Plasmodium Of Physarum Polycephalum Research Articles

Relation between learning process and morphology of transport tube network in plasmodium of Physarum polycephalum.

The question of whether a single-celled organism without a brain could have functions such as learning and memory has been the subject of much debate in recent years. The plasmodium of the true slime mold, Physarum polycephalum, is an ideal model organism for such a question. The plasmodium exhibits behaviors that resemble intelligence, including solving mazes, mimicking optimal rail transportation networks, predicting the weather, and solving traveling salesman problems. In addition, the plasmodium has recently been shown to have the simplest form of learning: habituation. In the experiments in which plasmodia were repeatedly allowed to cross bridges containing aversive chemicals, the habituation behavior has been confirmed. It has been shown that the habituation process involves chemicals that are stored internally. However, it is not clear how these chemicals result in change in the behavior of plasmodium during habituation learning. This study focused on the transport tube network formed in plasmodium during the above experiments. Then, the role of the network morphology in the habituation learning process was investigated. The results showed that the network morphology changes from tree to mesh type during habituation learning, and disrupting the learned network reduces habituation behavior. In addition, it was shown that the thickness oscillation frequency depends on the network morphology. The study found that in the plasmodium of P. polycephalum, a primitive organism without a brain, transport tube networks, instead of neuronal networks, play an important role in habituation learning and the resulting decision making.

Observation of Autonomous Behavioral Selection in Physarum Plasmodium

The plasmodium of Physarum polycephalum is a unicellular and multinuclear giant amoeba with computational abilities. The plasmodium has been widely used as a model organism in the field of bio-computing; however, its ability to perform computation related to its biological nature itself in the essential sense has not yet been fully realized. Therefore, in this study, we focused on the phenomenon in which a plasmodium trapped in a closed space surrounded by repellent substances escapes from the field by changing its own behavior rules. We demonstrated that this phenomenon is bio-computationally important in that it may enable the implementation of biological characteristics in computing.

Externalized memory in slime mould and the extended (non-neuronal) mind

The hypothesis of extended cognition (HEC) claims that the cognitive processes that materially realise thinking are sometimes partially constituted by entities that are located external to an agent’s body in its local environment. We show how proponents of HEC need not claim that an agent must have a central nervous system, or physically instantiate processes organised in such a way as to play a causal role equivalent to that of the brain if that agent is to be capable of cognition. Focusing on the case of spatial memory, we make our argument by taking a close look at the striking example of Physarum Polycephalum plasmodium (i.e., slime mould) which uses self-produced non-living extracellular slime trails to navigate its environment. We will argue that the use of externalized spatial memory by basal organisms like Physarum is an example of extended cognition. Moreover, it is a possible evolutionary precursor to the use of internal spatial memory and recall in animals thus demonstrating how extended cognition may have emerged early in evolutionary history.

Effective mixing due to oscillatory laminar flow in tubular networks of plasmodial slime moulds

The plasmodium of the unicellular slime mould Physarum polycephalum forms an extended vascular network in which protoplasm is transported through the giant cell due to peristaltic pumping. The flow in the veins is always parabolic and it performs shuttle streaming, i.e., the flow reverses its direction periodically. However, particles suspended in the protoplasm are effectively and rapidly distributed within the cell. To elucidate how an effective mixing can be achieved in such a microfluidic system with Poiseuille flow, we performed micro-particle imaging velocimetry experiments and advected virtual tracers in the determined time-dependent flow fields. Two factors were found to be crucial for effective mixing: (i) flow splitting and flow reversals occurring at junctions of veins and (ii) small delays in the reversals of flows in the veins at a junction. These factors enhance the distribution of fluid volumes and hence promote mixing due to chaotic advection. From the residence time distributions of particles at a junction, it is estimated that about 10% of the volume is effectively redistributed at a junction during one period of the shuttle streaming. We presume that the principles of mixing unravelled in P. polycephalum represent a promising approach to achieve efficient mixing in man-made microfluidic devices.

PORA: A Physarum-inspired obstacle-avoiding routing algorithm for integrated circuit design

The plasmodium of Physarum polycephalum, a large, amoeboid cell, has attracted much attention recently due to its intelligent behaviors in pathfinding, danger avoidance, and network construction. Inspired by the biological behaviors of this primitive organism, in this study, we explore the optimization capability of Physarum polycephalum systematically and present the first Physarum-inspired obstacle-avoiding routing algorithm for the physical design of integrated circuits. We simulate the foraging behaviors of Physarum polycephalum using a novel nutrition absorption/consumption mathematical model, thereby presenting an efficient routing tool called Physarum router. With the proposed routing approach, for a given set of pin vertices and a given set of on-chip functional modules, a rectilinear Steiner minimal tree connecting all the pin vertices while avoiding the blockage of functional modules can be constructed automatically. Furthermore, several heuristics including a divide-and-conquer strategy, a non-pin leaf node pruning strategy, a dynamic parameter strategy, etc., are integrated into the proposed algorithm to fundamentally improve the performance of the Physarum router. Simulation results on multiple benchmarks confirm that the proposed algorithm leads to shorter wirelength compared with several state-of-the-art methods.

Biased Lévy-walk pattern in the exploratory behavior of the Physarum plasmodium

The plasmodium of Physarum polycephalum is a unicellular and multinuclear giant amoeba. The plasmodium has the ability to sense and adapt to many kinds of environmental stimuli, and its optimization behavior in closed spaces has been analyzed extensively. However, few studies have tested the behavior of the plasmodium in an open spaces, despite the biological importance of the adaptability of biological entities in such conditions. Accordingly, we established an experimental setup with a very large and strictly homogeneous substrate and observed the long-term exploratory behavior of the plasmodium. As a result, we found that the movement of the plasmodium was consistent with a Lévy-walk, but with anisotropic bias.

Slime Mould Games Based on Rough Set Theory

Abstract We define games on the medium of plasmodia of slime mould, unicellular organisms that look like giant amoebae. The plasmodia try to occupy all the food pieces they can detect. Thus, two different plasmodia can compete with each other. In particular, we consider game-theoretically how plasmodia of Physarum polycephalum and Badhamia utricularis fight for food. Placing food pieces at different locations determines the behavior of plasmodia. In this way, we can program the plasmodia of Physarum polycephalum and Badhamia utricularis by placing food, and we can examine their motion as a Physarum machine-an abstract machine where states are represented as food pieces and transitions among states are represented as movements of plasmodia from one piece to another. Hence, this machine is treated as a natural transition system. The behavior of the Physarum machine in the form of a transition system can be interpreted in terms of rough set theory that enables modeling some ambiguities in motions of plasmodia. The problem is that there is always an ambiguity which direction of plasmodium propagation is currently chosen: one or several concurrent ones, i.e., whether we deal with a sequential, concurrent or massively parallel motion. We propose to manage this ambiguity using rough set theory. Firstly, we define the region of plasmodium interest as a rough set; secondly, we consider concurrent transitions determined by these regions as a context-based game; thirdly, we define strategies in this game as a rough set; fourthly, we show how these results can be interpreted as a Go game.

Decidable and undecidable arithmetic functions in actin filament networks

The plasmodium of Physarum polycephalum is very sensitive to its environment, and reacts to stimuli with appropriate motions. Both the sensory and motor stages of these reactions are explained by hydrodynamic processes, based on fluid dynamics, with the participation of actin filament networks. This paper is devoted to actin filament networks as a computational medium. The point is that actin filaments, with contributions from many other proteins like myosin, are sensitive to extracellular stimuli (attractants as well as repellents), and appear and disappear at different places in the cell to change aspects of the cell structure—e.g. its shape. By assembling and disassembling actin filaments, some unicellular organisms, like Amoeba proteus, can move in response to various stimuli. As a result, these organisms can be considered a simple reversible logic gate—extracellular signals being its inputs and motions its outputs. In this way, we can implement various logic gates on amoeboid behaviours. These networks can embody arithmetic functions within p-adic valued logic. Furthermore, within these networks we can define the so-called diagonalization for deducing undecidable arithmetic functions.

Biological activities and chemical compositions of slime tracks and crude exopolysaccharides isolated from plasmodia of Physarum polycephalum and Physarella oblonga

BackgroundThe myxomycetes derive their common name (slime molds) from the multinucleate trophic stage (plasmodium) in the life cycle, which typically produces a noticeable amount of slimy materials, some of which is normally left behind as a “slime track” as the plasmodium migrates over the surface of a particular substrate. The study reported herein apparently represents the first attempt to investigate the chemical composition and biological activities of slime tracks and the exopolysaccharides (EPS) which cover the surface of the plasmodia of Physarum polycephalum and Physarella oblonga.ResultsChemical analyses indicated that the slime tracks and samples of the EPS consist largely of carbohydrates, proteins and various sulphate groups. Galactose, glucose and rhamnose are the monomers of the cabohydrates present. The slime tracks of both species and the EPS of Phy. oblonga contained rhamnose, but the EPS of Ph. polycephalum had glucose as the major monomer. In term of biological activities, the slime tracks displayed no antimicrobial activity, low anticancer activity and only moderate antioxidant activity. However, EPSs from both species showed remarkable antimicrobial activities, especially toward Candida albicans (zone of inhibition ≥20 mm). Minimum inhibitory concentrations of this fungus were found to be 2560 μg/mL and 1280 μg/mL for EPS from Phy. oblonga and Ph. polycephalum, respectively. These EPS samples also showed moderate antioxidant activities. However, they both displayed cytotoxicity towards MCF-7 and HepG2 cancer cells. Notably, EPS isolated from the plasmodium of Phy. oblonga inhibited the cell growth of MCF-7 and HepG2 at the half inhibitory concentration (IC50) of 1.22 and 1.11 mg/mL, respectively.ConclusionsEPS from Ph. polycephalum plasmodium could be a potential source of antifungal compounds, and EPS from Phy. oblonga could be a potential source of anticancer compounds.

Response to various periods of mechanical stimuli in Physarum plasmodium

Response to mechanical stimuli is a fundamental and critical ability for living cells to survive in hazardous conditions or to form adaptive and functional structures against force(s) from the environment. Although this ability has been extensively studied by molecular biology strategies, it is also important to investigate the ability from the viewpoint of biological rhythm phenomena so as to reveal the mechanisms that underlie these phenomena. Here, we use the plasmodium of the true slime mold Physarum polycephalum as the experimental system for investigating this ability. The plasmodium was repetitively stretched for various periods during which its locomotion speed was observed. Since the plasmodium has inherent oscillation cycles of protoplasmic streaming and thickness variation, how the plasmodium responds to various periods of external stretching stimuli can shed light on the other biological rhythm phenomena. The experimental results show that the plasmodium exhibits response to periodic mechanical stimulation and changes its locomotion speed depending on the period of the stretching stimuli.

Interrelation between respiratory and contractile activity of Physarum polycephalum

Different types of endoplasmic oscillatory activity of Physarum polycephalum plasmodium driven by external influences were investigated. Shuttle velocity oscillations of the endoplasm in an isolated plasmodium strand have been analysed using short-time Fourier (STFT) and wavelet transform. Spectral characteristics calculated from the obtained data allowed us to reveal two internal harmonic oscillators with frequencies differing twice with high accuracy (~2%), or one oscillator in which the frequency doubled with the phase shift. The amplitudes and phases of these harmonics only determine contractile activity, self-organisation and migration of the strand. Inhibitors of the cellular respiration (KCN-SHAM) were applied to demonstrate the interrelation between respiratory pathways with contractile activity. Both internal oscillators showed high sensitivity to the respiratory inhibitors: fast cessation of oscillation in the presence of inhibitors and gradual recovery when they have been removed.

Studies of the phase gradient at the boundary of the phase diffusion equation, motivated by peculiar wave patterns of rhythmic contraction in the amoeboid movement of Physarum polycephalum

The boundary of a cell is the interface with its surroundings and plays a key role in controlling the cell movement adaptations to different environments. We propose a study of the boundary effects on the patterns and waves of the rhythmic contractions in plasmodia of Physarum polycephalum, a tractable model organism of the amoeboid type. Boundary effects are defined as the effects of both the boundary conditions and the boundary shape. The rhythmicity of contraction can be modulated by local stimulation of temperature, light and chemicals, and by local deformation of cell shape via mechanosensitive ion channels as well. First, we examined the effects of boundary cell shapes in the case of a special shape resembling a tadpole, while requiring that the natural frequency in the proximity of the boundary is slightly higher and uniform. The simulation model reproduced the approximate propagated wave, from the tail to the head, while the inward waves were observed only near the periphery of the head section of the tadpole-shape. A key finding was that the frequency of the rhythmic contractions depended on the local shape of cell boundary. This implies that the boundary conditions of the phase were not always homogeneous. To understand the dependency, we reduced the two-dimensional model into a one-dimensional continuum model with Neumann boundary conditions. Here, the boundary conditions reflect the frequency distribution at the boundary. We described the analytic solutions and calculated the relationship between the boundary conditions and the wave propagation for a one-dimensional model of the continuous oscillatory field and a discrete coupled oscillator system. The results obtained may not be limited to cell movement of Physarum, but may be applicable to the other physical systems since the analysis used a generic phase diffusion equation.

Transition from isotropic to digitated growth modulates network formation in Physarum polycephalum

Some organisms, including fungi, ants, and slime molds, explore their environment and forage by forming interconnected networks. The plasmodium of the slime mold Physarum polycephalum is a large unicellular amoeboid organism that grows a tubular spatial network through which nutrients, body mass, and chemical signals are transported. Individual plasmodia are capable of sophisticated behaviours such as optimizing their network connectivity and dynamics using only decentralized information processing. In this study, we used a population of plasmodia that interconnect through time to analyse the dynamical interactions between growth of individual plasmodia and global network formation. Our results showed how initial conditions, such as the distance between plasmodia, their size, or the presence and quality of food, affect the emerging network connectivity.

The autowave electromechanical activity of the Physarum polycephalum plasmodium

The aim of this work is to clarify the role of the electrical activity of the Physarum polycephalum plasmodium in the control of the contractile activity and self-organization of the directed locomotion. This single-celled organism with a non-excitable membrane is a classic object that is used in studies of amoeboid motility. Its patterns of motor behavior and signal systems are common for many tissue cells. The presence of 50 mM KCl in an agar substrate under half of a separate plasmodial strand strongly inhibits the formation of the frontal zone and leads to sharp morphological polarization of the strand, which suggests the involvement of electrical processes in the autowave self-organization of the plasmodial structure. The gigantic sizes of the plasmodium make it possible to record its electrical activity simultaneously at different parts of the cell. It has been established that potentials and currents at parts of the plasmodium that are distant from each other oscillate synchronously and differ only in the shape of the signals, probably due to differences in the phases or the number of excited harmonics. We recorded currents (~50 pA) of single ion channels of the plasmodial membrane using the classical local voltage-clamp method. It has been found that the oscillation spectrum of the current that is generated by the plasmodium has high-frequency fluctuations, which are probably connected with periodic detachments of the membrane from the cytoskeleton during the formation and growth of the pseudopodia. It has been also shown that neomycin, a substrate inhibitor of phospholipase C, prevents oscillations of both the mechanical and electrical activity of the plasmodium. This is consistent with its well-established ability to inhibit mechanosensitive Ca2+ channels, which are apparently present in the plasmodial membrane. These data indicate the presence of a general signal system that is linked with the dynamics of the membrane- cytoskeleton association, which could be involved in the galvano- and chemotaxis of amoeboid cells.

Towards Slime Mould Based Computer

In this paper, I theoretically summarize, which behavioral possibilities the plasmodium of Physarum polycephalum has in order to be considered the medium of computation. I show that plasmodia can be represented as a natural implementation of different abstract automata: cellular automata, Kolmogorov–Uspensky machines, Schönhage’s storage modification machines, random-access machines. As a programming language for simulating Physarum plasmodium behavior, process calculus can be used.

Decision-making ability of Physarum polycephalum enhanced by its coordinated spatiotemporal oscillatory dynamics

An amoeboid unicellular organism, a plasmodium of the true slime mold Physarum polycephalum, exhibits complex spatiotemporal oscillatory dynamics and sophisticated information processing capabilities while deforming its amorphous body. We previously devised an ‘amoeba-based computer (ABC),’ that implemented optical feedback control to lead this amoeboid organism to search for a solution to the traveling salesman problem (TSP). In the ABC, the shortest TSP route (the optimal solution) is represented by the shape of the organism in which the body area (nutrient absorption) is maximized while the risk of being exposed to aversive light stimuli is minimized. The shortness of the TSP route found by ABC, therefore, serves as a quantitative measure of the optimality of the decision made by the organism. However, it remains unclear how the decision-making ability of the organism originates from the oscillatory dynamics of the organism. We investigated the number of coexisting traveling waves in the spatiotemporal patterns of the oscillatory dynamics of the organism. We show that a shorter TSP route can be found when the organism exhibits a lower number of traveling waves. The results imply that the oscillatory dynamics are highly coordinated throughout the global body. Based on the results, we discuss the fact that the decision-making ability of the organism can be enhanced not by uncorrelated random fluctuations, but by its highly coordinated oscillatory dynamics.

On modulating the Physarum polycephalum plasmodium's electrical resistance, resting membrane potential and capacitance by application of nanoparticles and nanostructures

Physarum polycephalum is a model organism used in the creation of hybrid artificial-biological devices. Among its demonstrated uses in biocomputing it is able to grow self healing ‘wires’ which can be used to generate circuitry, especially following hybridisation with nano- and micro-scale circuit components. In this study P. polycephalum plasmodia were hybridised with nanomaterials; graphene oxide, carbon nanotubes, calcium phosphate and aluminium oxide. Observations were made on toxicological effects and alterations in electrical properties; mean potential, period, frequency, resistance and capacitance. Macroscopically, there was little evidence of toxic effects on P. polycephalum using any of these nanomaterials. Capacitance was increased substantially and electrical resistance decreased in carbon nanotube-treated plasmodia, with all results for other nanomaterials being lesser in magnitude. Our results demonstrate that carbon nanotubes are a suitable material for biohybridisation in the creation of conductive cellular pathways, whilst influencing their capacitance.

Physarum Polycephalum Syllogistic L-Systems and Judaic Roots of Unconventional Computing

Abstract We show that in Kabbalah, the esoteric teaching of Judaism, there were developed ideas of unconventional automata in which operations over characters of the Hebrew alphabet can simulate all real processes producing appropriate strings in accordance with some algorithms. These ideas may be used now in a syllogistic extension of Lindenmayer systems (L-systems), where we deal also with strings in the Kabbalistic-Leibnizean meaning. This extension is illustrated by the behavior of Physarum polycephalum plasmodia which can implement, first, the Aristotelian syllogistic and, second, a Talmudic syllogistic by qal wa-homer.

A power law in the exploratory behavior of the Physarum plasmodium

The plasmodium of Physarum polycephalum is a unicellular giant amoeba that grows up to macroscopic scale under appropriate condition, and is known to its computational abilities. In this study, we tried to observe the long-term exploratory behavior of the plasmodium in an open environment and to evaluate its efficiency. For this purpose, we developed an experimental system with an extendable substrate. As a result of the experiment, we found that the frequency distribution of the speed of plasmodial locomotion is fitted by power function. By simulation, we further tried to estimate the efficiency of the exploration implemented with the patterns from the plasmodium, and confirmed that it is actually effective.

Characterization of endoplasmic streaming in Physarum polycephalum using direction sensitive laser Doppler microscopy

Shuttle endoplasmic streaming in an isolated strand of Physarum polycephalum plasmodium under normal conditions and after treatment with cellular respiration inhibitors (KCN and SHAM) was investigated using sign-sensitive sensitive laser Doppler velocimetry. Spectral analysis (short-time Fourier transform) applied to the experimental velocity time dependencies V(t) of endoplasmic motility, reveals two distinct frequencies, ν1 and ν2, corresponding to two harmonic contributions in each V(t), meaning the presence of at list two internal oscillators. Treatment with the inhibitors causes full stop of the endoplasmic streaming with simultaneous suppression of both harmonic oscillators. After removal of the inhibitors system returns to its original state (as before treatment)—the activity of both peaks is gradually restored during 800 s. Despite the frequency values are different, the ratio, ν2/ν1, remains constant for all investigated cases and approximately is equal to two.