Random graph theory and neuropercolation for modeling brain oscillations at criticality.

Mathematical approaches are reviewed to interpret intermittent singular space-time dynamics observed in brain imaging experiments. The following aspects of brain dynamics are considered: nonlinear dynamics (chaos), phase transitions, and criticality. Probabilistic cellular automata and random graph models are described, which develop equations for the probability distributions of macroscopic state variables as an alternative to differential equations.

Hierarchical random cellular neural networks for system-level brain-like signal processing.

Sensory information processing and cognition in brains are modeled using dynamic systems theory. The brain's dynamic state is described by a trajectory evolving in a high-dimensional state space. We introduce a hierarchy of random cellular automata as the mathematical tools to describe the spatio-temporal dynamics of the cortex.

Genome-wide survey for PilR recognition sites of the metal-reducing prokaryote Geobacter sulfurreducens.

Geobacter sulfurreducens is a species from the bacterial family Geobacteraceae, members of which participate in bioenergy production and in environmental bioremediation. G. sulfurreducens pili are electrically conductive and are required for Fe(III) oxide reduction and for optimal current production in microbial fuel cells.

GSEL version 2, an online genome-wide query system of operon organization and regulatory sequence elements of Geobacter sulfurreducens.

Geobacter sulfurreducens is a model organism within the delta-Proteobacterial family Geobacteraceae, members of which can participate in environmental bioremediation of metal and organic waste contaminants and in production of bioenergy. In this report, we describe a new, significantly expanded and updated, version 2 of the GSEL (Geobacter Sequence Elements) database ( http://geobacter.org/research/gsel2/ and http://geobacter.

Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens.

Background: The role of the RNA polymerase sigma factor RpoN in regulation of gene expression in Geobacter sulfurreducens was investigated to better understand transcriptional regulatory networks as part of an effort to develop regulatory modules for genome-scale in silico models, which can predict the physiological responses of Geobacter species during groundwater bioremediation or electricity production.

Results: An rpoN deletion mutant could not be obtained under all conditions tested. In order to investigate the regulon of the G.

Narrow-band oscillations in probabilistic cellular automata.

Dynamical properties of neural populations are studied using probabilistic cellular automata. Previous work demonstrated the emergence of critical behavior as the function of system noise and density of long-range axonal connections. Finite-size scaling theory identified critical properties, which were consistent with properties of a weak Ising universality class.

Diversity of promoter elements in a Geobacter sulfurreducens mutant adapted to disruption in electron transfer.

The delta-proteobacterium, Geobacter sulfurreducens, can obtain energy by coupling the oxidation of organic matter to the reduction of insoluble Fe(III) or the anode of a microbial fuel cell. Because Fe(III) oxide or the anode surface, in contrast to oxygen, nitrate, or sulfate, is not soluble nor can it be reduced readily, Geobacter species have developed mechanisms which allow electrons to be delivered across outer membrane to the cell surface. OmcB is an outer-membrane c-type cytochrome important for G.

Genome-wide expression profiling in Geobacter sulfurreducens: identification of Fur and RpoS transcription regulatory sites in a relGsu mutant.

Rel(Gsu) is the single Geobacter sulfurreducens homolog of RelA and SpoT proteins found in many organisms. These proteins are involved in the regulation of levels of guanosine 3', 5' bispyrophosphate, ppGpp, a molecule that signals slow growth and stress response under nutrient limitation in bacteria. We used information obtained from genome-wide expression profiling of the rel(Gsu) deletion mutant to identify putative regulatory sites involved in transcription networks modulated by Rel(Gsu) or ppGpp.

Computational prediction of RpoS and RpoD regulatory sites in Geobacter sulfurreducens using sequence and gene expression information.

RpoS, the sigma S subunit of RNA polymerase, is vital during the growth and survival of Geobacter sulfurreducens under conditions typically encountered in its native subsurface environments. We investigated the conservation of sites that may be important for RpoS function in G. sulfurreducens.

Phase transitions in the neuropercolation model of neural populations with mixed local and non-local interactions.

We model the dynamical behavior of the neuropil, the densely interconnected neural tissue in the cortex, using neuropercolation approach. Neuropercolation generalizes phase transitions modeled by percolation theory of random graphs, motivated by properties of neurons and neural populations. The generalization includes (1) a noisy component in the percolation rule, (2) a novel depression function in addition to the usual arousal function, (3) non-local interactions among nodes arranged on a multi-dimensional lattice.