Controlling Pattern Formation in Nanoparticle Assemblies via Directed Solvent Dewetting

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

Modeling the skin pattern of fishes

Complicated patterns showing various spatial scales have been obtained in the past by coupling Turing systems in such a way that the scales of the independent systems resonate. This produces superimposed patterns with different length scales. Here we propose a model consisting of two identical reaction-diffusion systems coupled together in such a way that one of them produces a simple Turing pattern of spots or stripes, and the other traveling wave fronts that eventually become stationary. The basic idea is to assume that one of the systems becomes fixed after some time and serves as a source of morphogens for the other system. This mechanism produces patterns very similar to the pigmentation patterns observed in different species of stingrays and other fishes. The biological mechanisms that support the realization of this model are discussed.

Dynamic formation of SEBS copolymer submicrometric structures

Highly ordered A-B-A block copolymer arrangements in the submicrometric scale, resulting from dewetting and solvent evaporation of thin films, have inspired a variety of new applications in the nanometric world. Despite the progress observed in the control of such structures, the intricate scientific phenomena related to regular patterns formation are still not completely elucidated. SEBS is a standard example of a triblock copolymer that forms spontaneously impressive pattern arrangements. From macroscopic thin liquid films of SEBS solution, several physical effects and phenomena act synergistically to achieve well-arranged patterns of stripes and/or droplets. That is, concomitant with dewetting, solvent evaporation, and Marangoni effect, Rayleigh instability and phase separation also play important role in the pattern formation. These two last effects are difficult to be followed experimentally in the nanoscale, which render difficulties to the comprehension of the whole phenomenon. In this paper, we use computational methods for image analysis, which provide quantitative morphometric data of the patterns, specifically comprising stripes fragmentation into droplets. With the help of these computational techniques, we developed an explanation for the final part of the pattern formation, i.e. structural dynamics related to the stripes fragmentation. (C) 2010 Elsevier Ltd. All rights reserved.

Generation of the primary hair follicle pattern.

Hair follicles are spaced apart from one another at regular intervals through the skin. Although follicles are predominantly epidermal structures, classical tissue recombination experiments indicated that the underlying dermis defines their location during development. Although many molecules involved in hair follicle formation have been identified, the molecular interactions that determine the emergent property of pattern formation have remained elusive. We have used embryonic skin cultures to dissect signaling responses and patterning outcomes as the skin spatially organizes itself. We find that ectodysplasin receptor (Edar)-bone morphogenetic protein (BMP) signaling and transcriptional interactions are central to generation of the primary hair follicle pattern, with restriction of responsiveness, rather than localization of an inducing ligand, being the key driver in this process. The crux of this patterning mechanism is rapid Edar-positive feedback in the epidermis coupled with induction of dermal BMP4/7. The BMPs in turn repress epidermal Edar and hence follicle fate. Edar activation also induces connective tissue growth factor, an inhibitor of BMP signaling, allowing BMP action only at a distance from their site of synthesis. Consistent with this model, transgenic hyperactivation of Edar signaling leads to widespread overproduction of hair follicles. This Edar-BMP activation-inhibition mechanism appears to operate alongside a labile prepattern, suggesting that Edar-mediated stabilization of beta-catenin active foci is a key event in determining definitive follicle locations.

Pattern selection in a lattice of pulse-coupled oscillators

We study spatio-temporal pattern formation in a ring of N oscillators with inhibitory unidirectional pulselike interactions. The attractors of the dynamics are limit cycles where each oscillator fires once and only once. Since some of these limit cycles lead to the same pattern, we introduce the concept of pattern degeneracy to take it into account. Moreover, we give a qualitative estimation of the volume of the basin of attraction of each pattern by means of some probabilistic arguments and pattern degeneracy, and show how they are modified as we change the value of the coupling strength. In the limit of small coupling, our estimative formula gives a pefect agreement with numerical simulations.

Self-organization mechanisms for the formation on nearshore crescentic and transverse sand bars

The formation and development of transverse and crescentic sand bars in the coastal marine environment has been investigated by means of a nonlinear numerical model based on the shallow-water equations and on a simpli ed sediment transport parameterization. By assuming normally approaching waves and a saturated surf zone, rhythmic patterns develop from a planar slope where random perturbations of small amplitude have been superimposed. Two types of bedforms appear: one is a crescentic bar pattern centred around the breakpoint and the other, herein modelled for the rst time, is a transverse bar pattern. The feedback mechanism related to the formation and development of the patterns can be explained by coupling the water and sediment conservation equations. Basically, the waves stir up the sediment and keep it in suspension with a certain cross-shore distribution of depth-averaged concentration. Then, a current flowing with (against) the gradient of sediment concentration produces erosion (deposition). It is shown that inside the surf zone, these currents may occur due to the wave refraction and to the redistribution of wave breaking produced by the growing bedforms. Numerical simulations have been performed in order to understand the sensitivity of the pattern formation to the parameterization and to relate the hydro-morphodynamic input conditions to which of the patterns develops. It is suggested that crescentic bar growth would be favoured by high-energy conditions and ne sediment while transverse bars would grow for milder waves and coarser sediment. In intermediate conditions mixed patterns may occur.

Towards a unifying framework for pattern transformation in swarm systems

This paper identifies the major challenges in the area of pattern formation. The work is also motivated by the need for development of a single framework to surmount these challenges. A framework based on the control of macroscopic parameters is proposed. The issue of transformation of patterns is specifically considered. A definition for transformation and four special cases, namely elementary and geometrical transformations by repositioning all or some robots in the pattern are provided. Two feasible tools for pattern transformation namely, a macroscopic parameter method and a mathematical tool - Moebius transformation also known as the linear fractional transformation are introduced. The realization of the unifying framework considering planning and communication is reported.

A swarm pattern transformation method based on macroscopic parameter operations

The work reported in this paper is motivated by biomimetic inspiration - the transformation of patterns. The major issue addressed is the development of feasible methods for transformation based on a macroscopic tool. The general requirement for the feasibility of the transformation method is determined by classifying pattern formation approaches an their characteristics. A formal definition for pattern transformation is provided and four special cases namely, elementary and geometric transformation based on repositioning all and some robotic agents are introduced. A feasible method for transforming patterns geometrically, based on the macroscopic parameter operation of a swarm is considered. The transformation method is applied to a swarm model which lends itself to the transformation technique. Simulation studies are developed to validate the feasibility of the approach, and do indeed confirm the approach.

The relevance of the silica metabolizing enzyme silicatein-alpha to biomineralization and the formation of biogenic silica in siliceous sponges

Die technische Silikatproduktion erfordert in der Regel hohe Temperaturen und extreme pH-Werte. In der Natur hingegen haben insbesondere Kieselschwämme die außergewöhnliche Fähigkeit, ihr Silikatskelett, das aus einzelnen sogenannten Spiculae besteht, enzymatisch mittels des Proteins Silicatein zu synthetisieren. rnIm Inneren der Spiculae, im zentralen Kanal, befindet sich das Axialfilament, welches hauptsächlich aus Silicatein-α aufgebaut ist. Mittels Antikörperfärbungen und Elektronenmikroskopischen Analysen konnte festgestellt werden, dass Silicatein in mit Kieselsäure-gefüllten Zellorganellen (silicasomes) nachzuweisen ist. Mittels dieser Vakuolen kann das Enzym und die Kieselsäure aus der Zelle zu den Spiculae im extrazellulären Raum befördert werden, wo diese ihre endgültige Länge und Dicke erreichen. Zum ersten Mal konnte nachgewiesen werden, dass rekombinant hergestelltes Silicatein-α sowohl als Siliciumdioxid-Polymerase als auch Siliciumdioxid-Esterase wirkt. Mittels Massenspektroskopie konnte die enzymatische Polymerisation von Kieselsäure nachverfolgt werden. Durch Spaltung der Esterbindung des künstlichen Substrates Bis(p-aminophenoxy)-dimethylsilan war es möglich kinetische Parameter der Siliciumdioxid-Esterase-Aktivität des rekombinanten Silicateins zu ermitteln.rnZu den größten biogenen Silikatstukuren auf der Erde gehören die Kieselnadeln der Schwammklasse Hexactinellida. Nadelextrakte aus den Schwammklassen Demospongien (S. domuncula) und Hexactinellida (M. chuni) wurden miteinander verglichen um die potentielle Existenz von Silicatein oder Silicatein-ähnliche Molekülen und die dazu gehörige proteolytischen Aktivität nachzuweisen. Biochemische Analysen zeigten, dass das 27 kDA große isolierte Polypeptid in Monoraphis mehrere gemeinsame Merkmale mit den Silicateinen der Demospongien teilt. Dazu gehören die Größe und die Proteinase-Aktivität. rnUm die Frage zu klären, ob das axiale Filament selbst zur Formbildung der Skelettelemente beiträgt, wurde ein neues mildes Extraktionsverfahren eingeführt. Dieses Verfahren ermöglichte die Solubilisierung des nativen Silicateins aus den Spiculae. Die isolierten Silicateine lagen als Monomere (24 kDa) vor, die Dimere durch nicht-kovalente Bindungen ausbildeten. Darüber hinaus konnten durch PAGE-Gelelektrophorese Tetramere (95 kDa) und Hexamere (135 kDa) nachgewiesen werden. Die Monomere zeigten eine beträchtliche proteolytische Aktivität, die sich während der Polymerisationsphase des Proteins weiter erhöhte. Mit Hilfe der Lichtmikroskopie und Elektronenmikroskopie (TEM) konnte die Assemblierung der Proteine zu filamentartigen Strukturen gezeigt werden. Die Selbstorganisation der Silicatein-α-Monomeren scheint eine Basis für Form- und Musterbildung der wachsenden Nadeln zu bilden.rn Um die Rolle des kürzlich entdeckten Proteins Silintaphin-1, ein starker Interaktionspartner des Silicatein-α, während der Biosilifizierung zu klären, wurden Assemblierungs-Experimente mit den rekombinanten Proteinen in vitro durchgeführt. Zusätzlich wurde deren Effekt auf die Biosilikatsynthese untersucht. Elektronenmikroskopische Analysen ergaben, dass rekombinantes Silicatein-α zufällig verteilte Aggregate bildet, während die Koinkubation beider Proteine (molekulares Verhältnis 4:1) über fraktal artige Strukturen zu Filamenten führt. Auch die enzymatische Aktivität der Silicatein-α-vermittelte Biosilikatsynthese erhöhte sich in Gegenwart von Silintaphin-1 um das 5,3-fache. rn

Mechano-Chemical Aspects of Organ Formation in Arabidopsis thaliana: The Relationship between Auxin and Pectin

How instructive signals are translated into robust and predictable changes in growth is a central question in developmental biology. Recently, much interest has centered on the feedback between chemical instructions and mechanical changes for pattern formation in development. In plants, the patterned arrangement of aerial organs, or phyllotaxis, is instructed by the phytohormone auxin; however, it still remains to be seen how auxin is linked, at the apex, to the biochemical and mechanical changes of the cell wall required for organ outgrowth. Here, using Atomic Force Microscopy, we demonstrate that auxin reduces tissue rigidity prior to organ outgrowth in the shoot apex of Arabidopsis thaliana, and that the de-methyl-esterification of pectin is necessary for this reduction. We further show that development of functional organs produced by pectin-mediated ectopic wall softening requires auxin signaling. Lastly, we demonstrate that coordinated localization of the auxin transport protein, PIN1, is disrupted in a naked-apex produced by increasing cell wall rigidity. Our data indicates that a feedback loop between the instructive chemical auxin and cell wall mechanics may play a crucial role in phyllotactic patterning.

Pattern and process: competition causes regular spacing of individuals within plant populations

1 We used simulated and experimental plant populations to analyse mortality-driven pattern formation under size-dependent competition. Larger plants had an advantage under size-asymmetric but not under symmetric competition. Initial patterns were random or clumped. 2 The simulations were individual-based and spatially explicit. Size-dependent competition was modelled with different rules to partition overlapping zones of influence. 3 The experiment used genotypes of Arabidopsis thaliana with different morphological plasticity and hence size-dependent competition. Compared with wild types, transgenic individuals over-expressed phytochrome A and had decreased plasticity because of disabled phytochrome-mediated shade avoidance. Therefore, competition among transgenics was more asymmetric compared with wild-types. 4 Density-dependent mortality under symmetric competition did not substantially change the initial spatial pattern. Conversely, simulations under asymmetric competition and experimental patterns of transgenic over-expressors showed patterns of survivors that deviated substantially from random mortality independent of initial patterns. 5 Small-scale initial patterns of wild types were regular rather than random or clumped. We hypothesize that this small-scale regularity may be explained by early shade avoidance of seedlings in their cotyledon stage. 6 Our experimental results support predictions from an individual-based simulation model and support the conclusion that regular spatial patterns of surviving individuals should be interpreted as evidence for strong, asymmetric competitive interactions and subsequent density-dependent mortality.

Complex formation between stage-specific oocyte factors and a Xenopus mRNA localization element

It is a long-standing proposal that localization of maternal factors in eggs can provide the basis for pattern formation in the early embryo. The localized information can be stored as RNA, one example being Vg1 RNA, which is localized exclusively to the vegetal hemisphere of Xenopus oocytes and eggs. Localization of Vg1 mRNA is directed by a 340-nt sequence element contained within its 3′ untranslated region. To understand the mechanism of localization, I have tested whether factors from the oocyte interact specifically with the RNA localization sequence. Results presented here show that a set of oocyte proteins form complexes with the localization element both in vitro and in vivo. These proteins are specifically enriched in the stages of oogenesis during which localization occurs and recognize sub-elements of the RNA localization element that are essential for localization in vivo. These data suggest that formation of a localization-specific RNA–protein complex may be the first step in directing Vg1 mRNA to its subcellular destination.

Pattern generation by dissipative parametric instability

Nonlinear instabilities are responsible for spontaneous pattern formation in a vast number of natural and engineered systems, ranging from biology to galaxy buildup. We propose a new instability mechanism leading to pattern formation in spatially extended nonlinear systems, which is based on a periodic antiphase modulation of spectrally dependent losses arranged in a zigzag way: an effective filtering is imposed at symmetrically located wave numbers k and -k in alternating order. The properties of the dissipative parametric instability differ from the features of both key classical concepts of modulation instabilities, i.e., the Benjamin-Feir instability and the Faraday instabiltyity. We demonstrate how the dissipative parametric instability can lead to the formation of stable patterns in one- and two-dimensional systems. The proposed instability mechanism is generic and can naturally occur or can be implemented in various physical systems.

Time correlation function in systems with two coexisting biological species

We study a stochastic lattice model describing the dynamics of coexistence of two interacting biological species. The model comprehends the local processes of birth, death, and diffusion of individuals of each species and is grounded on interaction of the predator-prey type. The species coexistence can be of two types: With self-sustained coupled time oscillations of population densities and without oscillations. We perform numerical simulations of the model on a square lattice and analyze the temporal behavior of each species by computing the time correlation functions as well as the spectral densities. This analysis provides an appropriate characterization of the different types of coexistence. It is also used to examine linked population cycles in nature and in experiment.

Complex kinetics, high frequency oscillations and temperature compensation in the electro-oxidation of ethylene glycol on platinum

Despite the fact that the majority of the catalytic electro-oxidation of small organic molecules presents oscillatory kinetics under certain conditions, there are few systematic studies concerning the influence of experimental parameters on the oscillatory dynamics. Of the studies available, most are devoted to C1 molecules and just some scattered data are available for C2 molecules. We present in this work a comprehensive study of the electro-oxidation of ethylene glycol on polycrystalline platinum surfaces and in alkaline media. The system was studied by means of electrochemical impedance spectroscopy, cyclic voltammetry, and chronoamperometry, and the impact of parameters such as applied current, ethylene glycol concentration, and temperature were investigated. As in the case of other parent systems, the instabilities in this system were associated with a hidden negative differential resistance, as identified by impedance data. Very rich and robust dynamics were observed, including the presence of harmonic and mixed mode oscillations and chaotic states, in some parameter region. Oscillation frequencies of about 16 Hz characterized the fastest oscillations ever reported for the electro-oxidation of small organic molecules. Those high frequencies were strongly influenced by the electrolyte pH and far less affected by the EG concentration. The system was regularly dependent on temperature under voltammetric conditions but rather independent within the oscillatory regime.