Science.gov

Sample records for biological pattern formation

  1. On the mechanical theory for biological pattern formation

    NASA Astrophysics Data System (ADS)

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

    1993-02-01

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

  2. 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.

  3. 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

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

    ERIC Educational Resources Information Center

    Mayer, William V.; And Others

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

  5. 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.

  6. 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

  7. Pattern formation today

    PubMed Central

    Chuong, Cheng-Ming; Richardson, Michael K.

    2010-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  9. Pattern formation in Dictyostelium via the dynamics of cooperative biological entities

    NASA Astrophysics Data System (ADS)

    Kessler, David A.; Levine, Herbert

    1993-12-01

    The cellular slime mold Dictyostelium discoideum exhibits a variety of spatial patterns as it aggregates to form a multicellular slug. These patterns arise via the interaction of the aggregating amoebae, either via contact or as mediated by chemical signals involving cyclic adenosine monophosphate (AMP). We model this system as a set of reaction-diffusion equations coupled to dynamical biological entities (bions), each of which is endowed with signal receptors and response rules. Simulations of our model reveal a close correspondence with the observed structures. Also, the general framework we propose should be suitable for modeling other biological pattern-forming processes.

  10. 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.

  11. Distinguishing Pattern Formation Phenotypes: Applying Minkowski Functionals to Cell Biology Systems

    NASA Astrophysics Data System (ADS)

    Rericha, Erin; Guven, Can; Parent, Carole; Losert, Wolfgang

    2011-03-01

    Spatial Clustering of proteins within cells or cells themselves frequently occur in cell biology systems. However quantifying the underlying order and determining the regulators of these cluster patterns have proved difficult due to the inherent high noise levels in the systems. For instance the patterns formed by wild type and cyclic-AMP regulatory mutant Dictyostelium cells are visually distinctive, yet the large error bars in measurements of the fractal number, area, Euler number, eccentricity, and wavelength making it difficult to quantitatively distinguish between the patterns. We apply a spatial analysis technique based on Minkowski functionals and develop metrics which clearly separate wild type and mutant cell lines into distinct categories. Having such a metric facilitated the development of a computational model for cellular aggregation and its regulators. Supported by NIH-NGHS Nanotechnology (R01GM085574) and the Burroughs Wellcome Fund.

  12. Biologic Patterns of Disability.

    ERIC Educational Resources Information Center

    Granger, Carl V.; Linn, Richard T.

    2000-01-01

    Describes the use of Rasch analysis to elucidate biological patterns of disability present in the functional ability of persons undergoing medical rehabilitation. Uses two measures, one for inpatients and one for outpatients, to illustrate the approach and provides examples of some biological patterns of disability associated with specific types…

  13. [Pattern formation in microcosm: the role of self-assembly in complex biological envelopes development].

    PubMed

    Gabaraeva, N I; Hemsley, A R

    2010-01-01

    The data on the development of pollen/spore walls (of sporoderm) were reconsidered in the light of our hypothesis regarding a considerable role of self-assembling processes in the formation of this complex pattern. The premises that (1) glycocalyx (cell surface coating) is a self-assembling colloidal solution, and that (2) exine, formed on a glycocalyx framework, appears as a result of the self-assembly of the biopolymer (sporopollenin microemulsion), were independently suggested by the authors of this paper (Gabarayeva, 1990, 1993; Hemsley et al., 1992). Afterwards a joint hypothesis has been worked out which interpreted the processes of sporoderm development through regularities of colloidal chemistry. It was shown that all of the successive developmental stages, seen in transmission electron microscope (TEM) in the course of pollen wall development, correspond to successive micelle mesophases of a colloidal solution of surface-active substances which self-assemble when their concentration increases. Such an interpretation implies that all of the microstructures, observed in mature pollen walls (granules; rods-columellae; hexagonally packed layers of rods; bilayers, separated with a gap) are somewhat like "stiff history" of their appearance as a micellar sequence, immortalized by chemically resistant sporopollenin. Since self-assembling processes have nonlinear, spasmodic character, and microstructures of pollen wall, mentioned above, are arranged, as a rule, in successive layers, it has been suggested that these layers of heterogeneous microstructures occur as a result of the abrupt phase transitions typical for self-assembling micellar systems. PMID:20865932

  14. The role of mathematical models in understanding pattern formation in developmental biology.

    PubMed

    Umulis, David M; Othmer, Hans G

    2015-05-01

    In a Wall Street Journal article published on April 5, 2013, E. O. Wilson attempted to make the case that biologists do not really need to learn any mathematics-whenever they run into difficulty with numerical issues, they can find a technician (aka mathematician) to help them out of their difficulty. He formalizes this in Wilsons Principle No. 1: "It is far easier for scientists to acquire needed collaboration from mathematicians and statisticians than it is for mathematicians and statisticians to find scientists able to make use of their equations." This reflects a complete misunderstanding of the role of mathematics in all sciences throughout history. To Wilson, mathematics is mere number crunching, but as Galileo said long ago, "The laws of Nature are written in the language of mathematics[Formula: see text] the symbols are triangles, circles and other geometrical figures, without whose help it is impossible to comprehend a single word." Mathematics has moved beyond the geometry-based model of Galileo's time, and in a rebuttal to Wilson, E. Frenkel has pointed out the role of mathematics in synthesizing the general principles in science (Both point and counter-point are available in Wilson and Frenkel in Notices Am Math Soc 60(7):837-838, 2013). We will take this a step further and show how mathematics has been used to make new and experimentally verified discoveries in developmental biology and how mathematics is essential for understanding a problem that has puzzled experimentalists for decades-that of how organisms can scale in size. Mathematical analysis alone cannot "solve" these problems since the validation lies at the molecular level, but conversely, a growing number of questions in biology cannot be solved without mathematical analysis and modeling. Herein, we discuss a few examples of the productive intercourse between mathematics and biology. PMID:25280665

  15. The Role of Mathematical Models in Understanding Pattern Formation in Developmental Biology

    PubMed Central

    Umulis, David M.

    2016-01-01

    In a Wall Street Journal article published on April 5, 2013, E. O. Wilson attempted to make the case that biologists do not really need to learn any mathematics—whenever they run into difficulty with numerical issues, they can find a technician (aka mathematician) to help them out of their difficulty. He formalizes this in Wilsons Principle No. 1: “It is far easier for scientists to acquire needed collaboration from mathematicians and statisticians than it is for mathematicians and statisticians to find scientists able to make use of their equations.” This reflects a complete misunderstanding of the role of mathematics in all sciences throughout history. To Wilson, mathematics is mere number crunching, but as Galileo said long ago, “The laws of Nature are written in the language of mathematics…the symbols are triangles, circles and other geometrical figures, without whose help it is impossible to comprehend a single word.” Mathematics has moved beyond the geometry-based model of Galileo’s time, and in a rebuttal to Wilson, E. Frenkel has pointed out the role of mathematics in synthesizing the general principles in science (Both point and counter-point are available in Wilson and Frenkel in Notices Am Math Soc 60(7):837–838, 2013). We will take this a step further and show how mathematics has been used to make new and experimentally verified discoveries in developmental biology and how mathematics is essential for understanding a problem that has puzzled experimentalists for decades—that of how organisms can scale in size. Mathematical analysis alone cannot “solve” these problems since the validation lies at the molecular level, but conversely, a growing number of questions in biology cannot be solved without mathematical analysis and modeling. Herein, we discuss a few examples of the productive intercourse between mathematics and biology. PMID:25280665

  16. Pattern formation during vasculogenesis.

    PubMed

    Czirok, Andras; Little, Charles D

    2012-06-01

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

  17. Biological patterns: Novel indicators for pharmacological assays

    NASA Technical Reports Server (NTRS)

    Johnson, Jacqueline U.

    1991-01-01

    Variable gravity testing using the KC-135 demonstrated clearly that biological pattern formation was definitely shown to result from gravity alone, and not from oxygen gradients in solution. Motile pattern formation of spermatozoa are driven by alternate mechanisms, and apparently not affected by short-term changes in gravity. The chemical effects found appear to be secondary to the primary effect of gravity. Cryopreservation may be the remedy to the problem of 'spare' or 'standing order' biological samples for testing of space lab investigations, but further studies are necessary.

  18. Space Biology: Patterns of Life

    ERIC Educational Resources Information Center

    Salisbury, Frank B.

    1971-01-01

    Present knowledge about Mars is compared with past beliefs about the planet. Biological experiments that indicate life may exist on Mars are interpreted. Life patterns or biological features that might be postulated for extraterrestrial life are presented at the molecular, cellular, organism, and ecosystem levels. (DS)

  19. Pattern formation in centrosome assembly.

    PubMed

    Mahen, Robert; Venkitaraman, Ashok R

    2012-02-01

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

  20. 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.

  1. Pattern formation in multiplex networks

    PubMed Central

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

    2015-01-01

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

  2. 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).

  3. Pattern Formation in Convective Instabilities

    NASA Astrophysics Data System (ADS)

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

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

  4. 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

  5. Pattern Formation and Functionality in Swarm Models

    NASA Astrophysics Data System (ADS)

    Rauch, Erik; Millonas, Mark; Chialvo, Dante

    1996-03-01

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

  6. Mechanisms of scaling in pattern formation

    PubMed Central

    Umulis, David M.; Othmer, Hans G.

    2013-01-01

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

  7. Pattern formation in oscillatory media without lateral inhibition.

    PubMed

    Ali, Rehman; Harris, Jeremy; Ermentrout, Bard

    2016-07-01

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

  8. Pattern formations and optimal packing.

    PubMed

    Mityushev, Vladimir

    2016-04-01

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

  9. Waves and Patterns in Chemical and Biological Media

    NASA Astrophysics Data System (ADS)

    Swinney, Harry L.; Krinsky, Valentin I.

    1991-12-01

    These 28 contributions by leading researchers - from such diverse disciplines as chemistry, biology, physics, mathematics, and physiology - describe recent experiments, numerical simulations, and theoretical analyses of the formation of spatial patterns in chemical and biological systems. Chemical patterns have been systematically studied since the field was established by Alan Turing's landmark 1952 paper, "The chemical basis for morphogenesis," yet only recently have new experimental techniques and numerical analyses of reaction-diffusion equations opened the way to understanding stationary and traveling wave patterns. This collection summarizes the exciting developments in this rapidly growing field. It shows that some biological patterns have been found to be strikingly similar to patterns found in simple, well-controlled laboratory chemical systems, that new chemical reactor designs make it possible to sustain chemical patterns and to study transitions between different kinds of patterns, and that nearly 40 years after Turing's paper, the patterns predicted by Turing have finally been observed in laboratory experiments. Harry L. Swinney is Sid Richardson Foundation Regents Chair, Department of Physics, and Director of the Center for Nonlinear Dynamics at the University of Texas at Austin. Valentin I. Krinsky is Head of the Autowave Laboratory, Institute of Biological Physics, Academy of Sciences, Pushchino, USSR. Chapters cover: Spiral, Ring, and Scroll Patterns: Experiments. Spiral, Ring, and Scroll Patterns: Theory and Simulations. Fronts and Turing Patterns. Waves and Patterns in Biological Systems.

  10. Formation of superhydrophobic/superhydrophilic patterns by combination of nanostructure-imprinted perfluoropolymer and nanostructured silicon oxide for biological droplet generation

    NASA Astrophysics Data System (ADS)

    Kobayashi, Taizo; Shimizu, Kazunori; Kaizuma, Yoshihiro; Konishi, Satoshi

    2011-03-01

    In this letter, we report a technology for fabricating superhydrophobic/superhydrophilic patterns using a combination of a nanostructure-imprinted perfluoropolymer and nanostructured silicon oxide. In our previous study, we used a combination of hydrophobic and superhydrophilic materials. However, it was difficult to split low-surface-tension liquids such as biological liquids into droplets solely using hydrophobic/hydrophilic patterns. In this study, the contact angle of the hydrophobic region was enhanced from 109.3° to 155.6° by performing nanostructure imprinting on a damage-reduced perfluoropolymer. The developed superhydrophobic/superhydrophilic patterns allowed the splitting of even those media that contained fetal bovine serum into droplets of a desired shape.

  11. Zonal flow as pattern formation

    NASA Astrophysics Data System (ADS)

    Parker, Jeffrey B.; Krommes, John A.

    2013-10-01

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

  12. Zonal flow as pattern formation

    SciTech Connect

    Parker, Jeffrey B.; Krommes, John A.

    2013-10-15

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

  13. Formate Formation and Formate Conversion in Biological Fuels Production

    PubMed Central

    Crable, Bryan R.; Plugge, Caroline M.; McInerney, Michael J.; Stams, Alfons J. M.

    2011-01-01

    Biomethanation is a mature technology for fuel production. Fourth generation biofuels research will focus on sequestering CO2 and providing carbon-neutral or carbon-negative strategies to cope with dwindling fossil fuel supplies and environmental impact. Formate is an important intermediate in the methanogenic breakdown of complex organic material and serves as an important precursor for biological fuels production in the form of methane, hydrogen, and potentially methanol. Formate is produced by either CoA-dependent cleavage of pyruvate or enzymatic reduction of CO2 in an NADH- or ferredoxin-dependent manner. Formate is consumed through oxidation to CO2 and H2 or can be further reduced via the Wood-Ljungdahl pathway for carbon fixation or industrially for the production of methanol. Here, we review the enzymes involved in the interconversion of formate and discuss potential applications for biofuels production. PMID:21687599

  14. Magnetic Assisted Colloidal Pattern Formation

    NASA Astrophysics Data System (ADS)

    Yang, Ye

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

  15. Cellular pattern formation during Dictyostelium aggregation

    NASA Astrophysics Data System (ADS)

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

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

  16. 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

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

    PubMed

    McCullen, Nick; Wagenknecht, Thomas

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    McCullen, Nick; Wagenknecht, Thomas

    2016-06-01

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

  19. 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

  20. Frequent patterns mining in multiple biological sequences.

    PubMed

    Chen, Ling; Liu, Wei

    2013-10-01

    Existing algorithms for mining frequent patterns in multiple biosequences may generate multiple projected databases and short candidate patterns, which can increase computation time and memory requirement. In order to overcome such shortcomings, we propose a fast and efficient algorithm for mining frequent patterns in multiple biological sequences (MSPM). We first present the concept of a primary pattern, which can be extended to form larger patterns in the sequence. To detect frequent primary patterns, a prefix tree is constructed. Based on this prefix tree, a pattern-extending approach is also presented to mine frequent patterns without producing a large number of irrelevant candidate patterns. The experimental results show that the MSPM algorithm can achieve not only faster speed, but also higher quality results as compared with other methods. PMID:24034736

  1. Pattern Formation in Excitable Media

    NASA Astrophysics Data System (ADS)

    Reynolds, William Nash

    1992-01-01

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

  2. Single cell pattern formation and transient cytoskeletal arrays

    PubMed Central

    Bement, William M.; von Dassow, George

    2015-01-01

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

  3. 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

  4. Pattern formation in quantum networks

    NASA Astrophysics Data System (ADS)

    Kim, Ilki; Mahler, Günter

    1999-03-01

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

  5. Femtosecond laser patterning of biological materials

    NASA Astrophysics Data System (ADS)

    Grigoropoulos, Costas P.; Jeon, Hojeong; Hidai, Hirofumi; Hwang, David J.

    2011-03-01

    This paper aims at presenting a review of work at the Laser Thermal Laboratory on the microscopic laser modification of biological materials using ultrafast laser pulses. We have devised a new method for fabricating high aspect ratio patterns of varying height by using two-photon polymerization process in order to study contact guidance and directed growth of biological cells. Studies using NIH-3T3 and MDCK cells indicate that cell morphology on fiber scaffolds is influenced by the pattern of actin microfilament bundles. Cells experienced different strength of contact guidance depending on the ridge height. Cell morphology and motility was investigated on micronscale anisotropic cross patterns and parallel line patterns having different aspect ratios. A significant effect on cell alignment and directionality of migration was observed. Cell morphology and motility were influenced by the aspect ratio of the cross pattern, the grid size, and the ridge height. Cell contractility was examined microscopically in order to measure contractile forces generated by individual cells on self-standing fiber scaffolds.

  6. Blood drop patterns: Formation and applications.

    PubMed

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

    2016-05-01

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

  7. Pattern Formation in Driven Systems

    NASA Astrophysics Data System (ADS)

    Klymko, Katherine

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

  8. 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

  9. A biologically inspired model for pattern recognition*

    PubMed Central

    Gonzalez, Eduardo; Liljenström, Hans; Ruiz, Yusely; Li, Guang

    2010-01-01

    In this paper, a novel bionic model and its performance in pattern recognition are presented and discussed. The model is constructed from a bulb model and a three-layered cortical model, mimicking the main features of the olfactory system. The olfactory bulb and cortex models are connected by feedforward and feedback fibers with distributed delays. The Breast Cancer Wisconsin dataset consisting of data from 683 patients divided into benign and malignant classes is used to demonstrate the capacity of the model to learn and recognize patterns, even when these are deformed versions of the originally learned patterns. The performance of the novel model was compared with three artificial neural networks (ANNs), a back-propagation network, a support vector machine classifier, and a radial basis function classifier. All the ANNs and the olfactory bionic model were tested in a benchmark study of a standard dataset. Experimental results show that the bionic olfactory system model can learn and classify patterns based on a small training set and a few learning trials to reflect biological intelligence to some extent. PMID:20104646

  10. 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.

  11. Taming contact line instability for pattern formation.

    PubMed

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

    2016-01-01

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

  12. 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

  13. Taming contact line instability for pattern formation

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  14. Pattern formation in Active Polar Fluids

    NASA Astrophysics Data System (ADS)

    Gopinath, Arvind; Hagan, Michael; Baskaran, Aparna

    2011-03-01

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

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

    PubMed

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

    2005-08-01

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

  16. Evaporation-Induced Pattern Formation of Decanol Droplets.

    PubMed

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

    2016-05-17

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

  17. 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.

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

    PubMed

    Oikawa, Noriko; Kurita, Rei

    2016-01-01

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

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

    PubMed Central

    Oikawa, Noriko; Kurita, Rei

    2016-01-01

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

  20. 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.

  1. Pattern formation in drying drops of blood

    NASA Astrophysics Data System (ADS)

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

    2011-01-01

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

  2. Electrically induced structure formation and pattern transfer

    NASA Astrophysics Data System (ADS)

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

    2000-02-01

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

  3. Pattern formation during early floral development.

    PubMed

    Vaddepalli, Prasad; Scholz, Sebastian; Schneitz, Kay

    2015-06-01

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

  4. Regulation of Spatiotemporal Patterns by Biological Variability: General Principles and Applications to Dictyostelium discoideum.

    PubMed

    Grace, Miriam; Hütt, Marc-Thorsten

    2015-11-01

    Spatiotemporal patterns often emerge from local interactions in a self-organizing fashion. In biology, the resulting patterns are also subject to the influence of the systematic differences between the system's constituents (biological variability). This regulation of spatiotemporal patterns by biological variability is the topic of our review. We discuss several examples of correlations between cell properties and the self-organized spatiotemporal patterns, together with their relevance for biology. Our guiding, illustrative example will be spiral waves of cAMP in a colony of Dictyostelium discoideum cells. Analogous processes take place in diverse situations (such as cardiac tissue, where spiral waves occur in potentially fatal ventricular fibrillation) so a deeper understanding of this additional layer of self-organized pattern formation would be beneficial to a wide range of applications. One of the most striking differences between pattern-forming systems in physics or chemistry and those in biology is the potential importance of variability. In the former, system components are essentially identical with random fluctuations determining the details of the self-organization process and the resulting patterns. In biology, due to variability, the properties of potentially very few cells can have a driving influence on the resulting asymptotic collective state of the colony. Variability is one means of implementing a few-element control on the collective mode. Regulatory architectures, parameters of signaling cascades, and properties of structure formation processes can be "reverse-engineered" from observed spatiotemporal patterns, as different types of regulation and forms of interactions between the constituents can lead to markedly different correlations. The power of this biology-inspired view of pattern formation lies in building a bridge between two scales: the patterns as a collective state of a very large number of cells on the one hand, and the internal

  5. Regulation of Spatiotemporal Patterns by Biological Variability: General Principles and Applications to Dictyostelium discoideum

    PubMed Central

    Grace, Miriam; Hütt, Marc-Thorsten

    2015-01-01

    Spatiotemporal patterns often emerge from local interactions in a self-organizing fashion. In biology, the resulting patterns are also subject to the influence of the systematic differences between the system’s constituents (biological variability). This regulation of spatiotemporal patterns by biological variability is the topic of our review. We discuss several examples of correlations between cell properties and the self-organized spatiotemporal patterns, together with their relevance for biology. Our guiding, illustrative example will be spiral waves of cAMP in a colony of Dictyostelium discoideum cells. Analogous processes take place in diverse situations (such as cardiac tissue, where spiral waves occur in potentially fatal ventricular fibrillation) so a deeper understanding of this additional layer of self-organized pattern formation would be beneficial to a wide range of applications. One of the most striking differences between pattern-forming systems in physics or chemistry and those in biology is the potential importance of variability. In the former, system components are essentially identical with random fluctuations determining the details of the self-organization process and the resulting patterns. In biology, due to variability, the properties of potentially very few cells can have a driving influence on the resulting asymptotic collective state of the colony. Variability is one means of implementing a few-element control on the collective mode. Regulatory architectures, parameters of signaling cascades, and properties of structure formation processes can be "reverse-engineered" from observed spatiotemporal patterns, as different types of regulation and forms of interactions between the constituents can lead to markedly different correlations. The power of this biology-inspired view of pattern formation lies in building a bridge between two scales: the patterns as a collective state of a very large number of cells on the one hand, and the internal

  6. 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.

  7. Patterning and Compartment Formation in the Diencephalon

    PubMed Central

    Chatterjee, Mallika; Li, James Y. H.

    2012-01-01

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

  8. 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

  9. 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.

  10. Chiral pattern formation in compact microbial colonies

    NASA Astrophysics Data System (ADS)

    Korolev, Kirill; Bino George, Ashish

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

  11. Instabilities and pattern formation in crystal growth

    NASA Astrophysics Data System (ADS)

    Langer, J. S.

    1980-01-01

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

  12. Biological Superoxide In Manganese Oxide Formation

    NASA Astrophysics Data System (ADS)

    Hansel, C.; Learman, D.; Zeiner, C.; Santelli, C. M.

    2011-12-01

    Manganese (Mn) oxides are among the strongest sorbents and oxidants within the environment, controlling the fate and transport of numerous elements and the degradation of recalcitrant carbon. Both bacteria and fungi mediate the oxidation of Mn(II) to Mn(III/IV) oxides but the genetic and biochemical mechanisms responsible remain poorly understood. Furthermore, the physiological basis for microbial Mn(II) oxidation remains an enigma. We have recently reported that a common marine bacterium (Roseobacter sp. AzwK-3b) oxidizes Mn(II) via reaction with extracellular superoxide (O2-) produced during exponential growth. Here we expand this superoxide-mediated Mn(II) oxidation pathway to fungi, introducing a surprising homology between prokaryotic and eukaryotic metal redox processes. For instance, Stibella aciculosa, a common soil Ascomycete filamentous fungus, precipitates Mn oxides at the base of asexual reproductive structures (synnemata) used to support conidia (Figure 1). This distribution is a consequence of localized production of superoxide (and it's dismutation product hydrogen peroxide, H2O2), leading to abiotic oxidation of Mn(II) by superoxide. Disruption of NADPH oxidase activity using the oxidoreductase inhibitor DPI leads to diminished cell differentiation and subsequent Mn(II) oxidation inhibition. Addition of Cu(II) (an effective superoxide scavenger) leads to a concentration dependent decrease in Mn oxide formation. We predict that due to the widespread production of extracellular superoxide within the fungal and likely bacterial kingdoms, biological superoxide may be an important contributor to the cycling of Mn, as well as other metals (e.g., Hg, Fe). Current and future explorations of the genes and proteins involved in superoxide production and Mn(II) oxidation will ideally lend insight into the physiological and biochemical basis for these processes.

  13. Cooperativity To Increase Turing Pattern Space for Synthetic Biology

    PubMed Central

    2014-01-01

    It is hard to bridge the gap between mathematical formulations and biological implementations of Turing patterns, yet this is necessary for both understanding and engineering these networks with synthetic biology approaches. Here, we model a reaction–diffusion system with two morphogens in a monostable regime, inspired by components that we recently described in a synthetic biology study in mammalian cells.1 The model employs a single promoter to express both the activator and inhibitor genes and produces Turing patterns over large regions of parameter space, using biologically interpretable Hill function reactions. We applied a stability analysis and identified rules for choosing biologically tunable parameter relationships to increase the likelihood of successful patterning. We show how to control Turing pattern sizes and time evolution by manipulating the values for production and degradation relationships. More importantly, our analysis predicts that steep dose–response functions arising from cooperativity are mandatory for Turing patterns. Greater steepness increases parameter space and even reduces the requirement for differential diffusion between activator and inhibitor. These results demonstrate some of the limitations of linear scenarios for reaction–diffusion systems and will help to guide projects to engineer synthetic Turing patterns. PMID:25122550

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

    PubMed

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

    2015-06-01

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

  15. 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.

  16. 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

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

    PubMed Central

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

    2012-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Diambra, Luis; da Fontoura Costa, Luciano

    2006-03-01

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

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

    PubMed

    Diambra, Luis; Costa, Luciano da Fontoura

    2006-03-01

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

  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. 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.

  4. Pattern formation in flowing electrorheological fluids.

    PubMed

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

    2002-05-01

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

  5. Cellular pattern formation in circular domains.

    PubMed

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

    1997-09-01

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

  6. Pattern Formation in Growing Polar Bacteria

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

  7. Pattern Formation Exhibited by Biofilm Formation within Microfluidic Chambers

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2013-05-01

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

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

    PubMed

    Jones, Jeff

    2010-01-01

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

  10. Adolescent Sleep Patterns: Biological, Social, and Psychological Influences.

    ERIC Educational Resources Information Center

    Carskadon, Mary A., Ed.

    Noting that healthy, adequate sleep fosters longevity and the optimal use of waking hours, and that adolescents, although rarely included in previous studies of sleep, are among the most sleep-deprived populations, this book explores the genesis and development of sleep patterns during adolescence, including biological and cultural factors that…

  11. 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

  12. 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.

  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. 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.

  15. Hypoxic adipocytes pattern early heterotopic bone formation.

    PubMed

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

    2007-02-01

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

  16. Quantification of layered patterns with structural anisotropy: a comparison of biological and geological systems.

    PubMed

    Smolyar, I; Bromage, T; Wikelski, M

    2016-03-01

    Large-scale patterns evident from satellite images of aeolian landforms on Earth and other planets; those of intermediate scale in marine and terrestrial sand ripples and sediment profiles; and small-scale patterns such as lamellae in the bones of vertebrates and annuli in fish scales are each represented by layers of different thicknesses and lengths. Layered patterns are important because they form a record of the state of internal and external factors that regulate pattern formation in these geological and biological systems. It is therefore potentially possible to recognize trends, periodicities, and events in the history of the formation of these systems among the incremental sequences. Though the structures and sizes of these 2-D patterns are typically scale-free, they are also characteristically anisotropic; that is, the number of layers and their absolute thicknesses vary significantly during formation. The aim of the present work is to quantify the structure of layered patterns and to reveal similarities and differences in the processing and interpretation of layered landforms and biological systems. To reach this goal we used N-partite graph and Boolean functions to quantify the structure of layers and plot charts for "layer thickness vs. layer number" and "layer area vs. layer number". These charts serve as a source of information about events in the history of formation of layered systems. The concept of synchronization of layer formation across a 2-D plane is introduced to develop the procedure for plotting "layer thickness vs. layer number" and "layer area vs. layer number", which takes into account the structural anisotropy of layered patterns and increase signal-to-noise ratio in charts. Examples include landforms on Mars and Earth and incremental layers in human and iguana bones. PMID:27441261

  17. Pattern formation in quantum Turing machines

    NASA Astrophysics Data System (ADS)

    Kim, Ilki; Mahler, Günter

    1999-07-01

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

  18. 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.

  19. 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.

  20. Spatial pattern formation in the lung

    PubMed Central

    Donovan, Graham M.; Kritter, Thibaut

    2014-01-01

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

  1. Instability-induced pattern formation of photoactivated functional polymers

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-12-01

    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

  3. Using ILP to Identify Pathway Activation Patterns in Systems Biology

    PubMed Central

    Neaves, Samuel R; Millard, Louise A C; Tsoka, Sophia

    2016-01-01

    We show a logical aggregation method that, combined with propositionalization methods, can construct novel structured biological features from gene expression data. We do this to gain understanding of pathway mechanisms, for instance, those associated with a particular disease. We illustrate this method on the task of distinguishing between two types of lung cancer; Squamous Cell Carcinoma (SCC) and Adenocarcinoma (AC). We identify pathway activation patterns in pathways previously implicated in the development of cancers. Our method identified a model with comparable predictive performance to the winning algorithm of a recent challenge, while providing biologically relevant explanations that may be useful to a biologist. PMID:27478883

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

    PubMed

    Seirin Lee, Sungrim

    2016-09-01

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

  5. The relationship between growth and pattern formation

    PubMed Central

    Bryant, Susan V.

    2016-01-01

    Abstract Successful development depends on the creation of spatial gradients of transcription factors within developing fields, and images of graded distributions of gene products populate the pages of developmental biology journals. Therefore the challenge is to understand how the graded levels of intracellular transcription factors are generated across fields of cells. We propose that transcription factor gradients are generated as a result of an underlying gradient of cell cycle lengths. Very long cell cycles will permit accumulation of a high level of a gene product encoded by a large transcription unit, whereas shorter cell cycles will permit progressively fewer transcripts to be completed due to gating of transcription by the cell cycle. We also propose that the gradients of cell cycle lengths are generated by gradients of extracellular morphogens/growth factors. The model of cell cycle gated transcriptional regulation brings focus back to the functional role of morphogens as cell cycle regulators, and proposes a specific and testable mechanism by which morphogens, in their roles as growth factors (how they were originally discovered), also determine cell fate. PMID:27499882

  6. Pattern Formation in Spatially Discrete Systems

    NASA Astrophysics Data System (ADS)

    Méndez, Vicenç; Fedotov, Sergei; Horsthemke, Werner

    The preceding chapters have dealt with the spatiotemporal behavior of spatially continuous systems. We now turn our attention to the dynamical behavior and stability properties of spatially discrete systems. A wide variety of phenomena in chemistry, biology, physics, and other fields involve the coupling between nonlinear, discrete units. Examples include arrays of Josephson junctions, chains of coupled diode resonators, coupled chemical or biochemical reactors, myelinated nerve fibers, neuronal networks, and patchy ecosystems. Such networks of coupled nonlinear units often combine dynamical and structural complexity [422]. Cells in living tissues, for example, are arranged in a variety of geometries. One-dimensional rings of cells were already considered by Turing [440]. Other types of lattices, such as open-ended linear arrays, tubes, rectangular and hexagonal arrays, and irregular arrangements in two or three dimensions are also found, see for example [5]. Cells interact with adjacent cells in various distinct ways. For example, signaling between cells may occur via diffusion through gap junctions [352, 230] or by membrane-bound proteins, juxtacrine signaling [339, 340, 471].

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

    NASA Astrophysics Data System (ADS)

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

    2008-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-05-01

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

  9. Optimal Vortex Formation as a Unifying Principle in Biological Propulsion

    NASA Astrophysics Data System (ADS)

    Gharib, Morteza

    2004-11-01

    The dynamics of vortex formation in starting flows are governed by limiting physical processes that have been observed in experiments and numerical simulations. For several years it has been suggested that the principles of optimal vortex ring formation discovered in the laboratory might also occur naturally in biological systems. Pulsed-jet swimming (e.g. squid and jellyfish) and cardiac blood transport are among the most commonly cited examples of systems which could benefit from a strategy of optimal vortex ring formation. However, previous efforts to quantify the biological mechanisms of vortex formation have encountered difficulties in resolving the effects of transient boundary conditions such as valve and orifice motion. We have combined new vortex generation techniques with in vivo measurements to determine the effects of time-dependent boundary conditions on vortex formation by starting-flow propulsors. Results indicate that vortex formation across various biological systems is manipulated by these kinematics in order to maximize thrust and/or propulsive efficiency. Hence, it is important to include these effects in realistic models of the bio-fluid mechanics. We also examine possible extension of these results to organisms that generate more complex vortical structures, such as fishes and birds. An emphasis on observed vortex dynamics and transient boundary conditions facilitates quantitative comparisons across propulsion schemes irrespective of their individual biological functions.

  10. 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

  11. Optical pattern formation with a two-level nonlinearity

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

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

    NASA Astrophysics Data System (ADS)

    Golovin, Alexander A.; Nepomnyashchy, Alexander A.

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

  13. Pattern formation and morphology transitions in bacterial systems

    NASA Astrophysics Data System (ADS)

    Arouh, Scott

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

  14. Neural pattern formation in networks with dendritic structure

    NASA Astrophysics Data System (ADS)

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

    1998-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Sandfeld, Stefan; Zaiser, Michael

    2015-09-01

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

  16. Patterning and characterization of surfaces with organic and biological molecules by the scanning electrochemical microscope.

    PubMed

    Turyan, I; Matsue, T; Mandler, D

    2000-08-01

    A novel approach for micropatterning of surfaces with organic and biological microstructures using the scanning electrochemical microscope (SECM) is described. The approach is based on the introduction of the spatial resolution by local deposition of gold particles followed by monolayer formation and functionalization. Specifically, gold patterns were deposited locally on silicon wafers with the SECM as a result of the controlled anodic dissolution of a gold microelectrode. The gold patterns were further used as microsubstrates for assembling cystamine monolayers to which either fluoresceine isothiocyanate (FIT) or glucose oxidase (GOD) were covalently attached. Characterization of the organic monolayers, as well as the biological activity of the enzyme patterns, was carried out by fluorescence microscopy and the SECM, respectively. PMID:10952523

  17. Predicting spiral wave patterns from cell properties in a model of biological self-organization

    NASA Astrophysics Data System (ADS)

    Geberth, Daniel; Hütt, Marc-Thorsten

    2008-09-01

    In many biological systems, biological variability (i.e., systematic differences between the system components) can be expected to outrank statistical fluctuations in the shaping of self-organized patterns. In principle, the distribution of single-element properties should thus allow predicting features of such patterns. For a mathematical model of a paradigmatic and well-studied pattern formation process, spiral waves of cAMP signaling in colonies of the slime mold Dictyostelium discoideum, we explore this possibility and observe a pronounced anticorrelation between spiral waves and cell properties (namely, the firing rate) and particularly a clustering of spiral wave tips in regions devoid of spontaneously firing (pacemaker) cells. Furthermore, we observe local inhomogeneities in the distribution of spiral chiralities, again induced by the pacemaker distribution. We show that these findings can be explained by a simple geometrical model of spiral wave generation.

  18. Trapping and patterning of biological objects using photovoltaic tweezers

    NASA Astrophysics Data System (ADS)

    Jubera, M.; Elvira, I.; García-Cabañes, A.; Bella, J. L.; Carrascosa, M.

    2016-01-01

    Photovoltaic tweezers are a recently proposed technique for manipulation and patterning of micro- and nano-objects. It is based in the dielectrophoretic forces associated to the electric fields induced by illumination of certain ferroelectrics due to the bulk photovoltaic effect. The technique has been applied to the patterning of dielectric and metal micro- and nano-particles. In this work, we report the use of photovoltaic tweezers to pattern biological objects on LiNbO3:Fe. Specifically, spores and pollen grains and their nanometric fragments have been trapped and patterned. 1D and 2D arrangements have been achieved by deposition in air or from a hexane suspension. The quality of patterns obtained with nanometric fragments is even better than previous results using photovoltaic tweezers with inorganic micro- and nano-particles. In fact, 1D patterns with a period of 2 μm, almost half of the minimum reported period achieved with photovoltaic tweezers, have been obtained with pollen fragments.

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

    NASA Astrophysics Data System (ADS)

    Brutin, David; Sobac, Benjamin

    2011-11-01

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

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

    PubMed

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

    2015-07-14

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

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

    PubMed Central

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

    2015-01-01

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

  2. 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.

  3. Pattern formation via intermittence from microscopic deterministic dynamics

    NASA Astrophysics Data System (ADS)

    Hernández, Marco; Escaff, Daniel; Finger, Ricardo

    2012-05-01

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

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

    NASA Astrophysics Data System (ADS)

    Kenkre, V. M.

    2012-10-01

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

  5. Biological agent detection and identification using pattern recognition

    NASA Astrophysics Data System (ADS)

    Braun, Jerome J.; Glina, Yan; Judson, Nicholas; Transue, Kevin D.

    2005-05-01

    This paper discusses a novel approach for the automatic identification of biological agents. The essence of the approach is a combination of gene expression, microarray-based sensing, information fusion, machine learning and pattern recognition. Integration of these elements is a distinguishing aspect of the approach, leading to a number of significant advantages. Amongst them are the applicability to various agent types including bacteria, viruses, toxins, and other, ability to operate without the knowledge of a pathogen's genome sequence and without the need for bioagent-speciific materials or reagents, and a high level of extensibility. Furthermore, the approach allows detection of uncatalogued agents, including emerging pathogens. The approach offers a promising avenue for automatic identification of biological agents for applications such as medical diagnostics, bioforensics, and biodefense.

  6. 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

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

    PubMed

    Czirok, Andras

    2013-01-01

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

  8. Cortical Folding Pattern and its Consistency Induced by Biological Growth

    NASA Astrophysics Data System (ADS)

    Jalil Razavi, Mir; Zhang, Tuo; Liu, Tianming; Wang, Xianqiao

    2015-09-01

    Cortical folding, characterized by convex gyri and concave sulci, has an intrinsic relationship to the brain’s functional organization. Understanding the mechanism of the brain’s convoluted patterns can provide useful clues into normal and pathological brain function. In this paper, the cortical folding phenomenon is interpreted both analytically and computationally, and, in some cases, the findings are validated with experimental observations. The living human brain is modeled as a soft structure with a growing outer cortex and inner core to investigate its developmental mechanism. Analytical interpretations of differential growth of the brain model provide preliminary insight into critical growth ratios for instability and crease formation of the developing brain. Since the analytical approach cannot predict the evolution of cortical complex convolution after instability, non-linear finite element models are employed to study the crease formation and secondary morphological folds of the developing brain. Results demonstrate that the growth ratio of the cortex to core of the brain, the initial thickness, and material properties of both cortex and core have great impacts on the morphological patterns of the developing brain. Lastly, we discuss why cortical folding is highly correlated and consistent by presenting an intriguing gyri-sulci formation comparison.

  9. Cortical Folding Pattern and its Consistency Induced by Biological Growth

    PubMed Central

    Jalil Razavi, Mir; Zhang, Tuo; Liu, Tianming; Wang, Xianqiao

    2015-01-01

    Cortical folding, characterized by convex gyri and concave sulci, has an intrinsic relationship to the brain’s functional organization. Understanding the mechanism of the brain’s convoluted patterns can provide useful clues into normal and pathological brain function. In this paper, the cortical folding phenomenon is interpreted both analytically and computationally, and, in some cases, the findings are validated with experimental observations. The living human brain is modeled as a soft structure with a growing outer cortex and inner core to investigate its developmental mechanism. Analytical interpretations of differential growth of the brain model provide preliminary insight into critical growth ratios for instability and crease formation of the developing brain. Since the analytical approach cannot predict the evolution of cortical complex convolution after instability, non-linear finite element models are employed to study the crease formation and secondary morphological folds of the developing brain. Results demonstrate that the growth ratio of the cortex to core of the brain, the initial thickness, and material properties of both cortex and core have great impacts on the morphological patterns of the developing brain. Lastly, we discuss why cortical folding is highly correlated and consistent by presenting an intriguing gyri-sulci formation comparison. PMID:26404042

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

    PubMed

    Sherratt, Jonathan A; Mackenzie, Julia J

    2016-10-01

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

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

    PubMed

    Sundaresan, Venkatesan; Alandete-Saez, Monica

    2010-01-01

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

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

    PubMed

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

    2015-07-01

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

  13. 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.

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

    PubMed

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

    2014-10-01

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

  15. Nonequilibrium breakdown of a correlated insulator through pattern formation

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  16. 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.

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

    DOE PAGESBeta

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

    2015-01-23

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

  18. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2007-09-01

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

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

    PubMed

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

    2007-09-14

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

  1. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  3. Clustering and Pattern Formation in Chemorepulsive Active Colloids

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  4. Clustering and Pattern Formation in Chemorepulsive Active Colloids.

    PubMed

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

    2015-12-18

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

  5. Patterned Plasmonic Nanoparticle Arrays for Microfluidic and Multiplexed Biological Assays.

    PubMed

    He, Jie; Boegli, Michelle; Bruzas, Ian; Lum, William; Sagle, Laura

    2015-11-17

    For applications ranging from medical diagnostics and drug screening to chemical and biological warfare detection, inexpensive, rapid-readout, portable devices are required. Localized surface plasmon resonance (LSPR) technologies show substantial promise toward meeting these goals, but the generation of portable, multiplexed and/or microfluidic devices incorporating sensitive nanoparticle arrays is only in its infancy. Herein, we have combined photolithography with Hole Mask Colloidal lithography to pattern uniform nanoparticle arrays for both microfluidic and multiplexed devices. The first proof-of-concept study is carried out with 5- and 7-channel microfluidic devices to acquire one-shot binding curves and protein binding kinetic data. The second proof-of-concept study involved the fabrication of a 96-spot plate that can be inserted into a standard plate reader for the multiplexed detection of protein binding. This versatile fabrication technique should prove useful in next generation chips for bioassays and genetic screening. PMID:26494412

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  8. Modeling in pattern formation with applications to electrochemical phenomena

    NASA Astrophysics Data System (ADS)

    Stanton, Liam G.

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

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

    PubMed

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

    2012-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2002-03-01

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

  11. Spatial Pattern of Biological Soil Crust with Fractal Geometry

    NASA Astrophysics Data System (ADS)

    Ospina, Abelardo; Florentino, Adriana; Tarquis, Ana M.

    2015-04-01

    Soil surface characteristics are subjected to changes driven by several interactions between water, air, biotic and abiotic components. One of the examples of such interactions is provided through biological soil crusts (BSC) in arid and semi-arid environments. BSC are communities composed of cyanobacteria, fungi, mosses, lichens, algae and liverworts covering the soil surface and play an important role in ecosystem functioning. The characteristics and formation of these BSC influence the soil hydrological balance, control the mass of eroded sediment, increase stability of soil surface, and influence plant productivity through the modification of nitrogen and carbon cycle. This study focus on characterize the spatial arrangements of the BSC based on image analysis and fractal concepts. To this end, RGB images of different types of biological soil crust where taken, each image corresponding to an area of 3.6 cm2 with a resolution of 1024x1024 pixels. For each image and channel, mass dimension and entropy were calculated. Preliminary results indicate that fractal methods are useful to describe changes associated to different types of BSC. Further research is necessary to apply these methodologies to several situations.

  12. Pattern formation gains interest in the Earth sciences

    NASA Astrophysics Data System (ADS)

    Durant, Dolores G.

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

  13. Spontaneous Pattern Formation in an Antiferromagnetic Quantum Gas

    SciTech Connect

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

    2010-08-27

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

  14. 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.

  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. Multiscale analysis of pattern formation via intercellular signalling.

    PubMed

    O'Dea, R D; King, J R

    2011-06-01

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

  18. Processing biological literature with customizable Web services supporting interoperable formats

    PubMed Central

    Rak, Rafal; Batista-Navarro, Riza Theresa; Carter, Jacob; Rowley, Andrew; Ananiadou, Sophia

    2014-01-01

    Web services have become a popular means of interconnecting solutions for processing a body of scientific literature. This has fuelled research on high-level data exchange formats suitable for a given domain and ensuring the interoperability of Web services. In this article, we focus on the biological domain and consider four interoperability formats, BioC, BioNLP, XMI and RDF, that represent domain-specific and generic representations and include well-established as well as emerging specifications. We use the formats in the context of customizable Web services created in our Web-based, text-mining workbench Argo that features an ever-growing library of elementary analytics and capabilities to build and deploy Web services straight from a convenient graphical user interface. We demonstrate a 2-fold customization of Web services: by building task-specific processing pipelines from a repository of available analytics, and by configuring services to accept and produce a combination of input and output data interchange formats. We provide qualitative evaluation of the formats as well as quantitative evaluation of automatic analytics. The latter was carried out as part of our participation in the fourth edition of the BioCreative challenge. Our analytics built into Web services for recognizing biochemical concepts in BioC collections achieved the highest combined scores out of 10 participating teams. Database URL: http://argo.nactem.ac.uk. PMID:25006225

  19. Processing biological literature with customizable Web services supporting interoperable formats.

    PubMed

    Rak, Rafal; Batista-Navarro, Riza Theresa; Carter, Jacob; Rowley, Andrew; Ananiadou, Sophia

    2014-01-01

    Web services have become a popular means of interconnecting solutions for processing a body of scientific literature. This has fuelled research on high-level data exchange formats suitable for a given domain and ensuring the interoperability of Web services. In this article, we focus on the biological domain and consider four interoperability formats, BioC, BioNLP, XMI and RDF, that represent domain-specific and generic representations and include well-established as well as emerging specifications. We use the formats in the context of customizable Web services created in our Web-based, text-mining workbench Argo that features an ever-growing library of elementary analytics and capabilities to build and deploy Web services straight from a convenient graphical user interface. We demonstrate a 2-fold customization of Web services: by building task-specific processing pipelines from a repository of available analytics, and by configuring services to accept and produce a combination of input and output data interchange formats. We provide qualitative evaluation of the formats as well as quantitative evaluation of automatic analytics. The latter was carried out as part of our participation in the fourth edition of the BioCreative challenge. Our analytics built into Web services for recognizing biochemical concepts in BioC collections achieved the highest combined scores out of 10 participating teams. Database URL: http://argo.nactem.ac.uk. PMID:25006225

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

    PubMed Central

    Kioussi, Chrissa; Gross, Michael K.

    2008-01-01

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

  1. 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.

  2. Multiple stable states and pattern formation in tidal environments

    NASA Astrophysics Data System (ADS)

    Marani, M.

    2012-12-01

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

  3. 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

  4. 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.

  5. Biological traits and growth patterns of pejerrey Odontesthes argentinensis.

    PubMed

    Llompart, F M; Colautti, D C; Maiztegui, T; Cruz-Jiménez, A M; Baigún, C R M

    2013-02-01

    This study assesses for the first time the relationship between annual cycles of different biological indices with growth patterns of a marine pejerrey Odontesthes argentinensis population near its southern-distribution boundary in North Patagonia. The reproductive period is between September and November evidenced by an increase in the gonado-somatic index with a peak in October corresponding to spawning. The reproductive cycle was also coupled with metabolic processes related to energy allocation as shown by changes in the hepato-somatic index and body condition. Total length (L(T) ) at maturity was 270 for females and 282 mm for males, whereas fecundity was estimated at mean ±s.d. = 9380 ± 1797 mature oocytes. Based on the marginal increment analysis, most of the scales showed a maximum value during summer, with a sharp decline thereafter during autumn and winter, indicating that scale rings are formed during the latter period and only once a year. Growth fitted by the von Bertalanffy model for both males and females did not show significant differences and showed a rapid growth during the first 2 years. The shorter reproductive period compared with that of the northern O. argentinensis populations inhabiting tropical and subtropical areas was interpreted as an adjustment to temperate environmental conditions. The larger maximum L(T) and L(T) at first maturity are in agreement with the counter-gradient hypothesis and could be related to the selective effects of low temperature and a shorter growing season. This latitude dependency argues strongly against the application of the same fishing regulations for different O. argentinensis populations as a whole and reinforces the need to assess basic biological features at a population scale to promote local sustainable fisheries management. PMID:23398062

  6. Dynamics of laser induced metal nanoparticle and pattern formation

    SciTech Connect

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

    2015-02-09

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

  7. The role of optimal vortex formation in biological fluid transport

    PubMed Central

    Dabiri, John O; Gharib, Morteza

    2005-01-01

    Animal phyla that require macro-scale fluid transport for functioning have repeatedly and often independently converged on the use of jet flows. During flow initiation these jets form fluid vortex rings, which facilitate mass transfer by stationary pumps (e.g. cardiac chambers) and momentum transfer by mobile systems (e.g. jet-propelled swimmers). Previous research has shown that vortex rings generated in the laboratory can be optimized for efficiency or thrust, based on the jet length-to-diameter ratio (L/D), with peak performance occurring at 3.5biological jets achieve this optimization have been inconclusive, due to the inability to properly account for the diversity of jet kinematics found across animal phyla. We combine laboratory experiments, in situ observations and a framework that reduces the kinematics to a single parameter in order to quantitatively show that individual animal kinematics can be tuned in correlation with optimal vortex ring formation. This new approach identifies simple rules for effective fluid transport, facilitates comparative biological studies of jet flows across animal phyla irrespective of their specific functions and can be extended to unify theories of optimal jet-based and flapping-based vortex ring formation. PMID:16048770

  8. The role of optimal vortex formation in biological fluid transport.

    PubMed

    Dabiri, John O; Gharib, Morteza

    2005-08-01

    Animal phyla that require macro-scale fluid transport for functioning have repeatedly and often independently converged on the use of jet flows. During flow initiation these jets form fluid vortex rings, which facilitate mass transfer by stationary pumps (e.g. cardiac chambers) and momentum transfer by mobile systems (e.g. jet-propelled swimmers). Previous research has shown that vortex rings generated in the laboratory can be optimized for efficiency or thrust, based on the jet length-to-diameter ratio (L/D), with peak performance occurring at 3.5biological jets achieve this optimization have been inconclusive, due to the inability to properly account for the diversity of jet kinematics found across animal phyla. We combine laboratory experiments, in situ observations and a framework that reduces the kinematics to a single parameter in order to quantitatively show that individual animal kinematics can be tuned in correlation with optimal vortex ring formation. This new approach identifies simple rules for effective fluid transport, facilitates comparative biological studies of jet flows across animal phyla irrespective of their specific functions and can be extended to unify theories of optimal jet-based and flapping-based vortex ring formation. PMID:16048770

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

    PubMed

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

    2016-01-01

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

  10. 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

  11. 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.

  12. The theory of pattern formation on directed networks

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

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

    PubMed

    Dawes, J H P; Williams, J L M

    2016-07-01

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

  14. 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.

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

    PubMed

    Tan, P C; Jones, G W

    1990-01-01

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

  16. 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.

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

    NASA Astrophysics Data System (ADS)

    Gheorghiu, Nadina

    2003-10-01

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

  18. Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data

    PubMed Central

    Kyoda, Koji; Tohsato, Yukako; Ho, Kenneth H. L.; Onami, Shuichi

    2015-01-01

    Motivation: Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats. Results: We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis. Availability and implementation: A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/. Contact: sonami@riken.jp Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:25414366

  19. 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.

  20. Interfacial pattern formation in confined power-law fluids

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

  1. 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

  2. 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

  3. 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

  4. Patterns and controls on nitrogen cycling of biological soil crusts

    USGS Publications Warehouse

    Barger, Nichole N.; Zaady, Eli; Weber, Bettina; Garcia-Pichel, Ferran; Belnap, Jayne

    2016-01-01

    Biocrusts play a significant role in the nitrogen [N ] cycle within arid and semi-arid ecosystems, as they contribute major N inputs via biological fixation and dust capture, harbor internal N transformation processes, and direct N losses via N dissolved, gaseous and erosional loss processes (Fig. 1). Because soil N availability in arid and semi-arid ecosystems is generally low and may limit net primary production (NPP), especially during periods when adequate water is available, understanding the mechanisms and controls of N input and loss pathways in biocrusts is critically important to our broader understanding of N cycling in dryland environments. In particular, N cycling by biocrusts likely regulates short-term soil N availability to support vascular plant growth, as well as long-term N accumulation and maintenance of soil fertility. In this chapter, we review the influence of biocrust nutrient input, internal cycling, and loss pathways across a range of biomes. We examine linkages between N fixation capabilities of biocrust organisms and spatio-temporal patterns of soil N availability that may influence the longer-term productivity of dryland ecosystems. Lastly, biocrust influence on N loss pathways such as N gas loss, leakage of N compounds from biocrusts, and transfer in wind and water erosion are important to understand the maintenance of dryland soil fertility over longer time scales. Although great strides have been made in understanding the influence of biocrusts on ecosystem N cycling, there are important knowledge gaps in our understanding of the influence of biocrusts on ecosystem N cycling that should be the focus of future studies. Because work on the interaction of N cycling and biocrusts was reviewed in Belnap and Lange (2003), this chapter will focus primarily on research findings that have emerged over the last 15 years (2000-2015).

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

    PubMed

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

    2014-04-01

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

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

    PubMed

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

    2003-08-21

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

  7. 5-methylcytosine in RNA: detection, enzymatic formation and biological functions

    PubMed Central

    Motorin, Yuri; Lyko, Frank; Helm, Mark

    2010-01-01

    The nucleobase modification 5-methylcytosine (m5C) is widespread both in DNA and different cellular RNAs. The functions and enzymatic mechanisms of DNA m5C-methylation were extensively studied during the last decades. However, the location, the mechanism of formation and the cellular function(s) of the same modified nucleobase in RNA still remain to be elucidated. The recent development of a bisulfite sequencing approach for efficient m5C localization in various RNA molecules puts ribo-m5C in a highly privileged position as one of the few RNA modifications whose detection is amenable to PCR-based amplification and sequencing methods. Additional progress in the field also includes the characterization of several specific RNA methyltransferase enzymes in various organisms, and the discovery of a new and unexpected link between DNA and RNA m5C-methylation. Numerous putative RNA:m5C-MTases have now been identified and are awaiting characterization, including the identification of their RNA substrates and their related cellular functions. In order to bring these recent exciting developments into perspective, this review provides an ordered overview of the detection methods for RNA methylation, of the biochemistry, enzymology and molecular biology of the corresponding modification enzymes, and discusses perspectives for the emerging biological functions of these enzymes. PMID:20007150

  8. 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

  9. An Investigation of the Relative Effectiveness of Two Scheduling Patterns of an Introductory College Biology Course.

    ERIC Educational Resources Information Center

    Chanin, Lynne Sheppard

    Students in an introductory biology course had laboratory sessions in one of two patterns: as one three-hour session per week, or as two one-and-one-half hour sessions, one after each lecture. Each of the twelve instructors involved taught one section using each pattern. The Nelson Biology Test, the Watson-Glaser Critical Thinking Appraisal, and a…

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    1997-03-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

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

    DOE PAGESBeta

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

    2015-11-19

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

  16. 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.

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

    PubMed

    Martínez-García, Ricardo; Murgui, Clara; Hernández-García, Emilio; López, Cristóbal

    2015-01-01

    We study the spatial patterns formed by a system of interacting particles where the mobility of any individual is determined by the population crowding at two different spatial scales. In this way we model the behavior of some biological organisms (like mussels) that tend to cluster at short ranges as a defensive strategy, and strongly disperse if there is a high population pressure at large ranges for optimizing foraging. We perform stochastic simulations of a particle-level model of the system, and derive and analyze a continuous density description (a nonlinear diffusion equation). In both cases we show that this interplay of scale-dependent-behaviors gives rise to a rich formation of spatial patterns ranging from labyrinths to periodic cluster arrangements. In most cases these clusters have the very peculiar appearance of ring-like structures, i.e., organisms arranging in the perimeter of the clusters, which we discuss in detail. PMID:26147351

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

    NASA Astrophysics Data System (ADS)

    Baxter, George William, III

    1990-01-01

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

  19. 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.

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

    PubMed

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

    2015-04-21

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

  1. Ternary eutectic dendrites: Pattern formation and scaling properties

    SciTech Connect

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

    2015-04-21

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

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

    PubMed

    Potts, Jonathan R; Lewis, Mark A

    2016-01-01

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

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

    PubMed

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

    2016-03-01

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

  4. 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.

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

    PubMed

    Balavoine, Guillaume

    2014-01-01

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

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

    PubMed Central

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

    2012-01-01

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

  7. Refinement and Pattern Formation in Neural Circuits by the Interaction of Traveling Waves with Spike-Timing Dependent Plasticity.

    PubMed

    Bennett, James E M; Bair, Wyeth

    2015-08-01

    Traveling waves in the developing brain are a prominent source of highly correlated spiking activity that may instruct the refinement of neural circuits. A candidate mechanism for mediating such refinement is spike-timing dependent plasticity (STDP), which translates correlated activity patterns into changes in synaptic strength. To assess the potential of these phenomena to build useful structure in developing neural circuits, we examined the interaction of wave activity with STDP rules in simple, biologically plausible models of spiking neurons. We derive an expression for the synaptic strength dynamics showing that, by mapping the time dependence of STDP into spatial interactions, traveling waves can build periodic synaptic connectivity patterns into feedforward circuits with a broad class of experimentally observed STDP rules. The spatial scale of the connectivity patterns increases with wave speed and STDP time constants. We verify these results with simulations and demonstrate their robustness to likely sources of noise. We show how this pattern formation ability, which is analogous to solutions of reaction-diffusion systems that have been widely applied to biological pattern formation, can be harnessed to instruct the refinement of postsynaptic receptive fields. Our results hold for rich, complex wave patterns in two dimensions and over several orders of magnitude in wave speeds and STDP time constants, and they provide predictions that can be tested under existing experimental paradigms. Our model generalizes across brain areas and STDP rules, allowing broad application to the ubiquitous occurrence of traveling waves and to wave-like activity patterns induced by moving stimuli. PMID:26308406

  8. Refinement and Pattern Formation in Neural Circuits by the Interaction of Traveling Waves with Spike-Timing Dependent Plasticity

    PubMed Central

    Bennett, James E. M.; Bair, Wyeth

    2015-01-01

    Traveling waves in the developing brain are a prominent source of highly correlated spiking activity that may instruct the refinement of neural circuits. A candidate mechanism for mediating such refinement is spike-timing dependent plasticity (STDP), which translates correlated activity patterns into changes in synaptic strength. To assess the potential of these phenomena to build useful structure in developing neural circuits, we examined the interaction of wave activity with STDP rules in simple, biologically plausible models of spiking neurons. We derive an expression for the synaptic strength dynamics showing that, by mapping the time dependence of STDP into spatial interactions, traveling waves can build periodic synaptic connectivity patterns into feedforward circuits with a broad class of experimentally observed STDP rules. The spatial scale of the connectivity patterns increases with wave speed and STDP time constants. We verify these results with simulations and demonstrate their robustness to likely sources of noise. We show how this pattern formation ability, which is analogous to solutions of reaction-diffusion systems that have been widely applied to biological pattern formation, can be harnessed to instruct the refinement of postsynaptic receptive fields. Our results hold for rich, complex wave patterns in two dimensions and over several orders of magnitude in wave speeds and STDP time constants, and they provide predictions that can be tested under existing experimental paradigms. Our model generalizes across brain areas and STDP rules, allowing broad application to the ubiquitous occurrence of traveling waves and to wave-like activity patterns induced by moving stimuli. PMID:26308406

  9. A biologically active surface enzyme assembly that attenuates thrombus formation

    PubMed Central

    Qu, Zheng; Muthukrishnan, Sharmila; Urlam, Murali K.; Haller, Carolyn A.; Jordan, Sumanas W.; Kumar, Vivek A.; Marzec, Ulla M.; Elkasabi, Yaseen; Lahann, Joerg; Hanson, Stephen R.

    2013-01-01

    Activation of hemostatic pathways by blood-contacting materials remains a major hurdle in the development of clinically durable artificial organs and implantable devices. We postulate that surface-induced thrombosis may be attenuated by the reconstitution onto blood contacting surfaces of bioactive enzymes that regulate the production of thrombin, a central mediator of both clotting and platelet activation cascades. Thrombomodulin (TM), a transmembrane protein expressed by endothelial cells, is an established negative regulator of thrombin generation in the circulatory system. Traditional techniques to covalently immobilize enzymes on solid supports may modify residues contained within or near the catalytic site, thus reducing the bioactivity of surface enzyme assemblies. In this report, we present a molecular engineering and bioorthogonal chemistry approach to site-specifically immobilize a biologically active recombinant human TM fragment onto the luminal surface of small diameter prosthetic vascular grafts. Bioactivity and biostability of TM modified grafts is confirmed in vitro and the capacity of modified grafts to reduce platelet activation is demonstrated using a non-human primate model. These studies indicate that molecularly engineered interfaces that display TM actively limit surface-induced thrombus formation. PMID:23532366

  10. DETERMINATION OF APPARENT QUANTUM YIELD SPECTRA FOR THE FORMATION OF BIOLOGICALLY LABILE PHOTOPRODUCTS

    EPA Science Inventory

    Quantum yield spectra for the photochemical formation of biologically labile photoproducts from dissolved organic matter (DOM) have not been available previously, although they would greatly facilitate attempts to model photoproduct formation rates across latitudinal, seasonal, a...

  11. Switch and template pattern formation in a discrete reaction-diffusion system inspired by the Drosophila eye

    PubMed Central

    Pennington, Matthew W.; Lubensky, David K.

    2011-01-01

    We examine a spatially discrete reaction diffusion model based on the interactions that create a periodic pattern in the Drosophila eye imaginal disc. This model is known to be capable of generating a regular hexagonal pattern of gene expression behind a moving front, as observed in the fly system. In order to better understand the novel “switch and template” mechanism behind this pattern formation, we present here a detailed study of the model's behavior in one dimension, using a combination of analytic methods and numerical searches of parameter space. We find that patterns are created robustly provided that there is an appropriate separation of timescales and that self-activation is sufficiently strong, and we derive expressions in this limit for the front speed and the pattern wavelength. Moving fronts in pattern-forming systems near an initial linear instability generically select a unique pattern, but our model operates in a strongly nonlinear regime where the final pattern depends on the initial conditions as well as on parameter values. Our work highlights the important role that cellularization and cell-autonomous feedback can play in biological pattern formation. PMID:20862598

  12. Pathological pattern formation and cortical propagation of epileptic seizures

    PubMed Central

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

    2005-01-01

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

  13. Transcriptional Switches Direct Plant Organ Formation and Patterning

    PubMed Central

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

    2013-01-01

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

  14. Spatial pattern formation facilitates eradication of infectious diseases.

    PubMed

    Eisinger, Dirk; Thulke, Hans-Hermann

    2008-04-01

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

  15. Family formation patterns among migrant women in Sydney.

    PubMed

    Yusuf, F; Siedlecky, S

    1996-01-01

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

  16. Control of Oscillation Patterns in a Symmetric Coupled Biological Oscillator System

    NASA Astrophysics Data System (ADS)

    Takamatsu, Atsuko; Tanaka, Reiko; Yamamoto, Takatoki; Fujii, Teruo

    2003-08-01

    A chain of three-oscillator system was constructed with living biological oscillators of phasmodial slime mold, Physarum polycehalum and the oscillation patterns were analyzed by the symmetric Hopf bifurcation theory using group theory. Multi-stability of oscillation patterns was observed, even when the coupling strength was fixed. This suggests that the coupling strength is not an effective parameter to obtain a desired oscillation pattern among the multiple patterns. Here we propose a method to control oscillation patterns using resonance to external stimulus and demonstrate pattern switching induced by frequency resonance given to only one of oscillators in the system.

  17. Global patterns in threats to vertebrates by biological invasions.

    PubMed

    Bellard, C; Genovesi, P; Jeschke, J M

    2016-01-27

    Biological invasions as drivers of biodiversity loss have recently been challenged. Fundamentally, we must know where species that are threatened by invasive alien species (IAS) live, and the degree to which they are threatened. We report the first study linking 1372 vertebrates threatened by more than 200 IAS from the completely revised Global Invasive Species Database. New maps of the vulnerability of threatened vertebrates to IAS permit assessments of whether IAS have a major influence on biodiversity, and if so, which taxonomic groups are threatened and where they are threatened. We found that centres of IAS-threatened vertebrates are concentrated in the Americas, India, Indonesia, Australia and New Zealand. The areas in which IAS-threatened species are located do not fully match the current hotspots of invasions, or the current hotspots of threatened species. The relative importance of biological invasions as drivers of biodiversity loss clearly varies across regions and taxa, and changes over time, with mammals from India, Indonesia, Australia and Europe are increasingly being threatened by IAS. The chytrid fungus primarily threatens amphibians, whereas invasive mammals primarily threaten other vertebrates. The differences in IAS threats between regions and taxa can help efficiently target IAS, which is essential for achieving the Strategic Plan 2020 of the Convention on Biological Diversity. PMID:26817767

  18. Metal nanoclusters: Protein corona formation and implications for biological applications.

    PubMed

    Shang, Li; Nienhaus, Gerd Ulrich

    2016-06-01

    Metal nanoclusters (NCs) are a new type of nanoprobe with great potential in various biological applications. For biocompatible and efficient utilization of NCs, a thorough understanding of their interactions with biological systems is highly important. Herein, we focus on recent studies addressing interactions between metal NCs and proteins as well as implications for their further biological application. These findings show that protein adsorption not only affects the photophysical properties of NCs, but also influences their subsequent biological behavior, i.e., cellular uptake and cytotoxicity. Moreover, specific protein-NC interactions have also been harnessed to develop novel protein discrimination strategies. PMID:26408503

  19. A Comparative Atlas of Zooplankton: Biological Patterns in the Oceans

    NASA Astrophysics Data System (ADS)

    Biggs, Douglas C.

    Large-scale biogeographic trends in the distribution of marine zooplankton are the subject of this work. As the subtitle of this book clarifies, it is an illustrated compendium of distributional patterns rather than a taxonomic atlas of invertebrate zoology. About half the work is devoted to Mercator projection maps of global distribution of various species of zooplankton and of chemical and physical properties of their environment. The other half is a treatise on plankton ecology as it relates to speciation.

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

    PubMed

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

    2001-04-01

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

  2. Surface induced phase separation and pattern formation at the isotropic interface in chiral nematic liquid crystals.

    PubMed

    Zola, R S; Evangelista, L R; Yang, Y-C; Yang, D-K

    2013-02-01

    We study the pattern formation of a chiral nematic liquid crystal under a wetting transition. In the isotropic-liquid crystal transition, a surface-enhanced effect happens and a thin liquid crystal layer forms at the substrates of the cell. In this confined system, chirality, elastic anisotropy, surface anchoring, and wetting strength interplay. A striped pattern is formed due to the chiral nature of the material and the tilted anchoring at the isotropic boundary. As the wetting layer grows from cooling the sample, first the stripes rotate through a process where dislocation defects are formed. As the wetting layer grows further, the periodicity of the stripe structure changes, and finally a splitting of the stripes occurs. Because of the unique properties of this system, new insights about pitch-thickness ratio, interface anchoring, and elastic anisotropy effect are found. Since the anchoring at the isotropic boundary is weak, the critical ratio between the thickness of the wetting layer and the helical pitch is different from that reported in the literature. We also discover that the elastic anisotropy and elastic constant ratios play a critical role in stripe formation. Because of the similarity with biological fibrous composites (twisted plywood), our system may be used as a synthetic version to mimic the naturally occurring one. We carry out a simulation study to explain the experimental results. PMID:23414046

  3. Surface Induced Phase Separation and Pattern Formation at the Isotropic Interface in Chiral Nematic Liquid Crystals

    NASA Astrophysics Data System (ADS)

    Zola, R. S.; Evangelista, L. R.; Yang, Y.-C.; Yang, D.-K.

    2013-02-01

    We study the pattern formation of a chiral nematic liquid crystal under a wetting transition. In the isotropic-liquid crystal transition, a surface-enhanced effect happens and a thin liquid crystal layer forms at the substrates of the cell. In this confined system, chirality, elastic anisotropy, surface anchoring, and wetting strength interplay. A striped pattern is formed due to the chiral nature of the material and the tilted anchoring at the isotropic boundary. As the wetting layer grows from cooling the sample, first the stripes rotate through a process where dislocation defects are formed. As the wetting layer grows further, the periodicity of the stripe structure changes, and finally a splitting of the stripes occurs. Because of the unique properties of this system, new insights about pitch-thickness ratio, interface anchoring, and elastic anisotropy effect are found. Since the anchoring at the isotropic boundary is weak, the critical ratio between the thickness of the wetting layer and the helical pitch is different from that reported in the literature. We also discover that the elastic anisotropy and elastic constant ratios play a critical role in stripe formation. Because of the similarity with biological fibrous composites (twisted plywood), our system may be used as a synthetic version to mimic the naturally occurring one. We carry out a simulation study to explain the experimental results.

  4. Effects of Scoring by Section and Independent Scorers' Patterns on Scorer Reliability in Biology Essay Tests

    ERIC Educational Resources Information Center

    Ebuoh, Casmir N.; Ezeudu, S. A.

    2015-01-01

    The study investigated the effects of scoring by section, use of independent scorers and conventional patterns on scorer reliability in Biology essay tests. It was revealed from literature review that conventional pattern of scoring all items at a time in essay tests had been criticized for not being reliable. The study was true experimental study…

  5. Pattern Learning, Damage and Repair within Biological Neural Networks

    NASA Astrophysics Data System (ADS)

    Siu, Theodore; Fitzgerald O'Neill, Kate; Shinbrot, Troy

    2015-03-01

    Traumatic brain injury (TBI) causes damage to neural networks, potentially leading to disability or even death. Nearly one in ten of these patients die, and most of the remainder suffer from symptoms ranging from headaches and nausea to convulsions and paralysis. In vitro studies to develop treatments for TBI have limited in vivo applicability, and in vitro therapies have even proven to worsen the outcome of TBI patients. We propose that this disconnect between in vitro and in vivo outcomes may be associated with the fact that in vitro tests assess indirect measures of neuronal health, but do not investigate the actual function of neuronal networks. Therefore in this talk, we examine both in vitro and in silico neuronal networks that actually perform a function: pattern identification. We allow the networks to execute genetic, Hebbian, learning, and additionally, we examine the effects of damage and subsequent repair within our networks. We show that the length of repaired connections affects the overall pattern learning performance of the network and we propose therapies that may improve function following TBI in clinical settings.

  6. Combinatorial epigenetic patterns as quantitative predictors of chromatin biology

    PubMed Central

    2014-01-01

    Background Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is the most widely used method for characterizing the epigenetic states of chromatin on a genomic scale. With the recent availability of large genome-wide data sets, often comprising several epigenetic marks, novel approaches are required to explore functionally relevant interactions between histone modifications. Computational discovery of "chromatin states" defined by such combinatorial interactions enabled descriptive annotations of genomes, but more quantitative approaches are needed to progress towards predictive models. Results We propose non-negative matrix factorization (NMF) as a new unsupervised method to discover combinatorial patterns of epigenetic marks that frequently co-occur in subsets of genomic regions. We show that this small set of combinatorial "codes" can be effectively displayed and interpreted. NMF codes enable dimensionality reduction and have desirable statistical properties for regression and classification tasks. We demonstrate the utility of codes in the quantitative prediction of Pol2-binding and the discrimination between Pol2-bound promoters and enhancers. Finally, we show that specific codes can be linked to molecular pathways and targets of pluripotency genes during differentiation. Conclusions We have introduced and evaluated a new computational approach to represent combinatorial patterns of epigenetic marks as quantitative variables suitable for predictive modeling and supervised machine learning. To foster widespread adoption of this method we make it available as an open-source software-package – epicode at https://github.com/mcieslik-mctp/epicode. PMID:24472558

  7. Expression Patterns and Potential Biological Roles of Dip2a

    PubMed Central

    Palange, Norberto J.; Jia, Ruirui; Ma, Jun; Bah, Fatoumata Binta; Sah, Rajiv Kumar; Li, Dan; Wang, Daji; Bah, Fatoumata Binta Maci; Togo, Jacques; Jin, Honghong; Ban, Luying; Feng, Xuechao; Zheng, Yaowu

    2015-01-01

    Disconnected (disco)-interacting protein 2 homolog A is a member of the DIP2 protein family encoded by Dip2a gene. Dip2a expression pattern has never been systematically studied. Functions of Dip2a in embryonic development and adult are not known. To investigate Dip2a gene expression and function in embryo and adult, a Dip2a-LacZ mouse model was generated by insertion of β-Gal cDNA after Dip2a promoter using CRISPR/Cas9 technology. Dip2a-LacZ mouse was designed to be a lacZ reporter mouse as well as a Dip2a knockout mouse. Heterozygous mice were used to study endogenous Dip2a expression and homozygotes to study DIP2A-associated structure and function. LacZ staining indicated that Dip2a is broadly expressed in neuronal, reproductive and vascular tissues, as well as in heart, kidney, liver and lung. Results demonstrate that Dip2a is expressed in ectoderm-derived tissues in developing embryos. Adult tissues showed rich staining in neurons, mesenchymal, endothelial, smooth muscle cells and cardiomyocytes by cell types. The expression pattern highly overlaps with FSTL1 and supports previous report that DIP2A to be potential receptor of FSTL1 and its protective roles of cardiomyocytes. Broad and intense embryonic and adult expression of Dip2a has implied their multiple structural and physiological roles. PMID:26605542

  8. Expression Patterns and Potential Biological Roles of Dip2a.

    PubMed

    Zhang, Luqing; Mabwi, Humphrey A; Palange, Norberto J; Jia, Ruirui; Ma, Jun; Bah, Fatoumata Binta; Sah, Rajiv Kumar; Li, Dan; Wang, Daji; Bah, Fatoumata Binta Maci; Togo, Jacques; Jin, Honghong; Ban, Luying; Feng, Xuechao; Zheng, Yaowu

    2015-01-01

    Disconnected (disco)-interacting protein 2 homolog A is a member of the DIP2 protein family encoded by Dip2a gene. Dip2a expression pattern has never been systematically studied. Functions of Dip2a in embryonic development and adult are not known. To investigate Dip2a gene expression and function in embryo and adult, a Dip2a-LacZ mouse model was generated by insertion of β-Gal cDNA after Dip2a promoter using CRISPR/Cas9 technology. Dip2a-LacZ mouse was designed to be a lacZ reporter mouse as well as a Dip2a knockout mouse. Heterozygous mice were used to study endogenous Dip2a expression and homozygotes to study DIP2A-associated structure and function. LacZ staining indicated that Dip2a is broadly expressed in neuronal, reproductive and vascular tissues, as well as in heart, kidney, liver and lung. Results demonstrate that Dip2a is expressed in ectoderm-derived tissues in developing embryos. Adult tissues showed rich staining in neurons, mesenchymal, endothelial, smooth muscle cells and cardiomyocytes by cell types. The expression pattern highly overlaps with FSTL1 and supports previous report that DIP2A to be potential receptor of FSTL1 and its protective roles of cardiomyocytes. Broad and intense embryonic and adult expression of Dip2a has implied their multiple structural and physiological roles. PMID:26605542

  9. 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-biological

  10. The Search for More Effective Methods of Teaching High-School Biology to Slow Learners Through Interaction Analysis, Part II. The Effects of Various Constant Teaching Patterns

    ERIC Educational Resources Information Center

    Citron, Irvin M.; Barnes, Cyrus W.

    1970-01-01

    Presents the procedures, results, and conclusions of a study designed to determine whether constant patterns of teaching of various kinds over an extended period could affect concept formation, problem solving, and total achievement of slow learners in a high school biology course. (LC)

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

    NASA Astrophysics Data System (ADS)

    Pease, Leonard Franklin, III

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

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

    PubMed

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

    2016-04-20

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

  13. A "lookup table" schema for synthetic biological patterning.

    PubMed

    Reitz, Frederick B

    2012-05-01

    A schema is proposed by which the three-dimensional structure and temporal development of a biological organism might be encoded and implemented via a genetic "lookup table". In the schema, diffusive morphogen gradients and/or the global concentration of a quickly diffusing signal index sets of kinase genes having promoters with logarithmically diminished affinity for the signal. Specificity of indexing is enhanced via concomitant expression of phosphatases undoing phosphorylation by "neighboring" kinases of greater affinity. Combinations of thus-selected kinases in turn jointly activate, via multiple phosphorylation, a particular enzyme from a virtual, multi-dimensional array thereof, at locations and times specified within the "lookup table". In principle, such a scheme could be employed to specify arbitrary gross anatomy, surface pigmentation, and/or developmental sequencing, extending the burgeoning toolset of the nascent field of synthetic morphology. A model of two-dimensional surface coloration using this scheme is specified, and LabVIEW software for its exploration is described and made available. PMID:22350667

  14. 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.

  15. Additivity of light-scattering patterns of aggregated biological particles

    NASA Astrophysics Data System (ADS)

    Moskalensky, Alexander E.; Strokotov, Dmitry I.; Chernyshev, Andrei V.; Maltsev, Valeri P.; Yurkin, Maxim A.

    2014-08-01

    The paper is focused on light scattering by aggregates of optically soft particles with a size larger than the wavelength, in particular, blood platelets. We conducted a systematic simulation of light scattering by dimers and larger aggregates of blood platelets, each modeled as oblate spheroids, using the discrete dipole approximation. Two-dimensional (2-D) light scattering patterns (LSPs) and internal fields showed that the multiple scattering between constituent particles can be neglected. Additionally, we derived conditions of the scattering angle and orientation of the dimer, under which the averaging of the 2-D LSPs over the azimuthal scattering angle washes out interference in the far field, resulting in averaged LSPs of the aggregate being equal to the sum of that for its constituents. We verified theoretical conclusions using the averaged LSPs of blood platelets measured with the scanning flow cytometer (SFC). Moreover, we obtained similar results for a model system of aggregates of polystyrene beads, studied both experimentally and theoretically. Finally, we discussed the potential of discriminating platelet aggregates from monomers using the SFC.

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

    PubMed

    Newman, S A; Frisch, H L

    1979-08-17

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

  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. Video and HTML: Testing Online Tutorial Formats with Biology Students

    ERIC Educational Resources Information Center

    Craig, Cindy L.; Friehs, Curt G.

    2013-01-01

    This study compared two common types of online information literacy tutorials: a streaming media tutorial using animation and narration and a text-based tutorial with static images. Nine sections of an undergraduate biology lab class (234 students total) were instructed by a librarian on how to use the BIOSIS Previews database. Three sections…

  19. 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

  20. Simple and non-toxic fabrication of poly(vinyl alcohol)-patterned polymer surface for the formation of cell patterns

    NASA Astrophysics Data System (ADS)

    Hwang, In-Tae; Jin, Yu-Ran; Oh, Min-Suk; Jung, Chan-Hee; Choi, Jae-Hak

    2014-10-01

    In this study, a facile and non-toxic method for the formation of cell-adhesive poly(vinyl alcohol) (PVA) patterns on the surface of a non-biological polystyrene substrate (NPS) is developed to control cellular micro-organization. PVA thin films spin-coated onto the NPS are selectively irradiated with 150 keV H+ ions through a pattern mask and developed with deionized water to form negative-type PVA patterns. Well-defined stripe patterns of PVA with a width of 100 μm are created on the NPS at a higher fluence than 5 × 1015 ions/cm2, and their surface chemical compositions are changed by ion irradiation without any significant morphological change. Based on the results of the protein adsorption test and in vitro cell culture, cancer cells are preferentially adhered and proliferated onto the more hydrophilic PVA regions of the PVA-patterned NPS, resulting in well-defined cell patterns.

  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. PMID:15697484

  2. Intergenerational Patterns of Union Formation and Relationship Quality

    ERIC Educational Resources Information Center

    Sassler, Sharon; Cunningham, Anna; Lichter, Daniel T.

    2009-01-01

    The authors examine whether young adults who experienced their parents' divorce and new relationships have different relationship trajectories than those who spent their childhoods living with biological parents in married-couple families. The analysis is based on longitudinal reports from more than 1,500 children from Wave 1 of the 1987-1988…

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

    PubMed

    Ueno, Tomonaga; Yoshida, Ryo

    2011-06-01

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

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

    PubMed

    Hirashima, Tsuyoshi

    2016-10-21

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

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

    NASA Astrophysics Data System (ADS)

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

    2002-11-01

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

  6. Large-scale pattern formation in active particles suspensions: from interacting microtubules to swimming bacteria

    NASA Astrophysics Data System (ADS)

    Aranson, Igor

    2006-03-01

    We consider two biological systems of active particles exhibiting large-scale collective behavior: microtubules interacting with molecular motors and hydrodynamically entrained swimming bacteria. Starting from a generic stochastic microscopic model of inelastically colliding polar rods with an anisotropic interaction kernel, we derive set of equations for the local rods concentration and orientation. Above certain critical density of rods the model exhibits orientational instability and onset of large-scale coherence. For the microtubules and molecular motors system we demonstrate that the orientational instability leads to the formation of vortices and asters seen in recent experiments. Similar approach is applied to colonies of swimming bacteria Bacillus subtilis confined in thin fluid film. The model is formulated in term of two-dimensional equations for local density and orientation of bacteria coupled to the low Reynolds number Navier-Stokes equation for the fluid flow velocity. The collective swimming of bacteria is represented by additional source term in the Navier-Stokes equation. We demonstrate that this system exhibits formation of dynamic large-scale patterns with the typical scale determined by the density of bacteria.

  7. Biological Basis of Tree-Ring Formation: A Crash Course

    PubMed Central

    Rathgeber, Cyrille B. K.; Cuny, Henri E.; Fonti, Patrick

    2016-01-01

    Wood is of crucial importance for man and biosphere. In this mini review, we present the fundamental processes involved in tree-ring formation and intra-annual dynamics of cambial activity, along with the influences of the environmental factors. During wood formation, new xylem cells produced by the cambium are undergoing profound transformations, passing through successive differentiation stages, which enable them to perform their functions in trees. Xylem cell formation can be divided in five major phases: (1) the division of a cambial mother cell that creates a new cell; (2) the enlargement of this newly formed cell; (3) the deposition of its secondary wall; (4) the lignification of its cell wall; and finally, (5) its programmed cell death. In most regions of the world cambial activity follows a seasonal cycle. At the beginning of the growing season, when temperature increases, the cambium resumes activity, producing new xylem cells. These cells are disposed along radial files, and start their differentiation program according to their birth date, creating typical developmental strips in the forming xylem. The width of these strips smoothly changes along the growing season. Finally, when climatic conditions deteriorate (temperature or water availability in particular), cambial activity stops, soon followed by cell enlargement, and later on by secondary wall deposition. Without a clear understanding of the xylem formation process, it is not possible to comprehend how annual growth rings and typical wood structures are formed, recording normal seasonal variations of the environment as well as extreme climatic events. PMID:27303426

  8. A stochastic multicellular model identifies biological watermarks from disorders in self-organized patterns of phyllotaxis.

    PubMed

    Refahi, Yassin; Brunoud, Géraldine; Farcot, Etienne; Jean-Marie, Alain; Pulkkinen, Minna; Vernoux, Teva; Godin, Christophe

    2016-01-01

    Exploration of developmental mechanisms classically relies on analysis of pattern regularities. Whether disorders induced by biological noise may carry information on building principles of developmental systems is an important debated question. Here, we addressed theoretically this question using phyllotaxis, the geometric arrangement of plant aerial organs, as a model system. Phyllotaxis arises from reiterative organogenesis driven by lateral inhibitions at the shoot apex. Motivated by recurrent observations of disorders in phyllotaxis patterns, we revisited in depth the classical deterministic view of phyllotaxis. We developed a stochastic model of primordia initiation at the shoot apex, integrating locality and stochasticity in the patterning system. This stochastic model recapitulates phyllotactic patterns, both regular and irregular, and makes quantitative predictions on the nature of disorders arising from noise. We further show that disorders in phyllotaxis instruct us on the parameters governing phyllotaxis dynamics, thus that disorders can reveal biological watermarks of developmental systems. PMID:27380805

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

    NASA Astrophysics Data System (ADS)

    Rohlf, Thimo; Bornholdt, Stefan

    2005-12-01

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

  10. Pattern formation in the wake of triggered pushed fronts

    NASA Astrophysics Data System (ADS)

    Goh, Ryan; Scheel, Arnd

    2016-08-01

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