4,718 research outputs found
Road planning with slime mould: If Physarum built motorways it would route M6/M74 through Newcastle
Plasmodium of Physarum polycephalum is a single cell visible by unaided eye.
During its foraging behaviour the cell spans spatially distributed sources of
nutrients with a protoplasmic network. Geometrical structure of the
protoplasmic networks allows the plasmodium to optimize transfer of nutrients
between remote parts of its body, to distributively sense its environment, and
make a decentralized decision about further routes of migration. We consider
the ten most populated urban areas in United Kingdom and study what would be an
optimal layout of transport links between these urban areas from the
"plasmodium's point of view". We represent geographical locations of urban
areas by oat flakes, inoculate the plasmodium in Greater London area and
analyse the plasmodium's foraging behaviour. We simulate the behaviour of the
plasmodium using a particle collective which responds to the environmental
conditions to construct and minimise transport networks. Results of our scoping
experiments show that during its colonization of the experimental space the
plasmodium forms a protoplasmic network isomorphic to a network of major
motorways except the motorway linking England with Scotland. We also imitate
the reaction of transport network to disastrous events and show how the
transport network can be reconfigured during natural or artificial cataclysms.
The results of the present research lay a basis for future science of
bio-inspired urban and road planning.Comment: Submitted November (2009
Efficiency of a stirred chemical reaction in a closed vessel
We perform a numerical study of the reaction efficiency in a closed vessel.
Starting with a little spot of product, we compute the time needed to complete
the reaction in the container following an advection-reaction-diffusion
process. Inside the vessel it is present a cellular velocity field that
transports the reactants. If the size of the container is not very large
compared with the typical length of the velocity field one has a plateau of the
reaction time as a function of the strength of the velocity field, . This
plateau appears both in the stationary and in the time-dependent flow. A
comparison of the results for the finite system with the infinite case (for
which the front speed, , gives a simple estimate of the reacting time)
shows the dramatic effect of the finite size.Comment: 4 pages, 4 figure
Characteristics of pattern formation and evolution in approximations of physarum transport networks
Most studies of pattern formation place particular emphasis on its role in the development of complex multicellular body plans. In simpler organisms, however, pattern formation is intrinsic to growth and behavior. Inspired by one such organism, the true slime mold Physarum polycephalum, we present examples of complex emergent pattern formation and evolution formed by a population of simple particle-like agents. Using simple local behaviors based on Chemotaxis, the mobile agent population spontaneously forms complex and dynamic transport networks. By adjusting simple model parameters, maps of characteristic patterning are obtained. Certain areas of the parameter mapping yield particularly complex long term behaviors, including the circular contraction of network lacunae and bifurcation of network paths to maintain network connectivity. We demonstrate the formation of irregular spots and labyrinthine and reticulated patterns by chemoattraction. Other Turing-like patterning schemes were obtained by using chemorepulsion behaviors, including the self-organization of regular periodic arrays of spots, and striped patterns. We show that complex pattern types can be produced without resorting to the hierarchical coupling of reaction-diffusion mechanisms. We also present network behaviors arising from simple pre-patterning cues, giving simple examples of how the emergent pattern formation processes evolve into networks with functional and quasi-physical properties including tensionlike effects, network minimization behavior, and repair to network damage. The results are interpreted in relation to classical theories of biological pattern formation in natural systems, and we suggest mechanisms by which emergent pattern formation processes may be used as a method for spatially represented unconventional computation. © 2010 Massachusetts Institute of Technology
Towards Physarum Binary Adders
Plasmodium of \emph{Physarum polycephalum} is a single cell visible by
unaided eye. The plasmodium's foraging behaviour is interpreted in terms of
computation. Input data is a configuration of nutrients, result of computation
is a network of plasmodium's cytoplasmic tubes spanning sources of nutrients.
Tsuda et al (2004) experimentally demonstrated that basic logical gates can be
implemented in foraging behaviour of the plasmodium. We simplify the original
designs of the gates and show --- in computer models --- that the plasmodium is
capable for computation of two-input two-output gate and
three-input two-output . We assemble the
gates in a binary one-bit adder and demonstrate validity of the design using
computer simulation.Comment: Biosystems (2010), in press. Please download final version of the
paper from the Publishers's sit
Taxis of Artificial Swimmers in a Spatio-Temporally Modulated Activation Medium
Contrary to microbial taxis, where a tactic response to external stimuli is
controlled by complex chemical pathways acting like sensor-actuator loops,
taxis of artificial microswimmers is a purely stochastic effect associated with
a non-uniform activation of the particles' self-propulsion. We study the tactic
response of such swimmers in a spatio-temporally modulated activating medium by
means of both numerical and analytical techniques. In the opposite limits of
very fast and very slow rotational particle dynamics, we obtain analytic
approximations that closely reproduce the numerical description. A swimmer
drifts on average either parallel or anti-parallel to the propagation direction
of the activating pulses, depending on their speed and width. The drift in line
with the pulses is solely determined by the finite persistence length of the
active Brownian motion performed by the swimmer, whereas the drift in the
opposite direction results from the combination of ballistic and diffusive
properties of the swimmer's dynamics.Comment: 19 pages, 6 figures; Entropy (in press
Influences on the formation and evolution of Physarum polycephalum inspired emergent transport networks
The single-celled organism Physarum polycephalum efficiently constructs and minimises dynamical nutrient transport networks resembling proximity graphs in the Toussaint hierarchy. We present a particle model which collectively approximates the behaviour of Physarum. We demonstrate spontaneous transport network formation and complex network evolution using the model and show that the model collectively exhibits quasi-physical emergent properties, allowing it to be considered as a virtual computing material. This material is used as an unconventional method to approximate spatially represented geometry problems by representing network nodes as nutrient sources. We demonstrate three different methods for the construction, evolution and minimisation of Physarum-like transport networks which approximate Steiner trees, relative neighbourhood graphs, convex hulls and concave hulls. We extend the model to adapt population size in response to nutrient availability and show how network evolution is dependent on relative node position (specifically inter-node angle), sensor scaling and nutrient concentration. We track network evolution using a real-time method to record transport network topology in response to global differences in nutrient concentration. We show how Steiner nodes are utilised at low nutrient concentrations whereas direct connections to nutrients are favoured when nutrient concentration is high. The results suggest that the foraging and minimising behaviour of Physarum-like transport networks reflect complex interplay between nutrient concentration, nutrient location, maximising foraging area coverage and minimising transport distance. The properties and behaviour of the synthetic virtual plasmodium may be useful in future physical instances of distributed unconventional computing devices, and may also provide clues to the generation of emergent computation behaviour by Physarum. © Springer Science+Business Media B.V. 2010
Phoretic Motion of Spheroidal Particles Due To Self-Generated Solute Gradients
We study theoretically the phoretic motion of a spheroidal particle, which
generates solute gradients in the surrounding unbounded solvent via chemical
reactions active on its surface in a cap-like region centered at one of the
poles of the particle. We derive, within the constraints of the mapping to
classical diffusio-phoresis, an analytical expression for the phoretic velocity
of such an object. This allows us to analyze in detail the dependence of the
velocity on the aspect ratio of the polar and the equatorial diameters of the
particle and on the fraction of the particle surface contributing to the
chemical reaction. The particular cases of a sphere and of an approximation for
a needle-like particle, which are the most common shapes employed in
experimental realizations of such self-propelled objects, are obtained from the
general solution in the limits that the aspect ratio approaches one or becomes
very large, respectively.Comment: 18 pages, 5 figures, to appear in European Physical Journal
Validity of the Cauchy-Born rule applied to discrete cellular-scale models of biological tissues
The development of new models of biological tissues that consider cells in a discrete manner is becoming increasingly popular as an alternative to PDE-based continuum methods, although formal relationships between the discrete and continuum frameworks remain to be established. For crystal mechanics, the discrete-to-continuum bridge is often made by assuming that local atom displacements can be mapped homogeneously from the mesoscale deformation gradient, an assumption known as the Cauchy-Born rule (CBR). Although the CBR does not hold exactly for non-crystalline materials, it may still be used as a first order approximation for analytic calculations of effective stresses or strain energies. In this work, our goal is to investigate numerically the applicability of the CBR to 2-D cellular-scale models by assessing the mechanical behaviour of model biological tissues, including crystalline (honeycomb) and non-crystalline reference states. The numerical procedure consists in precribing an affine deformation on the boundary cells and computing the position of internal cells. The position of internal cells is then compared with the prediction of the CBR and an average deviation is calculated in the strain domain. For centre-based models, we show that the CBR holds exactly when the deformation gradient is relatively small and the reference stress-free configuration is defined by a honeycomb lattice. We show further that the CBR may be used approximately when the reference state is perturbed from the honeycomb configuration. By contrast, for vertex-based models, a similar analysis reveals that the CBR does not provide a good representation of the tissue mechanics, even when the reference configuration is defined by a honeycomb lattice. The paper concludes with a discussion of the implications of these results for concurrent discrete/continuous modelling, adaptation of atom-to-continuum (AtC) techniques to biological tissues and model classification
Clustering of microswimmers: Interplay of shape and hydrodynamics
The spatiotemporal dynamics in systems of active self-propelled particles is
controlled by the propulsion mechanism in combination with various direct
interactions, such as steric repulsion, hydrodynamics, and chemical fields.
Yet, these direct interactions are typically anisotropic, and come in different
'flavors', such as spherical and elongated particle shapes for steric
repulsion, pusher and puller flow fields for hydrodynamics, etc. The
combination of the various aspects is expected to lead to new emergent
behavior. However, it is a priori not evident whether shape and hydrodynamics
act synergistically or antagonistically to generate motility-induced clustering
(MIC) and phase separation (MIPS). We employ a model of prolate spheroidal
microswimmers - called squirmers - in quasi-two-dimensional confinement to
address this issue by mesoscale hydrodynamic simulations. For comparison,
non-hydrodynamic active Brownian particles (ABPs) are considered to elucidate
the contribution of hydrodynamic interactions on MIC and MIPS. For spherical
particles, the comparison between ABP and hydrodynamic-squirmer ensembles
reveals a suppression of MIPS due to hydrodynamic interactions. The fundamental
difference between ABPs and squirmers is attributed to an increased
reorientation of squirmers by hydrodynamic torques during their collisions. In
contrast, for elongated squirmers, hydrodynamics interactions enhance MIPS.
Thus, hydrodynamic interactions show opposing effects on MIPS for spherical and
elongated microswimmers
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