Inspired by the basic processes of molecular biology, our previous studies resulted in defining a configurable molecule implementing self-replication and self-repair mechanisms made up of simple processes. The goal of our paper is to add error detection features to the molecule in order to make it able to perform also built-in self-test mechanisms. The hardware description of the molecule with all its self-organizing mechanisms leads to the simulation of an image processing array dedicated to thresholding and boolean operations.

Living organisms are endowed with three structural principles: multicellular architecture, cellular division, and cellular differentiation. Implemented in digital according to these principles, our bit slice processors present self-organizing mechanisms like configuration, cloning, cicatrization, and regeneration. These mechanisms are made of simple processes such as growth, load, branching, repair, reset, and kill. The description of a configurable molecule implementing the self-organizing mechanisms and its application to an arithmetic and logic unit constitute the core of this paper.

The multicellular structure of biological organisms and the interpretation in each of their cells of a chemical program (the DNA string or genome ) is the source of inspiration for the Embryonics (embryonic electronics) project, whose final objective is the design of highly robust integrated circuits, endowed with properties usually associated with the living world: self-repair and self-replication. In this article, we provide an overview of our latest research in the domain of the self-replication of processing elements within a programmable logic substrate, a key prerequisite for achieving system-level fault tolerance in our bio-inspired approach.

In a traditional cellular automaton (CA) a cell is implemented by a rule table defining its state at the next time step, given its present state and those of its neighbors. The cell thus deals only with states. We present a novel CA where the cell handles data and signals. The cell is designed as a digital system comprising a processing unit and a control unit. This allows the realization of various growing structures, including self-replicating loops and biomorphs. We also describe the hardware implementation of these structures within our electronic wall for bio-inspired applications, the BioWall.

In 1953, Crick and Watson published their landmark paper revealing the detailed structure of the DNA double helix. Several years earlier, von Neumann embedded a very complex configuration, a universal interpreter-copier, into a cellular array. Astoundingly, the structure of this configuration, able to realize the self-replication of any computing machine, including a universal Turing machine, shares several common traits with the structure of living cells as defined by Crick and Watson's discovery. To commemorate the 100th anniversary of von Neumann's birth, this paper presents a macroscopic analysis of self-replication in computing machines using three examples. After describing self-replication in von Neumann's universal interpreter-copier, we will revisit the famous self-replicating loop designed by Langton in 1984. In order to overcome some of the major drawbacks of Langton's loop, namely, its lack of functionality and the fact that it is ill-adapted for a realization in electronic circuits, we present a novel self-replicating loop, the Tom Thumb loop. Endowed with the same capabilities as von Neumann's interpreter-copier, i.e., the possibility of replicating computing machines of any complexity, our loop is moreover specifically designed for the implementation of self-replicating structures in programmable digital logic.

Self-replicating loops presented to date are essentially worlds unto themselves, inaccessible to the observer once the replication process is launched. In this article we present the design of an interactive self-replicating loop of arbitrary size, wherein the user can physically control the loop's replication and induce its destruction. After introducing the BioWall, a reconfigurable electronic wall for bio-inspired applications, we describe the design of our novel loop and delineate its hardware implementation in the wall.

The growth and operation of all living beings are directed by the interpretation, in each of their cells, of a chemical program, the DNA string or genome. This process is the source of inspiration for the Embryonics (embryonic electronics) project, whose final objective is the design of highly robust integrated circuits, endowed with properties usually associated with the living world: self-repair (cicatrization) and self-replication. The Embryonics architecture is based on four hierarchical levels of organization. (1) The basic primitive of our system is the molecule, a multiplexer-based element of a novel programmable circuit. (2) A finite set of molecules makes up a cell, essentially a small processor with an associated memory. (3) A finite set of cells makes up an organism, an application-specific multiprocessor system. (4) The organism can itself replicate, giving rise to a population of identical organisms. We begin by describing in detail the implementation of an artificial cell characterized by a fixed architecture, showing that multicellular arrays can realize a variety of different organisms, all capable of self-replication and self-repair. In order to allow for a wide range of applications, we then introduce a flexible architecture, realized using a new type of fine-grained field-programmable gate array whose basic element, our molecule, is essentially a programmable multiplexer. We describe the implementation of such a molecule, with built-in self-test, and illustrate its use in realizing two applications: a modulo-4 reversible counter (a unicellular organism) and a timer ( a complex multicellular organism). We describe our ongoing research efforts to meet three challenges: a scientific challenge, that of implementing the original specifications formulated by John von Neumann for the conception of a self-replicating automaton; a technical challenge, that of realizing very robust integrated circuits capable of self-repair and self-replication; and a biological challenge, that of attempting to show that the microscopic architectures of artificial and natural organisms, i.e., their genomes, share common properties.

Field-programmable gate arrays (FPGAs) are large, fast integrated circuits-that can be modified, or configured, almost at any point by the end user. Within the domain of configurable computing, we distinguish between two modes of configurability: static-where the configurable processor's configuration string is loaded once at the outset, after which it does not change during execution of the task at hand, and dynamic-where the processor's configuration may change at any moment. This paper describes four applications in the domain of configurable computing, considering both static and dynamic systems, including: SPYDER (a reconfigurable processor development system), RENCO (a reconfigurable network computer), Firefly (an evolving machine), and the BioWatch (a self-repairing watch). While static configurability mainly aims at attaining the classical computing goal of improving performance, dynamic configurability might bring about an entirely new breed of hardware devices-ones that are able to adapt within dynamic environments.

If one considers life on Earth since its very beginning, three levels of organization can be distinguished: the phylogenetic level concerns the temporal evolution of the genetic programs within individuals and species, the ontogenetic level concerns the developmental process of a single multicellular organism, and the epigenetic level concerns the learning processes during an individual organism's lifetime. In analogy to nature, the space of bio-inspired hardware systems can be partitioned along these three axes, phylogeny, ontogeny, and epigenesis, giving rise to the POE model, recently introduced by M. Sipper et al. (1997). In this short paper we briefly present three FPGA-based systems, each situated along a different axis of the POE model.

Biological organisms are among the most intricate structures known to man, exhibiting highly complex behavior through the massively parallel cooperation of numerous relatively simple elements, the cells. As the development of computing systems approaches levels of complexity such that their synthesis begins to push the limits of human intelligence, engineers are starting to seek inspiration in nature for the design of computing systems, both at the software and at hardware levels. We present one such endeavor, notably an attempt to draw inspiration from biology in the design of a novel digital circuit: a field-programmable gate array (FPGA). This reconfigurable logic circuit will be endowed with two features motivated and guided by the behavior of biological systems: self-replication and self-repair.

The growth and the operation of all living beings are directed through the interpretation, in each of their cells, of a chemical program, the DNA string or genome. This process is the source of inspiration for the Embryonics (embryonic electronics) project, whose final objective is the conception of very large scale integrated circuits endowed with properties usually associated with the living world: self-repair (cicatrization) and self-replication. We begin by showing that any logic system can be represented by an ordered binary decision diagram (OBDD), and then embedded into a fine-grained field-programmable gate array (FPGA) whose basic cell is a multiplexer with programmable connections. The cellular array thus obtained is perfectly homogeneous: the function of each cell is defined by a configuration (or gene) and all the genes in the array, each associated with a pair of coordinates, make up the blueprint (or genome) of the artificial organism. In the second part of the project, we add to the basic cell a memory and an interpreter to, respectively, store and decode the complete genome. The interpreter extracts from the genome the gene of a particular cell as a function of its position in the array (its coordinates) and thus determines the exact configuration of the relative multiplexer. The considerable redundancy introduced by the presence of a genome in each cell has significant advantages: self-replication (the automatic production of one or more copies of the original organism) and self-repair (the automatic repair of one or more faulty cells) become relatively simple operations. The multiplexer-based FPGA cell and the interpreter are finally embedded into an electronic module; an array of such modules make it possible to demonstrate self-repair and self-replication.

If one considers life on Earth since its very beginning, three levels of organization can be distinguished: the phylogenetic level concerns the temporal evolution of the genetic programs within individuals and species, the ontogenetic level concerns the developmental process of a single multicellular organism, and the epigenetic level concerns the learning processes during an individual organism's lifetime. In analogy to nature, the space of bio-inspired hardware systems can be partitioned along these three axes-phylogeny, ontogeny and epigenesis (POE)-giving rise to the POE model. This paper is an exposition and examination of bio-inspired systems within the POE framework, with our goals being: (1) to present an overview of current-day research, (2) to demonstrate that the POE model can be used to classify bio-inspired systems, and (3) to identify possible directions for future research, derived from a POE outlook. We discuss each of the three axes separately, considering the systems created to date and plotting directions for continued progress along the axis in question.

A relaxation approach for producing a placement of transistors in a CMOS cell in a grid layout style from the circuit schematic diagram is described. For a given objective function, the approach leads to optimal results in most of the cases attempted. Unlike previous constructive approaches, this approach is iterative. It is also quite flexible. It can be used for unrestricted circuit types and can handle a variety of other important parameters affecting the wireability of the layout. The procedure is targeted for use in the automatic generation of custom and gate-array cell libraries.>

A method for analyzing a wide range of CMOS pass transistor circuits is presented. Based on concepts derived from analysis, synthesis algorithms are proposed. They have been implemented as a program called PAVOS which can solve relatively complex problems. A manual method is presented for handling simpler ones. An effective minimization of the circuit area is obtained by using incomplete transmission gates, i.e. gates composed of either PMOS or NMOS transistors, without degrading the circuit output signals. The specification or a circuit can contain high-impedance states and attractive don't-cares called don't-happen states. It is shown that well-known good-pass transistor circuits, which synthesize results from designers' experience and intuition, can easily be obtained with the described methods. It is suggested that synthesis algorithms for all kinds of logics can be obtained by making small modifications on PAVOS.>