scholarly journals The Role of Cytoplasmic Interactions in the Collective Polarization of Tissues and its Interplay with Cellular Geometry

2018 ◽  
Author(s):  
Shahriar Shadkhoo ◽  
Madhav Mani
Keyword(s):  
Large Scale ◽  
Planar Cell Polarity ◽  
Reaction Diffusion ◽  
Directional Information ◽  
Collective Response ◽  
Reaction Diffusion Model ◽  
Necessary And Sufficient ◽  
Molecular Components ◽  
Theory And Experiments

AbstractPlanar cell polarity (PCP), the ability of a tissue to polarize coherently over multicellular length scales, provides the directional information that guides a multitude of developmental processes at cellular and tissue levels. While it is manifest that cells utilize both intra-cellular and intercellular mechanisms, how they couple together to produce the collective response remains an active area of investigation. Exploring a phenomeno-logical reaction-diffusion model, we predict a crucial, and novel, role for cytoplasmic interactions in the large-scale correlations of cell polarities. We demonstrate that finite-range (i.e. nonlocal) cytoplasmic interactions are necessary and sufficient for the robust and long-range polarization of tissues — even in the absence of global cues — and are essential to the faithful detection of weak directional signals. Strikingly, our model re-capitulates an observed influence of anisotropic tissue geometries on the orientation of polarity. In order to facilitate a conversation between theory and experiments, we compare five distinct classes of in silico mutants with experimental observations. Within this context, we propose quantitative measures that can guide the search for the participant molecular components, and the identification of their roles in the collective polarization of tissues.

scholarly journals Reaction Diffusion and Chemotaxis for Decentralized Gathering on FPGAs

2009 ◽  
Vol 2009 ◽  
pp. 1-15 ◽  
Author(s):  
Bernard Girau ◽  
César Torres-Huitzil ◽  
Nikolaos Vlassopoulos ◽  
José Hugo Barrón-Zambrano
Keyword(s):  
Large Scale ◽  
Complex Dynamics ◽  
Diffusion Mechanism ◽  
Reaction Diffusion ◽  
Fpga Implementation ◽  
Cellular Slime Mold ◽  
Reaction Diffusion Model ◽  
Cellular Slime ◽  
Computational Resources ◽  
Embedded Implementation

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.

scholarly journals Reaction-diffusion model as framework for understanding the role of riboflavin in “eye defence” formulations

RSC Advances ◽  
2020 ◽  
Vol 10 (25) ◽  
pp. 14965-14971
Author(s):  
Francesca Di Nezza ◽  
Ciro Caruso ◽  
Ciro Costagliola ◽  
Luigi Ambrosone
Keyword(s):  
Diffusion Model ◽  
Reaction Diffusion ◽  
Eye Drops ◽  
Reaction Diffusion Model ◽  
Visible Spectra ◽  
Uv Visible

Analysis of UV-visible spectra, performed on commercial riboflavin-based eye drops, showed that absorbance is a saturating function of vitamin concentration.

Fracture pattern formation in frictional, cohesive, granular material

2010 ◽  
Vol 368 (1910) ◽  
pp. 95-118 ◽  
Author(s):  
Alison Ord ◽  
Bruce E. Hobbs
Keyword(s):  
Pattern Formation ◽  
Granular Media ◽  
Large Scale ◽  
High Stress ◽  
Reaction Diffusion ◽  
Fracture Pattern ◽  
Reaction Diffusion Equations ◽  
Three Dimensions ◽  
Localized Deformation

Naturally, deformed rocks commonly contain crack arrays (joints) forming patterns with systematic relationships to the large-scale deformation. Kinematically, joints can be mode-1, -2 or -3 or combinations of these, but there is no overarching theory for the development of the patterns. We develop a model motivated by dislocation pattern formation in metals. The problem is formulated in one dimension in terms of coupled reaction–diffusion equations, based on computer simulations of crack development in deformed granular media with cohesion. The cracks are treated as interacting defects, and the densities of defects diffuse through the rock mass. Of particular importance is the formation of cracks at high stresses associated with force-chain buckling and variants of this configuration; these cracks play the role of ‘inhibitors’ in reaction–diffusion relationships. Cracks forming at lower stresses act as relatively mobile defects. Patterns of localized deformation result from (i) competition between the growth of the density of ‘mobile’ defects and the inhibition of these defects by crack configurations forming at high stress and (ii) the diffusion of damage arising from these two populations each characterized by a different diffusion coefficient. The extension of this work to two and three dimensions is discussed.

Role of dark excitations in the nonequilibrium condensation of exciton polaritons in optically-pumped organic single crystal microcavities

2015 ◽  
Vol 29 (22) ◽  
pp. 1550157 ◽  
Author(s):  
Svitlana Zaster ◽  
Eric R. Bittner
Keyword(s):  
Reaction Diffusion ◽  
Optically Pumped ◽  
Reaction Diffusion Model ◽  
Exciton Polaritons ◽  
Organic Single Crystal ◽  
Dielectric Mirrors ◽  
Dynamical Regimes ◽  
Nonequilibrium Condensation ◽  
External Driving

We present a reaction/diffusion model for the formation of a lower polariton condensate in a microcavity containing an organic semiconducting molecular crystalline film. Our model–based upon an anthracene film sandwiched between two reflecting dielectric mirrors–consists of three coupled fields corresponding to a gas of excitons created by an external driving pulse, a reservoir of dark states formed by the nonemissive decay of excitons in to nearby electronic states, and a lower polariton condensate. We show that at finite temperature, the presence of the dark reservoir can augment the exciton population such that a lower critical pumping threshold is required to achieve the critical exciton densities required to sustain a stable condensate population. Using linear-stability analysis, we show that a variety of dynamical regimes can emerge depending upon the characteristics of the cavity and the lattice temperature.

scholarly journals Towards Biophysically-Based Neuromorphic Computing at Scale: Markov Abstractions of Electrochemical Reaction-Diffusion in Synaptic Transmission

2020 ◽  
Author(s):  
Margot Wagner ◽  
Thomas M. Bartol ◽  
Terrence J. Sejnowski ◽  
Gert Cauwenberghs
Keyword(s):  
Large Scale ◽  
Internal State ◽  
Reaction Diffusion ◽  
Space Representation ◽  
Chemical Synapse ◽  
Spatial And Temporal Scales ◽  
State Space Representation ◽  
Reaction Diffusion Model ◽  
Neuromorphic Hardware ◽  
The Brain

ABSTRACTProgress in computational neuroscience towards understanding brain function is challenged both by the complexity of molecular-scale electrochemical interactions at the level of individual neurons and synapses, and the dimensionality of network dynamics across the brain covering a vast range of spatial and temporal scales. Our work abstracts the highly detailed, biophysically realistic 3D reaction-diffusion model of a chemical synapse to a compact internal state space representation that maps onto parallel neuromorphic hardware for efficient emulation on very large scale, and offers near-equivalence in input-output dynamics while preserving biologically interpretable tunable parameters.

scholarly journals Nonclassical Kinetics in Constrained Geometries: Initial Distribution Effects

1998 ◽  
Vol 08 (05) ◽  
pp. 853-868 ◽  
Author(s):  
K. Lindenberg ◽  
A. H. Romero ◽  
J. M. Sancho
Keyword(s):  
Initial Density ◽  
Reaction Diffusion ◽  
Initial Distribution ◽  
Density Fluctuations ◽  
Time Behavior ◽  
Numerical Work ◽  
Irreversible Reaction ◽  
Long Wavelength ◽  
Reaction Diffusion Model

We present a detailed study of the effects of the initial distribution on the kinetic evolution of the irreversible reaction A+B→0 in one dimension. Our analytic as well as numerical work is based on a reaction–diffusion model of this reaction. We focus on the role of initial density fluctuations in the creation of the macroscopic patterns that lead to the well-known kinetic anomalies in this system. In particular, we discuss the role of the long wavelength components of the initial fluctuations in determining the long-time behavior of the system. We note that the frequently studied random initial distribution is but one of a variety of possible distributions leading to interesting anomalous behavior. Our discussion includes an initial distribution with correlated A-B pairs and one in which the initial distribution forms a fractal pattern. The former is an example of a distribution whose long wavelength components are suppressed, while the latter exemplifies one whose long wavelength components are enhanced, relative to those of the random distribution.

scholarly journals Source-sink dynamics can maintain mismatched range and bioclimatic limits even at large spatial scales

2020 ◽  
Author(s):  
Nikunj Goel ◽  
Timothy H. Keitt
Keyword(s):  
Spatial Scales ◽  
Reaction Diffusion ◽  
Dispersal Distance ◽  
Life Strategy ◽  
Stepping Stones ◽  
Reaction Diffusion Model ◽  
Primary Determinant ◽  
Source Sink ◽  
Bioclimatic Envelope

AbstractBioclimatic models assume that at broad spatial scales, climate is the primary determinant of species distribution. Meanwhile, processes such as source-sink dynamics can be ignored because they are thought to manifest at length scales comparable to species mean dispersal distance. We present a reaction-diffusion model to show species can use sink patches near the bioclimatic (or niche) limit as stepping-stones to occupy sinks much further than the mean dispersal distance, thereby extending the distribution far beyond the bioclimatic envelope. This mismatch between geographical and bioclimatic limits is mediated by the shape of the bioclimatic limit and may be significant for low growth sensitivity and fast dispersal life strategy. These findings challenge one of the core assumptions of the bioclimatic models. Therefore, we advocate that biogeographers consider the role of dispersal when using bioclimatic models to generate inferences about the ecological and evolutionary processes that determine the distribution of biota.

scholarly journals Markov Chain Abstractions of Electrochemical Reaction-Diffusion in Synaptic Transmission for Neuromorphic Computing

2021 ◽  
Vol 15 ◽  
Author(s):  
Margot Wagner ◽  
Thomas M. Bartol ◽  
Terrence J. Sejnowski ◽  
Gert Cauwenberghs
Keyword(s):  
Large Scale ◽  
Internal State ◽  
Reaction Diffusion ◽  
Space Representation ◽  
Chemical Synapse ◽  
Spatial And Temporal Scales ◽  
State Space Representation ◽  
Reaction Diffusion Model ◽  
Neuromorphic Hardware ◽  
The Brain

Progress in computational neuroscience toward understanding brain function is challenged both by the complexity of molecular-scale electrochemical interactions at the level of individual neurons and synapses and the dimensionality of network dynamics across the brain covering a vast range of spatial and temporal scales. Our work abstracts an existing highly detailed, biophysically realistic 3D reaction-diffusion model of a chemical synapse to a compact internal state space representation that maps onto parallel neuromorphic hardware for efficient emulation at a very large scale and offers near-equivalence in input-output dynamics while preserving biologically interpretable tunable parameters.

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