Acellular Slime Mold Physarum Polycephalum Research Articles

Different Morphotypes of Physarum polycephalum as Models for Chemotaxis and Locomotion.

The acellular slime mold Physarum polycephalum is a large, unicellular amoeba, which, due to its huge size, is well suited to investigate chemotaxis and cellular locomotion. The myxomycete has an astonishing behavioral repertoire and is highly responsive to changes in its environment, which map to changes in its tubular network, internal cytoplasm flow, and cytoskeleton. The behavioral repertoire includes problem-solving, decision-making, and memory. P. polycephalum's chemo- and phototaxis are especially well studied. This chapter describes how to cultivate different morphotypes of P. polycephalum (micro-, meso-, and macroplasmodia). Furthermore, the setup of a chemotaxis experiment and the acquisition and analysis of chemotaxis data is described.

Improved slime mould algorithm with elitist strategy and its application to structural optimization with natural frequency constraints

An improved slime mould algorithm (ISMA) is proposed and applied to the size optimization of truss structures with natural frequency constraints. The slime mould algorithm is a recently proposed metaheuristic inspired by the morphological changes of the acellular slime mould Physarum polycephalum while foraging. This algorithm has been successfully applied to some real-world optimization problems in science and industry. However, it is found that the classical SMA suffers from slow convergence and often converges prematurely to non-optimal solutions, especially for large-scale optimization problems. Compared to the classical SMA, two main improvements are introduced in the proposed ISMA: (1) In the replacement phase of the ISMA, an elitist strategy is adopted to replace the generational replacement strategy of the classical SMA. The elitist strategy aims to increase the convergence rate of the ISMA. (2) A slight modification is made to the exploration phase of the classical SMA to ensure a vast exploration of the search space. The suggested modification enables the ISMA to overcome the shortcoming of the premature convergence of the classical SMA. Finally, the efficiency and robustness of the ISMA are demonstrated through three large-scale benchmark dome trusses with natural frequency constraints. To our knowledge, this is the first time to apply SMA to structural optimization. It is shown that the proposed ISMA overcomes the problems of premature convergence and slow convergence rate of the classical SMA. Numerical results show that the ISMA outperforms the classical SMA and shows superior or comparable performance to other reported methods.

Slime molds response to carbon nanotubes exposure: from internalization to behavior

Carbon nanotubes (CNTs) offer attractive opportunities due to their physical, electrical, mechanical, optical, and thermal properties. They are used in a wide range of applications and are found in numerous consumer products. On the downside, their increasing presence in the environment poses potential threats to living organisms and ecosystems. The aim of this study was to evaluate the toxicity of double-walled carbon nanotubes (DWCNTs) on a new model system: the acellular slime mold Physarum polycephalum. Despite its ecological significance, its simplicity of organization, and its behavioral complexity, exposure of such organisms to nanoparticles has been poorly investigated. Slime molds were exposed to DWCNTs using three routes of exposure (topical, food, environment). We first demonstrated that DWCNTs were rapidly internalized by slime molds especially when DWCNTs were mixed with the food or spread out in the environment. Secondly, we showed that a 6-week exposure to DWCNTs did not lead to bioaccumulation nor did it lead to persistence in the slime molds when they entered a resting stage. Thirdly, we revealed that 2 days following exposure, DWCNTs were almost entirely excreted from the slime molds. Lastly, we uncovered that DWCNTs exposure altered the migration speed, the pseudopods formation, and the expansion rate of the slime molds. Our results extend our current knowledge of CNTs cytotoxicity and introduce P. polycephalum as an ideal organism for nanotoxicology.

Experience shapes future foraging decisions in a brainless organism

The ability to change one’s behaviour based on past experience has obvious fitness benefits. Drawing from past experience requires some kind of information storage and retrieval. The acellular slime mould Physarum polycephalum has previously been shown to use stored information about negative stimuli. Here, we repeatedly exposed the slime mould to three stimuli with differing levels of potential risk: light, salt and lavender. We asked if the slime mould would change its foraging behaviour depending on the level of risk. In our experiment, taking risk yielded better food. We consistently selected individuals that made the same foraging decision (accepting risk or avoiding risk) over multiple trials. Hence, the same individuals were tested over a period of time, but only individuals that continued to make the same decision were allowed to continue. Regardless of selection regime, slime moulds in the light became more likely to select the food in the light over time, while those exposed to salt became more salt averse. Lavender had no effect. Our results can cautiously be interpreted as examples of non-associative learning, adding to a growing body of work showing that the absence of a central nervous system is no impediment to possessing sophisticated information processing.

Substrate and cell fusion influence on slime mold network dynamics

The acellular slime mold Physarum polycephalum provides an excellent model to study network formation, as its network is remodelled constantly in response to mass gain/loss and environmental conditions. How slime molds networks are built and fuse to allow for efficient exploration and adaptation to environmental conditions is still not fully understood. Here, we characterize the network organization of slime molds exploring homogeneous neutral, nutritive and adverse environments. We developed a fully automated image analysis method to extract the network topology and followed the slime molds before and after fusion. Our results show that: (1) slime molds build sparse networks with thin veins in a neutral environment and more compact networks with thicker veins in a nutritive or adverse environment; (2) slime molds construct long, efficient and resilient networks in neutral and adverse environments, whereas in nutritive environments, they build shorter and more centralized networks; and (3) slime molds fuse rapidly and establish multiple connections with their clone-mates in a neutral environment, whereas they display a late fusion with fewer connections in an adverse environment. Our study demonstrates that slime mold networks evolve continuously via pruning and reinforcement, adapting to different environmental conditions.

How to Observe the Inner Space of a Complex Biological System through Speculative Simulation

We present an approach for composition and performance with speculative complex biological systems. This iterative approach engages with both the content and the context of science through generative visual and sound art. We offer a conceptual framing as well as practical exercises, demonstrated in two cases. By distinguishing the system, its representation, and human observer(s), we clarify influences, material artifacts, and sources of tension. In the case of Dismantling, a live performance using a simulation adapted from a model of the acellular slime mold Physarum polycephalum, we explore a shifting locus of agency during the performance between the observer and the representation. In the case of Feed, a visual and sound installation realizing addiction as a multi-scale process, we explore the generative tension of re-use of a representation to engage with different systems. The underlying biological phenomena can be viewed as complex networks with powerful performative agency and multi-scale behaviors.

On the Convergence Time of a Natural Dynamics for Linear Programming

We consider a system of nonlinear ordinary differential equations for the solution of linear programming (LP) problems that was first proposed in the mathematical biology literature as a model for the foraging behavior of acellular slime mold Physarum polycephalum, and more recently considered as a method to solve LP instances. We study the convergence time of the continuous Physarum dynamics in the context of the linear programming problem, and derive a new time bound to approximate optimality that depends on the relative entropy between projected versions of the optimal point and of the initial point. The bound scales logarithmically with the LP cost coefficients and linearly with the inverse of the relative accuracy, establishing the efficiency of the dynamics for arbitrary LP instances with positive costs.

Information Transfer During Food Choice in the Slime Mold Physarum polycephalum

Throughout evolution, living systems have developed mechanisms to make adaptive decisions in the face of complex and changing environmental conditions. Most organisms make such decisions despite lacking a neural architecture. This is the case of the acellular slime mold Physarum polycephalum that has demonstrated remarkable information processing and problem-solving abilities. Previous studies suggest that the membrane of P. polycephalum plays an important role in integrating and processing information leading to the selection of a resource to exploit. The cyclical contraction-relaxation pattern of the membrane changes with the local quality of the environment, and individual contractile regions within a P. polycephalum can entrain neighboring regions, providing a potential mechanism for information processing and propagation. In this study, we use an information-theoretic tool, transfer entropy, to study the flow of information in single tubule segments of P. polycephalum in a binary choice between two food sources. We test P. polycephalum tubules in two food choice conditions, where the two available options are either symmetric in their nutrient concentrations or with one more concentrated in nutrients than the other (i.e., asymmetric). We measure the contractile pattern of the P. polycephalum membrane and use these data to explore the direction and amount of information transfer along the tubule as a function of the cell’s final decision. We find that the direction of information transfer is different in the two experimental conditions, and the amount of information transferred is inversely proportional to the distance between different contractile regions. Our results show that regions playing a leading role in information transfer changes with the decision-making challenges faced by P. polycephalum.

Symmetry breaking and inter-clonal behavioural variability in a slime mould.

Cells are dynamic systems capable of switching from isotropic growth to polarized growth even in the absence of any pre-existing external asymmetry. Here, we study this process of symmetry breaking in the acellular slime mould Physarum polycephalum. In these experiments, slime moulds could grow on two identical opposed sources of calcium. We highlighted a positive correlation between growth dynamic, level of symmetry breaking and calcium concentration. We identified three populations of slime moulds within our clonal lineage with similar symmetry breaking behaviours but different motility characteristics. These behavioural differences between slime moulds emerged in the absence of any environmental differences. Such behavioural plasticity could generate cellular diversity, which can be critical for survival.

Electroporation of DNA into Physarum polycephalum Mitochondria: Effects on Transcription and RNA Editing in Isolated Organelles.

Mitochondrial RNAs in the acellular slime mold Physarum polycephalum contain nucleotides that are not encoded in the mitochondrial genes from which they are transcribed. These site-specific changes are quite extensive, comprising ~4% of the residues within mRNAs and ~2% of rRNAs and tRNAs. These “extra” nucleotides are added co-transcriptionally, but the means by which this is accomplished have not been elucidated. The cox1 mRNA also contains four sites of C to U changes, which occur post-transcriptionally, most likely via targeted deamination. The currently available in vitro systems for studying P. polycephalum editing are limited in that the template is the entire ~63,000 bp mitochondrial genome. This presents a significant challenge when trying to define the signals that specify editing sites. In an attempt to overcome this issue, a method for introducing DNA into isolated P. polycephalum mitochondria via electroporation has been developed. Exogenous DNA is expressed, but the transcripts synthesized from these templates are not edited under the conditions tested. However, transcripts derived from the mitochondrial genome are accurately edited after electroporation, indicating that the editing machinery is still functional. These findings suggest that this method may ultimately provide a feasible approach to elucidating editing signals.

Slime mould processors, logic gates and sensors.

A heterotic, or hybrid, computation implies that two or more substrates of different physical nature are merged into a single device with indistinguishable parts. These hybrid devices then undertake coherent acts on programmable and sensible processing of information. We study the potential of heterotic computers using slime mould acting under the guidance of chemical, mechanical and optical stimuli. Plasmodium of acellular slime mould Physarum polycephalum is a gigantic single cell visible to the unaided eye. The cell shows a rich spectrum of behavioural morphological patterns in response to changing environmental conditions. Given data represented by chemical or physical stimuli, we can employ and modify the behaviour of the slime mould to make it solve a range of computing and sensing tasks. We overview results of laboratory experimental studies on prototyping of the slime mould morphological processors for approximation of Voronoi diagrams, planar shapes and solving mazes, and discuss logic gates implemented via collision of active growing zones and tactile responses of P. polycephalum. We also overview a range of electronic components--memristor, chemical, tactile and colour sensors-made of the slime mould.

Patterns of cell thickness oscillations during directional migration of Physarum polycephalum.

The functional relationship between the velocity of cell locomotion and intracellular spatial patterns of thickness oscillations in the acellular slime mould Physarum polycephalum was studied. The freely migrating plasmodial cells of 300-800 µm length were tadpole-shaped and displayed thickness oscillations along their longitudinal (body) axis. Two distinct patterns of intracellular thickness oscillations were observed in dependence on the locomotive velocity. The first mode consisted of a single travelling wave that propagated from the rear to the front of the cell. This pattern occurred when the plasmodium migrated slowly. The second mode was a multinodal standing wave that was found during events of fast propagation. Transitions between these two types of cell thickness oscillation patterns took place in narrow propagation velocity intervals. We discuss the possible mechanism leading to these patterns, which are conjectured to modulate both the intracellular pressure and the velocity of free locomotion of the cell.

Dynamics of frontal extension of an amoeboid cell

The acellular slime mould Physarum polycephalum forms giant plasmodia that consist of an apical zone, which is succeeded by a vast network of veins where protoplasm is periodically transported back and forth. The apical zone is formed by a dense layer of viscoelastic cell material, whose leading edge is characterized by the development of undulations, which are called fingers. The dynamics of finger formation and evolution was studied. The front is characterized by alternating events of front advancement and stagnation, which are reflected in the development of the fingers. Therefore, the dynamics of the front was divided into two distinct, periodically alternating regimes. The dispersion relations, i.e., the growth rates of fingers of different wavelengths, observed in these two regimes were found to be symmetric, except for the sign of the growth rates. Furthermore, finger splitting occurred once the fingers reached a critical curvature. Our findings are discussed in terms of the intracellular dynamics of this slime mould.

Evolving Transport Networks With Cellular Automata Models Inspired by Slime Mould.

Man-made transport networks and their design are closely related to the shortest path problem and considered amongst the most debated problems of computational intelligence. Apart from using conventional or bio-inspired computer algorithms, many researchers tried to solve this kind of problem using biological computing substrates, gas-discharge solvers, prototypes of a mobile droplet, and hot ice computers. In this aspect, another example of biological computer is the plasmodium of acellular slime mould Physarum polycephalum (P. polycephalum), which is a large single cell visible by an unaided eye and has been proven as a reliable living substrate for implementing biological computing devices for computational geometry, graph-theoretical problems, and optimization and imitation of transport networks. Although P. polycephalum is easy to experiment with, computing devices built with the living slime mould are extremely slow; it takes slime mould days to execute a computation. Consequently, mapping key computing mechanisms of the slime mould onto silicon would allow us to produce efficient bio-inspired computing devices to tackle with hard to solve computational intelligence problems like the aforementioned. Toward this direction, a cellular automaton (CA)-based, Physarum-inspired, network designing model is proposed. This novel CA-based model is inspired by the propagating strategy, the formation of tubular networks, and the computing abilities of the plasmodium of P. polycephalum. The results delivered by the CA model demonstrate a good match with several previously published results of experimental laboratory studies on imitation of man-made transport networks with P. polycephalum. Consequently, the proposed CA model can be used as a virtual, easy-to-access, and biomimicking laboratory emulator that will economize large time periods needed for biological experiments while producing networks almost identical to the tubular networks of the real-slime mould.

Slime mould electronic oscillators

We construct electronic oscillator from acellular slime mould Physarum polycephalum. The slime mould oscillator is made of two electrodes connected by a protoplasmic tube of the living slime mould. A protoplasmic tube has an average resistance of 3MOhm. The tube’s resistance is changing over time due to peristaltic contractile activity of the tube. The resistance of the protoplasmic tube oscillates with average period of 73s and average amplitude of 0.6MOhm. We present experimental laboratory results on dynamics of Physarum oscillator under direct current voltage up to 15V and speculate that slime mould P. polycephalum can be employed as a living electrical oscillator in biological and hybrid circuits.

Slime mold microfluidic logical gates

We demonstrate how logical operations can be implemented in ensembles of protoplasmic tubes of acellular slime mold Physarum polycephalum. The tactile response of the protoplasmic tubes is used to actuate analogs of two- and four-input logical gates and memory devices. The slime mold tube logical gates display results of logical operations by blocking flow in mechanically stimulated tube fragments and redirecting the flow to output tube fragments. We demonstrate how XOR and NOR gates are constructed. We also exemplify circuits of hybrid gates and a memory device. The slime mold based gates are non-electronic, simple and inexpensive, and several gates can be realized simultaneously at sites where protoplasmic tubes merge.

Physarum wires: Self-growing self-repairing smart wires made from slime mould

Purpose We report experimental laboratory studies on developing conductive pathways, or wires, using protoplasmic tubes of plasmodium of acellular slime mould Physarum polycephalum.

Towards slime mould colour sensor: Recognition of colours by Physarum polycephalum

Acellular slime mould Physarum polycephalum is a popular now user-friendly living substrate for designing of future and emergent sensing and computing devices. P. polycephalum exhibits regular patterns of oscillations of its surface electrical potential. The oscillation patterns are changed when the slime mould is subjected to mechanical, chemical, electrical or optical stimuli. We evaluate feasibility of slime-mould based colour sensors by illuminating Physarum with red, green, blue and white colours and analysing patterns of the slime mould’s electrical potential oscillations. We define that the slime mould recognises a colour if it reacts to illumination with the colour by a unique changes in amplitude and periods of oscillatory activity. In laboratory experiments we found that the slime mould recognises red and blue colour. The slime mould does not differentiate between green and white colours. The slime mould also recognises when red colour is switched off. We also map colours to diversity of the oscillations: illumination with a white colour increases diversity of amplitudes and periods of oscillations, other colours studied increase diversity either of amplitude or period.

Slimeware: Engineering Devices with Slime Mold

The plasmodium of the acellular slime mold Physarum polycephalum is a gigantic single cell visible to the unaided eye. The cell shows a rich spectrum of behavioral patterns in response to environmental conditions. In a series of simple experiments we demonstrate how to make computing, sensing, and actuating devices from the slime mold. We show how to program living slime mold machines by configurations of repelling and attracting gradients and demonstrate the workability of the living machines on tasks of computational geometry, logic, and arithmetic.

Simulating strange attraction of acellular slime mould Physarum polycephaum to herbal tablets

Plasmodium of acellular slime mould Physarum polycephalum exhibits traits of wave-like behaviour. The plasmodium’s behaviour can be finely tuned in laboratory experiments by using herbal tablets. A single tablet acts as a fixed attractor: plasmodium propagates towards the tablet, envelops the tablet with its body and stays around the tablet for several days. Being presented with several tablets the plasmodium executes limit cycle like motions. The plasmodium performs sophisticated routines of movement around tablets: rotation, splitting, and annihilation. We use the two-variable Oregonator model to simulate the plasmodium behaviour in the presence of the herbal tablets. Numerical experiments confirm that using long-distance attracting and short-distance repelling fields we can organise arbitrary movement of plasmodia.