Science.gov

Sample records for aspect pattern formation

  1. 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

  2. Dorsal and ventral aspects of the most caudal medullary reticular formation have differential roles in modulation and formation of the respiratory motor pattern in rat.

    PubMed

    Jones, Sarah E; Stanić, Davor; Dutschmann, Mathias

    2016-12-01

    The respiratory pattern generator of mammals is anatomically organized in lateral respiratory columns (LRCs) within the brainstem. LRC compartments serve specific functions in respiratory pattern and rhythm generation. While the caudal medullary reticular formation (cMRF) has respiratory functions reportedly related to the mediation of expulsive respiratory reflexes, it remains unclear whether neurons of the cMRF functionally belong to the LRC. In the present study we specifically investigated the respiratory functions of the cMRF. Tract tracing shows that the cMRF has substantial connectivity with key compartments of the LRC, particularly the parafacial respiratory group and the Kölliker-Fuse nuclei. These neurons have a loose topography and are located in the ventral and dorsal cMRF. Systematic mapping of the cMRF with glutamate stimulation revealed potent respiratory modulation of the respiratory motor pattern from both dorsal and ventral injection sites. Pharmacological inhibition of the cMRF with the GABA-receptor agonist isoguvacine produced significant and robust changes to the baseline respiratory motor pattern (decreased laryngeal post-inspiratory and abdominal expiratory motor activity, delayed inspiratory off-switch and increased respiratory frequency) after dorsal cMRF injection, while ventral injections had no effect. The present data indicate that the ventral cMRF is not an integral part of the respiratory pattern generator and merely serves as a relay for sensory and/or higher command-related modulation of respiration. On the contrary, the dorsal aspect of the cMRF clearly has a functional role in respiratory pattern formation. These findings revive the largely abandoned concept of a dorsal respiratory group that contributes to the generation of the respiratory motor pattern.

  3. Patterns in small aspect ratio Bénard-Marangoni convection.

    PubMed

    Ramón, M L; Maza, D; Mancini, H L

    1999-10-01

    An experimental study of pattern formation in Bénard-Marangoni convection with small aspect ratio containers and high Prandtl number fluids is presented. The observed stationary patterns complete previous experimental works performed at different values of aspect ratio and supercriticality. Detailed experimental studies of the flow in some single structures are described, and spatial bifurcations between different stationary planforms for a fixed aspect ratio are shown. These experimental results agree qualitatively with linear theory analysis and with some previous numerical works about boundary conditions effects.

  4. Understanding Alliance Formation Patterns

    DTIC Science & Technology

    2015-12-01

    most of the alliance formations throughout history. Using logistic regression models and statistical analysis for different historical periods from... historical periods, especially under conditions of war and peace and based on the polarity of the international system. The approach presented in the...alliance formation, historical periods, geographical proximity, trade exchange, regime type, national material capability, system-level conditions 15

  5. Excitability dependent pattern formation

    NASA Astrophysics Data System (ADS)

    Prabhakara, Kaumudi; Gholami, Azam; Bodenschatz, Eberhard

    2014-03-01

    On starvation, the amoebae Dictyostelium discoideum emit the chemo-attractant cyclic adenosine monophosphate (cAMP) at specific frequencies. The neighboring amoebae sense cAMP through membrane receptors and produce their own cAMP. Soon the cells synchronize and move via chemotaxis along the gradient of cAMP. The response of the amoebae to the emission of cAMP is seen as spiral waves or target patterns under a dark field microscope. The causal reasons for the selection of one or the other patterns are still unclear. Here we present a possible explanation based on excitability. The excitability of the amoebae depends on the starvation time because the gene expression changes with starvation. Cells starved for longer times are more excitable. In this work, we mix cells of different excitabilities to study the dependence of the emergent patterns on the excitability. Preliminary results show a transition from spirals to target patterns for specific excitabilities. A phase map of the patterns for different combinations of excitability and number densities is obtained. We compare our findings with numerical simulations of existing theoretical models.

  6. Pattern formation at liquid interfaces

    NASA Astrophysics Data System (ADS)

    Heidel, Barbara; Knobler, Charles M.

    1990-01-01

    Quantitative experimental investigations of pattern formation at a liquid interface are described. The reaction studied is the photoreduction of Fe 3+ in aqueous solution and the subsequent formation of Turnbull's Blue. Both the wavelength of the pattern and the time at which the break in homogeneity occurs have been studied as functions of the concentrations of the reactants and the viscosity of the solvent. Many of the features of the process are consistent with a mechanism in which autocatalysis is enhanced by double diffusion. Preliminary studies of pattern formation in the KI/starch/chloralhydrate system are also presented.

  7. Anisotropic assembly and pattern formation

    NASA Astrophysics Data System (ADS)

    von Brecht, James H.; Uminsky, David T.

    2017-01-01

    We investigate the role of anisotropy in two classes of individual-based models for self-organization, collective behavior and self-assembly. We accomplish this via first-order dynamical systems of pairwise interacting particles that incorporate anisotropic interactions. At a continuum level, these models represent the natural anisotropic variants of the well-known aggregation equation. We leverage this framework to analyze the impact of anisotropic effects upon the self-assembly of co-dimension one equilibrium structures, such as micelles and vesicles. Our analytical results reveal the regularizing effect of anisotropy, and isolate the contexts in which anisotropic effects are necessary to achieve dynamical stability of co-dimension one structures. Our results therefore place theoretical limits on when anisotropic effects can be safely neglected. We also explore whether anisotropic effects suffice to induce pattern formation in such particle systems. We conclude with brief numerical studies that highlight various aspects of the models we introduce, elucidate their phase structure and partially validate the analysis we provide.

  8. 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

  9. Modeling generic aspects of ideal fibril formation

    NASA Astrophysics Data System (ADS)

    Michel, D.

    2016-01-01

    Many different proteins self-aggregate into insoluble fibrils growing apically by reversible addition of elementary building blocks. But beyond this common principle, the modalities of fibril formation are very disparate, with various intermediate forms which can be reshuffled by minor modifications of physico-chemical conditions or amino-acid sequences. To bypass this complexity, the multifaceted phenomenon of fibril formation is reduced here to its most elementary principles defined for a linear prototype of fibril. Selected generic features, including nucleation, elongation, and conformational recruitment, are modeled using minimalist hypotheses and tools, by separating equilibrium from kinetic aspects and in vitro from in vivo conditions. These reductionist approaches allow to bring out known and new rudiments, including the kinetic and equilibrium effects of nucleation, the dual influence of elongation on nucleation, the kinetic limitations on nucleation and fibril numbers, and the accumulation of complexes in vivo by rescue from degradation. Overlooked aspects of these processes are also pointed: the exponential distribution of fibril lengths can be recovered using various models because it is attributable to randomness only. It is also suggested that the same term "critical concentration" is used for different things, involved in either nucleation or elongation.

  10. Modeling generic aspects of ideal fibril formation

    SciTech Connect

    Michel, D.

    2016-01-21

    Many different proteins self-aggregate into insoluble fibrils growing apically by reversible addition of elementary building blocks. But beyond this common principle, the modalities of fibril formation are very disparate, with various intermediate forms which can be reshuffled by minor modifications of physico-chemical conditions or amino-acid sequences. To bypass this complexity, the multifaceted phenomenon of fibril formation is reduced here to its most elementary principles defined for a linear prototype of fibril. Selected generic features, including nucleation, elongation, and conformational recruitment, are modeled using minimalist hypotheses and tools, by separating equilibrium from kinetic aspects and in vitro from in vivo conditions. These reductionist approaches allow to bring out known and new rudiments, including the kinetic and equilibrium effects of nucleation, the dual influence of elongation on nucleation, the kinetic limitations on nucleation and fibril numbers, and the accumulation of complexes in vivo by rescue from degradation. Overlooked aspects of these processes are also pointed: the exponential distribution of fibril lengths can be recovered using various models because it is attributable to randomness only. It is also suggested that the same term “critical concentration” is used for different things, involved in either nucleation or elongation.

  11. Pattern formations and optimal packing.

    PubMed

    Mityushev, Vladimir

    2016-04-01

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

  12. 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.

  13. Theory of electrochemical pattern formation

    NASA Astrophysics Data System (ADS)

    Christoph, J.; Eiswirth, M.

    2002-03-01

    The spatial coupling in electrochemical systems is mediated by ion migration under the influence of the electric field. Since field effects spread very rapidly, every point of an electrode can communicate with every other one practically instantaneously through migration coupling. Based on mathematical potential theory we present the derivation of a generally applicable reaction-migration equation, which describes the coupling via an integral over the whole electrode area. The corresponding coupling function depends only on the geometry of the electrode setup and has been computed for commonly used electrode shapes (such as ring, disk, ribbon or rectangle). The pattern formation observed in electrochemical systems in the bistable, excitable and oscillatory regime can be reproduced in computer simulations, and the types of patterns occurring under different geometries can be rationalized.

  14. 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

  15. The reliance of insolation pattern on surface aspect

    NASA Astrophysics Data System (ADS)

    Saad, N. Md; Hamid, J. R. Abdul; Mohd Suldi, A.

    2014-02-01

    The Sun's radiated energy is an important source in realizing the green technology concept construction. When interacting with the atmosphere and objects on the Earth's surface incoming solar radiation (insolation) will create insolation patterns that are ambiguous and as a result need to be investigated further. This paper explores the insolation pattern and ambiguities against topographic surfaces in the context of direct, diffuse, and reflectance irradiance. The topography is modeled from LiDAR data as Digital Surface Model (DSM) and Digital Terrain Model (DTM). The generated DSM and DTM were converted to Triangular Irregular Network (TIN) format within the Arc GIS environment before the insolation pattern could be visualized. The slope and aspect of the topography has an impact on the insolation which is the emphasis of this paper. The main outcome from the study is the insolation map and plots of relationship between the insolation and surface aspect. The findings from this study should contribute to the sustainable practices of green building technology.

  16. 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").

  17. Plasma Chemical Aspects Of Dust Formation In Hydrocarbon Plasmas

    SciTech Connect

    Berndt, J.; Kovacevic, E.; Stepanovic, O.; Stefanovic, I.; Winter, J.

    2008-09-07

    This contribution deals with some plasma chemical aspects of dust formation in hydrocarbon plasmas. The interplay between dust formation and plasma chemistry will be discussed by means of different experimental results. One specific example concerns the formation of benzene and the role of atomic hydrogen for plasma chemical processes and dust formation in hydrocarbon discharges.

  18. 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).

  19. Some aspects of core formation in Mercury

    NASA Technical Reports Server (NTRS)

    Solomon, S. C.

    1976-01-01

    Some questions dealing with the nature and history of a large metallic core within Mercury are considered. These include the existence of a core, its size, whether it is fluid or solid, the timescale for core formation, the geological consequences of core formation, and whether such consequences are consistent with the surface geology. Several indirect lines of evidence are discussed which suggest the presence of a large iron-rich core. A core-formation model is examined in which core infall is accompanied by an increase of 17 km in planetary radius, an increase of 700 K in mean internal temperature, and substantial melting of the mantle. It is argued that if the core differentiated from an originally homogeneous planet, that event must have predated the oldest geological units comprising most of the planetary surface. A convective dynamo model for the source of Mercury's magnetic field is shown to conflict with cosmochemical models that do not predict a substantial radiogenic heat source in the core.

  20. Molecular aspects of bile formation and cholestasis.

    PubMed

    Arrese, Marco; Trauner, Michael

    2003-12-01

    Recent insights into the cellular and molecular mechanisms that control the function and regulation of hepatobiliary transport have led to a greater understanding of the physiological significance of bile secretion. Individual carriers for bile acids and other organic anions in both liver and intestine have now been cloned from several species. In addition, complex networks of signals that regulate key enzymes and membrane transporters located in cells that participate in the metabolism or transport of biliary constituents are being unraveled. This knowledge has major implications for the pathogenesis of cholestatic liver diseases. Here, we review recent information on molecular aspects of hepatobiliary secretory function and its regulation in cholestasis. Potential implications of this knowledge for the design of new therapies of cholestatic disorders are also discussed.

  1. Pattern Formation in Excitable Media

    NASA Astrophysics Data System (ADS)

    Mikhailov, Alexander S.

    1997-03-01

    In this talk I give a short review of the history and the current state of theoretical research on spiral wave patterns in excitable media. I start with the theoretical model of wave propagation in excitable media proposed in 1946 by Wiener and Rosenblueth(N. Wiener and A. Rosenblueth, The mathematical formulation of the problem of conduction of impulses in a network of connected excitable elements, specifically in cardiac muscle, Arch. Inst. Cardiol. Mexico 16 (1946) 205). This model describes spiral waves rotating around obstacles. I show how, by taking additionally into account curvature effects and gradual recovery of the medium after passage of an excitation wave, the model is generalized to describe freely rotating spiral waves and the breakup which produces spirals. In the context of this kinematic model, complex dynamics of spiral waves, i.e. their meandering, drift and resonance, is discussed. Instabilities of spiral waves in confined geometries, i.e. inside a circular region and on a sphere, are analyzed. At the end, I show how spiral waves in such systems can be efficiently controlled by application of a delayed global feedback. The talk is based on the review paper(A. S. Mikhailov, V. A. Davydov, and V. S. Zykov, Complex dynamics of spiral waves and motion of curves, Physica D 70 (1994) 1) and the monograph(A. S. Mikhailov, Foundations of Synergetics I, 2nd revised edition (Springer, Berlin, 1994)).

  2. 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.

  3. Fabrication of Very-High-Aspect-Ratio Microstructures in Complex Patterns by Photoelectrochemical Etching

    SciTech Connect

    Sun, GY; Zhao, X; Kim, CJ

    2012-12-01

    We have fabricated very-high-aspect-ratio (VHAR) silicon and metal microstructures in complex geometric patterns. The recently developed surfactant-added tetramethylammonium hydroxide etching allows the formation of V-grooves in any pattern, i.e., not limited by the crystal direction, on a silicon surface. As the resulting sharp pits allow very deep photoelectrochemical etching, VHAR silicon microstructures (4-mu m-wide and over-300-mu m-deep trenches) are successfully fabricated in complex patterns (spiral and zigzag demonstrated), overcoming the prevailing limitations of simple pores and straight trenches. Furthermore, by filling the VHAR silicon mold with nickel and removing the silicon, high-aspect-ratio metal microstructures of complex patterns are also obtained. These VHAR microstructures in complex patterns, which are structurally much stronger than the simple posts and straight plates, overcome the stiction problem even when densely populated. [2012-0042

  4. 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

  5. Pattern formation in prey-taxis systems.

    PubMed

    Lee, J M; Hillen, T; Lewis, M A

    2009-11-01

    In this paper, we consider spatial predator-prey models with diffusion and prey-taxis. We investigate necessary conditions for pattern formation using a variety of non-linear functional responses, linear and non-linear predator death terms, linear and non-linear prey-taxis sensitivities, and logistic growth or growth with an Allee effect for the prey. We identify combinations of the above non-linearities that lead to spatial pattern formation and we give numerical examples. It turns out that prey-taxis stabilizes the system and for large prey-taxis sensitivity we do not observe pattern formation. We also study and find necessary conditions for global stability for a type I functional response, logistic growth for the prey, non-linear predator death terms, and non-linear prey-taxis sensitivity.

  6. 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.

  7. N7 logic via patterning using templated DSA: implementation aspects

    NASA Astrophysics Data System (ADS)

    Bekaert, J.; Doise, J.; Gronheid, R.; Ryckaert, J.; Vandenberghe, G.; Fenger, G.; Her, Y. J.; Cao, Y.

    2015-07-01

    In recent years, major advancements have been made in the directed self-assembly (DSA) of block copolymers (BCP). Insertion of DSA for IC fabrication is seriously considered for the 7 nm node. At this node the DSA technology could alleviate costs for multiple patterning and limit the number of masks that would be required per layer. At imec, multiple approaches for inserting DSA into the 7 nm node are considered. One of the most straightforward approaches for implementation would be for via patterning through templated DSA; a grapho-epitaxy flow using cylindrical phase BCP material resulting in contact hole multiplication within a litho-defined pre-pattern. To be implemented for 7 nm node via patterning, not only the appropriate process flow needs to be available, but also DSA-aware mask decomposition is required. In this paper, several aspects of the imec approach for implementing templated DSA will be discussed, including experimental demonstration of density effect mitigation, DSA hole pattern transfer and double DSA patterning, creation of a compact DSA model. Using an actual 7 nm node logic layout, we derive DSA-friendly design rules in a logical way from a lithographer's view point. A concrete assessment is provided on how DSA-friendly design could potentially reduce the number of Via masks for a place-and-routed N7 logic pattern.

  8. 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

  9. 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

  10. Circulation patterns in open, wide and deep lacustrine embayments with different aspect ratios

    NASA Astrophysics Data System (ADS)

    Razmi, Amir Mehdi; Barry, David Andrew; Lemmin, Ulrich

    2013-04-01

    Numerical simulations were carried out to examine the effect of different horizontal aspect ratios on wind-induced circulation within open, wide and deep lacustrine embayments. Two adjacent embayments in Lake Geneva, Switzerland, located between Morges and Lausanne on the north shore of the lake, were compared. These embayments were selected because of their similar exposure with respect to wind forcing. However, their aspect ratios are different, making them ideal case studies to evaluate the impact of the aspect ratio on the resulting circulation pattern. A previously validated 3D hydrodynamic model (Delft3D-FLOW) was employed to simulate currents in the lake for the year 2010. Detailed over-lake maps of wind, temperature and humidity were used as input to drive the model. The embayments were compared in terms of circulation patterns and conditions leading to gyre formation. Furthermore, we carried out a systematic comparison, focusing on the embayment aspect ratio by constructing different "synthetic" embayments with aspect ratios in the range 1 - 4. Subsequently, the flow field within these embayments was computed for typical meteorological regimes (dominant wind regimes and seasonality). In particular, the generation of gyres was compared for different cases. The results revealed that, even for large aspect ratios (~ 3), wind-induced circulation can still occur in open, wide, and deep lacustrine embayments. The results showed that, as expected, gyres are formed less frequently as the embayment aspect ratio increases. For this reason, gyres are much more probable in the Morges embayment than in Vidy Bay.

  11. 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.

  12. Quantum pattern formation dynamics of photoinduced nucleation

    NASA Astrophysics Data System (ADS)

    Ishida, Kunio; Nasu, Keiichiro

    2008-06-01

    We study the dynamics of quantum pattern formation processes in molecular crystals which is concomitant with photoinduced nucleation. Since the nucleation process in coherent regime is driven by the nonadiabatic transition in each molecule followed by the propagation of phonons, it is necessary to take into account the quantum nature of both electrons and phonons in order to pursue the dynamics of the system. Therefore, we employ a model of localized electrons coupled with a quantized phonon mode and solve the time-dependent Schrödinger equation numerically. We found that there is a minimal size of clusters of excited molecules which triggers the photoinduced nucleation process; i.e., nucleation does not take place unless sufficient photoexcitation energy is concentrated within a narrow area of the system. We show that this result means that the spatial distribution of photoexcited molecules plays an important role in the nonlinearity of the dynamics and also in the optical properties observed in experiments. We calculate the conversion ratio, the rate of cluster formation, and correlation functions to reveal the dynamical properties of the pattern formation process; the initial dynamics of the photoinduced structural change is discussed from the viewpoint of pattern formation.

  13. Global aspects of the formation of γ Cephei b

    NASA Astrophysics Data System (ADS)

    Eggl, Siegfried; Gyergyovits, Markus; Pilat-Lohinger, Elke

    2011-11-01

    Discoveries of extrasolar planets in tight binaries are of great scientific value since these systems can be used to gain new insights in planetary development processes. Gamma Cephei, one of the most thoroughly investigated double star systems is hosting a Jovian planet at a distance of about 2 AU from its primary, a 1.4 solar-mass K1 III-IV star (Neuhäuser et al. 2007; Torres 2007). We comprise aspects of dynamical stability, disc heating processes and different giant planet (GP) formation scenarios in order to gain a better understanding of the open questions that remain in explaining the formation of gamma Cephei b.

  14. 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.

  15. Emergent pattern formation in an interstitial biofilm

    NASA Astrophysics Data System (ADS)

    Zachreson, Cameron; Wolff, Christian; Whitchurch, Cynthia B.; Toth, Milos

    2017-01-01

    Collective behavior of bacterial colonies plays critical roles in adaptability, survivability, biofilm expansion and infection. We employ an individual-based model of an interstitial biofilm to study emergent pattern formation based on the assumptions that rod-shaped bacteria furrow through a viscous environment and excrete extracellular polymeric substances which bias their rate of motion. Because the bacteria furrow through their environment, the substratum stiffness is a key control parameter behind the formation of distinct morphological patterns. By systematically varying this property (which we quantify with a stiffness coefficient γ ), we show that subtle changes in the substratum stiffness can give rise to a stable state characterized by a high degree of local order and long-range pattern formation. The ordered state exhibits characteristics typically associated with bacterial fitness advantages, even though it is induced by changes in environmental conditions rather than changes in biological parameters. Our findings are applicable to a broad range of biofilms and provide insights into the relationship between bacterial movement and their environment, and basic mechanisms behind self-organization of biophysical systems.

  16. 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

  17. 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

  18. 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.

  19. Pattern formation in cell membrane adhesion

    NASA Astrophysics Data System (ADS)

    Discher, Dennis; Hategan, A.; Sengupta, K.; Sackmann, E.

    2004-03-01

    Strong adhesion of highly active cells often nucleates focal adhesions or related structures that are, over time, reinforced by cytoskeleton (actin, etc.). Red cells lack such complex adhesion systems, but they are shown here to also exhibit complex spatial patterns within an adhesive contact zone. While strong adhesion and spreading of the red cell to a dense poly-L-lysine surface appears complete in < 1 s by reflective interference microscopy, over longer times of 10-15 min or more distinct patterns in fluorescently labeled membrane components emerge. The fluorescent lipid Fl-PE (fluorescein phosphoethanolamine), in particular, is seen to diffuse and reorganize (eg. worm-like domains of <500 nm) within the contact zone, independent of whether the cell is intact or ruptured. Lipid patterns are accompanied by visible perturbations in band 3 distribution and weaker perturbations in membrane skeleton actin. Although fluorescent poly-L-lysine is shown to be uniform under cells, pressing down on the membrane quenches the lipid patterns and reveals the topographical basis for pattern formation. Regions of strong contact are thus separated by regions where the membrane is more distant from the surface.

  20. 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.

  1. Kinetics of lamellar formation on sparsely stripped patterns

    NASA Astrophysics Data System (ADS)

    Xie, Nan; Li, Weihua; Zhang, Hongdong; Qiu, Feng; Shi, An-Chang

    2013-11-01

    Chemical epitaxy based on the self-assembly of block copolymers is viewed as a promising technique to achieve ordered patterns on a large scale. Herein, we study the kinetics of lamellar formation of block copolymers under the direction of sparsely stripped patterns using cell dynamics simulations of the time-dependent Ginzburg-Landau theory. First, a scaling law is unveiled with the ordering time of lamellae, tp, with respect to the multiples between the periods of lamellae and stripe patterns, which is consistent with the power law evolution of the correlation length existing in the bulk phase of lamellae. Second, the tolerative windows of perfect order, with deviation from integer multiples, are also estimated from the aspect of kinetics. The results of the ordering time and tolerative windows are of great interest for relevant experiments or applications. Finally, a two-stage evolution is explored during the pattern formation of chemical epitaxy by probing into the evolution of defects, which is of fundamental interest for us to understand the coarsening kinetics of block copolymers under the direction of chemical patterns.

  2. 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.

  3. Singularity-Driven Pattern Formation by Bacteria

    NASA Astrophysics Data System (ADS)

    Brenner, Michael P.; Betterton, M. D.

    2000-03-01

    Under special conditions bacteria excrete an attractant and aggregate. The patterns formation is driven by the formation of singularities. The high density regions initially collapse into cylindrical structures, which subsequently destabilize and break up into spherical aggregates. This paper presents a theoretical description of the process. Cylindrical collapse is marginal, which leads to corrections to the collapse laws expected from dimensional analysis. The instability of a collapsing cylinder is composed of two stages: Initially, slow modulations to the cylinder develop, which correspond to a variation of the collapse time along the cylinder axis. Ultimately, one point on the cylinder pinches off. At this final stage of the instability, a front propagates from the pinch into the remainder of the cylinder. The spacing of the resulting spherical aggregates is determined by the front propagation.

  4. 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

  5. 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.

  6. Sandpile formation and patterning by revolving rivers

    NASA Astrophysics Data System (ADS)

    Altshuler, Ernesto; Ramos, Osvanny; Bassler, Kevin; Batista-Leyva, Alfo; Rivera, Aramis

    2002-03-01

    Here we report a remarkable new mechanism of pile formation, which eventually involves patterning. If sand from "Santa Teresa", Cuba, is poured into a cylindrical container with radious 4-6 cm, or smaller, the pile does not build through avalanches, but instead by a "revolving river" mechanism. This novel mechanism can be described as the deposition of a conical layer a few grains thick, which "wraps" the pile clockwise or counterclockwise, depending on the initial conditions. The "growing edge" of the layer consists of a continuous river of sand that flows from the apex of the pile to the base and is a few mm wide. The axial symmetry of the system is spontaneously broken as the direction of the river, clockwise or counterclockwise, is chosen. If the radius of the container is larger than 6-7 cm, the river becomes "intermittent". However, on average, it continues to revolve around the pile, as in the case of the continuous regime observed in smaller piles. The intermittent appearance of the rivers produces an undulating pattern on the pile surface resembling those recently observed for rapid granular flows on an inclined plane, but clearly caused by different mechanisms.

  7. 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

  8. Pattern formation in rotating Bénard convection

    NASA Astrophysics Data System (ADS)

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

    1992-12-01

    Using an extension of the Swift-Hohenberg equation we study pattern formation in the Bénard experiment close to the onset of convection in the case of rotating cylindrical fluid containers. For small Taylor numbers we emphasize the existence of slowly rotating patterns and describe behaviour exhibiting defect motion. Finally, we study pattern formation close to the Küppers-Lortz instability. The instability is nucleated at defects and proceeds through front propagation into the bulk patterns.

  9. 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.

  10. Electrohydrodynamic pressure enhanced by free space charge for electrically induced structure formation with high aspect ratio.

    PubMed

    Tian, Hongmiao; Wang, Chunhui; Shao, Jinyou; Ding, Yucheng; Li, Xiangming

    2014-10-28

    Electrically induced structure formation (EISF) is an interesting and unique approach for generating a microstructured duplicate from a rheological polymer by a spatially modulated electric field induced by a patterned template. Most of the research on EISF have so far used various dielectric polymers (with an electrical conductivity smaller than 10(-10) S/m that can be considered a perfect dielectric), on which the electric field induces a Maxwell stress only due to the dipoles (or bounded charges) in the polymer molecules, leading to a structure with a small aspect ratio. This paper presents a different approach for improving the aspect ratio allowed in EISF by doping organic salt into the perfect dielectric polymer, i.e., turning the perfect dielectric into a leaky dielectric, considering the fact that the free space charges enriched in the leaky dielectric polymer can make an additional contribution to the Maxwell stress, i.e., electrohydrodynamic pressure, which is desirable for high aspect ratio structuring. Our numerical simulations and experimental tests have shown that a leaky dielectric polymer, with a small conductivity comparable to that of deionized water, can be much more effective at being electrohydrodynamically deformed into a high aspect ratio in comparison with a perfect dielectric polymer when both of them have roughly the same dielectric constant.

  11. Diapycnal Transport and Pattern Formation in Double-Diffusive Convection

    DTIC Science & Technology

    2015-12-01

    TRANSPORT AND PATTERN FORMATION IN DOUBLE-DIFFUSIVE CONVECTION by Erick L. Edwards December 2015 Dissertation Supervisor Timour Radko THIS...Dissertation 4. TITLE AND SUBTITLE DIAPYCNAL TRANSPORT AND PATTERN FORMATION IN DOUBLE- DIFFUSIVE CONVECTION 5. FUNDING NUMBERS 6. AUTHOR(S...is unlimited 12b. DISTRIBUTION CODE 13. ABSTRACT (maximum 200 words) This work analyzes the role of double-diffusive convection

  12. 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.

  13. 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.

  14. The daytime breath hydrogen profile: technical aspects and normal pattern.

    PubMed

    Kneepkens, C M; Vonk, R J; Bijleveld, C M; Fernandes, J

    1985-04-30

    A method is described for breath sampling which can be used for breath hydrogen estimations not only in clinical practice, but also at home. Sampling of end-expiratory air is performed using a 10-ml syringe with a side hole. The samples are transferred to 3-ml vacuum tubes, which can be stored and mailed without significant loss of hydrogen. The hydrogen concentration is estimated gas chromatographically using 0.4 ml of sampled air. This method was used to assess the breath hydrogen pattern under normal circumstances: the daytime breath hydrogen profile. Fourteen children sampled their breath at 30-min intervals during one full day, and recorded diet and activity. The normal daytime breath hydrogen profile showed a typical pattern. Morning values were low, but the evening values were markedly increased in half of the children. These patterns differed markedly from those registered in three children with carbohydrate malabsorption. The daytime breath hydrogen profile, which is easy to perform and applicable at home, might provide valuable additional information in the investigation of children with suspected carbohydrate malabsorption.

  15. Comparing investigation of pattern formation in glow and streamer DBD

    NASA Astrophysics Data System (ADS)

    Li, Ben; Ouyang, Jiting

    2016-11-01

    In this paper, we investigate the behaviors of patterns in dielectric barrier discharge (DBD) in glow and streamer regimes under different operating conditions (driving frequency and voltage) and external electric/magnetic field to explore the similarity and difference of pattern formation. It is found that patterns in both glow and streamer DBDs can be homogenized by decreasing the driving frequency to a low level. But filamentary streamers can still appear at low frequency when the voltage is much higher. With an additional lateral electric field, patterns in both regimes can be homogenized. However, an axial magnetic field makes the glow DBD homogeneous, while the streamer DBD decreases in filamentary size. In both regimes, dynamics and distribution of the space charges, rather than the surface charges, play the predominant role in the formation of DBD patterns. But the surface charges may also play an important role in pattern formation, especially in streamer DBD.

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

    PubMed

    Seirin Lee, Sungrim

    2016-09-07

    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.

  18. Static and Dynamic Aspects of Black Silicon Formation

    NASA Astrophysics Data System (ADS)

    Abi Saab, David; Basset, Philippe; Pierotti, Matthew J.; Trawick, Matthew L.; Angelescu, Dan E.

    2014-12-01

    We present a combination of experimental data and modeling that explains some of the important characteristics of black silicon (BSi) developed in cryogenic reactive ion etching (RIE) processes, including static properties (dependence of resulting topography on process parameters) and dynamic aspects (evolution of topography with process time). We generate a phase diagram predicting the RIE parameter combinations giving rise to different BSi geometries and show that the topographic details of BSi explain the metamaterial characteristics that are responsible for its low reflectivity. In particular, the unique combination of needle and hole features of various heights and depths, which is captured by our model and confirmed by focused ion beam nanotomography, creates a uniquely smooth transition in refractive index. The model also correctly describes dynamical characteristics, such as the dependence of aspect ratio on process time, and the prediction of new etching fronts appearing at topographical saddle points during the incipient stages of BSi development—a phenomenon reported here for the first time.

  19. Pattern formation and coarsening in crystalline membranes

    NASA Astrophysics Data System (ADS)

    Vega, Daniel A.; Pezzutti, Aldo D.

    2011-03-01

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

  20. Formation of High Aspect Ratio Microcoil Using Dipping Method

    NASA Astrophysics Data System (ADS)

    Noda, Daiji; Yamashita, Shuhei; Matsumoto, Yoshifumi; Setomoto, Masaru; Hattori, Tadashi

    Coils are used in many electronic devices as inductors in mobile units such as mobile phone, digital cameras, etc. Inductance and quality factor of coils are very important value of the performance. Therefore, the requests for coils are small size, high inductance, low power consumption, etc. However, coils are unsuitable for miniaturization because of its structure. Therefore, we have proposed and developed the microcoils of high aspect ratio with the dipping method and an X-ray lithography technique. In dipping method, centrifugal force and highly viscous photoresist solution were key points to evenly apply resist in the form of thick film on metal bar. The film thickness of resist on bar was achieved about 50 μm after single coating. Using these techniques, we succeeded in creating threaded groove structure with 10 μm lines and spaces on 1 mm brass bar. In this case, the aspect ratio was achieved five. It is very expected the high performance microcoil with high aspect ratio lines could be manufactured in spite of the miniature size.

  1. 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

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

    PubMed

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

    2014-12-02

    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. Pattern Formation in Drying Drops of Polyelectrolyte - Salt Solutions

    NASA Astrophysics Data System (ADS)

    Kaya, Deniz; Belyi, Vladimir A.

    2005-03-01

    We use optical microscopy, AFM, and SEM to investigate salt patterns formed during evaporation of aqueous solutions of sodium poly(styrene sulfonate) and sodium chloride (NaPSS/NaCl). Observed patterns exhibit significantly larger variety than in the simple "drying coffee drop" experiments. We find that varying the concentration ratios of polyelectrolyte/salt solutions leads to formation of qualitatively different patterns, including radially grown salt deposits, concentric rings of salt and other structures. Our results indicate that these patterns are also sensitive to evaporation rate of the droplet. However molecular weight of the polymer appears to have little to no effect on the observed patterns.

  4. (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)

  5. 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

  6. 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.

  7. Harnessing Localized Ridges for High-Aspect-Ratio Hierarchical Patterns with Dynamic Tunability and Multifunctionality

    PubMed Central

    Cao, Changyong; Chan, Hon Fai; Zang, Jianfeng; Leong, Kam W.; Zhao, Xuanhe

    2014-01-01

    We invent a simple method for fabricating high-aspect-ratio, hierarchical and dynamically tunable surface patterns by harnessing localized-ridge instabilities in gold nanofilms coated on elastomer substrates (a); develop a theoretical model to calculate the critical parameters (e.g. wavelength and amplitude) for designing the new patterns (b); and demonstrate novel applications of the patterns as super-hydrophobic coatings (c) and biomimetic cell-culture substrates (d) capable of on-demand tunability. PMID:24339233

  8. Argon ion beam induced surface pattern formation on Si

    SciTech Connect

    Hofsäss, H.; Bobes, O.; Zhang, K.

    2016-01-21

    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 10{sup 18} ions/cm{sup 2}. 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.

  9. Theoretical aspects of product formation from the NCO + NO reaction

    SciTech Connect

    Lin, M.C.; He, Y. ); Melius, C.F. )

    1993-09-09

    The reaction of NCO with NO, an important elementary process involved in the reduction of NO[sub x] by HNCO, has been studied theoretically using the BAC-MP4 technique in conjunction with RRKM calculations. The computed molecular structures and thermochemical data for various intermediates and transition states suggest that the reaction takes place primarily via the singlet, ground electronic state OCNNO molecule according to the following mechanism; (step a) NCO + NO [leftrightarrow] [sup 1]OCNNO [yields] N[sub 2]O + CO; (step b) NCO + NO [leftrightarrow] [sup 1]OCNNO [yields] c-OCNNO[minus] N[sub 2] + CO[sub 2]. The formation of N[sub 2]O + CO occurs by the fragmentation of the singlet OCNNO intermediate step (a), whereas the production of N[sub 2] + CO[sub 2] by cyclization-fragmentation occurs via step b. The tight transition states leading to the formation of these products, coupled with the loose entrance channel, give rise to the experimentally observed strong negative temperature dependence which can be quantitatively accounted for by the results of RRKM calculations based on the BAC-MP4 data. The experimentally measured product branching ratio for channels a and b could be accounted for theoretically by lowering the calculated energy barrier for step a by 3.6 kcal/mol, corresponding to about 15% of the barrier height. 22 refs., 3 figs., 5 tabs.

  10. Formation of co-crystals: Kinetic and thermodynamic aspects

    NASA Astrophysics Data System (ADS)

    Gagnière, E.; Mangin, D.; Puel, F.; Rivoire, A.; Monnier, O.; Garcia, E.; Klein, J. P.

    2009-04-01

    Co-crystallisation is a recent method of great interest for the pharmaceutical industry, since pharmaceutical co-crystals represent useful materials for drug products. In this study, an active pharmaceutical ingredient (carbamazepine (CBZ)) co-crystallized with a vitamin (nicotinamide (NCT)) was chosen as a model substance. This work was focused on the construction of a phase diagram for the system CBZ/NCT, split in six domains for kinetic reasons (the different solid phases which might appear during the crystallisation) and in four domains according to thermodynamic aspects (the stable final phase obtained). Although co-crystals are not ionic compounds, the supersaturation of co-crystals can be evaluated by considering the solubility product. Batch crystallisation operations were carried out in a stirred vessel equipped with an in situ video probe. This latter device was a powerful analysis tool to monitor the CBZ/NCT co-crystals and single CBZ crystals since these two crystalline phases grown in ethanol exhibited needle and platelet habits. As concerns kinetics, the different solid phases which might appear during the experiments were observed and competed against each others. In accordance with thermodynamics, the stable solid form was obtained at the end of the operation. Finally some preliminary results indicate that the nucleation of co-crystals may be favoured by the presence of CBZ crystals. Epitaxial relationships between CBZ/NCT co-crystals and CBZ crystals were suspected.

  11. 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...

  12. The role of hydrological transience in peatland pattern formation

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

    The sloping flanks of peatlands are commonly patterned with non-random, contour-parallel stripes of distinct microhabitats 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, to explore the controls over peatland patterning. Our models each consist of three submodels, which simulate: peatland water tables in a gridded landscape; a simple representation of microhabitat 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 captured some aspect of real peatland behaviour that generates patterning. Recently-buried peat layers may remain hydrologically active despite no longer reflecting current vegetation patterns, providing a form of ecological memory. Furthermore, the models were highly sensitive to the assumed values of peat hydraulic properties, which we take to indicate that the models are missing an important negative feedback between peat

  13. 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.

  14. Robust ecological pattern formation induced by demographic noise

    NASA Astrophysics Data System (ADS)

    Butler, Thomas; Goldenfeld, Nigel

    2010-03-01

    We demonstrate that demographic noise can induce persistent spatial pattern formation and temporal oscillations in the Levin-Segel predator-prey model for plankton-herbivore population dynamics. Although the model exhibits a Turing instability in mean field theory, demographic noise greatly enlarges the region of parameter space where pattern formation occurs. To distinguish between patterns generated by fluctuations and those present at the mean field level in real ecosystems, we calculate the power spectrum in the noise-driven case and predict the presence of fat tails not present in the mean field case. These results may account for the prevalence of large-scale ecological patterns, beyond that expected from traditional non-stochastic approaches.

  15. Robust ecological pattern formation induced by demographic noise.

    PubMed

    Butler, Thomas; Goldenfeld, Nigel

    2009-09-01

    We demonstrate that demographic noise can induce persistent spatial pattern formation and temporal oscillations in the Levin-Segel predator-prey model for plankton-herbivore population dynamics. Although the model exhibits a Turing instability in mean-field theory, demographic noise greatly enlarges the region of parameter space where pattern formation occurs. To distinguish between patterns generated by fluctuations and those present at the mean-field level in real ecosystems, we calculate the power spectrum in the noise-driven case and predict the presence of fat tails not present in the mean-field case. These results may account for the prevalence of large-scale ecological patterns, beyond that expected from traditional nonstochastic approaches.

  16. Robust ecological pattern formation induced by demographic noise

    NASA Astrophysics Data System (ADS)

    Butler, Thomas; Goldenfeld, Nigel

    2009-09-01

    We demonstrate that demographic noise can induce persistent spatial pattern formation and temporal oscillations in the Levin-Segel predator-prey model for plankton-herbivore population dynamics. Although the model exhibits a Turing instability in mean-field theory, demographic noise greatly enlarges the region of parameter space where pattern formation occurs. To distinguish between patterns generated by fluctuations and those present at the mean-field level in real ecosystems, we calculate the power spectrum in the noise-driven case and predict the presence of fat tails not present in the mean-field case. These results may account for the prevalence of large-scale ecological patterns, beyond that expected from traditional nonstochastic approaches.

  17. Vegetation pattern formation of a water-biomass model

    NASA Astrophysics Data System (ADS)

    Wang, Xiaoli; Wang, Wendi; Zhang, Guohong

    2017-01-01

    In this paper, a mathematical model with diffusion and cross-diffusion is proposed to describe the interaction between the vegetation and the soil water. Based on the view of Turing pattern, we discuss the conditions of the diffusion-induced instability and the cross-diffusion-induced instability of a homogenous uniform steady state. We find that either a fast diffusion speed of water or a great hydraulic diffusivity due to the suction of roots may drive the instability of the homogenous steady state. Furthermore, we find that both the rain-fall rate and the infiltration feedback parameter can induce the transitions among the vegetation state, pattern formation and bare soil state. It is also found that the "terrain slope" may cause the instability of the homogenous steady state and drive the formation of periodic stripe pattern. Consequently, the diversity of dryland vegetation in reality can be explained as a result of pattern solutions of the model.

  18. 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

  19. Dynamic aspects of the ozone anomalies formation in the Antarctic region

    NASA Astrophysics Data System (ADS)

    Lapo, Palina; Svetashev, Alexander; Krasouski, Alexander; Barodka, Siarhei

    2013-04-01

    The ozone layer is a unique shield protecting all living creatures on our planet. However, it has become subject of active research only after the first ozone hole was discovered over Antarctica. Ozone layer depletion over Antarctica is an even more acute problem, since Antarctica is the only continent having a very endemic, rich nature with least human impact. It has been shown that extreme temperature conditions in polar stratosphere and polar stratospheric clouds formation in addition to photochemical reactions involving ozone and ozone-depleting substances act as a primary cause of ozone-layer depletion. In the present study we review the dynamic aspects of ozone anomalies formation in the Antarctic region by numerical simulation. For that purpose we consider the ozone hole which formed over Antarctica in the period of September-October 2011. Using the WRF modelling system and its PolarWRF modification, we simulate meteorological situation over Antarctica in the time periods of ozone hole formation and destruction, and also in the time period when the ozone hole is absent. Based on the modelling results, we argue that a cold air mass (anticyclone) formed over the territory of Antarctica during the formation of the ozone hole. Absence of solar irradiation and strong cooling of the atmosphere contribute to formation of such meteorological conditions during the Antarctic winter. In the stratosphere there is a region of low atmospheric pressure, which is clearly visible on a pressure topography map. Under the effect of the tropospheric and the stratospheric vortices, air patches movement leads to ozone concentration decrease and formation of the ozone anomalies. From the WRF system modelling results we calculate several basic meteorological characteristics and analyze surface maps and aerological (skew-T) diagrams for atmospheric variables with the NCL scripting language. We conclude that atmospheric dynamics has an impact on ozone depression. Also, we evaluate the

  20. 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

  1. ASPECT

    EPA Pesticide Factsheets

    Able to deploy within one hour of notification, EPA's Airborne Spectral Photometric Environmental Collection Technology (ASPECT) is the nation’s only airborne real-time chemical and radiological detection, infrared and photographic imagery platform.

  2. 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.

  3. Spontaneous pattern formation in broad-area lasers

    NASA Astrophysics Data System (ADS)

    Krents, Anton; Anchikov, Dmitry; Molevich, Nonna; Pakhomov, Anton

    2016-10-01

    The paper studies the spontaneous formation of nonlinear optical patterns in broad area lasers. Spatiotemporal transverse dynamics of the laser is described by the Maxwell-Bloch equations (MBE). The instability of the steady-state solution leads to pattern formation. Two different types of instabilities were observed analytically (Hopf and wave). 2D numerical simulation of the MBE with the random initial conditions has been performed using a split-step Fourier method and periodic boundary conditions. Hopf instability leads to homogeneous oscillations, spatiotemporal chaos and spiral waves. In the case of wave instability, the direct numerical simulation showed that space-time (periodic, quasi-periodic, or chaotic) modulation of the uniform profile is observed. The characteristic sizes of excited patterns are in good agreement with analytical predictions. The nonlinear interaction of four travelling waves forms a square optical vortex lattice similar to the vortex lattices observed in superconductors and Bose Einstein condensate.

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

    PubMed

    Sundaresan, Venkatesan; Alandete-Saez, Monica

    2010-01-01

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

  5. 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

  6. 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.

  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

    2014-10-05

    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.

  9. Simulating discrete models of pattern formation by ion beam sputtering.

    PubMed

    Hartmann, Alexander K; Kree, Reiner; Yasseri, Taha

    2009-06-03

    A class of simple, (2+1)-dimensional, discrete models is reviewed, which allow us to study the evolution of surface patterns on solid substrates during ion beam sputtering (IBS). The models are based on the same assumptions about the erosion process as the existing continuum theories. Several distinct physical mechanisms of surface diffusion are added, which allow us to study the interplay of erosion-driven and diffusion-driven pattern formation. We present results from our own work on evolution scenarios of ripple patterns, especially for longer timescales, where nonlinear effects become important. Furthermore we review kinetic phase diagrams, both with and without sample rotation, which depict the systematic dependence of surface patterns on the shape of energy depositing collision cascades after ion impact. Finally, we discuss some results from more recent work on surface diffusion with Ehrlich-Schwoebel barriers as the driving force for pattern formation during IBS and on Monte Carlo simulations of IBS with codeposition of surfactant atoms.

  10. Effect of slot aspect ratio on droplet formation from silicon straight-through microchannels.

    PubMed

    Kobayashi, Isao; Mukataka, Sukekuni; Nakajima, Mitsutoshi

    2004-11-01

    We recently proposed a novel technique for preparing monodisperse emulsions using an array of microfabricated through-holes with an oblong section; we called this array a straight-through microchannel (MC). This paper reports how the slot aspect ratio of the straight-through MC affects droplet formation characteristics. Straight-through MCs with different slot aspect ratios and equivalent diameters of about 20 microm were used. Experimental observation showed that slot aspect ratios exceeding a threshold of approximately 3 were needed to successfully prepare monodisperse emulsions with coefficients of variation below 2%.

  11. 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.

  12. Boundary-layer model of pattern formation in solidification

    NASA Technical Reports Server (NTRS)

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

    1984-01-01

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

  13. Pattern formation and collective effects in populations of magnetic microswimmers

    NASA Astrophysics Data System (ADS)

    Vach, Peter J.; Walker, Debora; Fischer, Peer; Fratzl, Peter; Faivre, Damien

    2017-03-01

    Self-propelled particles are one prototype of synthetic active matter used to understand complex biological processes, such as the coordination of movement in bacterial colonies or schools of fishes. Collective patterns such as clusters were observed for such systems, reproducing features of biological organization. However, one limitation of this model is that the synthetic assemblies are made of identical individuals. Here we introduce an active system based on magnetic particles at colloidal scales. We use identical but also randomly-shaped magnetic micropropellers and show that they exhibit dynamic and reversible pattern formation.

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

    DOE PAGES

    Zhou, Caizhi; Reichhardt, Charles; Olson Reichhardt, Cynthia 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

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. Modeling cell-death patterning during biofilm formation

    NASA Astrophysics Data System (ADS)

    Ghosh, Pushpita; Ben-Jacob, Eshel; Levine, Herbert

    2013-12-01

    Self-organization by bacterial cells often leads to the formation of a highly complex spatially-structured biofilm. In such a bacterial biofilm, cells adhere to each other and are embedded in a self-produced extracellular matrix (ECM). Bacillus substilis bacteria utilize localized cell-death patterns which focuses mechanical forces to form wrinkled sheet-like structures in three dimensions. A most intriguing feature underlying this biofilm formation is that vertical buckling and ridge location is biased to occur in region of high cell-death. Here we present a spatially extended model to investigate the role of the bacterial secreted ECM during the biofilm formation and the self-organization of cell-death. Using this reaction-diffusion model we show that the interaction between the cell's motion and the ECM concentration gives rise to a self-trapping instability, leading to variety of cell-death patterns. The resultant spot patterns generated by our model are shown to be in semi-quantitative agreement with recent experimental observation.

  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. Liquid crystalline pattern formation in drying droplets of biopolymers

    NASA Astrophysics Data System (ADS)

    Smalyukh, Ivan; Zribi, Olena; Butler, John; Lavrentovich, Oleg; Wong, Gerard

    2006-03-01

    When a droplet of DNA in water dries out, a ring-like deposit is observed along the perimeter, similar to the stains in spilled drops of coffee. However, the dried ring of DNA is a self-similar birefringent pattern composed of extended molecules. We examine dynamics of the pattern formation at the droplet's rim. This gives us an insight into the underlining physics. During the major part of drying process the contact line is pinned so that DNA molecules are brought to the perimeter and extended by the radial capillary flow. Lyotropic nematic phase is formed in which highly concentrated DNA aligns along the triple line to minimize elastic energy. When the contact angle becomes small, the contact line starts to retract and the radial dilative stress causes buckling distortions at the rim which then propagate deep into the elastic liquid- crystalline medium and give rise to the pattern.

  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. 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.

  4. Rimming flows and pattern formation inside rapidly rotating cylinder

    NASA Astrophysics Data System (ADS)

    Polezhaev, Denis; Dyakova, Veronika; Kozlov, Victor

    2014-11-01

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

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

    PubMed Central

    Tamulonis, Carlos; Kaandorp, Jaap

    2014-01-01

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

  6. 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

  7. 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.

  8. Different Aspects of {sup 24}Mg Formation and Decay Using a Radioactive {sup 13}N Beam

    SciTech Connect

    P. Figuera; F. Amorini; W. Bradfield-Smith; M. Cabibbo; G. Cardella; T. Davinson; A. Di Pietro; W. Galster; P. Leleux; A. Musumarra; A Ninane; M. Papa; G. Pappalardo; F. Rizzo; A.C. Shotter; C. Sukosd; S. Tudisco; P.J. Woods

    2000-12-31

    Different aspects of the formation and decay of {sup 24}Mg in the collision {sup 13}N+{sup 11}B have been studied using a large solid angle and highly segmented Silicon strip detector. Results concerning the fusion cross section, the 6 {alpha} decay of {sup 24}Mg and the GDR gamma ray emission are discussed.

  9. 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

  10. 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.

  11. 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.

  12. Fractal pattern formation in metallic ink sessile droplets

    NASA Astrophysics Data System (ADS)

    Hadj-Achour, Miloud; Brutin, David

    2014-11-01

    We report a fingering instability that occurs during the spreading and evaporation of a nanosuspension droplet. The patterns has a fractal structure similar to those reported by N. Shahidzadeh-Bonn et al. (2008) for salt crystallisation, during evaporation of saturated Na2SO4 on a hydrophilic surface. The fingering instability has been widely studied for both Newtonian and non-Newtonian fluids. However, we describe for the first time that a fingering instability is observed for the spreading of a nanosuspension sessile droplet. We demonstrate that in certain cases, the contact line evolves through different spreading regimes according to J. De Coninck et al. (2001) with an enhancement in the evaporation rate due the formation of the fractal patterns.

  13. Pattern formation in transparent media using ultrashort laser pulses

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

  14. Flow-Induced Control of Pattern Formation in Chemical Systems

    NASA Astrophysics Data System (ADS)

    Berenstein, Igal; Beta, Carsten

    Since Alan Turing's seminal paper in 1952, the study of spatio-temporal patterns that arise in systems of reacting and diffusing components has grown into an immense and vibrant realm of scientific research. This field includes not only chemical systems but spans many areas of science as diverse as cell and developmental biology, ecology, geosciences, or semiconductor physics. For several decades research in this field has concentrated on the vast variety of patterns that can emerge in reaction-diffusion systems and on the underlying instabilities. In the 1990s, stimulated by the pioneering work of Ott, Grebogi and Yorke, control of pattern formation arose as a new topical focus and gradually developed into an entire new field of research. On the one hand, research interests concentrated on control and suppression of undesired dynamical states, in particular on control of chaos. On the other hand, the design and engineering of particular space-time patterns became a major focus in this field that motivates ongoing scientific effort until today...

  15. 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

  16. Pattern formation and mixing in three-dimensional film flow

    NASA Astrophysics Data System (ADS)

    Heining, C.; Pollak, T.; Aksel, N.

    2012-04-01

    The effect of inertia on gravity-driven free surface flow over different three-dimensional periodic corrugations is considered analytically, numerically and experimentally. In the case of high bottom amplitudes, compared to the film thickness, the results predict complex free surface structures especially in cases where the topography is not fully flooded by the liquid film. The investigation of the flow field shows a rich variety of pattern formation phenomena depending on the interplay between the geometry of the topography and the inertia of the film. Finally, we show how the complex topographical structure enhances the laminar mixing within the film.

  17. Growth Anisotropy and Pattern Formation in Metal Epitaxy

    NASA Astrophysics Data System (ADS)

    Jorritsma, Louis C.; Bijnagte, Matthieu; Rosenfeld, Georg; Poelsema, Bene

    1997-02-01

    Evidence for the formation of growth induced, ordered checkerboardlike arrangements of mesas has been obtained. These patterns develop on a metal substrate with square symmetry after deposition of tens of monolayers. Its origin is traced back to laterally anisotropic advance rates of island edges in combination with slope selection. The foundation for the mesa arrangement is already laid just after coalescence of the adatom islands in the first monolayer. The results are exemplified in a high resolution surface diffraction study for the growth of Cu on Cu(001).

  18. 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.

  19. Pattern formation in granular binary mixtures under shear flow

    NASA Astrophysics Data System (ADS)

    Gao, Xin; Narteau, Clement; Rozier, Olivier

    2013-04-01

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

  20. High aspect ratio patterning of photosensitive polyimide with low thermal expansion coefficient and low dielectric constant

    NASA Astrophysics Data System (ADS)

    Dick, Andrew R.; Bell, William K.; Luke, Brendan; Maines, Erin; Mueller, Brennen; Rawlings, Brandon; Kohl, Paul A.; Grant Willson, C.

    2016-07-01

    A photosensitive polyimide system based on amine catalyzed imidization of a precursor poly(amic ester) is described. The material is based on the meta ethyl ester of pyromellitic dianhydride and 2,2' bis(trifluoromethyl)benzidine. It acts as a negative tone resist when formulated with a photobase generator. The material exhibits a dielectric constant of 3.0 in the gigahertz range, a coefficient of thermal expansion of 6±2 ppm/K, and can be patterned to aspect ratios of >2 when formulated with a highly quantum efficient cinnamide type photobase generator.

  1. 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.

  2. 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.

  3. Biological surface engineering: a simple system for cell pattern formation.

    PubMed

    Zhang, S; Yan, L; Altman, M; Lässle, M; Nugent, H; Frankel, F; Lauffenburger, D A; Whitesides, G M; Rich, A

    1999-07-01

    Biological surface engineering using synthetic biological materials has a great potential for advances in our understanding of complex biological phenomena. We developed a simple system to engineer biologically relevant surfaces using a combination of self-assembling oligopeptide monolayers and microcontact printing (muCP). We designed and synthesized two oligopeptides containing a cell adhesion motif (RADS)n (n = 2 and 3) at the N-terminus, followed by an oligo(alanine) linker and a cysteine residue at the C-terminus. The thiol group of cysteine allows the oligopeptides to attach covalently onto a gold-coated surface to form monolayers. We then microfabricated a variety of surface patterns using the cell adhesion peptides in combination with hexa-ethylene glycol thiolate which resist non-specific adsorption of proteins and cells. The resulting patterns consist of areas either supporting or inhibiting cell adhesion, thus they are capable of aligning cells in a well-defined manner, leading to specific cell array and pattern formations.

  4. Micron-scale pattern formation in prestressed polygonal films

    NASA Astrophysics Data System (ADS)

    Annabattula, R. K.; Onck, P. R.

    2011-02-01

    In this paper we explore the spontaneous formation of micropatterns in thin prestressed polygonal films using finite element simulations. We study films with different size, thickness, and shape, including square, rectangular, pentagonal, and hexagonal films. Patterns form when the films release the internal eigenstrain by buckling-up, after which the films bond-back to the substrate. After an initial symmetric evolution of the buckling profile, the symmetry of the deflection pattern breaks when the wavelength of wriggles near the film edges decreases. During bond back the deflection morphology converges to a fourfold, fivefold, and sixfold ridging pattern for the square, pentagonal and hexagonal films, respectively, showing a close resemblance with experimental film systems of similar size and shape. Rectangular films of large length to width ratio go through a transition in buckling shapes from the initial Euler mode, through the varicose mode into the antisymmetric telephone-cord mode. For all the film shapes, the ratio of the film height to the effective film width scales with the square root of eigenstrain and is independent of thickness. The bond-back mechanism determines the final wrinkle morphology and is governed by the eigenstrain value at the end of the buckling-up stage and the dimensionless parameter (Γ /EWeq)(Weq/t)3, relating the interface energy to the strain energy in the film.

  5. 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

  6. 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

  7. Pattern formation in granular binary mixtures under shear flow

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  8. 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

  9. Pattern formation induced by a differential shear flow

    NASA Astrophysics Data System (ADS)

    Stucchi, L.; Vasquez, Desiderio A.

    2013-02-01

    Fluid flow advecting one substance while others are immobilized can generate an instability in a homogeneous steady state of a reaction-diffusion-advection system. This differential-flow instability leads to the formation of steady spatial patterns in a moving reference frame. We study the effects of shear flow on this instability by considering two layers of fluid moving independently from each other, but allowing the substances to diffuse along and across the layers. We find that shear flow can generate instabilities even if the average flow velocity is zero for both substances. These instabilities are strongly dependent on which substance is advected by the shear flow. We explain these effects using the results of Taylor dispersion, where an effective diffusivity is enhanced by shear flow.

  10. 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

  11. 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.

  12. 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.

  13. Modulational instability and pattern formation in discrete dissipative systems.

    PubMed

    Mohamadou, Alidou; Kofané, Timoléon Crépin

    2006-04-01

    We report in this paper the study of modulated wave trains in the one-dimensional (1D) discrete Ginzburg-Landau model. The full linear stability analysis of the nonlinear plane wave solutions is performed by considering both the wave vector (q) of the basic states and the wave vector (Q) of the perturbations as free parameters. In particular, it is shown that a threshold exists for the amplitude and above this threshold, the induced modulational instability leads to the formation of ordered and disordered patterns. The theoretical findings have been numerically tested through direct simulations and have been found to be in agreement with the theoretical prediction. We show numerically that modulational instability is also an indicator of the presence of discrete solitons as were early predicted to exist in Ginzburg-Landau lattices.

  14. 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.

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

    DOE PAGES

    Geslin, Pierre -Antoine; McCue, Ian; Gaskey, Bernard; ...

    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

  16. Maternal control of pattern formation in early Caenorhabditis elegans embryos.

    PubMed

    Bowerman, B

    1998-01-01

    Genetic screens for recessive, maternal-effect, embryonic-lethal mutations have identified about 25 genes that control early steps of pattern formation in the nematode Caenorhabditis elegans. These maternal genes are discussed as belonging to one of three groups. The par group genes establish and maintain polarity in the one-cell zygote in response to sperm entry, defining an anterior/posterior body axis at least in part through interactions with the cyto-skeleton mediated by cortically localized proteins. Blastomere identity group genes act down-stream of the par group to specify the identities of individual embryonic cells, or blastomeres, using both cell autonomous and non-cell autonomous mechanisms. Requirements for the blastomere identity genes are consistent with previous studies suggesting that early asymmetric cleavages in the C. elegans embryo generate six "founder" cells that account for much of the C. elegans body plan. Intermediate group genes, most recently identified, may link the establishment of polarity in the zygote by par group genes to the localization of blastomere identity group gene functions. This review summarizes the known requirements for the members of each group, although it seems clear that additional regulatory genes controlling pattern formation in the early embryo have yet to be identified. An emerging challenge is to link the function of the genes in these three groups into interacting pathways that can account for the specification of the six founder cell identities in the early embryo, five of which produce somatic cell types and one of which produces the germline.

  17. 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

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  19. 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.

  20. 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.

  1. 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.

  2. Basic Aspects of the Formation and Activation of Boron Junctions Using Plasma Immersion Ion Implantation

    SciTech Connect

    Zschaetzsch, G.; Vandervorst, W.; Hoffmann, T.; Goossens, J.; Everaert, J.-L.; Agua Borniquel, J. I. del; Poon, T.

    2008-11-03

    This study investigates the basic aspects of junction formation using Plasma Immersion Ion Implantation using BF{sub 3} and addresses the role of (pre)amorphization, C(F)-co-implantation, plasma parameters (bias, dose) and the thermal anneal cycle (spike versus msec laser anneal). The basic physics are studied using Secondary Ion Mass Spectrometry, sheet resistance and using four point probe and RsL. Profiles with junction depths ranging from 10-12 nm and sheet resistance values below 800 Ohm/sq are readily achievable.

  3. Pattern formation and evolution in thin polymer films

    NASA Astrophysics Data System (ADS)

    Masson, Jean-Loup Didier

    2001-07-01

    Thin polymer films are important for many technologies. They are used as coatings, adhesives, lubricants and for device technologies, such as polymer based light-emitting diodes. Several concerns arise when processing and using thin polymer films. Properties of thin polymer films (e.g., viscosity, diffusion, glass transition temperature) are different from bulk properties due to finite size effects (e.g., confinement of the chains) and to interfacial interactions (e.g., presence of the free surface and the substrate). Moreover, the stability of the film on the substrate is of concern. Thin polymer films, of thickness h < 100 nm, fabricated on a substrate may rupture under destabilizing forces, such as van der Waals forces. Rupturing exposes the underlying substrate and the exposed regions will grow, provided that the spreading coefficient is negative. This process is known as dewetting. Thus far, two dewetting morphologies have been identified but little is understood about their formation and evolution. The first morphology consists of circular holes throughout the film and the second morphology is reminiscent of patterns associated with spinodal decomposition processes. In this research, we investigated four problems. First, we examined fundamental questions related to the formation and evolution of patterns on the substrate. We documented the existence of different dynamic stages of evolution associated with different driving forces for both "conventional" morphologies (circular holes and "spinodal-like"). Second, we discovered a new morphology that occurs in a thin random copolymer film on a silicon substrate. This morphology results from heterogeneous interactions of the chain segments with the substrate. Third, we examined flow processes in thin polymer films (chain dynamics near surfaces). We show that a fingering instability develop spontaneously at the moving liquid front when the film is below a critical thickness that depends on the length of the chains

  4. 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

  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. Formation Control of Multi-agent Systems via Distributed Pattern Decision

    NASA Astrophysics Data System (ADS)

    Sakurama, Kazunori; Azuma, Shun-Ichi; Sugie, Toshiharu

    This paper deals with a formation control problem of networked multi-agent systems via distributed pattern decision. We assume that several formation patterns are given without a leader which decides what formation pattern the group of agents should form. Each agent has to individually decide a possible formation pattern by watching the configuration of his neighborhood. Our control objective is to achieve one of the given formation patterns as a result of the distributed pattern decisions. We propose a new objective function consisting of formation errors on the cliques of networks, and design a formation controller based on the gradient flow of this clique-based objective function. The effectiveness of the proposed method is illustrated by simulations.

  7. Spatial pattern formation facilitates eradication of infectious diseases.

    PubMed

    Eisinger, Dirk; Thulke, Hans-Hermann

    2008-04-01

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

  8. Gradient-driven diffusion and pattern formation in crowded mixtures

    NASA Astrophysics Data System (ADS)

    Nandigrami, Prithviraj; Grove, Brandy; Konya, Andrew; Selinger, Robin L. B.

    2017-02-01

    Gradient-driven diffusion in crowded, multicomponent mixtures is a topic of high interest because of its role in biological processes such as transport in cell membranes. In partially phase-separated solutions, gradient-driven diffusion affects microstructure, which in turn affects diffusivity; a key question is how this complex coupling controls both transport and pattern formation. To examine these mechanisms, we study a two-dimensional multicomponent lattice gas model, where "tracer" molecules diffuse between a source and a sink separated by a solution of sticky "crowder" molecules that cluster to form dynamically evolving obstacles. In the high-temperature limit, crowders and tracers are miscible, and transport may be predicted analytically. At intermediate temperatures, crowders phase separate into clusters that drift toward the tracer sink. As a result, steady-state tracer diffusivity depends nonmonotonically on both temperature and crowder density, and we observe a variety of complex microstructures. In the low-temperature limit, crowders rapidly aggregate to form obstacles that are kinetically arrested; if crowder density is near the percolation threshold, resulting tracer diffusivity shows scaling behavior with the same scaling exponent as the random resistor network model. Though highly idealized, this simple model reveals fundamental mechanisms governing coupled gradient-driven diffusion, phase separation, and microstructural evolution in crowded mixtures.

  9. Pattern Formation in Dewetting Nanoparticle/Polymer Bilayers

    NASA Astrophysics Data System (ADS)

    Esker, Alan; Paul, Rituparna; Karabiyik, Ufuk; Swift, Michael; Hottle, John

    2008-03-01

    Comprised of inorganic cores and flexible organic coronae with 1 -- 2 nm diameter monodisperse sizes, polyhedral oligomeric silsesquioxanes (POSS) are ideal model nanofillers. Our discovery that one POSS derivative, trisilanolphenyl-POSS (TPP), can form Langmuir-Blodgett (LB) films on hydrophobic substrates, allows us to create thin film bilayers of precisely controlled thickness and architecture. Work with poly(t-butylacrylate) (PtBA)/TPP bilayers reveals a two-step dewetting mechanism in which the upper TPP layer dewets first, followed by the formation of isolated holes with intricate, fractal, nanofiller aggregates. Like the PtBA/TPP bilayers, polystyrene (PS)/TPP bilayers also undergo a two-step dewetting mechanism. However, the upper TPP layer initially forms cracks that may arise from mismatches in thermal expansion coefficients. These cracks then serve as nucleation sites for complete dewetting of the entire bilayer. Understanding the rich diversity of surface patterns that can be formed from relatively simple processes is a key feature of this work.

  10. Mechanistic Aspects in the Formation, Growth and Surface Functionalization of Metal Oxide Nanoparticles in Organic Solvents.

    PubMed

    Niederberger, Markus; Deshmukh, Rupali

    2017-04-04

    The synthesis of metal oxide nanoparticles in organic solvents, so-called nonaqueous (or nonhydrolytic) processes represent powerful alternatives to aqueous approaches and have become an independent research field. 10 years ago, when we published our first review on organic reaction pathways in nonaqueous sol-gel approaches,[1] the number of examples was relatively limited. Nowadays, it is almost impossible to provide an exhaustive overview. Here we review the development of the last few years, without neglecting pioneering examples, which help to follow the historical development. The importance of a profound understanding of mechanistic aspects of nanoparticle crystallization and formation mechanisms can't be overestimated, when it comes to the design of rational synthesis concepts under minimization of trial-and-error experiments. The main reason for the progress in mechanistic understanding lies in the availability of characterization tools that make it possible to monitor chemical reactions from the dissolution of the precursor to the nucleation and growth of the nanoparticles, by ex-situ methods involving sampling after different reaction times, but more and more also by in-situ studies. After a short introduction to experimental aspects of nonaqueous sol-gel routes to metal oxide nanoparticles, we provide an overview of the main and basic organic reaction pathways in these approaches. Afterwards, we summarize the main characterization methods to study formation mechanisms, and then we discuss in great depth the chemical formation mechanisms of many different types of metal oxide nanoparticles. The review concludes with a paragraph on selected crystallization mechanisms reported for nonaqueous systems and a few illustrative examples of nonaqueous sol-gel concepts applied to surface chemistry.

  11. Faraday instability and nonlinear pattern formation of a two-layer system: A reduced model

    NASA Astrophysics Data System (ADS)

    Bestehorn, Michael; Pototsky, Andrey

    2016-10-01

    Stability and pattern formation of a two-layer liquid system with large aspect ratio subjected to vertical harmonic oscillations is studied by means of an integrated boundary layer model. The lower layer rests on an oscillating solid substrate, the upper layer is separated by a deformable interface from the lower layer and bounded at the top with a second, free interface to the ambient passive air. The model is derived from the Navier-Stokes equations in long-wave approximation, including inertial terms. Applying a Floquet analysis, linear stability charts and dispersion relations are computed and compared with results from the full linearized Navier-Stokes equations and the long-wave approximation. Nonlinear Faraday patterns simultaneously occurring at the interface and at the film surface are studied by numerically solving the integrated boundary layer model in two and three spatial dimensions. For gravitationally stable two-layer films with a lighter fluid on top of the heavier fluid, we find squares, hexagons, quasiperiodic patterns with eightfold symmetry as well as localized states in the form of large scale depletion regions or finite depth holes, occurring at the interface and surface. For a Rayleigh-Taylor unstable combination (heavier fluid above the light one) we show that external vibration increases the lifetime of the film by delaying or completely suppressing the film rupture.

  12. 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.

  13. Pattern formation of Rayleigh-Bénard convection of cold water near its density maximum in a vertical cylindrical container.

    PubMed

    Li, You-Rong; Ouyang, Yu-Qing; Hu, Yu-Peng

    2012-10-01

    In order to understand the onset of convective instability and multiple stable convection patterns of buoyancy-driven convection of cold water near its density maximum in a vertical cylindrical container heated from below, a series of three-dimensional numerical simulations were performed. The aspect ratio of the container was 2 and Prandtl number of cold water was 11.57. The sidewall was considered to be perfectly adiabatic, and the density inversion parameter was fixed at 0.3. The result shows that the density inversion phenomenon in cold water has an important effect on the critical Rayleigh number for the onset of convection and the pattern formation at higher Rayleigh numbers. When the Rayleigh number varies from 3×10(3) to 1.2×10(5), eight stable, steady convection patterns are obtained under different initial conditions. The coexistence of multiple stable steady flow patterns is also observed within some specific ranges of the Rayleigh number.

  14. Versatile pattern generation of periodic, high aspect ratio Si nanostructure arrays with sub-50-nm resolution on a wafer scale

    PubMed Central

    2013-01-01

    We report on a method of fabricating variable patterns of periodic, high aspect ratio silicon nanostructures with sub-50-nm resolution on a wafer scale. The approach marries step-and-repeat nanoimprint lithography (NIL) and metal-catalyzed electroless etching (MCEE), enabling near perfectly ordered Si nanostructure arrays of user-defined patterns to be controllably and rapidly generated on a wafer scale. Periodic features possessing circular, hexagonal, and rectangular cross-sections with lateral dimensions down to sub-50 nm, in hexagonal or square array configurations and high array packing densities up to 5.13 × 107 structures/mm2 not achievable by conventional UV photolithography are fabricated using this top-down approach. By suitably tuning the duration of catalytic etching, variable aspect ratio Si nanostructures can be formed. As the etched Si pattern depends largely on the NIL mould which is patterned by electron beam lithography (EBL), the technique can be used to form patterns not possible with self-assembly methods, nanosphere, and interference lithography for replication on a wafer scale. Good chemical resistance of the nanoimprinted mask and adhesion to the Si substrate facilitate good pattern transfer and preserve the smooth top surface morphology of the Si nanostructures as shown in TEM. This approach is suitable for generating Si nanostructures of controlled dimensions and patterns, with high aspect ratio on a wafer level suitable for semiconductor device production. PMID:24289275

  15. Investigation of Vortical Flow Patterns in the Near Field of a Dynamic Low-Aspect-Ratio Cylinder

    NASA Astrophysics Data System (ADS)

    Gildersleeve, Samantha; Amitay, Michael

    2016-11-01

    The flowfield and associated flow structures of a low-aspect-ratio cylindrical pin were investigated experimentally in the near-field as the pin underwent wall-normal periodic oscillations. Under dynamic conditions, the pin is driven at the natural wake shedding frequency with an amplitude of 33% of its mean height. Additionally, a static pin was also tested at various mean heights of 0.5, 1.0, and 1.5 times the local boundary layer thickness to explore the effect of the mean height on the flowfield. Three-dimensional flowfields were reconstructed and analyzed from SPIV measurements where data were collected along streamwise planes for several spanwise locations under static and dynamic conditions. The study focuses on the incoming boundary layer as it interacts with the pin, as well as two main vortical formations: the arch-type vortex and the horseshoe vortex. Under dynamic conditions, the upstream boundary layer is thinner, relative to the baseline, and the downwash in the wake increases, resulting in a reduced wake deficit. These results indicate enhanced strength of the aforementioned vortical flow patterns under dynamic conditions. The flow structures in the near-field of the static/dynamic cylinder will be discussed in further detail. Supported by The Boeing Company.

  16. Convection-driven pattern formation in grass (Invited)

    NASA Astrophysics Data System (ADS)

    Daniels, K. E.; Thompson, S. E.

    2010-12-01

    Spatial patterns of 'dead' lawn grass have often been ascribed to Turing-type reaction-diffusion processes related to water scarcity. However, morphologically-similar patterns can also result from fluid convection. Therefore, we present an alternative hypothesis: that the air within the grass canopy is unstable to a convective instability, such that chill damage caused by falling cold air is responsible for the creation of brown and green bands of grass. We model the grass as a uniform porous medium of upright cylindrical rods subject to a temperature gradient and find that the resulting patterns are consistent with several features of small-scale vegetation patterns, including their length scale, rapid onset and transient nature. Finally, the predictions are found to be consistent with measurements made for a particular instance of lawn-patterning in North Carolina. We close by discussing the implications for other plant species. Lawn grass patterning at Duke University.

  17. Pattern formation in dielectric barrier discharges with different dielectric materials

    SciTech Connect

    Dong, L. F.; Fan, W. L.; Wang, S.; Ji, Y. F.; Liu, Z. W.; Chen, Q.

    2011-03-15

    The influence of dielectric material on the bifurcation and spatiotemporal dynamics of the patterns in dielectric barrier discharge in argon/air at atmospheric pressure is studied. It is found that pattern bifurcation sequences are different with different dielectric materials. The spatiotemporal dynamics of the hexagonal pattern in dielectric barrier discharge depends on the dielectric material. The hexagon pattern with glass dielectric is an interleaving of two rectangular sublattices appearing at different moments. The hexagon pattern with quartz dielectric is composed of one set of hexagonal lattice discharging twice in one half cycle of the applied voltage, one is at the rising edge and the other at the falling edge. It results in that the accumulation of wall charges in individual microdischarges in a hexagon pattern with quartz dielectric is greater than that with glass dielectric, which is in agreement with the electron density measurement by Stark broadening of Ar I 696.54 nm.

  18. Pattern formation during development of the embryonic cerebellum

    PubMed Central

    Dastjerdi, F. V.; Consalez, G. G.; Hawkes, R.

    2012-01-01

    The patterning of the embryonic cerebellum is vital to establish the elaborate zone and stripe architecture of the adult. This review considers early stages in cerebellar Purkinje cell patterning, from the organization of the ventricular zone to the development of Purkinje cell clusters—the precursors of the adult stripes. PMID:22493569

  19. Giant Amplification of Noise in Fluctuation-Induced Pattern Formation

    NASA Astrophysics Data System (ADS)

    Biancalani, Tommaso; Jafarpour, Farshid; Goldenfeld, Nigel

    2017-01-01

    The amplitude of fluctuation-induced patterns might be expected to be proportional to the strength of the driving noise, suggesting that such patterns would be difficult to observe in nature. Here, we show that a large class of spatially extended dynamical systems driven by intrinsic noise can exhibit giant amplification, yielding patterns whose amplitude is comparable to that of deterministic Turing instabilities. The giant amplification results from the interplay between noise and nonorthogonal eigenvectors of the linear stability matrix, yielding transients that grow with time, and which, when driven by the ever-present intrinsic noise, lead to persistent large amplitude patterns. This mechanism shows that fluctuation-induced Turing patterns are observable, and are not strongly limited by the amplitude of demographic stochasticity nor by the value of the diffusion coefficients.

  20. 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.

  1. Binding the Generations: Household Formation Patterns among Vietnamese Refugees.

    ERIC Educational Resources Information Center

    Haines, David W.

    2002-01-01

    Examines key features of Vietnamese refugees' household formation, reviewing sociohistorical data on household formation and structure in southern Vietnam during the period of the Republic, comparing these data with more recent data on southern and northern Vietnam, and considering U.S. Vietnamese refugee households based on the Office of Refugee…

  2. Convection-driven pattern formation in lawn grasses

    NASA Astrophysics Data System (ADS)

    Thompson, Sally; Daniels, Karen

    2009-11-01

    Spatial patterns of 'dead' lawn grass have often been ascribed to Turing-type reaction-diffusion processes related to water scarcity. We present an alternative hypothesis: that the air within the grass canopy is unstable to a convective instability, such that chill damage caused by falling cold air is responsible for the creation of brown and green bands of grass. This hypothesis is consistent with several features of small-scale vegetation patterns, including their length scale, rapid onset and transient nature. We find that the predictions of a porous medium convection model based are consistent with measurements made for a particular instance of lawn-patterning in North Carolina.

  3. Dynamics of formation of symmetrical patterns by chemotactic bacteria

    NASA Astrophysics Data System (ADS)

    Budrene, Elena O.; Berg, Howard C.

    1995-07-01

    MOTILE cells of Escherichia coli aggregate to form stable patterns of remarkable regularity when grown from a single point on certain substrates. Central to this self-organization is chemotaxis, the motion of bacteria along gradients of a chemical attractant that the cells themselves excrete1. Here we show how these complex patterns develop. The long-range spatial order arises from interactions between two multicellular aggregate structures: a 'swarm ring' that expands radially, and focal aggregates that have lower mobility. Patterning occurs through alternating domination by these two sources of excreted attractant (which we identify here as aspartate). The pattern geometries vary in a systematic way, depending on how long an aggregate remains active; this depends, in turn, on the initial concentration of substrate (here, succinate).

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

    PubMed Central

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

    2012-01-01

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

  5. Effects of Growth and Mutation on Pattern Formation in Tissues

    PubMed Central

    Mengel Pers, Benedicte; Krishna, Sandeep; Chakraborty, Sagar; Pigolotti, Simone; Sekara, Vedran; Semsey, Szabolcs; Jensen, Mogens H.

    2012-01-01

    In many developing tissues, neighboring cells enter different developmental pathways, resulting in a fine-grained pattern of different cell states. The most common mechanism that generates such patterns is lateral inhibition, for example through Delta-Notch coupling. In this work, we simulate growth of tissues consisting of a hexagonal arrangement of cells laterally inhibiting their neighbors. We find that tissue growth by cell division and cell migration tends to produce ordered patterns, whereas lateral growth leads to disordered, patchy patterns. Ordered patterns are very robust to mutations (gene silencing or activation) in single cells. In contrast, mutation in a cell of a disordered tissue can produce a larger and more widespread perturbation of the pattern. In tissues where ordered and disordered patches coexist, the perturbations spread mostly at boundaries between patches. If cell division occurs on time scales faster than the degradation time, disordered patches will appear. Our work suggests that careful experimental characterization of the disorder in tissues could pinpoint where and how the tissue is susceptible to large-scale damage even from single cell mutations. PMID:23144963

  6. 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

  7. New Aspects of the Formation of the β Pictoris Moving Group

    NASA Astrophysics Data System (ADS)

    Ortega, V. G.; de la Reza, R.; Jilinski, E.; Bazzanella, B.

    2004-07-01

    In a previous work, we explored the possibility that the β Pictoris moving group (BPMG), consisting of low-mass post-T Tauri stars, was formed near the Scorpius-Centaurus OB association. The cause of the formation could be a Type II supernova exploding either in Lower Centaurus Crux (LCC) or the Upper Centaurus Lupus (UCL), the two older subgroups of that association. Here we present new results for BPMG. A more detailed analysis of the orbit confinement in this group leads to a star distribution pattern at birth that can be considered as a representation of the density distribution in the natal cloud. We also propose a plausible origin for the supernova that could have triggered the star formation in BPMG by finding the past position of the runaway star HIP 46950. We find that this scenario is capable of explaining the origin of all the members of BPMG proposed by Zuckerman and coworkers and by Song and coworkers, with the exception of HIP 79881, which is probably an old main-sequence interloper.

  8. 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.

  9. 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.

  10. 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.

  11. Size segregated ring pattern formation in particle impactors

    NASA Astrophysics Data System (ADS)

    Saylor, J. R.; Fredericks, S. A.

    2016-11-01

    Typical particle impactors consist of a nozzle that directs a particle laden flow onto a plate, and is designed to capture particles greater than a cutoff diameter. Connected in series as a cascade, with each impactor designed to have a progressively smaller cutoff diameter, the particle size distribution can be measured. Typical impactors utilize a nozzle-to-plate distance S that is on the order of one nozzle diameter W, S / W 1 , and give a nominally Gaussian particle deposition pattern on the plate. We explored conditions where S / W < < 1 and observed deposition patterns consisting of very fine rings. Moreover, we found that the ring diameter increased with decreasing particle diameter and the ring thickness increased with particle diameter. These results suggest a potential method for sizing particles by using the mature technology of impactors in a different way. Potential mechanisms for how these ring patterns are formed will be discussed. We note that prior studies have observed conditions where particle deposition patterns exhibited "halos". These halos appear less distinct than the rings we have observed, and it is unclear whether they are related.

  12. Family Formation and Dissolution Patterns: Rural-Urban Differences.

    ERIC Educational Resources Information Center

    Bacon, Lloyd

    Patterns of relationships among the variables of pregnancy status at marriage, marital dissolution probabilities, residence and migration status, and race were ascertained. The data source was the 1967 Survey of Economic Opportunity, a large national probability sample expanded to U.S. population parameters. Relationships among these variables…

  13. 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

  14. Parameter domains for spots and stripes in mechanical models for biological pattern formation

    NASA Astrophysics Data System (ADS)

    Zhu, M.; Murray, J. D.

    1995-07-01

    Mechanochemical models for biological pattern formation have been applied to the development of a variety of patterning problems, such as feather germ primordia and cartilage formation in the vertebrate limb. Linear analysis has been the main technique for assessing the pattern formation potential of these models to date. In this paper we carry out a nonlinear analysis and numerical simulations of a generic model in two spatial dimensions. With these methods, we obtain conditions for generating specific spatial patterns such as stripes and spots, and divide the parameter space into domains giving rise to distinct types of pattern. We accomplish our goal through a study of model parameter domains by showing how different mechanical forces affect spatial patterning.

  15. 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

  16. Drying Mediated Pattern Formation From a Restricted Geometry

    NASA Astrophysics Data System (ADS)

    Xu, Jun

    2005-03-01

    There is much interest in causing patterns (of dyes, nanoparticles, or polymers) to emerge spontaneously on surfaces. A main characteristic pattern known as the ``coffee ring'' formed when the contact line of an evaporating drop becomes pinned, ensuring that liquid evaporating from the edge is replenished by liquid from the interior, so that outward flow carries the nonvolatile dispersion to the edge. Here we report the remarkable observation that a complex structure consisting of a periodic family of hundreds of concentric rings with definite spacing can be achieved when solvent evaporates irreversible from a restricted geometry. Each ring is approximately nanometers high and micron wide. The observed micron size rings are governed by the imposed geometry, the solution concentration and the solvent properties. The mechanism, which is believed to be a series of successive pinning and depinning of the contact line as solvent evaporates, will be discussed. This simple yet novel approach affords a means to produce and organize surface patterns in a well-ordered gradient fashion.

  17. 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.

  18. 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.

  19. 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''.

  20. Spatial pattern formation induced by Gaussian white noise.

    PubMed

    Scarsoglio, Stefania; Laio, Francesco; D'Odorico, Paolo; Ridolfi, Luca

    2011-02-01

    The ability of Gaussian noise to induce ordered states in dynamical systems is here presented in an overview of the main stochastic mechanisms able to generate spatial patterns. These mechanisms involve: (i) a deterministic local dynamics term, accounting for the local rate of variation of the field variable, (ii) a noise component (additive or multiplicative) accounting for the unavoidable environmental disturbances, and (iii) a linear spatial coupling component, which provides spatial coherence and takes into account diffusion mechanisms. We investigate these dynamics using analytical tools, such as mean-field theory, linear stability analysis and structure function analysis, and use numerical simulations to confirm these analytical results.

  1. Pattern formation and growth kinetics in eutectic systems

    NASA Astrophysics Data System (ADS)

    Teng, Jing

    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 rod, 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

  2. Pattern formation in granular and granular-fluid flows

    NASA Astrophysics Data System (ADS)

    Duong, Nhat-Hang P.

    Particles and suspensions of particles in fluids are regularly used in many engineering disciplines such as catalysis and reaction engineering, environmental engineering, pharmaceutical engineering, etc. A few issues that are commonly encountered include ensuring homogeneity in pharmaceutical suspensions, predicting particle transport in atmospheric and effluent streams, and manufacturing uniform composite materials. Yet the fundamental study of particle motions in granular media or in highly concentrated granular suspensions has received little attention. Relevant issues of research interest include development of adaptive models that permit wide ranges of particle concentrations, improvement of analyses that allow physical interpretation of particle motions in any medium, of scales ranging from particle size to system size, and accurate validation of theoretical with experimental data. Given the above shortcomings, this dissertation will focus on investigating basic transport behavior of particles in fluids and developing predictive models for granular media and granular suspensions. Emphasis will be given to combining experiments with computations through examples of pattern forming phenomena in a granular medium and a dense granular-fluid system. The background motivation and the objectives of this dissertation are stated in the opening chapter 1. The next three chapters address these objectives in detail. First, chapter 2 presents experimental evidence, descriptions, and characteristics of novel patterns in a dense granular suspension. This is followed by chapter 3 in which a mean-field continuum model is derived to further elucidate the reported patterning phenomena. Chapter 4 uncovers several novel granular patterns experimentally and is concluded with a coarse-grained phenomenological model for granular surface flows. Lastly, chapter 5 closes the dissertation with conclusions and possible future directions. This work provides additional understanding and

  3. 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

  4. Automated numerical simulation of biological pattern formation based on visual feedback simulation framework

    PubMed Central

    Sun, Mingzhu; Xu, Hui; Zeng, Xingjuan; Zhao, Xin

    2017-01-01

    There are various fantastic biological phenomena in biological pattern formation. Mathematical modeling using reaction-diffusion partial differential equation systems is employed to study the mechanism of pattern formation. However, model parameter selection is both difficult and time consuming. In this paper, a visual feedback simulation framework is proposed to calculate the parameters of a mathematical model automatically based on the basic principle of feedback control. In the simulation framework, the simulation results are visualized, and the image features are extracted as the system feedback. Then, the unknown model parameters are obtained by comparing the image features of the simulation image and the target biological pattern. Considering two typical applications, the visual feedback simulation framework is applied to fulfill pattern formation simulations for vascular mesenchymal cells and lung development. In the simulation framework, the spot, stripe, labyrinthine patterns of vascular mesenchymal cells, the normal branching pattern and the branching pattern lacking side branching for lung branching are obtained in a finite number of iterations. The simulation results indicate that it is easy to achieve the simulation targets, especially when the simulation patterns are sensitive to the model parameters. Moreover, this simulation framework can expand to other types of biological pattern formation. PMID:28225811

  5. 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

  6. 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.

  7. [Family formation in Flanders: new patterns, different timing].

    PubMed

    Lee, H Y; Rajulton, F; Wijewickrema, S; Lesthaeghe, R

    1987-01-01

    "The article presents a statistical study of the starting age and the speed of transitions in the process of family formation in Flanders. It contrasts two sets of generations, three groups according to educational achievement and three groups with differing religious practice. The methodology of shifted proportional hazard models is used and transition probabilities are fed into a semi-Markovian chain. Higher educational achievement results in later starting points, but not in a differing pace once started. By contrast, lower religious involvement speeds up the transitions to first sexual contact and premarital cohabitation, while it considerably retards the transition to parenthood among the generations born after 1950." (SUMMARY IN ENG AND FRE)

  8. [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.

  9. [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.

  10. Radial-pattern formation in the polycarbonate substratum of recordable compact disks

    NASA Astrophysics Data System (ADS)

    Tanimura, M.; Ishikawa, I.; Tachibana, M.; Shinozaki, K.; Kojima, K.

    2001-09-01

    A radial pattern is found to form in the polycarbonate (PC) substratum of a recordable compact disk. Characteristic features of the pattern are that it is composed of about 80 needle-like regions, the shape of which closely resembles a thin film. In addition, white light is found to scatter at the needle-like region/matrix boundaries. This suggests that the PC substratum may have inferior transparency due to the formation of this pattern. Thus, it is important to understand the bifurcation of the radial-pattern formation from the viewpoint of materials science and engineering. Based on the mechanics of the PC viscous fluid, it has been found that the bifurcation of the pattern formation has a Reynolds number of about 10-3.

  11. STELLAR ELEMENTAL ABUNDANCE PATTERNS: IMPLICATIONS FOR PLANET FORMATION

    SciTech Connect

    Chambers, J. E.

    2010-11-20

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

  12. 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

  13. Longitudinal Relations between Personality Traits and Aspects of Identity Formation during Adolescence

    ERIC Educational Resources Information Center

    Hill, Patrick L.; Allemand, Mathias; Grob, Sabine Zehnder; Peng, Aristide; Morgenthaler, Christoph; Kappler, Christoph

    2013-01-01

    The current study focused on three aspects of identity development relevant to the adolescent years: being an authentic person, perceiving control over and consistency in one's environment, and having consistent expectations from close others. In a two-wave study of adolescents (n = 750), we examined how these aspects change over the course of a…

  14. 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.

  15. 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.

  16. Controlled spin pattern formation in multistable cavity-polariton systems

    NASA Astrophysics Data System (ADS)

    Gavrilov, S. S.; Kulakovskii, V. D.

    2016-12-01

    Theoretical studies are performed of planar cavity-polariton systems under resonant optical excitation. We show that if the cavity is spatially anisotropic, the polariton spin is highly sensitive to the pump polarization direction, which can be used to modulate the circular polarization of the output light. In particular, when the right- and left-circular components of the incident wave have equal intensities and mutually opposite angular momenta, the pump has strictly linear yet angle-dependent polarization and as such brings about a periodic angular variation of the polariton spin. Free motion of polaritons is the other factor determining the shape of the cavity-field distribution. Such externally driven and highly tunable spin patterns represent a counterpart of spin shaping in nonresonantly excited Bose-Einstein condensates of cavity polaritons.

  17. 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.

  18. Pattern formation due to non-linear vortex diffusion

    NASA Astrophysics Data System (ADS)

    Wijngaarden, Rinke J.; Surdeanu, R.; Huijbregtse, J. M.; Rector, J. H.; Dam, B.; Einfeld, J.; Wördenweber, R.; Griessen, R.

    Penetration of magnetic flux in YBa 2Cu 3O 7 superconducting thin films in an external magnetic field is visualized using a magneto-optic technique. A variety of flux patterns due to non-linear vortex diffusion is observed: (1) Roughening of the flux front with scaling exponents identical to those observed in burning paper including two distinct regimes where respectively spatial disorder and temporal disorder dominate. In the latter regime Kardar-Parisi-Zhang behavior is found. (2) Fractal penetration of flux with Hausdorff dimension depending on the critical current anisotropy. (3) Penetration as ‘flux-rivers’. (4) The occurrence of commensurate and incommensurate channels in films with anti-dots as predicted in numerical simulations by Reichhardt, Olson and Nori. It is shown that most of the observed behavior is related to the non-linear diffusion of vortices by comparison with simulations of the non-linear diffusion equation appropriate for vortices.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. Fractal pattern formation in the Ziff Gulari Barshad model

    NASA Astrophysics Data System (ADS)

    Provata, A.; Noussiou, V. K.

    2007-02-01

    The dynamics of the Ziff-Gulari-Barshad (ZGB) model is studied on three different two-dimensional (2D) lattices: square (sq) lattice, hexagonal-honeycomb (hex-hon) lattice and purely hexagonal (hex) lattice. The effects of the support geometry on the steady state and the dynamics are assessed. In all 2D lattice geometries the ZGB model is shown to exhibit non-equilibrium phase transitions of the first and second order, but the critical values of the kinetic parameters depend crucially on the substrate geometry. Clustering and island formation are observed in all ranges of parameters, but the clusters are fractal only outside the active catalytic region. The fractal dimensions depend on the kinetic parameters.

  4. Pattern formation at liquid interfaces II. The KI/chloral hydrate/starch system

    NASA Astrophysics Data System (ADS)

    Liu, Cliff Zeh-Wen; Knobler, Charles M.

    1992-02-01

    Measurements are reported of pattern formation at a liquid interface produced by a photochemical reaction involving the system KI/chloral hydrate/ starch. The dependence of the wavelength on the concentrations of the reactants, the viscosity, and the height of the sample has been examined. It is concluded that the pattern is produced by a hydrodynamic mechanism.

  5. Surface pattern formation during MeV energy ion beam irradiation

    SciTech Connect

    Srivastava, S. K.; Nair, K. G. M.; Kannan, R. Kamala; Kamruddin, M.; Panigrahi, B. K.; Tyagi, A. K.

    2012-06-05

    Surface patterning during high energy heavy ion irradiation is a relatively recent observation. We report in this paper the results of a study on the formation of self organized ripple patterns on silica surface irradiated with MeV energy gold ions.

  6. 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.

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

    NASA Astrophysics Data System (ADS)

    Betterton, Meredith Diane

    2000-11-01

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

  8. 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

  9. Pattern formation and temporal undulations of plane magnetic droplet

    NASA Astrophysics Data System (ADS)

    Singh, Chamkor; Das, Arup Kumar; Das, Prasanta Kumar

    2016-11-01

    In this study, we numerically investigate the time-dependent response of a ferrofluid droplet under an impulsively applied uniform magnetic field in a zero gravity environment. It is identified that two characteristic non-dimensional groups, namely, the Laplace number La and the magnetic Bond number Bom , primarily influence the response of the droplet. It is found that the nature of the time response can be either monotonic or undulating depending on the parameters. The transition between the two is smooth. In addition to the previously well-known regimes of elliptic and acicular ferrofluid droplet shapes, a new regime on the La - Bom plane is found where we observe some unique bifurcating patterns at the poles of the droplet. The temporal aperiodic to periodic mode transition on the La - Bom plane is found to be governed by La and the spatial droplet deformation and its final equilibrium configuration is found to be governed by Bom . The mechanism behind the elliptic to non-elliptic or elliptic to bifurcated shape transitions is discussed. The authors gratefully acknowledge the support of the Council of Scientific and Industrial Research, New Delhi, India, for the present work.

  10. 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.

  11. Non-linear diffusion and pattern formation in vortex matter

    NASA Astrophysics Data System (ADS)

    Wijngaarden, Rinke J.; Surdeanu, R.; Huijbregtse, J. M.; Rector, J. H.; Dam, B.; Griessen, R.; Einfeld, J.; Woerdenweber, R.

    2000-03-01

    Penetration of magnetic flux in YBa_2Cu_3O7 superconducting thin films and crystals in externally applied magnetic fields is visualized with a magneto-optical technique. A variety of flux patterns due to non-linear vortex behavior is observed: 1. Roughening of the flux front^1 with scaling exponents identical to those observed in burning paper^2. Two regimes are found where respectively spatial disorder and temporal disorder dominate. In the latter regime Kardar-Parisi-Zhang behavior is found. 2. Roughening of the flux profile similar to the Oslo model for rice-piles. 3. Fractal penetration of flux^3 with Hausdorff dimension depending on the critical current anisotropy. 4. Penetration as 'flux-rivers'. 5. The occurrence of commensurate and incommensurate channels in films with anti-dots as predicted in numerical simulations by Reichhardt, Olson and Nori^4. By comparison with numerical simulations, it is shown that most of the observed behavior can be explained in terms of non-linear diffusion of vortices. ^1R. Surdeanu, R.J. Wijngaarden, E. Visser, J.M. Huijbregtse, J.H. Rector, B. Dam and R. Griessen, Phys.Rev. Lett. 83 (1999) 2054 ^2J. Maunuksela, M. Myllys, O.-P. Kähkönen, J. Timonen, N. Provatas, M.J. Alava, T. Ala-Nissila, Phys. Rev. Lett. 79, 1515 (1997) ^3R. Surdeanu, R.J. Wijngaarden, B. Dam, J. Rector, R. Griessen, C. Rossel, Z.F. Ren and J.H. Wang, Phys Rev B 58 (1998) 12467 ^4C. Reichhardt, C.J. Olson and F. Nori, Phys. Rev. B 58, 6534 (1998)

  12. Pattern formation in stochastic systems: Magnetized billiards and mitotic spindles

    NASA Astrophysics Data System (ADS)

    Schaffner, Stuart C.

    vital for spindle formation.

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

    PubMed Central

    Xu, Li; Zhang, Guang; Cui, Haoyue

    2016-01-01

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

  14. A biochemical hypothesis on the formation of fingerprints using a turing patterns approach

    PubMed Central

    2011-01-01

    Background Fingerprints represent a particular characteristic for each individual. Characteristic patterns are also formed on the palms of the hands and soles of the feet. Their origin and development is still unknown but it is believed to have a strong genetic component, although it is not the only thing determining its formation. Each fingerprint is a papillary drawing composed by papillae and rete ridges (crests). This paper proposes a phenomenological model describing fingerprint pattern formation using reaction diffusion equations with Turing space parameters. Results Several numerical examples were solved regarding simplified finger geometries to study pattern formation. The finite element method was used for numerical solution, in conjunction with the Newton-Raphson method to approximate nonlinear partial differential equations. Conclusions The numerical examples showed that the model could represent the formation of different types of fingerprint characteristics in each individual. PMID:21711537

  15. How Temporal and Spatial Aspects of Presenting Visualizations Affect Learning about Locomotion Patterns

    ERIC Educational Resources Information Center

    Imhof, Birgit; Scheiter, Katharina; Edelmann, Jorg; Gerjets, Peter

    2012-01-01

    Two studies investigated the effectiveness of dynamic and static visualizations for a perceptual learning task (locomotion pattern classification). In Study 1, seventy-five students viewed either dynamic, static-sequential, or static-simultaneous visualizations. For tasks of intermediate difficulty, dynamic visualizations led to better…

  16. 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

  17. Formation of bromate in sulfate radical based oxidation: mechanistic aspects and suppression by dissolved organic matter.

    PubMed

    Lutze, Holger V; Bakkour, Rani; Kerlin, Nils; von Sonntag, Clemens; Schmidt, Torsten C

    2014-04-15

    Sulfate radical based oxidation is discussed being a potential alternative to hydroxyl radical based oxidation for pollutant control in water treatment. However, formation of undesired by-products, has hardly been addressed in the current literature, which is an issue in other oxidative processes such as bromate formation in ozonation of bromide containing water (US-EPA and EU drinking water standard of bromate: 10 μg L(-1)). Sulfate radicals react fast with bromide (k = 3.5 × 10(9) M(-1) s(-1)) which could also yield bromate as final product. The mechanism of bromate formation in aqueous solution in presence of sulfate radicals has been investigated in the present paper. Further experiments were performed in presence of humic acids and in surface water for investigating the relevance of bromate formation in context of pollutant control. The formation of bromate by sulfate radicals resembles the well described mechanism of the hydroxyl radical based bromate formation. In both cases hypobromous acid is a requisite intermediate. In presence of organic matter formation of bromate is effectively suppressed. That can be explained by formation of superoxide formed in the reaction of sulfate radicals plus aromatic moieties of organic matter, since superoxide reduces hypobromous acid yielding bromine atoms and bromide. Hence formation of bromate can be neglected in sulfate radical based oxidation at typical conditions of water treatment.

  18. 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.

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

    PubMed

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

    2004-01-01

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

  20. 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

  1. Chirality as a physical aspect of structure formation in biological macromolecular systems

    NASA Astrophysics Data System (ADS)

    Malyshko, E. V.; Tverdislov, V. A.

    2016-08-01

    A novel regularity of hierarchical structures is found in the formation of chiral biological macromolecular systems. The formation of structures with alternating chirality (helical structures) serves as an instrument of stratification. The ability of a carbon atom to form chiral compounds is an important factor that determined the carbon basis of living systems on the Earth as well as their development through a series of chiral bifurcations. In the course of biological evolution, the helical structures became basic elements of the molecular machines in the cell. The discreteness of structural levels allowed the mechanical degrees of freedom formation in the molecular machines in the cell.

  2. Wavelength Analysis of Interface between Two Miscible Solutions Observed in Formation of Fractal Pattern

    NASA Astrophysics Data System (ADS)

    Shimokawa, Michiko; Takami, Toshiya

    2014-04-01

    When a droplet of a higher-density solution (HDS) is placed on top of a lower-density solution (LDS), the HDS draws a fractal pattern on the surface of the LDS. Before the fractal pattern is formed, a stick-like pattern with a periodic structure emerges in a region surrounding the surface pattern due to interfacial instability. We experimentally measure the wavelength of this stick-like pattern. The wavelength increases with the volume of the HDS and is independent of the viscosities of the two solutions. To understand the stick generation, we propose a model of miscible viscous fingering whose boundary conditions are similar to those of the experiments. The wavelength obtained from the model agrees with the experimentally obtained wavelength. The formation of the fractal pattern is discussed by comparing it with the viscous fingering.

  3. 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.

  4. 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

  5. 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.

  6. 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

  7. Spinodal instability and pattern formation in thin liquid films confined between two plates.

    PubMed

    Verma, Ruhi; Sharma, Ashutosh; Banerjee, Indrani; Kargupta, Kajari

    2006-04-01

    The instability, morphology and pattern formation engendered by the van der Waals force in a thin liquid film of thickness h confined between two closely placed solid surfaces (at distance d > h) are investigated based on nonlinear 3D simulations. The initial and the final stages of dewetting and pattern formation are found to be crucially dependent on the volumetric (thickness) ratio of air and liquid and its deviation from the location of the maximum of the spinodal parameter versus volumetric ratio curve. On a low energy surface, relatively thinner films and wider air gaps favor initial dewetting of the lower plate by the formation of holes, whereas thicker films with thinner air gaps initially evolve by the formation of columns/bridges that join the upper plate. In the later stage of evolution, the initial holes in thinner films evolve into columns/drops, while a rapid coalescence of columns in the thicker films eventually causes formation of holes. Thus, a phase inversion, either from liquid-in-air to air-in-liquid dispersion or vice versa, occurs during the final stages of evolution. A thin film confined between two high-energy solid surfaces forms columns (bridges) only when its mean thickness, h0, is greater than a critical thickness (hc) or the air gap is smaller than a critical distance. The patterns can be aligned by using a topographically patterned confining surface. Conditions on pattern periodicity, amplitude, and the volumetric ratio of air and liquid in the gap are explored for the formation of various types of ordered patterns including annular rings of columns, concentric ripples, parallel channels and a rectangular array of complex features. The results are of significance in soft lithographies such as LISA, soft stamping and capillary force lithography.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Drinking pattern and socio-cultural aspects on immune response: an overview.

    PubMed

    Romeo, Javier; Wärnberg, Julia; Marcos, Ascensión

    2010-08-01

    Social acceptance of drinking involves social and cultural roles and has important implications for public health. Since extensive evidence indicates that alcohol possesses immunomodulatory properties, scientists have recently debated the influence of alcohol consumption on the immune response, particularly in countries where drinking in a social setting is a part of cultural identity. Experimental and clinical data support the conclusion that alcohol is a potent immunomodulator. While high alcohol consumption suppresses a wide range of immune responses, leading to an increased incidence of a number of infectious diseases, moderate alcohol consumption may have a beneficial impact on the immune system, compared to alcohol abuse or abstinence, most likely due to the multiple components of polyphenol-rich alcoholic contributing to the protective effect seen for moderate alcohol consumption on CVD and the immune system. Despite this, the scientific literature appears to be concerned about the diseases associated with excessive drinking in some societies and cultures. Thus, the present review recognizes the importance to consider social and cultural aspects of drinking when examining the whole dimension of alcohol consumption (amount, beverage type, frequency and variability), in order to estimate global risk of consequences on host defence to better understand alcohol-related harm or benefit.

  13. Microlens formation in microgel/gold colloid composite materials via photothermal patterning.

    PubMed

    Jones, Clinton D; Serpe, Michael J; Schroeder, Laura; Lyon, L Andrew

    2003-05-07

    We report on the nature of photothermally patterned regions inside self-assembled hydrogel nanoparticle materials containing coassembled colloidal Au. These composite materials are prepared from approximately 226-nm diameter particles composed of the environmentally responsive polymer, poly(N-isopropylacrylamide) (pNIPAm). Upon centrifugation to achieve a proper volume fraction, these close-packed assemblies display a sharp Bragg diffraction peak in the midvisible region of the spectrum and can be reversibly converted into a nondiffracting glassy material as the temperature is raised above the characteristic phase transition temperature of the polymer. The addition of 16-nm colloidal Au prior to centrifugation allows the homogeneous distribution of metal nanoparticles throughout the close-packed material. Localized heating is then possible upon excitation of the Au plasmon absorption with a frequency doubled Nd:YAG laser (lambda = 532 nm). Such localized heating events lead to patterned regions of ordered crystalline phases inside of bulk glassy phases. We illustrate that the nature of the locally patterned area results in the formation of a microlens due to density/refractive index gradient in the patterned crystalline region. The Gaussian power distribution of the incident beam is thought to be a contributing factor in the microlens formation. Microlens formation is shown by observing interference patterns similar to Newton's rings, which change over time as the region is formed. A true hallmark of the lens is also demonstrated by focusing an image through the patterned structure.

  14. Temporal Patterns of Ant Diversity across a Mountain with Climatically Contrasting Aspects in the Tropics of Africa

    PubMed Central

    Munyai, Thinandavha Caswell; Foord, Stefan Hendrik

    2015-01-01

    Factors that drive species richness over space and time are still poorly understood and are often context specific. Identifying these drivers for ant diversity has become particularly relevant within the context of contemporary global change events. We report on a long-term bi-annual (wet and dry seasons), standardized sampling of epigeal ants over a five year period on the mesic and arid aspects of an inselberg (Soutpansberg Mountain Range) in the tropics of Africa. We detail seasonal, annual and long-term trends of species density, test the relative contribution of geometric constraints, energy, available area, climate, local environmental variables, time, and space in explaining ant species density patterns through Generalized Linear Mixed Models (GLMM) where replicates were included as random factors to account for temporal pseudo-replication. Seasonal patterns were very variable and we found evidence of decreased seasonal variation in species density with increased elevation. The extent and significance of a decrease in species density with increased elevation varied with season. Annual patterns point to an increase in ant diversity over time. Ant density patterns were positively correlated with mean monthly temperature but geometric constraints dominated model performance while soil characteristics were minor correlates. These drivers and correlates accounted for all the spatio-temporal variability in the database. Ant diversity was therefore mainly determined by geometric constraints and temperature while soil characteristics (clay and carbon content) accounted for smaller but significant amounts of variation. This study documents the role of season, elevation and their interaction in affecting ant species densities while highlighting the importance of neutral processes and temperature in driving these patterns. PMID:25774670

  15. Temporal patterns of ant diversity across a mountain with climatically contrasting aspects in the tropics of Africa.

    PubMed

    Munyai, Thinandavha Caswell; Foord, Stefan Hendrik

    2015-01-01

    Factors that drive species richness over space and time are still poorly understood and are often context specific. Identifying these drivers for ant diversity has become particularly relevant within the context of contemporary global change events. We report on a long-term bi-annual (wet and dry seasons), standardized sampling of epigeal ants over a five year period on the mesic and arid aspects of an inselberg (Soutpansberg Mountain Range) in the tropics of Africa. We detail seasonal, annual and long-term trends of species density, test the relative contribution of geometric constraints, energy, available area, climate, local environmental variables, time, and space in explaining ant species density patterns through Generalized Linear Mixed Models (GLMM) where replicates were included as random factors to account for temporal pseudo-replication. Seasonal patterns were very variable and we found evidence of decreased seasonal variation in species density with increased elevation. The extent and significance of a decrease in species density with increased elevation varied with season. Annual patterns point to an increase in ant diversity over time. Ant density patterns were positively correlated with mean monthly temperature but geometric constraints dominated model performance while soil characteristics were minor correlates. These drivers and correlates accounted for all the spatio-temporal variability in the database. Ant diversity was therefore mainly determined by geometric constraints and temperature while soil characteristics (clay and carbon content) accounted for smaller but significant amounts of variation. This study documents the role of season, elevation and their interaction in affecting ant species densities while highlighting the importance of neutral processes and temperature in driving these patterns.

  16. The RADICLELESS1 gene is required for vascular pattern formation in rice.

    PubMed

    Scarpella, Enrico; Rueb, Saskia; Meijer, Annemarie H

    2003-02-01

    The molecular mechanisms through which the complex patterns of plant vascular tissues are established are largely unknown. The highly ordered, yet simple, striate array of veins of rice leaves represents an attractive system to study the dynamics underlying pattern formation. Here we show that mutation in the RADICLELESS1 (RAL1) gene results in distinctive vascular pattern defects. In ral1 embryonic scutella, secondary veins are absent and in the prematurely aborted and discontinuous primary veins, cells are misaligned to each other. In ral1 leaves, longitudinal and commissural (transverse) veins display altered spacing and the commissural veins additionally show atypical branching and interruptions in their continuity. The vascular pattern alterations of ral1 occur in the context of normally shaped leaf primordia. Anatomical inspection and analysis of the expression of the procambium specification marker Oshox1-GUS and of the auxin-inducible reporter DR5-GUS demonstrates that all the vascular patterning aberrations of ral1 originate from defects in the procambium, which represents the earliest identifiable stage of vascular development. Furthermore, the ral1 mutant is unique in that procambium formation in leaf primordium development is delayed. Finally, the ral1 vascular patterning distortions are associated with a defective response to auxin and with an enhanced sensitivity to cytokinin. ral1 is the first mutant impaired in both procambium development and vascular patterning to be isolated in a monocot species.

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

    NASA Astrophysics Data System (ADS)

    Ewing, R. C.; Kocurek, G.

    2015-12-01

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

  18. 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.

  19. Aspects of glycosidic bond formation in aqueous solution: chemical bonding and the role of water.

    PubMed

    Stubbs, John M; Marx, Dominik

    2005-04-22

    A model of the specific acid-catalyzed glycosidic bond formation in liquid water at ambient conditions is studied based on constrained Car-Parrinello ab initio molecular dynamics. Specifically the reaction of alpha-D-glucopyranose and methanol is found to proceed by a D(N)A(N) mechanism. The D(N) step consists of a concerted protonation of the O(1) hydroxyl leaving group; this process results in the breaking of the C(1)-O(1) bond, and oxocarbenium ion formation involving C(1)=O(5). The second step, A(N), is the formation of the C(1)-O(m) glycosidic bond, deprotonation of the methanol hydroxyl group O(m)H(m), and re-formation of the C(1)-O(5) single bond. A focus of this study is the analysis of the electronic structure during this condensed phase reaction relying on both Boys/Wannier localized orbitals and the electron localization function ELF. This analysis allows the clear elucidation of the chemical bonding features of the intermediate bracketed by the D(N) and A(N) steps, which is a non-solvent equilibrated oxocarbenium cation. Most interestingly, it is found that the oxygen in the pyranose ring becomes "desolvated" upon double bond/oxocarbenium formation, whereas it is engaged in the hydrogen-bonded water network before and after this period. This demonstrates that hydrogen bonding and thus the aqueous solvent play an active role in this reaction implying that microsolvation studies in the gas phase, both theoretical and experimental, might lead to qualitatively different reaction mechanisms compared to solution.

  20. Studies on the mechanism of retinoid-induced pattern duplications in the early chick limb bud: temporal and spatial aspects

    PubMed Central

    1985-01-01

    All-trans-retinoic acid causes striking digit pattern changes when it is continuously released from a bead implanted in the anterior margin of an early chick wing bud. In addition to the normal set of digits (234), extra digits form in a mirror-symmetrical arrangement, creating digit patterns such as a 432234. These retinoic acid-induced pattern duplications closely mimic those found after grafts of polarizing region cells to the same positions with regard to dose-response, timing, and positional effects. To elucidate the mechanism by which retinoic acid induces these pattern duplications, we have studied the temporal and spatial distribution of all-trans-retinoic acid and its potent analogue TTNPB in these limb buds. We find that the induction process is biphasic: there is an 8-h lag phase followed by a 6-h duplication phase, during which additional digits are irreversibly specified in the sequence digit 2, digit 3, digit 4. On average, formation of each digit seems to require between 1 and 2 h. The tissue concentrations, metabolic pattern, and spatial distribution of all- trans-retinoic acid and TTNPB in the limb rapidly reach a steady state, in which the continuous release of the retinoid is balanced by loss from metabolism and blood circulation. Pulse-chase experiments reveal that the half-time of clearance from the bud is 20 min for all-trans- retinoic acid and 80 min for TTNPB. Manipulations that change the experimentally induced steep concentration gradient of TTNPB suggest that a graded distribution of retinoid concentrations across the limb is required during the duplication phase to induce changes in the digit pattern. The extensive similarities between results obtained with retinoids and with polarizing region grafts raise the possibility that retinoic acid serves as a natural "morphogen" in the limb. PMID:4055899

  1. 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…

  2. 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.

  3. The Impact of Course Delivery Format on Wellness Patterns of University Students

    ERIC Educational Resources Information Center

    Everhart, Kim; Dimon, Chelsea

    2013-01-01

    University students (N = 103) enrolled in multiple wellness courses at a small northeastern public university completed a questionnaire measuring wellness patterns at the beginning and end of a wellness course delivered totally on line (web-based), in the traditional classroom, or in a mix of the two formats (blended). Attrition of participants…

  4. Global bifurcation analysis and pattern formation in homogeneous diffusive predator-prey systems

    NASA Astrophysics Data System (ADS)

    Wang, Jinfeng; Wei, Junjie; Shi, Junping

    2016-02-01

    The dynamics of a general diffusive predator-prey system is considered. Existence and nonexistence of non-constant positive steady state solutions are shown to identify the ranges of parameters of spatial pattern formation. Bifurcations of spatially homogeneous and nonhomogeneous periodic solutions as well as non-constant steady state solutions are studied.

  5. Is sputtering relevant for ion-induced self-organized pattern formation?

    NASA Astrophysics Data System (ADS)

    Hofsäss, Hans; Bobes, Omar; Zhang, Kun

    2013-04-01

    Recently it was reported that ion-induced mass redistribution rather than sputtering would solely determine ripple pattern formation of ion-irradiated surfaces. We investigate the pattern formation on Si irradiated with Xe ions with energies of 5 and 10 keV. Sputter yield and collision cascade characteristics vary strongly as function of ion energy, ion mass and substrate material and allow us to investigate the contributions of curvature dependent erosion as well as mass redistribution. The experimental results are compared with calculations of the curvature coefficients Sx and Sy. Parameters required for the calculations are extracted from Monte Carlo simulations with program SDTrimSP. The calculated curvature coefficients show that mass redistribution is dominant for parallel ripple formation in most cases. The angle where the pattern orientation changes from parallel to perpendicular ripples is however related to curvature dependent sputtering. We discuss the possibilities to tune the different contributions to pattern formation and examine the possibility to completely eliminate mass redistribution effects.

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

    SciTech Connect

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

    1999-07-06

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

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

    DOE PAGES

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

    2009-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-03-01

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

  9. Histological aspects of the "fixed-particle" model of stone formation: animal studies.

    PubMed

    Khan, Saeed R

    2017-02-01

    Crystallization by itself is not harmful as long as the crystals are not retained in the kidneys and are allowed to pass freely down the renal tubules to be excreted in the urine. A number of theories have been proposed, and studies performed, to determine the mechanisms involved in crystal retention within the kidneys. It has been suggested that urinary transit through the nephron is too fast for crystals to grow large enough to be retained. Thus, free particle mechanism alone cannot lead to stone formation, and there must be a mechanism for crystal fixation within the kidneys. Animal model studies suggest that crystal retention is possible through both the free- and fixed-particle mechanisms. Crystal-cell interaction leads to pathological changes which promote crystal attachment to either epithelial cells or their basement membrane. Alternatively, crystals aggregate and produce large enough particles to block the tubules particularly at sites, where urinary flow is affected because of changes in the luminal diameter of the tubule. Crystal deposits plugging the openings of the ducts of Bellini may be the result of such a phenomenon. Intratubular crystals translocating to renal interstitium may produce osteogenic changes in the epithelial or endothelial cells resulting in the formation of the Randall's plaques. Thus, fixation appears to be either through the formation of Randall's plugs, crystal plugs clogging the openings of the ducts of Bellini or sub-epithelial crystal deposits, and the Randall's plaques.

  10. Pattern formation based on complex coupling mechanism in dielectric barrier discharge

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

    The pattern formation of cinque-dice square superlattice pattern (CDSSP) is investigated based on the complex coupling mechanism in a dielectric barrier discharge (DBD) system. The spatio-temporal structure of CDSSP obtained by using an intensified-charge coupled device indicates that CDSSP is an interleaving of two kinds of subpatterns (mixture of rectangle and square, and dot-line square) which discharge twice in one half voltage, respectively. Selected by the complex coupling of two subpatterns, the CDSSP can be formed and shows good stability. This investigation based on gas discharge theory together with nonlinear theory may provide a deeper understanding for the nonlinear characteristics and even the formation mechanism of patterns in DBD.

  11. 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

  12. Spatial and temporal behavior of pattern formations and defect motions in the electrohydrodynamic instability of nematic liquid crystals

    NASA Astrophysics Data System (ADS)

    Kai, Shoichi; Chizumi, Nobuyuki; Kohno, Mitsuhiro

    1989-12-01

    Pattern-formation processes and the associated defect motions are experimentally studied for various rectangular cells with aspect ratios Γ ranging from 8 to 15 in the electrohydrodynamic instability (EHD). Wave-number selection arises from the competition between the most rapidly growing mode kc, which dominates initially, and the final stable mode km in the Williams domain (WD) state, which is influenced by the cell boundaries as well as nonlinear effects. Defect motion is associated with such competitive growth into the final stage. The fluctuating Williams domains (FWD's) are strongly related to the oscillatory gliding motion of defects. A temporally nonperiodic change of the number of defects is observed in the FWD state with a power spectrum of 1/f type (defect chaos). For a step change in the external voltage, a clear threshold for the onset of FWD is determined. On the other hand, when the voltage is increased continuously no defect is formed at the threshold for WD, and nondecaying defect motion starts at a certain threshold value. A large hysteresis is observed near the onset of FWD. The step change of the external field leads to defect formation more easily than the continuous change. A detailed phase diagram of stable convective patterns in the plane spanned by the threshold voltage and the applied frequency is presented. The characteristic behavior of defect motions, for example, its oscillatory activity of gliding and climbing motions, is strongly related to the pattern following the second pattern instability. In the case of the strong gliding oscillation, a pattern with temporal order appears above the second threshold. Contrary to this, in the case of the weakly oscillatory motion of defects, a stationary pattern is usually observed above its threshold. The magnetic field suppresses the defect chaos and stabilizes the system, that is, the threshold of the applied electric field for the onset of EHD is raised when the magnetic field is increased

  13. Interlinked nonlinear subnetworks underlie the formation of robust cellular patterns in Arabidopsis epidermis: a dynamic spatial model

    PubMed Central

    Benítez, Mariana; Espinosa-Soto, Carlos; Padilla-Longoria, Pablo; Alvarez-Buylla, Elena R

    2008-01-01

    Background Dynamical models are instrumental for exploring the way information required to generate robust developmental patterns arises from complex interactions among genetic and non-genetic factors. We address this fundamental issue of developmental biology studying the leaf and root epidermis of Arabidopsis. We propose an experimentally-grounded model of gene regulatory networks (GRNs) that are coupled by protein diffusion and comprise a meta-GRN implemented on cellularised domains. Results Steady states of the meta-GRN model correspond to gene expression profiles typical of hair and non-hair epidermal cells. The simulations also render spatial patterns that match the cellular arrangements observed in root and leaf epidermis. As in actual plants, such patterns are robust in the face of diverse perturbations. We validated the model by checking that it also reproduced the patterns of reported mutants. The meta-GRN model shows that interlinked sub-networks contribute redundantly to the formation of robust hair patterns and permits to advance novel and testable predictions regarding the effect of cell shape, signalling pathways and additional gene interactions affecting spatial cell-patterning. Conclusion The spatial meta-GRN model integrates available experimental data and contributes to further understanding of the Arabidopsis epidermal system. It also provides a systems biology framework to explore the interplay among sub-networks of a GRN, cell-to-cell communication, cell shape and domain traits, which could help understanding of general aspects of patterning processes. For instance, our model suggests that the information needed for cell fate determination emerges from dynamic processes that depend upon molecular components inside and outside differentiating cells, suggesting that the classical distinction of lineage versus positional cell differentiation may be instrumental but rather artificial. It also suggests that interlinkage of nonlinear and redundant

  14. Modeling Elevation and Aspect Controls on Emerging Ecohydrologic Processes and Ecosystem Patterns Using the Component-based Landlab Framework

    NASA Astrophysics Data System (ADS)

    Nudurupati, S. S.; Istanbulluoglu, E.; Adams, J. M.; Hobley, D. E. J.; Gasparini, N. M.; Tucker, G. E.; Hutton, E. W. H.

    2014-12-01

    Topography plays a commanding role on the organization of ecohydrologic processes and resulting vegetation patterns. In southwestern United States, climate conditions lead to terrain aspect- and elevation-controlled ecosystems, with mesic north-facing and xeric south-facing vegetation types; and changes in biodiversity as a function of elevation from shrublands in low desert elevations, to mixed grass/shrublands in mid elevations, and forests at high elevations and ridge tops. These observed patterns have been attributed to differences in topography-mediated local soil moisture availability, micro-climatology, and life history processes of plants that control chances of plant establishment and survival. While ecohydrologic models represent local vegetation dynamics in sufficient detail up to sub-hourly time scales, plant life history and competition for space and resources has not been adequately represented in models. In this study we develop an ecohydrologic cellular automata model within the Landlab component-based modeling framework. This model couples local vegetation dynamics (biomass production, death) and plant establishment and competition processes for resources and space. This model is used to study the vegetation organization in a semiarid New Mexico catchment where elevation and hillslope aspect play a defining role on plant types. Processes that lead to observed plant types across the landscape are examined by initializing the domain with randomly assigned plant types and systematically changing model parameters that couple plant response with soil moisture dynamics. Climate perturbation experiments are conducted to examine the plant response in space and time. Understanding the inherently transient ecohydrologic systems is critical to improve predictions of climate change impacts on ecosystems.

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

    PubMed

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

    2016-01-01

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

  16. Kinetic aspects of the formation of aluminium oxide by use of a microwave-induced plasma.

    PubMed

    Quade, A; Steffen, H; Hippler, R; Wulff, H

    2002-10-01

    The oxidation of thin aluminium layers in a microwave plasma has been investigated to determine the kinetics of oxide growth. Thin Al-coatings were oxidized by means of a variety of gas mixtures, characterized by different partial pressures of oxygen, in microwave-induced plasmas of different power. To study the whole kinetic process the Al-metal and the oxide formed were investigated by means of a combination of grazing incidence X-ray reflectometry (GIXR) and grazing incidence X-ray diffractometry (GIXRD). XPS and FTIR spectroscopy confirmed the formation of stoichiometric Al(2)O(3). The alumina formed is X-ray amorphous. Quantitative description of oxide formation was achieved indirectly by determination of the decrease in the integrated intensity of the Al(111)-peak and the total thickness of the whole coating. These values enabled calculation of kinetic data. It was found that oxide growth was a combination of two simultaneous processes - diffusion and sputter processes. The diffusion coefficient D (cm(2) s(-1)) and the sputter rate S (nm s(-1)) were determined. The effect of the composition of the gas mixture, microwave power, and concentration of activated oxygen species on the oxidation process will be discussed. For calculation of the activation energy, E(A), of this plasma-enhanced diffusion process the temperature-dependence of D was investigated.

  17. Structural aspects of glass-formation in Ni-Nb melts

    SciTech Connect

    Holland-Moritz, D.; Yang, F.; Gegner, J.; Meyer, A.; Hansen, T.; Ruiz-Martín, M. D.

    2014-05-28

    We report on investigations of the static structure factors of glass-forming Ni{sub 59.5}Nb{sub 40.5} alloy melts by combination of the containerless processing technique of electrostatic levitation with neutron diffraction. By application of the isotopic substitution method, the full set of partial structure factors was determined. The short-range order in liquid Ni{sub 59.5}Nb{sub 40.5} is characterized by a large nearest neighbor coordination number of Z{sub NN} = 14.3 and a chemical short-range order with an affinity for the formation of heterogeneous Nb-Ni nearest neighbors. The structure factors observed here in the liquid state closely resemble those reported for amorphous Nb-Ni solids. The comparison with earlier results on the short-range structure in Zr-based glass-forming melts suggests that a large local density of packing, chemical order, and structural frustration are, amongst others, common structural properties of these metallic glass-forming systems, which favor glass-formation.

  18. Genericity aspects of black hole formation in the collapse of spherically symmetric slightly inhomogeneous perfect fluids

    NASA Astrophysics Data System (ADS)

    Satin, Seema; Malafarina, Daniele; Joshi, Pankaj S.

    2016-12-01

    We study the complete gravitational collapse of a class of spherically symmetric inhomogeneous perfect fluid models obtained by introducing small radial perturbations in an otherwise homogeneous matter cloud. Our aim here is to study the genericity and stability of the formation of black holes and locally naked singularities in collapse. While the occurrence of naked singularities is known for many models of collapse, the key issue now in focus is genericity and stability of these outcomes. Towards this purpose, we study how the introduction of a somewhat general class of small inhomogeneities in homogeneous collapse leading to a black hole can change the final outcome to a naked singularity. The key feature that we assume for the perturbation profile is that of a mass profile that is separable in radial and temporal coordinates. The known models of dust and homogeneous perfect fluid collapse can be obtained from this choice of the mass profile as special cases. This choice is very general and physically well motivated and we show that this class of collapse models leads to the formation of a naked singularity as the final state.

  19. Influence of different aspect ratios on the structural and electrical properties of GaN thin films grown on nanoscale-patterned sapphire substrates

    NASA Astrophysics Data System (ADS)

    Lee, Fang-Wei; Ke, Wen-Cheng; Cheng, Chun-Hong; Liao, Bo-Wei; Chen, Wei-Kuo

    2016-07-01

    This study presents GaN thin films grown on nanoscale-patterned sapphire substrates (NPSSs) with different aspect ratios (ARs) using a homemade metal-organic chemical vapor deposition system. The anodic aluminum oxide (AAO) technique is used to prepare the dry etching mask. The cross-sectional view of the scanning electron microscope image shows that voids exist between the interface of the GaN thin film and the high-AR (i.e. ∼2) NPSS. In contrast, patterns on the low-AR (∼0.7) NPSS are filled full of GaN. The formation of voids on the high-AR NPSS is believed to be due to the enhancement of the lateral growth in the initial growth stage, and the quick-merging GaN thin film blocks the precursors from continuing to supply the bottom of the pattern. The atomic force microscopy images of GaN on bare sapphire show a layer-by-layer surface morphology, which becomes a step-flow surface morphology for GaN on a high-AR NPSS. The edge-type threading dislocation density can be reduced from 7.1 × 108 cm-2 for GaN on bare sapphire to 4.9 × 108 cm-2 for GaN on a high-AR NPSS. In addition, the carrier mobility increases from 85 cm2/Vs for GaN on bare sapphire to 199 cm2/Vs for GaN on a high-AR NPSS. However, the increased screw-type threading dislocation density for GaN on a low-AR NPSS is due to the competition of lateral growth on the flat-top patterns and vertical growth on the bottom of the patterns that causes the material quality of the GaN thin film to degenerate. Thus, the experimental results indicate that the AR of the particular patterning of a NPSS plays a crucial role in achieving GaN thin film with a high crystalline quality.

  20. Self-organized nanostructured spherulitic crystal pattern formation in Belousov-Zhabotinsky type reaction system

    NASA Astrophysics Data System (ADS)

    Srivastava, Rohit; Srivastava, P. K.

    2013-11-01

    We report the formation of self-organized nanostructured spherulitic crystal pattern in a modified Belousov-Zhabotinsky (BZ) type system. In liquid phase, we observed the reaction system to exhibit well distinguishable spatial patterns including stripe and hexagonal structures. The solid phase nucleation was found to occur in the colloidal phase and nanostructured spherulitic crystal patterns were obtained as one of the final products. Transmission electron microscopy, scanning electron microscopy, optical microscopy, powder X-ray diffraction and Fourier transform infrared spectroscopy were used to characterize the spherulitic crystal pattern. The average diameter of the grown crystals was found to be ˜30-100 nm. In situ UV-Visible spectroscopic measurement exhibited damped oscillatory nature corresponding to ferroin in the reaction system. This oscillation was found to be well conjugated to the spherulitic structures. The paper elucidates the roles of the various possible factors behind such phase-transformation along with the plausible explanation of the corresponding reaction pathways.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  2. 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

  3. Some aspects of double layer formation in a plasma constrained by a magnetic mirror

    NASA Technical Reports Server (NTRS)

    Lennartsson, W.

    1987-01-01

    The shift from wave-generated anomalous resistivity toward the more large-scale effects of magnetic confinement of current carrying plasmas was inspired by the more extensive data on auroral particle distribution functions that were made available, data that may often seem consistent with a dissipation-free acceleration of auroral electrons over an extended altitude range. Efforts to interpret these data have brought new vigor to the concept that a smooth and static electric field can be self-consistently generated by suitable pitch angle anisotropies among the high altitude particle populations, different for electrons and ions, and that such an electric field is both necessary and sufficient to maintain the plasma in a quasi-neutral steady state. Certain aspects of this concept are reviewed and criticized, both from a general theoretical standpoint and from the standpoint of what is known about the magnetospheric environment. It is argued that this concept has flaws and that the actual physical problem is considerably more complicated, requiring a more complex electric field, possibly including double layer structures.

  4. 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)

  5. 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.

  6. Artificial selection on egg size perturbs early pattern formation in Drosophila melanogaster.

    PubMed

    Miles, Cecelia M; Lott, Susan E; Hendriks, Cris L Luengo; Ludwig, Michael Z; Manu; Williams, Calvin L; Kreitman, Martin

    2011-01-01

    Pattern formation in Drosophila embryogenesis has been widely investigated as a developmental and evolutionary model of robustness. To ask whether genetic variation for pattern formation is suppressed in this system, artificial selection for divergent egg size was used to challenge the scaling of even-skipped (eve) pattern formation in mitotic cycle 14 (stage 5) embryos of Drosophila melanogaster. Three-dimensional confocal imaging revealed shifts in the allometry of eve pair-rule stripes along both anterior–posterior (A–P) and dorsoventral (D–V) axes as a correlated response to egg size selection, indicating the availability of genetic variation for this buffered trait. Environmental perturbation was not required for the manifestation of this variation. The number of nuclei at the cellular blastoderm stage also changed in response to selection, with large-egg selected lines having more than 1000 additional nuclei relative to small-egg lines. This increase in nuclear number in larger eggs does not scale with egg size, however, as nuclear density is inversely correlated with egg length. Nuclear density varies along the A–P axis but does not correlate with the shift in eve stripe allometry between the selection treatments. Despite its macroevolutionary conservation, both eve stripe patterning and blastoderm cell number vary genetically both within and between closely related species.

  7. Nanoscale tomographic reconstruction of the subsurface mechanical properties of low-k high-aspect ratio patterns

    NASA Astrophysics Data System (ADS)

    Stan, Gheorghe; Mays, Ebony; Yoo, Hui Jae; King, Sean W.

    2016-12-01

    In this work, intermittent contact resonance atomic force microscopy (ICR-AFM) was performed on high-aspect ratio a-SiOC:H patterned fins (100 nm in height and width from 20 to 90 nm) to map the depth and width dependencies of the material stiffness. The spatial resolution and depth sensitivity of the measurements were assessed from tomographic cross-sections over various regions of interest within the 3D space of the measurements. Furthermore, the depth-dependence of the measured contact stiffness over the scanned area was used to determine the sub-surface variation of the elastic modulus at each point in the scan. This was achieved by iteratively adjusting the local elastic profile until the depth dependence of the resulted contact stiffness matched the depth dependence of the contact stiffness measured by ICR-AFM at that location. The results of this analysis were assembled into nanoscale sub-surface tomographic images of the elastic modulus of the investigated SiOC:H patterns. A new 3D structure-property representation emerged from these tomographic images with direct evidence for the alterations sustained by the structures during processing.

  8. The influence of aspect ratio and stroke pattern on force generation of a bat-inspired membrane wing.

    PubMed

    Schunk, Cosima; Swartz, Sharon M; Breuer, Kenneth S

    2017-02-06

    Aspect ratio (AR) is one parameter used to predict the flight performance of a bat species based on wing shape. Bats with high AR wings are thought to have superior lift-to-drag ratios and are therefore predicted to be able to fly faster or to sustain longer flights. By contrast, bats with lower AR wings are usually thought to exhibit higher manoeuvrability. However, the half-span ARs of most bat wings fall into a narrow range of about 2.5-4.5. Furthermore, these predictions do not take into account the wide variation in flapping motion observed in bats. To examine the influence of different stroke patterns, we measured lift and drag of highly compliant membrane wings with different bat-relevant ARs. A two degrees of freedom shoulder joint allowed for independent control of flapping amplitude and wing sweep. We tested five models with the same variations of stroke patterns, flapping frequencies and wind speed velocities. Our results suggest that within the relatively small AR range of bat wings, AR has no clear effect on force generation. Instead, the generation of lift by our simple model mostly depends on wingbeat frequency, flapping amplitude and freestream velocity; drag is mostly affected by the flapping amplitude.

  9. Mechanistic aspects of the nucleophilic substitution of pectin. On the formation of chloromethane.

    PubMed

    Sailaukhanuly, Yerbolat; Sárossy, Zsuzsa; Carlsen, Lars; Egsgaard, Helge

    2014-09-01

    Chloromethane, accounting for approximately 16% of the tropospheric chlorine, is mainly coming from natural sources. However anthropogenic activities, such as combustion of biomass may contribute significantly as well. The present study focuses on the thermal solid state reaction between pectin, an important constituent of biomass, and chloride ions as found in alkali metal chlorides. The formation of chloromethane is evident with the amount formed being linear with respect to chloride if pectin is in great excess. Thus the reaction is explained as a pseudo first order SN2 reaction between the chloride ion and the methyl ester moiety in pectin. It is suggested that the polymeric nature of pectin plays an active role by an enhanced transport of halides along the carbohydrate chain. Optimal reaction temperature is around 210°C. At higher temperatures the yield of chloromethane decreases due to a thermal decomposition of the pectin. The possible influence of the type of cation is discussed.

  10. Thermodynamic aspects of the coating formation through mechanochemical synthesis in vibration technology systems

    NASA Astrophysics Data System (ADS)

    Shtyn, S. U.; Lebedev, V. A.; Gorlenko, A. O.

    2017-02-01

    On the basis of thermodynamic concepts of the process, we proposed an energy model that reflects the mechanochemical essence of coating forming in terms of vibration technology systems, which takes into account the contribution to the formation of the coating, the increase of unavailable energy due to the growth of entropy, the increase in the energy of elastic-plastic crystal lattice distortion as a result of the mechanical influence of working environment indenters, surface layer internal energy change which occurs as a result of chemical interaction of the contacting media. We proposed adhesion strength of the local volume modified through processing as a criterion of the energy condition of the formed coating. We established analytical dependence which helps to obtain the coating strength of the material required by operating conditions.

  11. The upper Bow Island (Blackleaf) Formation of southwestern Alberta: Geological aspects and exploration approaches

    SciTech Connect

    Putnam, P.E.; Christensen, S.L. )

    1991-06-01

    The upper parts of the Bow Island Formation (Albian) of southwestern Alberta are significant gas reservoirs. The main westernmost reservoir zone is part of a complex package of interbedded lenticular sandstones, mudstones, and localized chert pebble conglomerates. The depositional setting for these sediments comprised a wave-dominated shoreline with conglomerates found proximal to drowned river mouths. The coarse nature of the upper Bow Island is related to tectonic movements associated with Crowsnest (Vaughn) volcanism. Conglomerates form the most impressive Bow Island reservoirs because of their thickness (up to 25 m) and petrophysical properties (17% porosity, 24 d permeability). Diagenesis dominantly comprises compaction features within grain-supported conglomerates. Increasing quartz content is related to decreasing grain size and is associated with porosity occlusion by quartz overgrowths. Bow Island reservoirs in southwestern Alberta are cool (under 50C) and significantly underpressured (0.2 psi). The high permeabilities and low pressures at depths of 1,000 to 1,500 m suggest the potential for formation damage is high, and many wells in the region were targeted for deeper, high-pressure zones. In spite of the low pressures, however, many Bow Island wells are capable of excellent gas deliveries with individual well recoveries of up to 10 bcf. All significant Bow Island porosity in the deepest, undisturbed parts of southwestern Alberta is gas saturated with updip aquifers flanking the gas. Seismic definition of the thickest Bow Island targets is feasible but has been hampered, in part, by difficult surface conditions and a prior emphasis on deeper targets.

  12. Studies on a novel mask technique with high selectivity and aspect-ratio patterns for HgCdTe trenches ICP etching

    NASA Astrophysics Data System (ADS)

    Ye, Z. H.; Hu, W. D.; Li, Y.; Huang, J.; Yin, W. T.; Lin, C.; Hu, X. N.; Ding, R. J.; Chen, X. S.; Lu, W.; He, L.

    2012-06-01

    A novel mask technique, combining high selectivity silicon dioxide patterns over high aspect-ratio photoresist (PR) patterns has been exploited to perform mesa etching for device delineation and electrical isolation of HgCdTe third-generation infrared focal plane arrays (IRFPAs). High-density silicon dioxide film covering high aspect-ratio PR patterns was deposited at the temperature of 80°C and silicon dioxide film patterns over high aspect-ratio PR patterns of HgCdTe etching samples was developed by standard photolithography and wet chemical etch. Scanning electron microscopy (SEM) shows that the surfaces of inductively coupled plasma (ICP) etched samples are quite clean and smooth. The etching selectivity between the novel mask and HgCdTe of the samples is increased to above 32: 1 while the side-wall impact of etching plasma is suppressed by the high aspect ratio patterns. These results show that the combined patterning of silicon dioxide film and thick PR film is a readily available and promising masking technique for HgCdTe mesa etching.

  13. Formation and characteristics of patterns in atmospheric-pressure radio-frequency dielectric barrier discharge plasma

    NASA Astrophysics Data System (ADS)

    Yang, Lizhen; Liu, Zhongwei; Mao, Zhiguo; Li, Sen; Chen, Qiang

    2017-01-01

    The patterns in radio-frequency dielectric barrier discharge (RF DBD) are studied at atmospheric pressure of argon (Ar) or helium (He) mixed with nitrogen (N2) gas. When a small amount of N2 is mixed with He or Ar gas, discharge patterns are formed. In a N2/He gas mixture, besides the filament discharge that forms patterns, a glow background discharge is also observed, whereas only the filament discharge forms patterns in a N2/Ar gas mixture. The resolution of the hexagonal pattern as a function of applied power and gas flow rate is then explored. On the basis of spatial-temporal images taken using an intensified charge-coupled device (ICCD), we find that there is no interleaving of two transient hexagon sublattices in N2/Ar or N2/He plasma in RF DBD patterns, which are totally different from those in which surface charges dominated in the mid-frequency DBD plasma. This supports our hypothesis that the bulk charges dominate the pattern formation in RF DBD.

  14. The remodeling pattern of human mandibular alveolar bone during prenatal formation from 19 to 270mm CRL.

    PubMed

    Radlanski, Ralf J; Renz, Herbert; Tsengelsaikhan, Nyamdorj; Schuster, Felix; Zimmermann, Camilla A

    2016-05-01

    The underlying mechanisms of human bone morphogenesis leading to a topologically specific shape remain unknown, despite increasing knowledge of the basic molecular aspects of bone formation and its regulation. The formation of the alveolar bone, which houses the dental primordia, and later the dental roots, may serve as a model to approach general questions of bone formation. Twenty-five heads of human embryos and fetuses (Radlanski-Collection, Berlin) ranging from 19mm to 270mm (crown-rump-length) CRL were prepared as histological serial sections. For each stage, virtual 3D-reconstructions were made in order to study the morphogenesis of the mandibular molar primordia with their surrounding bone. Special focus was given to recording the bone-remodeling pattern, as diagnosed from the histological sections. In early stages (19-31mm CRL) developing bone was characterized by appositional only. At 41, in the canine region, mm CRL bony extensions were found forming on the bottom of the trough. Besides general apposition, regions with resting surfaces were also found. At a fetal size of 53mm CRL, septa have developed and led to a compartment for canine development. Furthermore, one shared compartment for the incisor primordia and another shared compartment for the molars also developed. Moreover, the inner surfaces of the dental crypts showed resorption of bone. From this stage on, a general pattern became established such that the compartmentalizing ridges and septa between all of the dental primordia and the brims of the crypts were noted, and were due to appositional growth of bone, while the crypts enlarged on their inner surfaces by resorption. By 160mm CRL, the dental primordia were larger, and all of the bony septa had become reduced in size. The primordia for the permanent teeth became visible at 225mm CRL and shared the crypts of their corresponding deciduous primordia.

  15. 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.

  16. New aspects of absorption line formation in intervening turbulent clouds - I. General principles

    NASA Astrophysics Data System (ADS)

    Levshakov, Sergei A.; Kegel, Wilhelm H.

    1997-07-01

    We study the formation of absorption lines in intervening clouds with stochastic velocity fields, accounting for the fact that actually only one line of sight is observed. Our results show that the introduction of the finite velocity correlation length leads to a new type of absorption line profiles which are asymmetric in general, may have different shifts of the centres of gravity, and look like barely resolved blends, i.e. could be interpreted in a standard Voigt fitting analysis as being caused by several independent clouds with different physical parameters. Numerical results are presented for the HI Lyalpha line with N_Hi=10^12,10^14,10^15 and 10^16cm^-2, T_kin=10^4 K, and different sets of turbulent parameters. The intensity fluctuations within the line profile caused by `turbulent noise' are investigated and the confidence belts for the absorption lines are calculated. We conclude that an exact measurement of the column densities of the absorbing atoms N_a from the observed values of the optical depths tau lambda is actually impossible for the case of the correlated velocity field. One can only determine a range of values within which N_a is to be found with a certain probability.

  17. Delineation of the Key Aspects in the Regulation of Epithelial Monolayer Formation

    PubMed Central

    Aschauer, Lydia; Gruber, Leonhard N.; Pfaller, Walter; Limonciel, Alice; Athersuch, Toby J.; Cavill, Rachel; Khan, Abdulhameed; Gstraunthaler, Gerhard; Grillari, Johannes; Grillari, Regina; Hewitt, Philip; Leonard, Martin O.; Wilmes, Anja

    2013-01-01

    The formation, maintenance, and repair of epithelial barriers are of critical importance for whole-body homeostasis. However, the molecular events involved in epithelial tissue maturation are not fully established. To this end, we investigated the molecular processes involved in renal epithelial proximal-tubule monolayer maturation utilizing transcriptomic, metabolomic, and functional parameters. We uncovered profound dynamic alterations in transcriptional regulation, energy metabolism, and nutrient utilization over the maturation process. Proliferating cells exhibited high glycolytic rates and high transcript levels for fatty acid synthesis genes (FASN), whereas matured cells had low glycolytic rates, increased oxidative capacity, and preferentially expressed genes for beta oxidation. There were dynamic alterations in the expression and localization of several adherens (CDH1, -4, and -16) and tight junction (TJP3 and CLDN2 and -10) proteins. Genes involved in differentiated proximal-tubule function, cilium biogenesis (BBS1), and transport (ATP1A1 and ATP1B1) exhibited increased expression during epithelial maturation. Using TransAM transcription factor activity assays, we could demonstrate that p53 and FOXO1 were highly active in matured cells, whereas HIF1A and c-MYC were highly active in proliferating cells. The data presented here will be invaluable in the further delineation of the complex dynamic cellular processes involved in epithelial cell regulation. PMID:23608536

  18. 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

  19. 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.

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

    SciTech Connect

    Qiao, Yajun; Li, Ben; Ouyang, Jiting

    2016-01-15

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

  1. New geological aspects for freshwater seepage and formation in Eckernförde Bay, western Baltic

    NASA Astrophysics Data System (ADS)

    Jensen, Jørn B.; Kuijpers, Antoon; Bennike, Ole; Laier, Troels; Werner, Friedrich

    2002-10-01

    The subsurface geology relevant to the submarine freshwater seepage in Eckernförde Bay has been investigated using shallow seismic instruments and vibrocoring. Detailed surveying revealed that the pockmarks are aligned like pearls on a string or densely clustered in furrow-like structures depending on the glacial and postglacial setting of the underlying strata. Two possible aquifers have been verified: The older Miocene sand aquifer is partly sealed by a till unit forming the central part of the Mittelgrund. The younger aquifer consists of a mixture of glacial till and meltwater sediments partly sealed by till and partly by lateglacial galciolacustrine silt and clay sediments. The investigations imply that connections exist between the aquifers and that groundwater leakage takes place in the marginal zones of the bay due to thinning and coarsening of the sediment composition of the lateglacial seal. Within the seepage areas, the pockmarks are restricted to areas covered by unconsolidated Holocene mud of low thickness' that are easy to penetrate by artesian groundwater. Macrofossil studies and AMS 14C dating of the lateglacial and Holocene units reveal that the Mittelgrund shoal of glacial origin has been modified by coastal processes and formation of cuspate foreland deposits during the subsequent palaeo-lake phases of 15-20 m below the present sea level (b.s.l.). The lake phases correlate in time with the regional Baltic Ice Lake highstand about 10,000 14C years BP and the Ancylus Lake highstand about 9200 14C years BP. This means that local contemporary lakes existed or the western margin of the regional lakes can be moved considerably further west than expected hitherto. In the earliest phase of the Littorina Sea transgression, the Mittelgrund shoal was exposed to coastal erosion once more before the final drowning and the initiation of mud sedimentation in the surrounding basins took place.

  2. Pattern formation in the flow between two horizontal coaxial cylinders with a partially filled gap

    NASA Astrophysics Data System (ADS)

    Mutabazi, Innocent; Hegseth, John J.; Andereck, C. David; Wesfreid, Jose E.

    1988-11-01

    Flow between two horizontal coaxial cylinders with a partially filled gap is subject to several types of centrifugal instabilities which lead to the formation of a variety of spatial patterns. An experimental investigation has shown that there are five distinct branches of primary instabilities occurring in the system and that four codimension-2 points are easily reached. Theoretical predictions are in qualitative agreement with the observations.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. Density of founder cells affects spatial pattern formation and cooperation in Bacillus subtilis biofilms.

    PubMed

    van Gestel, Jordi; Weissing, Franz J; Kuipers, Oscar P; Kovács, Akos T

    2014-10-01

    In nature, most bacteria live in surface-attached sedentary communities known as biofilms. Biofilms are often studied with respect to bacterial interactions. Many cells inhabiting biofilms are assumed to express 'cooperative traits', like the secretion of extracellular polysaccharides (EPS). These traits can enhance biofilm-related properties, such as stress resilience or colony expansion, while being costly to the cells that express them. In well-mixed populations cooperation is difficult to achieve, because non-cooperative individuals can reap the benefits of cooperation without having to pay the costs. The physical process of biofilm growth can, however, result in the spatial segregation of cooperative from non-cooperative individuals. This segregation can prevent non-cooperative cells from exploiting cooperative neighbors. Here we examine the interaction between spatial pattern formation and cooperation in Bacillus subtilis biofilms. We show, experimentally and by mathematical modeling, that the density of cells at the onset of biofilm growth affects pattern formation during biofilm growth. At low initial cell densities, co-cultured strains strongly segregate in space, whereas spatial segregation does not occur at high initial cell densities. As a consequence, EPS-producing cells have a competitive advantage over non-cooperative mutants when biofilms are initiated at a low density of founder cells, whereas EPS-deficient cells have an advantage at high cell densities. These results underline the importance of spatial pattern formation for competition among bacterial strains and the evolution of microbial cooperation.

  8. 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.

  9. Kinetic Monte Carlo simulation of self-organized pattern formation induced by ion beam sputtering using crater functions

    NASA Astrophysics Data System (ADS)

    Yang, Zhangcan; Lively, Michael A.; Allain, Jean Paul

    2015-02-01

    The production of self-organized nanostructures by ion beam sputtering has been of keen interest to researchers for many decades. Despite numerous experimental and theoretical efforts to understand ion-induced nanostructures, there are still many basic questions open to discussion, such as the role of erosion or curvature-dependent sputtering. In this work, a hybrid MD/kMC (molecular dynamics/kinetic Monte Carlo) multiscale atomistic model is developed to investigate these knowledge gaps, and its predictive ability is validated across the experimental parameter space. This model uses crater functions, which were obtained from MD simulations, to model the prompt mass redistribution due to single-ion impacts. Defect migration, which is missing from previous models that use crater functions, is treated by a kMC Arrhenius method. Using this model, a systematic study was performed for silicon bombarded by Ar+ ions of various energies (100 eV, 250 eV, 500 eV, 700 eV, and 1000 eV) at incidence angles of 0∘ to 80∘. The simulation results were compared with experimental findings, showing good agreement in many aspects of surface evolution, such as the phase diagram. The underestimation of the ripple wavelength by the simulations suggests that surface diffusion is not the main smoothening mechanism for ion-induced pattern formation. Furthermore, the simulated results were compared with moment-description continuum theory and found to give better results, as the simulation did not suffer from the same mathematical inconsistencies as the continuum model. The key finding was that redistributive effects are dominant in the formation of flat surfaces and parallel-mode ripples, but erosive effects are dominant at high angles when perpendicular-mode ripples are formed. Ion irradiation with simultaneous sample rotation was also simulated, resulting in arrays of square-ordered dots. The patterns obtained from sample rotation were strongly correlated to the rotation speed and to

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

    PubMed

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

    2014-08-08

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

  11. Formation of Ceramic Nanoparticle Patterns Using Electrohydrodynamic Jet Printing with Pin-to-Pin Electrodes

    NASA Astrophysics Data System (ADS)

    Lee, Dae-Young; Yu, Jae-Hun; Shin, Yun-Soo; Park, Dongho; Yu, Tae-U.; Hwang, Jungho

    2008-03-01

    As one of the direct write technologies, electrohydrodynamic jet printing was used in obtaining fine ceramic lines. We used pin electrodes of various diameters, each of which was located below the substrate, and analyzed the effects of pin diameter on Al2O3 nanoparticle one- and two-dimensional patterns formed with pin (nozzle)-to-pin (ground) electrodes. The onset voltage required to start the formation of a pattern for a 1-µm-diameter electrode was fourfold lower than the voltage required for a 1000-µm-diameter electrode. Additionally, an Al2O3 nanoparticle pattern with a uniform width as fine as 25 µm was obtained despite using the very large diameter of the nozzle (920 µm) used.

  12. 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

  13. 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.

  14. Turing pattern formation in the chlorine dioxide-iodine- malonic acid reaction-diffusion system

    NASA Astrophysics Data System (ADS)

    Setayeshgar, Sima

    The formation of localized structures in the chlorine dioxide-idodine-malonic acid (CDIMA) reaction-diffusion system is investigated numerically using a realistic model of this system. We analyze the one-dimensional patterns formed along the gradients imposed by boundary feeds, and study their linear stability to symmetry- breaking perturbations (the Turing instability) in the plane transverse to these gradients. We establish that an often-invoked simple local linear analysis which neglects longitudinal diffusion is inappropriate for predicting the linear stability of these patterns. Using a fully nonuniform analysis, we investigate the structure of the patterns formed along the gradients and their stability to transverse Turing pattern formation as a function of the values of two control parameters: the malonic acid feed concentration and the size of the reactor in the dimension along the gradients. The results from this investigation are compared with existing experimental results. We also verify that the two-variable reduction of the chemical model employed in the linear stability analysis is justified. Finally, we present numerical solution of the CDIMA system in two dimensions which is in qualitative agreement with experiments. This result also confirms our linear stability analysis, while demonstrating the feasibility of numerical exploration of realistic chemical models.

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

    PubMed Central

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

    2015-01-01

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

  16. 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

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

    PubMed Central

    Muñoz-García, Javier

    2016-01-01

    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

  18. Thermodynamic Aspects of the Formation of Sulfate Minerals from Hot Gaseous Phase

    NASA Astrophysics Data System (ADS)

    Giere, R.; Majzlan, J.

    2006-12-01

    Minerals may form by solid-state reactions or by dissolution and precipitation from a fluid phase, be it magma, aqueous medium, or gas. The latter phase was traditionally not considered as important as the other ones, although it may be essential in some geological environments. Components of minerals (e.g., sulfur) are commonly transported by hot gases in volcanoes. Others may form in burning coal dumps or by burning fossil fuels for energy production. We have identified a number of minerals which precipitated from the hot gases escaping into the atmosphere from the smoke stack of a coal-fired power plant. This power plant uses coal or a mixture of coal and used tires to produce electricity. The phases identified by TEM are anglesite (PbSO4), gunningite (ZnSO4?H2O), anhydrite (CaSO4), and yavapaiite (KFe(SO4)2). In addition to these crystalline phases, amorphous sulfate materials and soot have been identified. All these materials were captured by filtering the escaping gases beyond the last filters intended to remove any particles from the gas stream. Therefore, they must have formed by precipitation from the hot gas and may present a significant pollution load in the vicinity of power plants. Verhulst et al. (1996) have shown that several metals are most likely transported as chloride complexes in the gas phase. Their assumption correlates well with the finding that the chloride-richer coal+tire mixture increases considerably amounts of emitted metals. Using thermodynamic data for these and other sulfate minerals, we are trying to understand and model the precipitation process of these minerals from hot gases at ambient pressures. In this contribution, we focus on the mineral mikasaite (trigonal Fe2(SO4)3). This mineral has been reported only from burning coal dumps (Miura et al. 1994). Using acid-solution calorimetry, we have determined the enthalpy of formation of mikasaite from elements at T = 298.15 K. We have further estimated the standard entropy of this

  19. Segment polarity gene expression in a myriapod reveals conserved and diverged aspects of early head patterning in arthropods.

    PubMed

    Janssen, Ralf

    2012-09-01

    Arthropods show two kinds of developmental mode. In the so-called long germ developmental mode (as exemplified by the fly Drosophila), all segments are formed almost simultaneously from a preexisting field of cells. In contrast, in the so-called short germ developmental mode (as exemplified by the vast majority of arthropods), only the anterior segments are patterned similarly as in Drosophila, and posterior segments are added in a single or double segmental periodicity from a posterior segment addition zone (SAZ). The addition of segments from the SAZ is controlled by dynamic waves of gene activity. Recent studies on a spider have revealed that a similar dynamic process, involving expression of the segment polarity gene (SPG) hedgehog (hh), is involved in the formation of the anterior head segments. The present study shows that in the myriapod Glomeris marginata the early expression of hh is also in a broad anterior domain, but this domain corresponds only to the ocular and antennal segment. It does not, like in spiders, represent expression in the posterior adjacent segment. In contrast, the anterior hh pattern is conserved in Glomeris and insects. All investigated myriapod SPGs and associated factors are expressed with delay in the premandibular (tritocerebral) segment. This delay is exclusively found in insects and myriapods, but not in chelicerates, crustaceans and onychophorans. Therefore, it may represent a synapomorphy uniting insects and myriapods (Atelocerata hypothesis), contradicting the leading opinion that suggests a sister relationship of crustaceans and insects (Pancrustacea hypothesis). In Glomeris embryos, the SPG engrailed is first expressed in the mandibular segment. This feature is conserved in representatives of all arthropod classes suggesting that the mandibular segment may have a special function in anterior patterning.

  20. Ultra-high aspect ratio poly-Si FinFET using an improved spacer formation technique

    NASA Astrophysics Data System (ADS)

    Liu, Libin; Liang, Renrong; Wang, Jing; Xu, Jun

    2017-04-01

    An improved spacer formation technique was proposed and developed to fabricate poly-Si fin field-effect transistors (FinFETs) with an ultra-high aspect ratio. The as-demonstrated FinFETs have a fin channel with a width and height of 22 nm and 230 nm, respectively, corresponding to an aspect ratio of 10.5. The electrical and temperature properties of the FinFETs are described in detail in this paper. The poly-Si FinFETs exhibit a steep subthreshold swing (196 mV/dec), a low leakage current (∼10-14 A), a high on/off current ratio (2.2 × 107 at VDS = 0.1 V), and a low drain-induced barrier lowering effect (0.28 V). The excellent switching characteristics are attributed to the ultrathin channel body and the multi-gate structure combined with high-k Al2O3 dielectric. Furthermore, the electron field-effective mobility increases as the temperature increases. An analytical fitting model was derived and was utilized to account for this phenomenon. The fitting results indicate that the positive temperature coefficient originates from the grain boundary-controlled mechanism in the low gate voltage regime.

  1. Dynamic auxin transport patterns preceding vein formation revealed by live-imaging of Arabidopsis leaf primordia

    PubMed Central

    Marcos, Danielle; Berleth, Thomas

    2014-01-01

    Self-regulatory patterning mechanisms capable of generating biologically meaningful, yet unpredictable cellular patterns offer unique opportunities for obtaining mathematical descriptions of underlying patterning systems properties. The networks of higher-order veins in leaf primordia constitute such a self-regulatory system. During the formation of higher-order veins, vascular precursors are selected from a homogenous field of subepidermal cells in unpredictable positions to eventually connect in complex cellular networks. Auxin transport routes have been implicated in this selection process, but understanding of their role in vascular patterning has been limited by our inability to monitor early auxin transport dynamics in vivo. Here we describe a live-imaging system in emerging Arabidopsis thaliana leaves that uses a PIN1:GFP reporter to visualize auxin transport routes and an Athb8:YFP reporter as a marker for vascular commitment. Live-imaging revealed common features initiating the formation of all higher-order veins. The formation of broad PIN1 expression domains is followed by their restriction, leading to sustained, elevated PIN1 expression in incipient procambial cells files, which then express Athb8. Higher-order PIN1 expression domains (hPEDs) are initiated as freely ending domains that extend toward each other and sometimes fuse with them, creating connected domains. During the restriction and specification phase, cells in wider hPEDs are partitioned into vascular and non-vascular fates: Central cells acquire a coordinated cell axis and express elevated PIN1 levels as well as the pre-procambial marker Athb8, while edge cells downregulate PIN1 and remain isodiametric. The dynamic nature of the early selection process is underscored by the instability of early hPEDs, which can result in dramatic changes in vascular network architecture prior to Athb8 expression, which is correlated with the promotion onto vascular cell fate. PMID:24966861

  2. Nonlinear theory of pattern formation in ferrofluid films at high field strengths.

    PubMed

    Richardi, J; Pileni, M P

    2004-01-01

    When a magnetic field is applied to a thin layer of a suspension of magnetic nanoparticles (ferrofluid), the formation of labyrinthine and hexagonal patterns is observed. We introduce a theory to describe ferrofluid patterns at high field, where a nonlinear relationship between field and magnetization is expected. The computational difficulties due to the use of a nonlinear magnetization curve are solved by a reformulation of the magnetic energy equation. The evolution of the pattern size at intermediate and very high fields can be understood by an analysis of limiting cases of the magnetization curve. In particular, at a very high field the pattern size reaches a constant saturation value which has been recently confirmed by experiments. The field for the onset of a nonlinear behavior is shifted to higher field strength due to a demagnetization effect. This can partially explain the ability of linear approaches to reproduce experimental data even at a high field. Finally, the impact of the nonlinearity of the magnetization curve on the transition between hexagonal and labyrinthine patterns is discussed.

  3. 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.

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

    PubMed

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

    2010-02-26

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

  5. Spatial Self-Organization of Ecosystems: Integrating Multiple Mechanisms of Regular-Pattern Formation.

    PubMed

    Pringle, Robert M; Tarnita, Corina E

    2017-01-31

    Large-scale regular vegetation patterns are common in nature, but their causes are disputed. Whereas recent theory focuses on scale-dependent feedbacks as a potentially universal mechanism, earlier studies suggest that many regular spatial patterns result from territorial interference competition between colonies of social-insect ecosystem engineers, leading to hexagonally overdispersed nest sites and associated vegetation. Evidence for this latter mechanism is scattered throughout decades of disparate literature and lacks a unified conceptual framework, fueling skepticism about its generality in debates over the origins of patterned landscapes. We review these mechanisms and debates, finding evidence that spotted and gapped vegetation patterns generated by ants, termites, and other subterranean animals are globally widespread, locally important for ecosystem functioning, and consistent with models of intraspecific territoriality. Because these and other mechanisms of regular-pattern formation are not mutually exclusive and can coexist and interact at different scales, the prevailing theoretical outlook on spatial self-organization in ecology must expand to incorporate the dynamic interplay of multiple processes.

  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. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2008-03-01

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

  9. 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

  10. Role of Glycosyltransferases in Pollen Wall Primexine Formation and Exine Patterning1[OPEN

    PubMed Central

    Li, Wenhua L.; Liu, Yuanyuan

    2017-01-01

    The pollen cell wall is important for protection of male sperm from physical stresses and consists of an inner gametophyte-derived intine layer and a sporophyte-derived exine layer. The polymeric constituents of the robust exine are termed sporopollenin. The mechanisms by which sporopollenin is anchored onto microspores and polymerized in specific patterns are unknown, but the primexine, a transient cell wall matrix formed on the surface of microspores at the late tetrad stage, is hypothesized to play a key role. Arabidopsis (Arabidopsis thaliana) spongy (spg) and uneven pattern of exine (upex) mutants exhibit defective and irregular exine patterns. SPG2 (synonymous with IRREGULAR XYLEM9-LIKE [IRX9L]) encodes a family GT43 glycosyltransferase involved in xylan backbone biosynthesis, while UPEX1 encodes a family GT31 glycosyltransferase likely involved in galactosylation of arabinogalactan proteins. Imaging of developing irx9l microspores showed that the earliest detectable defect was in primexine formation. Furthermore, wild-type microspores contained primexine-localized epitopes indicative of the presence of xylan, but these were absent in irx9l. These data, together with the spg phenotype of a mutant in IRX14L, which also plays a role in xylan backbone elongation, indicate the presence of xylan in pollen wall primexine, which plays a role in exine patterning on the microspore surface. We observed an aberrant primexine and irregular patterns of incipient sporopollenin deposition in upex1, suggesting that primexine-localized arabinogalactan proteins could play roles in sporopollenin adhesion and patterning early in microspore wall development. Our data provide new insights into the biochemical and functional properties of the primexine component of the microspore cell wall. PMID:27495941

  11. Embryonic requirements for ErbB signaling in neural crest development and adult pigment pattern formation

    PubMed Central

    Budi, Erine H.; Patterson, Larissa B.; Parichy, David M.

    2009-01-01

    SUMMARY Vertebrate pigment cells are derived from neural crest cells and are a useful system for studying neural crest-derived traits during post-embryonic development. In zebrafish, neural crest-derived melanophores differentiate during embryogenesis to produce stripes in the early larva. Dramatic changes to the pigment pattern occur subsequently during the larva-to-adult transformation, or metamorphosis. At this time, embryonic melanophores are replaced by newly differentiating metamorphic melanophores that form the adult stripes. Mutants with normal embryonic/early larval pigment patterns but defective adult patterns identify factors required uniquely to establish, maintain, or recruit the latent precursors to metamorphic melanophores. We show that one such mutant, picasso, lacks most metamorphic melanophores and results from mutations in the ErbB gene erbb3b, encoding an EGFR-like receptor tyrosine kinase. To identify critical periods for ErbB activities, we treated fish with pharmacological ErbB inhibitors and also knocked-down erbb3b by morpholino injection. These analyses reveal an embryonic critical period for ErbB signaling in promoting later pigment pattern metamorphosis, despite the normal patterning of embryonic/early larval melanophores. We further demonstrate a peak requirement during neural crest migration that correlates with early defects in neural crest pathfinding and peripheral ganglion formation. Finally, we show that erbb3b activities are both autonomous and non-autonomous to the metamorphic melanophore lineage. These data identify a very early, embryonic, requirement for erbb3b in the development of much later metamorphic melanophores, and suggest complex modes by which ErbB signals promote adult pigment pattern development. PMID:18508863

  12. Disappearing Scales in Carps: Re-Visiting Kirpichnikov's Model on the Genetics of Scale Pattern Formation

    PubMed Central

    Goh, Chin Heng; Kathiresan, Purushothaman; Németh, Sándor; Jeney, Zsigmond; Bercsényi, Miklós; Orbán, László

    2013-01-01

    The body of most fishes is fully covered by scales that typically form tight, partially overlapping rows. While some of the genes controlling the formation and growth of fish scales have been studied, very little is known about the genetic mechanisms regulating scale pattern formation. Although the existence of two genes with two pairs of alleles (S&s and N&n) regulating scale coverage in cyprinids has been predicted by Kirpichnikov and colleagues nearly eighty years ago, their identity was unknown until recently. In 2009, the ‘S’ gene was found to be a paralog of fibroblast growth factor receptor 1, fgfr1a1, while the second gene called ‘N’ has not yet been identified. We re-visited the original model of Kirpichnikov that proposed four major scale pattern types and observed a high degree of variation within the so-called scattered phenotype due to which this group was divided into two sub-types: classical mirror and irregular. We also analyzed the survival rates of offspring groups and found a distinct difference between Asian and European crosses. Whereas nude × nude crosses involving at least one parent of Asian origin or hybrid with Asian parent(s) showed the 25% early lethality predicted by Kirpichnikov (due to the lethality of the NN genotype), those with two Hungarian nude parents did not. We further extended Kirpichnikov's work by correlating changes in phenotype (scale-pattern) to the deformations of fins and losses of pharyngeal teeth. We observed phenotypic changes which were not restricted to nudes, as described by Kirpichnikov, but were also present in mirrors (and presumably in linears as well; not analyzed in detail here). We propose that the gradation of phenotypes observed within the scattered group is caused by a gradually decreasing level of signaling (a dose-dependent effect) probably due to a concerted action of multiple pathways involved in scale formation. PMID:24386179

  13. 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.

  14. Continuous fine pattern formation by screen-offset printing using a silicone blanket

    NASA Astrophysics Data System (ADS)

    Nomura, Ken-ichi; Kusaka, Yasuyuki; Ushijima, Hirobumi; Nagase, Kazuro; Ikedo, Hiroaki; Mitsui, Ryosuke; Takahashi, Seiya; Nakajima, Shin-ichiro; Iwata, Shiro

    2014-09-01

    Screen-offset printing combines screen-printing on a silicone blanket with transference of the print from the blanket to a substrate. The blanket absorbs organic solvents in the ink, and therefore, the ink does not disperse through the material. This prevents blurring and allows fine patterns with widths of a few tens of micrometres to be produced. However, continuous printing deteriorates the pattern’s shape, which may be a result of decay in the absorption abilities of the blanket. Thus, we have developed a new technique for refreshing the blanket by substituting high-boiling-point solvents present on the blanket surface with low-boiling-point solvents. We analyse the efficacy of this technique, and demonstrate continuous fine pattern formation for 100 screen-offset printing processes.

  15. Formation of mixed and patterned self-assembled films of alkylphosphonates on commercially pure titanium surfaces

    NASA Astrophysics Data System (ADS)

    Rudzka, Katarzyna; Sanchez Treviño, Alda Y.; Rodríguez-Valverde, Miguel A.; Cabrerizo-Vílchez, Miguel A.

    2016-12-01

    Titanium is extensively employed in biomedical devices, in particular as implant. The self-assembly of alkylphosphonates on titanium surfaces enable the specific adsorption of biomolecules to adapt the implant response against external stimuli. In this work, chemically-tailored cpTi surfaces were prepared by self-assembly of alkylphosphonate molecules. By bringing together attributes of two grafting molecules, aqueous mixtures of two alkylphosphonates were used to obtain mixed self-assembled films. Single self-assembled films were also altered by laser abrasion to produce chemically patterned cpTi surfaces. Both mixed and patterned self-assembled films were confirmed by AFM, ESEM and X-ray photoelectron spectroscopy. Water contact angle measurements also revealed the composition of the self-assembly films. Chemical functionalization with two grafting phosphonate molecules and laser surface engineering may be combined to guide the bone-like formation on cpTi, and the future biological response in the host.

  16. 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.

  17. 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.

  18. Mechanisms for spatio-temporal pattern formation in highway traffic models.

    PubMed

    Wilson, R Eddie

    2008-06-13

    A key qualitative requirement for highway traffic models is the ability to replicate a type of traffic jam popularly referred to as a phantom jam, shock wave or stop-and-go wave. Despite over 50 years of modelling, the precise mechanisms for the generation and propagation of stop-and-go waves and the associated spatio-temporal patterns are in dispute. However, the increasing availability of empirical datasets, such as those collected from motorway incident detection and automatic signalling system (MIDAS) inductance loops in the UK or the next-generation simulation trajectory data (NGSIM) project in the USA, means that we can expect to resolve these questions definitively in the next few years. This paper will survey the essence of the competing explanations of highway traffic pattern formation and introduce and analyse a new mechanism, based on dynamical systems theory and bistability, which can help resolve the conflict.

  19. Polymer Wall Formation Using Liquid-Crystal/Polymer Phase Separation Induced on Patterned Polyimide Films

    NASA Astrophysics Data System (ADS)

    Murashige, Takeshi; Fujikake, Hideo; Sato, Hiroto; Kikuchi, Hiroshi; Kurita, Taiichiro; Sato, Fumio

    2004-12-01

    We could form lattice-shaped polymer walls in a liquid crystal (LC) layer through the thermal phase separation of an LC/polystyrene solution between substrates with polyimide films etched by short-wavelength ultraviolet irradiation using a photomask. The LC wetting difference between the polyimide and substrate surfaces caused the coalescence of growing LC droplets on patterned polyimide films with the progress of phase separation. Consequently, polymer walls were formed on substrate surface areas without polyimide films. The shape of the polymer wall formed became sharp with the use of rubbed polyimide films because the nucleation of growing LC droplets concentrated on the patterned polyimide films. It is thought that the increase in the alignment order of LC molecules in the solution near the rubbed polyimide films promotes the formation of LC molecular aggregation, which becomes the growth nuclei of LC droplets.

  20. Pattern formation during the evaporation of a colloidal nanoliter drop: a numerical and experimental study

    NASA Astrophysics Data System (ADS)

    Bhardwaj, Rajneesh; Fang, Xiaohua; Attinger, Daniel

    2009-07-01

    An efficient way to precisely pattern particles on solid surfaces is to dispense and evaporate colloidal drops, as for bioassays. The dried deposits often exhibit complex structures exemplified by the coffee ring pattern, where most particles have accumulated at the periphery of the deposit. In this work, the formation of deposits during the drying of nanoliter colloidal drops on a flat substrate is investigated numerically and experimentally. A finite-element numerical model is developed that solves the Navier-Stokes, heat and mass transport equations in a Lagrangian framework. The diffusion of vapor in the atmosphere is solved numerically, providing an exact boundary condition for the evaporative flux at the droplet-air interface. Laplace stresses and thermal Marangoni stresses are accounted for. The particle concentration is tracked by solving a continuum advection-diffusion equation. Wetting line motion and the interaction of the free surface of the drop with the growing deposit are modeled based on criteria on wetting angles. Numerical results for evaporation times and flow field are in very good agreement with published experimental and theoretical results. We also performed transient visualization experiments of water and isopropanol drops loaded with polystyrene microspheres evaporating on glass and polydimethylsiloxane substrates, respectively. Measured evaporation times, deposit shapes and sizes and flow fields are in very good agreement with the numerical results. Different flow patterns caused by the competition of Marangoni loops and radial flow are shown to determine the deposit shape to be either a ring-like pattern or a homogeneous bump.

  1. Spatiotemporal pattern formation in a prey-predator model under environmental driving forces

    NASA Astrophysics Data System (ADS)

    Sirohi, Anuj Kumar; Banerjee, Malay; Chakraborti, Anirban

    2015-09-01

    Many existing studies on pattern formation in the reaction-diffusion systems rely on deterministic models. However, environmental noise is often a major factor which leads to significant changes in the spatiotemporal dynamics. In this paper, we focus on the spatiotemporal patterns produced by the predator-prey model with ratio-dependent functional response and density dependent death rate of predator. We get the reaction-diffusion equations incorporating the self-diffusion terms, corresponding to random movement of the individuals within two dimensional habitats, into the growth equations for the prey and predator population. In order to have the noise added model, small amplitude heterogeneous perturbations to the linear intrinsic growth rates are introduced using uncorrelated Gaussian white noise terms. For the noise added system, we then observe spatial patterns for the parameter values lying outside the Turing instability region. With thorough numerical simulations we characterize the patterns corresponding to Turing and Turing-Hopf domain and study their dependence on different system parameters like noise-intensity, etc.

  2. 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.

  3. Pattern Formation in Polymerizing Actin Flocks: Spirals, Spots, and Waves without Nonlinear Chemistry

    NASA Astrophysics Data System (ADS)

    Le Goff, T.; Liebchen, B.; Marenduzzo, D.

    2016-12-01

    We propose a model solely based on actin treadmilling and polymerization which describes many characteristic states of actin-wave formation: spots, spirals, and traveling waves. In our model, as in experiments on cells recovering motility following actin depolymerization, we choose an isotropic low-density initial condition; polymerization of actin filaments then raises the density towards the Onsager threshold where they align. We show that this alignment, in turn, destabilizes the isotropic phase and generically induces transient actin spots or spirals as part of the dynamical pathway towards a polarized phase which can either be uniform or consist of a series of actin-wave trains (flocks). Our results uncover a universal route to actin-wave formation in the absence of any system-specific nonlinear biochemistry, and it may help to understand the mechanism underlying the observation of actin spots and waves in vivo. They also suggest a minimal setup to design similar patterns in vitro.

  4. 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.

  5. Laser patterning of diamond. Part II. Surface nondiamond carbon formation and its removal

    NASA Astrophysics Data System (ADS)

    Smedley, John; Jaye, Cherno; Bohon, Jen; Rao, Triveni; Fischer, Daniel A.

    2009-06-01

    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 ˜60 nm. Ozone cleaning was used to remove the nondiamond carbon layer.

  6. Pattern formation in binary fluid mixtures induced by short-range competing interactions

    NASA Astrophysics Data System (ADS)

    Bores, Cecilia; Lomba, Enrique; Perera, Aurélien; Almarza, Noé G.

    2015-08-01

    Molecular dynamics simulations and integral equation calculations of a simple equimolar mixture of diatomic molecules and monomers interacting via attractive and repulsive short-range potentials show the existence of pattern formation (microheterogeneity), mostly due to depletion forces away from the demixing region. Effective site-site potentials extracted from the pair correlation functions using an inverse Monte Carlo approach and an integral equation inversion procedure exhibit the features characteristic of a short-range attractive and a long-range repulsive potential. When charges are incorporated into the model, this becomes a coarse grained representation of a room temperature ionic liquid, and as expected, intermediate range order becomes more pronounced and stable.

  7. A simple model of thermal crack pattern formation using the coupled criterion

    NASA Astrophysics Data System (ADS)

    Leguillon, Dominique

    2013-06-01

    Different mechanisms (cooling, drying, and ageing) lead to the formation of crack patterns on the surface of some materials that are very difficult to describe in detail. We propose a model based on the coupled criterion using two necessary conditions for the nucleation of cracks: an energy condition and a stress condition. This model is applied to a simple example: a plate fixed to a rigid substrate and cooled down on its top face. During slow cooling, it highlights the ability of forming a first lattice of cracks and the subdivision thereof. It also shows that, in a rapid cooling (quenching), the higher the temperature drop, the tighter the cracks network.

  8. 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.

  9. 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.

  10. 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.

  11. Hydrologic Connectivity as a Window into Pattern Conditions and Formation Processes in Aquatic Ecosystems

    NASA Astrophysics Data System (ADS)

    Larsen, L. G.; Choi, J.; Nungesser, M. K.; Harvey, J. W.

    2011-12-01

    Patterned aquatic ecosystems exhibit different types and degrees of hydrologic connectivity, from isolated open-water patches in some inland marshes, to cross-slope strings and flarks of striped fens, to along-slope ridges and sloughs of low-gradient subtropical wetlands, to dendritic channels of coastal marshes. The nature and degree of this connectivity are closely linked to landscape function. For example, hydrologic connectivity perpendicular to river channel thalwegs relates to the exchange of sediment and nutrients between channels and floodplains, whereas connectivity parallel to a dominant flow direction affects fish migration or the likelihood of contaminant transport. Characteristics of hydrologic connectivity reflect not only the results of landscape pattern but also the mechanisms responsible for pattern creation. Quantifying those connectivity characteristics provides a robust means to identify landscapes likely formed under a consistent set of processes or to compare the output of landscape simulation models to actual landscapes in order to determine whether the models capture the most relevant landscape formation processes. However, established methods for quantifying isotropic patch connectivity are often ill suited for strongly patterned landscapes or hydroscapes in which directional flow is important. Using graph theory principles, we developed two alternative indices of directional hydrologic connectivity: the maximum flow index (MFI) and directional connectivity index (DCI), which quantify the connectivity of flow paths along a particular axis of interest. The MFI is sensitive to the existence of any hydrologic connection along the direction of interest, whereas the DCI is sensitive to the linearity of connections along that direction. Curves of directional connectivity over a range of angular bearings provide a quantitative, information-dense representation of landscape structure that can be related to subtle differences in the physical

  12. Formation and reverberation of sequential neural activity patterns evoked by sensory stimulation are enhanced during cortical desynchronization.

    PubMed

    Bermudez Contreras, Edgar J; Schjetnan, Andrea Gomez Palacio; Muhammad, Arif; Bartho, Peter; McNaughton, Bruce L; Kolb, Bryan; Gruber, Aaron J; Luczak, Artur

    2013-08-07

    Memory formation is hypothesized to involve the generation of event-specific neural activity patterns during learning and the subsequent spontaneous reactivation of these patterns. Here, we present evidence that these processes can also be observed in urethane-anesthetized rats and are enhanced by desynchronized brain state evoked by tail pinch, subcortical carbachol infusion, or systemic amphetamine administration. During desynchronization, we found that repeated tactile or auditory stimulation evoked unique sequential patterns of neural firing in somatosensory and auditory cortex and that these patterns then reoccurred during subsequent spontaneous activity, similar to what we have observed in awake animals. Furthermore, the formation of these patterns was blocked by an NMDA receptor antagonist, suggesting that the phenomenon depends on synaptic plasticity. These results suggest that anesthetized animals with a desynchronized brain state could serve as a convenient model for studying stimulus-induced plasticity to improve our understanding of memory formation and replay in the brain.

  13. 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).

  14. 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.

  15. Control of distributed autonomous robotic systems using principles of pattern formation in nature and pedestrian behavior.

    PubMed

    Molnar, P; Starke, J

    2001-01-01

    Self-organized and error-resistant control of distributed autonomous robotic units in a manufacturing environment with obstacles where the robotic units have to be assigned to manufacturing targets in a cost effective way, is achieved by using two fundamental principles of nature. First, the selection behavior of modes is used which appears in pattern formation of physical, chemical and biological systems. Coupled selection equations based on these pattern formation principles can be used as dynamical system approach to assignment problems. These differential equations guarantee feasibility of the obtained solutions which is of great importance in industrial applications. Second, a model of behavioral forces is used, which has been successfully applied to describe self-organized crowd behavior of pedestrians. This novel approach includes collision avoidance as well as error resistivity. In particular, in systems where failures are of concern, the suggested approach outperforms conventional methods in covering up for sudden external changes like breakdowns of some robotic units. The capability of this system is demonstrated in computer simulations.

  16. 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.

  17. NF2/Merlin is required for the axial pattern formation in the Xenopus laevis embryo.

    PubMed

    Zhu, Xuechen; Min, Zheying; Tan, Renbo; Tao, Qinghua

    2015-11-01

    The NF2 gene product Merlin is a FERM-domain protein possessing a broad tumor-suppressing function. NF2/Merlin has been implicated in regulating multiple signaling pathways critical for cell growth and survival. However, it remains unknown whether NF2/Merlin regulates Wnt/β-catenin signaling during vertebrate embryogenesis. Here we demonstrate that NF2/Merlin is required for body pattern formation in the Xenopus laevis embryo. Depletion of the maternal NF2/Merlin enhances organizer gene expression dependent on the presence of β-catenin, and causes dorsanteriorized development; Morpholino antisense oligo-mediated knockdown of the zygotic NF2/Merlin shifts posterior genes anteriorwards and reduces the anterior development. We further demonstrate that targeted depletion of NF2 in the presumptive dorsal tissues increases the levels of nuclear β-catenin in the neural epithelial cells. Biochemical analyses reveal that NF2 depletion promotes the production of active β-catenin and concurrently decreases the level of N-terminally phosphorylated β-catenin under the stimulation of the endogenous Wnt signaling. Our findings suggest that NF2/Merlin negatively regulates the Wnt/β-catenin signaling activity during the pattern formation in early X. laevis embryos.

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

    PubMed

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

    2013-09-03

    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.

  19. Metamorphic pattern of the Cretaceous Celica Formation, SW Ecuador, and its geodynamic implications

    NASA Astrophysics Data System (ADS)

    Aguirre, Luis

    1992-04-01

    The volcanic rocks of the Cretaceous Celica Formation of southern Ecuador are affected by a weak although widespread alteration. The chemical study of the secondary chemical phases present in andesitic and basaltic lava flows reveals that this alteration corresponds to very low-grade metamorphism comprising the zeolite and the prehnite-pumpellyite facies. Main features of this metamorphism are: weak lithostatic pressure, moderate to steep thermal gradient, high ƒ O2, low value of the seawater/rock ratio and total absence of deformation. These characteristics are typically present in other volcanic suites of similar age and composition along the Andes and correspond to the pattern of metamorphism developed in extensional settings (diastathermal metamorphism) linked to various degrees of thinning of the continental crust. Based on this metamorphic pattern, a geodynamic model is proposed in which the Celica Formation is interpreted as an ensialic, aborted, marginal basin developed on strongly attenuated continental crust at the border of the South American plate. The relationship between the Ecuadorian and Colombian volcanic suites of Cretaceous age present along the Western Cordillera is discussed in the light of the model suggested.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. A possible formation mechanism of rampart-like ejecta pattern in a laboratory

    NASA Astrophysics Data System (ADS)

    Suzuki, A.; Kadono, T.; Nakamura, A. M.; Arakawa, M.; Wada, K.; Yamamoto, S.

    2011-12-01

    The ejecta morphologies around impact craters represent highly diverse appearance on the surface of solid bodies in our Solar System. It is considered that the varied ejecta morphologies result from the environments such as the atmospheric pressure, the volatile content in the subsurface, because they affect the emplacement process of the ejecta. Clarifying the relationships between the ejecta morphologies and the formation processes and environments could constrain the ancient surface environment and the evolution of the planets. We have investigated the ejecta patterns around the impact craters which formed on a glass beads layer in a laboratory, and found that the patterns depend on impact velocity, atmospheric pressure, and initial state of packing of the target [Suzuki et al., 2010, JpGU abstract]. Now, we focus on one of the ejecta patterns which has a petal-like (or sometimes concentric) ridges on the distal edge of the continuous ejecta. This ejecta pattern looks very similar to the rampart ejecta morphology observed around Martian impact craters [e.g. Barlow et al., 2000]. The experiments are conducted with the small light gas gun placed in Kobe University, Japan. The projectile is a cylinder with a diameter of 10 mm and a height of 10 mm, and is made of aluminum, nylon, or stainless. The target is a layer of glass beads (nearly uniform diameter) in a tub with ~28 cm in diameter. The bulk density is about 1.7 g/cm^3. The following three parameters are varied: 1) the diameter of the target glass beads (50, 100, 420 microns), 2) the ambient atmospheric pressure in the chamber (from ~500 Pa to atmospheric pressure), 3) the impact velocity of the projectile (from a few to ~120 m/s). In our experiments, the rampart-like ridged patterns are observed within the following conditions: 1) the diameter of the target glass beads is 50 and 100 microns, 2) the ambient pressure in the chamber is higher than ~10^4 Pa, and 3) the impact velocity is higher than 16 m

  5. 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.

  6. Pattern Formation and Strong Nonlinear Interactions in Exciton-Polariton Condensates

    NASA Astrophysics Data System (ADS)

    Ge, Li; Nersisyan, Ani; Oztop, Baris; Tureci, Hakan

    2014-03-01

    Exciton-polaritons generated by light-induced potentials can spontaneously condense into macroscopic quantum states that display nontrivial spatial and temporal density modulation. While these patterns and their dynamics can be reproduced through the solution of the generalized Gross-Pitaevskii equation, a predictive theory of their thresholds, oscillation frequencies, and multi-pattern interactions has so far been lacking. Here we represent such an approach based on current-carrying quasi-modes of the non-Hermitian potential induced by the pump. The presented theory allows us to capture the patterns formed in the steady-state directly and account for nonlinearities exactly. We find a simple but powerful expression for thresholds of condensation and the associated frequencies of oscillations, quantifying the contribution of particle formation, leakage, and interactions. We also show that the evolution of the condensate with increasing pump strength is strongly geometry dependent and can display contrasting features such as enhancement or reduction of the spatial localization of the condensate. We acknowledge support by DARPA under Grant No. N66001-11-1-4162 and NSF under CAREER Grant No. DMR-1151810.

  7. An updated kernel-based Turing model for studying the mechanisms of biological pattern formation.

    PubMed

    Kondo, Shigeru

    2017-02-07

    The reaction-diffusion model presented by Alan Turing has recently been supported by experimental data and accepted by most biologists. However, scientists have recognized shortcomings when the model is used as the working hypothesis in biological experiments, particularly in studies in which the underlying molecular network is not fully understood. To address some such problems, this report proposes a new version of the Turing model. This alternative model is not represented by partial differential equations, but rather by the shape of an activation-inhibition kernel. Therefore, it is named the kernel-based Turing model (KT model). Simulation of the KT model with kernels of various shapes showed that it can generate all standard variations of the stable 2D patterns (spot, stripes and network), as well as some complex patterns that are difficult to generate with conventional mathematical models. The KT model can be used even when the detailed mechanism is poorly known, as the interaction kernel can often be detected by a simple experiment and the KT model simulation can be performed based on that experimental data. These properties of the KT model complement the shortcomings of conventional models and will contribute to the understanding of biological pattern formation.

  8. 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. .

  9. Spermidine, but not spermine, is essential for pigment pattern formation in zebrafish.

    PubMed

    Frohnhöfer, Hans Georg; Geiger-Rudolph, Silke; Pattky, Martin; Meixner, Martin; Huhn, Carolin; Maischein, Hans-Martin; Geisler, Robert; Gehring, Ines; Maderspacher, Florian; Nüsslein-Volhard, Christiane; Irion, Uwe

    2016-06-15

    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.

  10. 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

  11. In situ formation and photo patterning of emissive quantum dots in small organic molecules

    NASA Astrophysics Data System (ADS)

    Bansal, Ashu K.; Sajjad, Muhammad T.; Antolini, Francesco; Stroea, Lenuta; Gečys, Paulius; Raciukaitis, Gediminas; André, Pascal; Hirzer, Andreas; Schmidt, Volker; Ortolani, Luca; Toffanin, Stefano; Allard, Sybille; Scherf, Ullrich; Samuel, Ifor D. W.

    2015-06-01

    Nanostructured composites of inorganic and organic materials are attracting extensive interest for electronic and optoelectronic device applications. Here we report a novel method for the fabrication and patterning of metal selenide nanoparticles in organic semiconductor films that is compatible with solution processable large area device manufacturing. Our approach is based upon the controlled in situ decomposition of a cadmium selenide precursor complex in a film of the electron transporting material 1,3,5-tris(N-phenyl-benzimidazol-2-yl)-benzene (TPBI) by thermal and optical methods. In particular, we show that the photoluminescence quantum yield (PLQY) of the thermally converted CdSe quantum dots (QDs) in the TPBI film is up to 15%. We also show that laser illumination can form the QDs from the precursor. This is an important result as it enables direct laser patterning (DLP) of the QDs. DLP was performed on these nanocomposites using a picosecond laser. Confocal microscopy shows the formation of emissive QDs after laser irradiation. The optical and structural properties of the QDs were also analysed by means of UV-Vis, PL spectroscopy and transmission electron microscopy (TEM). The results show that the QDs are well distributed across the film and their emission can be tuned over a wide range by varying the temperature or irradiated laser power on the blend films. Our findings provide a route to the low cost patterning of hybrid electroluminescent devices.

  12. 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

  13. 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.

  14. Stability and pattern formation for competing populations with asymmetric nonlocal coupling.

    PubMed

    Tanzy, M C; Volpert, V A; Bayliss, A; Nehrkorn, M E

    2013-11-01

    We consider a model of two competing species with asymmetric nonlocal coupling in a competition for resources. The nonlocal coupling is via convolution integrals and the asymmetry is via convolution kernel functions which are not even functions of their arguments. The nonlocality is due to species mobility, so that at any fixed point in space the competition for resources depends not just on the populations at that point but on a suitably weighted average of the populations. We introduce two parameters, δ, describing the extent of the coupling, with δ=0 corresponding to local coupling, and α, describing the extent of the asymmetry, with α=0 corresponding to symmetric nonlocal interactions. We consider the case where the model admits a stable coexistence equilibrium solution. We perform a linear stability analysis and show that this solution can be destabilized by sufficient nonlocality, i.e., when δ increases beyond a critical value. We consider two specific kernel functions, (i) an asymmetric Gaussian and (ii) an asymmetric stepfunction. We compute the stability boundary as a function of α, and for δ beyond the stability boundary we determine unstable wavenumber bands. We compute nonlinear patterns for δ significantly beyond the stability boundary. Patterns consist of arrays of islands, regions of nonzero population, separated by either near-deadzones where the populations are small, but nonzero, or by deadzones where populations are exponentially small and essentially extinct. We find solutions consisting of propagating traveling waves of islands, solutions exhibiting colony formation, where a colony is formed just ahead of an island and eventually grows as the parent island decays, and modulated traveling waves, where competition between the two species allows propagation and inhibits colony formation. We explain colony formation and the modulated traveling waves as due to a positive feedback mechanism associated with small variations in the amplitude of

  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. Pattern formation of down-built salt structures: insights from 3D numerical models

    NASA Astrophysics Data System (ADS)

    Fernandez, Naiara; Kaus, Boris

    2015-04-01

    Many salt diapirs are thought to have formed as a result of down-building, which implies that the top of the diapir remained close to the surface during sediment deposition. This process is largely three-dimensional and in order to better understand what controls the patterns that form as a result of this down-building process, we here perform three-dimensional numerical models and compare the results with analytical models. In our models, we vary several parameters such as initial salt thickness, sedimentation rate, salt viscosity, salt-sediment viscosity contrast as well as the density of sediments. Down-building of three-dimensional diapirs only occurs for a certain range of parameters and is favored by lower sediment/salt viscosity contrasts and sedimentation rates in agreement with analytical predictions and findings from previous 2D models. However, the models show that the sedimentation rate has an additional effect on the formation and evolution of three-dimensional diapir patterns. At low sedimentation rates, salt ridges that form during early model stages remain preserved at later stages as well. For higher sedimentation rates, the initial salt ridges break up and form finger-like diapirs at the junction of salt ridges, which results in different salt exposure patterns at the surface. Once the initial pattern of diapirs is formed, higher sedimentation rate can also result in covered diapirs if the diapir extrusion velocity is insufficiently large. We quantify the effect of sedimentation rate on the number of diapirs exposed at the surface as well as on their spacing. In some cases, this final pattern is distinctly different from the initial polygonal pattern. We also study the extrusion of salt through time in the simulations, and show that it can be related to the geometries of the sedimentary layers surrounding the diapirs. Acknowledgements. Funding was provided by the European Research Council under the European Community's Seventh Framework Program

  17. New patterns of family formation in Italy. Which tools for which interpretations?

    PubMed

    Micheli, G A

    1996-01-01

    This paper presents a detailed discussion of the impact of World War II on subsequent fertility behavior a generation later in Italy. The changes in fertility were delayed and induced by a transgenerational process precipitated by war. War anomie and anomie in the rules of family formation are "symptoms" and not effects of the broad structural changes and historical upheavals during the 30 years of war. Fertility behavior is not construed to be an inevitable outcome of causal processes, but as alternative responses to life situations. The author bases this explanatory model of macrodemographic processes on a variant of Brown and Harris' etiological model that explains the occurrence of depression. It is argued that demographic models of European fertility are needed that acknowledge "a radical form of war that acts on reciprocity systems susceptible to change" and "intervenes to modify the subsequent transgenerational (family) relations." A research design is not now available that relies on the tools of history and anthropology. Thus, the demography of fertility may be reduced to a "mere bookkeeping of vital statistical data or simple economics of resources." The author's new pattern of family formation in Italy considers the "regional family culture and structure to be symptom-formation factors relating to the war and transformations in systems of family relations and exchange." These family changes are linked to war anomie and "changes in the logic of transition strategies from suppression to disconfirmation." War anomie is linked with a generational impact that intervenes in the relationship between changes in the logic of transition strategies and the decline in births. The decline in births is the response to background factors, precipitating events, and symptom-formation or structural factors. The author states that the second demographic transition does not represent a break with prior urban lifestyles and does not modify general trends continuing from the

  18. Spontaneous formation of 10-μm-scale periodic patterns in transverse-scanning femtosecond laser processing.

    PubMed

    Matsuo, Shigeki; Hashimoto, Shuichi

    2015-01-12

    We report spontaneous formation of 10-μm-scale periodic patterns in transverse-scanning femtosecond (fs) laser processing inside a glass substrate. The formation of the periodic patterns was critically dependent on the distance of the focus from the back surface; they formed only when fs pulses were focused slightly inside (∼ a few micrometers) from the back surface. The periods ranged from 7 to 16 μm, which is much longer than the distance between neighboring irradiation spots (0.1-1 μm in the present experiments), the diameter of the individual modified spots (about 2 μm), and the wavelength (0.8 μm). The patterns formed without any intentional modulation; just by scanning the sample at a constant speed during irradiation of fs laser pulses. The dependence on scanning speed and repetition rate of the laser were also investigated, and a possible formation scenario for this "long" periodic pattern was described.

  19. 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.

  20. Dynamic models of biological pattern formation have some surprising implications for understanding the epigenetics of development.

    PubMed

    Molenaar, Peter C M; Lo, Lawrence

    2013-01-01

    Nonlinear epigenetic processes are conceived of in terms of self-organizing dynamic models of biological pattern formation. Epigenetic processes thus conceived generate substantial subject-specific structural variation, for instance, in growing brain networks. It is shown that standard quantitative genetic modeling based on analyses of interindividual phenotypic variation misclassifies the variation generated by nonlinear epigenetic processes as being due to specific environmental influences. A new quantitative genetic model, iFACE, is introduced to correctly identify the structural variation generated by self-organizing epigenetic processes. iFACE is based on time series analysis of intraindividual variation of a single pair of genetically related subjects. The results of an application of iFACE to multilead EEG obtained with a single dizygotic twin pair is presented.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Ion beam induced surface pattern formation and stable travelling wave solutions.

    PubMed

    Numazawa, Satoshi; Smith, Roger

    2013-03-06

    The formation of ripple structures on ion bombarded semiconductor surfaces is examined theoretically. Previous models are discussed and a new nonlinear model is formulated, based on the infinitesimal local atomic relocation induced by elastic nuclear collisions in the early stages of collision cascades and an associated density change in the near surface region. Within this framework ripple structures are shown to form without the necessity to invoke surface diffusion or large sputtering as important mechanisms. The model can also be extended to the case where sputtering is important, and it is shown that in this case certain 'magic' angles can occur at which the ripple patterns are most clearly defined. The results are in very good agreement with experimental observations.

  6. 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

  7. 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.

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

    NASA Astrophysics Data System (ADS)

    Wang, Qi; Song, Yang; Shao, Lingjie

    2017-02-01

    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.

  9. Pattern formation of second harmonic conical waves in a nonlinear medium with extended defect structure.

    PubMed

    Lin, Y C; Su, K W; Huang, K F; Chen, Y F

    2014-11-17

    We experimentally demonstrate the propagation of the conical second harmonic fields generated from a nonlinear crystal with extended defects to investigate their pattern formation. The generated second harmonic waves are found to be the interference of multiple Bessel-like beams that originate from distinct longitudinal layers inside the crystal. To reconstruct the experimental results, we model the individual Bessel-like beam to be the superposition of an ensemble of identical decentered Gaussian waves with random phases. We present that the randomness of the phases leads the Bessel-like beams to show wave profiles with different extent of localization. Moreover, we use the coherent superposition of the developed wave functions with a phase factor to manifest the interference of multiple Bessel-like beams. The relative phases among the Bessel-like beams are shown to be closely related to the near and far-field patterns. With the experimental observations and the theoretical model, the relative phases are decided to successfully reconstruct the propagation characteristics of the multiple Bessel-like beams.

  10. 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.

  11. 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.

  12. Signaling, transcriptional regulation, and asynchronous pattern formation governing plant xylem development

    PubMed Central

    FUKUDA, Hiroo

    2016-01-01

    In plants, vascular stem cells continue to give rise to all xylem and phloem cells, which constitute the plant vascular system. During plant vascular development, the peptide, tracheary element differentiation inhibitory factor (TDIF), regulates vascular stem cell fate in a non-cell-autonomous fashion. TDIF promotes vascular stem cell proliferation through up-regulating the transcription factor gene WUS-related HOMEOBOX4, and it suppresses xylem differentiation from vascular stem cells through the activation of Glycogen Synthase Kinase 3 proteins. VASCULAR-RELATED NAC-DOMAIN6 and 7 (VND6 and 7) are master transcription factors, and ectopic expression of VND6 and VND7 in various plants induces differentiation of different types of cells into metaxylem and protoxylem tracheary elements, respectively. These genes up-regulate genes involved in both patterned secondary cell wall formation and programmed cell death to form tracheary elements. Secondary wall patterns are formed by localized deposition of cellulose microfibrils, which is guided by cortical microtubules. Local activation of the small G-protein, Rho-type 11 determines distribution of cortical microtubules. PMID:26972600

  13. 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.

  14. Pattern formation, synchronization, and outbreak of biodiversity in cyclically competing games

    NASA Astrophysics Data System (ADS)

    Wang, Wen-Xu; Ni, Xuan; Lai, Ying-Cheng; Grebogi, Celso

    2011-01-01

    Species in nature are typically mobile over diverse distance scales, examples of which range from bacteria run to long-distance animal migrations. These behaviors can have a significant impact on biodiversity. Addressing the role of migration in biodiversity microscopically is fundamental but remains a challenging problem in interdisciplinary science. We incorporate both intra- and inter-patch migrations in stochastic games of cyclic competitions and find that the interplay between the migrations at the local and global scales can lead to robust species coexistence characterized dynamically by the occurrence of remarkable target-wave patterns in the absence of any external control. The waves can emerge from either mixed populations or isolated species in different patches, regardless of the size and the location of the migration target. We also find that, even in a single-species system, target waves can arise from rare mutations, leading to an outbreak of biodiversity. A surprising phenomenon is that target waves in different patches can exhibit synchronization and time-delayed synchronization, where the latter potentially enables the prediction of future evolutionary dynamics. We provide a physical theory based on the spatiotemporal organization of the target waves to explain the synchronization phenomena. We also investigate the basins of coexistence and extinction to establish the robustness of biodiversity through migrations. Our results are relevant to issues of general and broader interest such as pattern formation, control in excitable systems, and the origin of order arising from self-organization in social and natural systems.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Intracellular Trafficking in Drosophila Visual System Development: A Basis for Pattern Formation Through Simple Mechanisms

    PubMed Central

    Chan, Chih-Chiang; Epstein, Daniel; Hiesinger, P. Robin

    2012-01-01

    Intracellular trafficking underlies cellular functions ranging from membrane remodeling to receptor activation. During multicellular organ development, these basic cell biological functions are required as both passive machinery and active signaling regulators. Exocytosis, endocytosis, and recycling of several key signaling receptors have long been known to actively regulate morphogenesis and pattern formation during Drosophila eye development. Hence, intracellular membrane trafficking not only sets the cell biological stage for receptor-mediated signaling but also actively controls signaling through spatiotemporally regulated receptor localization. In contrast to eye development, the role of intracellular trafficking for the establishment of the eye-to-brain connectivity map has only recently received more attention. It is still poorly understood how guidance receptors are spatiotemporally regulated to serve as meaningful synapse formation signals. Yet, the Drosophila visual system provides some of the most striking examples for the regulatory role of intracellular trafficking during multicellular organ development. In this review we will first highlight the experimental and conceptual advances that motivate the study of intracellular trafficking during Drosophila visual system development. We will then illuminate the development of the eye, the eye-to-brain connectivity map and the optic lobe from the perspective of cell biological dynamics. Finally, we provide a conceptual framework that seeks to explain how the interplay of simple genetically encoded intracellular trafficking events governs the seemingly complex cellular behaviors, which in turn determine the developmental product. PMID:21714102

  1. Seasonal and temporal patterns of NDMA formation potentials in surface waters.

    PubMed

    Uzun, Habibullah; Kim, Daekyun; Karanfil, Tanju

    2015-02-01

    The seasonal and temporal patterns of N-nitrosodimethylamine (NDMA) formation potentials (FPs) were examined with water samples collected monthly for 21 month period in 12 surface waters. This long term study allowed monitoring the patterns of NDMA FPs under dynamic weather conditions (e.g., rainy and dry periods) covering several seasons. Anthropogenically impacted waters which were determined by high sucralose levels (>100 ng/L) had higher NDMA FPs than limited impacted sources (<100 ng/L). In most sources, NDMA FP showed more variability in spring months, while seasonal mean values remained relatively consistent. The study also showed that watershed characteristics played an important role in the seasonal and temporal patterns. In the two dam-controlled river systems (SW A and G), the NDMA FP levels at the downstream sampling locations were controlled by the NDMA levels in the dams independent of either the increases in discharge rates due to water releases from the dams prior to or during the heavy rain events or intermittent high NDMA FP levels observed at the upstream of dams. The large reservoirs and impoundments on rivers examined in this study appeared serving as an equalization basin for NDMA precursors. On the other hand, in a river without an upstream reservoir (SW E), the NDMA levels were influenced by the ratio of an upstream wastewater treatment plant (WWTP) effluent discharge to the river discharge rate. The impact of WWTP effluent decreased during the high river flow periods due to rain events. Linear regression with independent variables DOC, DON, and sucralose yielded poor correlations with NDMA FP (R(2) < 0.27). Multiple linear regression analysis using DOC and log [sucralose] yielded a better correlation with NDMA FP (R(2) = 0.53).

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

    PubMed

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

    2007-03-14

    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 (3.0 nm), 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 (12.0 nm), the crystallization of PEO dominates the surface morphology. For films with thickness between these two values, microphase separation and crystallization can simultaneously occur.

  3. 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.

  4. Geologically Controlled Isotope-Time Patterns Reveal Early Differentiation and Crust Formation Processes

    NASA Astrophysics Data System (ADS)

    Bennett, V. C.; Nutman, A. P.

    2014-12-01

    The mechanisms of continental crust production and evolution in the early Earth remain controversial, as are questions of the relative roles of early differentiation versus subsequent tectonic procssing in creating Earth's chemical signatures. Here we present geologic observations integrated with whole rock major, trace element and Sm-Nd isotopic signatures and combined with U-Pb and Lu-Hf isotopic compositions of zircon populations from the same rocks, from the most extensive early rock record comprising the 3.9 Ga to 3.6 Ga terranes of southwest Greenland. These data reveal repeated patterns of formation of juvenile TTG crust and associated mafic and ultramafic rocks in convergent margin settings followed by formation of more evolved granites [1]. Our new zircon Lu-Hf data from rare 3.6-3.7 Ga tonalites within the Itsaq Gneiss Complex, obtained from single component, non-migmatitic gneisses with simple zircon populations, limited within sample Hf isotopic variability and accurate U-Pb ages, now document extraction of juvenile tonalites from a near chondritic mantle source between 3.9 Ga and 3.6 Ga. The more evolved, granitic rocks in each area show slightly negative initial ɛHf in accord with crustal reworking of the older (3.8-3.9 Ga) gniesses. There is no evidence for Hadean material in the sources of the granitoids. The Hf isotope-time patterns are consistent with juvenile crust production from a mantle source that experienced only modest amounts of prior crustal extraction. They are distinct from those predicted by reprocessing of an enriched Hadean mafic crust, as has been proposed for this region [2] and for the source of the Hadean Jack Hills zircons [3]. The well-documented, time decreasing, positive 142Nd anomalies [e.g., 4] from these rocks are further evidence of crustal derivation from a convecting mantle source, rather than reworking of an enriched mafic lithosphere. The 143Nd isotopic -time patterns are more complex, reflecting the interplay

  5. 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

  6. Resembling a "natural formation pattern" of chlorinated dibenzo-p-dioxins by varying the experimental conditions of hydrothermal carbonization.

    PubMed

    Tirler, Werner; Basso, Albino

    2013-11-01

    Until several years ago dioxins were considered as just an unwanted by product of anthropogenic activities and stigmatized as the symbol of man-made environmental pollution. Natural processes, such as forest fires, can emit dioxins, but compared to industrial processes, usually very low quantities are emitted. However after a case of food contamination occurred in the United States of America in 1996 caused by kaolinitic clay a discussion on the provenience started. Besides the relatively high concentration also an unusual PCDD/F distribution pattern was found in these ball clay samples. This specific pattern related to none of the known anthropogenic sources for these contaminants and, in relation to a supposed natural formation, later it was named "natural formation pattern". Hydrothermal carbonization (HTC) can transform biomass within hours into a brown coal-like product which resembles naturally occurring coal formation. HTC can also transform an already present PCDD/F contamination in a way to obtain a "natural formation pattern" characterized by an unusual high ratio between 1,2,3,7,8,9-HxCDD and 1,2,3,6,7,8-HxCDD and the absence of almost all chlorinated dibenzofurans. By varying the experimental conditions of the HTC process applied to sewage sludge samples contaminated with PCDD/Fs from anthropogenic sources, beside the "natural formation pattern" at a temperatures of 255 °C, a remarkable increase of the toxicity based on WHO-TEQ was observed.

  7. From Dynamic Expression Patterns to Boundary Formation in the Presomitic Mesoderm

    PubMed Central

    Tiedemann, Hendrik B.; Schneltzer, Elida; Zeiser, Stefan; Hoesel, Bastian; Beckers, Johannes; Przemeck, Gerhard K. H.; de Angelis, Martin Hrabě

    2012-01-01

    The segmentation of the vertebrate body is laid down during early embryogenesis. The formation of signaling gradients, the periodic expression of genes of the Notch-, Fgf- and Wnt-pathways and their interplay in the unsegmented presomitic mesoderm (PSM) precedes the rhythmic budding of nascent somites at its anterior end, which later develops into epithelialized structures, the somites. Although many in silico models describing partial aspects of somitogenesis already exist, simulations of a complete causal chain from gene expression in the growth zone via the interaction of multiple cells to segmentation are rare. Here, we present an enhanced gene regulatory network (GRN) for mice in a simulation program that models the growing PSM by many virtual cells and integrates WNT3A and FGF8 gradient formation, periodic gene expression and Delta/Notch signaling. Assuming Hes7 as core of the somitogenesis clock and LFNG as modulator, we postulate a negative feedback of HES7 on Dll1 leading to an oscillating Dll1 expression as seen in vivo. Furthermore, we are able to simulate the experimentally observed wave of activated NOTCH (NICD) as a result of the interactions in the GRN. We esteem our model as robust for a wide range of parameter values with the Hes7 mRNA and protein decays exerting a strong influence on the core oscillator. Moreover, our model predicts interference between Hes1 and HES7 oscillators when their intrinsic frequencies differ. In conclusion, we have built a comprehensive model of somitogenesis with HES7 as core oscillator that is able to reproduce many experimentally observed data in mice. PMID:22761566

  8. An investigation of the formation patterns of the ionospheric F3 layer in low and equatorial latitudes

    NASA Astrophysics Data System (ADS)

    Zhu, Jie; Zhao, Biqiang; Wan, Weixing; Ning, Baiqi

    2013-09-01

    Ionogram traces with the F3 layer in different latitude do not always seem similar. In our work, we tend to describe morphological features of traces with the F3 layer in magnetic low-latitude region and near magnetic equator through the quantitative investigation of the diurnal variation and latitude dependence of two morphologically characteristic parameters - the foF2-to-foF3 ratio and the difference between h‧F3 and h‧F2 - in geomagnetically quiet period. The distribution of two formation patterns (pattern A and pattern B are defined with increasing F3 peak density and with nearly constant or decreasing F3 peak density respectively as the peak moving upward around the onset of the F3 layer’s occurrence) of the F3 layer is also investigated based on statistics of formation patterns of the F3 layer in Sanya and Kwajalein in 2011. The ideal equinoctial distribution (without the summer-to-winter neutral wind) of those patterns is symmetrical about magnetic equator with pattern A in magnetic low-latitude region and pattern B near magnetic equator. When taking the summer-to-winter neutral wind which resists (enhances) the plasma diffusion to higher latitude in the windward (leeward) into consideration in a solstice, pattern A could be observed near magnetic equator in summer hemisphere and pattern B in magnetic low-latitude region in winter hemisphere compared with the ideal distribution in the equinox.

  9. 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

  10. 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.

  11. 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

  12. Pattern formation in B-cell immune networks: Domains and dots in shape-space

    NASA Astrophysics Data System (ADS)

    Noest, A. J.; Takumi, K.; de Boer, R.

    1997-02-01

    The immune system contains many types of B-cells, which can activate each other if the shapes and surface properties of their receptors (or antibodies) match well. The dynamics of the resulting network is analysed using a recently derived B-cell activation function which captures the effects of the binding and crosslinking of B-cell receptors. All receptor/antibody shapes are parametrised by a continuous ‘shape-space’, such that matching pairs of shapes interact locally. The model produces a variety of activation patterns across shape-space for a wide range of parameters. The spatio-temporal structures differ qualitatively from those seen with a previously used type of activation function. In either case, the pattern formation can largely be understood analytically, by first solving exactly for the various uniform fixed solutions, and then computing the evolution of spatially modulated perturbations. For the more realistic activation function, the following scenario is found. Most (random) initial conditions first lead to the formation of coarse domains, of three possible types: the ‘virgin’-(V) state, the ‘ {immune}/{suppresed}’ ( {I}/{S)-state }, and its reverse ( {S}/{I}) . V-domains are stable, but the other two types are unstable to spatial perturbations with a wavelength which is of the order of the interaction range. In the second stage, this instability causes big {I}/{S}- and {S}/{I-domains } to split up into arrays of small ‘dots’ which preserve the {I}/{S-asymmetry } of their parent domain. These dots are stable, even in isolation, which allows them to act as a ‘memory’ for previously encountered antigens. No stable dots are obtained when the model is made to emulate the simpler activation function which has been used widely in earlier models. With this less realistic choice, unstable waves propagate from the boundaries of coarse {I}/{S-domains }, eventually filling up most of shape-space. This instability was previously described as

  13. Light-mediated Formation and Patterning of Hydrogels for Cell Culture Applications

    PubMed Central

    Sawicki, Lisa A.; Kloxin, April M.

    2016-01-01

    Click chemistries have been investigated for use in numerous biomaterials applications, including drug delivery, tissue engineering, and cell culture. In particular, light-mediated click reactions, such as photoinitiated thiol−ene and thiol−yne reactions, afford spatiotemporal control over material properties and allow the design of systems with a high degree of user-directed property control. Fabrication and modification of hydrogel-based biomaterials using the precision afforded by light and the versatility offered by these thiol−X photoclick chemistries are of growing interest, particularly for the culture of cells within well-defined, biomimetic microenvironments. Here, we describe methods for the photoencapsulation of cells and subsequent photopatterning of biochemical cues within hydrogel matrices using versatile and modular building blocks polymerized by a thiol−ene photoclick reaction. Specifically, an approach is presented for constructing hydrogels from allyloxycarbonyl (Alloc)-functionalized peptide crosslinks and pendant peptide moieties and thiol-functionalized poly(ethylene glycol) (PEG) that rapidly polymerize in the presence of lithium acylphosphinate photoinitiator and cytocompatible doses of long wavelength ultraviolet (UV) light. Facile techniques to visualize photopatterning and quantify the concentration of peptides added are described. Additionally, methods are established for encapsulating cells, specifically human mesenchymal stem cells, and determining their viability and activity. While the formation and initial patterning of thiol-alloc hydrogels are shown here, these techniques broadly may be applied to a number of other light and radical-initiated material systems (e.g., thiol-norbornene, thiol-acrylate) to generate patterned substrates. PMID:27768057

  14. 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.

  15. 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.

  16. Arthroscopic patterns of the poster-medial aspect of the knee joint: classification of the gastrocnemius-semimembranosus gateway and its relationship with Baker’s cyst

    PubMed Central

    Calvisi, Vittorio; Zoccali, Carmine

    2016-01-01

    Summary Background The gastrocnemius-semimembranosus bursa may communicate with the knee joint. The arthroscopic anatomy of the posteromedial aspect varies depending on the angle of the oblique popliteal ligament, the level at which it crosses the medial gastrocnemius tendon, and its relationship with the capsular joint and synovia. The aim of this paper is to identify possible patterns, and to evaluate their characteristics and their relationship with Baker’s cyst. Methods data archived from 185 consecutive arthroscopies were evaluated; an anatomic description and classification was carried out; the percentages of association with BC and the associated pathologies were reported. Results The different anatomies were classified into six groups based on the relationship above the medial gastrocnemius tendon, the capsular joint and synovia. The prevalence of Baker’s cyst was 28.3%. The main associated intra-articular pathological condition was the contemporary presence of a meniscal tear and chondropathy. Conclusion Exploration of the posterior aspect of the knee must be performed routinely. Knowing the possible anatomy patterns of the posteromedial arthroscopic aspect of the knee joint could help to identify the cyst and its gateway, thus facilitating its treatment. Level of the evidence III. PMID:28217572

  17. Micro-patterned surfaces reduce bacterial colonization and biofilm formation in vitro: Potential for enhancing endotracheal tube designs

    PubMed Central

    2014-01-01

    Background Ventilator-associated pneumonia (VAP) is a leading hospital acquired infection in intensive care units despite improved patient care practices and advancements in endotracheal tube (ETT) designs. The ETT provides a conduit for bacterial access to the lower respiratory tract and a substratum for biofilm formation, both of which lead to VAP. A novel microscopic ordered surface topography, the Sharklet micro-pattern, has been shown to decrease surface attachment of numerous microorganisms, and may provide an alternative strategy for VAP prevention if included on the surface of an ETT. To evaluate the feasibility of this micro-pattern for this application, the microbial range of performance was investigated in addition to biofilm studies with and without a mucin-rich medium to simulate the tracheal environment in vitro. Methods The top five pathogens associated with ETT-related pneumonia, Methicillin-Resistant Staphylococcus aureus (MRSA), Pseudomonas aeruginosa, Klebsiella pneumonia, Acinetobacter baumannii, and Escherichia coli, were evaluated for attachment to micro-patterned and un-patterned silicone surfaces in a short-term colonization assay. Two key pathogens, MRSA and Pseudomonas aeruginosa, were evaluated for biofilm formation in a nutrient rich broth for four days and minimal media for 24 hours, respectively, on each surface type. P. aeruginosa was further evaluated for biofilm formation on each surface type in a mucin-modified medium mimicking tracheal mucosal secretions. Results are reported as percent reductions and significance is based on t-tests and ANOVA models of log reductions. All experiments were replicated at least three times. Results Micro-patterned surfaces demonstrated reductions in microbial colonization for a broad range of species, with up to 99.9% (p < 0.05) reduction compared to un-patterned controls. Biofilm formation was also reduced, with 67% (p = 0.12) and 52% (p = 0.05) reductions in MRSA and P. aeruginosa

  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. Low-temperature plasma etching of high aspect-ratio densely packed 15 to sub-10 nm silicon features derived from PS-PDMS block copolymer patterns.

    PubMed

    Liu, Zuwei; Gu, Xiaodan; Hwu, Justin; Sassolini, Simone; Olynick, Deirdre L

    2014-07-18

    The combination of block copolymer (BCP) lithography and plasma etching offers a gateway to densely packed sub-10 nm features for advanced nanotechnology. Despite the advances in BCP lithography, plasma pattern transfer remains a major challenge. We use controlled and low substrate temperatures during plasma etching of a chromium hard mask and then the underlying substrate as a route to high aspect ratio sub-10 nm silicon features derived from BCP lithography. Siloxane masks were fabricated using poly(styrene-b-siloxane) (PS-PDMS) BCP to create either line-type masks or, with the addition of low molecular weight PS-OH homopolymer, dot-type masks. Temperature control was essential for preventing mask migration and controlling the etched feature's shape. Vertical silicon wire features (15 nm with feature-to-feature spacing of 26 nm) were etched with aspect ratios up to 17 : 1; higher aspect ratios were limited by the collapse of nanoscale silicon structures. Sub-10 nm fin structures were etched with aspect ratios greater than 10 : 1. Transmission electron microscopy images of the wires reveal a crystalline silicon core with an amorphous surface layer, just slightly thicker than a native oxide.

  20. Daily Access to Sucrose Impairs Aspects of Spatial Memory Tasks Reliant on Pattern Separation and Neural Proliferation in Rats

    ERIC Educational Resources Information Center

    Reichelt, Amy C.; Morris, Margaret J.; Westbrook, Reginald Frederick

    2016-01-01

    High sugar diets reduce hippocampal neurogenesis, which is required for minimizing interference between memories, a process that involves "pattern separation." We provided rats with 2 h daily access to a sucrose solution for 28 d and assessed their performance on a spatial memory task. Sucrose consuming rats discriminated between objects…

  1. 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.

  2. Formation of Ga droplets on patterned GaAs (100) by molecular beam epitaxy.

    PubMed

    Li, Ming-Yu; Hirono, Yusuke; Koukourinkova, Sabina D; Sui, Mao; Song, Sangmin; Kim, Eun-Soo; Lee, Jihoon; Salamo, Gregory J

    2012-10-03

    In this paper, the formation of Ga droplets on photo-lithographically patterned GaAs (100) and the control of the size and density of Ga droplets by droplet epitaxy using molecular beam epitaxy are demonstrated. In extension of our previous result from the journal Physical Status Solidi A, volume 209 in 2012, the sharp contrast of the size and density of Ga droplets is clearly observed by high-resolution scanning electron microscope, atomic force microscope, and energy dispersive X-ray spectrometry. Also, additional monolayer (ML) coverage is added to strength the result. The density of droplets is an order of magnitude higher on the trench area (etched area), while the size of droplets is much larger on the strip top area (un-etched area). A systematic variation of ML coverage results in an establishment of the control of size and density of Ga droplets. The cross-sectional line profile analysis and root mean square roughness analysis show that the trench area (etched area) is approximately six times rougher. The atomic surface roughness is suggested to be the main cause of the sharp contrast of the size and density of Ga droplets and is discussed in terms of surface diffusion.

  3. 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.

  4. Pattern formation of Dictystelium discoideum in the presence of laminar flow and cAMP pulses

    NASA Astrophysics Data System (ADS)

    Gholami, Azam; Steinbock, Oliver; Zykov, Vladimir; Bodenschatz, Eberhard

    2014-03-01

    Dictyostelium discoideum (D.d) amobae undergo starvation-induced multicellular development in which single cells aggregate chemotactically towards cAMP signals emitted periodically from an aggregation center. We are investigating spatiotemporal pattern formation of D.d. cells under the presence of a laminar flow. Starved cells are loaded into a straight millifluidic device with an external flow and cell response to the signaling molecule cAMP is monitored indirectly using dark-field microscopy. The observed contraction waves develop simultaneously over the entire channel, are propagating only in flow direction, and have curved wave fronts resembling the parabolic flow profile. The wave dynamics analysis shows that the wave velocity is locked to the flow velocity and yields a wave period of T0 6 min, which matches the typical oscillation period of extracellular cAMP in spatial homogeneous, well-stirred systems. We apply a small cAMP perturbation at the inlet region of the channel and observe the spatiotemporal response of the cells as the pulse is propagating down the channel. The results show that D.d. cells are in the oscillatory regime and the system can be forced within resonance tongue. We compared our results with analytical and numerical analysis of Goldbeter model.

  5. Quantitative universality and non-local interactions in neural pattern formation

    NASA Astrophysics Data System (ADS)

    Kaschube, Matthias; Schnabel, Michael; Loewel, Siegrid; Coppola, David; White, Leonard; Wolf, Fred

    2008-03-01

    The occurrence of universal quantitative laws in a strongly interacting multi-component system indicates that its behavior can be elucidated through the identification of general mathematical principles rather than by the detailed characterization of its individual components. Here we demonstrate that universal quantitative laws govern the spatial layout of orientation selective neurons in the visual cortex in three mammalian species separated in evolution by more than 50 million years. Most suggestive of a mathematical structure underlying this universality, the average number of pinwheel centers per orientation hyper-column in all three species is statistically indistinguishable from the constant π. Mathematical models of neural pattern formation can reproduce all observed universal quantitative laws if non-local interactions are dominant, indicating that non-local interactions are constitutive in visual cortical development. The spatial layout adheres to these laws even if visual cortical organization exhibits marked overall inhomogeneities and when neuronal response properties are experimentally altered. These results demonstrate that mathematical principles can shape the organization of the brain as powerfully as an organism's genetic make-up.

  6. 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

  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. Polar pattern formation in driven filament systems requires non-binary particle collisions

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

    From the self-organization of the cytoskeleton to the synchronous motion of bird flocks, living matter has the extraordinary ability to behave in a concerted manner. The Boltzmann equation for self-propelled particles is frequently used in silico to link a system’s meso- or macroscopic behaviour to the microscopic dynamics of its constituents. But so far such studies have relied on an assumption of simplified binary collisions owing to a lack of experimental data suggesting otherwise. We report here experimentally determined binary-collision statistics by studying a recently introduced molecular system, the high-density actomyosin motility assay. We demonstrate that the alignment induced by binary collisions is too weak to account for the observed ordering transition. The transition density for polar pattern formation decreases quadratically with filament length, indicating that multi-filament collisions drive the observed ordering phenomenon and that a gas-like picture cannot explain the transition of the system to polar order. Our findings demonstrate that the unique properties of biological active-matter systems require a description that goes well beyond that developed in the framework of kinetic theories.

  9. Heterotypic interactions regulate cell shape and density during color pattern formation in zebrafish

    PubMed Central

    Mahalwar, Prateek; Singh, Ajeet Pratap; Fadeev, Andrey; Nüsslein-Volhard, Christiane

    2016-01-01

    ABSTRACT The conspicuous striped coloration of zebrafish is produced by cell-cell interactions among three different types of chromatophores: black melanophores, orange/yellow xanthophores and silvery/blue iridophores. During color pattern formation xanthophores undergo dramatic cell shape transitions and acquire different densities, leading to compact and orange xanthophores at high density in the light stripes, and stellate, faintly pigmented xanthophores at low density in the dark stripes. Here, we investigate the mechanistic basis of these cell behaviors in vivo, and show that local, heterotypic interactions with dense iridophores regulate xanthophore cell shape transition and density. Genetic analysis reveals a cell-autonomous requirement of gap junctions composed of Cx41.8 and Cx39.4 in xanthophores for their iridophore-dependent cell shape transition and increase in density in light-stripe regions. Initial melanophore-xanthophore interactions are independent of these gap junctions; however, subsequently they are also required to induce the acquisition of stellate shapes in xanthophores of the dark stripes. In summary, we conclude that, whereas homotypic interactions regulate xanthophore coverage in the skin, their cell shape transitions and density is regulated by gap junction-mediated, heterotypic interactions with iridophores and melanophores. PMID:27742608

  10. Shrink film patterning by craft cutter: complete plastic chips with high resolution/high-aspect ratio channel.

    PubMed

    Taylor, Douglas; Dyer, David; Lew, Valerie; Khine, Michelle

    2010-09-21

    This paper presents a rapid, ultra-low-cost approach to fabricate microfluidic devices using a polyolefin shrink film and a digital craft cutter. The shrinking process (with a 95% reduction in area) results in relatively uniform and consistent microfluidic channels with smooth surfaces, vertical sidewalls, and high aspect ratio channels with lateral resolutions well beyond the tool used to cut them. The thermal bonding of the layers results in strongly bonded devices. Complex microfluidic designs are easily designed on the fly and protein assays are also readily integrated into the device. Full device characterization including channel consistency, optical properties, and bonding strength are assessed in this technical note.

  11. 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

  12. Three Aspects of PLATO Use at Chanute AFB: CBE Production Techniques, Computer-Aided Management, Formative Development of CBE Lessons.

    ERIC Educational Resources Information Center

    Klecka, Joseph A.

    This report describes various aspects of lesson production and use of the PLATO system at Chanute Air Force Base. The first chapter considers four major factors influencing lesson production: (1) implementation of the "lean approach," (2) the Instructional Systems Development (ISD) role in lesson production, (3) the transfer of…

  13. Formation and control of line defects caused by tectonics of water droplet arrays during self-organized honeycomb-patterned polymer film formation.

    PubMed

    Yamazaki, Hidekazu; Ito, Koju; Yabu, Hiroshi; Shimomura, Masatsugu

    2014-04-28

    This study describes the formation of macro-scale defects of the honeycomb-patterned polymer film and we discovered two types of new line defects which differ from the defects reported in the past studies. We examined the formation mechanisms of the line defects and clarified two types of formation mechanisms of the "Divergent" mode line defects and the "Convergent" mode line defects caused by the "tectonics" of water droplet arrays on polymer solutions. The regions causing the macro-scale line defects are made clear in the phase diagram represented by the radius and the density of the micro-scale water droplets. In addition, the results of our calculations made it possible to theoretically predict the water droplet growth time for the water droplets to grow to the ideal size for uniform packing that is necessary for fabrication of the defect-free honeycomb-patterned polymer film. With the use of these techniques, A4-sized, defect-free, honeycomb-patterned polymer films can be fabricated.

  14. 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

  15. Pigment Pattern Formation in the Guppy, Poecilia reticulata, Involves the Kita and Csf1ra Receptor Tyrosine Kinases

    PubMed Central

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

    2013-01-01

    Males of the guppy (Poecilia reticulata) vary tremendously in their ornamental patterns, which are thought to have evolved in response to a complex interplay between natural and sexual selection. Although the selection pressures acting on the color patterns of the guppy have been extensively studied, little is known about the genes that control their ontogeny. Over 50 years ago, two autosomal color loci, blue and golden, were described, both of which play a decisive role in the formation of the guppy color pattern. Orange pigmentation is absent in the skin of guppies with a lesion in blue, suggesting a defect in xanthophore development. In golden mutants, the development of the melanophore pattern during embryogenesis and after birth is affected. Here, we show that blue and golden correspond to guppy orthologs of colony-stimulating factor 1 receptor a (csf1ra; previously called fms) and kita. Most excitingly, we found that both genes are required for the development of the black ornaments of guppy males, which in the case of csf1ra might be mediated by xanthophore–melanophore interactions. Furthermore, we provide evidence that two temporally and genetically distinct melanophore populations contribute to the adult camouflage pattern expressed in both sexes: one early appearing and kita-dependent and the other late-developing and kita-independent. The identification of csf1ra and kita mutants provides the first molecular insights into pigment pattern formation in this important model species for ecological and evolutionary genetics. PMID:23666934

  16. 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.

  17. Ancestral Patterning of Tergite Formation in a Centipede Suggests Derived Mode of Trunk Segmentation in Trilobites

    PubMed Central

    Ortega-Hernández, Javier; Brena, Carlo

    2012-01-01

    Trilobites have a rich and abundant fossil record, but little is known about the intrinsic mechanisms that orchestrate their body organization. To date, there is disagreement regarding the correspondence, or lack thereof, of the segmental units that constitute the trilobite trunk and their associated exoskeletal elements. The phylogenetic position of trilobites within total-group Euarthropoda, however, allows inferences about the underlying organization in these extinct taxa to be made, as some of the fundamental genetic processes for constructing the trunk segments are remarkably conserved among living arthropods. One example is the expression of the segment polarity gene engrailed, which at embryonic and early postembryonic stages is expressed in extant panarthropods (i.e. tardigrades, onychophorans, euarthropods) as transverse stripes that define the posteriormost region of each trunk segment. Due to its conservative morphology and allegedly primitive trunk tagmosis, we have utilized the centipede Strigamia maritima to study the correspondence between the expression of engrailed during late embryonic to postembryonic stages, and the development of the dorsal exoskeletal plates (i.e. tergites). The results corroborate the close correlation between the formation of the tergite borders and the dorsal expression of engrailed, and suggest that this association represents a symplesiomorphy within Euarthropoda. This correspondence between the genetic and phenetic levels enables making accurate inferences about the dorsoventral expression domains of engrailed in the trunk of exceptionally preserved trilobites and their close relatives, and is suggestive of the widespread occurrence of a distinct type of genetic segmental mismatch in these extinct arthropods. The metameric organization of the digestive tract in trilobites provides further support to this new interpretation. The wider evolutionary implications of these findings suggest the presence of a derived

  18. 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

  19. 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.

  20. Aerosol patterns and aerosol-cloud-interactions off the West African Coast based on the A-train formation

    NASA Astrophysics Data System (ADS)

    Fuchs, Julia; Bendix, Jörg; Cermak, Jan

    2013-04-01

    In this study, spatial and temporal aerosol patterns off the Western African coast are characterized and related to cloud properties, based on satellite data Atmospheric aerosols play a key role in atmospheric processes and influence our environmental system in a complex way. Their identification, characterization, transport patterns as well as their interactions with clouds pose major challenges. Especially the last aspect reveals major uncertainties in terms of the Earth's radiation budget as reported in the IPCC's Fourth Assessment Report (IPCC, 2007). Western and Southern Africa are dominated by two well-known source types of atmospheric aerosols. First, the Saharan Desert is the world's largest aeolian dust emitting source region. Second, biomass burning aerosol is commonly transported off-shore further south (Kaufman et al., 2005). Both aerosol types influence Earth's climate in different manners and can be detected by the MODIS (MODerate resolution Imaging Spectrometer) sensor onboard the EOS platforms as they propagate to the Central and Southern Atlantic. The motivation of this study was to reveal the seasonal pattern of the Saharan dust transport based on an observation period of 11 years and trying to explain the meteorological mechanisms. North African dust plumes are transported along a latitude of 19°N in July and 6°N in January. The seasonally fluctuating intensities adapt to the annual cycle of wind and precipitation regimes. A strong relationship is found between the spatial shift of the Azores High and the Saharan dust load over the middle Atlantic Ocean. Monthly Aerosol Optical Thickness products of Terra MODIS and NCEP-DOE (National Centers for Environmental Predictions) Reanalysis II data are used for this purpose. The relationship between aerosol and cloud droplet parameters is blurred by high sensitivities to aerosol size and composition (Feingold, 2003; McFiggans et al., 2006) as well as meteorological context (Ackerman et al., 2004

  1. Aspects of the palynology of the Chinle Formation (Upper Triassic), Colorado Plateau, Arizona, Utah, and New Mexico

    USGS Publications Warehouse

    Scott, Richard A.

    1982-01-01

    This study deals with 16 palynological samples from Arizona, New Mexico, and Utah, that represent six members of the Chinle Formation of Late Triassic age. The samples, in ascending sequence, show a gradual change in the spore-bisaccate ratio from a preponderance of spores to numerical dominance of bisaccate pollen grains. This change is interpreted to indicate a climatic trend toward increasing aridity. The trend is thought to represent the decreasing energy phase of the oldest of three depositional cycles posited by Lupe (1977, 1979). The late Karnian age indicated for the Chinle Formation by pollen and spores is based on material from the lower part of the formation, leaving open the possibility that the upper part of the Chinle may be younger.

  2. Regeneration and pattern formation - an interview with Susan Bryant. Interviewed by Richardson, Michael K and Chuong, Cheng-Ming.

    PubMed

    Bryant, Susan

    2009-01-01

    Susan Bryant is one of the leading researchers in regeneration and pattern formation. Born in England in 1943, she studied biology at Kings College, London (UK). After a Ph.D. with Angus Bellairs on caudal autotomy and regeneration in lizards, she researched urodele regeneration in Marcus Singer's lab at Case Western Reserve University. Then, at the University of California, Irvine, she adopted the axolotl as a research model for limb regeneration and pattern formation. Her work supported models involving the intercalation of positional values in a polar coordinate system. Fibroblasts, often regarded as "junk" cells, are seen by Susan Bryant as central to patterning. She argues that fibroblasts express positional values needed for regeneration. She also argues that vertebrate species capable of regeneration have evolved steps to plug back into developmental programmes. Susan Bryant thinks that regeneration is essential for a full understanding of development, and believes that developmental biology has suffered though not embracing regeneration. She also believes that deeper knowledge of pattern formation will bring advances in emerging field of tissue engineering. Since 2000, she has served as Dean of Biological Sciences and more recently, as Vice Chancellor for Research, at UC Irvine (USA). She is an advocate of equal opportunities for women and other under-represented groups in academia. She lives in California with husband David Gardiner, her scientific partner for over 20 years. They have two children. We interviewed Susan Bryant in her office in Irvine on October 5th, 2007.

  3. 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.

  4. Formation and Development of the Pre-Professional Training System of Foreign Medical Applicants in Ukraine (Historical and Educational Aspect)

    ERIC Educational Resources Information Center

    Proskurkina, Iana

    2014-01-01

    The growing number of foreign applicants looking forward to getting education in Ukrainian medical universities makes us find the ways how to improve and make effective the pre-professional training system of foreign medical applicants for further education. The article deals with the issues of the history of formation and development of the…

  5. Psychological Aspects of the Formation of an Individual's Secondary Linguistic Identity in the Professional Training of Linguists

    ERIC Educational Resources Information Center

    Nechaev, Nikolai Nikolaevich

    2016-01-01

    The article is devoted to one of the major problems of educational psychology: the professional training of specialists in intercultural communication. The proposed approach allows us to uncover the significance of the concept of "linguistic consciousness" and methods governing its application to the process of the formation of the…

  6. Formation of Polychlorinated Biphenyls on Secondary Copper Production Fly Ash: Mechanistic Aspects and Correlation to Other Persistent Organic Pollutants

    PubMed Central

    Jiang, Xiaoxu; Liu, Guorui; Wang, Mei; Zheng, Minghui

    2015-01-01

    Emission of unintentionally formed polychlorinated biphenyls (PCBs) from industrial thermal processes is a global issue. Because the production and use of technical PCB mixtures has been banned, industrial thermal processes have become increasingly important sources of PCBs. Among these processes, secondary copper smelting is an important PCB source in China. In the present study, the potential for fly ash-mediated formation of PCBs in the secondary copper industry, and the mechanisms involved, were studied in laboratory thermochemical experiments. The total PCB concentrations were 37–70 times higher than the initial concentrations. Thermochemical reactions on the fly ash amplified the potential toxic equivalents of PCBs. The formation of PCBs over time and the effect of temperature were investigated. Based on analyses of PCB homologue profiles with different reaction conditions, a chlorination mechanism was proposed for forming PCBs in addition to a de novo synthesis mechanism. The chlorination pathway was supported by close correlations between each pair of adjacent homologue groups. Formation of PCBs and multiple persistent organic pollutants, including polychlorinated dibenzo-p-dioxins, polychlorinated dibenzofurans and polychlorinated naphthalenes, occurred during the tests, indicating that these compounds may share similar formation mechanisms. PMID:26374495

  7. Formation of Polychlorinated Biphenyls on Secondary Copper Production Fly Ash: Mechanistic Aspects and Correlation to Other Persistent Organic Pollutants

    NASA Astrophysics Data System (ADS)

    Jiang, Xiaoxu; Liu, Guorui; Wang, Mei; Zheng, Minghui

    2015-09-01

    Emission of unintentionally formed polychlorinated biphenyls (PCBs) from industrial thermal processes is a global issue. Because the production and use of technical PCB mixtures has been banned, industrial thermal processes have become increasingly important sources of PCBs. Among these processes, secondary copper smelting is an important PCB source in China. In the present study, the potential for fly ash-mediated formation of PCBs in the secondary copper industry, and the mechanisms involved, were studied in laboratory thermochemical experiments. The total PCB concentrations were 37-70 times higher than the initial concentrations. Thermochemical reactions on the fly ash amplified the potential toxic equivalents of PCBs. The formation of PCBs over time and the effect of temperature were investigated. Based on analyses of PCB homologue profiles with different reaction conditions, a chlorination mechanism was proposed for forming PCBs in addition to a de novo synthesis mechanism. The chlorination pathway was supported by close correlations between each pair of adjacent homologue groups. Formation of PCBs and multiple persistent organic pollutants, including polychlorinated dibenzo-p-dioxins, polychlorinated dibenzofurans and polychlorinated naphthalenes, occurred during the tests, indicating that these compounds may share similar formation mechanisms.

  8. Visual number beats abstract numerical magnitude: format-dependent representation of Arabic digits and dot patterns in human parietal cortex.

    PubMed

    Bulthé, Jessica; De Smedt, Bert; Op de Beeck, Hans P

    2015-07-01

    In numerical cognition, there is a well-known but contested hypothesis that proposes an abstract representation of numerical magnitude in human intraparietal sulcus (IPS). On the other hand, researchers of object cognition have suggested another hypothesis for brain activity in IPS during the processing of number, namely that this activity simply correlates with the number of visual objects or units that are perceived. We contrasted these two accounts by analyzing multivoxel activity patterns elicited by dot patterns and Arabic digits of different magnitudes while participants were explicitly processing the represented numerical magnitude. The activity pattern elicited by the digit "8" was more similar to the activity pattern elicited by one dot (with which the digit shares the number of visual units but not the magnitude) compared to the activity pattern elicited by eight dots, with which the digit shares the represented abstract numerical magnitude. A multivoxel pattern classifier trained to differentiate one dot from eight dots classified all Arabic digits in the one-dot pattern category, irrespective of the numerical magnitude symbolized by the digit. These results were consistently obtained for different digits in IPS, its subregions, and many other brain regions. As predicted from object cognition theories, the number of presented visual units forms the link between the parietal activation elicited by symbolic and nonsymbolic numbers. The current study is difficult to reconcile with the hypothesis that parietal activation elicited by numbers would reflect a format-independent representation of number.

  9. Time-stratigraphic aspects of a formation: Interpretation of surficial Pleistocene deposits by analogy with Holocene paralic deposits, southeastern Delaware

    NASA Astrophysics Data System (ADS)

    Demarest, J. M.; Biggs, R. B.; Kraft, J. C.

    1981-08-01

    Pleistocene shoreline deposits in close spatial and temporal proximity to Holocene deposits permit detailed interpretation of the development of Pleistocene coastal deposits when a modern-ancient analog approach is used. Peak sea levels during the past 1 m.y. or more have allowed the preservation of transgressive shoreline systems, here referred to as paralic units, along the inner continental margin. These Pleistocene paralic units are similar to Holocene coastal deposits now forming on Delmarva Peninsula. The Omar Formation (early to late Pleistocene age) incorporates at least four juxtaposed, transgressive, paralic units of different ages, each containing deposits of lagoonal sands and muds, tidal marsh, barrier sands and gravels, tidal delta sands and silty sands, and tidal channel sands and gravels. The successive paralic units become younger in the seaward direction. Thus, although the Omar Formation in the study area is almost entirely made up of transgressive deposits produced during rising sea levels, in a longer time frame it forms a progradational sequence. Only about 2% to 5% of the elapsed time during the deposition of the studied part of the Omar Formation is represented by sedimentary units. The internal time-stratigraphy of the Omar Formation is extremely complex. This makes the time-stratigraphic interpretation of any one outcrop or drill hole difficult. Any lithologic change may represent a wide variety of time gaps, from minutes to tens of thousands of years. The analog approach, in which sedimentary lithosome mapping is used, allows one to infer a time-stratigraphic framework of the deposits. These concepts can aid in the interpretation of depositional history of older paralic deposits and the nature of the development of certain types of clastic formations.

  10. Poly (methyl methacrylate) Formation and Patterning Initiated by Synchrotron X-ray Illumination

    SciTech Connect

    Xiao, J.; Je, J. H.; Wang, C. H.; Yang, T. Y.; Hwu, Y.

    2007-01-19

    A facile radiation method was developed to obtain micro-sized poly (methyl methacrylate) (PMMA) particles and create patterned coating on different substrates by a synchrotron x-ray induced dispersion polymerization. The polymerization of MMA monomer and well defined patterning was successfully realized. The produced PMMA particles and patterning were characterized by Fourier transformation infrared (FTIR), 1H-Nuclear Magnetic Resonance (NMR), and Scanning Electron Microscope (SEM). The observed patterning contrast essentially derived from a variation of size, density and morphology of particles and the type of substrate materials used.

  11. Patterns of biofilm formation in intermittent and permanent streams: analysis of biofilm structure and metabolism

    NASA Astrophysics Data System (ADS)

    Artigas, J.; Schwartz, T.; Kirchen, S.; Romaní, A. M.; Fund, K.; Obst, U.; Sabater, S.

    2009-04-01

    The development and functioning of benthic microbial communities in streams is largely dependent on the hydrological conditions. Climate change projections predict that the hydrological characteristics will probably be affected because of the rainfall regime. Hence, rivers from the Mediterranean region will become more similar to those draining arid or desert regions, while temperate streams will suffer of higher water flow fluctuations. In this study, we compared the process of biofilm formation between an intermittent (the Fuirosos, Mediterranean) and a permanent (the Walzbach, Central European) stream. Specifically, we analyzed the succession of bacterial and algal populations in the biofilm through bacterial rDNA sequences analysis (16S rDNA and 16S-23S intergenic sequence) and diatom taxa identification over a 60-days colonization experiment. Moreover, changes in biofilm structural (microbial biomass and extracellular polysaccharide content) and metabolic (extracellular enzyme activities) parameters were also analyzed. The successional patterns of microbial populations in the Fuirosos showed clear discontinutities coinciding with flood episodes while at the Walzbach the time sequence was more gradual. Although both study sites were forested, greater microbial biomass standing stock (algal and bacterial) and greater species biodiversity was detected during biofilm development at the Mediterranean site. The higher bacterial biodiversity may be related to the potential effect of flooding episodes in reducing biological interactions in complex microbial communities, such as the competitive exclusion of species. Moreover, the presence of rapid colonizing diatom species might be an adaptation to hydrological changes. In contrast, species competition could define the more stable environments, such as that observed in the Central European stream. Overall, the hystorical evolutionary pressure from the different bioclimatic regions could be also affecting the microbial

  12. Resurfacing time of terrestrial surfaces by the formation and maturation of polygonal patterned ground

    NASA Astrophysics Data System (ADS)

    Sletten, R. S.; Hallet, B.; Fletcher, R. C.

    2003-04-01

    To help interpret the polygonal patterned ground on Mars, we present recent findings about a similar form of patterned ground in a particularly cold and arid region on Earth, the Dry Valleys of Antarctica. In this region, distinct arrays of interconnected polygons, which we refer to herein simply as patterned ground, characterize many surfaces, reflecting a subsurface network of interconnected, subvertical wedges of sand that grow incrementally as sand progressively fills soil fractures. The fractures form initially as thermoelastic stresses arise during periods of rapid cooling of frozen ground, and they continue to open and close in response to thermal cycles. We describe the initiation and maturation of the patterned ground using data for the growth of sand wedges and for the evolution of crack patterns and microrelief over time scales ranging up to 106 years.

  13. Acrylamide formation from asparagine under low-moisture Maillard reaction conditions. 1. Physical and chemical aspects in crystalline model systems.

    PubMed

    Robert, Fabien; Vuataz, Gilles; Pollien, Philippe; Saucy, Françoise; Alonso, Maria-Isabelle; Bauwens, Isabelle; Blank, Imre

    2004-11-03

    The formation of acrylamide in crystalline model systems based on asparagine and reducing sugars was investigated under low-moisture reaction conditions. The acrylamide amounts were correlated with physical changes occurring during the reaction. Molecular mobility of the precursors turned out to be a critical parameter in solid systems, which is linked to the melting behavior and the release of crystallization water of the reaction sample. Heating binary mixtures of asparagine monohydrate and anhydrous reducing sugars led to higher acrylamide amounts in the presence of fructose compared to glucose. Differential scanning calorimetry measurements performed in open systems indicated melting of fructose at 126 degrees C, whereas glucose and galactose fused at 157 and 172 degrees C, respectively. However, glucose was the most reactive and fructose the least efficient sugar in anhydrous liquid systems, indicating that at given molecular mobility the chemical reactivity of the sugar was the major driver in acrylamide formation. Furthermore, reaction time and temperature were found to be covariant parameters: acrylamide was preferably formed by reacting glucose and asparagine at 120 degrees C for 60 min, whereas 160 degrees C was required at shorter reaction time (5 min). These results suggest that, in addition to the chemical reactivity of ingredients, their physical state as well as reaction temperature and time would influence the formation of acrylamide during food processing.

  14. Topographic Controls on Spatial Patterns of Soil Texture and Moisture in a Semi-arid Montane Catchment with Aspect-Dependent Vegetation

    NASA Astrophysics Data System (ADS)

    Lehman, B. M.; Niemann, J. D.

    2008-12-01

    Soil moisture exerts significant control over the partitioning of latent and sensible energy fluxes, the magnitude of both vertical and lateral water fluxes, the physiological and water-use characteristics of vegetation, and nutrient cycling. Considerable progress has been made in determining how soil characteristics, topography, and vegetation influence spatial patterns of soil moisture in humid environments at the catchment, hillslope, and plant scales. However, understanding of the controls on soil moisture patterns beyond the plant scale in semi-arid environments remains more limited. This study examines the relationships between the spatial patterns of near surface soil moisture (upper 5 cm), terrain indices, and soil properties in a small, semi-arid, montane catchment. The 8 ha catchment, located in the Cache La Poudre River Canyon in north-central Colorado, has a total relief of 115 m and an average elevation of 2193 m. It is characterized by steep slopes and shallow, gravelly/sandy soils with scattered granite outcroppings. Depth to bedrock ranges from 0 m to greater than 1 m. Vegetation in the catchment is highly correlated with topographic aspect. In particular, north-facing hillslopes are predominately vegetated by ponderosa pines, while south-facing slopes are mostly vegetated by several shrub species. Soil samples were collected at a 30 m resolution to characterize soil texture and bulk density, and several datasets consisting of more than 300 point measurements of soil moisture were collected using time domain reflectometry (TDR) between Fall 2007 and Summer 2008 at a 15 m resolution. Results from soil textural analysis performed with sieving and the ASTM standard hydrometer method show that soil texture is finer on the north-facing hillslope than on the south-facing hillslope. Cos(aspect) is the best univariate predictor of silts, while slope is the best predictor of coarser fractions up to fine gravel. Bulk density increases with depth but shows no

  15. A new mechanism for spatial pattern formation via lateral and protrusion-mediated lateral signalling

    PubMed Central

    Hunter, Ginger L.; Baum, Buzz

    2016-01-01

    Tissue organization and patterning are critical during development when genetically identical cells take on different fates. Lateral signalling plays an important role in this process by helping to generate self-organized spatial patterns in an otherwise uniform collection of cells. Recent data suggest that lateral signalling can be mediated both by junctional contacts between neighbouring cells and via cellular protrusions that allow non-neighbouring cells to interact with one another at a distance. However, it remains unclear precisely how signalling mediated by these distinct types of cell–cell contact can physically contribute to the generation of complex patterns without the assistance of diffusible morphogens or pre-patterns. To explore this question, in this work we develop a model of lateral signalling based on a single receptor/ligand pair as exemplified by Notch and Delta. We show that allowing the signalling kinetics to differ at junctional versus protrusion-mediated contacts, an assumption inspired by recent data which show that the cleavage of Notch in several systems requires both Delta binding and the application of mechanical force, permits individual cells to act to promote both lateral activation and lateral inhibition. Strikingly, under this model, in which Delta can sequester Notch, a variety of patterns resembling those typical of reaction–diffusion systems is observed, together with more unusual patterns that arise when we consider changes in signalling kinetics, and in the length and distribution of protrusions. Importantly, these patterns are self-organizing—so that local interactions drive tissue-scale patterning. Together, these data show that protrusions can, in principle, generate different types of patterns in addition to contributing to long-range signalling and to pattern refinement. PMID:27807273

  16. Instability criteria and pattern formation in the complex Ginzburg-Landau equation with higher-order terms.

    PubMed

    Mohamadou, Alidou; Ayissi, Bebe Emilienne; Kofané, Timoléon Crépin

    2006-10-01

    We study the modulational instability and spatial pattern formation in extended media, taking the one-dimensional complex Ginzburg-Landau equation with higher-order terms as a perturbation of the nonlinear Schrödinger equation as a model. By stability analysis for the original partial differential equation, we derive its stability condition as well as the threshold for amplitude perturbations and we show how nonlinear higher-order terms qualitatively change the behavior of the system. The analytical results are found to be in agreement with numerical findings. Modulational instability mediates pattern formation through the lattice. The main feature of the traveling plane waves is its disintegration in pulse train during the propagation through the system.

  17. Real-time nonlinear feedback control of pattern formation in (bio)chemical reaction-diffusion processes: a model study.

    PubMed

    Brandt-Pollmann, U; Lebiedz, D; Diehl, M; Sager, S; Schlöder, J

    2005-09-01

    Theoretical and experimental studies related to manipulation of pattern formation in self-organizing reaction-diffusion processes by appropriate control stimuli become increasingly important both in chemical engineering and cellular biochemistry. In a model study, we demonstrate here exemplarily the application of an efficient nonlinear model predictive control (NMPC) algorithm to real-time optimal feedback control of pattern formation in a bacterial chemotaxis system modeled by nonlinear partial differential equations. The corresponding drift-diffusion model type is representative for many (bio)chemical systems involving nonlinear reaction dynamics and nonlinear diffusion. We show how the computed optimal feedback control strategy exploits the system inherent physical property of wave propagation to achieve desired control aims. We discuss various applications of our approach to optimal control of spatiotemporal dynamics.

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

    SciTech Connect

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

    2013-10-15

    The paper discusses current filamentation and formation of current structures (in particular, hexagonal current patterns) in discharges of the Townsend and glow types. The aim of the paper, which is in part a review, is to reveal basic reasons for formation of current patterns in different cases, namely, in dielectric barrier discharge, discharge with semiconductor cathode, and micro-discharge between metallic electrodes. Pursuing this goal, we give a very brief review of observations and discuss only those theoretical, computational, and experimental papers that shed light on the physical mechanisms involved. The mechanisms are under weak currents—the thermal expansion of the gas as a result of Joule heating; under enhanced currents—the electric field and ionization rate redistribution induced by space charge. Both mechanisms lead to instability of the homogeneous discharges. In addition, we present new results of numerical simulations of observed short-living current filaments which are chaotic in space and time.

  19. Real-time nonlinear feedback control of pattern formation in (bio)chemical reaction-diffusion processes: A model study

    NASA Astrophysics Data System (ADS)

    Brandt-Pollmann, U.; Lebiedz, D.; Diehl, M.; Sager, S.; Schlöder, J.

    2005-09-01

    Theoretical and experimental studies related to manipulation of pattern formation in self-organizing reaction-diffusion processes by appropriate control stimuli become increasingly important both in chemical engineering and cellular biochemistry. In a model study, we demonstrate here exemplarily the application of an efficient nonlinear model predictive control (NMPC) algorithm to real-time optimal feedback control of pattern formation in a bacterial chemotaxis system modeled by nonlinear partial differential equations. The corresponding drift-diffusion model type is representative for many (bio)chemical systems involving nonlinear reaction dynamics and nonlinear diffusion. We show how the computed optimal feedback control strategy exploits the system inherent physical property of wave propagation to achieve desired control aims. We discuss various applications of our approach to optimal control of spatiotemporal dynamics.

  20. 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

  1. Pattern formation of a reaction-diffusion system with self-consistent flow in the amoeboid organism Physarum plasmodium

    NASA Astrophysics Data System (ADS)

    Yamada, Hiroyasu; Nakagaki, Toshiyuki; Ito, Masami

    1999-01-01

    The amoeboid organism, the plasmodium of Physarum polycephalum, moves by forming a spatiotemporal pattern of contraction oscillators. This biological system can be regarded as a reaction-diffusion system with spatial interaction via active flow of protoplasmic sol in the cell. We present a reaction-diffusion system with self-consistent flow on the basis of the physiological evidence that the flow is determined by contraction patterns in the plasmodium. Such a coupling of reaction, diffusion, and advection is characteristic of biological systems, and is expected to be related to control mechanisms of amoeboid behavior. Using weakly nonlinear analysis, we show that the envelope dynamics obeys the complex Ginzburg-Landau (CGL) equation when a bifurcation occurs at finite wave number. The flow term affects the nonlinear term of the CGL equation through the critical wave number squared. A physiological role of pattern formation with the flow is discussed.

  2. Pattern formation and flow control of fine particles by laser-scanning micromanipulation.

    PubMed

    Sasaki, K; Koshioka, M; Misawa, H; Kitamura, N; Masuhara, H

    1991-10-01

    A novel micromanipulation technique is proposed for aligning fine particles on micrometer-scale spatial patterns and for moving the particles continuously along the formed patterns. This technique is based on the repetitive scanning of a focused trapping laser beam. The velocity of the particle flow can be controlled by scan speed and laser power. The origin of the driving force is considered theoretically and experimentally.

  3. Macroscopically structured polymer formation governed by spatial patterns in the Belousov Zhabotinsky reaction

    NASA Astrophysics Data System (ADS)

    Kalishyn, Yevhen Yu.; Khavrus, Vyacheslav O.; Strizhak, Peter E.; Seipel, Michael; Münster, Arno F.

    2002-09-01

    We report the formation of macroscopically structured cross-linked polyacrylamide hydrogel in the Belousov-Zhabotinsky (BZ) system (oxidation of malonic acid by bromate catalyzed by ferroin). Here, acrylamide, the cross-linker bis-acrylamide, and polymerization initiator are added into the BZ system. We show that the formation of waves and ripples in the polymer is governed by spatial structures emerging in the BZ system. Without any spatial structures in the BZ system only the formation of a spatially uniform polymer is observed. Without cross-linker, a spatially uniform polymer was observed as well. Structured polymer formation is caused by the interaction of chemical reactions in the BZ system and the polymerization process including gelation and cross-linking of the monomer units.

  4. The effect of landscape position and aspect on chemical weathering and soil formation: contrasting field and model results

    NASA Astrophysics Data System (ADS)

    Vanwalleghem, Tom; Román, Andrea; Giráldez, Juan

    2016-04-01

    Interest in modelling pedogenesis has increased greatly over the past few years, with the emergence of detailed pedon-scale models (e.g. Soilgen) on the one hand and landscape-scale models (e.g. marm3D, MILESD, LORICA) on the other. Pore water chemistry and chemical weathering is not (well) represented in the latter and needs to be improved in order to adequately model the evolution of soils and of the critical zone. The objective of this work is to analyse the spatial variability of chemical weathering and to develop a new soil landscape model that accounts for this. Here, we present field and model results from the Santa Clotilde Critical Zone Observatory, S Spain. A new model, MILESD2, was developed to integrate the effect of landscape evolution and soil formation. This model is based on a daily spatially-explicit soil water balance. Average soil water content, temperature and deep percolation fluxes are linked to weathering and soil formation processes. Model input (temperature and precipitation) for the last 25 000 years was generated on a daily time by combining palaeoclimate data and the WXGEN weather generator. The soil-landscape model was applied to a 48 km2 semi-natural catchment in Southern Spain, with soils developed on granite. Model-generated runoff was used for a first validation against discharge observations. Next, soil formation output was contrasted against experimental data from 10 soil profiles along two catenas. Field data showed an important variation in mobile regolith thickness, between 0,44 and 1,10m, and in chemical weathering along the catena. Southern slopes were characterized by shallower, stonier and carbon-poor soils, while soils on north-facing slopes were deeper, more fine-textured and had a higher carbon content. Chemical depletion fraction was found to vary between 0,41 and 0,72. The lowest overall weathering intensity was found on plateau positions. South facing slopes revealed slightly lower weathering compared to north facing

  5. Reservoir quality, sediment source, and regional aspects of Norphlet Formation, South State Line field, Greene County, Mississippi

    SciTech Connect

    Thomson, A.; Stancliffe, R.J.; Shew, R.D.

    1987-05-01

    South State Line field, discovered in 1970, is centrally located in the productive Jurassic Norphlet trend of the eastern Gulf Coast. The Norphlet Formation at South State Line has produced gas and condensate from normally pressured eolian sandstones at depths of more than 17,900 ft (5455 m). The 600-ft- (183-m) thick Norphlet Formation is composed of 100% sandstone and consists of two reservoir types: a poorer quality upper sandstone having low permeability (0.6 md) and a good-quality lower sandstone with better permeability (15.5 md). The upper sandstone exhibits tighter compaction of framework grains and more cement than the lower sandstone. Significantly, the upper sandstone contains authigenic illite (which promotes pressure solution), whereas the lower sandstone contains authigenic chlorite (which inhibits cementation and possibly pressure solution). On a regional scale, illite is the principal diagenetic clay mineral in the western area of the Norphlet trend (Mississippi to Texas), whereas chlorite is the principal diagenetic clay mineral in the east (Alabama to Florida). Not surprisingly, reservoir quality is poorer in the western portion of the trend. A comparison of framework grains in the upper and lower sandstones shows no significant compositional differences. Both are mature arkosic sandstones with a transitional-continental source (eastern Appalachians). No evidence was seen of a quartz-rich Ouachita or cratonic source. Volcanic and plutonic rock fragments are slightly more abundant in the lower sandstone, possibly reflecting a shifting of compositional terranes within a single source area along the eastern side of the Appalachians. The lower Norphlet sandstone may have been derived from Triassic volcanics, whereas the upper sandstone may have been derived from a more metamorphic source.

  6. Laser-induced superhydrophobic grid patterns on PDMS for droplet arrays formation

    NASA Astrophysics Data System (ADS)

    Farshchian, Bahador; Gatabi, Javad R.; Bernick, Steven M.; Park, Sooyeon; Lee, Gwan-Hyoung; Droopad, Ravindranath; Kim, Namwon

    2017-02-01

    We demonstrate a facile single step laser treatment process to render a polydimethylsiloxane (PDMS) surface superhydrophobic. By synchronizing a pulsed nanosecond laser source with a motorized stage, superhydrophobic grid patterns were written on the surface of PDMS. Hierarchical micro and nanostructures were formed in the irradiated areas while non-irradiated areas were covered by nanostructures due to deposition of ablated particles. Arrays of droplets form spontaneously on the laser-patterned PDMS with superhydrophobic grid pattern when the PDMS sample is simply immersed in and withdrawn from water due to different wetting properties of the irradiated and non-irradiated areas. The effects of withdrawal speed and pitch size of superhydrophobic grid on the size of formed droplets were investigated experimentally. The droplet size increases initially with increasing the withdrawal speed and then does not change significantly beyond certain points. Moreover, larger droplets are formed by increasing the pitch size of the superhydrophobic grid. The droplet arrays formed on the laser-patterned PDMS with wettability contrast can be used potentially for patterning of particles, chemicals, and bio-molecules and also for cell screening applications.

  7. Experimental study on flame pattern formation and combustion completeness in a radial microchannel

    NASA Astrophysics Data System (ADS)

    Fan, Aiwu; Minaev, Sergey; Kumar, Sudarshan; Liu, Wei; Maruta, Kaoru

    2007-12-01

    Combustion behavior in a radial microchannel with a gap of 2.0 mm and a diameter of 50 mm was experimentally investigated. In order to simulate the heat recirculation, which is an essential strategy in microscale combustion devices, positive temperature gradients along the radial flow direction were given to the microchannel by an external heat source. A methane-air mixture was supplied from the center of the top plate through a 4.0 mm diameter delivery tube. A variety of flame patterns, including a stable circular flame and several unstable flame patterns termed unstable circular flame, single and double pelton-like flames, traveling flame and triple flame, were observed in the experiments. The regime diagram of all these flame patterns is presented in this paper. Some characteristics of the various flame patterns, such as the radii of stable and unstable circular flames, major combustion products and combustion efficiencies of all these flame patterns, were also investigated. Furthermore, the effect of the heat recirculation on combustion stability was studied by changing the wall temperature levels.

  8. Stochastic reaction and diffusion on growing domains: Understanding the breakdown of robust pattern formation

    NASA Astrophysics Data System (ADS)

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

    2011-10-01

    Many biological patterns, from population densities to animal coat markings, can be thought of as heterogeneous spatiotemporal distributions of mobile agents. Many mathematical models have been proposed to account for the emergence of this complexity, but, in general, they have consisted of deterministic systems of differential equations, which do not take into account the stochastic nature of population interactions. One particular, pertinent criticism of these deterministic systems is that the exhibited patterns can often be highly sensitive to changes in initial conditions, domain geometry, parameter values, etc. Due to this sensitivity, we seek to understand the effects of stochasticity and growth on paradigm biological patterning models. In this paper, we extend spatial Fourier analysis and growing domain mapping techniques to encompass stochastic Turing systems. Through this we find that the stochastic systems are able to realize much richer dynamics than their deterministic counterparts, in that patterns are able to exist outside the standard Turing parameter range. Further, it is seen that the inherent stochasticity in the reactions appears to be more important than the noise generated by growth, when considering which wave modes are excited. Finally, although growth is able to generate robust pattern sequences in the deterministic case, we see that stochastic effects destroy this mechanism for conferring robustness. However, through Fourier analysis we are able to suggest a reason behind this lack of robustness and identify possible mechanisms by which to reclaim it.

  9. Phosphorus Zoning Patterns and the Formation of Olivine-Hosted Melt Inclusions

    NASA Astrophysics Data System (ADS)

    Milman-Barris, M. S.; Baker, M.; Beckett, J.; Sobolev, A.; Vielzeuf, D.; Stolper, E.

    2006-12-01

    composition produced ol (to ~2 mm in size) with coupled zoning of P, Al, and Cr; some show oscillatory or sector-zoning. Nearly all experimental ol grains have embayments and interior melt pools (up to 1 mm in longest dimension). While many of these are likely in contact with far-field melt, some may be isolated (i.e., true inclusions). Interior melt pools have aspect ratios of 1-40; the more elongate pools are similar in appearance to those of [3]. Enclosed, interior melt pools are surrounded by P-poor ol, but near P-rich ol. Also, boundaries between high- and low-P zones are often deflected in the vicinity of melt pools. These observations are reminiscent of inclusions observed in Hawaiian ol phenocrysts. Our experiments show that P-zoning in ol and associated interior melt pools can be produced by simple linear cooling histories. The proximity of melt inclusions to P-rich zones in both Hawaiian and experimental ol points to the importance of rapid growth in the formation of both features. Cross-cutting (and perhaps replacement) of high-P features in ol by the low-P zones surrounding natural melt inclusions may reflect trapping of melt inclusions in pits formed by localized dissolution of growing ol, recrystallization of high-energy ol adjacent to melt inclusions after trapping, and/or melting/reprecipitation of ol adjacent to trapped melt inclusions due to transient thermal gradients. [1] Sobolev et al. (2000) Nature 404, 986-990. [2] Norman et al. (2002) Chem. Geol. 183, 143-68. [3] Faure &Schiano (2005) EPSL 236, 882-98.

  10. Influence of pinning effects on the electrochemical formation of silver patterns in agarose-containing sols and gels.

    PubMed

    Pasquale, M A; Saracco, G P; Marchiano, S L; Arvia, A J

    2005-11-03

    The formation of silver patterns via electrolysis from aqueous silver sulfate + x% w/v agarose sol and gel media, with and without supporting electrolyte, in a quasi-two-dimensional (2D) cylindrical cell at room temperature, is utilized as a reference system to investigate the complexity of pinning effects. From pattern morphology and electrochemical data, both delocalized and localized pinning in the bulk dominate the drift of the growth front, depending on the concentration of agarose in the heterogeneous media. Delocalized pinning results from mobile, small agarose aggregates at the growth front and from their accumulation by the front drift. For gels, localized pinning comes from their own percolated structure. A depinning/pinning transition is observed in going from sols to gels. The relative contribution of diffusion and advection in mass-transport-controlled silver electrodeposition depends on the plating bath composition. On the other hand, silver ion attachment to the cathode appears to be interfered with by some screening caused by weakly adsorbed, mobile agarose aggregates at the metal surface without slowing down the rate of the electron-transfer step at the cathode. Their relative contribution of a delocalized, localized pinning and screening effect to a great extent determines the morphology and transition in the growth mode of silver patterns in both media. The analysis of charge and current transients and the corresponding silver pattern morphologies for open and dense radial patterns is made. Results are qualitatively simulated with a novel, rather simple cellular automaton algorithm.

  11. 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.

  12. Flow-driven instabilities during aggregation and pattern formation of Dictyostelium Discoideum: Experiments and modeling

    NASA Astrophysics Data System (ADS)

    Gholami, Azam; Steinbock, Oliver; Zykov, Vladimir; Bodenschatz, Eberhard

    2013-03-01

    We report the first experimental verification of the Differential Flow Induced Chemical Instability (DIFICI) in a signaling chemotactic biological population, where a differential flow induces traveling waves in the signaling pattern. The traveling wave speed was observed to be proportional to the flow velocity while the wave period was 7 min, which is comparable to that of starved Dictyostelium cells. Analysis and numerical simulations of the Goldbeter model show that the resulting DIFICI wave patterns appear in the oscillatory regime. In the experiments, we observe that the DIFICI wave pattern disappears after 4-5 h of starvation. We extrapolated the Goldbeter model to the experimental situation. This suggests that the dynamics switches from the oscillatory to the excitable regime as the DIFICI waves disappear in the experiment.

  13. Pattern formation on membranes and its role in bacterial cell division.

    PubMed

    Kretschmer, Simon; Schwille, Petra

    2016-02-01

    Bacterial cell division is arguably one of the most central processes in biology. Despite the identification of many important molecular players, surprisingly little is yet known about the underlying physicochemical mechanisms. However, self-organized protein patterns play key roles during division of Escherichia coli, where division is initiated by the directed localization of FtsZ to the cell middle by an inhibitor gradient arising from pole-to-pole oscillations of MinCDE proteins. In vitro reconstitution studies have established that both the Min system and FtsZ with its membrane adaptor FtsA form dynamic energy-dependent patterns on membranes. Furthermore, recent in vivo and in vitro approaches have shown that Min patterns display rich dynamics in diverse geometries and respond to the progress of cytokinesis.

  14. Pattern formation in the instability of a vicinal surface by the drift of adatoms

    NASA Astrophysics Data System (ADS)

    Sato, Masahide; Uwaha, Makio

    1999-12-01

    We study the behavior of steps in a vicinal face with drift of adsorbed atoms (adatoms) by an external field. When the drift is in the downhill direction and its velocity exceeds critical values, vxc and vyc, the vicinal face is linearly unstable to long-wavelength fluctuations parallel and/or perpendicular to the steps. By taking the continuum limit of the step-flow model, we derive an anisotropic Kuramoto-Sivashinsky equation with propagative terms, which describes the motion of an unstable vicinal face. Its numerical solution shows ripples or a zigzag pattern expected from the linear analysis. Nonlinearity becomes important in the late stage and, depending on the condition, various patterns are formed: regular step bunches, a hill and valley structure tilted from the initial step direction, mounds, and a chaotic pattern.

  15. Linking Pattern Formation and Alternative Stable States: Ecohydrologic Thresholds and Critical Transitions in the Everglades Peatlands

    NASA Astrophysics Data System (ADS)

    Heffernan, J. B.; Ross, M. S.; Sah, J. P.; Isherwood, E.; Cohen, M. J.

    2015-12-01

    Spatial patterning occurs in a variety of ecosystems, and is important for the functional properties of landscapes; for testing spatial models of ecological processes; and as an indicator of landscape condition and resilience. Theory suggests that regular patterns arise from coupled local- and landscape-scale feedbacks that can also create multiple stable landscape states. In the Florida Everglades, hydrologic modification has degraded much of the historically-extensive ridge-slough landscape, a patterned peatland mosaic with distinct, flow-parallel patches. However, in the Everglades and in general, the hypothesis that patterned landscapes have homogeneous alternative states has little direct empirical support. Here we use microtopographic and vegetative heterogeneity, and their relation to hydrologic conditions, to infer the existence of multiple landscape equilibria and identify the hydrologic thresholds for critical transitions between these states. Dual relationships between elevation variance and water depth, and bi-modal distributions of both elevation variance and plant community distinctness, are consistent with generic predictions of multiple states, and covariation between these measures suggests that microtopography is the leading indicator of landscape degradation. Furthermore, a simple ecohydrologic multiple-state model correctly predicts the hydrologic thresholds for persistence of distinct ridges and sloughs. Predicted ridge-slough elevation differences and their relation to water depth are much greater than observed in the contemporary Everglades, but correspond closely with historical observations of pre-drainage conditions. These multiple lines of evidence represent the broadest and most direct support for the link between regular spatial pattern and landscape-scale alternative states in any ecosystem, and suggest that other patterned landscapes could undergo sudden collapse in response to changing environmental conditions. Hydrologic thresholds

  16. Pattern formation in icosahedral virus capsids: the papova viruses and Nudaurelia capensis beta virus.

    PubMed Central

    Marzec, C J; Day, L A

    1993-01-01

    The capsids of the spherical viruses all show underlying icosahedral symmetry, yet they differ markedly in capsomere shape and in capsomere position and orientation. The capsid patterns presented by the capsomere shapes, positions, and orientations of three viruses (papilloma, SV40, and N beta V) have been generated dynamically through a bottom-up procedure which provides a basis for understanding the patterns. A capsomere shape is represented in two-dimensional cross-section by a mass or charge density on the surface of a sphere, given by an expansion in spherical harmonics, and referred to herein as a morphological unit (MU). A capsid pattern is represented by an icosahedrally symmetrical superposition of such densities, determined by the positions and orientations of its MUs on the spherical surface. The fitness of an arrangement of MUs is measured by an interaction integral through which all capsid elements interact with each other via an arbitrary function of distance. A capsid pattern is generated by allowing the correct number of approximately shaped MUs to move dynamically on the sphere, positioning themselves until an extremum of the fitness function is attained. The resulting patterns are largely independent of the details of both the capsomere representation and the interaction function; thus the patterns produced are generic. The simplest useful fitness function is sigma 2, the average square of the mass (or charge) density, a minimum of which corresponds to a "uniformly spaced" MU distribution; to good approximation, the electrostatic free energy of charged capsomeres, calculated from the linearized Poisson-Boltzmann equation, is proportional to sigma 2. With disks as MUs, the model generates the coordinated lattices familiar from the quasi-equivalence theory, indexed by triangulation numbers. Using fivefold MUs, the model generates the patterns observed at different radii within the T = 7 capsid of papilloma and at the surface of SV40; threefold MUs

  17. Influence of Carbohydrates on Quantitative Aspects of Growth and Embryo Formation in Wild Carrot Suspension Cultures 12

    PubMed Central

    Verma, Devi C.; Dougall, Donald K.

    1977-01-01

    Wild carrot (Daucus carota L.) cell suspensions were grown on a mineral salt medium supplemented with 10 mmmyoinositol in the presence and absence of 2.25 μm 2,4-dichlorophenoxyacetic acid (2,4-D), and a variety of carbon sources. The data obtained on growth and embryo number in the absence of 2,4-D show that wild carrot suspensions were able to utilize sucrose, glucose, fructose, galactose, mannose, maltose, raffinose, or stachyose as a carbon source. A highly significant correlation between dry weight and embryo number was obtained regardless of the carbohydrate source suggesting the involvement of a common intermediate in the metabolism of the various sugars. In the presence of 2.25 μm 2,4-D, embryo formation was suppressed. Time course of dry weights obtained in the presence and absence of 2,4-D show that 2,4-D increased the growth rate of the tissue when glucose, fructose, mannose, or stachyose was used as the carbon source. The growth rates on other sugars remained unchanged under these conditions. PMID:16659793

  18. Comparison of defect cluster accumulation and pattern formation in irradiated copper and nickel

    SciTech Connect

    Zinkle, S.J.; Snead, L.L.; Edwards, D.J.

    1995-04-01

    The objective of this study is to compare the contrasting behavior of defect cluster formation in neutron-irradiated copper and nickel specimens. Transmission electron microscopy was used to examine the density and spatial distribution of defect clusters produced in copper and nickel as the result of fission neutron irradiation to damage levels of 0.01 to 0.25 displacements per atom (dpa) at irradiation temperature between 50 and 230{degrees}C. A comparison with published results in the literature indicates that defect cluster wall formation occurs in nickel irradiated at 0.2 to 0.4 T{sub M} in a wide variety of irradiation spectra. Defect cluster wall formation apparently only occurs in copper during low temperature irradiation with electrons and light ions. These results are discussed in terms of the thermal spike model for energetic displacement cascades.

  19. Pattern dependence of void formation on electromigration in Mg-containing Al-Si alloys

    NASA Astrophysics Data System (ADS)

    Akiya, Masahiro; Saitoh, Kazuhiro; Sakai, Kazuya

    2001-11-01

    The pattern dependence of alternating wide and narrow stripe structures was demonstrated in the investigation of electromigration mechanisms. Magnesium accumulated in the portion of the stripe near the cathode and gradually decreased toward the anode. A fatal large void appeared at the current change point near the cathode.

  20. Glycerol etherification over highly active CaO-based materials: new mechanistic aspects and related colloidal particle formation.

    PubMed

    Ruppert, Agnieszka M; Meeldijk, Johannes D; Kuipers, Bonny W M; Erné, Ben H; Weckhuysen, Bert M

    2008-01-01

    Glycerol is an attractive renewable building block for the synthesis of di- and triglycerols, which have numerous applications in the cosmetic and pharmaceutical industries. In this work, the selective etherification of glycerol to di- and triglycerol was studied in the presence of alkaline earth metal oxides and the data are compared with those obtained with Na2CO3 as a homogeneous catalyst. It was found that glycerol conversion increased with increasing catalyst basicity; that is, the conversion increases in the order: MgO90 % at 60 % conversion) are obtained over CaO, SrO, and BaO. For these catalysts no substantial acrolein formation was observed. Furthermore, at the start of the reaction mainly linear diglycerol was produced, whereas at higher conversion degrees branched diglycerol started to form. In another series of experiments different types of CaO materials were prepared. It was found that these CaO-based materials not only differed in their surface area and number of basic sites, but also in their Lewis acid strength. Within this series the CaO material possessing the strongest Lewis acid sites had the highest catalytic activity, comparable to that of BaO, pointing towards the important role of Lewis acidity for this etherification reaction. Based on these observations a plausible alternative reaction scheme for glycerol etherification is presented, which considers the facilitation of the hydroxyl leaving process. Finally, the stability of the catalytic solids under study was investigated and it was found that colloidal CaO particles of about 50-100 nm can be spontaneously generated during reaction. Catalytic testing of these CaO colloids, after isolation from the reaction medium, revealed a very high etherification activity. Understanding the nature of these Ca-based colloids opens new opportunities for investigating supported colloidal particle catalysts to take advantage of both

  1. Patterns and sources of variation in pollen deposition and pollen tube formation in flowers of the endemic monoecious shrub Cnidoscolus souzae (Euphorbiaceae).

    PubMed

    Arceo-Gómez, G; Alonso, C; Abdala-Roberts, L; Parra-Tabla, V

    2016-07-01

    Pollen deposition and pollen tube formation are key components of angiosperm reproduction but intraspecific variation in these has rarely been quantified. Documenting and partitioning (populations, plants and flowers) natural variation in these two aspects of plant reproduction can help uncover spatial mosaics of reproductive success and underlying causes. In this study, we assess variation in pollen deposition and pollen tube formation for the endemic monoecious shrub Cnidoscolus souzae throughout its distribution range in Mexico, and determine how this variation is structured among populations, plants and flowers. We also infer the relative importance of pollen quantity and quality in determining pollination success in this species. While we found no evidence suggesting that pollen receipt limits C. souzae reproduction across 19 populations, we did find extensive variation in pollen load size and pollen tube number per flower. Total variation in pollen receipt and pollen tube number was mostly explained by intra-individual and among-population variance. Furthermore, pollen load size had a stronger effect on the number of pollen tubes at the base of the style than pollen germination rate, suggesting that pollen quantity may be more important than quality for pollen tube success in C. souzae. Our results suggest that both small within-plant flower differences and broad-scale differences in community attributes can play an important role in determining pollination success. We emphasise the need to evaluate patterns and sources of variation in pollen deposition and pollen tube formation as a first step in understanding the causes of variation in pollination success over broad spatial scales.

  2. The influence of projectile ion induced chemistry on surface pattern formation

    NASA Astrophysics Data System (ADS)

    Karmakar, Prasanta; Satpati, Biswarup

    2016-07-01

    We report the critical role of projectile induced chemical inhomogeneity on surface nanostructure formation. Experimental inconsistency is common for low energy ion beam induced nanostructure formation in the presence of uncontrolled and complex contamination. To explore the precise role of contamination on such structure formation during low energy ion bombardment, a simple and clean experimental study is performed by selecting mono-element semiconductors as the target and chemically inert or reactive ion beams as the projectile as well as the source of controlled contamination. It is shown by Atomic Force Microscopy, Cross-sectional Transmission Electron Microscopy, and Electron Energy Loss Spectroscopy measurements that bombardment of nitrogen-like reactive ions on Silicon and Germanium surfaces forms a chemical compound at impact zones. Continuous bombardment of the same ions generates surface instability due to unequal sputtering and non-uniform re-arrangement of the elemental atom and compound. This instability leads to ripple formation during ion bombardment. For Argon-like chemically inert ion bombardment, the chemical inhomogeneity induced boost is absent; as a result, no ripples are observed in the same ion energy and fluence.

  3. A photo-oxidation mechanism for patterning and hologram formation in conjugated polymer/glass composites

    NASA Astrophysics Data System (ADS)

    Levi, Ofer; Perepelitsa, Galina; Davidov, Dan; Shalom, Shoshy; Benjamin, Iris; Neumann, Ronny; Agranat, Aharon J.; Avny, Yair

    2000-08-01

    Improved diffraction efficiency was observed in holograms stored in disordered conjugated polymer/glass composites. The conjugated polymers used were alkoxy substituted poly(phenylenevinylne) analogs and the glass matrices were zirconia-organosilica xerogels. Investigation of the mechanism of hologram formation revealed evidence of a photochromic process consisting of light induced photo-oxidation (bleaching) of the embedded conjugated polymer resulting in the formation of an absorption grating and a phase grating. Investigation of the hologram formation revealed that the process was oxygen dependent. Oxygen removal increases hologram formation time by more than an order of magnitude and halves the total hologram efficiency. The oxygen dependence was also highly correlated with photobleaching of the samples and beam interaction of the writing beams. The chemical transformations upon photobleaching were shown by infrared and Raman spectroscopy to involve chain scission and oxidation of the polymer at the vinylic position of the conjugated polymer. Film preparation of the composites was optimized showing a tenfold improvement in the holographic properties compared to our previous results. The optimized treatment method allows for a high, >20%, diffraction efficiency, η, to be obtained for the 2.5-μm-thick polymer/glass films. Light sensitivity was compared for several polymer/glass composites and was correlated to the absorption curves and holographic diffraction efficiency showing that the new composites and film preparation techniques are promising for holographic materials sensitive in the blue and ultraviolet spectral regions. A method of information fixing by preventing oxygen entry to the composite film resulted in a fourfold increase of the erasure time. These findings suggest that holograms can be fixed for a long term by nonoxygen permeable coating, applied after hologram formation.

  4. Pattern formation in 3-D numerical models of down-built diapirs initiated by a Rayleigh-Taylor instability

    NASA Astrophysics Data System (ADS)

    Fernandez, Naiara; Kaus, Boris J. P.

    2015-08-01

    Many salt diapirs are thought to have formed as a result of down-building, which implies that the top of the diapir remained close to the surface during syn-halokinetic sediment deposition. Down-building is largely a 3-D process and in order to better understand what controls the patterns of the diapirs that form by this process, we here perform 3-D numerical models of down-built diapirs initiated by the gravity instability in linear viscous materials and compare the results with analytical models. We vary several parameters of the numerical models such as initial salt thickness, sedimentation rate, salt viscosity, salt-sediment viscosity ratio as well as the density of sediments. Down-building of 3-D diapirs only occurs for a certain range of parameters and is favoured by lower sediment/salt viscosity contrasts and sedimentation rates in agreement with analytical predictions and findings from previous 2-D models. However, the models show that the sedimentation rate has an additional effect on the formation and evolution of 3-D diapir patterns. At low sedimentation rates, salt ridges that form during early model stages remain preserved at later stages as well. For higher sedimentation rates, the initial salt ridges are covered up and finger-like diapirs form at their junctions, which results in different salt exposure patterns at the surface. Once the initial pattern of diapirs is formed, higher sedimentation rate can also result in covered diapirs if the diapir extrusion velocity is insufficiently large. We quantify the effect of sedimentation rate on the number of diapirs exposed at the surface as well as on their spacing and we explain the observations with analytical predictions using thick-plate analytical models. In some cases, this final pattern is distinctly different from the initial polygonal pattern.

  5. Nanostructure Formation by controlled dewetting on patterned substrates: A combined theoretical, modeling and experimental study

    PubMed Central

    Lu, Liang-Xing; Wang, Ying-Min; Srinivasan, Bharathi Madurai; Asbahi, Mohamed; Yang, Joel K. W.; Zhang, Yong-Wei

    2016-01-01

    We perform systematic two-dimensional energetic analysis to study the stability of various nanostructures formed by dewetting solid films deposited on patterned substrates. Our analytical results show that by controlling system parameters such as the substrate surface pattern, film thickness and wetting angle, a variety of equilibrium nanostructures can be obtained. Phase diagrams are presented to show the complex relations between these system parameters and various nanostructure morphologies. We further carry out both phase field simulations and dewetting experiments to validate the analytically derived phase diagrams. Good agreements between the results from our energetic analyses and those from our phase field simulations and experiments verify our analysis. Hence, the phase diagrams presented here provide guidelines for using solid-state dewetting as a tool to achieve various nanostructures. PMID:27580943

  6. Formation of superwetting surface with line-patterned nanostructure on sapphire induced by femtosecond laser

    NASA Astrophysics Data System (ADS)

    Yin, Kai; Duan, Ji'an; Sun, Xiaoyan; Wang, Cong; Luo, Zhi

    2015-04-01

    In this study, an effective approach is presented for the fabrication of line-patterned superwetting surface on sapphire by using a femtosecond laser. The fabricated surface shows a powerful capillary action by which water could be rapidly sucked into the as-prepared surface structures and spread even on the vertical surface against gravitation. In addition, the effects of the period and the dimensions of the microgrooves on surface wettability are investigated. It is demonstrated that the wettability can be significantly enhanced in the case when the sizable line-patterned nanostructures exist. This work could provide a facile and promising strategy for enhancing the performance of heat dissipation in the electronic devices substrate.

  7. Intramolecular vibrations and noise effects on pattern formation in a molecular helix.

    PubMed

    Fouda, H P Ekobena; Tabi, C B; Mohamadou, A; Kofané, T C

    2011-09-21

    Modulational instability in a biexciton molecular chain is addressed. We show that the model can be reduced to a set of three coupled equations: two nonlinear Schrödinger equations and a Boussinesq equation. The linear stability analysis of continuous wave solutions of the coupled systems is performed and the growth rate of instability is found numerically. Simulations of the full discrete systems reveal some behaviors of modulational instability, since wave patterns are observed for the excitons and the phonon spectrum. We also take the effect of thermal fluctuations into account and we numerically study both the stability and the instability of the plane waves under 300 K. The plane wave is found to be stable under modulation, but displays a gradual increase of the wave amplitudes. Under modulation, the same behaviors are observed and wave patterns are found to resist thermal fluctuations, which is in agreement with earlier research on localized structure stability under thermal noise.

  8. Composite catalyst surfaces: Effect of inert and active heterogeneities on pattern formation

    SciTech Connect

    Baer, M.; Bangia, A.K.; Kevrekidis, I.G.; Haas, G.; Rotermund, H.H.; Ertl, G.

    1996-12-05

    Spatiotemporal dynamics in reaction-diffusion systems can be altered through the properties (reactivity, diffusivity) of the medium in which they occur. We construct active heterogeneous media (composite catalytic surfaces with inert as well as active illusions) using microelectronics fabrication techniques and study the spatiotemporal dynamics of heterogeneous catalytic reactions on these catalysts. In parallel, we perform simulations as well as numerical stability and bifurcation analysis of these patterns using mechanistic models. At the limit of large heterogeneity `grain size` (compared to the wavelength of spontaneously arising structures) the interaction patterns with inert or active boundaries dominates (e.g., pinning, transmission, and boundary breakup of spirals, interaction of pulses with corners, `pacemaker` effects). At the opposite limit of very small or very finely distributed heterogeneity, effective behavior is observed (slight modulation of pulses, nearly uniform oscillations, effective spirals). Some representative studies of transitions between the two limits are presented. 48 refs., 11 figs.

  9. Pattern Formation, Defect Motions and Onset of Defect Chaos in the Electrohydrodynamic Instability of Nematic Liquid Crystals

    NASA Astrophysics Data System (ADS)

    Kai, Shoichi; Chizumi, Nobuyuki; Kohno, Mitsuhiro

    1989-10-01

    Pattern formation processes and the associated defect motion are experimentally studied for various rectangular cells in the electrohydrodynamic instability. Wavenumber selection arises from the competition between the growth of the most rapidly growing mode and the finally stable mode in the Williams domain (WD) state. Defect motion is associated with such a competitive growth into the final stage. The fluctuating WD (FWD) is strongly related to the oscillatory gliding motion of defects. Temporally nonperiodic change of the number of defects is observed in the FWD state with a power spectrum of 1/f type (defect chaos). A large hysteresis is observed near the onset of FWD. A detailed phase diagram of stable convective patterns in the plane spanned by the threshold voltage and the applied frequency is presented with the characteristic behavior of defect motions.

  10. Studying the optical second-order interference pattern formation process with classical light in the photon counting regime.

    PubMed

    He, Yuchen; Liu, Jianbin; Zhang, Songlin; Wang, Wentao; Bai, Bin; Le, Mingnan; Xu, Zhuo

    2015-12-01

    The formation process of the second-order interference pattern is studied experimentally in the photon counting regime by superposing two independent single-mode continuous-wave lasers. Two-photon interference based on the superposition principle in Feynman's path integral theory is employed to interpret the experimental results. The second-order interference pattern of classical light can be formulated when, with high probability, there are only two photons in the interferometer at one time. The studies are helpful in understanding the second-order interference of classical light in the language of photons. The method and conclusions can be generalized to the third- and higher-order interference of light and interference of massive particles.

  11. Regulation of pattern formation and gene amplification during Drosophila oogenesis by the miR-318 microRNA.

    PubMed

    Ge, Wanzhong; Deng, Qiannan; Guo, Ting; Hong, Xin; Kugler, Jan-Michael; Yang, Xiaohang; Cohen, Stephen M

    2015-05-01

    Pattern formation during epithelial development requires the coordination of multiple signaling pathways. Here, we investigate the functions of an ovary-enriched miRNA, miR-318, in epithelial development during Drosophila oogenesis. mir-318 maternal loss-of-function mutants were female-sterile and laid eggs with abnormal morphology. Removal of mir-318 disrupted the dorsal-anterior follicle cell patterning, resulting in abnormal dorsal appendages. mir-318 mutant females also produced thin and fragile eggshells due to impaired chorion gene amplification. We provide evidence that the ecdysone signaling pathway activates expression of miR-318 and that miR-318 cooperates with Tramtrack69 to control the switch from endocycling to chorion gene amplification during differentiation of the follicular epithelium. The multiple functions of miR-318 in oogenesis illustrate the importance of miRNAs in maintaining cell fate and in promoting the developmental transition in the female follicular epithelium.

  12. Formation of coffee-stain patterns at the nanoscale: The role of nanoparticle solubility and solvent evaporation rate

    NASA Astrophysics Data System (ADS)

    Zhang, Jianguo; Milzetti, Jasmin; Leroy, Frédéric; Müller-Plathe, Florian

    2017-03-01

    When droplets of nanoparticle suspension evaporate from surfaces, they leave behind a deposit of nanoparticles. The mechanism of evaporation-induced pattern formation in the deposit is studied by molecular dynamics simulations for sessile nanodroplets. The influence of the interaction between nanoparticles and liquid molecules and the influence of the evaporation rate on the final deposition pattern are addressed. When the nanoparticle-liquid interaction is weaker than the liquid-liquid interaction, an interaction-driven or evaporation-induced layer of nanoparticles appears at the liquid-vapor interface and eventually collapses onto the solid surface to form a uniform deposit independently of the evaporation rate. When the nanoparticle-liquid and liquid-liquid interactions are comparable, the nanoparticles are dispersed inside the droplet and evaporation takes place with the contact line pinned at a surface defect. In such a case, a pattern with an approximate ring-like shape is found with fast evaporation, while a more uniform distribution is observed with slower evaporation. When the liquid-nanoparticle interaction is stronger than the liquid-liquid interaction, evaporation always occurs with receding contact line. The final deposition pattern changes from volcano-like to pancake-like with decreasing evaporation rate. These findings might help to design nanoscale structures like nanopatterns or nanowires on surface through controlled solvent evaporation.

  13. Formation of coffee-stain patterns at the nanoscale: The role of nanoparticle solubility and solvent evaporation rate.

    PubMed

    Zhang, Jianguo; Milzetti, Jasmin; Leroy, Frédéric; Müller-Plathe, Florian

    2017-03-21

    When droplets of nanoparticle suspension evaporate from surfaces, they leave behind a deposit of nanoparticles. The mechanism of evaporation-induced pattern formation in the deposit is studied by molecular dynamics simulations for sessile nanodroplets. The influence of the interaction between nanoparticles and liquid molecules and the influence of the evaporation rate on the final deposition pattern are addressed. When the nanoparticle-liquid interaction is weaker than the liquid-liquid interaction, an interaction-driven or evaporation-induced layer of nanoparticles appears at the liquid-vapor interface and eventually collapses onto the solid surface to form a uniform deposit independently of the evaporation rate. When the nanoparticle-liquid and liquid-liquid interactions are comparable, the nanoparticles are dispersed inside the droplet and evaporation takes place with the contact line pinned at a surface defect. In such a case, a pattern with an approximate ring-like shape is found with fast evaporation, while a more uniform distribution is observed with slower evaporation. When the liquid-nanoparticle interaction is stronger than the liquid-liquid interaction, evaporation always occurs with receding contact line. The final deposition pattern changes from volcano-like to pancake-like with decreasing evaporation rate. These findings might help to design nanoscale structures like nanopatterns or nanowires on surface through controlled solvent evaporation.

  14. Pattern formation at multiple spatial scales drives the resilience of mussel bed ecosystems.

    PubMed

    Liu, Quan-Xing; Herman, Peter M J; Mooij, Wolf M; Huisman, Jef; Scheffer, Marten; Olff, Han; van de Koppel, Johan

    2014-10-22

    Self-organized complexity at multiple spatial scales is a distinctive characteristic of biological systems. Yet, little is known about how different self-organizing processes operating at different spatial scales interact to determine ecosystem functioning. Here we show that the interplay between self-organizing processes at individual and ecosystem level is a key determinant of the functioning and resilience of mussel beds. In mussel beds, self-organization generates spatial patterns at two characteristic spatial scales: small-scale net-shaped patterns due to behavioural aggregation of individuals, and large-scale banded patterns due to the interplay of between-mussel facilitation and resource depletion. Model analysis reveals that the interaction between these behavioural and ecosystem-level mechanisms increases mussel bed resilience, enables persistence under deteriorating conditions and makes them less prone to catastrophic collapse. Our analysis highlights that interactions between different forms of self-organization at multiple spatial scales may enhance the intrinsic ability of ecosystems to withstand both natural and human-induced disturbances.

  15. Endogenous electromagnetic fields in plant leaves: a new hypothesis for vascular pattern formation.

    PubMed

    Pietak, Alexis Mari

    2011-06-01

    Electromagnetic (EM) phenomena have long been implicated in biological development, but few detailed, practical mechanisms have been put forth to connect electromagnetism with morphogenetic processes. This work describes a new hypothesis for plant leaf veination, whereby an endogenous electric field forming as a result of a coherent Frohlich process, and corresponding to an EM resonant mode of the developing leaf structure, is capable of instigating leaf vascularisation. In order to test the feasibility of this hypothesis, a three-dimensional, EM finite-element model (FEM) of a leaf primordium was constructed to determine if suitable resonant modes were physically possible for geometric and physical parameters similar to those of developing leaf tissue. Using the FEM model, resonant EM modes with patterns of relevance to developing leaf vein modalities were detected. On account of the existence of shared geometric signatures in a leaf's vascular pattern and the electric field component of EM resonant modes supported by a developing leaf structure, further theoretical and experimental investigations are warranted. Significantly, this hypothesis is not limited to leaf vascular patterning, but may be applicable to a variety of morphogenetic phenomena in a number of living systems.

  16. Mesoscale pattern formation of self-propelled rods with velocity reversal

    NASA Astrophysics Data System (ADS)

    Großmann, Robert; Peruani, Fernando; Bär, Markus

    2016-11-01

    We study self-propelled particles with velocity reversal interacting by uniaxial (nematic) alignment within a coarse-grained hydrodynamic theory. Combining analytical and numerical continuation techniques, we show that the physics of this active system is essentially controlled by the reversal frequency. In particular, we find that elongated, high-density, ordered patterns, called bands, emerge via subcritical bifurcations from spatially homogeneous states. Our analysis reveals further that the interaction of bands is weakly attractive and, consequently, bands fuse upon collision in analogy with nonequilibrium nucleation processes. Moreover, we demonstrate that a renormalized positive line tension can be assigned to stable bands below a critical reversal rate, beyond which they are transversally unstable. In addition, we discuss the kinetic roughening of bands as well as their nonlinear dynamics close to the threshold of transversal instability. Altogether, the reduction of the multiparticle system onto the dynamics of bands provides a unified framework to understand the emergence and stability of nonequilibrium patterns in this self-propelled particle system. In this regard, our results constitute a proof of principle in favor of the hypothesis in microbiology that velocity reversal of gliding rod-shaped bacteria regulates the transitions between various self-organized patterns observed during the bacterial life cycle.

  17. The logic of plant vascular patterning. Polarity, continuity and plasticity in the formation of the veins and of their networks.

    PubMed

    Scarpella, Enrico

    2017-03-02

    The problem of long-distance transport is solved in many multicellular organisms by tissue networks such as the vascular networks of plants. Because tissue networks transport from one tissue area to another, they are polar and continuous; most of them, including plant vascular networks, are also plastic. Surprisingly, the formation of tissue networks is in most cases just as polar, continuous and plastic. Available evidence suggests that the polarity, continuity and plasticity of plant vascular networks and their formation could be accounted for by a patterning process that combines: (i) excess of developmental alternatives competing for a limiting cell-polarizing signal; (ii) positive feedback between cell polarization and continuous, cell-to-cell transport of the cell-polarizing signal; and (iii) gradual restriction of differentiation that increasingly removes the cell-polarizing signal.

  18. Dorsoventral patterning by the Chordin-BMP pathway: a unified model from a pattern-formation perspective for Drosophila, vertebrates, sea urchins and Nematostella.

    PubMed

    Meinhardt, Hans

    2015-09-01

    Conserved from Cnidarians to vertebrates, the dorsoventral (DV) axis is patterned by the Chordin-BMP pathway. However, the functions of the pathway's components are very different in different phyla. By modeling it is shown that many observations can be integrated by the assumption that BMP, acting as an inhibitory component in more ancestral systems, became a necessary and activating component for the generation of a secondary and antipodal-located signaling center. The different realizations seen in vertebrates, Drosophila, sea urchins and Nematostella allow reconstruction of a chain of modifications during evolution. BMP-signaling is proposed to be based on a pattern-forming reaction of the activator-depleted substrate type in which BMP-signaling acts via pSmad as the local self-enhancing component and the depletion of the highly mobile BMP-Chordin complex as the long-ranging antagonistic component. Due to the rapid removal of the BMP/Chordin complex during BMP-signaling, an oriented transport and "shuttling" results, although only ordinary diffusion is involved. The system can be self-organizing, allowing organizer formation even from near homogeneous initial situations. Organizers may regenerate after removal. Although connected with some losses of self-regulation, for large embryos as in amphibians, the employment of maternal determinants is an efficient strategy to make sure that only a single organizer of each type is generated. The generation of dorsoventral positional information along a long-extended anteroposterior (AP) axis cannot be achieved directly by a single patch-like organizer. Nature found different solutions for this task. Corresponding models provide a rationale for the well-known reversal in the dorsoventral patterning between vertebrates and insects.

  19. Dealloying of Platinum-Aluminum Thin Films: Dynamics of Pattern Formation

    NASA Astrophysics Data System (ADS)

    Galinski, Henning; Ryll, Thomas; Schlagenhauf, Lukas; Rechberger, Felix; Ying, Sun; Gauckler, Ludwig J.; Mornaghini, Flavio C. F.; Ries, Yasmina; Spolenak, Ralph; Döbeli, Max

    2011-11-01

    The application of focused ion beam (FIB) nanotomography and Rutherford backscattering spectroscopy (RBS) to dealloyed platinum-aluminum thin films allows for an in-depth analysis of the dominating physical mechanisms of nanoporosity formation during the dealloying process. The porosity formation due to the dissolution of the less noble aluminum in the alloy is treated as result of a reaction-diffusion system. The RBS and FIB analysis yields that the porosity evolution has to be regarded as superposition of two independent processes, a linearly propagating diffusion front with a uniform speed and a slower dissolution process in regions which have already been passed by the diffusion front. The experimentally observed front evolution is captured by the Fisher-Kolmogorov-Petrovskii-Piskounov (FKPP). The slower dissolution is represented by a zero-order rate law which causes a gradual porosity in the thin film.

  20. Geochemical patterns and microbial contribution to iron plaque formation in the rice plant rhizosphere

    NASA Astrophysics Data System (ADS)

    Maisch, Markus; Murata, Chihiro; Unger, Julia; Kappler, Andreas; Schmidt, Caroline

    2015-04-01

    Rice is the major food source for more than half of the world population and 80 percent of the worldwide rice cultivation is performed on water logged paddy soils. The establishment of reducing conditions in the soil and across the soil-water interface not only stimulates the microbial production and release of the greenhouse gas methane. These settings also create optimal conditions for microbial iron(III) reduction and therefore saturate the system with reduced ferrous iron. Through the reduction and dissolution of ferric minerals that are characterized by their high surface activity, sorbed nutrients and contaminants (e.g. arsenic) will be mobilized and are thus available for uptake by plants. Rice plants have evolved a strategy to release oxygen from their roots in order to prevent iron toxification in highly ferrous environments. The release of oxygen to the reduced paddy soil causes ferric iron plaque formation on the rice roots and finally increases the sorption capacity for toxic metals. To this date the geochemical and microbiological processes that control the formation of iron plaque are not deciphered. It has been hypothesized that iron(II)-oxidizing bacteria play a potential role in the iron(III) mineral formation along the roots. However, not much is known about the actual processes, mineral products, and geochemical gradients that establish within the rhizosphere. In the present study we have developed a growth set-up that allows the co-cultivation of rice plants and iron(II)-oxidizing bacteria, as well as the visual observation and in situ measurement of geochemical parameters. Oxygen and dissolved iron(II) gradients have been measured using microelectrodes and show geochemical hot spots that offer optimal growth conditions for microaerophilic iron(II) oxidizers. First mineral identification attempts of iron plaque have been performed using Mössbauer spectroscopy and microscopy. The obtained results on mineraology and crystallinity have been

  1. Reef facies distribution patterns, Pleistocene (125 Ka) Falmouth Formation, Rio Bueno, Jamaica, W. I

    SciTech Connect

    Precht, W.F. ); Hoyt, W.H. )

    1991-03-01

    Detailed paleoecologic and sedimentologic studies of the well-exposed, Pleistocene (125 Ka) Falmouth Formation from Rio Bueno, Jamaica, where undertaken to define both temporal and spatial changes in reef architecture. Analyses of samples reveal an overall shallowing - upwards motif and a distinct lateral zonation of reefal facies similar to those observed in Recent fringing-reef and bank-barrier reef complexes from the eastern and western sides of Discovery Bay, Jamaica, respectively. The Falmouth Formation that crops out on the eastern shore of Rio Bueno Harbor is continually exposed (north-south) for approximately 0.5 km in length. The top of the reef exposure is approximately +4.5 m above MSL. This height correlates directly with sea level maxima for the Sangamon in Jamaica based upon a wavecut notch in the Hopegate Formation at the top of the Falmouth onlap surface. Interpretation of these deposits indicates that no lagoon or back-reef facies were present and that there was a gradation of energy regimes from high-to-low, north-to-south within this true fringing reef complex. Detailed sedimentologic analysis of thin-sections from all the above lithologies confirms the aforementioned paleoenvironmental interpretations. This study emphasizes the usefulness of modern counterparts in Pleistocene reef analysis and interpretation, and allows for an understanding of temporal (vertical) and spatial (horizontal) variations due to both physical disturbance and local sea level history that are preserved in these reefal deposits.

  2. Evaluating the influence of different aspects of habitat fragmentation on mating patterns and pollen dispersal in the bird-pollinated Banksia sphaerocarpa var. caesia.

    PubMed

    Llorens, T M; Byrne, M; Yates, C J; Nistelberger, H M; Coates, D J

    2012-01-01

    Habitat fragmentation can significantly affect mating and pollen dispersal patterns in plant populations, although the differential effects of the various aspects of fragmentation are poorly understood. In this study, we used eight microsatellite loci to investigate the effect of fragmentation on the mating system and pollen dispersal within one large and eight small population remnants of Banksia sphaerocarpa var. caesia, a bird-pollinated shrub in the southern agricultural region of Western Australia. The large population had a much larger neighbourhood size and lower selfing rate, maternal pollen pool differentiation and within-plot mean pollen dispersal distance than the small populations. Outcrossing was consistently high and ranged from 85.7% ± 2.6 to 98.5% ± 0.9, and mating patterns suggested nearest-neighbour pollination. Pollen immigration into small populations ranged from 2.8% ± 1.8 to 16.5% ± 3.2. Using the small populations, we tested for correlations between various fragmentation variables and mating system and pollen dispersal parameters. We found significant negative linear relationships between population isolation and outcrossing rate; population shape and neighbourhood size; and conspecific density and mean pollen dispersal distance. There were significant positive linear relationships between population shape and pollen pool differentiation and between population size and number of different fathers per seed crop. Our results suggest that birds may use a series of fragmented populations as a vegetation corridor while foraging across the landscape and that population connectivity is a critical determinant of pollinator visitation. Our results also suggest that the effect of a linear population shape on the mating system and pollen dispersal is routinely underestimated.

  3. Suppression of transient enhanced diffusion in sub-micron patterned silicon template by dislocation loops formation

    SciTech Connect

    Hu, Kuan-Kan; Woon, Wei Yen; Chang, Ruey-Dar

    2015-10-15

    We investigate the evolution of two dimensional transient enhanced diffusion (TED) of phosphorus in sub-micron scale patterned silicon template. Samples doped with low dose phosphorus with and without high dose silicon self-implantation, were annealed for various durations. Dopant diffusion is probed with plane-view scanning capacitance microscopy. The measurement revealed two phases of TED. Significant suppression in the second phase TED is observed for samples with high dose self-implantation. Transmission electron microscopy suggests the suppressed TED is related to the evolution of end of range defect formed around ion implantation sidewalls.

  4. Chemical patterning of Ag(111): Spatially confined oxide formation induced by electron beam irradiation

    SciTech Connect

    Guenther, S.; Reichelt, R.; Wintterlin, J.; Barinov, A.; Mentes, T. O.; Nino, M. A.; Locatelli, A.

    2008-12-08

    Low energy electron irradiation of a Ag(111) surface during NO{sub 2} adsorption at 300 K induces formation of Ag oxide. Using a spatially confined electron beam, small Ag{sub 2}O spots could be grown with a sharp, {approx}100 nm wide, boundary to the nonirradiated metallic surface. Since the structure size will mainly depend on the sharpness of the irradiating electron beam, this process has the potential of a single step nanostructuring process. Temperature treatment offers an easy way to manipulate the boundary between oxide and metallic silver by steering a chemical front.

  5. Pattern formation of microtubules and motors: Inelastic interaction of polar rods

    NASA Astrophysics Data System (ADS)

    Aranson, Igor S.; Tsimring, Lev S.

    2005-05-01

    We derive a model describing spatiotemporal organization of an array of microtubules interacting via molecular motors. Starting from a stochastic model of inelastic polar rods with a generic anisotropic interaction kernel we obtain a set of equations for the local rods concentration and orientation. At large enough mean density of rods and concentration of motors, the model describes orientational instability. We demonstrate that the orientational instability leads to the formation of vortices and (for large density and/or kernel anisotropy) asters seen in recent experiments.

  6. An experimental study of the flow pattern and heat transport behavior in horizontal convection with large Rayleigh number and small aspect ratio

    NASA Astrophysics Data System (ADS)

    Xia, Ke-Qing; Huang, Shi-Di

    2014-11-01

    Horizontal convection is a simple conceptual model to understand the role of buoyancy in the Meridional Overturning Circulation (MOC). Here we report an experimental study of the flow pattern and heat transport behavior in horizontal convection with Rayleigh number Ra up to 2 ×1012 and aspect ratio of 0.1 using a long apparatus. Flow visualization studies reveal that it is not necessary for the returning flow to penetrate the strong stratification in the thermal BLs, suggesting that much less energy may be required to maintain a global circulation than is generally believed. Moreover, both the heat transport efficiency and thermal BL thicknesses are found to follow a 0.3 power law, which indicates a stronger heat transport in horizontal convection with large Ra number than is suggested in the literature. These findings on horizontal convection may be relevant to the driving mechanism of the MOC. This work is supported by the Hong Kong Research Grants Council under Grant No. CUHK403811.

  7. Endothelial pattern formation in hybrid constructs of additive manufactured porous rigid scaffolds and cell-laden hydrogels for orthopedic applications.

    PubMed

    Shanjani, Yaser; Kang, Yunqing; Zarnescu, Livia; Ellerbee Bowden, Audrey K; Koh, Jeong-Tae; Ker, Dai Fei Elmer; Yang, Yunzhi

    2017-01-01

    Vascularization of tissue engineering constructs (TECs) in vitro is of critical importance for ensuring effective and satisfactory clinical outcomes upon implantation of TECs. Biomechanical properties of TECs have remarkable influence on the in vitro vascularization of TECs. This work utilized in vitro experiments and finite element analysis to investigate endothelial patterns in hybrid constructs of soft collagen gels and rigid macroporous poly(ε-caprolactone)-β-tricalcium phosphate (PCL-β-TCP) scaffold seeded/embedded with human umbilical vein endothelial cells (HUVECs) for bone tissue engineering applications. We first fabricated and characterized well-defined porous PCL-β-TCP scaffolds with identical pore size (500µm) but different strut sizes (200 and 400µm) using additive manufacturing (AM) technology, and then assessed the HUVEC׳s proliferation and morphogenesis within collagen, PCL-β-TCP scaffold, and the collagen-scaffold hybrid construct. Results showed that, in the hybrid construct, the cell population in the collagen component dropped by day 7 but then increased by day 14. Also, cells migrated onto the struts of the scaffold component, proliferated over time, and formed networks on the thinner struts (i.e., 200µm). Also, the thinner struts resulted in formation of long linear cellular cords structures within the pores. Finite element simulation demonstrated principal stress patterns similar to the observed cell-network pattern. It is probable that the scaffold component modulated patterns of principal stresses in the collagen component as biomechanical cues for reorganization of cell network patterns. Also, the scaffold component significantly improved the mechanical integrity of hydrogel component in the hybrid construct for weight-bearing applications. These results have collectively indicated that the manipulation of micro-architecture of scaffold could be an effective means to further regulate and guide desired cellular response in hybrid