Tomohiro Shirakawa

On simultaneous construction of Voronoi diagram and delaunay triangulation by physarum polycephalum

We experimentally demonstrate that both Voronoi diagram and its dual graph Delaunay triangulation are simultaneously constructed — for specific conditions — in cultures of plasmodium, a vegetative state of Physarum polycephalum. Every point of a given planar data set is represented by a tiny mass of plasmodium. The plasmodia spread from their initial locations but, in certain conditions, stop spreading when they encounter plasmodia originated from different locations. Thus space loci not occupied by the plasmodia represent edges of Voronoi diagram of the given planar set. At the same time, the plasmodia originating at neighboring locations form merging protoplasmic tubes, where the strongest tubes approximate Delaunay triangulation of the given planar set. The problems are solved by plasmodium only for limited data sets, however the results presented lay a sound ground for further investigations.

UNIVERSAL COMPUTATION WITH LIMITED RESOURCES: BELOUSOV–ZHABOTINSKY AND PHYSARUM COMPUTERS

Using the examples of an excitable chemical system (the Belousov–Zhabotinsky medium) and plasmodium of Physarum polycephalum we show that universal computation in a geometrically unconstrained medium is only possible when resources (excitability or concentration of nutrients) are limited. In situations of limited resources the systems studied develop traveling localizations. These localizations are the elementary units of dynamical logical circuits in collision-based computing architectures.

Minimal model of a cell connecting amoebic motion and adaptive transport networks

A cell is a minimal self-sustaining system that can move and compute. Previous work has shown that a unicellular slime mold, Physarum, can be utilized as a biological computer based on cytoplasmic flow encapsulated by a membrane. Although the interplay between the modification of the boundary of a cell and the cytoplasmic flow surrounded by the boundary plays a key role in Physarum computing, no model of a cell has been developed to describe this interplay. Here we propose a toy model of a cell that shows amoebic motion and can solve a maze, Steiner minimum tree problem and a spanning tree problem. Only by assuming that cytoplasm is hardened after passing external matter (or softened part) through a cell, the shape of the cell and the cytoplasmic flow can be changed. Without cytoplasm hardening, a cell is easily destroyed. This suggests that cytoplasmic hardening and/or sol-gel transformation caused by external perturbation can keep a cell in a critical state leading to a wide variety of shapes and motion.

An adaptive and robust biological network based on the vacant-particle transportation model

A living system reveals local computing by referring to a whole system beyond the exploration-exploitation dilemma. The slime mold, Physarum polycephalum, uses protoplasmic flow to change its own outer shape, which yields the boundary condition and forms an adaptive and robust network. This observation suggests that the whole Physarum can be represented as a local protoplasmic flow system. Here, we show that a system composed of particles, which move and are modified based upon the particle transformation that contains the relationship between the parts and the whole, can emulate the network formed by Physarum. This system balances the exploration-exploitation trade-off and shows a scale-free sub-domain. By decreasing the number of particles, our model, VP-S, can emulate the Physarum adaptive network as it is attracted to a food stimulus. By increasing the number of particles, our model, VP-D, can emulate the pattern of a growing Physarum. The patterns produced by our model were compared with those of the Physarum pattern quantitatively, which showed that both patterns balance exploration with exploitation. This model should have a wide applicability to study biological collective phenomena in general.

An associative learning experiment using the plasmodium of Physarum polycephalum

Abstract The plasmodium of Physarum polycephalum is a unicellular and multinuclear giant amoeba that shows adaptive behaviors. To test the presence of memory and learning ability in the plasmodium, we performed an associative learning experiment using the unicellular organism. The plasmodium in this experiment seemed to acquire a reversed thermotactic property, a new preference for the lower temperature. The result implied a possibility of unicellular learning, though in a preliminary way. We also discuss a possible mechanism of learning by the organism.

A model of network formation by Physarum plasmodium: Interplay between cell mobility and morphogenesis

The plasmodium of Physarum polycephalum has attracted much attention due its intelligent adaptive behavior. In this study, we constructed a model of the organism and attempted to simulate its locomotion and morphogenetic behavior. By modifying our previous model, we were able to get closer to the actual behavior. We also compared the behavior of the model with that of the real organism, demonstrating remarkable similarity between the two.

Multi-scaled adaptability in motility and pattern formation of the Physarum plasmodium

The plasmodium of Physarum polycephalum is a unicellular and multinuclear giant amoeba that has macroscopic size, and by this particular nature the organism is attracting a lot of attention in the research fields such as systems science, nature-inspired bio-computing and swarm behavioural study. In this paper, we investigated how the plasmodium generates new motility and morphology, and found that there are allometric relationships between the cell volume and morphology, and between cell size and cell motility. We further discuss how these relationships are realised, and these relationships are deeply connected to the organisms benefit of being a large-scale unicellular organism.

Kanizsa illusory contours appearing in the plasmodium pattern of Physarum polycephalum.

The plasmodium of Physarum polycephalum is often used in the implementation of non-linear computation to solve optimization problems, and this organismal feature was not used in this analysis to compute perception and/or sensation in humans. In this paper, we focused on the Kanizsa illusion, which is a well-known visual illusion resulting from the differentiation-integration of the visual field, and compared the illusion with the adaptive network in the plasmodium of P. polycephalum. We demonstrated that the network pattern mimicking the Kanizsa illusion can be produced by an asynchronous automata-fashioned model of the foraging slime mold and by the real plasmodia of P. polycephalum. Because the protoplasm of the plasmodium is transported depending on both local and global computation, it may contain differentiation-integration processes. In this sense, we can extend the idea of perception and computation.

Construction of living cellular automata using the Physarum plasmodium

The plasmodium of Physarum polycephalum is a unicellular and multinuclear giant amoeba that has an amorphous cell body. To clearly observe how the plasmodium makes decisions in its motile and exploratory behaviours, we developed a new experimental system to pseudo-discretize the motility of the organism. In our experimental space that has agar surfaces arranged in a two-dimensional lattice, the continuous and omnidirectional movement of the plasmodium was limited to the stepwise one, and the direction of the locomotion was also limited to four neighbours. In such an experimental system, a cellular automata-like system was constructed using the living cell. We further analysed the exploratory behaviours of the plasmodium by duplicating the experimental results in the simulation models of cellular automata. As a result, it was revealed that the behaviours of the plasmodium are not reproduced by only local state transition rules; and for the reproduction, a kind of historical rule setting is needed.

Novel taxis of the Physarum plasmodium and a taxis-based simulation of Physarum swarm

The plasmodium of Physarum polycephalum is a unicellular and multinuclear giant amoeba. We investigated the behavior of the plasmodium in magnetic field and found that the organism has magnetotaxis. Based on this new finding, we further studied how the taxis benefit the survival of the plasmodium using a simple swarm model. The result from the model implies that the magnetotaxis promotes prompt swarming of the plasmodia and at the same time facilitates the effective exploration of the space on which the cells crawl.