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    <description>recent bookmarks from Vaguery</description>
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	<rdf:li rdf:resource="http://dev.biologists.org/content/140/20/4119.long"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1709.05546"/>
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  </channel><item rdf:about="https://arxiv.org/abs/2407.05991">
    <title>[2407.05991] Multi-Texture Synthesis through Signal Responsive Neural Cellular Automata</title>
    <dc:date>2026-02-21T20:35:23+00:00</dc:date>
    <link>https://arxiv.org/abs/2407.05991</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Neural Cellular Automata (NCA) have proven to be effective in a variety of fields, with numerous biologically inspired applications. One of the fields, in which NCAs perform well is the generation of textures, modelling global patterns from local interactions governed by uniform and coherent rules. This paper aims to enhance the usability of NCAs in texture synthesis by addressing a shortcoming of current NCA architectures for texture generation, which requires separately trained NCA for each individual texture. In this work, we train a single NCA for the evolution of multiple textures, based on individual examples. Our solution provides texture information in the state of each cell, in the form of an internally coded genomic signal, which enables the NCA to generate the expected texture. Such a neural cellular automaton not only maintains its regenerative capability but also allows for interpolation between learned textures and supports grafting techniques. This demonstrates the ability to edit generated textures and the potential for them to merge and coexist within the same automaton. We also address questions related to the influence of the genomic information and the cost function on the evolution of the NCA.
]]></description>
<dc:subject>pattern-formation generative-models generative-art neural-networks rather-interesting cellular-automata image-generation machine-learning note:distance-metric consider:code</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:da851ce41a6f/</dc:identifier>
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	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:generative-models"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:generative-art"/>
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	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cellular-automata"/>
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	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:machine-learning"/>
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<item rdf:about="https://arxiv.org/abs/2408.03458">
    <title>[2408.03458] Complex Dynamics in Reaction-Phase Separation Systems</title>
    <dc:date>2025-08-17T14:15:14+00:00</dc:date>
    <link>https://arxiv.org/abs/2408.03458</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We investigate the emergence of sustained spatio-temporal behaviors in reaction-phase separation systems. We focus on binary systems, in which either one or both species can phase separate, and we discuss the stability of the homogeneous state determining the conditions for the emergence of a Hopf-type bifurcation. We then examine the effects of a specific autocatalytic chemical reaction, and computationally determine the full solutions to the partial differential equations. We find that when both species phase separate, sustained pulsed dynamics arise in one dimension. When considered in two dimensions, the system generates persistent, complex dynamic droplets, which do not generally appear if only one of the species can phase separate. We finally discuss the emergence of dynamics with complex features, which can be understood using the framework of a cellular automata.
]]></description>
<dc:subject>pattern-formation reaction-diffusion-systems nonlinear-dynamics rather-interesting simulation to-simulate to-write-about consider:object-boundaries</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:bd6e5c1bf1b4/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:reaction-diffusion-systems"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
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	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:object-boundaries"/>
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<item rdf:about="https://arxiv.org/abs/2106.09471">
    <title>[2106.09471] A skeleton model to enumerate standard puzzle sequences</title>
    <dc:date>2022-01-01T13:33:43+00:00</dc:date>
    <link>https://arxiv.org/abs/2106.09471</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Guo-Niu Han [arXiv:2006.14070 [math.CO]] has introduced a new combinatorial object named standard puzzle. We use digraphs to show the relations between numbers in standard puzzles and propose a skeleton model. By this model, we solve the enumeration problem of over fifty thousand standard puzzle sequences. Most of them can be represented by classical numbers, such as Catalan numbers, double factorials, Secant numbers and so on. Also, we prove several identities in standard puzzle sequences.
]]></description>
<dc:subject>number-theory representation pattern-formation to-understand to-write-about to-simulate consider:sampling</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:57da769c7352/</dc:identifier>
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<item rdf:about="https://arxiv.org/abs/2003.06339">
    <title>[2003.06339] Extreme boundary conditions and random tilings</title>
    <dc:date>2021-07-04T11:29:13+00:00</dc:date>
    <link>https://arxiv.org/abs/2003.06339</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Standard statistical mechanical or condensed matter arguments tell us that bulk properties of a physical system do not depend too much on boundary conditions. Random tilings of large regions provide counterexamples to such intuition, as illustrated by the famous 'arctic circle theorem' for dimer coverings in two dimensions. In these notes, I discuss such examples in the context of critical phenomena, and their relation to 1+1d quantum particle models. All those turn out to share a common feature: they are inhomogeneous, in the sense that local densities now depend on position in the bulk. I explain how such problems may be understood using variational (or hydrodynamic) arguments, how to treat long range correlations, and how non trivial edge behavior can occur. While all this is done on the example of the dimer model, the results presented here have much greater generality. In that sense the dimer model serves as an opportunity to discuss broader methods and results. [These notes require only a basic knowledge of statistical mechanics.]
]]></description>
<dc:subject>domino-tiling nonlinear-dynamics rather-interesting constraint-satisfaction pattern-formation boundary-effects relaxation-studies to-write-about consider:visualization consider:polyomino-boundaries</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:80c6c164bba9/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:domino-tiling"/>
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	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:boundary-effects"/>
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	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:polyomino-boundaries"/>
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<item rdf:about="https://arxiv.org/abs/cond-mat/0001457">
    <title>[cond-mat/0001457] Compaction of Rods: Relaxation and Ordering in Vibrated, Anisotropic Granular Material</title>
    <dc:date>2020-10-15T10:32:33+00:00</dc:date>
    <link>https://arxiv.org/abs/cond-mat/0001457</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We report on experiments to measure the temporal and spatial evolution of packing arrangements of anisotropic, cylindrical granular material, using high-resolution capacitive monitoring. In these experiments, the particle configurations start from an initially disordered, low-packing-fraction state and under vertical vibrations evolve to a dense, highly ordered, nematic state in which the long particle axes align with the vertical tube walls. We find that the orientational ordering process is reflected in a characteristic, steep rise in the local packing fraction. At any given height inside the packing, the ordering is initiated at the container walls and proceeds inward. We explore the evolution of the local as well as the height-averaged packing fraction as a function of vibration parameters and compare our results to relaxation experiments conducted on spherically shaped granular materials.
]]></description>
<dc:subject>granular-materials packing self-organization pattern-formation nonlinear-dynamics physics! experiment rather-interesting phase-transitions</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:f2214283ad66/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:granular-materials"/>
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	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
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<item rdf:about="https://arxiv.org/abs/cond-mat/0203236">
    <title>[cond-mat/0203236] Vortices in vibrated granular rods</title>
    <dc:date>2020-10-15T10:30:33+00:00</dc:date>
    <link>https://arxiv.org/abs/cond-mat/0203236</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We report the experimental observation of novel vortex patterns in vertically vibrated granular rods. Above a critical packing fraction, moving ordered domains of nearly vertical rods spontaneously form and coexist with horizontal rods. The domains of vertical rods coarsen in time to form large vortices. We investigate the conditions under which the vortices occur by varying the number of rods, vibration amplitude and frequency. The size of the vortices increases with the number of rods. We characterize the growth of the ordered domains by measuring the area fraction of the ordered regions as a function of time. A {\em void filling} model is presented to describe the nucleation and growth of the vertical domains. We track the ends of the vertical rods and obtain the velocity fields of the vortices. The rotation speed of the rods is observed to depend on the vibration velocity of the container and on the packing. To investigate the impact of the direction of driving on the observed phenomena, we performed experiments with the container vibrated horizontally. Although vertical domains form, vortices are not observed. We therefore argue that the motion is generated due to the interaction of the inclination of the rods with the bottom of a vertically vibrated container. We also perform simple experiments with a single row of rods in an annulus. These experiments directly demonstrate that the rod motion is generated when the rods are inclined from the vertical, and is always in the direction of the inclination.
]]></description>
<dc:subject>granular-materials nonlinear-dynamics rather-interesting looking-to-see condensed-matter self-organization pattern-formation</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:351157b6a0ab/</dc:identifier>
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	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
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	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:condensed-matter"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1709.10043">
    <title>[1709.10043] Revealing new dynamical patterns in a reaction-diffusion model with cyclic competition via a novel computational framework</title>
    <dc:date>2020-08-05T16:25:00+00:00</dc:date>
    <link>https://arxiv.org/abs/1709.10043</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Understanding how patterns and travelling waves form in chemical and biological reaction-diffusion models is an area which has been widely researched, yet is still experiencing fast development. Surprisingly enough, we still do not have a clear understanding about all possible types of dynamical regimes in classical reaction-diffusion models such as Lotka-Volterra competition models with spatial dependence. In this work, we demonstrate some new types of wave propagation and pattern formation in a classical three species cyclic competition model with spatial diffusion, which have been so far missed in the literature. These new patterns are characterised by a high regularity in space, but are different from patterns previously known to exist in reaction-diffusion models, and may have important applications in improving our understanding of biological pattern formation and invasion theory. Finding these new patterns is made technically possible by using an automatic adaptive finite element method driven by a novel a posteriori error estimate which is proven to provide a reliable bound for the error of the numerical method. We demonstrate how this numerical framework allows us to easily explore the dynamical patterns both in two and three spatial dimensions.
]]></description>
<dc:subject>pattern-formation Turing-systems reaction-networks rather-interesting simulation to-understand to-simulate pattern-discovery consider:feature-discovery</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:4712e9eddddb/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:Turing-systems"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:reaction-networks"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-understand"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-discovery"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:feature-discovery"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://www.pnas.org/content/117/1/43">
    <title>Mechanics unlocks the morphogenetic puzzle of interlocking bivalved shells | PNAS</title>
    <dc:date>2020-05-02T14:51:20+00:00</dc:date>
    <link>https://www.pnas.org/content/117/1/43</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Brachiopods and mollusks are 2 shell-bearing phyla that diverged from a common shell-less ancestor more than 540 million years ago. Brachiopods and bivalve mollusks have also convergently evolved a bivalved shell that displays an apparently mundane, yet striking feature from a developmental point of view: When the shell is closed, the 2 valve edges meet each other in a commissure that forms a continuum with no gaps or overlaps despite the fact that each valve, secreted by 2 mantle lobes, may present antisymmetric ornamental patterns of varying regularity and size. Interlocking is maintained throughout the entirety of development, even when the shell edge exhibits significant irregularity due to injury or other environmental influences, which suggests a dynamic physical process of pattern formation that cannot be genetically specified. Here, we derive a mathematical framework, based on the physics of shell growth, to explain how this interlocking pattern is created and regulated by mechanical instabilities. By close consideration of the geometry and mechanics of 2 lobes of the mantle, constrained both by the rigid shell that they secrete and by each other, we uncover the mechanistic basis for the interlocking pattern. Our modeling framework recovers and explains a large diversity of shell forms and highlights how parametric variations in the growth process result in morphological variation. Beyond the basic interlocking mechanism, we also consider the intricate and striking multiscale-patterned edge in certain brachiopods. We show that this pattern can be explained as a secondary instability that matches morphological trends and data.

]]></description>
<dc:subject>developmental-biology evo-devo rather-interesting pattern-formation theoretical-biology dynamical-systems performance-measure to-write-about to-simulate</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:4fb2b291258e/</dc:identifier>
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	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:theoretical-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:dynamical-systems"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:performance-measure"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
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</item>
<item rdf:about="https://onlinelibrary.wiley.com/doi/10.1111/mmi.14316#.XO-2r2gTpiU.twitter">
    <title>Division plane placement in pleomorphic archaea is dynamically coupled to cell shape - Walsh - - Molecular Microbiology - Wiley Online Library</title>
    <dc:date>2019-06-03T10:41:35+00:00</dc:date>
    <link>https://onlinelibrary.wiley.com/doi/10.1111/mmi.14316#.XO-2r2gTpiU.twitter</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[One mechanism for achieving accurate placement of the cell division machinery is via Turing patterns, where non‐linear molecular interactions spontaneously produce spatiotemporal concentration gradients. The resulting patterns are dictated by cell shape. For example, the Min system of Escherichia coli shows spatiotemporal oscillation between cell poles, leaving a mid‐cell zone for division. The universality of pattern‐forming mechanisms in divisome placement is currently unclear. We examined the location of the division plane in two pleomorphic archaea, Haloferax volcanii and Haloarcula japonica, and show that it correlates with the predictions of Turing patterning. Time‐lapse analysis of H. volcanii shows that divisome locations after successive rounds of division are dynamically determined by daughter cell shape. For H. volcanii, we show that the location of DNA does not influence division plane location, ruling out nucleoid occlusion. Triangular cells provide a stringent test for Turing patterning, where there is a bifurcation in division plane orientation. For the two archaea examined, most triangular cells divide as predicted by a Turing mechanism, however, in some cases multiple division planes are observed resulting in cells dividing into three viable progeny. Our results suggest that the division site placement is consistent with a Turing patterning system in these archaea.

]]></description>
<dc:subject>cell-biology pattern-formation rather-interesting cytoskeleton microbiology to-simulate</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:de3ce800d2ad/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cell-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cytoskeleton"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:microbiology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1811.03557">
    <title>[1811.03557] Efficient Numerical Algorithms based on Difference Potentials for Chemotaxis Systems in 3D</title>
    <dc:date>2019-02-23T12:06:17+00:00</dc:date>
    <link>https://arxiv.org/abs/1811.03557</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[In this work, we propose efficient and accurate numerical algorithms based on Difference Potentials Method for numerical solution of chemotaxis systems and related models in 3D. The developed algorithms handle 3D irregular geometry with the use of only Cartesian meshes and employ Fast Poisson Solvers. In addition, to further enhance computational efficiency of the methods, we design a Difference-Potentials-based domain decomposition approach which allows mesh adaptivity and easy parallelization of the algorithm in space. Extensive numerical experiments are presented to illustrate the accuracy, efficiency and robustness of the developed numerical algorithms.]]></description>
<dc:subject>theoretical-biology pattern-formation reaction-diffusion finite-elements self-organization rather-interesting simulation representation</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:f5ea1887a0d3/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:theoretical-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:reaction-diffusion"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:finite-elements"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:representation"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://dev.biologists.org/content/140/20/4119.long">
    <title>Studies of morphogens: keep calm and carry on | Development</title>
    <dc:date>2019-01-22T00:25:31+00:00</dc:date>
    <link>http://dev.biologists.org/content/140/20/4119.long</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Morphogens are signaling factors that direct cell fate and tissue development at a distance from their source, and various modes of transport and interpretation have been suggested for morphogens. The recent EMBO Workshop on ‘Morphogen gradients’, which took place in Oxford, UK in June 2013, centered on the formation and interpretation of such morphogen gradients during development. This meeting allowed an exchange of views in light of recent results. Here, we provide a brief overview of the talks, organized in relation to several major themes of discussion at the meeting: (1) morphogen gradient formation; (2) morphogen gradient interpretation; (3) signaling networks and feedback in morphogenesis; (4) emergence of patterns; (5) scaling of patterns; (6) the control of growth; and (7) new techniques in the field.

]]></description>
<dc:subject>developmental-biology pattern-formation Turing-systems actual-biology Drosophila nostalgia-but-not-much</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:1430bfd44bf3/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:developmental-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:Turing-systems"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:actual-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:Drosophila"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nostalgia-but-not-much"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1709.05546">
    <title>[1709.05546] A computational study of the mechanisms of growth-driven folding patterns on shells, with application to the developing brain</title>
    <dc:date>2018-01-15T12:15:36+00:00</dc:date>
    <link>https://arxiv.org/abs/1709.05546</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We consider the mechanisms by which folds, or sulci (troughs) and gyri (crests), develop in the brain. This feature, common to many gyrencephalic species including humans, has attracted recent attention from soft matter physicists. It occurs due to inhomogeneous, and predominantly tangential, growth of the cortex, which causes circumferential compression, leading to a bifurcation of the solution path to a folded configuration. The problem can be framed as one of buckling in the regime of linearized elasticity. However, the brain is a very soft solid, which is subject to large strains due to inhomogeneous growth. As a consequence, the morphomechanics of the developing brain demonstrates an extensive post-bifurcation regime. Nonlinear elasticity studies of growth-driven brain folding have established the conditions necessary for the onset of folding, and for its progression to configurations broadly resembling gyrencephalic brains. The reference, unfolded, configurations in these treatments have a high degree of symmetry--typically, ellipsoidal. Depending on the boundary conditions, the folded configurations have symmetric or anti-symmetric patterns. However, these configurations do not approximate the actual morphology of, e.g., human brains, which display unsymmetric folding. More importantly, from a neurodevelopmental standpoint, many of the unsymmetric sulci and gyri are notably robust in their locations. Here, we initiate studies on the physical mechanisms and geometry that control the development of primary sulci and gyri. In this preliminary communication we carry out computations with idealized geometries, boundary conditions and parameters, seeking a pattern resembling one of the first folds to form: the Central Sulcus.
]]></description>
<dc:subject>pattern-formation developmental-biology biological-engineering rather-interesting nonlinear-dynamics to-write-about to-model</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:3a9440273692/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:developmental-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:biological-engineering"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-model"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1706.08422">
    <title>[1706.08422] Spatial effects in meta-food-webs</title>
    <dc:date>2017-09-26T15:06:11+00:00</dc:date>
    <link>https://arxiv.org/abs/1706.08422</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[In ecology it is widely recognised that many landscapes comprise a network of discrete patches of habitat. The species that inhabit the patches interact with each other through a foodweb, the network of feeding interactions. The meta-foodweb model proposed by Pillai et al. combines the feeding relationships at each patch with the dispersal of species between patches, such that the whole system is represented by a network of networks. Previous work on meta-foodwebs has focussed on landscape networks that do not have an explicit spatial embedding, but in real landscapes the patches are usually distributed in space. Here we compare the dispersal of a meta-foodweb on \ER networks, that do not have a spatial embedding, and random geometric networks, that do have a spatial embedding. We found that local structure and large network distances in spatially embedded networks, lead to meso-scale patterns of patch occupation by both specialist and omnivorous species. In particular, we found that spatial separations make the coexistence of competing species more likely. Our results highlight the effects of spatial embeddings for meta-foodweb models, and the need for new analytical approaches to them.
]]></description>
<dc:subject>food-webs ecology theoretical-biology graph-theory network-theory agent-based nonlinear-dynamics pattern-formation</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:f2b46e5105c0/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:food-webs"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:ecology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:theoretical-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:graph-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:network-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:agent-based"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1704.00347">
    <title>[1704.00347] Self-organization of charged particles in circular geometry</title>
    <dc:date>2017-06-17T12:20:08+00:00</dc:date>
    <link>https://arxiv.org/abs/1704.00347</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[The basic principles of self-organization of one-component charged particles, confined in disk and circular parabolic potentials, are proposed. A system of equations is derived, that allows us to determine equilibrium configurations for an arbitrary, but finite, number of charged particles that are distributed over several rings. Our approach reduces significantly the computational effort in minimizing the energy of equilibrium configurations and demonstrates a remarkable agreement with the values provided by molecular dynamics calculations. With the increase of particle number n>180 we find a steady formation of a centered hexagonal lattice that smoothly transforms to valence circular rings in the ground state configurations for both potentials.
]]></description>
<dc:subject>self-organization physics experiment simulation simplicity rather-interesting to-write-about pattern-formation stamp-collecting</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:72692d04b43e/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:physics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:experiment"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simplicity"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:stamp-collecting"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1610.01461">
    <title>[1610.01461] Cooperative Output Regulation of Linear Multi-agent Systems with Communication Constraints</title>
    <dc:date>2017-02-25T12:25:14+00:00</dc:date>
    <link>https://arxiv.org/abs/1610.01461</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[In this paper, we consider the cooperative output regulation problem for heterogeneous linear multi-agent systems in the presence of communication constraints. Under standard assumptions on the agents dynamics, we propose a distributed control algorithm relying on intermittent and asynchronous discrete-time information exchange that can be subject to unknown time-varying delays and information losses. We show that cooperative output regulation can be reached for arbitrary characteristics of the discrete-time communication process and under mild assumptions on the interconnection topology between agents. A numerical example is given to illustrate the effectiveness of our theoretical results.
]]></description>
<dc:subject>collective-behavior control-theory rather-interesting agent-based pattern-formation engineering-design nudge-targets consider:feature-discovery consider:looking-to-see to-write-about</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:3debc1192a76/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:collective-behavior"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:control-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:agent-based"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:engineering-design"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:feature-discovery"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:looking-to-see"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1304.8035">
    <title>[1304.8035] Construction of local structure maps for cellular automata</title>
    <dc:date>2017-02-04T11:34:04+00:00</dc:date>
    <link>https://arxiv.org/abs/1304.8035</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[The paper formalizes and extends the idea of local structure approximation for cellular automata originally proposed by Gutowitz et. al. We start with a review of the construction of a probability measure on the set of bi-infinite strings over a finite alphabet of N symbols. We then demonstrate that for a shift-invariant probability measure, probabilities of all blocks of length up to k can be expressed by (N−1)Nk−1 linearly independent block probabilities. Two choices of these independent blocks are discussed in detail, one in which we choose the longest possible blocks ("long form") and one in which we choose the shortest possible blocks ("short form"). We then proceed to review the method which allows to approximate probabilities of blocks longer than k by blocks of length k or less. This approximation, known as Bayesian extension or Markov measure, is then used to construct approximate orbits of shift-invariant probability measures under the action of probabilistic or deterministic cellular automaton. We show that the aforementioned approximate orbit is completely determined by an (N−1)Nk−1-dimensional map. When the short form of block probabilities is used, this map takes particularly simple form, often revealing important features of a particular cellular automaton.]]></description>
<dc:subject>cellular-automata combinatorics pattern-formation information-theory rather-interesting to-write-about</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:33fa4617e8a8/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cellular-automata"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:combinatorics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:information-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1701.01361">
    <title>[1701.01361] Rhombic Tilings and Primordia Fronts of Phyllotaxis</title>
    <dc:date>2017-01-24T12:03:11+00:00</dc:date>
    <link>https://arxiv.org/abs/1701.01361</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We introduce and study properties of phyllotactic and rhombic tilings on the cylin- der. These are discrete sets of points that generalize cylindrical lattices. Rhombic tilings appear as periodic orbits of a discrete dynamical system S that models plant pattern formation by stacking disks of equal radius on the cylinder. This system has the advantage of allowing several disks at the same level, and thus multi-jugate config- urations. We provide partial results toward proving that the attractor for S is entirely composed of rhombic tilings and is a strongly normally attracting branched manifold and conjecture that this attractor persists topologically in nearby systems. A key tool in understanding the geometry of tilings and the dynamics of S is the concept of pri- mordia front, which is a closed ring of tangent disks around the cylinder. We show how fronts determine the dynamics, including transitions of parastichy numbers, and might explain the Fibonacci number of petals often encountered in compositae.
]]></description>
<dc:subject>phyllotaxis tiling pattern-formation biologically-inspired mathematics rather-interesting stamp-collecting</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:61b31a8d41d8/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:phyllotaxis"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:tiling"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:biologically-inspired"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:mathematics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:stamp-collecting"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1604.08658">
    <title>[1604.08658] Dependence between External Path-Length and Size in Random Tries</title>
    <dc:date>2016-06-06T10:51:01+00:00</dc:date>
    <link>http://arxiv.org/abs/1604.08658</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We study the size and the external path length of random tries and show that they are asymptotically independent in the asymmetric case but strongly dependent with small periodic fluctuations in the symmetric case. Such an unexpected behavior is in sharp contrast to the previously known results that the internal path length is totally positively correlated to the size and that both tend to the same normal limit law. These two examples provide concrete instances of bivariate normal distributions (as limit laws) whose correlation is 0, 1 and periodically oscillating.
]]></description>
<dc:subject>probability-theory data-structures looking-to-see computer-science pattern-formation rather-odd nudge-targets consider:looking-to-see</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:afbaa87eac66/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:probability-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:data-structures"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:looking-to-see"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:computer-science"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-odd"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:looking-to-see"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1605.06093">
    <title>[1605.06093] Square Formation by Asynchronous Oblivious Robots</title>
    <dc:date>2016-05-29T13:37:10+00:00</dc:date>
    <link>http://arxiv.org/abs/1605.06093</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[A fundamental problem in Distributed Computing is the Pattern Formation problem, where some independent mobile entities, called robots, have to rearrange themselves in such a way as to form a given figure from every possible (non-degenerate) initial configuration. 
In the present paper, we consider robots that operate in the Euclidean plane and are dimensionless, anonymous, oblivious, silent, asynchronous, disoriented, non-chiral, and non-rigid. For this very elementary type of robots, the feasibility of the Pattern Formation problem has been settled, either in the positive or in the negative, for every possible pattern, except for one case: the Square Formation problem by a team of four robots. 
Here we solve this last case by giving a Square Formation algorithm and proving its correctness. Our contribution represents the concluding chapter in a long thread of research. Our results imply that in the context of the Pattern Formation problem for mobile robots, features such as synchronicity, chirality, and rigidity are computationally irrelevant.
]]></description>
<dc:subject>planning self-organization distributed-processing collective-intelligence pattern-formation emergent-design nudge-targets consider:looking-to-see</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:63613dd565d3/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:planning"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:distributed-processing"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:collective-intelligence"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:emergent-design"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:looking-to-see"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1605.06589">
    <title>[1605.06589] Large compact clusters and fast dynamics in coupled nonequilibrium systems</title>
    <dc:date>2016-05-28T21:01:32+00:00</dc:date>
    <link>http://arxiv.org/abs/1605.06589</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We demonstrate particle clustering on macroscopic scales in a coupled nonequilibrium system where two species of particles are advected by a fluctuating landscape and modify the landscape in the process. The phase diagram generated by varying the particle-landscape coupling, valid for all particle density and in both one and two dimensions, shows novel nonequilibrium phases. While particle species are completely phase separated, the landscape develops macroscopically ordered regions coexisting with a disordered region, resulting in coarsening and steady state dynamics on time scales which grow algebraically with size, not seen earlier in systems with pure domains.
]]></description>
<dc:subject>self-organization condensed-matter pattern-formation nonlinear-dynamics nudge-targets simulation consider:robustness consider:looking-to-see</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:6e676bf68cda/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:condensed-matter"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:robustness"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:looking-to-see"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1601.02918">
    <title>[1601.02918] Spatial self-organization in hybrid models of multicellular adhesion</title>
    <dc:date>2016-03-21T11:05:08+00:00</dc:date>
    <link>http://arxiv.org/abs/1601.02918</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Spatial self-organization emerges in distributed systems exhibiting local interactions when nonlinearities and the appropriate propagation of signals are at work. These kinds of phenomena can be modeled with different frameworks, typically cellular automata or reaction-diffusion systems. A different class of dynamical processes involves the correlated movement of agents over space, which can be mediated through chemotactic movement or minimization of cell-cell interaction energy. A classic example of the latter is given by the formation of spatially segregated assemblies when cells display differential adhesion. Here we consider a new class of dynamical models, involving cell adhesion among two stochastically exchangeable cell states as a minimal model capable of exhibiting well-defined, ordered spatial patterns. Our results suggest that a whole space of pattern-forming rules is hosted by the combination of physical differential adhesion and the value of probabilities modulating cell phenotypic switching, showing that Turing-like patterns can be obtained without resorting to reaction-diffusion processes. If the model is expanded allowing cells to proliferate and die in an environment where diffusible nutrient and toxic waste are at play, different phases are observed, characterized by regularly spaced patterns. The analysis of the parameter space reveals that certain phases reach higher population levels than other modes of organization. A detailed exploration of the mean-field theory is also presented. Finally we let populations of cells with different adhesion matrices compete for reproduction, showing that, in our model, structural organization can improve the fitness of a given cell population. The implications of these results for ecological and evolutionary models of pattern formation and the emergence of multicellularity are outlined.
]]></description>
<dc:subject>cellular-automata pattern-formation rather-interesting theoretical-biology hey-I-know-this-guy good-to-see-somebody-finally-do-this nudge-targets consider:writing-up</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:138fee1159ce/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cellular-automata"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:theoretical-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:hey-I-know-this-guy"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:good-to-see-somebody-finally-do-this"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:writing-up"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1508.06898">
    <title>[1508.06898] Topological Microstructure Analysis Using Persistence Landscapes</title>
    <dc:date>2016-02-27T11:43:29+00:00</dc:date>
    <link>http://arxiv.org/abs/1508.06898</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Phase separation mechanisms can produce a variety of complicated and intricate microstructures, which often can be difficult to characterize in a quantitative way. In recent years, a number of novel topological metrics for microstructures have been proposed, which measure essential connectivity information and are based on techniques from algebraic topology. Such metrics are inherently computable using computational homology, provided the microstructures are discretized using a thresholding process. However, while in many cases the thresholding is straightforward, noise and measurement errors can lead to misleading metric values. In such situations, persistence landscapes have been proposed as a natural topology metric. Common to all of these approaches is the enormous data reduction, which passes from complicated patterns to discrete information. It is therefore natural to wonder what type of information is actually retained by the topology. In the present paper, we demonstrate that averaged persistence landscapes can be used to recover central system information in the Cahn-Hilliard theory of phase separation. More precisely, we show that topological information of evolving microstructures alone suffices to accurately detect both concentration information and the actual decomposition stage of a data snapshot. Considering that persistent homology only measures discrete connectivity information, regardless of the size of the topological features, these results indicate that the system parameters in a phase separation process affect the topology considerably more than anticipated. We believe that the methods discussed in this paper could provide a valuable tool for relating experimental data to model simulations.
]]></description>
<dc:subject>nonlinear-dynamics information-theory topology (somehow) abstraction to-understand pattern-discovery pattern-formation</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:14e3c1328e9b/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:information-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:topology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:(somehow)"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:abstraction"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-understand"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-discovery"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1601.01468">
    <title>[1601.01468] Phyllotaxis: a framework for foam topological evolution</title>
    <dc:date>2016-01-16T00:59:07+00:00</dc:date>
    <link>http://arxiv.org/abs/1601.01468</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Phyllotaxis describes the arrangement of florets, scales or leaves in composite flowers or plants (daisy, aster, sunflower, pinecone, pineapple). As a structure, it is a geometrical foam, the most homogeneous and densest covering of a large disk by Voronoi cells (the florets), constructed by a simple algorithm: Points placed regularly on a generative spiral constitute a spiral lattice, and phyllotaxis is the tiling by the Voronoi cells of the spiral lattice. Locally, neighboring cells are organized as three whorls or parastichies, labeled with successive Fibonacci numbers. The structure is encoded as the sequence of the shapes (number of sides) of the successive Voronoi cells on the generative spiral. We show that sequence and organization are independent of the position of the initial point on the generative spiral, that is invariant under disappearance (T2) of the first Voronoi cell or, conversely, under creation of a first cell, that is under growth. This independence shows how a foam is able to respond to a shear stress, notably through grain boundaries that are layers of square cells slightly truncated into heptagons, pentagons and hexagons, meeting at four-corner vertices, critical points of T1 elementary topological transformations.
]]></description>
<dc:subject>computational-geometry theoretical-biology pattern-formation physics dynamical-systems rather-interesting phyllotaxis</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:e2e6a053c0ec/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:computational-geometry"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:theoretical-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:physics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:dynamical-systems"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:phyllotaxis"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1512.05199">
    <title>[1512.05199] Extension of cellular automata by introducing an algorithm of recursive estimation of neighbors</title>
    <dc:date>2015-12-24T01:41:04+00:00</dc:date>
    <link>http://arxiv.org/abs/1512.05199</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[This study focuses on an extended model of a standard cellular automaton (CA) that includes an extra index consisting of a radius that defines a perception area for each cell in addition to the radius defined by the CA rule. Extended standard CA rules form a sequence ordered by this index, which includes the CA rule as its first term. This extension aims at constructing a model that can be used within the CA framework to study the relationship between information processing and pattern formation in collective systems. Although the extension presented here is merely an extrapolation to a CA with a larger rule neighborhood, the extra radius can be interpreted as an individual difference of each cell, which provides a new perspective to CA. Some pattern formations in extended one-dimensional elementary CAs and two-dimensional Life-like CAs are presented. It is expected that the extended CA can be applied to various simulations of complex systems and other fields.
]]></description>
<dc:subject>cellular-automata self-organization pattern-formation artificial-life Wolframism to-do nudge-targets consider:looking-to-see</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:2e8bcad2b737/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cellular-automata"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:artificial-life"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:Wolframism"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-do"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:looking-to-see"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1407.8070">
    <title>[1407.8070] Weak chimeras in minimal networks of coupled phase oscillators</title>
    <dc:date>2015-11-01T09:33:53+00:00</dc:date>
    <link>http://arxiv.org/abs/1407.8070</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We suggest a definition for a type of chimera state that appears in networks of indistinguishable phase oscillators. Defining a "weak chimera" as a type of invariant set showing partial frequency synchronization, we show that this means they cannot appear in phase oscillator networks that are either globally coupled or too small. We exhibit various networks of four, six and ten indistinguishable oscillators where weak chimeras exist with various dynamics and stabilities. We examine the role of Kuramoto-Sakaguchi coupling in giving degenerate (neutrally stable) families of weak chimera states in these example networks.
]]></description>
<dc:subject>nonlinear-dynamics coupled-oscillators classification emergence feature-extraction pattern-formation rather-interesting nudge-targets</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:e6b627e9a3cb/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:coupled-oscillators"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:classification"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:emergence"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:feature-extraction"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1505.07168">
    <title>[1505.07168] Getting Close Without Touching: Near-Gathering for Autonomous Mobile Robots</title>
    <dc:date>2015-09-12T13:09:42+00:00</dc:date>
    <link>http://arxiv.org/abs/1505.07168</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[In this paper we study the Near-Gathering problem for a finite set of dimensionless, deterministic, asynchronous, anonymous, oblivious and autonomous mobile robots with limited visibility moving in the Euclidean plane in Look-Compute-Move (LCM) cycles. In this problem, the robots have to get close enough to each other, so that every robot can see all the others, without touching (i.e., colliding with) any other robot. The importance of solving the Near-Gathering problem is that it makes it possible to overcome the restriction of having robots with limited visibility. Hence it allows to exploit all the studies (the majority, actually) done on this topic in the unlimited visibility setting. Indeed, after the robots get close enough to each other, they are able to see all the robots in the system, a scenario that is similar to the one where the robots have unlimited visibility. 
We present the first (deterministic) algorithm for the Near-Gathering problem, to the best of our knowledge, which allows a set of autonomous mobile robots to nearly gather within finite time without ever colliding. Our algorithm assumes some reasonable conditions on the input configuration (the Near-Gathering problem is easily seen to be unsolvable in general). Further, all the robots are assumed to have a compass (hence they agree on the "North" direction), but they do not necessarily have the same handedness (hence they may disagree on the clockwise direction). 
We also show how the robots can detect termination, i.e., detect when the Near-Gathering problem has been solved. This is crucial when the robots have to perform a generic task after having nearly gathered. We show that termination detection can be obtained even if the total number of robots is unknown to the robots themselves (i.e., it is not a parameter of the algorithm), and robots have no way to explicitly communicate.
]]></description>
<dc:subject>robotics collective-intelligence swarms planning algorithms pattern-formation optimization nudge-targets consider:rediscovery</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:5e4aa6afc28a/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:robotics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:collective-intelligence"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:swarms"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:planning"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:algorithms"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:optimization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:rediscovery"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1501.03769">
    <title>[1501.03769] Control of transversal instabilities in reaction-diffusion systems</title>
    <dc:date>2015-09-06T10:56:19+00:00</dc:date>
    <link>http://arxiv.org/abs/1501.03769</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[In two-dimensional reaction-diffusion systems, local curvature perturbations in the shape of traveling waves are typically damped out and disappear in the course of time. If, however, the inhibitor diffuses much faster than the activator, transversal instabilities can arise, leading from flat to folded, spatio-temporally modulated wave shapes and to spreading spiral turbulence. For experimentally relevant parameter values, the photosensitive Belousov-Zhabotinsky reaction (PBZR) does not exhibit transversal wave instabilities. Here, we propose a mechanism to artificially induce these instabilities via a wave shape dependent spatio-temporal feedback loop, and study the emerging wave patterns. In numerical simulations with the modified Oregonator model for the PBZR using experimentally realistic parameter values we demonstrate the feasibility of this control scheme. Conversely, in a piecewise-linear version of the FitzHugh-Nagumo model transversal instabilities and spiral turbulence in the uncontrolled system are shown to be suppressed in the presence of control, thereby stabilising flat wave propagation.
]]></description>
<dc:subject>self-organization reaction-diffusion pattern-formation nonlinear-dynamics reaction-networks engineering-design rather-interesting nudge-targets consider:robustness</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:2b089215eccb/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:reaction-diffusion"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:reaction-networks"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:engineering-design"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:robustness"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1508.06768">
    <title>[1508.06768] Effects of Boundary Conditions on Single-File Pedestrian Flow</title>
    <dc:date>2015-08-29T11:28:49+00:00</dc:date>
    <link>http://arxiv.org/abs/1508.06768</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[In this paper we investigate effects of boundary conditions on one dimensional pedestrian flow which involves purely longitudinal interactions. Qualitatively, stop-and-go waves are observed under closed boundary condition and dissolve when the boundary is open. To get more detailed information the fundamental diagrams of the open and closed systems are compared using Voronoi-based measurement method. Higher maximal specific flow is observed from the pedestrian movement at open boundary condition.
]]></description>
<dc:subject>self-organization pattern-formation pedestrians complex-systems nonlinear-dynamics collective-behavior nudge-targets consider:feature-discovery</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:4a6a807674f4/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pedestrians"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complex-systems"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:collective-behavior"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:feature-discovery"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1404.4289">
    <title>[1404.4289] Nonlocal control of pulse propagation in excitable media</title>
    <dc:date>2015-08-27T10:40:48+00:00</dc:date>
    <link>http://arxiv.org/abs/1404.4289</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We study the effects of nonlocal control of pulse propagation in excitable media. As a generic example for an excitable medium the FitzHugh-Nagumo model with diffusion in the activator variable is considered. Nonlocal coupling in form of an integral term with a spatial kernel is added. We find that the nonlocal coupling modifies the propagating pulses of the reaction-diffusion system such that a variety of spatio-temporal patterns are generated including acceleration, deceleration, suppression, or generation of pulses, multiple pulses, and blinking pulse trains. It is shown that one can observe these effects for various choices of the integral kernel and the coupling scheme, provided that the control strength and spatial extension of the integral kernel is appropriate. In addition, an analytical procedure is developed to describe the stability borders of the spatially homogeneous steady state in control parameter space in dependence on the parameters of the nonlocal coupling.
]]></description>
<dc:subject>pattern-formation nonlinear-dynamics engineering-design rather-interesting perturbation nudge-targets consider:rediscovery</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:63fcc57e7659/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:engineering-design"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:perturbation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:rediscovery"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1508.01219">
    <title>[1508.01219] Adhesion Induced Instabilities and Pattern Formation in Thin Films of Elastomers and Gels</title>
    <dc:date>2015-08-22T12:18:42+00:00</dc:date>
    <link>http://arxiv.org/abs/1508.01219</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[A hydrostatically stressed soft elastic film circumvents the imposed constraint by undergoing a morphological instability, the wavelength of which is dictated by the minimization of the surface and the elastic strain energies of the film. While for a single film, the wavelength is entirely dependent on its thickness, a co-operative energy minimization dictates that the wavelength depends on both the elastic moduli and thicknesses of two contacting films. The wavelength can also depend on the material properties of a film if its surface tension has a pronounced effect in comparison to its elasticity. When such a confined film is subjected to a continually increasing normal displacement, the morphological patterns evolve into cracks, which, in turn, govern the adhesive fracture behavior of the interface. While, in general, the thickness provides the relevant length scale underlying the well-known Griffith-Kendall criterion of debonding of a rigid disc from a confined film, it is modified non-trivially by the elasto-capillary number for an ultra-soft film. Depending upon the degree of confinement and the spatial distribution of external stress, various analogs of the canonical instability patterns in liquid systems can also be reproduced with thin confined elastic films.
]]></description>
<dc:subject>physics! pattern-formation materials-science experiment</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:4436b6bbbf3d/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:physics!"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:materials-science"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:experiment"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1210.7019">
    <title>[1210.7019] Labyrinthine clustering in a spatial rock-paper-scissors ecosystem</title>
    <dc:date>2015-07-31T11:51:25+00:00</dc:date>
    <link>http://arxiv.org/abs/1210.7019</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[The spatial rock-paper-scissors ecosystem, where three species interact cyclically, is a model example of how spatial structure can maintain biodiversity. We here consider such a system for a broad range of interaction rates. When one species grows very slowly, this species and its prey dominate the system by self-organizing into a labyrinthine configuration in which the third species propagates. The cluster size distributions of the two dominating species have heavy tails and the configuration is stabilized through a complex, spatial feedback loop. We introduce a new statistical measure that quantifies the amount of clustering in the spatial system by comparison with its mean field approximation. Hereby, we are able to quantitatively explain how the labyrinthine configuration slows down the dynamics and stabilizes the system.
]]></description>
<dc:subject>rock-paper-scissors roshambo artificial-life agent-based self-organization pattern-formation hey-I-know-this-guy nudge-targets</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:efbb46bae065/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rock-paper-scissors"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:roshambo"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:artificial-life"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:agent-based"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:hey-I-know-this-guy"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1212.5414">
    <title>[1212.5414] Asymptotic domino statistics in the Aztec diamond</title>
    <dc:date>2015-07-20T12:11:08+00:00</dc:date>
    <link>http://arxiv.org/abs/1212.5414</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We study random domino tilings of the Aztec diamond with different weights for horizontal and vertical dominoes. A domino tiling of an Aztec diamond can also be described by a particle system which is a determinantal process. We give a relation between the correlation kernel for this process and the inverse Kasteleyn matrix of the Aztec diamond. This gives a formula for the inverse Kasteleyn matrix which generalizes a result of Helfgott. As an application, we investigate the asymptotics of the process formed by the southern dominoes close to the frozen boundary. We find that at the northern boundary, the southern domino process converges to a thinned Airy point process. At the southern boundary, the process of holes of the southern domino process converges to a multiple point process that we call the thickened Airy point process. We also study the convergence of the domino process in the unfrozen region to the limiting Gibbs measure.
]]></description>
<dc:subject>tiling combinatorics pattern-formation rather-interesting statistical-physics nudge-targets consider:looking-to-see</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:ed2bb3c21be2/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:tiling"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:combinatorics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:statistical-physics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:looking-to-see"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1506.06698">
    <title>[1506.06698] Emergent collective chemotaxis without single-cell gradient sensing</title>
    <dc:date>2015-06-27T13:54:03+00:00</dc:date>
    <link>http://arxiv.org/abs/1506.06698</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Many eukaryotic cells chemotax, sensing and following chemical gradients. However, even if single cells do not chemotax significantly, small clusters may still follow a gradient; this behavior is observed in neural crest cells and during border cell migration in Drosophila, but its origin remains puzzling. Here, we study this "collective guidance" analytically and computationally. We show collective chemotaxis can exist without single-cell chemotaxis if contact inhibition of locomotion (CIL), where cells polarize away from cell-cell contact, is regulated by the chemoattractant. We present explicit formulas for how cluster velocity and chemotactic index depend on the number and organization of cells in the cluster. Pairs of cells will have velocities that are strongly dependent on the cell pair's orientation: this provides a simple test for the presence of collective guidance in neural crest cells and other systems. We also study cluster-level adaptation, amplification, and cohesion via co-attraction.
]]></description>
<dc:subject>theoretical-biology collective-intelligence pattern-formation adaptive-control simulation artificial-life nudge-targets consider:rediscovery</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:1dad1eabb5ce/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:theoretical-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:collective-intelligence"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:adaptive-control"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:artificial-life"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:rediscovery"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1503.03321">
    <title>[1503.03321] The Kinetic Basis of Morphogenesis</title>
    <dc:date>2015-04-09T11:59:13+00:00</dc:date>
    <link>http://arxiv.org/abs/1503.03321</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[It has been shown recently (Shalygo, 2014) that stationary and dynamic patterns can arise in the proposed one-component model of the analog (continuous state) kinetic automaton, or a kinon for short, defined as a reflexive dynamical system with active transport. This paper presents the extensions of the model, which increase further its complexity and tunability, and shows that the extended kinon model can produce spatio-temporal patterns pertaining not only to pattern formation but also to morphogenesis in real physical and biological systems. It indicates the possible applicability of the model to morphogenetic engineering and robotics.
]]></description>
<dc:subject>artificial-life pattern-formation developmental-biology done-pretty-much-wrong reaction-diffusion nudge-targets representation meh to-correct</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:cb18c8099a64/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:artificial-life"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:developmental-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:done-pretty-much-wrong"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:reaction-diffusion"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:representation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:meh"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-correct"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1412.8501">
    <title>[1412.8501] Formation Games of Reliable Networks</title>
    <dc:date>2015-03-10T10:47:59+00:00</dc:date>
    <link>http://arxiv.org/abs/1412.8501</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We establish a network formation game for the Internet's Autonomous System (AS) interconnection topology. The game includes different types of players, accounting for the heterogeneity of ASs in the Internet. We incorporate reliability considerations in the player's utility function, and analyze static properties of the game as well as its dynamic evolution. We provide dynamic analysis of its topological quantities, and explain the prevalence of some "network motifs" in the Internet graph. We assess our predictions with real-world data.
]]></description>
<dc:subject>graph-theory network-theory game-theory dynamical-systems simulation pattern-formation nudge-targets</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:1948ec553113/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:graph-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:network-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:game-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:dynamical-systems"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1410.7623">
    <title>[1410.7623] An island of stability in a sea of fingers: emergent large-scale features of the viscous flow instability</title>
    <dc:date>2015-03-05T10:59:21+00:00</dc:date>
    <link>http://arxiv.org/abs/1410.7623</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[The displacement of a more viscous fluid by a less viscous one in a quasi-two dimensional geometry leads to the formation of complex fingering patterns. This fingering has been characterized by a most unstable wavelength, λc, which depends on the viscosity difference between the two immiscible fluids and sets the characteristic width of the fingers. How the finger length grows after the instability occurs is an equally important, but previously overlooked, aspect that characterizes the global features of the patterns. As the lower viscosity fluid is injected, we show that there is a stable inner region where the outer fluid is completely displaced. The ratio of the finger length to the radius of this stable region depends only on the viscosity ratio of the fluids and is decoupled from λc.
]]></description>
<dc:subject>physics self-organization pattern-formation experiment modeling nudge-targets fluid-dynamics</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:1a45c19b8565/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:physics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:experiment"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:modeling"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:fluid-dynamics"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1403.6204">
    <title>[1403.6204] Chimera states: Coexistence of coherence and incoherence in networks of coupled oscillators</title>
    <dc:date>2015-02-07T12:34:07+00:00</dc:date>
    <link>http://arxiv.org/abs/1403.6204</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[A chimera state is a spatio-temporal pattern in a network of identical coupled oscillators in which synchronous and asynchronous oscillation coexist. This state of broken symmetry, which usually coexists with a stable spatially symmetric state, has intrigued the nonlinear dynamics community since its discovery in the early 2000s. Recent experiments have led to increasing interest in the origin and dynamics of these states. Here we review the history of research on chimera states and highlight major advances in understanding their behaviour.
]]></description>
<dc:subject>coupled-oscillators pattern-formation nonlinear-dynamics nudge-targets network-theory engineering-design</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:9165f7363963/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:coupled-oscillators"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:network-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:engineering-design"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1501.01509">
    <title>[1501.01509] Pattern phase diagram for 2D arrays of coupled limit-cycle oscillators</title>
    <dc:date>2015-02-06T12:12:28+00:00</dc:date>
    <link>http://arxiv.org/abs/1501.01509</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Arrays of coupled limit-cycle oscillators represent a paradigmatic example for studying synchronization and pattern formation. They are also of direct relevance in the context of currently emerging experiments on nano- and optomechanical oscillator arrays. We find that the full dynamical equations for the phase dynamics of such an array go beyond previously studied Kuramoto-type equations. We analyze the evolution of the phase field in a two-dimensional array and obtain a "phase diagram" for the resulting stationary and non-stationary patterns. The possible observation in optomechanical arrays is discussed briefly.
]]></description>
<dc:subject>coupled-oscillators pattern-formation phase-transitions butterfly-collecting nudge-targets consider:recognizers consider:variations consider:robustness rather-interesting nonlinear-dynamics</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:7ad7badf7db2/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:coupled-oscillators"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:phase-transitions"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:butterfly-collecting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:recognizers"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:variations"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:robustness"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1402.6669">
    <title>[1402.6669] Long-range correlations in a locally driven exclusion process</title>
    <dc:date>2015-02-06T11:58:21+00:00</dc:date>
    <link>http://arxiv.org/abs/1402.6669</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We show that the presence of a driven bond in an otherwise diffusive lattice gas with simple exclusion interaction results in long-range density-density correlation in its stationary state. In dimensions d>1 we show that in the thermodynamic limit this correlation decays as C(r,s)∼(r2+s2)−d at large distances r and s away from the drive with |r−s|>>1. This is derived using an electrostatic analogy whereby C(r,s) is expressed as the potential due to a configuration of electrostatic charges distributed in 2d-dimension. At bulk density ρ=1/2 we show that the potential is that of a localized quadrupolar charge. At other densities the same is correct in leading order in the strength of the drive and is argued numerically to be valid at higher orders.
]]></description>
<dc:subject>lattice-gas cellular-automata simulation thermodynamics complexology pattern-formation nudge-targets consider:reasons-to-move-the-excitation</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:6fb0e5c6245a/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:lattice-gas"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cellular-automata"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:thermodynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:reasons-to-move-the-excitation"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1403.0697">
    <title>[1403.0697] Aggregation and Segregation of Confined Active Particles</title>
    <dc:date>2015-01-19T11:42:39+00:00</dc:date>
    <link>http://arxiv.org/abs/1403.0697</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We simulate a model of self-propelled disks with soft repulsive interactions confined to a box in two dimensions. For small rotational diffusion rates, monodisperse disks spontaneously accumulate at the walls. At low densities, interaction forces between particles are strongly inhomogeneous, and a simple model predicts how these inhomogeneities alter the equation of state. At higher densities, collective effects become important. We observe signatures of a jamming transition at a packing fraction ϕ∼0.88, which is also the jamming point for non-active athermal monodisperse disks. At this ϕ, the system develops a critical finite active speed necessary for wall aggregation. At packing fractions above ϕ∼0.6, the pressure decreases with increasing density, suggesting that strong interactions between particles are affecting the equation of state well below the jamming transition. A mixture of bidisperse disks segregates in the absence of any adhesion, identifying a new mechanism that could contribute to cell sorting in embryonic development.
]]></description>
<dc:subject>active-matter self-organization pattern-formation nudge-targets biologically-inspired emergent-design</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:b3d6b61ea357/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:active-matter"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:biologically-inspired"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:emergent-design"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1401.1315">
    <title>[1401.1315] Emergent spatial structures in flocking models: a dynamical system insight</title>
    <dc:date>2014-12-21T13:33:05+00:00</dc:date>
    <link>http://arxiv.org/abs/1401.1315</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We show that hydrodynamic theories of polar active matter generically possess inhomogeneous traveling solutions. We introduce a unifying dynamical-system framework to establish the shape of these intrinsically nonlinear patterns, and show that they correspond to those hitherto observed in experiments and numerical simulations: periodic density waves, and solitonic bands, or polar-liquid droplets both cruising in isotropic phases. We elucidate their respective multiplicity and mutual relations, as well as their existence domain.
]]></description>
<dc:subject>swarms artificial-life ethology simulation pattern-formation rather-interesting</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:6c381e2f80e9/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:swarms"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:artificial-life"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:ethology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1401.4085">
    <title>[1401.4085] Bending of Sparklers</title>
    <dc:date>2014-12-18T11:24:27+00:00</dc:date>
    <link>http://arxiv.org/abs/1401.4085</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[A new equation is proposed to explain the curvature of spent sparklers. We found the state of a segment of the sparkler to depend strongly on the state of its spent segments. The equation is nearly able to produce the sparkler shape for a range of lengths and for all elevation angles. The method proposed here is likely to explain any phenomena in nature related to an evolving length scale associated with some material that becomes progressively stiff or dry, such as the growth of resin exuded from trees. The equation can produce a very rich spectrum of shapes by varying material parameters (density, temperature-dependent strength), heating temperature, elevation angle, and gravitational acceleration. This might provide new insights into explaining many shapes in nature or man-made structures.
]]></description>
<dc:subject>physics dynamical-systems rather-interesting simulation pattern-formation</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:f2be2e62ca3c/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:physics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:dynamical-systems"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1412.1070">
    <title>[1412.1070] The Self-Organization of Grid Cells in 3D</title>
    <dc:date>2014-12-08T11:49:15+00:00</dc:date>
    <link>http://arxiv.org/abs/1412.1070</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[What sort of grid cells do we expect to see in bats exploring a three-dimensional environment? How long will it take for them to emerge? We address these questions within our self-organization model based on firing-rate adaptation. The model indicates that the answer to the first question may be simple, and to the second one rather complex. The mathematical analysis of the simplified version of the model points at asymptotic states resembling FCC and HCP crystal structures, which are calculated to be very close to each other in terms of cost function. The simulation of the full model, however, shows that the approach to such asymptotic states involves several sub-processes over distinct time scales. The smoothing of the initially irregular multiple fields of individual units and their arrangement into hexagonal grids over certain best planes are observed to occur relatively fast, even in large 3D volumes. The correct mutual orientation of the planes, however, and the coordinated arrangement of different units, take a longer time, with the network showing no sign of convergence towards either a pure FCC or HCP ordering.
]]></description>
<dc:subject>self-organization theoretical-biology ethology pattern-formation rather-interesting collective-intelligence</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:8a2b74b1d33e/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:theoretical-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:ethology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:collective-intelligence"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1407.6426">
    <title>[1407.6426] Pattern Formation with a Compartmental Lateral Inhibition System</title>
    <dc:date>2014-12-02T11:57:01+00:00</dc:date>
    <link>http://arxiv.org/abs/1407.6426</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We propose a compartmental lateral inhibition system that generates contrasting patterns of gene expression between neighboring compartments. The system consists of a set of compartments interconnected by channels. Each compartment contains a colony of cells that produce diffusible molecules to be detected by the neighboring colony, and each cell is equipped with an inhibitory circuit that reduces its production when the detected signal is stronger. We develop a technique to analyze the steady-state patterns emerging from this lateral inhibition system and apply it to a specific implementation. The analysis shows that the proposed system indeed exhibits contrasting patterns within realistic parameter ranges.
]]></description>
<dc:subject>theoretical-biology systems-biology developmental-biology models formalization pattern-formation parameter-tuning nudge-targets</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:4f0ca27a9453/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:theoretical-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:systems-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:developmental-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:models"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:formalization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:parameter-tuning"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1403.7146">
    <title>[1403.7146] Pattern analysis in a benthic bacteria-nutrient system</title>
    <dc:date>2014-11-27T17:16:50+00:00</dc:date>
    <link>http://arxiv.org/abs/1403.7146</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We study pattern formation in a reaction-diffusion system for a benthic bacteria-nutrient model in a marine sediment, which originally contains some spatially varying coefficients and with these shows some layering of patterns. Using the Landau reduction for the system with homogeneous coefficients, we locally analyze Turing bifurcations in 1D and 2D. Moreover, we use the software {\tt pde2path} to compute the corresponding branches globally and find a number of snaking branches of patterns over patterns. 
This shows that spatially varying patterns are not necessarily due to spatially varying coefficients.
]]></description>
<dc:subject>self-organization pattern-formation community-assembly simulation theoretical-biology rather-interesting Turing-systems</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:885cecb3f952/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:community-assembly"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:theoretical-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:Turing-systems"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1401.6466">
    <title>[1401.6466] Periodic ordering of clusters and stripes in a two-dimensional lattice model. II. Results of Monte Carlo simulation</title>
    <dc:date>2014-11-27T12:05:30+00:00</dc:date>
    <link>http://arxiv.org/abs/1401.6466</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[The triangular lattice model with nearest-neighbor attraction and third-neighbor repulsion, introduced in [J. Pekalski, A. Ciach and N. G. Almarza, arXiv:1401.0801 [cond-mat.soft]] is studied by Monte Carlo simulation. Introduction of appropriate order parameters allowed us to construct a phase diagram, where different phases with patterns made of clusters, bubbles or stripes are thermodynamically stable. We observe, in particular, two distinct lamellar phases - the less ordered one with global orientational order and the more ordered one with both orientational and translational order. Our results concern spontaneous pattern formation on solid surfaces, fluid interfaces or membranes that is driven by competing interactions between adsorbing particles or molecules.
]]></description>
<dc:subject>pattern-formation self-organization simulation stamp-collecting rather-interesting physics nudge-targets biological-engineering consider:engineering-design consider:variants-in-this-context consider:stress-testing-pattern-detectors consider:pattern-detectors</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:0288273ee937/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:stamp-collecting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:physics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:biological-engineering"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:engineering-design"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:variants-in-this-context"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:stress-testing-pattern-detectors"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:pattern-detectors"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1304.7301">
    <title>[1304.7301] Percolation and Disorder-Resistance in Cellular Automata</title>
    <dc:date>2014-11-27T01:35:33+00:00</dc:date>
    <link>http://arxiv.org/abs/1304.7301</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We rigorously prove a form of disorder-resistance for a class of one-dimensional cellular automaton rules, including some that arise as boundary dynamics of two-dimensional solidification rules. Specifically, when started from a random initial seed on an interval of length L, with probability tending to one as L goes to infinity, the evolution is a replicator. That is, a region of space-time of density one is filled with a spatially and temporally periodic pattern, punctuated by a finite set of other finite patterns repeated at a fractal set of locations. On the other hand, the same rules exhibit provably more complex evolution from some seeds, while from other seeds their behavior is apparently chaotic. A principal tool is a new variant of percolation theory, in the context of additive cellular automata from random initial states.
]]></description>
<dc:subject>cellular-automata order-and-chaos nonlinear-dynamics pattern-discovery pattern-formation narrative seeing-things (in-a-good-way) nudge-targets consider:pattern-detectors consider:generalizations</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:313bccba6a54/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cellular-automata"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:order-and-chaos"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-discovery"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:narrative"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:seeing-things"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:(in-a-good-way)"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:pattern-detectors"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:generalizations"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1402.3168">
    <title>[1402.3168] Calculating Voronoi diagrams using simple chemical reactions</title>
    <dc:date>2014-10-08T20:27:01+00:00</dc:date>
    <link>http://arxiv.org/abs/1402.3168</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[This paper overviews work on the use of simple chemical reactions to calculate Voronoi diagrams and undertake other related geometric calculations. This work highlights that this type of specialised chemical processor is a model example of a parallel processor. For example increasing the complexity of the input data within a given area does not increase the computation time. These processors are also able to calculate two or more Voronoi diagrams in parallel. Due to the specific chemical reactions involved and the relative strength of reaction with the substrate (and cross-reactivity with the products) these processors are also capable of calculating Voronoi diagrams sequentially from distinct chemical inputs. The chemical processors are capable of calculating a range of generalised Voronoi diagrams (either from circular drops of chemical or other geometric shapes made from adsorbent substrates soaked in reagent), skeletonisation of planar shapes and weighted Voronoi diagrams (e.g. additively weighted Voronoi diagrams, Multiplicitavely weighted Crystal growth Voronoi diagrams). The paper will also discuss some limitations of these processors. These chemical processors constitute a class of pattern forming reactions which have parallels with those observed in natural systems. It is possible that specialised chemical processors of this general type could be useful for synthesising functional structured materials.
]]></description>
<dc:subject>reaction-diffusion self-organization pattern-formation chemistry computational-geometry algorithms algorithms-sortof philosophy-of-engineering nanotechnology materials-science rather-interesting</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:41d785b92b51/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:reaction-diffusion"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:chemistry"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:computational-geometry"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:algorithms"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:algorithms-sortof"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:philosophy-of-engineering"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nanotechnology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:materials-science"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1401.4475">
    <title>[1401.4475] Controlled self-assembly of periodic and aperiodic cluster crystals</title>
    <dc:date>2014-09-28T11:43:49+00:00</dc:date>
    <link>http://arxiv.org/abs/1401.4475</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Soft particles are known to overlap and form stable clusters that self-assemble into periodic crystalline phases with density-independent lattice constants. We use molecular dynamics simulations in two dimensions to demonstrate that, through a judicious design of an isotropic pair potential, one can control the ordering of the clusters and generate a variety of phases, including decagonal and dodecagonal quasicrystals. Our results confirm analytical predictions based on a mean-field approximation, providing insight into the stabilization of quasicrystals in soft macromolecular systems, and suggesting a practical approach for their controlled self-assembly in laboratory realizations using synthesized soft-matter particles.
]]></description>
<dc:subject>molecular-design self-organization self-assembly nanotechnology simulation condensed-matter pattern-formation nudge-targets consider:diversity-of-particles</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:a9917f955e14/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:molecular-design"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-assembly"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nanotechnology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:condensed-matter"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:diversity-of-particles"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1408.6828">
    <title>[1408.6828] Cyclic dominance in evolutionary games: A review</title>
    <dc:date>2014-09-05T12:28:17+00:00</dc:date>
    <link>http://arxiv.org/abs/1408.6828</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Rock is wrapped by paper, paper is cut by scissors, and scissors are crushed by rock. This simple game is popular among children and adults to decide on trivial disputes that have no obvious winner, but cyclic dominance is also at the heart of predator-prey interactions, the mating strategy of side-blotched lizards, the overgrowth of marine sessile organisms, and the competition in microbial populations. Cyclical interactions also emerge spontaneously in evolutionary games entailing volunteering, reward, punishment, and in fact are common when the competing strategies are three or more regardless of the particularities of the game. Here we review recent advances on the rock-paper-scissors and related evolutionary games, focusing in particular on pattern formation, the impact of mobility, and the spontaneous emergence of cyclic dominance. We also review mean-field and zero-dimensional rock-paper-scissors models and the application of the complex Ginzburg-Landau equation, and we highlight the importance and usefulness of statistical physics for the successful study of large-scale ecological systems. Directions for future research, related for example to dynamical effects of coevolutionary rules and invasion reversals due to multi-point interactions, are outlined as well.
]]></description>
<dc:subject>evolutionary-economics artificial-life pattern-formation complexology review self-organization pretty roshambo</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:55519eaa2898/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:evolutionary-economics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:artificial-life"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:review"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pretty"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:roshambo"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1212.1740">
    <title>[1212.1740] A Graph Partitioning Approach to Predict Patterns in Lateral Inhibition Systems</title>
    <dc:date>2014-08-22T12:32:16+00:00</dc:date>
    <link>http://arxiv.org/abs/1212.1740</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We analyze pattern formation on a network of cells where each cell inhibits its neighbors through cell-to-cell contact signaling. The network is modeled as an interconnection of identical dynamical subsystems each of which represents the signaling reactions in a cell. We search for steady state patterns by partitioning the graph vertices into disjoint classes, where the cells in the same class have the same final fate. To prove the existence of steady states with this structure, we use results from monotone systems theory. Finally, we analyze the stability of these patterns with a block decomposition based on the graph partition.
]]></description>
<dc:subject>pattern-formation prediction models complex-systems emergent-design nudge-targets rather-interesting discrete-mathematics dynamical-systems</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:882eaa11291b/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:prediction"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:models"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complex-systems"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:emergent-design"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:discrete-mathematics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:dynamical-systems"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1401.0413">
    <title>[1401.0413] Spatial patterns of competing random walkers</title>
    <dc:date>2014-08-09T11:48:08+00:00</dc:date>
    <link>http://arxiv.org/abs/1401.0413</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We review recent results obtained from simple individual-based models of biological competition in which birth and death rates of an organism depend on the presence of other competing organisms close to it. In addition the individuals perform random walks of different types (Gaussian diffusion and L\'{e}vy flights). We focus on how competition and random motions affect each other, from which spatial instabilities and extinctions arise. Under suitable conditions, competitive interactions lead to clustering of individuals and periodic pattern formation. Random motion has a homogenizing effect and then delays this clustering instability. When individuals from species differing in their random walk characteristics are allowed to compete together, the ones with a tendency to form narrower clusters get a competitive advantage over the others. Mean-field deterministic equations are analyzed and compared with the outcome of the individual-based simulations.
]]></description>
<dc:subject>self-organization pattern-formation random-walks agent-based simulation ecology nudge-targets consider:rule-discovery computational-geometry</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:2057b12c4f5c/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:random-walks"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:agent-based"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:ecology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:rule-discovery"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:computational-geometry"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1403.0351">
    <title>[1403.0351] Turing Instability and Pattern Formation in an Activator-Inhibitor System with Nonlinear Diffusion</title>
    <dc:date>2014-05-02T11:39:19+00:00</dc:date>
    <link>http://arxiv.org/abs/1403.0351</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[In this work we study the effect of density dependent nonlinear diffusion on pattern formation in the Lengyel--Epstein system. Via the linear stability analysis we determine both the Turing and the Hopf instability boundaries and we show how nonlinear diffusion intensifies the tendency to pattern formation; %favors the mechanism of pattern formation with respect to the classical linear diffusion case; in particular, unlike the case of classical linear diffusion, the Turing instability can occur even when diffusion of the inhibitor is significantly slower than activator's one. In the Turing pattern region we perform the WNL multiple scales analysis to derive the equations for the amplitude of the stationary pattern, both in the supercritical and in the subcritical case. Moreover, we compute the complex Ginzburg-Landau equation in the vicinity of the Hopf bifurcation point as it gives a slow spatio-temporal modulation of the phase and amplitude of the homogeneous oscillatory solution.
]]></description>
<dc:subject>turing-patterns pattern-formation reaction-networks self-organization simulation physics</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:2ef5a86b98ed/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:turing-patterns"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:reaction-networks"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:physics"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1401.1704">
    <title>[1401.1704] Spatiotemporal Oscillation Patterns in the Collective Relaxation Dynamics of Interacting Particles in Periodic Potentials</title>
    <dc:date>2014-04-24T11:06:30+00:00</dc:date>
    <link>http://arxiv.org/abs/1401.1704</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We demonstrate the emergence of self-organized structures in the course of the relaxation of an initially excited, dissipative and finite chain of interacting particles in a periodic potential towards its many particle equilibrium configuration. Specifically we observe a transition from an in phase correlated motion via phase randomized oscillations towards oscillations with a phase difference π between adjacent particles thereby yielding the growth of long time transient spatiotemporal oscillation patterns. Parameter modifications allow for designing these patterns, including steady states and even states that combine in phase and correlated out of phase oscillations along the chain. The complex relaxation dynamics is based on finite size effects together with an evolution running from the nonlinear to the linear regime thereby providing a highly unbalanced population of the center of mass and relative motion.]]></description>
<dc:subject>self-organization pattern-formation coupled-oscillators simulation nudge-targets consider:inhomogeneities consider:relating-to-cellular-automata</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:0bd34a47302b/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:coupled-oscillators"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:inhomogeneities"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:relating-to-cellular-automata"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1401.1888">
    <title>[1401.1888] Dynamical Models of Stock Prices Based on Technical Trading Rules Part I: The Models</title>
    <dc:date>2014-01-23T13:08:56+00:00</dc:date>
    <link>http://arxiv.org/abs/1401.1888</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[In this paper we use fuzzy systems theory to convert the technical trading rules commonly used by stock practitioners into excess demand functions which are then used to drive the price dynamics. The technical trading rules are recorded in natural languages where fuzzy words and vague expressions abound. In Part I of this paper, we will show the details of how to transform the technical trading heuristics into nonlinear dynamic equations. First, we define fuzzy sets to represent the fuzzy terms in the technical trading rules; second, we translate each technical trading heuristic into a group of fuzzy IF-THEN rules; third, we combine the fuzzy IF-THEN rules in a group into a fuzzy system; and finally, the linear combination of these fuzzy systems is used as the excess demand function in the price dynamic equation. We transform a wide variety of technical trading rules into fuzzy systems, including moving average rules, support and resistance rules, trend line rules, big buyer, big seller and manipulator rules, band and stop rules, and volume and relative strength rules. Simulation results show that the price dynamics driven by these technical trading rules are complex and chaotic, and some common phenomena in real stock prices such as jumps, trending and self-fulfilling appear naturally.
]]></description>
<dc:subject>agent-based technical-analysis self-organization markets pattern-discovery pattern-formation the-mangle-in-practice nudge-targets simulation interesting</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:fb561a0d16d4/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:agent-based"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:technical-analysis"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:markets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-discovery"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:the-mangle-in-practice"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:interesting"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1310.0293">
    <title>[1310.0293] Periodic structures in binary mixtures enforced by Janus particles</title>
    <dc:date>2013-11-27T15:33:43+00:00</dc:date>
    <link>http://arxiv.org/abs/1310.0293</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Phase separation in binary mixtures in the presence of Janus particles has been studied in terms of a Cahn-Hilliard model coupled to the Langevin equations describing the particle dynamics. We demonstrate that the phase separation process is arrested leading to unexpected regular stripe patterns in the concentration field. The underlying pattern forming mechanism has been elucidated: The twofold absorption properties on the surface of Janus particles with respect to the two components of a binary mixture trigger in their neighborhood spatial concentration variations. They result in an effective interaction between the particles mediated by the binary mixture. Our findings open a route to design composite materials with nanoscale lamellar morphologies where the pattern wavelength can be tuned by changing the wetting properties of the Janus particles.
]]></description>
<dc:subject>self-organization pattern-formation nanotechnology biological-engineering self-assembly simulation nudge-targets</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:7c84cac608ee/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nanotechnology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:biological-engineering"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-assembly"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1302.4014">
    <title>[1302.4014] Digital morphogenesis via Schelling segregation</title>
    <dc:date>2013-11-03T12:40:39+00:00</dc:date>
    <link>http://arxiv.org/abs/1302.4014</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Schelling's model of segregation looks to explain the way in which particles or agents of two types may come to arrange themselves spatially into configurations consisting of large homogeneous clusters, i.e.\ connected regions consisting of only one type. As one of the earliest agent based models studied by economists and perhaps the most famous model of self-organising behaviour, it also has direct links to areas at the interface between computer science and statistical mechanics, such as the Ising model and the study of contagion and cascading phenomena in networks. 
While the model has been extensively studied it has largely resisted rigorous analysis, prior results from the literature generally pertaining to variants of the model which are tweaked so as to be amenable to standard techniques from statistical mechanics or stochastic evolutionary game theory. In \cite{BK}, Brandt, Immorlica, Kamath and Kleinberg provided the first rigorous analysis of the unperturbed model, for a specific set of input parameters. Here we provide a rigorous analysis of the model's behaviour much more generally and establish some surprising forms of threshold behaviour, notably the existence of situations where an \emph{increased} level of intolerance for neighbouring agents of opposite type leads almost certainly to \emph{decreased} segregation.
]]></description>
<dc:subject>artificial-life pattern-formation design-patterns collective-intelligence nudge-targets algorithms</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:db71366f6c73/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:artificial-life"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:design-patterns"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:collective-intelligence"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:algorithms"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1310.8272">
    <title>[1310.8272] Active Brownian agents with concentration-dependent chemotactic sensitivity</title>
    <dc:date>2013-11-03T11:10:31+00:00</dc:date>
    <link>http://arxiv.org/abs/1310.8272</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We study a biologically motivated model of overdamped, autochemotactic Brownian agents with concentration-dependent chemotactic sensitivity. The agents in our model move stochastically and produce a chemical ligand at their current position. The ligand concentration obeys a reaction-diffusion equation and acts as a chemoattractant for the agents, which bias their motion towards higher concentrations of the dynamically altered chemical field. We explore the impact of concentration-dependent response to chemoattractant gradients on large-scale pattern formation, by deriving a coarse-grained macroscopic description of the individual based model, and compare the conditions for emergence of inhomogeneous solutions for different variants of the chemotactic sensitivity. We focus primarily on the so-called "Receptor Law" sensitivity, which models a non-linear decrease of chemotactic sensitivity with increasing ligand concentration. Our results reveal qualitative differences between the "Receptor-Law", the constant chemotactic response and the so-called "Log-Law", with respect to stability of the homogeneous solution, as well as the emergence of different patterns (labyrinthine structures, clusters and bubbles) via spinodal-decomposition or nucleation. We discuss two limiting cases, where the model can be reduced to the dynamics of single species: (I) the agent density governed by an density-dependent effective diffusion coefficient and (II) the ligand-field with an effective bistable, time-dependent reaction rate. In the end, we turn to single clusters of agents, studying domain growth and determining mean characteristics of the stationary inhomogeneous state. Analytical results are confirmed and extended by large-scale GPU simulations of the individual based model.
]]></description>
<dc:subject>self-organization biological-engineering collective-intelligence simulation nudge-targets reaction-diffusion pattern-formation</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:0827385af112/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:biological-engineering"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:collective-intelligence"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:reaction-diffusion"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1209.1529">
    <title>[1209.1529] Diagonal patterns and chevron effect in intersecting traffic flows</title>
    <dc:date>2013-09-08T14:19:31+00:00</dc:date>
    <link>http://arxiv.org/abs/1209.1529</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We study a lattice model of two perpendicular intersecting flows of pedestrians represented by hard core particles of two types, eastbound (`$\pE$') and northbound (`$\pN$'). Each flow takes place on a strip of width $M$ so that the intersection is an $M\times M$ square lattice. In experiment and simulation there occurs on this square spontaneous formation of a diagonal pattern of alternating $\pE$ and $\pN$ particles. We show that this pattern formation may be understood in terms of a linear instability of the corresponding mean field equations. A refined investigation reveals that the pattern actually consists of chevrons rather than straight diagonals. We explain this effect as the consequence of the existence of a nonlinear mode sustained by the interaction between the two types of particles.
]]></description>
<dc:subject>self-organization traffic emergent-design pattern-formation agent-based nudge-targets</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:6632a4b19a11/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:traffic"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:emergent-design"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:agent-based"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1301.4190">
    <title>[1301.4190] Phyllotaxis, Pushed Pattern-Forming Fronts and Optimal Packing</title>
    <dc:date>2013-04-26T22:15:27+00:00</dc:date>
    <link>http://arxiv.org/abs/1301.4190</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We demonstrate that the pattern forming partial differential equation derived from the auxin distribution model proposed by Meyerowitz, Traas and others gives rise to all spiral phyllotaxis properties observed on plants. We show how the advancing pushed pattern front chooses spiral families enumerated by Fibonacci sequences with all attendant self similar properties and connect the results with the optimal packing based algorithms previously used to explain phyllotaxis. Our results allow us to make experimentally testable predictions.
]]></description>
<dc:subject>pattern-formation phyllotaxis self-organization dynamical-systems nudge-targets biological-engineering biologically-inspired</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:8bd01b0317f4/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:phyllotaxis"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:dynamical-systems"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:biological-engineering"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:biologically-inspired"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1211.6582">
    <title>[1211.6582] Emergence of large scale structure in planetary turbulence</title>
    <dc:date>2013-04-21T15:15:03+00:00</dc:date>
    <link>http://arxiv.org/abs/1211.6582</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Planetary and magnetohydrodynamic drift-wave turbulence is observed to self-organize into large scale structures such as zonal jets and coherent vortices. In this Letter we present a non-equilibrium statistical theory, the Stochastic Structural Stability theory (SSST), that can make predictions for the formation and finite amplitude equilibration of non-zonal and zonal structures (lattice and stripe patterns) in homogeneous turbulence. This theory reveals that the emergence of large scale structure is the result of an instability of the interaction between the coherent flow and the associated turbulent field. Comparison of the theory with nonlinear simulations of a barotropic flow in a beta-plane channel with turbulence sustained by isotropic random stirring, demonstrates that SSST predicts the threshold parameters at which the coherent structures emerge as well as the characteristics of the emerging structures (scale, amplitude, phase speed). It is shown that non-zonal structures (lattice states or zonons) emerge at lower energy input rates of the stirring compared to zonal flows (stripe states) and their emergence affects the dynamics of jet formation.
]]></description>
<dc:subject>meteorology astronomy emergence nonlinear-dynamics fluid-dynamics pattern-formation</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:8e637892aa47/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:meteorology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:astronomy"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:emergence"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:fluid-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1207.1864">
    <title>[1207.1864] Pattern formation in the dipolar Ising model on a two-dimensional honeycomb lattice</title>
    <dc:date>2012-08-29T11:08:32+00:00</dc:date>
    <link>http://arxiv.org/abs/1207.1864</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We present Monte Carlo simulation results for a two-dimensional Ising model with ferromagnetic nearest-neighbor couplings and a competing long-range dipolar interaction on a honeycomb lattice. Both structural and thermodynamic properties are very similar to the case of a square lattice, with the exception that structures reflect the sixfold rotational symmetry of the underlying honeycomb lattice. To deal with the long-range nature of the dipolar interaction we also present a simple method of evaluating effective interaction coefficients, which can be regarded as a more straightforward alternative to the prevalent Ewald summation techniques.]]></description>
<dc:subject>ising-model pattern-formation self-organization lattice-effects</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:9a64ef32ce00/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:ising-model"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:lattice-effects"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1201.5440">
    <title>[1201.5440] Self-assembly of anisotropic soft particles in two dimensions</title>
    <dc:date>2012-01-27T13:37:26+00:00</dc:date>
    <link>http://arxiv.org/abs/1201.5440</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA["The self assembly of core-corona discs interacting via anisotropic potentials is investigated using Monte Carlo computer simulations. A minimal interaction potential that incorporates anisotropy in a simple way is introduced. It consists in a core-corona architecture in which the center of the core is shifted with respect to the center of the corona. Anisotropy can thus be tuned by progressively shifting the position of the core. Despite its simplicity, the system self organize in a rich variety of structures including stripes, triangular and rectangular lattices, and unusual plastic crystals. Our results indicate that the amount of anisotropy does not alter the lattice spacing and only influences the type of clustering (stripes, micells, etc.) of the individual particles."]]></description>
<dc:subject>self-assembly biologically-inspired simulation pattern-formation condensed-matter</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:a69592e63de5/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-assembly"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:biologically-inspired"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:condensed-matter"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1201.4417">
    <title>[1201.4417] Instabilities and Patterns in Coupled Reaction-Diffusion Layers</title>
    <dc:date>2012-01-26T14:06:58+00:00</dc:date>
    <link>http://arxiv.org/abs/1201.4417</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA["We study instabilities and pattern formation in reaction-diffusion layers that are diffusively coupled. For two-layer systems of identical two-component reactions, we analyze the stability of homogeneous steady states by exploiting the block symmetric structure of the linear problem. There are eight possible primary bifurcation scenarios, including a Turing-Turing bifurcation that involves two disparate length scales whose ratio may be tuned via the inter-layer coupling. For systems of $n$-component layers and non-identical layers, the linear problem's block form allows approximate decomposition into lower-dimensional linear problems if the coupling is sufficiently weak. As an example, we apply these results to a two-layer Brusselator system. The competing length scales engineered within the linear problem are readily apparent in numerical simulations of the full system. Selecting a $sqrt{2}$:1 length scale ratio produces an unusual steady square pattern."]]></description>
<dc:subject>cute emergent-design pattern-formation complexology nudge-targets nonlinear-dynamics</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:7c05c8698a13/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cute"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:emergent-design"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://www.pnas.org/cgi/content/abstract/104/17/6974">
    <title>Complex spatial group patterns result from different animal communication mechanisms</title>
    <dc:date>2008-01-04T14:39:59+00:00</dc:date>
    <link>http://www.pnas.org/cgi/content/abstract/104/17/6974</link>
    <dc:creator>Vaguery</dc:creator><dc:subject>flocking artificial-life complex-systems complexology pattern-formation exploration algorithms biologically-inspired</dc:subject>
<dc:identifier>https://pinboard.in/u:Vaguery/b:f1ae619a74da/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:flocking"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:artificial-life"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complex-systems"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-formation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:exploration"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:algorithms"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:biologically-inspired"/>
</rdf:Bag></taxo:topics>
</item>
</rdf:RDF>