Axonal Computations

Axons functionally link the somato-dendritic compartment to synaptic terminals. Structurally and functionally diverse, they accomplish a central role in determining the delays and reliability with which neuronal ensembles communicate. By combining their active and passive biophysical properties, they ensure a plethora of physiological computations. In this review, we revisit the biophysics of generation and propagation of electrical signals in the axon and their dynamics. We further place the computational abilities of axons in the context of intracellular and intercellular coupling. We discuss how, by means of sophisticated biophysical mechanisms, axons expand the repertoire of axonal computation, and thereby, of neural computation

Quantum Genetics, Quantum Automata and Quantum Computation

The concepts of quantum automata and quantum computation are studied in the context of quantum genetics and genetic networks with nonlinear dynamics. In a previous publication (Baianu,1971a) the formal concept of quantum automaton was introduced and its possible implications for genetic and metabolic activities in living cells and organisms were considered. This was followed by a report on quantum and abstract, symbolic computation based on the theory of categories, functors and natural transformations (Baianu,1971b). The notions of topological semigroup, quantum automaton,or quantum computer, were then suggested with a view to their potential applications to the analogous simulation of biological systems, and especially genetic activities and nonlinear dynamics in genetic networks. Further, detailed studies of nonlinear dynamics in genetic networks were carried out in categories of n-valued, Lukasiewicz Logic Algebras that showed significant dissimilarities (Baianu, 1977) from Bolean models of human neural networks (McCullough and Pitts,1945). Molecular models in terms of categories, functors and natural transformations were then formulated for uni-molecular chemical transformations, multi-molecular chemical and biochemical transformations (Baianu, 1983,2004a). Previous applications of computer modeling, classical automata theory, and relational biology to molecular biology, oncogenesis and medicine were extensively reviewed and several important conclusions were reached regarding both the potential and limitations of the computation-assisted modeling of biological systems, and especially complex organisms such as Homo sapiens sapiens(Baianu,1987). Novel approaches to solving the realization problems of Relational Biology models in Complex System Biology are introduced in terms of natural transformations between functors of such molecular categories. Several applications of such natural transformations of functors were then presented to protein biosynthesis, embryogenesis and nuclear transplant experiments. Other possible realizations in Molecular Biology and Relational Biology of Organisms are here suggested in terms of quantum automata models of Quantum Genetics and Interactomics. Future developments of this novel approach are likely to also include: Fuzzy Relations in Biology and Epigenomics, Relational Biology modeling of Complex Immunological and Hormonal regulatory systems, n-categories and Topoi of Lukasiewicz Logic Algebras and Intuitionistic Logic (Heyting) Algebras for modeling nonlinear dynamics and cognitive processes in complex neural networks that are present in the human brain, as well as stochastic modeling of genetic networks in Lukasiewicz Logic Algebras

Computation vs. Information Processing: Why Their Difference Matters to Cognitive Science

Since the cognitive revolution, it’s become commonplace that cognition involves both computation and information processing. Is this one claim or two? Is computation the same as information processing? The two terms are often used interchangeably, but this usage masks important differences. In this paper, we distinguish information processing from computation and examine some of their mutual relations, shedding light on the role each can play in a theory of cognition. We recommend that theorists of cognition be explicit and careful in choosing\ud notions of computation and information and connecting them together. Much confusion can be avoided by doing so

Quantum Genetics and Quantum Automata Models of Quantum-Molecular Evolution Involved in the Evolution of Organisms and Species

Previous theoretical or general approaches to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 and further developed in several recent articles. The representation of genomes and Interactome networks in categories of many-valued logic LMn –algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata. Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an internal re-structuring of major submodules of the genome and Interactome networks related to cell cycling and cell growth. Contrary to the commonly held view of `standard’ Darwinist models of evolution, the evolution of organisms and species occurs through coupled multi-molecular transformations induced not only by the environment but actually realized through internal re-organizations of genome and interactome networks. The biological, evolutionary processes involve certain epigenetic transformations that are responsible for phenotypic expression of the genome and Interactome transformations initiated at the quantum-molecular level. It can thus be said that only quantum genetics can provide correct explanations of evolutionary processes that are initiated at the quantum--multi-molecular levels and propagate to the higher levels of organismal and species evolution.

Biological evolution should be therefore regarded as a multi-scale process which is initiated by underlying quantum (coupled) multi-molecular transformations of the genomic and interactomic networks, followed by specific phenotypic transformations at the level of organism and the variable biogroupoids associated with the evolution of species which are essential to the survival of the species. The theoretical framework introduced in this article also paves the way to a Quantitative Biology approach to biological evolution at the quantum-molecular, as well as at the organismal and species levels. This is quite a substantial modification of the 'established’ modern Darwinist, and also of several so-called `molecular evolution’ theories

TopologyNet: Topology based deep convolutional neural networks for biomolecular property predictions

Although deep learning approaches have had tremendous success in image, video and audio processing, computer vision, and speech recognition, their applications to three-dimensional (3D) biomolecular structural data sets have been hindered by the entangled geometric complexity and biological complexity. We introduce topology, i.e., element specific persistent homology (ESPH), to untangle geometric complexity and biological complexity. ESPH represents 3D complex geometry by one-dimensional (1D) topological invariants and retains crucial biological information via a multichannel image representation. It is able to reveal hidden structure-function relationships in biomolecules. We further integrate ESPH and convolutional neural networks to construct a multichannel topological neural network (TopologyNet) for the predictions of protein-ligand binding affinities and protein stability changes upon mutation. To overcome the limitations to deep learning arising from small and noisy training sets, we present a multitask topological convolutional neural network (MT-TCNN). We demonstrate that the present TopologyNet architectures outperform other state-of-the-art methods in the predictions of protein-ligand binding affinities, globular protein mutation impacts, and membrane protein mutation impacts.Comment: 20 pages, 8 figures, 5 table

Quantum Mechanics of 'Conscious Energy'

This paper is aiming to investigate the physical substrate of conscious process. It will attempt to find out: How does conscious process establish relations between their external stimuli and internal stimuli in order to create reality? How does consciousness devoid of new sensory input result to its new quantum effects? And how does conscious process gain mass in brain? This paper will also try to locate the origins of consciousness at the level of neurons along with the quantum effects of conscious process

Universal neural field computation

Turing machines and G\"odel numbers are important pillars of the theory of computation. Thus, any computational architecture needs to show how it could relate to Turing machines and how stable implementations of Turing computation are possible. In this chapter, we implement universal Turing computation in a neural field environment. To this end, we employ the canonical symbologram representation of a Turing machine obtained from a G\"odel encoding of its symbolic repertoire and generalized shifts. The resulting nonlinear dynamical automaton (NDA) is a piecewise affine-linear map acting on the unit square that is partitioned into rectangular domains. Instead of looking at point dynamics in phase space, we then consider functional dynamics of probability distributions functions (p.d.f.s) over phase space. This is generally described by a Frobenius-Perron integral transformation that can be regarded as a neural field equation over the unit square as feature space of a dynamic field theory (DFT). Solving the Frobenius-Perron equation yields that uniform p.d.f.s with rectangular support are mapped onto uniform p.d.f.s with rectangular support, again. We call the resulting representation \emph{dynamic field automaton}.Comment: 21 pages; 6 figures. arXiv admin note: text overlap with arXiv:1204.546