COMPUTER SIMULATION AND COMPUTABILITY OF BIOLOGICAL SYSTEMS

The ability to simulate a biological organism by employing a computer is related to the ability of the computer to calculate the behavior of such a dynamical system, or the "computability" of the system.* However, the two questions of computability and simulation are not equivalent. Since the question of computability can be given a precise answer in terms of recursive functions, automata theory and dynamical systems, it will be appropriate to consider it first. The more elusive question of adequate simulation of biological systems by a computer will be then addressed and a possible connection between the two answers given will be considered. A conjecture is formulated that suggests the possibility of employing an algebraic-topological, "quantum" computer (Baianu, 1971b) for analogous and symbolic simulations of biological systems that may include chaotic processes that are not, in genral, either recursively or digitally computable. Depending on the biological network being modelled, such as the Human Genome/Cell Interactome or a trillion-cell Cognitive Neural Network system, the appropriate logical structure for such simulations might be either the Quantum MV-Logic (QMV) discussed in recent publications (Chiara, 2004, and references cited therein)or Lukasiewicz Logic Algebras that were shown to be isomorphic to MV-logic algebras (Georgescu et al, 2001)

Minimally Constrained Stable Switched Systems and Application to Co-simulation

We propose an algorithm to restrict the switching signals of a constrained switched system in order to guarantee its stability, while at the same time attempting to keep the largest possible set of allowed switching signals. Our work is motivated by applications to (co-)simulation, where numerical stability is a hard constraint, but should be attained by restricting as little as possible the allowed behaviours of the simulators. We apply our results to certify the stability of an adaptive co-simulation orchestration algorithm, which selects the optimal switching signal at run-time, as a function of (varying) performance and accuracy requirements.Comment: Technical report complementing the following conference publication: Gomes, Cl\'audio, Beno\^it Legat, Rapha\"el Jungers, and Hans Vangheluwe. "Minimally Constrained Stable Switched Systems and Application to Co-Simulation." In IEEE Conference on Decision and Control. Miami Beach, FL, USA, 201

Nonlinear Models of Neural and Genetic Network Dynamics:\ud \ud Natural Transformations of Łukasiewicz Logic LM-Algebras in a Łukasiewicz-Topos as Representations of Neural Network Development and Neoplastic Transformations \ud

A categorical and Łukasiewicz-Topos framework for Algebraic Logic models of nonlinear dynamics in complex functional systems such as Neural Networks, Cell Genome and Interactome Networks is introduced. Łukasiewicz Algebraic Logic models of both neural and genetic networks and signaling pathways in cells are formulated in terms of nonlinear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks. An algebraic formulation of variable next-state/transfer functions is extended to a Łukasiewicz Topos with an N-valued Łukasiewicz Algebraic Logic subobject classifier description that represents non-random and nonlinear network activities as well as their transformations in developmental processes and carcinogenesis.\u

Human-Robot Trust Integrated Task Allocation and Symbolic Motion planning for Heterogeneous Multi-robot Systems

This paper presents a human-robot trust integrated task allocation and motion planning framework for multi-robot systems (MRS) in performing a set of tasks concurrently. A set of task specifications in parallel are conjuncted with MRS to synthesize a task allocation automaton. Each transition of the task allocation automaton is associated with the total trust value of human in corresponding robots. Here, the human-robot trust model is constructed with a dynamic Bayesian network (DBN) by considering individual robot performance, safety coefficient, human cognitive workload and overall evaluation of task allocation. Hence, a task allocation path with maximum encoded human-robot trust can be searched based on the current trust value of each robot in the task allocation automaton. Symbolic motion planning (SMP) is implemented for each robot after they obtain the sequence of actions. The task allocation path can be intermittently updated with this DBN based trust model. The overall strategy is demonstrated by a simulation with 5 robots and 3 parallel subtask automata

Łukasiewicz-Topos Models of Neural Networks, Cell Genome and Interactome Nonlinear Dynamic Models

A categorical and Łukasiewicz-Topos framework for Algebraic Logic models of nonlinear dynamics in complex functional systems such as Neural Networks, Cell Genome and Interactome Networks is introduced. Łukasiewicz Algebraic Logic models of both neural and genetic networks and signaling pathways in cells are formulated in terms of nonlinear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks. An algebraic formulation of variable 'next-state functions' is extended to a Łukasiewicz Topos with an n-valued Łukasiewicz Algebraic Logic subobject classifier description that represents non-random and nonlinear network activities as well as their transformations in developmental processes and carcinogenesis

Neural Networks, Cell Genome and Interactome Nonlinear Dynamic Models

Operational logic and bioinformatics models of nonlinear dynamics in complex functional systems such as neural networks, genomes and cell interactomes are proposed. Łukasiewicz Algebraic Logic models of genetic networks and signaling pathways in cells are formulated in terms of nonlinear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks. An algebraic formulation of variable 'next-state functions' is extended to a Łukasiewicz Topos with an n-valued Łukasiewicz Algebraic Logic subobject classifier description that represents non-random and nonlinear network activities as well as their transformations in developmental processes and carcinogenesis