Amoeba-inspired analog electronic computing system integrating resistance crossbar for solving the travelling salesman problem.

Combinatorial optimization to search for the best solution across a vast number of legal candidates requires the development of a domain-specific computing architecture that can exploit the computational power of physical processes, as conventional general-purpose computers are not powerful enough. Recently, Ising machines that execute quantum annealing or related mechanisms for rapid search have attracted attention. These machines, however, are hard to map application problems into their architecture, and often converge even at an illegal candidate.

Remarkable problem-solving ability of unicellular amoeboid organism and its mechanism.

Choosing a better move correctly and quickly is a fundamental skill of living organisms that corresponds to solving a computationally demanding problem. A unicellular plasmodium of searches for a solution to the travelling salesman problem (TSP) by changing its shape to minimize the risk of being exposed to aversive light stimuli. In our previous studies, we reported the results on the eight-city TSP solution.

Size-Dependent Affinity of Glycine and Its Short Oligomers to Pyrite Surface: A Model for Prebiotic Accumulation of Amino Acid Oligomers on a Mineral Surface.

The interaction strength of progressively longer oligomers of glycine, (Gly), di-Gly, tri-Gly, and penta-Gly, with a natural pyrite surface was directly measured using the force mode of an atomic force microscope (AFM). In recent years, selective activation of abiotically formed amino acids on mineral surfaces, especially that of pyrite, has been proposed as an important step in many origins of life scenarios. To investigate such notions, we used AFM-based force measurements to probe possible non-covalent interactions between pyrite and amino acids, starting from the simplest amino acid, Gly.

Estimating the capacity for production of formamide by radioactive minerals on the prebiotic Earth.

Water creates special problems for prebiotic chemistry, as it is thermodynamically favorable for amide and phosphodiester bonds to hydrolyze. The availability of alternative solvents with more favorable properties for the formation of prebiotic molecules on the early Earth may have helped bypass this so-called "water paradox". Formamide (FA) is one such solvent, and can serve as a nucleobase precursor, but it is difficult to envision how FA could have been generated in large quantities or accumulated in terrestrial surface environments.

Flat-band light dynamics in Stub photonic lattices.

We experimentally study a Stub photonic lattice and excite their localized linear states originated from an isolated Flat Band at the center of the linear spectrum. By exciting these modes in different regions of the lattice, we observe that they do not diffract across the system and remain well trapped after propagating along the crystal. By using their wave nature, we are able to combine - in phase and out of phase - two neighbor states into a coherent superposition.

Common and Potentially Prebiotic Origin for Precursors of Nucleotide Synthesis and Activation.

We have recently shown that 2-aminoimidazole is a superior nucleotide activating group for nonenzymatic RNA copying. Here we describe a prebiotic synthesis of 2-aminoimidazole that shares a common mechanistic pathway with that of 2-aminooxazole, a previously described key intermediate in prebiotic nucleotide synthesis. In the presence of glycolaldehyde, cyanamide, phosphate and ammonium ion, both 2-aminoimidazole and 2-aminooxazole are produced, with higher concentrations of ammonium ion and acidic pH favoring the former.

Random walk with chaotically driven bias.

We investigate two types of random walks with a fluctuating probability (bias) in which the random walker jumps to the right. One is a 'time-quenched framework' using bias time series such as periodic, quasi-periodic, and chaotic time series (chaotically driven bias). The other is a 'time-annealed framework' using the fluctuating bias generated by a stochastic process, which is not quenched in time.

The Abiotic Chemistry of Thiolated Acetate Derivatives and the Origin of Life.

Thioesters and thioacetic acid (TAA) have been invoked as key reagents for the origin of life as activated forms of acetate analogous to acetyl-CoA. These species could have served as high-energy group-transfer reagents and allowed carbon insertions to form higher molecular weight compounds such as pyruvate. The apparent antiquity of the Wood-Ljungdahl CO2 fixation pathway and its presence in organisms which inhabit hydrothermal (HT) environments has also led to suggestions that there may be a connection between the abiotic chemistry of compounds similar to TAA and the origins of metabolism.

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.

A Strategy for Origins of Life Research.

Contents 1. Introduction 1.1.

Single-photon decision maker.

Decision making is critical in our daily lives and for society in general and is finding evermore practical applications in information and communication technologies. Herein, we demonstrate experimentally that single photons can be used to make decisions in uncertain, dynamically changing environments. Using a nitrogen-vacancy in a nanodiamond as a single-photon source, we demonstrate the decision-making capability by solving the multi-armed bandit problem.

A Principled Approach to the Origin Problem.

The key issue of the origin of life is the origin of a complex system rather than the abiotic formation of various organic substances, small and large. To consider this "origin problem" it is advantageous to abstract some principles from biology and statistical physics to guide our approach. Referring to these principles, we aim to construct a chemical system called "protometabolism," which would be a precursor of metabolism.

Amoeba-Inspired Heuristic Search Dynamics for Exploring Chemical Reaction Paths.

We propose a nature-inspired model for simulating chemical reactions in a computationally resource-saving manner. The model was developed by extending our previously proposed heuristic search algorithm, called "AmoebaSAT [Aono et al. 2013]," which was inspired by the spatiotemporal dynamics of a single-celled amoeboid organism that exhibits sophisticated computing capabilities in adapting to its environment efficiently [Zhu et al.

Chaotic oscillation and random-number generation based on nanoscale optical-energy transfer.

By using nanoscale energy-transfer dynamics and density matrix formalism, we demonstrate theoretically and numerically that chaotic oscillation and random-number generation occur in a nanoscale system. The physical system consists of a pair of quantum dots (QDs), with one QD smaller than the other, between which energy transfers via optical near-field interactions. When the system is pumped by continuous-wave radiation and incorporates a timing delay between two energy transfers within the system, it emits optical pulses.

Amoeba-inspired Tug-of-War algorithms for exploration-exploitation dilemma in extended Bandit Problem.

The true slime mold Physarum polycephalum, a single-celled amoeboid organism, is capable of efficiently allocating a constant amount of intracellular resource to its pseudopod-like branches that best fit the environment where dynamic light stimuli are applied. Inspired by the resource allocation process, the authors formulated a concurrent search algorithm, called the Tug-of-War (TOW) model, for maximizing the profit in the multi-armed Bandit Problem (BP). A player (gambler) of the BP should decide as quickly and accurately as possible which slot machine to invest in out of the N machines and faces an "exploration-exploitation dilemma.

Decision maker based on nanoscale photo-excitation transfer.

Decision-making is one of the most important intellectual abilities of the human brain. Here we propose an efficient decision-making system which uses optical energy transfer between quantum dots (QDs) mediated by optical near-field interactions occurring at scales far below the wavelength of light. The simulation results indicate that our system outperforms the softmax rule, which is known as the best-fitting algorithm for human decision-making behaviour.

Information physics fundamentals of nanophotonics.

Nanophotonics has been extensively studied with the aim of unveiling and exploiting light-matter interactions that occur at a scale below the diffraction limit of light, and recent progress made in experimental technologies--both in nanomaterial fabrication and characterization--is driving further advancements in the field. From the viewpoint of information, on the other hand, novel architectures, design and analysis principles, and even novel computing paradigms should be considered so that we can fully benefit from the potential of nanophotonics. This paper examines the information physics aspects of nanophotonics.

Amoeba-inspired nanoarchitectonic computing: solving intractable computational problems using nanoscale photoexcitation transfer dynamics.

Biologically inspired computing devices and architectures are expected to overcome the limitations of conventional technologies in terms of solving computationally demanding problems, adapting to complex environments, reducing energy consumption, and so on. We previously demonstrated that a primitive single-celled amoeba (a plasmodial slime mold), which exhibits complex spatiotemporal oscillatory dynamics and sophisticated computing capabilities, can be used to search for a solution to a very hard combinatorial optimization problem. We successfully extracted the essential spatiotemporal dynamics by which the amoeba solves the problem.

Amoeba-based computing for traveling salesman problem: long-term correlations between spatially separated individual cells of Physarum polycephalum.

A single-celled, multi-nucleated amoeboid organism, a plasmodium of the true slime mold Physarum polycephalum, can perform sophisticated computing by exhibiting complex spatiotemporal oscillatory dynamics while deforming its amorphous body. We previously devised an "amoeba-based computer (ABC)" to quantitatively evaluate the optimization capability of the amoeboid organism in searching for a solution to the traveling salesman problem (TSP) under optical feedback control. In ABC, the organism changes its shape to find a high quality solution (a relatively shorter TSP route) by alternately expanding and contracting its pseudopod-like branches that exhibit local photoavoidance behavior.

Two-dimensional self-assembled structures of melamine and melem at the aqueous solution-Au(111) interface.

Self-assembled structures of melamine and the condensed melamine derivative melem were investigated at aqueous solution-Au(111) interfaces by cyclic voltammetry and in situ scanning tunneling microscopy (STM) observation. The adsorption/desorption behaviors of both molecules on Au(111) surfaces could be controlled by varying the electrochemical potential and solution concentration. In the negative potential region, self-assembled structures of melem and melamine were constructed by double hydrogen bonding systems between nitrogen atoms of triazine rings and amine groups.

Tug-of-war model for the two-bandit problem: nonlocally-correlated parallel exploration via resource conservation.

We propose a model - the "tug-of-war (TOW) model" - to conduct unique parallel searches using many nonlocally-correlated search agents. The model is based on the property of a single-celled amoeba, the true slime mold Physarum, which maintains a constant intracellular resource volume while collecting environmental information by concurrently expanding and shrinking its branches. The conservation law entails a "nonlocal correlation" among the branches, i.

Spontaneous mode switching in coupled oscillators competing for constant amounts of resources.

We propose a widely applicable scheme of coupling that models competitions among dynamical systems for fixed amounts of resources. Two oscillators coupled in this way synchronize in antiphase. Three oscillators coupled circularly show a number of oscillation modes such as rotation and partially in-phase synchronization.

Simulation of neurocomputing based on the photophobic reactions of Euglena with optical feedback stimulation.

To explore possible forms of unconventional computers that have high capacities for adaptation and exploration, we propose a new approach to developing a biocomputer based on the photophobic reactions of microbes (Euglena gracilis), and perform the Monte-Carlo simulation of Euglena-based neural network computing, involving virtual optical feedback to the Euglena cells. The photophobic reactions of Euglena are obtained experimentally, and incorporated in the simulation, together with a feedback algorithm with a modified Hopfield-Tank model for solving a 4-city traveling salesman problem. The simulation shows high performances in terms of (1) reaching one of the best solutions of the problem, and (2) searching for a number of solutions via dynamic transition among the solutions.

Spontaneous deadlock breaking on amoeba-based neurocomputer.

Any artificial concurrent computing system involves a potential risk of "deadlock" that its multiple processes sharing common computational resources are stuck in starved conditions, if simultaneous accesses of the processes to the resources were unconditionally permitted. To avoid the deadlock, it is necessary to set up some form of central control protocol capable of appropriately regulating the resource allocation. On the other hand, many decentralized biological systems also perform concurrent computing based on interactions of components sharing limited amounts of available resources.

Robust and emergent Physarum logical-computing.

There have been many attempts for realization of emergent computing, but the notion of emergent computing is still ambiguous. In an open system, emergence and an error cannot be specified distinctly, because they are dependent on the dis-equilibration process between local and global behaviors. To manifest such an aspect, we implement a Boolean gate as a biological device made of slime mold Physarum polycephalum.