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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. Pattern Formation in Materials

    NASA Astrophysics Data System (ADS)

    Karma, Alain

    2011-04-01

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

  4. 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.

  5. Understanding Alliance Formation Patterns

    DTIC Science & Technology

    2015-12-01

    different periods. The thesis concludes that alliance formation behaviors differ depending on the prevailing system- level conditions in the different...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

  6. Pattern Formation in Hydrozoa

    NASA Astrophysics Data System (ADS)

    Berking, Stefan

    The fresh water polyp Hydra is famous for its ability to regenerate missing structures. Even aggregates of single cells transform eventually into normally shaped animals. This indicates a communication within the tissue and within the aggregates which determines the spatial pattern of gene expression. Such pattern-forming systems are thought to play a decisive role in the control of self-organization during embryogenesis. Marine and fresh water hydrozoa appear to allow an access to such a system. Although the molecular components are still mostly unknown, the regulatory properties of the pattern-forming system are increasingly well understood, and this may help eventually to identify the components involved.

  7. 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.

  8. 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.

  9. Dynamics of interfacial pattern formation

    NASA Technical Reports Server (NTRS)

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

    1983-01-01

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

  10. 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.

  11. Pattern formation in the geosciences.

    PubMed

    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.

  12. 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

  13. 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.

  14. 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.

  15. Pattern formation in Salt Playa

    NASA Astrophysics Data System (ADS)

    Lasser, Jana; Goehring, Lucas; Nield, Joanna

    2017-04-01

    Salt Playa, or crusts, often exhibit polygonal salt-ridge patterns with a diameter of roughly 1 m. Several mechanisms, like cracking or wrinkling of the surface crust have been discussed, but none of these can explain the scale of the observed patterns. We investigate a theory where we link the crust pattern to buoyancy-driven flows in the porous ground beneath them. In this model, salinity gradients arise due to evaporation at the ground surface. These gradients lead to the formation of convection cells, much like the convection caused by temperature gradients. The spatial scaling of these convection rolls significantly depends on the evaporation rate, while the onset of convection is controlled by the permeability of the soil. Here we will show a link between surface salt patterns and subsurface dynamics. We investigate the onset of convection, the scaling of convection cells, and the formation of salt crusts in a sandy soil confined to a Hele-Shaw cell in analogue experiments and link subsurface concentration gradients to surface crust patterns by means of a field study. The aim of the experiments and the field study is to explore how porous media convection can affect salt crust patterns in arid environments.

  16. Pattern formation in optical resonators

    NASA Astrophysics Data System (ADS)

    Weiss, C. O.; Larionova, Ye

    2007-02-01

    We review pattern formation in optical resonators. The emphasis is on 'particle-like' structures such as vortices or spatial solitons. On the one hand, similarities impose themselves with other fields of physics (condensed matter, phase transitions, particle physics, fluds/super fluids). On the other hand the feedback is led by the resonator mirrors to bi- and multi-stability of the spatial field structure, which is the basic ingredient for optical information processing. The spatial dimension or the 'parallelism' is the strength of optics compared to electronics (and will have to be employed to fully use the advantages optics offers in information processing). But even in the 'serial' processing tasks of telecoms (e.g. information buffering) spatial resonator solitons can do better than the schemes proposed so far—including 'slow light'. Pattern formation in optical resonators will likely be the key to brain-like information processing like cognition, learning and association; to complement the precise but limited algorithmic capabilities of electronic processing. But even in the short term it will be useful for solving serial optical processing problems. The prospects for technical uses of pattern formation in resonators are one motivation for this research. The fundamental similarities with other fields of physics, on the other hand, inspire transfer of concepts between fields; something that has always proven fruitful for gaining deeper insights or for solving technical problems.

  17. Fold pattern formation in 3D

    NASA Astrophysics Data System (ADS)

    Schmid, Daniel W.; Dabrowski, Marcin; Krotkiewski, Marcin

    2010-05-01

    The vast majority of studies concerned with folding focus on 2D and assume that the resulting fold structures are cylindrically extended in the out of place direction. This simplification is often justified as fold aspect ratios, length/width, are quite large. However, folds always exhibit finite aspect ratios and it is unclear what controls this (cf. Fletcher 1995). Surprisingly little is known about the fold pattern formation in 3D for different in-plane loading conditions. Even more complicated is the pattern formation when several folding events are superposed. Let us take the example of a plane strain pure shear superposed by the same kind of deformation but rotated by 90 degrees. The text book prediction for this event is the formation of an egg carton structure; relevant analogue models either agree and produce type 1 interference patterns or contradict and produce type 2. In order to map out 3D fold pattern formation we have performed a systematic parameter space investigation using BILAMIN, our efficient unstructured mesh finite element Stokes solver. BILAMIN is capable of solving problems with more than half a billion unknowns. This allows us to study fold patterns that emerge in randomly (red noise) perturbed layers. We classify the resulting structures with differential geometry tools. Our results show that there is a relationship between fold aspect ratio and in-plane loading conditions. We propose that this finding can be used to determine the complete parameter set potentially contained in the geometry of three dimensional folds: mechanical properties of natural rocks, maximum strain, and relative strength of the in-plane far-field load components. Furthermore, we show how folds in 3D amplify and that there is a second deformation mode, besides continuous amplification, where compression leads to a lateral rearrangement of blocks of folds. Finally, we demonstrate that the textbook prediction of egg carton shaped dome and basin structures resulting

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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").

  4. 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.

  5. 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).

  6. Kinetic Aspects of Formation of Carbonitride Layer

    NASA Astrophysics Data System (ADS)

    Gryzunov, V. I.; Priymak, E. Yu.; Firsova, N. V.; Emel'yanova, T. V.

    2017-07-01

    The laws of formation and growth of carbonitride layer in steels 40G2, 38KhMA, 40KhN2MA, and 09GSF at a temperature of 560°C are studied. Metallographic methods are used to determine its composition, location and length. Equations for computing the lengths of the carbonitride phase and of the layer due to surface cyaniding are derived.

  7. 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.

  8. Some aspects of hydrate formation and wetting.

    PubMed

    Fotland, P; Askvik, K M

    2008-05-01

    Experimental observations of gas hydrate formation have shown that, in the initial nucleation and crystallization process, water-oil emulsions may be generated, destabilized or even inverted. These phenomena are consistent with the effects of particles on emulsions. In this work we relate experimental observations of hydrate formation to the phenomenon of wettability. It is shown that details of hydrate wetting are important for both the morphology and the kinetics of the formed hydrates. For the cases of hydrate lenses and spheres, it is shown that the various wetting states can be illustrated and analyzed by using wetting diagrams. Metastability is a function of the surface energies of the hydrate formation, i.e., the wetting state, and it is shown that in some cases metastability vanishes, and thus hydrates nucleates instantly at all positive driving forces. The magnitude of buoyancy and turbulence forces acting on a hydrate sphere are compared to the capillary force and it is concluded that capillary energy dominates when the hydrate spheres is less than 1 mm.

  9. 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.

  10. 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.

  11. 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)).

  12. 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. Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.

  13. Spontaneous Pattern Formation with Incoherent White Light

    NASA Astrophysics Data System (ADS)

    Schwartz, Tal; Carmon, Tal; Buljan, Hrvoje; Segev, Mordechai

    2004-11-01

    We present the first experimental observation of modulation instability and spontaneous pattern formation with incoherent white light emitted from an incandescent light bulb. We show experimentally that modulation instability of white light propagating in a noninstantaneous self-focusing medium is a collective effect, where the entire temporal spectrum of the light beam becomes unstable at the same threshold value and collectively forms a pattern with a single periodicity. We experimentally demonstrate that the temporal spectrum of the evolving perturbation self-adjusts to match the collective pattern formation phenomenon.

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. Sarcomeric Pattern Formation by Actin Cluster Coalescence

    PubMed Central

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

    2012-01-01

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

  8. 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.

  9. 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.

  10. 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

  11. Geometry-induced protein pattern formation

    PubMed Central

    Thalmeier, Dominik; Halatek, Jacob; Frey, Erwin

    2016-01-01

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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. The LLE, pattern formation and a novel coherent source

    NASA Astrophysics Data System (ADS)

    Castelli, Fabrizio; Brambilla, Massimo; Gatti, Alessandra; Prati, Franco; Lugiato, Luigi A.

    2017-04-01

    The LLE was introduced in order to provide a paradigmatic model for spontaneous spatial pattern formation in the field of nonlinear optics. In the first part of this paper we describe in details its historical evolution. We underline, first of all, that the multimode instability of optical bistability represents an important precursor of the LLE. Next, we illustrate how the original LLE was conceived in order to describe pattern formation in the planes transverse with respect to the longitudinal direction of propagation of light in the nonlinear medium contained in the optical cavity. We emphasize, in particular, the crucial role of the low transmission limit (also called mean field limit or uniform field limit in the literature) in determining the simplicity of the equation. In discussing transverse pattern formation in the LLE, we underline incidentally the presence of very important quantum aspects related to squeezing of quantum fluctuations and to quantum imaging. We consider not only the case of global patterns but also localized structures (cavity solitons and their control). Then we turn to the temporal/longitudinal version of the LLE, formulated by Haelterman et al. [H. Haelterman, S. Trillo, S. Wabnitz, Opt. Commun. 91, 401 (1992)], and to its equivalence with the transverse LLE in 1D, discussing especially the phenomenon of temporal cavity solitons, their experimental observation and their control. Finally for the first part we turn to the very recent topic of broadband frequency combs, observed in a versatile multiwavelength coherent source (driven Kerr microcavity), which is raising a lot of interest and of research activities because of its very favourable physical characteristics, which support quite promising applicative perspectives. Kerr microcavities realize in an ideal manner the basic assumptions of the LLE, and the spontaneous formation of travelling patterns along the microcavity is the crucial mechanism which creates the combs and governs

  19. 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.

  20. Periodic Pattern Formation of Bacterial Colonies

    NASA Astrophysics Data System (ADS)

    Itoh, Hiroto; Wakita, Jun-ichi; Matsuyama, Tohey; Matsushita, Mitsugu

    1999-04-01

    We have experimentally investigated pattern formation of colonies ofbacterial species Proteus mirabilis, which is famous forforming concentric-ring-like colonies.The colony grows cyclically with the interface repeating an advance anda stop alternately on a surface of a solid agar medium.We distinguish three phases (initial lag phase, the followingmigration and consolidation phases that appear alternately) for the colony growth.When we cut a colony just behind a migrating front shortly after the migrationstarted, the migration ended earlier and the following consolidationlasted longer.However, the following cycles were not influenced by the cut, i.e., thephases of the migration and consolidation were not affected.Global chemical signals governing the colony formation from thecenter were not found to exist.We also quantitatively checked phase entrainment by letting two coloniescollide with each other and found that it does not take place in macroscopic scales.All these experimental results suggest that the most important factorfor the migration is the cell population density.

  1. 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

  2. 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.

  3. 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.

  4. Pattern formation in a sandpile of ternary granular mixtures

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  5. Pattern formation 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Chemical aspects of the formation of the solar system

    NASA Technical Reports Server (NTRS)

    Arrhenius, G.

    1978-01-01

    Application of Alfven's theory for the formation of the solar system and the constraints imposed by the chemical composition of space materials are discussed with reference to chemical processes involved in the formation of the solar system. Evidence for the chemical properties of the space medium and the chemical consequences of the postulated physical differentiation processes are outlined, and interpretations based on structure and composition of meteorite material are indicated. A large range of topics, including processes involving chemical differentiation, temperature effects, and isotope fractionation, are examined.

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

    NASA Technical Reports Server (NTRS)

    Langer, J. S.

    1989-01-01

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

  14. 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.

  15. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

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

  17. 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

  18. 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.

  19. 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.

  20. (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)

  1. 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.

  2. 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

  3. 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.

  4. Vascular tissue differentiation and pattern formation in plants.

    PubMed

    Ye, Zheng-Hua

    2002-01-01

    Vascular tissues, xylem and phloem, are differentiated from meristematic cells, procambium, and vascular cambium. Auxin and cytokinin have been considered essential for vascular tissue differentiation; this is supported by recent molecular and genetic analyses. Xylogenesis has long been used as a model for study of cell differentiation, and many genes involved in late stages of tracheary element formation have been characterized. A number of mutants affecting vascular differentiation and pattern formation have been isolated in Arabidopsis. Studies of some of these mutants have suggested that vascular tissue organization within the bundles and vascular pattern formation at the organ level are regulated by positional information.

  5. 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.

  6. Polariton Pattern Formation and Photon Statistics of the Associated Emission

    NASA Astrophysics Data System (ADS)

    Whittaker, C. E.; Dzurnak, B.; Egorov, O. A.; Buonaiuto, G.; Walker, P. M.; Cancellieri, E.; Whittaker, D. M.; Clarke, E.; Gavrilov, S. S.; Skolnick, M. S.; Krizhanovskii, D. N.

    2017-07-01

    We report on the formation of a diverse family of transverse spatial polygon patterns in a microcavity polariton fluid under coherent driving by a blue-detuned pump. Patterns emerge spontaneously as a result of energy-degenerate polariton-polariton scattering from the pump state to interfering high-order vortex and antivortex modes, breaking azimuthal symmetry. The interplay between a multimode parametric instability and intrinsic optical bistability leads to a sharp spike in the value of second-order coherence g(2 )(0 ) of the emitted light, which we attribute to the strongly superlinear kinetics of the underlying scattering processes driving the formation of patterns. We show numerically by means of a linear stability analysis how the growth of parametric instabilities in our system can lead to spontaneous symmetry breaking, predicting the formation and competition of different pattern states in good agreement with experimental observations.

  7. 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.

  8. 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

  9. 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...

  10. 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

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. Pattern formation in a ferroin-bromate system

    NASA Astrophysics Data System (ADS)

    Showalter, Kenneth

    1980-10-01

    Stationary mosaic patterns may spontaneously develop in a thin film of solution containing H2SO4, NaBrO3, KBr, ferroin, and 4-cyclohexene-1,2-dicarboxylic acid. The pattern formation is affected by initial reactant concentrations and depends on the generation of elemental bromine. Depending on initial reactant concentrations, a vivid nonsynchronous oxidation transition may also occur. Results of experiments designed to distinguish between physical and chemical mechanisms are presented.

  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. 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.

  20. Controlled Pattern Formation in Carbon Nanotube Arrays Using Liquid Interfaces

    NASA Astrophysics Data System (ADS)

    Sansom, Elijah; Noca, Flavio; Zhou, Jijie; Trevino, Lydia; Gharib, Morteza

    2004-11-01

    Thin liquid films undergoing evaporation and dewetting are subject to instabilities and film breakup. Such films may potentially be used to pattern small particles, even nanometer size ones. This possibility is investigated by studying drying liquid films within mats of vertically oriented carbon nanotubes while varying experimental conditions. Liquids of different surfactant concentration, surface tension, wettability, and viscosity are used while simultaneously varying evaporation rates. Rearrangements of the carbon nanotubes into interesting and perhaps useful patterns of uniformly distributed holes are produced, and controllability of these patterns is demonstrated. Lateral capillary forces acting on the partially immersed carbon nanotubes at the liquid interface and dewetting instabilities inherent in the film are the apparent cause of these patterns. Simple, controlled pattern formation is highly desirable in production of carbon nanotube devices as well as other nanoparticle systems.

  1. 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

  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. Raked Pattern TARs: Evolution and Formation of a Unique Pattern in an Active Sediment Transport Environment

    NASA Astrophysics Data System (ADS)

    Foroutan, M.; Zimbelman, J. R.

    2016-12-01

    Sedimentation patterns vary with geographic settings, varying fluid regimes and climate conditions. Decoding resultant bedform patterns in aeolian and fluvial environments is one way for extracting the history and formation processes, as well as recognizing the climate change in the region. Some of these patterns are common but some are quite unique comparing what we generally expect from these bedforms on different planets. In this study we describe a quite rare pattern in a pristine region in the Lut desert of Iran named "raked pattern" mega-ripples / TAR-like features, similar to patterns on Mars. We describe this unique pattern and explore their formation by remote sensing analysis and looking at their evolution through multi-temporal satellite images on both planets. These `raked'-appearing TAR-like features have been found on flat beds, but close to highly eroded features such as yardangs. They are oriented perpendicular to the prevailing wind direction, and consist of small equally spaced bedforms, with wavelength and space between mid-points of the features all equal. The `raked' landforms are neatly aligned in parallel groups (i.e., of about 10-30 features in each group) throughout the area; the TAR-like features have sharp boundaries and each patch has an overall `spindle' shape. The `raked' pattern could be evidence of two successive aeolian formation episodes, a special type of topography in the upwind side, or an indication of considerable change in wind direction. We explored these scenarios by studying repeated images during 8 years and monitored their changes. Some regions have been identified with clear evolution through initiation of these patterns in a highly active aeolian region. This curious pattern has not been identified or documented in the literature. Our results show interesting evolutionary stages arose from multi-modal particle size and sediment transport environment for this pattern that implies the formation process for the same

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

    PubMed

    Sherratt, Jonathan A; Mackenzie, Julia J

    2016-10-07

    In the Wadden Sea, mussel beds self-organise into spatial patterns consisting of bands parallel to the shore. A leading explanation for this phenomenon is that mussel aggregation reduces losses from dislodgement and predation, because of the adherence of mussels to one another. Previous mathematical modelling has shown that this can lead to spatial patterning when it is coupled to the advection from the open sea of algae-the main food source for mussels in the Wadden Sea. A complicating factor in this process is that the advection of algae will actually oscillate with the tidal flow. This has been excluded from previous modelling studies, and the present paper concerns the implications of this oscillation for pattern formation. The authors initially consider piecewise constant ("square-tooth") oscillations in advection, which enables analytical investigation of the conditions for pattern formation. They then build on this to study the more realistic case of sinusoidal oscillations. Their analysis shows that future research on the details of pattern formation in mussel beds will require an in-depth understanding of how the tides affect long-range inhibition among mussels. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. 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.

  6. 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.

  7. Dewetting-mediated pattern formation inside the coffee ring

    NASA Astrophysics Data System (ADS)

    Li, Weibin; Lan, Ding; Wang, Yuren

    2017-04-01

    The rearrangement of particles in the final stage of droplet evaporation has been investigated by utilizing differential interference contrast microscopy and the formation mechanism of a network pattern inside a coffee ring has been revealed. A tailored substrate with a circular hydrophilic domain is prepared to obtain thin liquid film containing monolayer particles. Real-time bottom-view images show that the evolution of a dry patch could be divided into three stages: rupture initiation, dry patch expansion, and drying of the residual liquid. A growing number of dry patches will repeat these stages to form the network patterns inside the ringlike stain. It can be shown that the suction effect promotes the rupture of the liquid film and the formation of the dry patch. The particle-assembling process is totally controlled by the liquid film dewetting and dominated by the surface tension of the liquid film, which eventually determine the ultimate deposition patterns.

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

    NASA Astrophysics Data System (ADS)

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

    2012-07-01

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

  9. Dynamic Pattern Formation in Electron-Beam-Induced Etching [Emergent formation of dynamic topographic patterns in electron beam induced etching

    DOE PAGES

    Martin, Aiden A.; Bahm, Alan; Bishop, James; ...

    2015-12-15

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

  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. 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

  12. Modeling of pattern development during fibronectin nanofibril formation.

    PubMed

    Pompe, Tilo; Starruss, Jörn; Bobeth, Manfred; Pompe, Wolfgang

    2006-09-01

    Formation of fibrillar fibronectin networks is a major process during embryogenesis and tissue formation, but the molecular details of fibril assembly remain poorly understood. Based on current ideas of fibronectin fibrillogenesis, a stochastic model was developed to enlighten the mechanism of the formation of paired fibronectin nanofibrils by adherent endothelial cells, which has been observed recently. The development of fibronectin clusters and fibrils was investigated by means of Monte Carlo simulations, including diffusion-controlled aggregation and myosin-driven transport of fibronectin-integrin complexes in the vicinity of a focal adhesion. Different evolving growth patterns were summarized in a morphological diagram as a function of the fibronectin substrate and fibronectin-fibronectin interaction energies. The formation of paired nanofibrils was found to occur in a certain region of interaction parameters. Beyond this region branched fibronectin clusters as well as tear-off of fibronectin fibrils were observed.

  13. 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.

  14. Pattern formation of stationary transcellular ionic currents in Fucus

    PubMed Central

    Léonetti, M.; Dubois-Violette, E.; Homblé, F.

    2004-01-01

    Stationary and nonstationary spatiotemporal pattern formations emerging from the cellular electric activity are a common feature of biological cells and tissues. The nonstationary ones are well explained in the framework of the cable model. Inversely, the formation of the widespread self-organized stationary patterns of transcellular ionic currents remains elusive, despite their importance in cell polarization, apical growth, and morphogenesis. For example, the nature of the breaking symmetry in the Fucus zygote, a model organism for the experimental investigation of embryonic pattern formation, is still an open question. Using an electrodiffusive model, we report here an unexpected property of the cellular electric activity: a phase-space domain that gives rise to stationary patterns of transcellular ionic currents at finite wavelength. The cable model cannot predict this instability. In agreement with experiments, the characteristic time is an ionic diffusive one (<2 min). The critical radius is of the same order of magnitude as the cell radius (30 μm). The generic salient features are a global positive differential conductance, a negative differential conductance for one ion, and a difference between the diffusive coefficients. Although different, this mechanism is reminiscent of Turing instability. PMID:15232004

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. Clustering and Pattern Formation in Chemorepulsive Active Colloids.

    PubMed

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

    2015-12-18

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

  20. 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.

  1. 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

  2. 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.

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

    PubMed Central

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

    2015-01-01

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

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. Langmuir films of chiral lipid molecules and Pattern Formation .

    NASA Astrophysics Data System (ADS)

    Basnet, Prem; Mann, Elizabeth; Chaieb, Sahraoui

    2009-03-01

    Langmuir films of 1,2-bis(10,12 Tricosadiynoyl)-sn-Glycero-3-Phosphoethanolamine form spiral and target patterns when compressed between two movable barriers in a Langmuir trough above 30^0C, up to the chain-melting transition at ˜37^0C. The critical pressure, at which spirals appear, increases with temperature. The patterns themselves also depend on temperature, with single-armed spirals with many defects forming near 30^0C and defect-free target patterns at higher temperatures. The mechanism of spiral formation could be a competition among elasticity, chirality, and the boundary conditions at the core of the domains. Optical anisotropy and the growth rate of internal structures test this suggested mechanism. .

  14. 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.

  15. 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

  16. Rimming flows and pattern formation inside rapidly rotating cylinder

    NASA Astrophysics Data System (ADS)

    Polezhaev, Denis; Dyakova, Veronika; Kozlov, Victor

    2014-11-01

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

  17. Fluctuations and Pattern Formation in Fluids with Competing Interactions

    NASA Astrophysics Data System (ADS)

    Imperio, A.; Pini, D.; Reatto, L.

    2007-08-01

    One of the most interesting phenomena in the soft-matter realm consists in the spontaneous formation of super-molecular structures (microphases) in condition of thermodynamic equilibrium. A simple mechanism responsible for this self-organization or pattern formation is based on the competition between attractive and repulsive forces with different length scales in the microscopic potential, typically, a short-range attraction against a longer-range repulsion. We analyse this problem by simulations in 2D fluids. We find that, as the temperature is lowered, liquid-vapor phase separation is inhibited by the competition between attraction and repulsion, and replaced by a transition to non-homogeneous phases. The structure of the fluid shows well defined signatures of the presence of both intra- and inter-cluster correlations. Even when the competition between attraction and repulsion is not so strong as to cause microphase formation, it still induces large density fluctuations in a wide region of the temperature-density plane. In this large-fluctuation regime, pattern formation can be triggered by a weak external modulating field.

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

    SciTech Connect

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

    2009-06-02

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

  19. 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.

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. Pattern formation in diffusive excitable systems under magnetic flow effects

    NASA Astrophysics Data System (ADS)

    Mvogo, Alain; Takembo, Clovis N.; Ekobena Fouda, H. P.; Kofané, Timoléon C.

    2017-07-01

    We study the spatiotemporal formation of patterns in a diffusive FitzHugh-Nagumo network where the effect of electromagnetic induction has been introduced in the standard mathematical model by using magnetic flux, and the modulation of magnetic flux on membrane potential is realized by using memristor coupling. We use the multi-scale expansion to show that the system equations can be reduced to a single differential-difference nonlinear equation. The linear stability analysis is performed and discussed with emphasis on the impact of magnetic flux. It is observed that the effect of memristor coupling importantly modifies the features of modulational instability. Our analytical results are supported by the numerical experiments, which reveal that the improved model can lead to nonlinear quasi-periodic spatiotemporal patterns with some features of synchronization. It is observed also the generation of pulses and rhythmics behaviors like breathing or swimming which are important in brain researches.

  5. 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.

  6. The theory of pattern formation on directed networks.

    PubMed

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

    2014-07-31

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

  7. 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.

  8. Pattern formation in reverse smouldering combustion: a homogenisation approach

    NASA Astrophysics Data System (ADS)

    Rowland Ijioma, Ekeoma; Muntean, Adrian; Ogawa, Toshiyuki

    2013-04-01

    The development of fingering char patterns on the surface of porous thin materials has been investigated in the framework of reverse combustion. This macroscopic characteristic feature of combustible media has also been studied experimentally and through the use of phenomenological models. However, not much attention has been given to the behaviour of the emerging patterns based on characteristic material properties. Starting from a microscopic description of the combustion process, macroscopic models of reverse combustion that are derived by the application of the homogenisation technique are presented. Using proper scaling by means of a small scale parameter ɛ, the results of the formal asymptotic procedure are justified by qualitative multiscale numerical simulations at the microscopic and macroscopic levels. We consider two equilibrium models that are based on effective conductivity contrasts, in a simple adiabatic situation, to investigate the formation of unstable fingering patterns on the surface of a charred material. The behaviour of the emerging patterns is analysed using primarily the Péclet and Lewis numbers as control parameters.

  9. 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...

  10. 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.

  11. 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).

  12. 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.

  13. 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.

  14. 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

  15. G-jitter Effects on Transport and Pattern Formation

    NASA Technical Reports Server (NTRS)

    Schatz, Michael F.

    2003-01-01

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

  16. Predicting Bed Pattern Formation at Duck, North Carolina

    NASA Astrophysics Data System (ADS)

    Dodd, N.; van Leeuwen, S. M.; Calvete, D.; Tiessen, M.; Falques, A.

    2006-12-01

    The many field campaigns over the last twenty years have given us great insight into natural beach change. The advent of ARGUS imaging techniques has further contributed enormously to our knowledge of morphological pattern formation, such as cusps, mega-cusps, and transverse, oblique and crescentic bars. More recently work on understanding the physics of the formation of such morphodynamical features has led to the development of stability models, which have yielded insight into the initial growth, and the kinematics of these bed-forms. In this presentation we shall discuss the application of such a model (MORFO60: see Calvete et al, 2005) to observations from Duck, North Carolina. Initial results over about 5 months of data from Duck indicate that results (migration rates, and pattern spacings) are consistent with observations, and that meaningful predictions cluster around periods of high wave energy. Simulations for the whole of 1998 are presently underway. The purpose is to test the viability of the approach under field conditions.

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

    PubMed Central

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

    2013-01-01

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

  18. Principles of branch formation and branch patterning in Hydrozoa.

    PubMed

    Berking, Stefan

    2006-01-01

    The freshwater polyp Hydra produces buds which separate from the parent. Other Hydrozoa produce branches which remain connected to the parent, thus forming a colony. Some Hydrozoa grow by means of an organ that is like a shoot apical meristem. Others display a sympodial type of growth. In this article, I propose that these different types of branches are organized by a common pattern-forming system. This system has self-organizing properties. It causes branch tip formation and is kept active in the tip when the tip finally differentiates into a hypostome of a polyp. The system does not cause structure formation directly but rather, determines a tissue property called positional value, in such a way that a gradient of values forms in the tissue of the bud or branch. The local value determines the local morphodynamic processes, including differentiation of the hypostome (highest positional value), tentacles and basal disc and of the exoskeleton pattern along the shoot. A high positional value favors the onset of a new self-organizing process and by lateral inhibition, such a process prevents the initiation of a further process in its surroundings. Small quantitative differences in the range of the signals involved determine whether a bud or a branch forms and whether monopodial and sympodial growth follows.

  19. An overview on common aspects influencing the dissipation pattern of pesticides: a review.

    PubMed

    Farha, Waziha; Abd El-Aty, A M; Rahman, Md Musfiqur; Shin, Ho-Chul; Shim, Jae-Han

    2016-12-01

    The common aspects and processes influencing dissipation kinetics of pesticides are determinants of their fate in the environment. Nowadays, with increasing population, the demand for food and fodder crops has also increased. With the development in science and technology, the methods of controlling pests may improve, but the major role played by the environment cannot be altered, i.e. the environmental factors, climatic conditions, and geology of areas under cultivation. Plants play a crucial role in the dissipation kinetics, as they may vary in species and characteristics. Differences in physico-chemical properties, such as formulation, bioavailability, and efficacy of the pesticide, may result in variable dissipation patterns even under the same environmental conditions. While modelling the dissipation kinetics for any specific pesticide applied to any specific crop, each factor must be considered. This review focusses on the variability observed across common factors, i.e. environmental aspects, plant-associated facts, and observed characteristics of chemical substances, influencing pesticide dissipation.

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. 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.

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

    PubMed

    Potts, Jonathan R; Lewis, Mark A

    2016-01-01

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

  7. 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.

  8. 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.

  9. 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

  10. Effect of environment fluctuations on pattern formation of single species.

    PubMed

    da Silva, L A; Colombo, E H; Anteneodo, C

    2014-07-01

    System-environment interactions are intrinsically nonlinear and dependent on the interplay between many degrees of freedom. The complexity may be even more pronounced when one aims to describe biologically motivated systems. In that case, it is useful to resort to simplified models relying on effective stochastic equations. A natural consideration is to assume that there is a noisy contribution from the environment, such that the parameters that characterize it are not constant but instead fluctuate around their characteristic values. From this perspective, we propose a stochastic generalization of the nonlocal Fisher-KPP equation where, as a first step, environmental fluctuations are Gaussian white noises, both in space and time. We apply analytical and numerical techniques to study how noise affects stability and pattern formation in this context. Particularly, we investigate noise-induced coherence by means of the complementary information provided by the dispersion relation and the structure function.

  11. 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.

  12. 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

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

    NASA Astrophysics Data System (ADS)

    Metcalfe, Guy; Shattuck, Mark

    1996-02-01

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

  14. 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. 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.

  16. Stochastic Simulations of Pattern Formation in Excitable Media

    PubMed Central

    Vigelius, Matthias; Meyer, Bernd

    2012-01-01

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

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.

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

    PubMed

    Balavoine, Guillaume

    2014-01-01

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

  3. 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.

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

    PubMed

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

    2015-04-21

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

  5. 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.

  6. Morphological and quantitative aspects of nodule formation in hemolymph of the blowfly Chrysomya megacephala (Fabricius, 1794).

    PubMed

    Faraldo, A C; Gregório, E A; Lello, E

    2008-03-01

    Insects manifest effective immune responses that include both cellular and humoral components. Morphological and quantitative aspects of cellular and humoral cooperation during nodule formation in Chrysomya megacephala hemolymph against Saccharomyces cerevisae yeast cells were demonstrated for the first time. The analyses were performed in non-injected larvae (NIL), saline-injected larvae (SIL) and yeast-injected larvae (YIL). The hemolymph of injected groups was collected 0.5, 1, 2, 4, 12, 24, 36, or 48-h post-injection. Morphological aspects of YIL nodulation were investigated using transmission electron microscopy (TEM). Quantitative analyses consisted of total (THC) and differential hemocyte counts (DHC) in all the groups and total yeast count (TYC) in YIL, which were performed in an improved Neubauer chamber. Nodule formation was initiated at approximately 2-h post-injection. Twelve hours after the injection, TEM revealed the presence of an amorphous membrane, at the same time that circulating hemocyte number decreased significantly contrasting the increase of yeast number. Our results showed the ability of C. megacephala hemolymph to perform humoral encapsulation when hemocyte population is insufficient to eliminate the microorganisms, warranting consideration in future investigations on the relative roles played by cellular and humoral elements of innate immunity of this calliphorid.

  7. Fly ash-mediated formation of polychlorinated naphthalenes during secondary copper smelting and mechanistic aspects.

    PubMed

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

    2015-01-01

    Thermal experiments (at 250-450 °C for 10-240 min) on fly ash from secondary copper smelting process (SeCu) were performed to study the polychlorinated naphthalene (PCN) formation in the post-zone of a secondary copper smelter. Unexpectedly high concentrations of PCNs were formed. Total PCN concentrations and toxic equivalents were 47-104 and 44-80 times higher than the initial concentration and toxic equivalent, respectively. The thermal disposal of SeCu fly ash should therefore be reconsidered. The kinetic of each homolog was determined under different thermal conditions. Less chlorinated homologs favored 350 °C and more chlorinated homologs favored higher temperature. Most of the homologs reached an equilibrium of formation and degradation within 30 min, except octachloronaphthalene which did not appear to reach such an equilibrium even after 240 min. Chlorine substitution of the formed PCNs was identified and a similar pattern was found in chlorination products starting with naphthalene and chlorine. Furthermore, inorganic chlorine and unsubstituted naphthalene were found in the reaction products, confirming that the formation of naphthalene and the chlorination of that naphthalene could occur and could be suggested to be an important PCN formation route. A detailed formation pathway from naphthalene through octachloronaphthalene is proposed. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. Blood vessels pattern heparan sulfate gradients between their apical and basolateral aspects.

    PubMed

    Stoler-Barak, Liat; Moussion, Christine; Shezen, Elias; Hatzav, Miki; Sixt, Michael; Alon, Ronen

    2014-01-01

    A hallmark of immune cell trafficking is directional guidance via gradients of soluble or surface bound chemokines. Vascular endothelial cells produce, transport and deposit either their own chemokines or chemokines produced by the underlying stroma. Endothelial heparan sulfate (HS) was suggested to be a critical scaffold for these chemokine pools, but it is unclear how steep chemokine gradients are sustained between the lumenal and ablumenal aspects of blood vessels. Addressing this question by semi-quantitative immunostaining of HS moieties around blood vessels with a pan anti-HS IgM mAb, we found a striking HS enrichment in the basal lamina of resting and inflamed post capillary skin venules, as well as in high endothelial venules (HEVs) of lymph nodes. Staining of skin vessels with a glycocalyx probe further suggested that their lumenal glycocalyx contains much lower HS density than their basolateral extracellular matrix (ECM). This polarized HS pattern was observed also in isolated resting and inflamed microvascular dermal cells. Notably, progressive skin inflammation resulted in massive ECM deposition and in further HS enrichment around skin post capillary venules and their associated pericytes. Inflammation-dependent HS enrichment was not compromised in mice deficient in the main HS degrading enzyme, heparanase. Our results suggest that the blood vasculature patterns steep gradients of HS scaffolds between their lumenal and basolateral endothelial aspects, and that inflammatory processes can further enrich the HS content nearby inflamed vessels. We propose that chemokine gradients between the lumenal and ablumenal sides of vessels could be favored by these sharp HS scaffold gradients.

  13. Blood Vessels Pattern Heparan Sulfate Gradients between Their Apical and Basolateral Aspects

    PubMed Central

    Stoler-Barak, Liat; Moussion, Christine; Shezen, Elias; Hatzav, Miki; Sixt, Michael; Alon, Ronen

    2014-01-01

    A hallmark of immune cell trafficking is directional guidance via gradients of soluble or surface bound chemokines. Vascular endothelial cells produce, transport and deposit either their own chemokines or chemokines produced by the underlying stroma. Endothelial heparan sulfate (HS) was suggested to be a critical scaffold for these chemokine pools, but it is unclear how steep chemokine gradients are sustained between the lumenal and ablumenal aspects of blood vessels. Addressing this question by semi-quantitative immunostaining of HS moieties around blood vessels with a pan anti-HS IgM mAb, we found a striking HS enrichment in the basal lamina of resting and inflamed post capillary skin venules, as well as in high endothelial venules (HEVs) of lymph nodes. Staining of skin vessels with a glycocalyx probe further suggested that their lumenal glycocalyx contains much lower HS density than their basolateral extracellular matrix (ECM). This polarized HS pattern was observed also in isolated resting and inflamed microvascular dermal cells. Notably, progressive skin inflammation resulted in massive ECM deposition and in further HS enrichment around skin post capillary venules and their associated pericytes. Inflammation-dependent HS enrichment was not compromised in mice deficient in the main HS degrading enzyme, heparanase. Our results suggest that the blood vasculature patterns steep gradients of HS scaffolds between their lumenal and basolateral endothelial aspects, and that inflammatory processes can further enrich the HS content nearby inflamed vessels. We propose that chemokine gradients between the lumenal and ablumenal sides of vessels could be favored by these sharp HS scaffold gradients. PMID:24465652

  14. Characteristic aspects of formation of new particles during the growth of monosize silica seeds

    SciTech Connect

    Chen, S.L.; Dong, P.; Yang, G.H.; Yang, J.Y.

    1996-06-01

    To prepare large monodisperse silica particles, it is necessary to grow silica seeds without the formation of new silica particles. Described in this paper are investigations of the characteristic aspects of formation of new particles during the growth of silica seeds through the hydrolysis and condensation of tetraethylorthosilicate. Experimental results indicated that with silica particles as seeds, under a given set of reaction conditions and total external surface area of seeds, the smaller the seed particles, the fewer the newly formed particles during seed growth. The larger the total surface area of the seeds, the fewer the newly formed particles during growth with the same diameter particles as seeds. The critical surface area of nucleation increases linearly with the diameter of seeds. Addition of a small amount of NaCl to the breeding solution can dramatically decrease the number of newly formed particles. From these experimental findings, it is believed that under the conditions of formation of new particles, seed growth during the early stage is controlled by diffusion of colloid-unstable condensed species carrying electric charges capable of overcoming electrostatic repulsion.

  15. 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.

  16. 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.

  17. Spatial pattern formation facilitates eradication of infectious diseases

    PubMed Central

    Eisinger, Dirk; Thulke, Hans-Hermann

    2008-01-01

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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

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

    PubMed

    Ho, Jian-Wei; Wee, Qixun; Dumond, Jarrett; Tay, Andrew; Chua, Soo-Jin

    2013-12-01

    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.

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

    NASA Astrophysics Data System (ADS)

    Ho, Jian-Wei; Wee, Qixun; Dumond, Jarrett; Tay, Andrew; Chua, Soo-Jin

    2013-12-01

    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.

  5. 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

  6. 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.

  7. Various aspects, patterns and risk factors in breast cancer patients of Balochistan.

    PubMed

    Baloch, Abdul Hameed; Shuja, Jameela; Daud, Shakeela; Ahmed, Muneer; Ahmad, Adeel; Tareen, Mehrullah; Khan, Farah; Kakar, Muhammad Azam; Baloch, Dost Mohammad; Kakar, Naseebullah; Naseeb, Hafiz Khush; Ahmad, Jamil

    2012-01-01

    Breast cancer is the commonest malignancy of females throughout the world with one million new cases each year. In Pakistan, the burden of breast cancer disease is high with late stage presentation being a common feature, more than half being stage III or stage IV. The objective of this study was to study various aspects, patterns and risk factors in breast cancer patients of Balochistan. Present study was performed on 134 patients of breast cancer who were registered in CENAR. The patients were interviewed by providing a questionnaire. Informed consent was taken from all the patients who took part in this study after explanation of the study aims. Body mass index (BMI) was calculated andbiopsy reports were obtained from patients files. All the cases were classified with respect to age, gender, ethnic group (Baloch, Pashtoon, Punjabi, Afghani, Hazara) BMI, cancer type, cancer grade, hormonal status, side of the cancer, fertility and marital status. Out of 134 patients, the most common ethnic group was Pashtoon with a total of 42 and the common age group was 41-50 years with a total of 51. Invasive ductal carcinoma (IDC) was the most common type, accounting for in 128 patients (95.5%) followed by invasive lobular carcinoma (ILC). Pashtoon was the most common ethnic group, IDC was common type and most of the patients had an ER/PR positive hormonal status.

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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…

  13. 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.

  14. 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).

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

    PubMed

    Czirok, Andras

    2013-01-01

    How vascular networks assemble is a fundamental problem of developmental biology that also has medical importance. To explain the organizational principles behind vascular patterning, we must understand how can tissue level structures be controlled through cell behavior patterns like motility and adhesion that, in turn, are determined by biochemical signal transduction processes? We discuss the various ideas that have been proposed as mechanisms for vascular network assembly: cell motility guided by extracellular matrix alignment (contact guidance), chemotaxis guided by paracrine and autocrine morphogens, and multicellular sprouting guided by cell-cell contacts. All of these processes yield emergent patterns, thus endothelial cells can form an interconnected structure autonomously, without guidance from an external pre-pattern. © 2013 Wiley Periodicals, Inc.

  16. 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

  17. 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

  18. 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

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

    SciTech Connect

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

    1994-10-01

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

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

    NASA Astrophysics Data System (ADS)

    Koch, A. J.; Meinhardt, H.

    1994-10-01

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

  1. 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.

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

    PubMed

    Jones, Jeff

    2010-01-01

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

  3. Viscoelasticity and pattern formations in stock market indices

    NASA Astrophysics Data System (ADS)

    Gündüz, Güngör; Gündüz, Aydın

    2017-06-01

    The viscoelastic and thermodynamic properties of four stock indices, namely, DJI, Nasdaq-100, Nasdaq-Composite, and S&P were analyzed for a period of 30 years from 1986 to 2015. The asset values (or index) can be placed into Aristotelian `potentiality-actuality' framework by using scattering diagram. Thus, the index values can be transformed into vectorial forms in a scattering diagram, and each vector can be split into its horizontal and vertical components. According to viscoelastic theory, the horizontal component represents the conservative, and the vertical component represents the dissipative behavior. The related storage and the loss modulus of these components are determined and then work-like and heat-like terms are calculated. It is found that the change of storage and loss modulus with Wiener noise (W) exhibit interesting patterns. The loss modulus shows a featherlike pattern, whereas the storage modulus shows figurative man-like pattern. These patterns are formed due to branchings in the system and imply that stock indices do have a kind of `fine-order' which can be detected when the change of modulus values are plotted with respect to Wiener noise. In theoretical calculations it is shown that the tips of the featherlike patterns stay at negative W values, but get closer to W = 0 as the drift in the system increases. The shift of the tip point from W = 0 indicates that the price change involves higher number of positive Wiener number corrections than the negative Wiener. The work-like and heat-like terms also exhibit patterns but with different appearance than modulus patterns. The decisional changes of people are reflected as the arrows in the scattering diagram and the propagation path of these vectors resemble the path of crack propagation. The distribution of the angle between two subsequent vectors shows a peak at 90°, indicating that the path mostly obeys the crack path occurring in hard objects. Entropy mimics the Wiener noise in the evolution

  4. 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…

  5. Pattern Formations in Polymer-Molecular Motor Networks

    NASA Astrophysics Data System (ADS)

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

    2001-03-01

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

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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

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

    PubMed

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

    2015-01-01

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

  12. 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.

  13. Exploring archetypal dynamics of pattern formation in cellular flames

    NASA Astrophysics Data System (ADS)

    Stone, Emily

    2002-01-01

    The application of archetypal analysis to high-dimensional data arising from video-taped images is presented. Included in the analysis are intermittent regimes which have not been analyzed previously by other statistical methods such as principal component analysis (PCA). A hybrid PCA/archetypes technique has been developed to overcome the difficulties of applying archetypes to data sets with points living in a space of dimension higher than about 500. The advantages of the method lie in the creation of patterns typical of the set as a whole, and an expression of the dynamics in terms of these patterns. Archetypes are particularly useful in identifying intermittent regimes, where low energy events that might be missed by a severe principal component truncation are none-the-less crucial to understanding the dynamics. They are part of a suite of data analysis techniques that can be used on dynamic data sets (such as FFT, PCA and other spectral decompositions). This hybrid method extends the application of archetypes to spatio-temporal dynamics in two-dimensional patterns.

  14. 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.

  15. Pattern formation in Dictyostelium discoideum aggregates in confined microenvironments

    NASA Astrophysics Data System (ADS)

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

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

  16. 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.

  17. 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…

  18. 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…

  19. Sex-Specific Pattern Formation During Early Drosophila Development

    PubMed Central

    Manu; Ludwig, Michael Z.; Kreitman, Martin

    2013-01-01

    The deleterious effects of different X-chromosome dosage in males and females are buffered by a process called dosage compensation, which in Drosophila is achieved through a doubling of X-linked transcription in males. The male-specific lethal complex mediates this process, but is known to act only after gastrulation. Recent work has shown that the transcription of X-linked genes is also upregulated in males prior to gastrulation; whether it results in functional dosage compensation is not known. Absent or partial early dosage compensation raises the possibility of sex-biased expression of key developmental genes, such as the segmentation genes controlling anteroposterior patterning. We assess the functional output of early dosage compensation by measuring the expression of even-skipped (eve) with high spatiotemporal resolution in male and female embryos. We show that eve has a sexually dimorphic pattern, suggesting an interaction with either X-chromosome dose or the sex determination system. By manipulating the gene copy number of an X-linked transcription factor, giant (gt), we traced sex-biased eve patterning to gt dose, indicating that early dosage compensation is functionally incomplete. Despite sex-biased eve expression, the gene networks downstream of eve are able to produce sex-independent segmentation, a point that we establish by measuring the proportions of segments in elongated germ-band embryos. Finally, we use a whole-locus eve transgene with modified cis regulation to demonstrate that segment proportions have a sex-dependent sensitivity to subtle changes in Eve expression. The sex independence of downstream segmentation despite this sensitivity to Eve expression implies that additional autosomal gene- or pathway-specific mechanisms are required to ameliorate the effects of partial early dosage compensation. PMID:23410834

  20. 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

  1. 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

  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 in the Belousov-Zhabotinsky-PAMAM dendrimer system.

    PubMed

    Roncaglia, Diana I; Carballido-Landeira, Jorge; Muñuzuri, Alberto P

    2011-04-28

    The Belousov-Zhabotinsky reaction was studied under the influence of nanometric confinements induced by a complex polymer, the PAMAM-G4 dendrimers. They are well-defined in both molecular weight and architecture and are capable of molecular inclusion, making "unimolecular active micelles". The effect of such nanocompartments in the BZ reaction is analyzed by changing both the excitability and the concentration of the dendrimer, obtaining a wide range of behaviours, ranging from stationary Turing-like patterns to time dependent structures, such as jumping waves or packet waves.

  4. Pattern formation in a complex plasma in high magnetic fields.

    PubMed

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

    2011-05-27

    Low-pressure room-temperature neon, argon, krypton, and air plasmas were studied in magnetic fields up to flux densities of 2.3 T. Filaments appeared parallel to the magnetic field lines, and patterns such as spirals and concentric circles formed in the perpendicular direction. We link these effects to the magnetization of the ions. We also used a layer of embedded microparticles as probes in the plasma. Their motion changed dramatically from a collective rotation of the whole ensemble in moderate magnetic fields to a rotation in several small vortices centered at the filaments. © 2011 American Physical Society

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. [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)

  10. Pattern guided structure formation in polymer films of asymmetric blends

    NASA Astrophysics Data System (ADS)

    Raczkowska, J.; Bernasik, A.; Budkowski, A.; Cyganik, P.; Rysz, J.; Raptis, I.; Czuba, P.

    2006-03-01

    Two off-critical blends of poly(2-vinylpyridine) and polystyrene, 2:3 and 3:2 (w:w) PVP:PS, were spin-cast (with varied domain scale R) onto periodically ( λ = 4 μm) patterned substrate. The pattern consisted of two alternating symmetric stripes: Au attracting PVP and neutral self-assembled monolayer. The resulting droplet-type morphologies were recorded with Scanning Force Microscopy and examined with integral geometry approach. PVP-rich islands of the 2:3 PVP:PS films form, for a wide R/ λ range, strongly anisotropic morphologies. They show up, for R/ λ ˜ 0.5, a weak λ/2-substructure of smaller PVP droplets in addition to the domains periodic with λ. The 3:2 blend exhibits morphologies with dominant λ-structure of PVP ribbons, which encircle PS droplets. For R/ λ ˜ 0.5, smaller PS domains are also present but no λ/2-substructure is formed. The | χE|-values of droplet surface density are reduced, as compared to homogeneous substrate, for the 3:2 blend (with | χE| → 0 for R ˜ λ). This effect is absent for the 2:3 mixture.

  11. [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.

  12. [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.

  13. Pattern Formation of Bacterial Colonies by Escherichia coli

    NASA Astrophysics Data System (ADS)

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

    2009-07-01

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

  14. 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.

  15. 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

  16. Modeling pattern formation in hydra: a route to understanding essential steps in development.

    PubMed

    Meinhardt, Hans

    2012-01-01

    Modeling of pattern formation in hydra has revealed basic mechanisms that underlie the reproducible generation of complex and self-regulating patterns. Organizing regions can be generated by a local self-enhancing reaction that is coupled with an inhibitory effect of longer range. Such reactions enable pattern formation even in an initially almost homogeneous assembly of cells. A long-ranging feedback of the organizer onto the competence to perform the pattern-forming reaction stabilizes the polar axial pattern during growth and allows for regeneration with preserved polarity. Hypostome formation is assumed to be under the control of two positive feedback loops in which Wnt3 is a common element. In addition to the well-established loop employing beta-catenin, a second cell-local loop is involved, possibly with Brachyury as an additional component. This model accounts for the different expression patterns of beta-catenin and Wnt3. Wnt molecules are proposed to play a dual role, functioning as activators and, after processing, as inhibitors. Since Wnt genes code for complete pattern-forming systems, gene duplication and diversification lead to a family of genes whose expression regions have a precise relation to each other. Tentacle formation is an example of positioning a second pattern-forming system by medium-ranging activation and local exclusion exerted by the primary system. A model for bud formation suggests that a transient pre-bud signal is involved that initiates the formation of the foot of the bud, close to the normal foot, as well as close to the bud tip. Many dynamic regulations, as observed in classical and molecular observations, are reproduced in computer simulations. A case is made that hydra can be regarded as a living fossil, documenting an evolutionary early axis formation before trunk formation and bilaterality were invented. Animated simulations are available in the supplementary information accompanying this paper.

  17. Morphology-induced collective behaviors: dynamic pattern formation in water-floating elements.

    PubMed

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

    2012-01-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2005-01-01

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

  20. 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.

  1. Developmental waves in myxobacteria: A distinctive pattern formation mechanism

    NASA Astrophysics Data System (ADS)

    Igoshin, Oleg A.; Neu, John; Oster, George

    2004-10-01

    In early stages of their development, starving myxobacteria organize their motion to produce a periodic pattern of traveling cell density waves. These waves arise from coordination of individual cell reversals by contact signaling when they collide. Unlike waves generated by reaction-diffusion instabilities, which annihilate on collision, myxobacteria waves appear to pass through one another unaffected. Here we analyze a mathematical model of these waves developed earlier [Igoshin , Proc. Natl. Acad. Sci. USA 98, 14 913 (2001)]. The mechanisms which generate and maintain the density waves are clearly revealed by tracing the reversal loci of individual cells. An evolution equation of reversal point density is derived in the weak-signaling limit. Linear stability analysis determines parameters favorable for the development of the waves. Numerical solutions demonstrate the stability of the fully developed nonlinear waves.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

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

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

    PubMed Central

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

    2013-01-01

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

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. Analytic model for ring pattern formation by bacterial swarmers

    NASA Astrophysics Data System (ADS)

    Arouh, Scott

    2001-03-01

    We analyze a model proposed by Medvedev, Kaper, and Kopell (the MKK model) for ring formation in two-dimensional bacterial colonies of Proteus mirabilis. We correct the model to formally include a feature crucial of the ring generation mechanism: a bacterial density threshold to the nonlinear diffusivity of the MKK model. We numerically integrate the model equations, and observe the logarithmic profiles of the bacterial densities near the front. These lead us to define a consolidation front distinct from the colony radius. We find that this consolidation front propagates outward toward the colony radius with a nearly constant velocity. We then implement the corrected MKK equations in two dimensions and compare our results with biological experiment. Our numerical results indicate that the two-dimensional corrected MKK model yields smooth (rather than branched) rings, and that colliding colonies merge if grown in phase but not if grown out of phase. We also introduce a model, based on coupling the MKK model to a nutrient field, for simulating experimentally observed branched rings.

  1. 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.

  2. 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)

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

    NASA Astrophysics Data System (ADS)

    Schaffner, Stuart C.

    vital for spindle formation.

  4. Synergetic aspects of gas-discharge: lateral patterns in dc systems with a high ohmic barrier

    NASA Astrophysics Data System (ADS)

    Purwins, H.-G.; Stollenwerk, L.

    2014-12-01

    The understanding of self-organized patterns in spatially extended nonlinear dissipative systems is one of the most challenging subjects in modern natural sciences. Such patterns are also referred to as dissipative structures. We review this phenomenon in planar low temperature dc gas-discharge devices with a high ohmic barrier. It is demonstrated that for these systems a deep qualitative understanding of dissipative structures can be obtained from the point of view of synergetics. At the same time, a major contribution can be made to the general understanding of dissipative structures. The discharge spaces of the experimentally investigated systems, to good approximation, have translational and rotational symmetry by contraction. Nevertheless, a given system may exhibit stable current density distributions and related patterns that break these symmetries. Among the experimentally observed fundamental patterns one finds homogeneous isotropic states, fronts, periodic patterns, labyrinth structures, rotating spirals, target patterns and localized filaments. In addition, structures are observed that have the former as elementary building blocks. Finally, defect structures as well as irregular patterns are common phenomena. Such structures have been detected in numerous other driven nonlinear dissipative systems, as there are ac gas-discharge devices, semiconductors, chemical solutions, electrical networks and biological systems. Therefore, from the experimental observations it is concluded that the patterns in planar low temperature dc gas-discharge devices exhibit universal behavior. From the theoretical point of view, dissipative structures of the aforementioned kind are also referred to as attractors. The possible sets of attractors are an important characteristic of the system. The number and/or qualitative nature of attractors may change when changing parameters. The related bifurcation behavior is a central issue of the synergetic approach chosen in the present

  5. 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

  6. 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

  7. Beard infantile hemangioma and subglottic involvement: are median pattern and telangiectatic aspect the clue?

    PubMed

    Piram, M; Hadj-Rabia, S; Boccara, O; Couloigner, V; Hamel-Teillac, D; Bodemer, C

    2016-12-01

    Identification of patient at risk of subglottic infantile hemangioma (IH) is challenging because subglottic IH can grow fast and cause airway obstruction with a fatal course. To refine the cutaneous IH pattern at risk of subglottic IH. Prospective and retrospective review of patients with cutaneous IH involving the beard area. IHs were classified in the bilateral pattern group (BH) or in the unilateral pattern group (UH). Infantile hemangioma topography, subtype (telangiectatic or tuberous), ear, nose and throat (ENT) manifestations and subglottic involvement were recorded. Thirty-one patients (21 BH and 10 UH) were included during a 20-year span. Nineteen patients (16 BH and 3 UH) had subglottic hemangioma. BH and UH group overlap on the median pattern (tongue, gum, lips, chin and neck). Median pattern, particularly the neck area and telangiectatic subtype of IH were significantly associated with subglottic involvement. Patients presenting with telangiectatic beard IH localized on the median area need early ENT exploration. They should be treated before respiratory symptoms occur. © 2016 European Academy of Dermatology and Venereology.

  8. 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

  9. 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.

  10. 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…

  11. 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…

  12. Chemical and rheological aspects of gel formation in the California Mastitis Test.

    PubMed

    Whyte, David; Walmsley, Michael; Liew, Alvin; Claycomb, Rod; Mein, Graeme

    2005-02-01

    The rheological properties of the CMT gel were analysed. Data are presented to demonstrate that the gel is a non-homogenous, visco-elastic, non-Newtonian fluid with rheopectic, and rheodestructive behaviour. The fundamental chemistry of the CMT is reviewed and a modified theory of gel formation is presented. The implications of the rheological properties and modified theory of gel formation for an automatic sensor are discussed.

  13. Understanding the molecular aspects of oriental obesity pattern differentiation using DNA microarray.

    PubMed

    Hong, Sun Woo; Yoo, Jae-Wook; Bose, Shambhunath; Park, Jung-Hyun; Han, Kyungsun; Kim, Soyoun; Lim, Chi-Yeon; Kim, Hojun; Lee, Dong-Ki

    2015-10-19

    Human constitution, the fundamental basis of oriental medicine, is categorized into different patterns for a particular disease according to the physical, physiological, and clinical characteristics of the individuals. Obesity, a condition of metabolic disorder, is classified according to six patterns in oriental medicine, as follows: spleen deficiency syndrome, phlegm fluid syndrome, yang deficiency syndrome (YDS), food accumulation syndrome (FAS), liver depression syndrome (LDS), and blood stasis syndrome. In oriental medicine, identification of the disease pattern for individual obese patients is performed on the basis of differentiation in obesity syndrome index and, accordingly, personalized treatment is provided to the patients. The aim of the current study was to understand the obesity patterns in oriental medicine from the genomic point of view via determining the gene expression signature of obese patients using peripheral blood mononuclear cells as the samples. The study was conducted in 23 South Korean obese subjects (19 female and four male) with BMI ≥25 kg/m(2). Identification of oriental obesity pattern was based on the software-guided evaluation of the responses of the subjects to a questionnaire developed by the Korean Institute of Oriental Medicine. The expression profiles of genes were determined using DNA microarray and the level of transcription of genes of interest was further evaluated using quantitative real-time PCR (qRT-PCR). Gene clustering analysis of the microarray data from the FAS, LDS, and YDS subjects exhibited disease pattern-specific upregulation of expression of several genes in a particular cluster. Further analysis of transcription of selected genes using qRT-PCR led to identification of specific genes, including prostaglandin endoperoxide synthase 2, G0/G1 switch 2, carcinoembryonic antigen-related cell adhesion molecule 3, cystein-serine-rich nuclear protein 1, and interleukin 8 receptor, alpha which were highly expressed in

  14. Hypothetical way of pollen aperture patterning. 2. Formation of polycolpate patterns and pseudoaperture geometry.

    PubMed

    Pozhidaev

    2000-05-01

    Deviant forms of polycolpate pollen, differing from the typical pattern in the number and arrangement of apertures, are found to be similar in distantly related dicotyledon taxa. The range of variation of common and deviant aperture patterns may be arranged as a continuous series, which may be described as a gradual and geometrically regular transformation of the deviant form with a meridional circular colpus to one of the common polycolpate conditions. Similar series have been observed in the taxa with colporate and pseudocolpate pollen. All possible spatial isomers and their mirror symmetrical variants of the deviant polycolpate and polypseudocolpate pollen have been predicted in terms of the suggested regularities of aperture multiplication. Some of them have been identified in the samples studied.

  15. 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.

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

    PubMed

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

    2012-01-07

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

  17. 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

  18. 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

  19. Virtual patients for assessing medical students--important aspects when considering the introduction of a new assessment format.

    PubMed

    Waldmann, Uta-Maria; Gulich, Markus Sebastian; Zeitler, Hans-Peter

    2008-02-01

    A case-based online assessment tool has been accomplished at the University of Ulm by simulating consultations with virtual patients in General Practice setting. After a successful pilot study, more data on validity were needed as one important step when considering introducing this assessment format to replace the regular written course exam. Five distinct sources of validity evidence are addressed: content, response process, internal structure, relationship to other variables and consequences. An examination simulation was conducted including all students (147) of the General Practice course, scores of three virtual patient cases compared with the written course exam and data gathered regarding usability, acceptance, content and structural characteristics, and consequences. All five aspects were supported by collected data. Correlation to the written exam was moderate with r = 0.36, correlation between the cases higher with r = 0.50-0.56. Although a direct comparison of written course exams and dealing with virtual patients is difficult in many aspects and the study setting as an exam simulation caused confounders, this new assessment format is supported by many aspects of validity evidence. Solving virtual clinical scenarios addresses other abilities, skills and knowledge than traditional written exams and since "assessment drives learning" it could have positive implications on teaching and learning alike.

  20. 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

  1. Numerical simulation of the zebra pattern formation on a three-dimensional model

    NASA Astrophysics Data System (ADS)

    Jeong, Darae; Li, Yibao; Choi, Yongho; Yoo, Minhyun; Kang, Dooyoung; Park, Junyoung; Choi, Jaewon; Kim, Junseok

    2017-06-01

    In this paper, we numerically investigate the zebra skin pattern formation on the surface of a zebra model in three-dimensional space. To model the pattern formation, we use the Lengyel-Epstein model which is a two component activator and inhibitor system. The concentration profiles of the Lengyel-Epstein model are obtained by solving the corresponding reaction-diffusion equation numerically using a finite difference method. We represent the zebra surface implicitly as the zero level set of a signed distance function and then solve the resulting system on a discrete narrow band domain containing the zebra skin. The values at boundary are dealt with an interpolation using the closet point method. We present the numerical method in detail and investigate the effect of the model parameters on the pattern formation on the surface of the zebra model.

  2. 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.

  3. Impact of degree mixing pattern on consensus formation in social networks

    NASA Astrophysics Data System (ADS)

    Liu, Xiao Fan; Tse, Chi Kong

    The consensus formation process in a social network is affected by a number of factors. This paper studies how the degree mixing pattern of a social network affects the consensus formation process. A social network of more than 50,000 nodes was sampled from the online social services website Twitter. Nodes in the Twitter user network are grouped by their in-degrees and out-degrees. A degree mixing correlation is proposed to measure the randomness of the mixing pattern for each degree group. The DeGroot model is used to simulate the consensus formation processes in the network. Simulation suggests that the non-random degree mixing pattern of social networks can slow down the rate of consensus.

  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. 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.

  6. 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.

  7. Induction of secondary axis in hydra revisited: New insights into pattern formation

    PubMed Central

    Kadu, Vishal; S. Ghaskadbi, Saroj; Ghaskadbi, Surendra

    2012-01-01

    In 1909, several years before the famous `Organizer’ experiments of Spemann and Mangold, Ethel Browne demonstrated induction of a secondary axis in hydra by grafting a hypostome. Based on this and subsequent work, in the late sixties, Lewis Wolpert proposed the theory of morphogen gradients and positional information. We have studied secondary axis induction by hypostome and foot tissue using three species of hydra as well as transgenic, GFP-expressing lines of hydra. We have found that pieces of hypostome and complete foot of a donor hydra can induce a secondary axis all along (in upper, middle or lower parts of) the body column of a host hydra, both within and across species with comparable rates. Thus, contrary to the available literature, our results show that the host hypostome does not completely inhibit the induction of a secondary axis. The length of the induced axis though is determined by the position of the graft. By using GFP-expressing lines of hydra we have demonstrated that host ectodermal and endodermal cells actively contribute to the secondary axis. On comparison, the hypostome was found to be a stronger and dominant Organizer than the foot. Foot grafting experiments show a transient increase in the host length as well as the distance between the two Organizers. The length becomes normal once the grafted foot reaches the budding zone. Our work brings out several new aspects of the role of positional cues in pattern formation in hydra that can be now be explored at cellular and molecular levels. PMID:24551754

  8. 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.

  9. The mechanism of Turing pattern formation in a positive feedback system with cross diffusion

    NASA Astrophysics Data System (ADS)

    Yang, Xiyan; Liu, Tuoqi; Zhang, Jiajun; Zhou, Tianshou

    2014-03-01

    In this paper, we analyze a reaction-diffusion (R-D) system with a double negative feedback loop and find cases where self diffusion alone cannot lead to Turing pattern formation but cross diffusion can. Specifically, we first derive a set of sufficient conditions for Turing instability by performing linear stability analysis, then plot two bifurcation diagrams that specifically identify Turing regions in the parameter phase plane, and finally numerically demonstrate representative Turing patterns according to the theoretical predictions. Our analysis combined with previous studies actually implies an interesting fact that Turing patterns can be generated not only in a class of monostable R-D systems where cross diffusion is not necessary but also in a class of bistable R-D systems where cross diffusion is necessary. In addition, our model would be a good candidate for experimentally testing Turing pattern formation from the viewpoint of synthetic biology.

  10. 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.

  11. 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.

  12. Double helix formation of oligoresorcinols in water: thermodynamic and kinetic aspects.

    PubMed

    Goto, Hidetoshi; Furusho, Yoshio; Miwa, Kazuhiro; Yashima, Eiji

    2009-04-08

    We previously reported that the oligoresorcinols formed double-stranded helices in neutral water through interstrand aromatic interactions. In the present study, we synthesized a new series of oligomers from the 2mer to the 15mer to explore the thermodynamics, kinetics, and mechanism of the double helix formation of the oligoresorcinols in water. The double helix formation was dependent on the chain length of the oligomers and significantly affected by solvent, pH, salt, and temperature. The free energy change (-DeltaG) for the double helix formation linearly increased with the chain length from the 4mer to the 11mer (DeltaDeltaG = -0.94 kcal mol(-1) unit(-1)), whereas it did not change for the oligomers longer than the 11mer. The van't Hoff analysis of the 9mer revealed that the double helix formation was an enthalpically driven process (DeltaH = -27 +/- 1.5 kcal mol(-1) and DeltaS = -70 +/- 5 cal mol(-1) K(-1)), which was consistent with the upfield shifts in the (1)H NMR spectra and the hypochromicity of the absorption spectra as a result of the interstrand aromatic interactions in water. Furthermore, the kinetic analysis of the chain exchange reaction between the double helices of the optically active and optically inactive 11mers revealed a small DeltaS(double dagger), suggesting that the chain exchange proceeds not via the dissociation-association pathway, but via the direct exchange pathway.

  13. Discovering local patterns of co - evolution: computational aspects and biological examples

    PubMed Central

    2010-01-01

    Background Co-evolution is the process in which two (or more) sets of orthologs exhibit a similar or correlative pattern of evolution. Co-evolution is a powerful way to learn about the functional interdependencies between sets of genes and cellular functions and to predict physical interactions. More generally, it can be used for answering fundamental questions about the evolution of biological systems. Orthologs that exhibit a strong signal of co-evolution in a certain part of the evolutionary tree may show a mild signal of co-evolution in other branches of the tree. The major reasons for this phenomenon are noise in the biological input, genes that gain or lose functions, and the fact that some measures of co-evolution relate to rare events such as positive selection. Previous publications in the field dealt with the problem of finding sets of genes that co-evolved along an entire underlying phylogenetic tree, without considering the fact that often co-evolution is local. Results In this work, we describe a new set of biological problems that are related to finding patterns of local co-evolution. We discuss their computational complexity and design algorithms for solving them. These algorithms outperform other bi-clustering methods as they are designed specifically for solving the set of problems mentioned above. We use our approach to trace the co-evolution of fungal, eukaryotic, and mammalian genes at high resolution across the different parts of the corresponding phylogenetic trees. Specifically, we discover regions in the fungi tree that are enriched with positive evolution. We show that metabolic genes exhibit a remarkable level of co-evolution and different patterns of co-evolution in various biological datasets. In addition, we find that protein complexes that are related to gene expression exhibit non-homogenous levels of co-evolution across different parts of the fungi evolutionary line. In the case of mammalian evolution, signaling pathways that are

  14. 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.

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

    PubMed

    Radlanski, Ralf J; Renz, Herbert

    2007-01-01

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

  16. 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.

  17. 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.

  18. 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.

  19. Chemical aspects of iron colloid plugging in quartz sands and implications for formation damage

    SciTech Connect

    Potter, J.M.; Dibble, W.E.

    1985-09-01

    A research direction having great potential for better understanding of formation damage is the influence of colloid plugging on fluid flow behavior in porous media. Using flow through experimental equipment, we have explored the dependence of the degree of ferric oxyhydroxide colloid plugging of quartz sand packs on the solution pH and anion type at a constant temperature of 208/sup 0/F (97.7/sup 0/C). At a pH of 5, permeability reductions were greatest in the order PO/sup 3//sub 4/-, SO/sup 2//sub 4/-, and Cl-. This order was reversed at a pH of 9. The results suggest that plugging occurs by two fundamentally different mechanisms. First, flocculation/coagulation of the ferric hydroxide leads to formation of filter cake in the low-pH case. Second, colloid/quartz surface interaction produces a more uniform accumulation of colloid throughout the core at higher pH's.

  20. Theoretical aspects of fluoride air contaminant formation in aluminium smelter potrooms.

    PubMed

    L'vov, Boris V; Polzik, Leonid K; Weinbruch, Stephan; Ellingsen, Dag G; Thomassen, Yngvar

    2005-05-01

    The amount of particulate fluorides evolved from aluminium electrolysis cells is not entirely accounted for by the fluorides entrained in the anode gas. The largest additional source of particulate fluoride formation is by direct evaporation of fluorides into the anode gas stream and subsequent condensation on the drops of electrolyte generated in the process of bubble burst. A theoretical model was used for the calculation of the main physical parameters responsible for the formation of particle nuclei when the hot anode-gas is mixed with ambient air. The results of these calculations are in agreement with experimental observations reported in the literature. In particular, the size distribution, composition and morphology of the nano-particles support the theory of a vapour condensation mechanism under conditions of extreme supersaturation, but further studies are necessary.

  1. 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.

  2. 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.

  3. Design and process aspects of laboratory scale SCF particle formation systems.

    PubMed

    Vemavarapu, Chandra; Mollan, Matthew J; Lodaya, Mayur; Needham, Thomas E

    2005-03-23

    Consistent production of solid drug materials of desired particle and crystallographic morphologies under cGMP conditions is a frequent challenge to pharmaceutical researchers. Supercritical fluid (SCF) technology gained significant attention in pharmaceutical research by not only showing a promise in this regard but also accommodating the principles of green chemistry. Given that this technology attained commercialization in coffee decaffeination and in the extraction of hops and other essential oils, a majority of the off-the-shelf SCF instrumentation is designed for extraction purposes. Only a selective few vendors appear to be in the early stages of manufacturing equipment designed for particle formation. The scarcity of information on the design and process engineering of laboratory scale equipment is recognized as a significant shortcoming to the technological progress. The purpose of this article is therefore to provide the information and resources necessary for startup research involving particle formation using supercritical fluids. The various stages of particle formation by supercritical fluid processing can be broadly classified into delivery, reaction, pre-expansion, expansion and collection. The importance of each of these processes in tailoring the particle morphology is discussed in this article along with presenting various alternatives to perform these operations.

  4. Free boundary problem for cell protrusion formations: theoretical and numerical aspects.

    PubMed

    Gallinato, Olivier; Ohta, Masahito; Poignard, Clair; Suzuki, Takashi

    2017-08-01

    In this paper, a free boundary problem for cell protrusion formation is studied theoretically and numerically. The cell membrane is precisely described thanks to a level set function, whose motion is due to specific signalling pathways. The aim is to model the chemical interactions between the cell and its environment, in the process of invadopodia or pseudopodia formation. The model consists of Laplace equation with Dirichlet condition inside the cell coupled to Laplace equation with Neumann condition in the outer domain. The actin polymerization is accounted for as the gradient of the inner signal, which drives the motion of the interface. We prove the well-posedness of our free boundary problem under a sign condition on the datum. This criterion ensures the consistency of the model, and provides conditions to focus on for any enrichment of the model. We then propose a new first order Cartesian finite-difference method to solve the problem. We eventually exhibit the main biological features that can be accounted for by the model: the formation of thin and elongated protrusions as for invadopodia, or larger protrusion as for pseudopodia, depending on the source term in the equation. The model provides the theoretical and numerical grounds for single cell migration modeling, whose formulation is valid in 2D and 3D. In particular, specific chemical reactions that occurred at the cell membrane could be precisely described in forthcoming works.

  5. 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.

  6. 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.

  7. Influence of oscillatory centrifugal forces on the mechanism of Turing pattern formation

    NASA Astrophysics Data System (ADS)

    Guiu-Souto, Jacobo; Muñuzuri, Alberto P.

    2015-01-01

    Constantly acting centrifugal forces on Turing pattern forming systems have been observed to induce orientation and wavelength changes on Turing structures. Here, we will consider a periodic modulation of such centrifugal forces and their effects on pattern formation. Depending on the oscillation period the system exhibits a wide variety of stationary (stripes, H0, etc.) or nonstationary patterns (black eyes, etc.), as well as transitions and instabilities such as Eckhaus, zigzag, etc. In this paper, a detailed description of the different patterns and patterning mechanisms will be described and understood within the previous context. The system considered is the Belousov-Zhabotinsky reaction encapsulated in AOT micelles modeled by the adapted version of the Oregonator model.

  8. 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.

  9. 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

  10. 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…

  11. 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.

  12. 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.

  13. 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…

  14. 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.

  15. 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.

  16. 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…

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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

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

    SciTech Connect

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

    2016-08-15

    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.

  4. Two-dimensionality of yeast colony expansion accompanied by pattern formation.

    PubMed

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

    2014-12-01

    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.

  5. 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

  6. 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.

  7. Pattern of socio-economic and health aspects among TB patients and controls.

    PubMed

    Kapoor, A K; Deepani, Vijit; Dhall, Meenal; Kapoor, Satwanti

    2016-10-01

    Socio-economic and health-related factors have a significant impact on tuberculosis (TB) incidence among population residing in resource-scare settings. To evaluate the pattern of socio-economic and health-related factors among TB patients and control in Delhi, India. The present cross-sectional study was performed among 893 TB patients (or cases) and 333 healthy disease-free controls. The data for the present study was obtained from several district TB centres in north, west and south Delhi. The collected data was edited, coded and statistical analysed with the help of SPSS 20.0 version. Illiteracy and primary education were significant risk factors being associated with a TB. Rented housing condition had an odds ratio (OR) of 1.4 (95% confidence interval [CI]: 1.09-1.89) compared to owned housing condition. 3-5 individuals per room were 3 times more likely to be associated with a case of TB (95% CI: 2.49-4.41). Migrant individuals were 13 times more likely to be associated with a case of TB (95% CI: 8.77-19.78) in comparison to settled population. Daily consumption of non-vegetarian food also significantly contributed to case of TB with an OR of 3.4 (95% CI: 2.51-4.72). Loss of appetite and family TB served as significant health-related factors associated with TB risk. Lower educational status, rented household, individuals per room (as a measure of overcrowding) and migratory status served as prominent risk factors for TB disease. Preference and frequency of non-vegetarian food being consumed, night sweating, weight loss, loss of appetite, earlier TB and family TB were principle health-related risk factors associated with TB disease. Copyright © 2016 Tuberculosis Association of India. Published by Elsevier B.V. All rights reserved.

  8. 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

  9. 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.

  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. Geologic and metallogenic aspects concerning the Nahuelbuta mountains banded iron formation, Chile

    NASA Astrophysics Data System (ADS)

    Oyarzún, R.; Clemmey, H.; Collao, S.

    1986-07-01

    Paleozoic banded-iron-formation (BIF) deposits occur within the Nahuelbuta-Queule Complex (south central Chile) which hosts the following stratigraphic units: Cabo Tirúa (green schists, mica schists, and metacherts), Lleu-Lleu (iron-bearing metacherts, mica schists, and serpentinites), and Colcura (metagraywackes and metapelites). The lithological, structural, and geochemical characteristics of the Lleu-Lleu and Cabo Tirúa units indicate that they were part of a tectonic mélange accreted to the South American paleocontinent during the Paleozoic. BIF ores are restricted to the Lleu-Lleu metacherts and are characterized by oxide-silicate-sulfide BIF facies. The iron-bearing metacherts present mineralogical and geochemical characteristics close to the volcanogenic BIF types and are thought to have been formed by submarine volcanic exhalative activity.

  12. 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.

  13. Molecular aspects of polyene- and sterol-dependent pore formation in thin lipid membranes.

    PubMed

    Dennis, V W; Stead, N W; Andreoli, T E

    1970-03-01

    Amphotericin B modifies the permeability properties of thin lipid membranes formed from solutions containing sheep red cell phospholipids and cholesterol. At 10(-6)M amphotericin B, the DC membrane resistance fell from approximately 10(8) to approximately 10(2) ohm-cm(2), and the membranes became Cl(-)-, rather than Na(+)-selective; the permeability coefficients for hydrophilic nonelectrolytes increased in inverse relationship to solute size, and the rate of water flow during osmosis increased 30-fold. These changes may be rationalized by assuming that the interaction of amphotericin B with membrane-bound sterol resulted in the formation of aqueous pores. N-acetylamphotericin B and the methyl ester of N-acetylamphotericin B, but not the smaller ring compounds, filipin, rimocidin, and PA-166, produced comparable permeability changes in identical membranes, and amphotericin B and its derivatives produced similar changes in the properties of membranes formed from phospholipid-free sterol solutions. However, amphotericin B did not affect ionic selectivity or water and nonelectrolyte permeability in membranes formed from solutions containing phospholipids and no added cholesterol, or when cholesterol was replaced by either cholesterol palmitate, dihydrotachysterol, epicholesterol, or Delta5-cholesten-3-one. Phospholipid-free sterol membranes exposed to amphotericin B or its derivatives were anion-selective, but the degree of Cl(-) selectivity varied among the compounds, and with the aqueous pH. The data are discussed with regard to, first, the nature of the polyene-sterol interactions which result in pore formation, and second, the functional groups on amphotericin B responsible for membrane anion selectivity.

  14. Molecular Aspects of Polyene- and Sterol-Dependent Pore Formation in Thin Lipid Membranes

    PubMed Central

    Dennis, Vincent W.; Stead, Nancy W.; Andreoli, Thomas E.

    1970-01-01

    Amphotericin B modifies the permeability properties of thin lipid membranes formed from solutions containing sheep red cell phospholipids and cholesterol. At 10-6 M amphotericin B, the DC membrane resistance fell from ≈108 to ≈102 ohm-cm2, and the membranes became Cl--, rather than Na+-selective; the permeability coefficients for hydrophilic nonelectrolytes increased in inverse relationship to solute size, and the rate of water flow during osmosis increased 30-fold. These changes may be rationalized by assuming that the interaction of amphotericin B with membrane-bound sterol resulted in the formation of aqueous pores. N-acetylamphotericin B and the methyl ester of N-acetylamphotericin B, but not the smaller ring compounds, filipin, rimocidin, and PA-166, produced comparable permeability changes in identical membranes, and amphotericin B and its derivatives produced similar changes in the properties of membranes formed from phospholipid-free sterol solutions. However, amphotericin B did not affect ionic selectivity or water and nonelectrolyte permeability in membranes formed from solutions containing phospholipids and no added cholesterol, or when cholesterol was replaced by either cholesterol palmitate, dihydrotachysterol, epicholesterol, or Δ5-cholesten-3-one. Phospholipid-free sterol membranes exposed to amphotericin B or its derivatives were anion-selective, but the degree of Cl- selectivity varied among the compounds, and with the aqueous pH. The data are discussed with regard to, first, the nature of the polyene-sterol interactions which result in pore formation, and second, the functional groups on amphotericin B responsible for membrane anion selectivity. PMID:4938534

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

    NASA Astrophysics Data System (ADS)

    Srivastava, Rohit; Srivastava, P. K.

    2014-03-01

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

  16. 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

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

    PubMed

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

    2008-11-17

    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. 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. 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 sub-networks in larger networks

  18. 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. © 2016 Elsevier Inc. All rights reserved.

  19. 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.

  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. 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.

  2. 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

  3. 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.

  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. Toll ligand Spätzle3 controls melanization in the stripe pattern formation in caterpillars.

    PubMed

    KonDo, Yûsuke; Yoda, Shinichi; Mizoguchi, Takayuki; Ando, Toshiya; Yamaguchi, Junichi; Yamamoto, Kimiko; Banno, Yutaka; Fujiwara, Haruhiko

    2017-08-01

    A stripe pattern is an aposematic or camouflage coloration often observed among various caterpillars. However, how this ecologically important pattern is formed is largely unknown. The silkworm dominant mutant Zebra (Ze) has a black stripe in the anterior margin of each dorsal segment. Here, fine linkage mapping of 3,135 larvae revealed a 63-kbp region responsible for the Ze locus, which contained three candidate genes, including the Toll ligand gene spätzle3 (spz-3). Both electroporation-mediated ectopic expression and RNAi analyses showed that, among candidate genes, only processed spz-3 induced melanin pigmentation and that Toll-8 was the candidate receptor gene of spz-3 This Toll ligand/receptor set is also involved in melanization of other mutant Striped (p(S) ), which has broader stripes. Additional knockdown of 5 other spz family and 10 Toll-related genes caused no drastic change in the pigmentation of either mutant, suggesting that only spz-3/Toll-8 is mainly involved in the melanization process rather than pattern formation. The downstream pigmentation gene yellow was specifically up-regulated in the striped region of the Ze mutant, but spz-3 showed no such region-specific expression. Toll signaling pathways are known to be involved in innate immunity, dorsoventral axis formation, and neurotrophic functions. This study provides direct evidence that a Toll signaling pathway is co-opted to control the melanization process and adaptive striped pattern formation in caterpillars.

  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. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  14. 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.

  15. 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.

  16. 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.

  17. A new computational approach to simulate pattern formation in Paenibacillus dendritiformis bacterial colonies

    NASA Astrophysics Data System (ADS)

    Tucker, Laura Jane

    Under the harsh conditions of limited nutrient and hard growth surface, Paenibacillus dendritiformis in agar plates form two classes of patterns (morphotypes). The first class, called the dendritic morphotype, has radially directed branches. The second class, called the chiral morphotype, exhibits uniform handedness. The dendritic morphotype has been modeled successfully using a continuum model on a regular lattice; however, a suitable computational approach was not known to solve a continuum chiral model. This work details a new computational approach to solving the chiral continuum model of pattern formation in P. dendritiformis. The approach utilizes a random computational lattice and new methods for calculating certain derivative terms found in the model.

  18. 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.

  19. 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

  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. 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.

  2. 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.

  3. Self-organized pattern formation at organic-inorganic interfaces during deposition: Experiment versus modeling

    NASA Astrophysics Data System (ADS)

    Szillat, F.; Mayr, S. G.

    2011-09-01

    Self-organized pattern formation during physical vapor deposition of organic materials onto rough inorganic substrates is characterized by a complex morphological evolution as a function of film thickness. We employ a combined experimental-theoretical study using atomic force microscopy and numerically solved continuum rate equations to address morphological evolution in the model system: poly(bisphenol A carbonate) on polycrystalline Cu. As the key ingredients for pattern formation, (i) curvature and interface potential driven surface diffusion, (ii) deposition noise, and (iii) interface boundary effects are identified. Good agreement of experiments and theory, fitting only the Hamaker constant and diffusivity within narrow physical parameter windows, corroborates the underlying physics and paves the way for computer-assisted interface engineering.

  4. Collective Behavior of Chiral Active Matter: Pattern Formation and Enhanced Flocking

    NASA Astrophysics Data System (ADS)

    Liebchen, Benno; Levis, Demian

    2017-08-01

    We generalize the Vicsek model to describe the collective behavior of polar circle swimmers with local alignment interactions. While the phase transition leading to collective motion in 2D (flocking) occurs at the same interaction to noise ratio as for linear swimmers, as we show, circular motion enhances the polarization in the ordered phase (enhanced flocking) and induces secondary instabilities leading to structure formation. Slow rotations promote macroscopic droplets with late time sizes proportional to the system size (indicating phase separation) whereas fast rotations generate patterns consisting of phase synchronized microflocks with a controllable characteristic size proportional to the average single-particle swimming radius. Our results defy the viewpoint that monofrequent rotations form a vapid extension of the Vicsek model and establish a generic route to pattern formation in chiral active matter with possible applications for understanding and designing rotating microflocks.

  5. 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

  6. Geochemical Aspects of Formation of Large Oil Deposits in the Volga-Ural Sedimentary Basin

    NASA Astrophysics Data System (ADS)

    Plotnikova, I.; Nosova, F.; Pronin, N.; Nosova, J.; Budkevich, T.

    2012-04-01

    C35/hC34, GAM / HOP, S27/S28/S29 (steranes), DIA / REG, Ts / Tm, MOR / HOP, NOR / HOP, TET / TRI, C29SSR, C29BBAA, C31HSR, S30STER, TRI / PENT, TRI / HOP. Comparison in the rock-oil system was performed primarily according to the parameters indicating the depositional environment of the source rock that contains syngenetic DOM - according to the coefficients that determine lithological conditions for the formation of the supposed oil-source bed strata (DIA / REG, Ts / Tm, NOR / HOP, TRI / HOP and STER / PENT). Biomarker ratios indicate a different type of sedimentation basins. Sediments, which accumulated DOM from Semilukskiy horizon, can be characterized by low clay content, or its absence, that is consistent with the carbonate type of cut of the horizon. The bacterial material that was accumulated under reducing conditions of sedimentation appeared to be the source of syngenetic OM. Chemofossils found in oils from Pashiyskiy horizon are typical of sedimentary strata that contain clay - for clastic rocks, which in the study area are mainly represented by deposits and Eyfel Givetian layers of the Middle Devonian and lowfransk substage of the Upper Devonian. The study of correlations obtained for the different coefficients of OM and oils showed that only the relationships between Ts/Tm and DIA/REG and between NOR/HOP and TRI/HOP are characteristic of close, almost similar values of correlation both for the dispersed organic matter and for oil. In all other cases, the character of the correlation of OM is significantly different from that of oil. The differences in values and ranges of biomarker ratios as well as the character of their correlation indicates the absence of genetic connection between the oil from Pashiyskiy horizon for the dispersed organic matter from Semilukskiy horizon. This conclusion is based on the study of five biomarker parameters (DIA/REG, Ts/Tm, NOR/HOP, TRI/HOP and STER/PENT). The research results described in the article clearly indicate the

  7. 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.

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

    PubMed Central

    Potts, Jonathan R.; Lewis, Mark A.

    2016-01-01

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

  10. 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.

  11. 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.

  12. 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.

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

    PubMed

    Chan, Pak Yuen; Goldenfeld, Nigel

    2007-10-01

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

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

    NASA Astrophysics Data System (ADS)

    Chan, Pak Yuen; Goldenfeld, Nigel

    2007-10-01

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

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

    PubMed

    Potts, Jonathan R; Lewis, Mark A

    2016-05-01

    Mechanistic home range analysis (MHRA) is a highly effective tool for understanding spacing patterns of animal populations. It has hitherto focused on populations where animals defend their territories by communicating indirectly, e.g. via scent marks. However, many animal populations defend their territories using direct interactions, such as ritualized aggression. To enable application of MHRA to such populations, we construct a model of direct territorial interactions, using linear stability analysis and energy methods to understand when territorial patterns may form. We show that spatial memory of past interactions is vital for pattern formation, as is memory of 'safe' places, where the animal has visited but not suffered recent territorial encounters. Additionally, the spatial range over which animals make decisions to move is key to understanding the size and shape of their resulting territories. Analysis using energy methods, on a simplified version of our system, shows that stability in the nonlinear system corresponds well to predictions of linear analysis. We also uncover a hysteresis in the process of territory formation, so that formation may depend crucially on initial space-use. Our analysis, in one dimension and two dimensions, provides mathematical groundwork required for extending MHRA to situations where territories are defended by direct encounters. © 2016 The Author(s).

  16. Modeling and interpreting speckle pattern formation in swept-source optical coherence tomography (Conference Presentation)

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

    We report on the development of a unified Monte-Carlo based computational model for exploring speckle pattern formation in swept-source optical coherence tomography (OCT). OCT is a well-established optical imaging modality capable of acquiring cross-sectional images of turbid media, including biological tissues, utilizing back scattered low coherence light. The obtained OCT images include characteristic features known as speckles. Currently, there is a growing interest to the OCT speckle patterns due to their potential application for quantitative analysis of medium's optical properties. Here we consider the mechanisms of OCT speckle patterns formation for swept-source OCT approaches and introduce further developments of a Monte-Carlo based model for simulation of OCT signals and images. The model takes into account polarization and coherent properties of light, mutual interference of back-scattering waves, and their interference with the reference waves. We present a corresponding detailed description of the algorithm for modeling these light-medium interactions. The developed model is employed for generation of swept-source OCT images, analysis of OCT speckle formation and interpretation of the experimental results. The obtained simulation results are compared with selected analytical solutions and experimental studies utilizing various sizes / concentrations of scattering microspheres.

  17. 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.

  18. 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

  19. Experimental investigation of the dynamics of spontaneous pattern formation during dendritic ice crystal growth

    NASA Astrophysics Data System (ADS)

    Tirmizi, Shakeel H.; Gill, William N.

    1989-06-01

    The dynamics of spontaneous pattern formation are studied experimentally by observing and recording the evolution of ice crystal patterns which grow freely in a supercooled melt. The sequence of evolution to dendrites is recorded in real time using cine-micrography. In the range of subcoolings from 0.06 to 0.29°C, all the patterns evolved as follows: Smooth disk → Perturbed disk → Disk dendrite → Partially developed dendrite → Fully developed dendrite. The initial smooth disk, the main branch and the side branches all developed perturbations beyond a critical size which depends on the subcooling. The combined effect of the destabilizing thermal gradients ahead of the growing crystal and the stabilizing Gibbs-Thompson capillarity effect dictates the critical size of the unstable structures in terms of the mean curvature of the interface. Detailed analysis of the evolving patterns was done using digital image analysis on the PRIME computer to determine both the manner in which the dendritic growth process replicates itself and the role which the shape and the movement of the interface play in the pattern formation process. Total arc length ST, total area A and the complexity ratio ξ = ST⧸√ A of evolving patterns were computed as a function of time and undercooling for each crystal image. These results permitted us to make some comparisons with theoretical models on pattern evolution. Three distinct phases of evolution were identified: the initial phase when the crystal structure is smooth and free of any perturbations and the complexity ratio is almost a constant, an intermediate phase when the crystal structure develops perturbations which grow quickly in number and in size and the complexity ratio increases rapidly and a final phase when the pattern approaches that of a fully developed dendrite which, on a global scale grows in a shape-perserving manner and has a slowly increasing complexity ratio which seems to approach an asymptote. Two factors were

  20. 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.

  1. 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.

  2. 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. Copyright © 2014, American Association for the Advancement of Science.

  3. 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

  4. 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

  5. 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

  6. 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.

  7. 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

  8. HGF, EGF and Dexamethasone induced gene expression patterns during formation of tissue in hepatic organoid cultures

    PubMed Central

    Michalopoulos, George K.; Bowen, William C.; Mulé, Karen; Luo, Jianhua

    2007-01-01

    Corticosteroids, HGF and EGF play important roles in hepatic biology. We have previously shown that these molecules are required for formation of tissue with specific histology in complex organoid cultures. Dexamethasone suppresses growth and induces hepatocyte maturation; HGF and EGF are needed for formation of the non-epithelial elements. All three are needed for formation of the biliary epithelium. The gene expression patterns by which corticosteroids, HGF and EGF mediate their effects in hepatic tissue formation are distinct. These patterns affect many gene families and are described in detail. In terms of main findings, Dexamethasone induces expression of both HNF4 and C/EBP-alpha, essential transcription factors for hepatocyte differentiation. It suppresses hepatocyte growth by suppressing many molecules associated with growth in liver and other tissues, including IL6, CXC-Chemokine receptor, Amphiregulin, COX-2, HIF, etc. HGF and EGF induce all members of the TGF-beta family. They also induced multiple CNS-related genes, probably associated with stellate cells. Dexamethasone, as well as HGF and EGF, induce expression of HNF6-beta, associated with biliary epithelium formation. Combined addition of all three molecules is associated with mature histology in which hepatocyte and biliary lineages are separate and HNF4 is expressed only in hepatocyte nuclei. In conclusion, the results provide new and often surprising information on the gene expression alterations by which corticosteroids, HGF and EGF exert their effects on formation of hepatic tissue. The results underscore the usefulness of the organoid cultures for generating information on histogenesis which cannot be obtained by other culture or whole animal models. PMID:12837037

  9. 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.

  10. 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

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

    NASA Astrophysics Data System (ADS)

    Nemeth, Richard S.; Kadison, Elizabeth

    2013-12-01

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

  12. 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.

  13. Pattern formation in a thread falling onto a moving belt: An ``elastic sewing machine''

    NASA Astrophysics Data System (ADS)

    Habibi, Mehdi; Najafi, Javad; Ribe, Neil M.

    2011-07-01

    We study the dynamics of instability and pattern formation in a slender elastic thread that is continuously fed onto a surface moving at constant speed V in its own plane. As V is decreased below a critical value Vc, the steady “dragged catenary” configuration of the thread becomes unstable to sinusoidal meanders and thence to a variety of more complex patterns including biperiodic meanders, figures of 8, “W,” “two-by-one,” and “two-by-two” patterns, and double coiling. Laboratory experiments are performed to determine the phase diagram of these patterns as a function of V, the thread feeding speed U, and the fall height H. The meandering state is quantified by measuring its amplitude and frequency as functions of V, which are consistent with a Hopf bifurcation. We formulate a numerical model for a slender elastic thread that predicts well the observed steady shapes but fails to predict the frequency of the onset of meandering, probably because of slippage of the thread relative to the belt. A comparison of our phase diagram with the analogous diagram for a thread of viscous fluid falling on a moving surface reveals many similarities, but each contains several patterns that are not found in the other.

  14. Mesoscopic study of the effects of gel concentration and materials on the formation of precipitation patterns.

    PubMed

    Chen, Li; Kang, Qinjun; He, Ya-Ling; Tao, Wen-Quan

    2012-08-14

    A mesoscopic model based on the lattice Boltzmann method (LBM) is proposed to simulate the formation of Liesegang precipitation patterns and investigate the effects of gel on the morphology of the precipitates. In this model, nucleation is introduced on the basis of Ostwald's supersaturation theory, and subsequent crystal growth on the precipitate surface is simulated using a crystal growth model by taking into account the heterogeneous reaction on the surface of the precipitate. This model can capture the porous structures of the precipitates and can take into account the effects of the gel concentration and material by adjusting the gel porosity and nucleation threshold. The density of the precipitate nodes in the model is limited. A wide range of precipitation patterns is predicted under different gel concentrations, including regular bands, treelike patterns, and for the first time with numerical models, transition patterns between regular bands and treelike patterns. Both the spacing law and the width law are carefully investigated with different gel concentrations and gel materials, and the obtained α in the width law (w(n) ≈ x(n)(α), where x(n) and w(n) are the position and the width of the nth band, respectively) is in the range of 0.58-0.67, sandwiched by previously predicted ranges.

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

    SciTech Connect

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

    2014-10-20

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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. Pattern formation in a thread falling onto a moving belt: an "elastic sewing machine".

    PubMed

    Habibi, Mehdi; Najafi, Javad; Ribe, Neil M

    2011-07-01

    We study the dynamics of instability and pattern formation in a slender elastic thread that is continuously fed onto a surface moving at constant speed V in its own plane. As V is decreased below a critical value V(c), the steady "dragged catenary" configuration of the thread becomes unstable to sinusoidal meanders and thence to a variety of more complex patterns including biperiodic meanders, figures of 8, "W," "two-by-one," and "two-by-two" patterns, and double coiling. Laboratory experiments are performed to determine the phase diagram of these patterns as a function of V, the thread feeding speed U, and the fall height H. The meandering state is quantified by measuring its amplitude and frequency as functions of V, which are consistent with a Hopf bifurcation. We formulate a numerical model for a slender elastic thread that predicts well the observed steady shapes but fails to predict the frequency of the onset of meandering, probably because of slippage of the thread relative to the belt. A comparison of our phase diagram with the analogous diagram for a thread of viscous fluid falling on a moving surface reveals many similarities, but each contains several patterns that are not found in the other.

  2. 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.

  3. Two-dimensional pattern formation in ionic liquids confined between graphene walls.

    PubMed

    Montes-Campos, Hadrián; Otero-Mato, José Manuel; Méndez-Morales, Trinidad; Cabeza, Oscar; Gallego, Luis J; Ciach, Alina; Varela, Luis M

    2017-09-20

    We perform molecular dynamics simulations of ionic liquids confined between graphene walls under a large variety of conditions (pure ionic liquids, mixtures with water and alcohols, mixtures with lithium salts and defective graphene walls). Our results show that the formation of striped and hexagonal patterns in the Stern layer can be considered as a general feature of ionic liquids at electrochemical interfaces, the transition between patterns being controlled by the net balance of charge in the innermost layer of adsorbed molecules. This explains previously reported experimental and computational results and, for the first time, why these pattern changes are triggered by any perturbation of the charge density at the innermost layer of the electric double layer (voltage and composition changes, and vacancies at the electrode walls, among others), which may help tuning electrode-ionic liquid interfaces. Using Monte Carlo simulations we show that such structures can be reproduced by a simple two-dimensional lattice model with only nearest-neighbour interactions, governed by highly screened ionic interactions and short-range and excluded volume interactions. We also show that the results of our simulations are consistent with those inferred from the Landau-Brazovskii theory of pattern formation in self-assembling systems. The presence of these patterns at the ionic liquid graphene-electrode interfaces may have a strong impact on the process of ionic transfer from the bulk mixtures to the electrodes, on the differential capacitance of the electrode-electrolyte double layer or on the rates of redox reactions at the electrodes, among other physicochemical properties, and is therefore an effect of great technological interest.

  4. An experimental test of well-described vegetation patterns across slope aspects using woodland herb transplants and manipulated abiotic drivers

    Treesearch

    Robert J. Warren

    2010-01-01

    • The ubiquitous transition of plant communities across slope aspects is a welldescribed, but rarely tested, ecological dynamic. Aspect position is often used as a proxy for microclimate changes in moisture, light and temperature, but these abiotic drivers are seldom decoupled and very rarely manipulated across slope aspects. • To investigate the mechanisms...

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

    NASA Astrophysics Data System (ADS)

    Jelsbak, Lars; Søgaard-Andersen, Lotte

    2002-02-01

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

  6. Clastic patterned ground in Lomonosov crater, Mars: examining fracture controlled formation mechanisms

    NASA Astrophysics Data System (ADS)

    Barrett, Alexander M.; Balme, Matthew R.; Patel, Manish R.; Hagermann, Axel

    2017-10-01

    The area surrounding Lomonosov crater on Mars has a high density of seemingly organised boulder patterns. These form seemingly sorted polygons and stripes within kilometre scale blockfields, patches of boulder strewn ground which are common across the Martian high latitudes. Several hypotheses have been suggested to explain the formation of clastic patterned ground on Mars. It has been proposed that these structures could have formed through freeze-thaw sorting, or conversely by the interaction of boulders with underlying fracture polygons. In this investigation a series of sites were examined to evaluate whether boulder patterns appear to be controlled by the distribution of underlying fractures and test the fracture control hypotheses for their formation. It was decided to focus on this suite of mechanisms as they are characterised by a clear morphological relationship, namely the presence of an underlying fracture network which can easily be evaluated over a large area. It was found that in the majority of examples at these sites did not exhibit fracture control. Although fractures were present at many sites there were very few sites where the fracture network appeared to be controlling the boulder distribution. In general these were not the sites with the best examples of organization, suggesting that the fracture control mechanisms are not the dominant geomorphic process organising the boulders in this area.

  7. Spatial patterning of endothelial cells and vascular network formation using ultrasound standing wave fields.

    PubMed

    Garvin, Kelley A; Dalecki, Diane; Yousefhussien, Mohammed; Helguera, Maria; Hocking, Denise C

    2013-08-01

    The spatial organization of cells is essential for proper tissue assembly and organ function. Thus, successful engineering of complex tissues and organs requires methods to control cell organization in three dimensions. In particular, technologies that facilitate endothelial cell alignment and vascular network formation in three-dimensional tissue constructs would provide a means to supply essential oxygen and nutrients to newly forming tissue. Acoustic radiation forces associated with ultrasound standing wave fields can rapidly and non-invasively organize cells into distinct multicellular planar bands within three-dimensional collagen gels. Results presented herein demonstrate that the spatial pattern of endothelial cells within three-dimensional collagen gels can be controlled by design of acoustic parameters of the sound field. Different ultrasound standing wave field exposure parameters were used to organize endothelial cells into either loosely aggregated or densely packed planar bands. The rate of vessel formation and the morphology of the resulting endothelial cell networks were affected by the initial density of the ultrasound-induced planar bands of cells. Ultrasound standing wave fields provide a rapid, non-invasive approach to pattern cells in three-dimensions and direct vascular network formation and morphology within engineered tissue constructs.

  8. NFI-C2 temporal-spatial expression and cellular localization pattern during tooth formation.

    PubMed

    Lamani, Ejvis; Gluhak-Heinrich, Jelica; MacDougall, Mary

    2015-12-01

    Currently, little is known regarding critical signaling pathways during later stages of tooth development, especially those associated with root formation. Nfi-c null mice, lacking molar roots, have implicated the transcription factor NFI-C as having an essential role in root development. Previously, we identified three NFI-C isoforms expressed in dental tissues with NFI-C2 being the major transcript. However, the expression pattern of the NFI-C2 protein is not characterized. In this study we performed in situ hybridization and immunohistochemistry using isoform specific probes. We show the production of a NFI-C2 peptide antibody, its characterization, the temporal-spatial expression pattern of the NFI-C2 protein during odontogenesis and sub-cellular localization in dental cells. Moderate NFI-C2 staining, as early as bud stage, was detected mostly in the condensing dental ectomesenchyme. This staining intensified within the dental pulp at later stages culminating in high expression in the dentin producing odontoblasts. The dental epithelium showed slight staining until cytodifferentiation of enamel organ into ameloblasts and stratum intermedium. During root formation NFI-C2 expression was high in the Hertwig's epithelial root sheath and later was found in the fully developed root and its supporting tissues. NFI-C2 cellular staining was cytosolic, associated with the Golgi, and nuclear. These data suggest a broader role for NFI-C during tooth formation than limited to root and periodontal ligament development. © 2015 Japanese Society of Developmental Biologists.

  9. Microscopic approach to the kinetics of pattern formation of charged molecules on surfaces

    SciTech Connect

    Kuzovkov, V. N.; Zvejnieks, G.; Kotomin, E. A.; Olvera de la Cruz, Monica

    2010-08-09

    A microscopic formalism based on computing many-particle densities is applied to the analysis of the diffusion-controlled kinetics of pattern formation in oppositely charged molecules on surfaces or adsorbed at interfaces with competing long-range Coulomb and short-range Lennard-Jones interactions. Particular attention is paid to the proper molecular treatment of energetic interactions driving pattern formation in inhomogeneous systems. The reverse Monte Carlo method is used to visualize the spatial molecular distribution based on the calculated radial distribution functions (joint correlation functions). We show the formation of charge domains for certain combinations of temperature and dynamical interaction parameters. The charge segregation evolves into quasicrystalline clusters of charges, due to the competing long- and short-range interactions. The clusters initially co-exist with a gas phase of charges that eventually add to the clusters, generating ”fingers” or line of charges of the same sign, very different than the nanopatterns expected by molecular dynamics in systems with competing interactions in two dimensions, such as strain or dipolar versus van der Waals interactions.

  10. Spatial patterning of endothelial cells and vascular network formation using ultrasound standing wave fields

    PubMed Central

    Garvin, Kelley A.; Dalecki, Diane; Yousefhussien, Mohammed; Helguera, Maria; Hocking, Denise C.

    2013-01-01

    The spatial organization of cells is essential for proper tissue assembly and organ function. Thus, successful engineering of complex tissues and organs requires methods to control cell organization in three dimensions. In particular, technologies that facilitate endothelial cell alignment and vascular network formation in three-dimensional tissue constructs would provide a means to supply essential oxygen and nutrients to newly forming tissue. Acoustic radiation forces associated with ultrasound standing wave fields can rapidly and non-invasively organize cells into distinct multicellular planar bands within three-dimensional collagen gels. Results presented herein demonstrate that the spatial pattern of endothelial cells within three-dimensional collagen gels can be controlled by design of acoustic parameters of the sound field. Different ultrasound standing wave field exposure parameters were used to organize endothelial cells into either loosely aggregated or densely packed planar bands. The rate of vessel formation and the morphology of the resulting endothelial cell networks were affected by the initial density of the ultrasound-induced planar bands of cells. Ultrasound standing wave fields provide a rapid, non-invasive approach to pattern cells in three-dimensions and direct vascular network formation and morphology within engineered tissue constructs. PMID:23927188

  11. 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

  12. 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.

  13. 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

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Statistical analysis and modeling of collective cell motion and pattern formation

    NASA Astrophysics Data System (ADS)

    Czirok, Andras; Szabo, Andras

    2009-03-01

    Cell motility and its guidance through cell-cell contacts is instrumental in vasculogenesis and in several other morphogenic processes as well. During vasculogenesis multicellular sprouts invade rapidly into avascular areas, eventually creating an interconnected network pattern. Epithelial cell sheets migrate during organogenesis or wound healing. These phenomena were studied with time-lapse microscopy both in vivo and in vitro. Statistical analysis of cell trajectories reveals that motile confluent cultures may behave either as vortical fluids or as deforming elastic sheets. The observed flow fields and pattern formation can be explained by our generalized cellular Potts model -- representing cell polarization and self-propulsion, links between the cytoskeleton of adjacent cells as well as an asymmetric preferential attraction to the surface of adjacent cells.

  1. 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.

  2. 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.

  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. Influence of computational domain size on the pattern formation of the phase field crystals

    NASA Astrophysics Data System (ADS)

    Starodumov, Ilya; Galenko, Peter; Alexandrov, Dmitri; Kropotin, Nikolai

    2017-04-01

    Modeling of crystallization process by the phase field crystal method (PFC) represents one of the important directions of modern computational materials science. This method makes it possible to research the formation of stable or metastable crystal structures. In this paper, we study the effect of computational domain size on the crystal pattern formation obtained as a result of computer simulation by the PFC method. In the current report, we show that if the size of a computational domain is changed, the result of modeling may be a structure in metastable phase instead of pure stable state. The authors present a possible theoretical justification for the observed effect and provide explanations on the possible modification of the PFC method to account for this phenomenon.

  5. 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.

  6. E × B shear pattern formation by radial propagation of heat flux wavesa)

    NASA Astrophysics Data System (ADS)

    Kosuga, Y.; Diamond, P. H.; Dif-Pradalier, G.; Gürcan, Ã.-. D.

    2014-05-01

    A novel theory to describe the formation of E ×B flow patterns by radially propagating heat flux waves is presented. A model for heat avalanche dynamics is extended to include a finite delay time between the instantaneous heat flux and the mean flux, based on an analogy between heat avalanche dynamics and traffic flow dynamics. The response time introduced here is an analogue of the drivers' response time in traffic dynamics. The microscopic foundation for the time delay is the time for mixing of the phase space density. The inclusion of the finite response time changes the model equation for avalanche dynamics from Burgers equation to a nonlinear telegraph equation. Based on the telegraph equation, the formation of heat flux jams is predicted. The growth rate and typical interval of jams are calculated. The connection of the jam interval to the typical step size of the E ×B staircase is discussed.

  7. 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.

  8. Moran's I quantifies spatio-temporal pattern formation in neural imaging data.

    PubMed

    Schmal, Christoph; Myung, Jihwan; Herzel, Hanspeter; Bordyugov, Grigory

    2017-10-01

    Neural activities of the brain occur through the formation of spatio-temporal patterns. In recent years, macroscopic neural imaging techniques have produced a large body of data on these patterned activities, yet a numerical measure of spatio-temporal coherence has often been reduced to the global order parameter, which does not uncover the degree of spatial correlation. Here, we propose to use the spatial autocorrelation measure Moran's I, which can be applied to capture dynamic signatures of spatial organization. We demonstrate the application of this technique to collective cellular circadian clock activities measured in the small network of the suprachiasmatic nucleus (SCN) in the hypothalamus. We found that Moran's I is a practical quantitative measure of the degree of spatial coherence in neural imaging data. Initially developed with a geographical context in mind, Moran's I accounts for the spatial organization of any interacting units. Moran's I can be modified in accordance with the characteristic length scale of a neural activity pattern. It allows a quantification of statistical significance levels for the observed patterns. We describe the technique applied to synthetic datasets and various experimental imaging time-series from cultured SCN explants. It is demonstrated that major characteristics of the collective state can be described by Moran's I and the traditional Kuramoto order parameter R in a complementary fashion. Python 2.7 code of illustrative examples can be found in the Supplementary Material. christoph.schmal@charite.de or grigory.bordyugov@hu-berlin.de. Supplementary data are available at Bioinformatics online.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Bone morphogenetic proteins, eye patterning, and retinocollicular map formation in the mouse

    PubMed Central

    Plas, Daniel T.; Dhande, Onkar; Lopez, Joshua E.; Murali, Deepa; Thaller, Christina; Henkemeyer, Mark; Furuta, Yasuhide; Overbeek, Paul; Crair, Michael C.

    2009-01-01

    Patterning events during early eye formation determine retinal cell fate and can dictate the behavior of retinal ganglion cell (RGC) axons as they navigate toward central brain targets. The temporally and spatially regulated expression of bone morphogenetic proteins (BMPs) and their receptors in the retina are thought to play a key role in this process, initiating gene expression cascades that distinguish different regions of the retina, particularly along the dorsoventral axis. Here, we examine the role of BMP and a potential downstream effector, EphB, in retinotopic map formation in the lateral geniculate nucleus (LGN) and superior colliculus (SC). RGC axon behaviors during retinotopic map formation in wild type mice are compared with those in several strains of mice with engineered defects of BMP and EphB signaling. Normal RGC axon sorting produces axon order in the optic tract that reflects the dorsoventral position of the parent RGCs in the eye. A dramatic consequence of disrupting BMP signaling is a missorting of RGC axons as they exit the optic chiasm. This sorting is not dependent on EphB. When BMP signaling in the developing eye is genetically modified, RGC order in the optic tract and targeting in the LGN and SC are correspondingly disrupted. These experiments show that BMP signaling regulates dorsoventral RGC cell fate, RGC axon behavior in the ascending optic tract and retinotopic map formation in the LGN and SC through mechanisms that are in part distinct from EphB signaling in the LGN and SC. PMID:18614674

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

    NASA Astrophysics Data System (ADS)

    Hou, Youmin; Zhou, Peng; Yao, Shuhuai

    2014-11-01

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

  17. Turing pattern formation on the sphere for a morphochemical reaction-diffusion model for electrodeposition

    NASA Astrophysics Data System (ADS)

    Lacitignola, Deborah; Bozzini, Benedetto; Frittelli, Massimo; Sgura, Ivonne

    2017-07-01

    The present paper deals with the pattern formation properties of a specific morpho-electrochemical reaction-diffusion model on a sphere. The physico-chemical background to this study is the morphological control of material electrodeposited onto spherical particles. The particular experimental case of interest refers to the optimization of novel metal-air flow batteries and addresses the electrodeposition of zinc onto inert spherical supports. Morphological control in this step of the high-energy battery operation is crucial to the energetic efficiency of the recharge process and to the durability of the whole energy-storage device. To rationalise this technological challenge within a mathematical modeling perspective, we consider the reaction-diffusion system for metal electrodeposition introduced in [Bozzini et al., J. Solid State Electr.17, 467-479 (2013)] and extend its study to spherical domains. Conditions are derived for the occurrence of the Turing instability phenomenon and the steady patterns emerging at the onset of Turing instability are investigated. The reaction-diffusion system on spherical domains is solved numerically by means of the Lumped Surface Finite Element Method (LSFEM) in space combined with the IMEX Euler method in time. The effect on pattern formation of variations in the domain size is investigated both qualitatively, by means of systematic numerical simulations, and quantitatively by introducing suitable indicators that allow to assign each pattern to a given morphological class. An experimental validation of the obtained results is finally presented for the case of zinc electrodeposition from alkaline zincate solutions onto copper spheres.

  18. 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.

  19. 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

  20. Stretch force guides finger-like pattern of bone formation in suture

    PubMed Central

    Kou, Xiao-Xing; Zhang, Ci; Zhang, Yi-Mei; Cui, Zhen; Wang, Xue-Dong; Liu, Yan; Liu, Da-Wei; Zhou, Yan-Heng

    2017-01-01

    Mechanical tension is widely applied on the suture to modulate the growth of craniofacial bones. Deeply understanding the features of bone formation in expanding sutures could help us to improve the outcomes of clinical treatment and avoid some side effects. Although there are reports that have uncovered some biological characteristics, the regular pattern of sutural bone formation in response to expansion forces is still unknown. Our study was to investigate the shape, arrangement and orientation of new bone formation in expanding sutures and explore related clinical implications. The premaxillary sutures of rat, which histologically resembles the sutures of human beings, became wider progressively under stretch force. Micro-CT detected new bones at day 3. Morphologically, these bones were forming in a finger-like pattern, projecting from the maxillae into the expanded sutures. There were about 4 finger-like bones appearing on the selected micro-CT sections at day 3 and this number increased to about 18 at day 7. The average length of these projections increased from 0.14 mm at day 3 to 0.81 mm at day 7. The volume of these bony protuberances increased to the highest level of 0.12 mm3 at day 7. HE staining demonstrated that these finger-like bones had thick bases connecting with the maxillae and thin fronts stretching into the expanded suture. Nasal sections had a higher frequency of finger-like bones occuring than the oral sections at day 3 and day 5. Masson-stained sections showed stretched fibers embedding into maxillary margins. Osteocalcin-positive osteoblasts changed their shapes from cuboidal to spindle and covered the surfaces of finger-like bones continuously. Alizarin red S and calcein deposited in the inner and outer layers of finger-like bones respectively, which showed that longer and larger bones formed on the nasal side of expanded sutures compared with the oral side. Interestingly, these finger-like bones were almost paralleling with the direction

  1. 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.

  2. 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.

  3. 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.

  4. Effects of confinement on pattern formation in two dimensional systems with competing interactions.

    PubMed

    Almarza, N G; Pe Combining Cedilla Kalski, J; Ciach, A

    2016-09-28

    Template-assisted pattern formation in monolayers of particles with competing short-range attraction and long-range repulsion interactions (SALR) is studied by Monte Carlo simulations in a simple generic model [N. G. Almarza et al., J. Chem. Phys., 2014, 140, 164708]. We focus on densities corresponding to formation of parallel stripes of particles and on monolayers laterally confined between straight parallel walls. We analyze both the morphology of the developed structures and the thermodynamic functions for broad ranges of temperature T and the separation L2 between the walls. At low temperature stripes parallel to the boundaries appear, with some corrugation when the distance between the walls does not match the bulk periodicity of the striped structure. The stripes integrity, however, is rarely broken for any L2. This structural order is lost at T = TK(L2) depending on L2 according to a Kelvin-like equation. Above the Kelvin temperature TK(L2) many topological defects such as breaking or branching of the stripes appear, but a certain anisotropy in the orientation of the stripes persists. Finally, at high temperature and away from the walls, the system behaves as an isotropic fluid of elongated clusters of various lengths and with various numbers of branches. For L2 optimal for the stripe pattern the heat capacity as a function of temperature takes the maximum at T = TK(L2).

  5. 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.

  6. 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).

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Arabidopsis thaliana miRNAs promote embryo pattern formation beginning in the zygote.

    PubMed

    Armenta-Medina, Alma; Lepe-Soltero, Daniel; Xiang, Daoquan; Datla, Raju; Abreu-Goodger, Cei; Gillmor, C Stewart

    2017-09-12

    miRNAs are essential regulators of cell identity, yet their role in early embryo development in plants remains largely unexplored. To determine the earliest stage at which miRNAs act to promote pattern formation in embryogenesis, we examined a series of mutant alleles in the Arabidopsis thaliana miRNA biogenesis enzymes DICER-LIKE 1 (DCL1), SERRATE (SE), and HYPONASTIC LEAVES 1 (HYL1). Cellular and patterning defects were observed in dcl1, se and hyl1 embryos from the zygote through the globular stage of embryogenesis. To identify miRNAs that are expressed in early embryogenesis, we sequenced mRNAs from globular stage Columbia wild type (wt) and se-1 embryos, and identified transcripts potentially corresponding to 100 miRNA precursors. Considering genome location and transcript increase between wt and se-1, 39 of these MIRNAs are predicted to be bona fide early embryo miRNAs. Among these are conserved miRNAs such as miR156, miR159, miR160, miR161, miR164, miR165, miR166, miR167, miR168, miR171, miR319, miR390 and miR394, as well as miRNAs whose function has never been characterized. Our analysis demonstrates that miRNAs promote pattern formation beginning in the zygote, and provides a comprehensive dataset for functional studies of individual miRNAs in Arabidopsis embryogenesis. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Dynamic Coupling of Pattern Formation and Morphogenesis in the Developing Vertebrate Retina

    PubMed Central

    Picker, Alexander; Cavodeassi, Florencia; Machate, Anja; Bernauer, Sabine; Hans, Stefan; Abe, Gembu; Kawakami, Koichi; Wilson, Stephen W.; Brand, Michael

    2009-01-01

    During embryonic development, pattern formation must be tightly synchronized with tissue morphogenesis to coordinate the establishment of the spatial identities of cells with their movements. In the vertebrate retina, patterning along the dorsal-ventral and nasal-temporal (anterior-posterior) axes is required for correct spatial representation in the retinotectal map. However, it is unknown how specification of axial cell positions in the retina occurs during the complex process of early eye morphogenesis. Studying zebrafish embryos, we show that morphogenetic tissue rearrangements during eye evagination result in progenitor cells in the nasal half of the retina primordium being brought into proximity to the sources of three fibroblast growth factors, Fgf8/3/24, outside the eye. Triple-mutant analysis shows that this combined Fgf signal fully controls nasal retina identity by regulating the nasal transcription factor Foxg1. Surprisingly, nasal-temporal axis specification occurs very early along the dorsal-ventral axis of the evaginating eye. By in vivo imaging GFP-tagged retinal progenitor cells, we find that subsequent eye morphogenesis requires gradual tissue compaction in the nasal half and directed cell movements into the temporal half of the retina. Balancing these processes drives the progressive alignment of the nasal-temporal retina axis with the anterior-posterior body axis and is controlled by a feed-forward effect of Fgf signaling on Foxg1-mediated cell cohesion. Thus, the mechanistic coupling and dynamic synchronization of tissue patterning with morphogenetic cell behavior through Fgf signaling leads to the graded allocation of cell positional identity in the eye, underlying retinotectal map formation. PMID:19823566

  15. Dynamic coupling of pattern formation and morphogenesis in the developing vertebrate retina.

    PubMed

    Picker, Alexander; Cavodeassi, Florencia; Machate, Anja; Bernauer, Sabine; Hans, Stefan; Abe, Gembu; Kawakami, Koichi; Wilson, Stephen W; Brand, Michael

    2009-10-01

    During embryonic development, pattern formation must be tightly synchronized with tissue morphogenesis to coordinate the establishment of the spatial identities of cells with their movements. In the vertebrate retina, patterning along the dorsal-ventral and nasal-temporal (anterior-posterior) axes is required for correct spatial representation in the retinotectal map. However, it is unknown how specification of axial cell positions in the retina occurs during the complex process of early eye morphogenesis. Studying zebrafish embryos, we show that morphogenetic tissue rearrangements during eye evagination result in progenitor cells in the nasal half of the retina primordium being brought into proximity to the sources of three fibroblast growth factors, Fgf8/3/24, outside the eye. Triple-mutant analysis shows that this combined Fgf signal fully controls nasal retina identity by regulating the nasal transcription factor Foxg1. Surprisingly, nasal-temporal axis specification occurs very early along the dorsal-ventral axis of the evaginating eye. By in vivo imaging GFP-tagged retinal progenitor cells, we find that subsequent eye morphogenesis requires gradual tissue compaction in the nasal half and directed cell movements into the temporal half of the retina. Balancing these processes drives the progressive alignment of the nasal-temporal retina axis with the anterior-posterior body axis and is controlled by a feed-forward effect of Fgf signaling on Foxg1-mediated cell cohesion. Thus, the mechanistic coupling and dynamic synchronization of tissue patterning with morphogenetic cell behavior through Fgf signaling leads to the graded allocation of cell positional identity in the eye, underlying retinotectal map formation.

  16. 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.

  17. 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

  18. 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.

  19. 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

  20. 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

  1. 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.

  2. Formation mechanisms of PNA-like teleconnection pattern in response to the Madden-Julian oscillation

    NASA Astrophysics Data System (ADS)

    Seo, K. H.; Lee, H. J.

    2016-12-01

    Formation mechanisms of PNA-like teleconnection pattern in response to the Madden-Julian oscillation (MJO) have been investigated with the GFDL dry model simulations. For this, the Rossby wave source (RWS) has been identified first and wave seeding has been performed using Rossby wave dispersion relationship. Results show that initial MJO phase 2-like diabatic forcing generates negative PNA-like pattern through negative RWS to the north of the enhanced convection over the equatorial Indian Ocean (IO) and positive RWS to the north of the suppressed convection over the equatorial western Pacific. It is of interest that the dibatic forcing over the IO generates another +RWS region at the exit of the jet stream through advection of the climatological relative vorticity by the northerly MJO winds. Ray tracing demonstrates explicit Rossby wave energy propagation over the PNA region. A series of simulations with different monopole forcing indicates that MJO phase-2 structure is most effective for the generation of -PNA pattern. The mechanisms for the surface warming over NA are discussed with the integration of the temperature equation and Rossby wave propagation.

  3. AN EFFICIENT, NON-LINEAR STABILITY ANALYSIS FOR DETECTING PATTERN FORMATION IN REACTION DIFFUSION SYSTEMS

    PubMed Central

    HOLMES, WILLIAM R.

    2014-01-01

    Reaction diffusion systems are often used to study pattern formation in biological systems. However, most methods for understanding their behavior are challenging and can rarely be applied to complex systems common in biological applications. I present a relatively simple and efficient, non-linear stability technique that greatly aids such analysis when rates of diffusion are substantially different. This technique reduces a system of reaction diffusion equations to a system of ordinary differential equations tracking the evolution of a large amplitude, spatially localized perturbation of a homogeneous steady state. Stability properties of this system, determined using standard bifurcation techniques and software, describe both linear and non-linear patterning regimes of the reaction diffusion system. I describe the class of systems this method can be applied to and demonstrate its application. Analysis of Schnakenberg and substrate inhibition models is performed to demonstrate the methods capabilities in simplified settings and show that even these simple models have non-linear patterning regimes not previously detected. The real power of this technique however is its simplicity and applicability to larger complex systems where other non-linear methods become intractable. This is demonstrated through analysis of a chemotaxis regulatory network comprised of interacting proteins and phospholipids. In each case, predictions of this method are verified against results of numerical simulation, linear stability, asymptotic, and / or full PDE bifurcation analyses. PMID:24158538

  4. Dynamic model based on voltage transfer curve for pattern formation in dielectric barrier glow discharge

    NASA Astrophysics Data System (ADS)

    Li, Ben; He, Feng; Duan, Xiaoxi; Ouyang, Jiting

    2015-12-01

    Simulation work is very important for understanding the formation of self-organized discharge patterns. Previous works have witnessed different models derived from other systems for simulation of discharge pattern, but most of these models are complicated and time-consuming. In this paper, we introduce a convenient phenomenological dynamic model based on the basic dynamic process of glow discharge and the voltage transfer curve (VTC) to study the dielectric barrier glow discharge (DBGD) pattern. VTC is an important characteristic of DBGD, which plots the change of wall voltage after a discharge as a function of the initial total gap voltage. In the modeling, the combined effect of the discharge conditions is included in VTC, and the activation-inhibition effect is expressed by a spatial interaction term. Besides, the model reduces the dimensionality of the system by just considering the integration effect of current flow. All these greatly facilitate the construction of this model. Numerical simulations turn out to be in good accordance with our previous fluid modeling and experimental result.

  5. 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.

  6. 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.

  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. 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.

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