11,209 research outputs found
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)
Simulating Membrane Systems in Digital Computers
* Work partially supported by contribution of EU commission Under The Fifth Framework Programme, project “MolCoNet” IST-2001-32008.Membrane Computing started with the analogy between some processes produced inside the
complex structure of living cells and computational processes. In the same way that in other branches of Natural
Computing, the model is extracted from nature but it is not clear whether or not the model must come back to
nature to be implemented. As in other cases in Natural Computing: Artificial Neural Networks, Genetic Algorithms,
etc; the models have been implemented in digital computers. Hence, some papers have been published
considering implementation of Membrane Computing in digital computers. This paper introduces an overview in
the field of simulation in Membrane Computing
The Mode of Computing
The Turing Machine is the paradigmatic case of computing machines, but there
are others, such as Artificial Neural Networks, Table Computing,
Relational-Indeterminate Computing and diverse forms of analogical computing,
each of which based on a particular underlying intuition of the phenomenon of
computing. This variety can be captured in terms of system levels,
re-interpreting and generalizing Newell's hierarchy, which includes the
knowledge level at the top and the symbol level immediately below it. In this
re-interpretation the knowledge level consists of human knowledge and the
symbol level is generalized into a new level that here is called The Mode of
Computing. Natural computing performed by the brains of humans and non-human
animals with a developed enough neural system should be understood in terms of
a hierarchy of system levels too. By analogy from standard computing machinery
there must be a system level above the neural circuitry levels and directly
below the knowledge level that is named here The mode of Natural Computing. A
central question for Cognition is the characterization of this mode. The Mode
of Computing provides a novel perspective on the phenomena of computing,
interpreting, the representational and non-representational views of cognition,
and consciousness.Comment: 35 pages, 8 figure
Open problems in artificial life
This article lists fourteen open problems in artificial life, each of which is a grand challenge requiring a major advance on a fundamental issue for its solution. Each problem is briefly explained, and, where deemed helpful, some promising paths to its solution are indicated
Towards Understanding the Origin of Genetic Languages
Molecular biology is a nanotechnology that works--it has worked for billions
of years and in an amazing variety of circumstances. At its core is a system
for acquiring, processing and communicating information that is universal, from
viruses and bacteria to human beings. Advances in genetics and experience in
designing computers have taken us to a stage where we can understand the
optimisation principles at the root of this system, from the availability of
basic building blocks to the execution of tasks. The languages of DNA and
proteins are argued to be the optimal solutions to the information processing
tasks they carry out. The analysis also suggests simpler predecessors to these
languages, and provides fascinating clues about their origin. Obviously, a
comprehensive unraveling of the puzzle of life would have a lot to say about
what we may design or convert ourselves into.Comment: (v1) 33 pages, contributed chapter to "Quantum Aspects of Life",
edited by D. Abbott, P. Davies and A. Pati, (v2) published version with some
editin
Design of testbed and emulation tools
The research summarized was concerned with the design of testbed and emulation tools suitable to assist in projecting, with reasonable accuracy, the expected performance of highly concurrent computing systems on large, complete applications. Such testbed and emulation tools are intended for the eventual use of those exploring new concurrent system architectures and organizations, either as users or as designers of such systems. While a range of alternatives was considered, a software based set of hierarchical tools was chosen to provide maximum flexibility, to ease in moving to new computers as technology improves and to take advantage of the inherent reliability and availability of commercially available computing systems
Simulation of networks of spiking neurons: A review of tools and strategies
We review different aspects of the simulation of spiking neural networks. We
start by reviewing the different types of simulation strategies and algorithms
that are currently implemented. We next review the precision of those
simulation strategies, in particular in cases where plasticity depends on the
exact timing of the spikes. We overview different simulators and simulation
environments presently available (restricted to those freely available, open
source and documented). For each simulation tool, its advantages and pitfalls
are reviewed, with an aim to allow the reader to identify which simulator is
appropriate for a given task. Finally, we provide a series of benchmark
simulations of different types of networks of spiking neurons, including
Hodgkin-Huxley type, integrate-and-fire models, interacting with current-based
or conductance-based synapses, using clock-driven or event-driven integration
strategies. The same set of models are implemented on the different simulators,
and the codes are made available. The ultimate goal of this review is to
provide a resource to facilitate identifying the appropriate integration
strategy and simulation tool to use for a given modeling problem related to
spiking neural networks.Comment: 49 pages, 24 figures, 1 table; review article, Journal of
Computational Neuroscience, in press (2007
Toward bio-inspired information processing with networks of nano-scale switching elements
Unconventional computing explores multi-scale platforms connecting
molecular-scale devices into networks for the development of scalable
neuromorphic architectures, often based on new materials and components with
new functionalities. We review some work investigating the functionalities of
locally connected networks of different types of switching elements as
computational substrates. In particular, we discuss reservoir computing with
networks of nonlinear nanoscale components. In usual neuromorphic paradigms,
the network synaptic weights are adjusted as a result of a training/learning
process. In reservoir computing, the non-linear network acts as a dynamical
system mixing and spreading the input signals over a large state space, and
only a readout layer is trained. We illustrate the most important concepts with
a few examples, featuring memristor networks with time-dependent and history
dependent resistances
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