Jacqueline Signorini

How a SIMD machine can implement a complex cellular automata? a case study: von Neumann's 29-state cellular automaton

This study is a part of an effort to simulate the 29-state self-reproducing cellular automaton described by John von Neumann in a manuscript that dates back to 1952. We are interested in the programming of very large SIMD arrays which, as a consequence of scaling them up, incorporate some features of cellular automata. Designing tools for programming them requires an experimental ground: considering that von Neumanns 29-state is the only known very large and complex cellular automaton, its simulation is a necessary first step. Embedded in a two-dimensional cellular array, using 29 states per cell and 5-cell neighborhood, this automaton exhibits the capabilities of universal computation and universal construction. This paper concentrates on the transition rule that governs the complex behavior of the 29-state automaton. We give a detailed presentation of its transition rule, with illustrative examples to ease its comprehension. We then discuss its implementation on a SIMD machine, using only 13 bits per processing element to encode the rule, each processing element corresponding to a cell. Finally, we present experimental results based upon the simulation of general-purpose components of the automaton: pulser, decoder, periodic pulser on the SIMD machine.

Complex Computing with Cellular Automata

There are two equally acceptable ways to describe the computational universe of cellular automata (CA), depending on whether one chooses to emphasize homogeneity or multiplicity. These two complementary approaches reflect a relationship between the organizational notions of insulation and interaction.

Object-Oriented Specification of Complex Bio-computing Processes: A Case Study of a Network of Proteolytic Enzymes

We propose a case study where a familiar but very complex and intrinsically woven bio-computing system – the blood clotting cascade – is specified using methods from software design known as object-oriented design (OOD). The specifications involve definition and inheritance of classes and methods and use design techniques from the most widely used OOD-language: the Unified Modeling Language (UML), as well as its Real-Time-UML extension.First, we emphasize the needs for a unified methodology to specify complex enough biological and biochemical processes. Then, using the blood clotting cascade as a example, we define the class diagrams which exhibit the static structure of procoagulant factors of proenzyme-enzyme conversions, and finally we give a dynamic model involving events, collaboration, synchronization and sequencing. We thus show that OOD can be used in fields very much beyond software design, gives the benefit of unified and sharable descriptions and, as a side effect, automatic generation of code templates for simulation software.

Object-oriented wound healing in the liver: a class-structured view of fibrogenesis and a glimpse of its evolution

We describe a very intricate case of highly correlated bio-processes: the liver fibrogenic cascade, by using a set of tools from object-oriented design (OOD). OOD methods were designed for the abstract specification of complex software prior to programming. It appears that OOD methods can be a fruitful tool for the abstract description of biological processes apparently quite far away from software engineering. We give a detailed view of the fibrogenic cascade within the liver using the now standard tool of OOD: Unified Modeling Language (UML) and one extension: Real-Time UML.OOD methods enforce the important role of concepts such as modularity, classes, methods and their inheritance hierarchies as well as primitives for concurrent process synchronization and cooperation. These concepts are surprisingly quite relevant for specifying bio-processes, and unexpectedly, they suggest an extension of the strict evolutionary explanation of the processes involved. As well as describing bio-structures and their interactions, we could consider evolutionary description of classes and processes. In particular, the OOD inheritance concept seems to be significant as an extension to gradualism. It suggests that DNA could encode, in Universal-Turing-Machine like fashion, the hierarchies of classes of molecular structures and perhaps the process templates associated with methods.

Object-oriented design for the specification of the blood clotting cascade: a class-structured view of bio-computing processes

We describe a very intricate case of interlocked bio-processes: the blood clotting cascade, by using a set of tools from object-oriented design (OOD). Originally, OOD has been designed for the abstract specification of complex software prior to programming. OOD brings a handful of concepts such as modularity, classes, methods and their inheritance hierarchies for concurrent process synchronization and cooperation. It appears that the set of OOD methods can be a very fruitful tool for the abstract description of biological processes apparently quite far away from software engineering. We give a moderately detailed view of the blood clotting cascade using the standard tool of OOD: Unified Modeling Language (UML) and its extension: Real-Time UML.

A computational model for perceptual grouping

A computational model for perceptual grouping is described, based on a single-instruction multiple-data (SIMD) machine, embedding a cellular automaton. The author shows that extraction of information and combination of perceptual features into higher-level grouping can be performed by SIMD computations. A description is given of a labeling procedure for the cellular automaton, based on the Huffman-Clowes system, where the labels are the states of the automation and the label combination rules its local transition rules.<<ETX>>

A routing model for the NCR GAPP

A routing model for the NCR Geometric Arithmetic Parallel Processor (GAPP) is described. The objective is to permit virtual reconfigurations of the array of processing elements (PEs) and nonlocal connections between arbitrarily distant PEs. The main feature of the model is the multiplexing of two instruction sets, over an additional pin, controlling either the SIMD (single-instruction, multiple-data-stream) machine or the set of router-cells organized as a hypercube network. A description is given of which structural changes are applied to the GAPP SIMD machine to support the routing scheme, and the operations concurrently executed by the router-cells for receiving, delivering or forwarding messages. A functional description of a semantic network which was designed expressly to test the routing model is given together with examples of its use.<<ETX>>