Computers from plants we never made. Speculations

We discuss possible designs and prototypes of computing systems that could be based on morphological development of roots, interaction of roots, and analog electrical computation with plants, and plant-derived electronic components. In morphological plant processors data are represented by initial configuration of roots and configurations of sources of attractants and repellents; results of computation are represented by topology of the roots' network. Computation is implemented by the roots following gradients of attractants and repellents, as well as interacting with each other. Problems solvable by plant roots, in principle, include shortest-path, minimum spanning tree, Voronoi diagram, $\alpha$-shapes, convex subdivision of concave polygons. Electrical properties of plants can be modified by loading the plants with functional nanoparticles or coating parts of plants of conductive polymers. Thus, we are in position to make living variable resistors, capacitors, operational amplifiers, multipliers, potentiometers and fixed-function generators. The electrically modified plants can implement summation, integration with respect to time, inversion, multiplication, exponentiation, logarithm, division. Mathematical and engineering problems to be solved can be represented in plant root networks of resistive or reaction elements. Developments in plant-based computing architectures will trigger emergence of a unique community of biologists, electronic engineering and computer scientists working together to produce living electronic devices which future green computers will be made of.Comment: The chapter will be published in "Inspired by Nature. Computing inspired by physics, chemistry and biology. Essays presented to Julian Miller on the occasion of his 60th birthday", Editors: Susan Stepney and Andrew Adamatzky (Springer, 2017

On hybrid circuits exploiting thermistive properties of slime mould

Slime mould Physarum polycephalum is a single cell visible by the unaided eye. Let the slime mould span two electrodes with a single protoplasmic tube: if the tube is heated to approximately ≈40 °C, the electrical resistance of the protoplasmic tube increases from ≈3 Mω to ≈10,000 Mω. The organisms resistance is not proportional nor correlated to the temperature of its environment. Slime mould can therefore not be considered as a thermistor but rather as a thermic switch. We employ the P. polycephalum thermic switch to prototype hybrid electrical analog summator, NAND gates, and cascade the gates into Flip-Flop latch. Computing operations performed on this bio-hybrid computing circuitry feature high repeatability, reproducibility and comparably low propagation delays

Quantitative transformation for implementation of adder circuits in physical systems

© 2015 Elsevier Ireland Ltd. Computing devices are composed of spatial arrangements of simple fundamental logic gates. These gates may be combined to form more complex adding circuits and, ultimately, complete computer systems. Implementing classical adding circuits using unconventional, or even living substrates such as slime mould Physarum polycephalum, is made difficult and often impractical by the challenges of branching fan-out of inputs and regions where circuit lines must cross without interference. In this report we explore whether it is possible to avoid spatial propagation, branching and crossing completely in the design of adding circuits. We analyse the input and output patterns of a single-bit full adder circuit. A simple quantitative transformation of the input patterns which considers the total number of bits in the input string allows us to map the respective input combinations to the correct outputs patterns of the full adder circuit, reducing the circuit combinations from a 2:1 mapping to a 1:1 mapping. The mapping of inputs to outputs also shows an incremental linear progression, suggesting its implementation in a range of physical systems. We demonstrate an example implementation, first in simulation, inspired by self-oscillatory dynamics of the acellular slime mould P. polycephalum. We then assess the potential implementation using plasmodium of slime mould itself. This simple transformation may enrich the potential for using unconventional computing substrates to implement digital circuits

On the development of slime mould morphological, intracellular and heterotic computing devices

The use of live biological substrates in the fabrication of unconventional computing (UC) devices is steadily transcending the barriers between science fiction and reality, but efforts in this direction are impeded by ethical considerations, the field’s restrictively broad multidisciplinarity and our incomplete knowledge of fundamental biological processes. As such, very few functional prototypes of biological UC devices have been produced to date. This thesis aims to demonstrate the computational polymorphism and polyfunctionality of a chosen biological substrate — slime mould Physarum polycephalum, an arguably ‘simple’ single-celled organism — and how these properties can be harnessed to create laboratory experimental prototypes of functionally-useful biological UC prototypes. Computing devices utilising live slime mould as their key constituent element can be developed into a) heterotic, or hybrid devices, which are based on electrical recognition of slime mould behaviour via machine-organism interfaces, b) whole-organism-scale morphological processors, whose output is the organism’s morphological adaptation to environmental stimuli (input) and c) intracellular processors wherein data are represented by energetic signalling events mediated by the cytoskeleton, a nano-scale protein network. It is demonstrated that each category of device is capable of implementing logic and furthermore, specific applications for each class may be engineered, such as image processing applications for morphological processors and biosensors in the case of heterotic devices. The results presented are supported by a range of computer modelling experiments using cellular automata and multi-agent modelling. We conclude that P. polycephalum is a polymorphic UC substrate insofar as it can process multimodal sensory input and polyfunctional in its demonstrable ability to undertake a variety of computing problems. Furthermore, our results are highly applicable to the study of other living UC substrates and will inform future work in UC, biosensing, and biomedicine

Teaching Memory Circuit Elements via Experiment-Based Learning

The class of memory circuit elements which comprises memristive, memcapacitive, and meminductive systems, is gaining considerable attention in a broad range of disciplines. This is due to the enormous flexibility these elements provide in solving diverse problems in analog/neuromorphic and digital/quantum computation; the possibility to use them in an integrated computing-memory paradigm, massively-parallel solution of different optimization problems, learning, neural networks, etc. The time is therefore ripe to introduce these elements to the next generation of physicists and engineers with appropriate teaching tools that can be easily implemented in undergraduate teaching laboratories. In this paper, we suggest the use of easy-to-build emulators to provide a hands-on experience for the students to learn the fundamental properties and realize several applications of these memelements. We provide explicit examples of problems that could be tackled with these emulators that range in difficulty from the demonstration of the basic properties of memristive, memcapacitive, and meminductive systems to logic/computation and cross-bar memory. The emulators can be built from off-the-shelf components, with a total cost of a few tens of dollars, thus providing a relatively inexpensive platform for the implementation of these exercises in the classroom. We anticipate that this experiment-based learning can be easily adopted and expanded by the instructors with many more case studies.Comment: IEEE Circuits and Systems Magazine (in press

On half-adders based on fusion of signal carriers: Excitation, fluidics, and electricity

Likely outcomes of a collision between two objects are annihilation, reflection or fusion. We show how to construct a one-bit adder with pattern that fuse on impact. A fusion gate has two inputs and three outputs. When a signal is generated on a single input the object propagates along its own output trajectory. When both inputs are activethe objects collide at a junction of input trajectories, fuse and propagate along dedicated output trajectory. Thus two outputs produce conjunction of one signal with negation of another signal; and, third output produces conjunction of input signals. By merging two outputs in one we make a one-bit half adder: one output is the conjunction of input signals, another output is the exclusive disjunction of the signals. We discuss blue-prints of the half-adders realised with two types of physical signal careers ---wave-fragments in excitable medium and high-velocity jet streams. We also propose an electrical circuits analogous of a fusion half-adder. By running fusion half-adders in reverse we find that, despite realising the same functions when in a straight mode, all devices implement different functions when their inputs swapped with outputs