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

Introduction to Iltis: An Interactive, Web-Based System for Teaching Logic

Logic is a foundation for many modern areas of computer science. In artificial intelligence, as a basis of database query languages, as well as in formal software and hardware verification --- modelling scenarios using logical formalisms and inferring new knowledge are important skills for going-to-be computer scientists. The Iltis project aims at providing a web-based, interactive system that supports teaching logical methods. In particular the system shall (a) support to learn to model knowledge and to infer new knowledge using propositional logic, modal logic and first-order logic, and (b) provide immediate feedback and support to students. This article presents a prototypical system that currently supports the above tasks for propositional logic. First impressions on its use in a second year logic course for computer science students are reported

Applying Formal Methods to Networking: Theory, Techniques and Applications

Despite its great importance, modern network infrastructure is remarkable for the lack of rigor in its engineering. The Internet which began as a research experiment was never designed to handle the users and applications it hosts today. The lack of formalization of the Internet architecture meant limited abstractions and modularity, especially for the control and management planes, thus requiring for every new need a new protocol built from scratch. This led to an unwieldy ossified Internet architecture resistant to any attempts at formal verification, and an Internet culture where expediency and pragmatism are favored over formal correctness. Fortunately, recent work in the space of clean slate Internet design---especially, the software defined networking (SDN) paradigm---offers the Internet community another chance to develop the right kind of architecture and abstractions. This has also led to a great resurgence in interest of applying formal methods to specification, verification, and synthesis of networking protocols and applications. In this paper, we present a self-contained tutorial of the formidable amount of work that has been done in formal methods, and present a survey of its applications to networking.Comment: 30 pages, submitted to IEEE Communications Surveys and Tutorial

Modeling and Verification of Agent based Adaptive Traffic Signal using Symbolic Model Verifier

This paper addresses the issue of modeling and verification of a Multi Agent System (MAS) scenario. We have considered an agent based adaptive traffic signal system. The system monitors the smooth flow of traffic at intersection of two road segment. After describing how the adaptive traffic signal system can efficiently be used and showing its advantages over traffic signals with predetermined periods, we have shown how we can transform this scenario into Finite State Machine (FSM). Once the system is transformed into a FSM, we have verified the specifications specified in Computational Tree Logic(CTL) using NuSMV as a model checking tool. Simulation results obtained from NuSMV showed us whether the system satisfied the specifications or not. It has also showed us the state where the system specification does not hold. Using which we traced back our system to find the source, leading to the specification violation. Finally, we again verified the modified system with NuSMV for its specifications.Comment: 13 pages, 6 figures, Submitted to International Journal of Computer Application (IJCA

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

Two Decades of Maude

This paper is a tribute to José Meseguer, from the rest of us in the Maude team, reviewing the past, the present, and the future of the language and system with which we have been working for around two decades under his leadership. After reviewing the origins and the language's main features, we present the latest additions to the language and some features currently under development. This paper is not an introduction to Maude, and some familiarity with it and with rewriting logic are indeed assumed.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Towards Intelligent Databases

This article is a presentation of the objectives and techniques of deductive databases. The deductive approach to databases aims at extending with intensional definitions other database paradigms that describe applications extensionaUy. We first show how constructive specifications can be expressed with deduction rules, and how normative conditions can be defined using integrity constraints. We outline the principles of bottom-up and top-down query answering procedures and present the techniques used for integrity checking. We then argue that it is often desirable to manage with a database system not only database applications, but also specifications of system components. We present such meta-level specifications and discuss their advantages over conventional approaches

Quantitative Verification: Formal Guarantees for Timeliness, Reliability and Performance

Computerised systems appear in almost all aspects of our daily lives, often in safety-critical scenarios such as embedded control systems in cars and aircraft or medical devices such as pacemakers and sensors. We are thus increasingly reliant on these systems working correctly, despite often operating in unpredictable or unreliable environments. Designers of such devices need ways to guarantee that they will operate in a reliable and efficient manner. Quantitative verification is a technique for analysing quantitative aspects of a system's design, such as timeliness, reliability or performance. It applies formal methods, based on a rigorous analysis of a mathematical model of the system, to automatically prove certain precisely specified properties, e.g. ``the airbag will always deploy within 20 milliseconds after a crash'' or ``the probability of both sensors failing simultaneously is less than 0.001''. The ability to formally guarantee quantitative properties of this kind is beneficial across a wide range of application domains. For example, in safety-critical systems, it may be essential to establish credible bounds on the probability with which certain failures or combinations of failures can occur. In embedded control systems, it is often important to comply with strict constraints on timing or resources. More generally, being able to derive guarantees on precisely specified levels of performance or efficiency is a valuable tool in the design of, for example, wireless networking protocols, robotic systems or power management algorithms, to name but a few. This report gives a short introduction to quantitative verification, focusing in particular on a widely used technique called model checking, and its generalisation to the analysis of quantitative aspects of a system such as timing, probabilistic behaviour or resource usage. The intended audience is industrial designers and developers of systems such as those highlighted above who could benefit from the application of quantitative verification,but lack expertise in formal verification or modelling