Coordinated optimization of visual cortical maps (II) Numerical studies

It is an attractive hypothesis that the spatial structure of visual cortical architecture can be explained by the coordinated optimization of multiple visual cortical maps representing orientation preference (OP), ocular dominance (OD), spatial frequency, or direction preference. In part (I) of this study we defined a class of analytically tractable coordinated optimization models and solved representative examples in which a spatially complex organization of the orientation preference map is induced by inter-map interactions. We found that attractor solutions near symmetry breaking threshold predict a highly ordered map layout and require a substantial OD bias for OP pinwheel stabilization. Here we examine in numerical simulations whether such models exhibit biologically more realistic spatially irregular solutions at a finite distance from threshold and when transients towards attractor states are considered. We also examine whether model behavior qualitatively changes when the spatial periodicities of the two maps are detuned and when considering more than 2 feature dimensions. Our numerical results support the view that neither minimal energy states nor intermediate transient states of our coordinated optimization models successfully explain the spatially irregular architecture of the visual cortex. We discuss several alternative scenarios and additional factors that may improve the agreement between model solutions and biological observations.Comment: 55 pages, 11 figures. arXiv admin note: substantial text overlap with arXiv:1102.335

Coordinated optimization of visual cortical maps : 2. Numerical studies

In the juvenile brain, the synaptic architecture of the visual cortex remains in a state of flux for months after the natural onset of vision and the initial emergence of feature selectivity in visual cortical neurons. It is an attractive hypothesis that visual cortical architecture is shaped during this extended period of juvenile plasticity by the coordinated optimization of multiple visual cortical maps such as orientation preference (OP), ocular dominance (OD), spatial frequency, or direction preference. In part (I) of this study we introduced a class of analytically tractable coordinated optimization models and solved representative examples, in which a spatially complex organization of the OP map is induced by interactions between the maps. We found that these solutions near symmetry breaking threshold predict a highly ordered map layout. Here we examine the time course of the convergence towards attractor states and optima of these models. In particular, we determine the timescales on which map optimization takes place and how these timescales can be compared to those of visual cortical development and plasticity. We also assess whether our models exhibit biologically more realistic, spatially irregular solutions at a finite distance from threshold, when the spatial periodicities of the two maps are detuned and when considering more than 2 feature dimensions. We show that, although maps typically undergo substantial rearrangement, no other solutions than pinwheel crystals and stripes dominate in the emerging layouts. Pinwheel crystallization takes place on a rather short timescale and can also occur for detuned wavelengths of different maps. Our numerical results thus support the view that neither minimal energy states nor intermediate transient states of our coordinated optimization models successfully explain the architecture of the visual cortex. We discuss several alternative scenarios that may improve the agreement between model solutions and biological observations

Elastic properties of proteins: insight on the folding process and evolutionary selection of native structures

We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full characterization of the spectrum and eigenmodes of vibration at various temperatures by merely exploiting the knowledge of the protein native structure. It is shown that the rate at which perturbations decay at the folding transition correlates well with experimental folding rates. This validation is carried out on a list of about 30 two-state folders. Furthermore, the qualitative analysis of residues mean square displacements (shown to accurately reproduce crystallographic data) provides a reliable and statistically accurate method to identify crucial folding sites/contacts. This novel strategy is validated against clinical data for HIV-1 Protease. Finally, we compare the spectra and eigenmodes of vibration of natural proteins against randomly-generated compact structures and regular random graphs. The comparison reveals a distinctive enhanced flexibility of natural structures accompanied by slow relaxation times at the folding temperature. The fact that these properties are intimately connected to the presence and assembly of secondary motifs hints at the special criteria adopted by evolution in the selection of viable folds.Comment: Revtex 17 pages, 13 eps figure

Biologically inspired distributed machine cognition: a new formal approach to hyperparallel computation

The irresistable march toward multiple-core chip technology presents currently intractable pdrogramming challenges. High level mental processes in many animals, and their analogs for social structures, appear similarly massively parallel, and recent mathematical models addressing them may be adaptable to the multi-core programming problem

The fuzzy boundary: the spatial definition of urban areas

Cities seem to have some kind of area structure, usually distinguished in terms of land use types, socio-economic variables, physical appearance or historical and culturalcharacteristics. Is there any possibility that urban areas could in general be differentiated from the spatial perspective? What is the nature of boundaries between areas in terms of space? These questions could be approached by the analysis of internal or contextual spatial structure, or the relation between the two. Most studies on area structure however had focused in the main on the internal area with a secondaryrole for the context. Is there any way in which we could give more explicit attention to the context, following the clue that had come out of the earlier studies?This paper is to try to develop spatial techniques for identifying area boundaries, and looking at their performance in both the traditional areas, such as the Central London and the Inner City of Beijing, and the new development of the London Docklands. It focuses on explicitly exploring the properties of contextual structure in the formation ofarea boundaries rather than simply the properties of internal structure. After much experimentation, a new technique was arrived at for exploring properties of the context. Each axial line or segment in the whole map is taken as the root of a graph, and the numbers of axial lines, or segments, found with increasing radius from the root is calculated, and expressed as a rate of change. This rate of change value is thenassigned to the original axial line and expressed through bands of color. The results show strong areal effects, in that groups of neighbouring lines tend to have similar coloring, and in many cases, these suggest natural areas.Through the case studies, this paper suggests that historic areas typically have what we will call fuzzy boundaries. Fuzzy boundaries arise from the way space is structured internally and how this relates to the external structure of space. Such boundaries can be effective in supporting functional differentiation of areas or the growth of areal identities and characters, but do not depend on the area being either spatially self contained or geometrically differentiated, or having clear spatial limits. It is the relation of urban areas and their further surroundings that determine fuzzy boundaries of these urban areas

A Survey on the Contributions of Software-Defined Networking to Traffic Engineering

Since the appearance of OpenFlow back in 2008, software-defined networking (SDN) has gained momentum. Although there are some discrepancies between the standards developing organizations working with SDN about what SDN is and how it is defined, they all outline traffic engineering (TE) as a key application. One of the most common objectives of TE is the congestion minimization, where techniques such as traffic splitting among multiple paths or advanced reservation systems are used. In such a scenario, this manuscript surveys the role of a comprehensive list of SDN protocols in TE solutions, in order to assess how these protocols can benefit TE. The SDN protocols have been categorized using the SDN architecture proposed by the open networking foundation, which differentiates among data-controller plane interfaces, application-controller plane interfaces, and management interfaces, in order to state how the interface type in which they operate influences TE. In addition, the impact of the SDN protocols on TE has been evaluated by comparing them with the path computation element (PCE)-based architecture. The PCE-based architecture has been selected to measure the impact of SDN on TE because it is the most novel TE architecture until the date, and because it already defines a set of metrics to measure the performance of TE solutions. We conclude that using the three types of interfaces simultaneously will result in more powerful and enhanced TE solutions, since they benefit TE in complementary ways.European Commission through the Horizon 2020 Research and Innovation Programme (GN4) under Grant 691567 Spanish Ministry of Economy and Competitiveness under the Secure Deployment of Services Over SDN and NFV-based Networks Project S&NSEC under Grant TEC2013-47960-C4-3-