scholarly journals Self-assembly and plasticity of synaptic domains through a reaction-diffusion mechanism

2015 ◽  
Vol 92 (3) ◽  
Author(s):  
Christoph A. Haselwandter ◽  
Mehran Kardar ◽  
Antoine Triller ◽  
Rava Azeredo da Silveira
2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Pedro E. S. Silva ◽  
Ricardo Chagas ◽  
Susete N. Fernandes ◽  
Pawel Pieranski ◽  
Robin L. B. Selinger ◽  
...  

AbstractCellulose-based systems are useful for many applications. However, the issue of self-organization under non-equilibrium conditions, which is ubiquitous in living matter, has scarcely been addressed in cellulose-based materials. Here, we show that quasi-2D preparations of a lyotropic cellulose-based cholesteric mesophase display travelling colourful patterns, which are generated by a chemical reaction-diffusion mechanism being simultaneous with the evaporation of solvents at the boundaries. These patterns involve spatial and temporal variation in the amplitude and sign of the helix´s pitch. We propose a simple model, based on a reaction-diffusion mechanism, which simulates the observed spatiotemporal colour behaviour.


Author(s):  
Rushil Pingali ◽  
Sourabh K. Saha

Abstract Two-photon lithography (TPL) is a polymerization-based direct laser writing process that is capable of fabricating arbitrarily complex three-dimensional (3D) structures with submicron features. Traditional TPL techniques have limited scalability due to the slow point-by-point serial writing scheme. The femtosecond projection TPL (FP-TPL) technique increases printing rate by a thousand times by enabling layer-by-layer parallelization. However, parallelization alters the time and the length scales of the underlying polymerization process. It is therefore challenging to apply the models of serial TPL to accurately predict process outcome during FP-TPL. To solve this problem, we have generated a finite element model of the polymerization process on the time and length scales relevant to FP-TPL. The model is based on the reaction-diffusion mechanism that underlies polymerization. We have applied this model to predict the geometry of nanowires printed under a variety of conditions and compared these predictions against empirical data. Our model accurately predicts the nanowire widths. However, accuracy of aspect ratio prediction is hindered by uncertain values of the chemical properties of the photopolymer. Nevertheless, our results demonstrate that the reaction-diffusion model can accurately capture the effect of controllable parameters on FP-TPL process outcome and can therefore be used for process control and optimization.


2009 ◽  
Vol 2009 ◽  
pp. 1-15 ◽  
Author(s):  
Bernard Girau ◽  
César Torres-Huitzil ◽  
Nikolaos Vlassopoulos ◽  
José Hugo Barrón-Zambrano

We consider here the feasibility of gathering multiple computational resources by means of decentralized and simple local rules. We study such decentralized gathering by means of a stochastic model inspired from biology: the aggregation of theDictyostelium discoideumcellular slime mold. The environment transmits information according to a reaction-diffusion mechanism and the agents move by following excitation fronts. Despite its simplicity this model exhibits interesting properties of self-organization and robustness to obstacles. We first describe the FPGA implementation of the environment alone, to perform large scale and rapid simulations of the complex dynamics of this reaction-diffusion model. Then we describe the FPGA implementation of the environment together with the agents, to study the major challenges that must be solved when designing a fast embedded implementation of the decentralized gathering model. We analyze the results according to the different goals of these hardware implementations.


Author(s):  
Bernard Richards

In his 1952 paper ‘The chemical basis of morphogenesis’ Turing postulated his now famous Morphogenesis Equation. He claimed that his theory would explain why plants and animals took the shapes they did. When I joined him, Turing suggested that I might solve his equation in three dimensions, a new problem. After many manipulations using rather sophisticated mathematics and one of the first factory-produced computers in the UK, I derived a series of solutions to Turing’s equation. I showed that these solutions explained the shapes of specimens of the marine creatures known as Radiolaria, and that they corresponded very closely to the actual spiny shapes of real radiolarians. My work provided further evidence for Turing’s theory of morphogenesis, and in particular for his belief that the external shapes exhibited by Radiolaria can be explained by his reaction–diffusion mechanism. While working in the Computing Machine Laboratory at the University of Manchester in the early 1950s, Alan Turing reignited the interests he had had in both botany and biology from his early youth. During his school-days he was more interested in the structure of the flowers on the school sports field than in the games played there (see Fig. 1.3). It is known that during the Second World War he discussed the problem of phyllotaxis (the arrangement of leaves and florets in plants), and then at Manchester he had some conversations with Claude Wardlaw, the Professor of Botany in the University. Turing was keen to take forward the work that D’Arcy Thompson had published in On Growth and Form in 1917. In his now-famous paper of 1952 Turing solved his own ‘Equation of Morphogenesis’ in two dimensions, and demonstrated a solution that could explain the ‘dappling’—the black-and-white patterns—on cows. The next step was for me to solve Turing’s equation in three dimensions. The two-dimensional case concerns only surface features of organisms, such as dappling, spots, and stripes, whereas the three-dimensional version concerns the overall shape of an organism. In 1953 I joined Turing as a research student in the University of Manchester, and he set me the task of solving his equation in three dimensions. A remarkable journey of collaboration began. Turing chatted to me in a very friendly fashion.


2020 ◽  
Vol 8 (48) ◽  
pp. 17417-17428
Author(s):  
Jiangtao Shi ◽  
Yue Zhao ◽  
Yue Wu ◽  
Jingyuan Chu ◽  
Xiao Tang ◽  
...  

In this work, pyrolysis behaviors dominated by the reaction–diffusion mechanism were investigated. And one-dimensional reaction–diffusion model is proposed.


1987 ◽  
Vol 65 (7) ◽  
pp. 1308-1319 ◽  
Author(s):  
Thurston C. Lacalli ◽  
Lionel G. Harrison

Morphogenesis following cell division in Micrasterias rotata is by outgrowth and repeated branching of a series of semicell lobes. Though successive branching events are qualitatively similar, they display changes in time and space scales, and these can be quantitated with the aid of autoradiographic patterns of labelled wall precursors that appear late in morphogenesis but which seem to represent its history. This enables us to consider branching as the conversion of a single centre of growth activity into two and to attempt to locate these centres precisely, in terms of both position and time of establishment. Temporal and spatial scales both decrease, by 75%, through a sequence of five branching events, in linear functional relationship to each other. This correlation points toward kinetic control of morphogenesis, i.e., the involvement of something like a reaction–diffusion mechanism. We analyse this possibility in terms of available reaction–diffusion theory to show how, after various simplifying assumptions, and if the time and space scales of branch formation are known, an effective diffusivity, [Formula: see text], for the patterning mechanism can be estimated. For M. rotata we obtain orders of magnitude: [Formula: see text], with an upper limit on the diffusivity of the faster diffusing of the two morphogenetic substances in the mechanism of ca. 1 × 10−7 cm2/s. These values implicate the cell membrane as the most probable site of pattern formation.


1998 ◽  
Vol 4 (1) ◽  
pp. 25-40 ◽  
Author(s):  
Jens Breyer ◽  
Jörg Ackermann ◽  
John McCaskill

Recently, new types of coupled isothermal polynucleotide amplification reactions for the investigation of in vitro evolution have been established that are based on the multi-enzyme 3SR reaction. Microstructured thin-film open bioreactors have been constructed in our laboratory to run these reactions spatially resolved in flow experiments. Artificial DNA/RNA chemistries close to the in vitro biochemistry of these systems have been developed, which we have studied in computer simulations in configurable hardware (NGEN). These artificial chemistries are described on the level of individual polynucleotide molecules, each with a defined sequence, and their complexes. The key feature of spatial pattern formation provides a weak stabilization of cooperative catalytic properties of the evolving molecules. Of great interest is the step to include extended self-assembly processes of flexible structures—allowing the additional stabilization of cooperation through semipermeable, flexible, self-organizing membrane boundaries. We show how programmable matter simulations of experimentally relevant molecular in vitro evolution can be extended to include the influence of self-assembling flexible membranes.


2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Matija Lovrak ◽  
Wouter E. J. Hendriksen ◽  
Chandan Maity ◽  
Serhii Mytnyk ◽  
Volkert van Steijn ◽  
...  

Abstract Self-assembly provides access to a variety of molecular materials, yet spatial control over structure formation remains difficult to achieve. Here we show how reaction–diffusion (RD) can be coupled to a molecular self-assembly process to generate macroscopic free-standing objects with control over shape, size, and functionality. In RD, two or more reactants diffuse from different positions to give rise to spatially defined structures on reaction. We demonstrate that RD can be used to locally control formation and self-assembly of hydrazone molecular gelators from their non-assembling precursors, leading to soft, free-standing hydrogel objects with sizes ranging from several hundred micrometres up to centimeters. Different chemical functionalities and gradients can easily be integrated in the hydrogel objects by using different reactants. Our methodology, together with the vast range of organic reactions and self-assembling building blocks, provides a general approach towards the programmed fabrication of soft microscale objects with controlled functionality and shape.


2017 ◽  
Vol 832 ◽  
pp. 666-696
Author(s):  
Lindsey T. Corson ◽  
David Pritchard

We describe a mathematical model of double-diffusive (thermosolutal) convection in a saturated porous layer, when the solubility of the solute depends on the temperature, and the porosity and permeability of the porous medium evolve through dissolution and precipitation. We present the results of linear and weakly nonlinear stability analyses and explore the longer-term development of the system numerically. When the solutal concentration gradient is destabilising, the dynamics are somewhat similar to those previously found for single-species convection (Ritchie & Pritchard, J. Fluid Mech., vol. 673, 2011, pp. 286–317), including the occurrence of subcritical instabilities driven by a reaction–diffusion mechanism. However, when the solutal concentration gradient is stabilising and the thermal gradient is destabilising, novel dynamics emerge. These include a vertical segregation of circulation cells and porosity perturbations near the onset of convection, and over longer time scales the formation of a low-permeability region in the middle of the layer, pierced by occasional high-permeability channels. Under these conditions, convection may die away to nearly zero for extended periods before resuming vigorously in localised regions at later times.


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