Convergence properties of optimal transport-based temporal networks

We study network properties of networks evolving in time based on optimal transport principles. These evolve from a structure covering uniformly a continuous space towards an optimal design in terms of optimal transport theory. At convergence, the networks should optimize the way resources are transported through it. As the network structure shapes in time towards optimality, its topological properties also change with it. The question is how do these change as we reach optimality. We study the behavior of various network properties on a number of network sequences evolving towards optimal design and find that the transport cost function converges earlier than network properties and that these monotonically decrease. This suggests a mechanism for designing optimal networks by compressing dense structures. We find a similar behavior in networks extracted from real images of the networks designed by the body shape of a slime mold evolving in time.Comment: 13 pages, 11 figure

Automated analysis of Physarum network structure and dynamics

We evaluate different ridge-enhancement and segmentation methods to automatically extract the network architecture from time-series of Physarum plasmodia withdrawing from an arena via a single exit. Whilst all methods gave reasonable results, judged by precision-recall analysis against a ground-truth skeleton, the mean phase angle (Feature Type) from intensity-independent, phase-congruency edge enhancement and watershed segmentation was the most robust to variation in threshold parameters. The resultant single pixel-wide segmented skeleton was converted to a graph representation as a set of weighted adjacency matrices containing the physical dimensions of each vein, and the inter-vein regions. We encapsulate the complete image processing and network analysis pipeline in a downloadable software package, and provide an extensive set of metrics that characterise the network structure, including hierarchical loop decomposition to analyse the nested structure of the developing network. In addition, the change in volume for each vein and intervening plasmodial sheet was used to predict the net flow across the network. The scaling relationships between predicted current, speed and shear force with vein radius were consistent with predictions from Murray's law. This work was presented at PhysNet 2015

Slime mould memristors

In laboratory experiments we demonstrate that protoplasmic tubes of acellular slime mould \emph{Physarum polycephalum} show current versus voltage profiles consistent with memristive systems and that the effect is due to the living protoplasm of the mould. This complements previous findings on memristive properties of other living systems (human skin and blood) and contributes to development of self-growing bio-electronic circuits. Distinctive asymmetric V-I curves which were occasionally observed when the internal current is on the same order as the driven current, are well-modelled by the concept of active memristors

Complex population dynamics in a spatial microbial ecosystem with Physarum polycephalum

This research addresses the interactions between the unicellular slime mold Physarum polycephalum and a red yeast in a spatial ecosystem over week-long imaging experiments. An inverse relationship between the growth rates of both species is shown, where P. polycephalum has positive growth when the red yeast has a negative growth rate and vice versa. The data also captures successional/oscillatory dynamics between both species. An advanced image analysis methodology for semantic segmentation is used to quantify population density over time, for all components of the ecosystem. We suggest that P. polycephalum is capable of exhibiting a sustainable feeding strategy by depositing a nutritive slime trail, allowing yeast to serve as a periodic food source. This opens a new direction of P. polycephalum research, where the population dynamics of spatial ecosystems can be readily quantified and complex ecological dynamics can be studied

Behavioural variation of acellular slime moulds

Protists are represented in every biome and have a diverse range of ecosystem roles.However, protists are severely under-represented in the scientific literature with fewstudies on how their diversity or behaviour affects ecosystem functioning. One group ofprotists, the acellular slime moulds, have been extensively studied for the behaviouralabilities of the model species Physarum polycephalum. Although the decision-making andproblem-solving abilities of P. polycephalum are well known, it is unclear whether thebehaviour of P. polycephalum is representative of acellular slime mould species andwhether their behaviour varies within individuals or strains. I investigated variations inacellular slime moulds at the species, strain and individual level and found a wide range ofvariability. Age affected two strains of P. polycephalum in a non-linear pattern and Iobserved age-related fluctuations in behaviour, physiology and cellular measures (Chapter1). I found a non-linear relationship between age and decision-making, as well as distinctdifferences in decision-making between strains (Chapter 2). I found variation in foragingbehaviour between three species of acellular slime moulds and each species also showed behavioural variation depending on the foraging environment as well as variations ininteractions between species (Chapter 3). I was able to observe facilitation betweenspecies where foraging success improved in the presence of other acellular slime mouldspecies (Chapter 3). The diversity of behaviour and physiology found within individualsand strains of P. polycephalum demonstrates the importance of including information onstrains and age in future behavioural investigations. In addition, variation in behaviourbetween species demonstrates the diversity of behaviour within this group of protists andhighlights the need for further research to understand how the behaviour of these protistsaffect species diversity and ecosystem functioning

The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling

Physarum polycephalum is a well-studied microbial eukaryote with unique experimental attributes relative to other experimental model organisms. It has a sophisticated life cycle with several distinct stages including amoebal, flagellated, and plasmodial cells. It is unusual in switching between open and closed mitosis according to specific life-cycle stages. Here we present the analysis of the genome of this enigmatic and important model organism and compare it with closely related species. The genome is littered with simple and complex repeats and the coding regions are frequently interrupted by introns with a mean size of 100 bases. Complemented with extensive transcriptome data, we define approximately 31,000 gene loci, providing unexpected insights into earlyeukaryoteevolution.Wedescribeextensiveuseofhistidinekinase-basedtwo-componentsystemsandtyrosinekinasesignaling, the presence of bacterial and plant type photoreceptors (phytochromes, cryptochrome, and phototropin) and of plant-type pentatricopeptide repeat proteins, as well as metabolic pathways, and a cell cycle control system typically found in more complex eukaryotes. Our analysis characterizes P. polycephalum as a prototypical eukaryote with features attributed to the last common ancestor of Amorphea, that is, the Amoebozoa and Opisthokonts. Specifically, the presence of tyrosine kinases inAcanthamoeba and Physarum as representatives of two distantly related subdivisions ofAmoebozoa argues against the later emergence of tyrosine kinase signaling in the opisthokont lineage and also against the acquisition by horizontal gene transfe

Intraspecific Variation In Two Cosmopolitan Myxomycetes, Didymium Squamulosum And Didymium Difforme (physarales: Didymiaceae)

The myxomycetes (plasmodial slime molds or myxogastrids) are one of three groups considered to be true slime molds (class Eumycetozoa sensu Olive 1975). Two vegetative states--amoebae and plasmodia--along with a spore-producing fruiting body characterize the life cycle of the myxomycetes. These organisms are associated with decaying plant material and are found in all terrestrial habitats worldwide. A number of species are considered cosmopolitan, being found worldwide, where they are associated with a diversity of microhabitats and substrates. A review of the literature, including molecular investigations in all three groups of slime molds, is presented, and this is followed by four original studies of the intraspecific variation that exists in two cosmopolitan species of myxomycetes. Molecular intraspecific variation in these two species, Didymium squamulosum (Alb. & Schwein.) Fr. and Didymium difforme (Pers.) S.F. Gray, was investigated using DNA sequence analysis. Initially, 14 specimens of Didymium squamulosum from widely distributed localities were examined, using the internal transcribed spacers (ITS) of nuclear ribosomal DNA (nrDNA). Although this genetic marker was found to be too variable for continued analysis, it did offer the first evidence that significant intraspecific variation exists within cosmopolitan species of myxomycetes. An additional genetic marker located within the mitochondrial small subunit (mtSSU) was investigated for 96 collections of Didymium squamulosum from worldwide localities and 56 collections of Didymium difforme distributed among three widely separated regions. For both species, conclusions were derived from molecular analyses using Bayesian methods and a haplotype network from TCS. It was concluded in both species that for this genetic marker no clear geographical assemblages emerged. While some sequences formed groups based on biogeography, there were a number of instances in which sequences from specimens that originated from distant geographical localities were more closely related to each other than to sequences from specimens obtained in nearby localities. In Didymium squamulosum, four morphological characters were observed for each collection and mapped onto the gene tree produced using Bayesian methods. While this species is known to have great diversity in morphology, no patterns emerged which would suggest that observed morphological diversity was related to molecular variation. This is the first molecular evidence that morphological diversity in a cosmopolitan species of myxomycete is the result of phenotypic plasticity rather than genetic divergence. Further evidence for phenotypic plasticity was obtained from an effort to culture each specimen of Didymium squamulosum spore-to-spore on agar, which resulted in only two successful cultures. In both cases, the fruiting bodies exhibited a degree of variation in morphological diversity that was different from the original specimen that had developed under natural conditions in the field

Preliminaries for distributed natural computing inspired by the slime mold Physarum Polycephalum

This doctoral thesis aims towards distributed natural computing inspired by the slime mold Physarum polycephalum. The vein networks formed by this organism presumably support efficient transport of protoplasmic fluid. Devising models which capture the natural efficiency of the organism and form a suitable basis for the development of natural computing algorithms is an interesting and challenging goal. We start working towards this goal by designing and executing wet-lab experi- ments geared towards producing a large number of images of the vein networks of P. polycephalum. Next, we turn the depicted vein networks into graphs using our own custom software called Nefi. This enables a detailed numerical study, yielding a catalogue of characterizing observables spanning a wide array of different graph properties. To share our results and data, i.e. raw experimental data, graphs and analysis results, we introduce a dedicated repository revolving around slime mold data, the Smgr. The purpose of this repository is to promote data reuse and to foster a practice of increased data sharing. Finally we present a model based on interacting electronic circuits including current controlled voltage sources, which mimics the emergent flow patterns observed in live P. polycephalum. The model is simple, distributed and robust to changes in the underlying network topology. Thus it constitutes a promising basis for the development of distributed natural computing algorithms.Diese Dissertation dient als Vorarbeit für den Entwurf von verteilten Algorithmen, inspiriert durch den Schleimpilz Physarum polycephalum. Es wird vermutet, dass die Venen-Netze dieses Organismus den effizienten Transport von protoplasmischer Flüssigkeit ermöglichen. Die Herleitung von Modellen, welche sowohl die natürliche Effizienz des Organismus widerspiegeln, als auch eine geeignete Basis für den Entwurf von Algorithmen bieten, gilt weiterhin als schwierig. Wir nähern uns diesem Ziel mittels Laborversuchen zur Produktion von zahlreichen Abbildungen von Venen-Netzwerken. Weiters führen wir die abgebildeten Netze in Graphen über. Hierfür verwenden wir unsere eigene Software, genannt Nefi. Diese ermöglicht eine numerische Studie der Graphen, welche einen Katalog von charakteristischen Grapheigenschaften liefert. Um die gewonnenen Erkenntnisse und Daten zu teilen, führen wir ein spezialisiertes Daten-Repository ein, genannt Smgr. Hiermit begünstigen wir die Wiederverwendung von Daten und fördern das Teilen derselben. Abschließend präsentieren wir ein Modell, basierend auf elektrischen Elementen, insbesondere stromabhängigen Spannungsquellen, welches die Flüsse von P. poly- cephalum nachahmt. Das Modell ist simpel, verteilt und robust gegenüber topolo- gischen änderungen. Aus diesen Gründen stellt es eine vielversprechende Basis für den Entwurf von verteilten Algorithmen dar