A Computational Investigation of Neural Dynamics and Network Structure

With the overall goal of illuminating the relationship between neural dynamics and neural network structure, this thesis presents a) a computer model of a network infrastructure capable of global broadcast and competition, and b) a study of various convergence properties of spike-timing dependent plasticity (STDP) in a recurrent neural network. The first part of the thesis explores the parameter space of a possible Global Neuronal Workspace (GNW) realised in a novel computational network model using stochastic connectivity. The structure of this model is analysed in light of the characteristic dynamics of a GNW: broadcast, reverberation, and competition. It is found even with careful consideration of the balance between excitation and inhibition, the structural choices do not allow agreement with the GNW dynamics, and the implications of this are addressed. An additional level of competition – access competition – is added, discussed, and found to be more conducive to winner-takes-all competition. The second part of the thesis investigates the formation of synaptic structure due to neural and synaptic dynamics. From previous theoretical and modelling work, it is predicted that homogeneous stimulation in a recurrent neural network with STDP will create a self-stabilising equilibrium amongst synaptic weights, while heterogeneous stimulation will induce structured synaptic changes. A new factor in modulating the synaptic weight equilibrium is suggested from the experimental evidence presented: anti-correlation due to inhibitory neurons. It is observed that the synaptic equilibrium creates competition amongst synapses, and those specifically stimulated during heterogeneous stimulation win out. Further investigation is carried out in order to assess the effect that more complex STDP rules would have on synaptic dynamics, varying parameters of a trace STDP model. There is little qualitative effect on synaptic dynamics under low frequency (< 25Hz) conditions, justifying the use of simple STDP until further experimental or theoretical evidence suggests otherwise

Flow alteration-ecology relationships in Ozark Highland streams: Consequences for fish, crayfish and macroinvertebrate assemblages

We examined flowalteration-ecology relationships in benthic macroinvertebrate, fish, and crayfish assemblages in Ozark Highland streams, USA, over two years with contrasting environmental conditions, a drought year (2012) and a flood year (2013). We hypothesized that: 1) there would be temporal variation in flow alteration-ecology relationships between the two years, 2) flow alteration-ecology relationshipswould be stronger during the drought year vs the flood year, and 3) fish assemblages would show the strongest relationships with flow alteration. We used a quantitative richest-targeted habitat (RTH) method and a qualitative multihabitat (QMH) method to collect macroinvertebrates at 16 USGS gaged sites during both years. We used backpack electrofishing to sample fish and crayfish at 17 sites in 2012 and 11 sites in 2013.Weused redundancy analysis to relate biological response metrics, including richness, diversity, density, and community-based metrics, to flow alteration.We found temporal variation in flow alteration-ecology relationships for all taxa, and that relationships differed greatly between assemblages. We found relationships were stronger for macroinvertebrates during the drought year but not for other assemblages, and that fish assemblage relationships were not stronger than the invertebrate taxa. Magnitude of average flow, frequency of high flow, magnitude of high flow, and duration of high flow were the most important categories of flow alteration metrics across taxa. Alteration of high and average flows was more important than alteration of low flows. Of 32 important flow alteration metrics across years and assemblages, 19 were significantly altered relative to expected values. Ecological responses differed substantially between drought and flood years, and this is likely to be exacerbated with predicted climate change scenarios. Differences in flow alteration-ecology relationships among taxonomic groups and temporal variation in relationships illustrate that a complex suite of variables should be considered for effective conservation of stream communities related to flow alteration

Multiscale Dynamics in Communities of Phase Oscillators

We investigate the dynamics of systems of many coupled phase oscillators with het- erogeneous frequencies. We suppose that the oscillators occur in M groups. Each oscillator is connected to other oscillators in its group with "attractive" coupling, such that the coupling promotes synchronization within the group. The coupling between oscillators in different groups is "repulsive"; i.e., their oscillation phases repel. To address this problem, we reduce the governing equations to a lower-dimensional form via the ansatz of Ott and Antonsen . We first consider the symmetric case where all group parameters are the same, and the attractive and repulsive coupling are also the same for each of the M groups. We find a manifold L of neutrally stable equilibria, and we show that all other equilibria are unstable. For M \geq 3, L has dimension M - 2, and for M = 2 it has dimension 1. To address the general asymmetric case, we then introduce small deviations from symmetry in the group and coupling param- eters. Doing a slow/fast timescale analysis, we obtain slow time evolution equations for the motion of the M groups on the manifold L. We use these equations to study the dynamics of the groups and compare the results with numerical simulations.Comment: 29 pages, 6 figure

Facilitate SIMD-Code-Generation in the Polyhedral Model by Hardware-aware Automatic Code-Transformation

Although Single Instruction Multiple Data (SIMD) units are available in general purpose processors already since the 1990s, state-of-the-art compilers are often still not capable to fully exploit them, i.e., they may miss to achieve the best possible performance. We present a new hardware-aware and adaptive loop tiling approach that is based on polyhedral transformations and explicitly dedicated to improve on auto-vectorization. It is an extension to the tiling algorithm implemented within the PluTo framework. In its default setting, PluTo uses static tile sizes and is already capable to enable the use of SIMD units but not primarily targeted to optimize it. We experimented with different tile sizes and found a strong relationship between their choice, cache size parameters and performance. Based on this, we designed an adaptive procedure that specifically tiles vectorizable loops with dynamically calculated sizes. The blocking is automatically fitted to the amount of data read in loop iterations, the available SIMD units and the cache sizes. The adaptive parts are built upon straightforward calculations that are experimentally verified and evaluated. Our results show significant improvements in the number of instructions vectorized, cache miss rates and, finally, running times

Growth-Induced In-Plane Uniaxial Anisotropy in V2_{2}O3_{3}/Ni Films

We report on a strain-induced and temperature dependent uniaxial anisotropy in V$_{2}$O$_{3}$/Ni hybrid thin films, manifested through the interfacial strain and sample microstructure, and its consequences on the angular dependent magnetization reversal. X-ray diffraction and reciprocal space maps identify the in-plane crystalline axes of the V$_{2}$O$_{3}$; atomic force and scanning electron microscopy reveal oriented rips in the film microstructure. Quasi-static magnetometry and dynamic ferromagnetic resonance measurements identify a uniaxial magnetic easy axis along the rips. Comparison with films grown on sapphire without rips shows a combined contribution from strain and microstructure in the V$_{2}$O$_{3}$/Ni films. Magnetization reversal characteristics captured by angular-dependent first order reversal curve measurements indicate a strong domain wall pinning along the direction orthogonal to the rips, inducing an angular-dependent change in the reversal mechanism. The resultant anisotropy is tunable with temperature and is most pronounced at room temperature, which is beneficial for potential device applications

Binding cooperativity of membrane adhesion receptors

The adhesion of cells is mediated by receptors and ligands anchored in apposing membranes. A central question is how to characterize the binding affinity of these membrane-anchored molecules. For soluble molecules, the binding affinity is typically quantified by the binding equilibrium constant K3D in the linear relation [RL] = K3D [R][L] between the volume concentration [RL] of bound complexes and the volume concentrations [R] and [L] of unbound molecules. For membrane-anchored molecules, it is often assumed by analogy that the area concentration of bound complexes [RL] is proportional to the product [R][L] of the area concentrations for the unbound receptor and ligand molecules. We show here (i) that this analogy is only valid for two planar membranes immobilized on rigid surfaces, and (ii) that the thermal roughness of flexible membranes leads to cooperative binding of receptors and ligands. In the case of flexible membranes, the area concentration [RL] of receptor-ligand bonds is proportional to the square of [R][L] for typical lengths and concentrations of receptors and ligands in cell adhesion zones. The cooperative binding helps to understand why different experimental methods for measuring the binding affinity of membrane-anchored molecules have led to values differing by several orders of magnitude.Comment: 9 pages, 4 figures; to appear in Soft Matte