Abstract State Machines 1988-1998: Commented ASM Bibliography

An annotated bibliography of papers which deal with or use Abstract State Machines (ASMs), as of January 1998.Comment: Also maintained as a BibTeX file at http://www.eecs.umich.edu/gasm

Categorical Ontology of Complex Systems, Meta-Systems and Theory of Levels: The Emergence of Life, Human Consciousness and Society

Single cell interactomics in simpler organisms, as well as somatic cell interactomics in multicellular organisms, involve biomolecular interactions in complex signalling pathways that were recently represented in modular terms by quantum automata with ‘reversible behavior’ representing normal cell cycling and division. Other implications of such quantum automata, modular modeling of signaling pathways and cell differentiation during development are in the fields of neural plasticity and brain development leading to quantum-weave dynamic patterns and specific molecular processes underlying extensive memory, learning, anticipation mechanisms and the emergence of human consciousness during the early brain development in children. Cell interactomics is here represented for the first time as a mixture of ‘classical’ states that determine molecular dynamics subject to Boltzmann statistics and ‘steady-state’, metabolic (multi-stable) manifolds, together with ‘configuration’ spaces of metastable quantum states emerging from complex quantum dynamics of interacting networks of biomolecules, such as proteins and nucleic acids that are now collectively defined as quantum interactomics. On the other hand, the time dependent evolution over several generations of cancer cells --that are generally known to undergo frequent and extensive genetic mutations and, indeed, suffer genomic transformations at the chromosome level (such as extensive chromosomal aberrations found in many colon cancers)-- cannot be correctly represented in the ‘standard’ terms of quantum automaton modules, as the normal somatic cells can. This significant difference at the cancer cell genomic level is therefore reflected in major changes in cancer cell interactomics often from one cancer cell ‘cycle’ to the next, and thus it requires substantial changes in the modeling strategies, mathematical tools and experimental designs aimed at understanding cancer mechanisms. Novel solutions to this important problem in carcinogenesis are proposed and experimental validation procedures are suggested. From a medical research and clinical standpoint, this approach has important consequences for addressing and preventing the development of cancer resistance to medical therapy in ongoing clinical trials involving stage III cancer patients, as well as improving the designs of future clinical trials for cancer treatments.\ud \ud \ud KEYWORDS: Emergence of Life and Human Consciousness;\ud Proteomics; Artificial Intelligence; Complex Systems Dynamics; Quantum Automata models and Quantum Interactomics; quantum-weave dynamic patterns underlying human consciousness; specific molecular processes underlying extensive memory, learning, anticipation mechanisms and human consciousness; emergence of human consciousness during the early brain development in children; Cancer cell ‘cycling’; interacting networks of proteins and nucleic acids; genetic mutations and chromosomal aberrations in cancers, such as colon cancer; development of cancer resistance to therapy; ongoing clinical trials involving stage III cancer patients’ possible improvements of the designs for future clinical trials and cancer treatments. \ud \u

Impact of positivity and complete positivity on accessibility of Markovian dynamics

We consider a two-dimensional quantum control system evolving under an entropy-increasing irreversible dynamics in the semigroup form. Considering a phenomenological approach to the dynamics, we show that the accessibility property of the system depends on whether its evolution is assumed to be positive or completely positive. In particular, we characterize the family of maps having different accessibility and show the impact of that property on observable quantities by means of a simple physical model.Comment: 11 pages, to appear in J. Phys.

The algebraic structure of geometric flows in two dimensions

There is a common description of different intrinsic geometric flows in two dimensions using Toda field equations associated to continual Lie algebras that incorporate the deformation variable t into their system. The Ricci flow admits zero curvature formulation in terms of an infinite dimensional algebra with Cartan operator d/dt. Likewise, the Calabi flow arises as Toda field equation associated to a supercontinual algebra with odd Cartan operator d/d \theta - \theta d/dt. Thus, taking the square root of the Cartan operator allows to connect the two distinct classes of geometric deformations of second and fourth order, respectively. The algebra is also used to construct formal solutions of the Calabi flow in terms of free fields by Backlund transformations, as for the Ricci flow. Some applications of the present framework to the general class of Robinson-Trautman metrics that describe spherical gravitational radiation in vacuum in four space-time dimensions are also discussed. Further iteration of the algorithm allows to construct an infinite hierarchy of higher order geometric flows, which are integrable in two dimensions and they admit immediate generalization to Kahler manifolds in all dimensions. These flows provide examples of more general deformations introduced by Calabi that preserve the Kahler class and minimize the quadratic curvature functional for extremal metrics.Comment: 54 page

The Genetic Code as a Periodic Table: Algebraic Aspects

The systematics of indices of physico-chemical properties of codons and amino acids across the genetic code are examined. Using a simple numerical labelling scheme for nucleic acid bases, data can be fitted as low-order polynomials of the 6 coordinates in the 64-dimensional codon weight space. The work confirms and extends recent studies by Siemion of amino acid conformational parameters. The connections between the present work, and recent studies of the genetic code structure using dynamical symmetry algebras, are pointed out.Comment: 26 pages Latex, 10 figures (4 ps, 6 Tex). Refereed version, small changes to discussion (conclusion unaltered). Minor alterations to format of figures and tables. To appear in BioSystem

A Combinatorial Bit Bang Leading to Quaternions

This paper describes in detail how (discrete) quaternions - ie. the abstract structure of 3-D space - emerge from, first, the Void, and thence from primitive combinatorial structures, using only the exclusion and co-occurrence of otherwise unspecified events. We show how this computational view supplements and provides an interpretation for the mathematical structures, and derive quark structure. The build-up is emergently hierarchical, compatible with both quantum mechanics and relativity, and can be extended upwards to the macroscopic. The mathematics is that of Clifford algebras emplaced in the homology-cohomology structure pioneered by Kron. Interestingly, the ideas presented here were originally developed by the author to resolve fundamental limitations of existing AI paradigms. As such, the approach can be used for learning, planning, vision, NLP, pattern recognition; and as well, for modelling, simulation, and implementation of complex systems, eg. biological.Comment: 23 pages, 4 figure