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

Towards a Physarum learning chip

Networks of protoplasmic tubes of organism Physarum polycehpalum are macro-scale structures which optimally span multiple food sources to avoid repellents yet maximize coverage of attractants. When data are presented by configurations of attractants and behaviour of the slime mould is tuned by a range of repellents, the organism preforms computation. It maps given data configuration into a protoplasmic network. To discover physical means of programming the slime mould computers we explore conductivity of the protoplasmic tubes; proposing that the network connectivity of protoplasmic tubes shows pathway-dependent plasticity. To demonstrate this we encourage the slime mould to span a grid of electrodes and apply AC stimuli to the network. Learning and weighted connections within a grid of electrodes is produced using negative and positive voltage stimulation of the network at desired nodes; low frequency (10 Hz) sinusoidal (0.5 V peak-to-peak) voltage increases connectivity between stimulated electrodes while decreasing connectivity elsewhere, high frequency (1000 Hz) sinusoidal (2.5 V peak-to-peak) voltage stimulation decreases network connectivity between stimulated electrodes. We corroborate in a particle model. This phenomenon may be used for computation in the same way that neural networks process information and has the potential to shed light on the dynamics of learning and information processing in non-neural metazoan somatic cell networks

Unconventional Computing and Music: An Investigation into Harnessing Physarum polycephalum

This thesis presents an investigation into developing musical systems with an Unconventional Computing substrate. Computer musicians have found it difficult to access the field of Unconventional Computing, which is likely due to its resource-intensive and complex nature. However, ongoing research is establishing the myxomycete Physarum polycephalum as a universally-accessible and versatile biological computing substrate. As such, the organism is a potential gateway for computer musicians to begin experimenting with aspects of Unconventional Computing. Physarum polycephalum, in its vegetative plasmodium form, is an amorphous unicellular organism that can respond with natural parallelism to the environmental conditions that surround it. This thesis explores the challenges and opportunities related to developing musical systems with Physarum polycephalum. As this area of inquiry is in its infancy, the research took inspiration from a common approach in Unconventional Computing: a journey of exploration and discovery. This journey consisted of a selection of waypoints that provided direction while allowing the research to explore applications of Physarum polycephalum in order to establish how it may be useful in Computer Music. These waypoints guided the research from adapting established prototypes for musical application to developing purpose-made musical demonstrators for use outside of the laboratory. Thus, the thesis reports on a series of Computer Music systems that explore one or more features of Physarum polycephalum's behaviour and physiology. First, the text presents an approach to algorithmic composition that exploits the organism's ability to form and reconfigure graph-like structures. Next, the thesis reports on systems that harness the plasmodium's electrical potential oscillations for sound synthesis and compositional tools. Finally, the thesis presents musical devices that encompass living plasmodium as electrical components. Where applicable, the thesis includes artefacts from demonstrations of these systems, some of which were developed in collaboration with a composer. The findings from this journey demonstrate that Physarum polycephalum is an appropriate substrate for computer musicians wanting to explore Unconventional Computing approaches creatively. Although Physarum polycephalum is relatively robust as a biological substrate, several obstacles arose during this project. This research addressed such obstacles by reviewing and selecting approaches that maintained the organism's accessibility to computer musicians. As a result, the work suggests methods for developing systems with the organism that are practical for the average music technologist and also beneficial to the wider group of scientists investigating Physarum polycephalum for other purposes.Plymouth University HumPA Studentshi

n-Alkyl Methacrylate Polymeric Memristors for Synaptic Response Modeling: Organic and Biologically Relevant Thin Films

There is a strong interest in organic materials for electrical devices due to several advantages that organic systems have over their inorganic counterparts including ease of processability and lower toxicity. Many of these organic materials can be utilized in the creation of thin-film devices that can be formed in high-throughput processes and with a very small profile. One such device that has emerged in recent years is the memristor which can be used in new computational concept or as a synaptic model. This work studies the alternating current (AC) and direct current (DC) electrical response of a number n-alkyl methacrylate polymers with a charge transporting pendant carbazole ring. The electrical properties of the polymers were studied as a function of n-alkyl length with n ranging from 2 to 11. The DC current (I)-voltage (V) response of the polymers was characterized by an erratic and bistable response, while their AC I-V response was a pinched hysteresis loop when measured between 1-100 Hz. For polymers with n \u3c 9, their pinched hysteresis loop is characterized by jump transitions indicative of bistability, while polymers with n ≥ 9 had a pinched hysteresis loop that is smooth in appearance. Dielectric spectroscopy on the polymers indicates that as the n-alkyl length is increased, the rotation flexibility of the carbazole moiety is enhanced. The n-alkyl methacrylate polymers with a pendant carbazole ring spaced n ≥ 9 exhibited a lower activation energy and temperature for the onset of ring motion and resulted in polymer-based memristors that exhibit electrical characteristics, such as incrementally adjustable conductivity, that are potential candidates for mimicking synaptic plasticity. Further characterization was done on similar methacrylate systems with oxygen-substituted side chains and the addition of bulky phenyl groups to the carbazole moieties. From this work, the most promising candidate for synaptic modeling behavior was taken and further examined. It was shown that this polymer could be pulsed through a multitude of conductivity states and demonstrated behavior consistent with the Hebbian Learning Rule upon the application of pre- and post-synaptic pulses. The system was further characterized for the effects of different spike rates and voltages before being utilized in a flexible device. Other thin-film devices as well as novel processing methods were also demonstrated in this work including a biologically based reserve battery and a printed diode utilizing pentacene. The battery utilized standard alkaline chemistry where the zinc and manganese oxide electrodes are formed using stencil printing. Fish eggs are used to sequester the electrolyte out of the system until the application of force to the device. This application of force bursts the fish eggs and allows the battery to function by introducing the electrolyte into the system. A printed diode is also demonstrated through the use of a miniemulsion process that allows for the dispersion of the material into aqueous solution. This pentacene emulsion in water can then be used as the basis for the formation of diodes in a variety of fabrication processes

Whole-Body Regeneration

This Open Access volume provides a comprehensive overview of the latest tools available to scientists to study the many facets of whole-body regeneration (WBR). The chapters in this book are organized into six parts. Part One provides a historical overview on the study of the WBR phenomena focusing on the primary challenges of this research. Parts Two and Three explore a series of non-vertebrate zoological contexts that provide experimental models for WBR, showing how they can be approached with cellular tools. Parts Four, Five, and Six discuss the future advancements of WBR, reporting about the cutting-edge techniques in genetics and omics used to dissect the underlying mechanisms of WBR, and systems biology approaches to reach a synthetic view of WBR. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and thorough, Whole-Body Regeneration: Methods and Protocols is a valuable resource for scientists and researchers who want to learn more about this important and developing field

Whole-Body Regeneration

This Open Access volume provides a comprehensive overview of the latest tools available to scientists to study the many facets of whole-body regeneration (WBR). The chapters in this book are organized into six parts. Part One provides a historical overview on the study of the WBR phenomena focusing on the primary challenges of this research. Parts Two and Three explore a series of non-vertebrate zoological contexts that provide experimental models for WBR, showing how they can be approached with cellular tools. Parts Four, Five, and Six discuss the future advancements of WBR, reporting about the cutting-edge techniques in genetics and omics used to dissect the underlying mechanisms of WBR, and systems biology approaches to reach a synthetic view of WBR. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and thorough, Whole-Body Regeneration: Methods and Protocols is a valuable resource for scientists and researchers who want to learn more about this important and developing field