Functional, clustered, feedforward, and mesoscale brain networks

The brain is a network spanning multiple scales from subcellular to macroscopic. In this thesis I present four projects studying brain networks at different levels of abstraction. The first involves determining a functional connectivity network based on neural spike trains and using a graph theoretical method to cluster groups of neurons into putative cell assemblies. In the second project I model neural networks at a microscopic level. Using diferent clustered wiring schemes, I show that almost identical spatiotemporal activity patterns can be observed, demonstrating that there is a broad neuro-architectural basis to attain structured spatiotemporal dynamics. Remarkably, irrespective of the precise topological mechanism, this behavior can be predicted by examining the spectral properties of the synaptic weight matrix. The third project introduces, via two circuit architectures, a new paradigm for feedforward processing in which inhibitory neurons have the complex and pivotal role in governing information flow in cortical network models. Finally, I analyze axonal projections in sleep deprived mice using data collected as part of the Allen Institute's Mesoscopic Connectivity Atlas. After normalizing for experimental variability, the results indicate there is no single explanatory difference in the mesoscale network between control and sleep deprived mice. Using machine learning techniques, however, animal classification could be done at levels significantly above chance. This reveals that intricate changes in connectivity do occur due to chronic sleep deprivation.

Design and Applications of a Decade-Spanning Terahertz Frequency Comb Spectrometer: Doppler-limited Rotational Spectroscopy of Methanol and Methanol-OD

This thesis details the design and applications of a terahertz (THz) frequency comb spectrometer. The spectrometer employs two offset locked Ti:Sapphire femtosecond oscillators with repetition rates of approximately 80 MHz, offset locked at 100 Hz to continuously sample a time delay of 12.5 ns at a maximum time delay resolution of 15.6 fs. These oscillators emit continuous pulse trains, allowing the generation of a THz pulse train by the master, or pump, oscillator and the sampling of this THz pulse train by the slave, or probe, oscillator via the electro-optic effect. Collecting a train of 16 consecutive THz pulses and taking the Fourier transform of this pulse train produces a decade-spanning frequency comb, from 0.25 to 2.5 THz, with a comb tooth width of 5 MHz and a comb tooth spacing of ~80 MHz. This frequency comb is suitable for Doppler-limited rotational spectroscopy of small molecules. Here, the data from 68 individual scans at slightly different pump oscillator repetition rates were combined, producing an interleaved THz frequency comb spectrum, with a maximum interval between comb teeth of 1.4 MHz, enabling THz frequency comb spectroscopy.

The accuracy of the THz frequency comb spectrometer was tested, achieving a root mean square error of 92 kHz measuring selected absorption center frequencies of water vapor at 10 mTorr, and a root mean square error of 150 kHz in measurements of a K-stack of acetonitrile. This accuracy is sufficient for fitting of measured transitions to a model Hamiltonian to generate a predicted spectrum for molecules of interest in the fields of astronomy and physical chemistry. As such, the rotational spectra of methanol and methanol-OD were acquired by the spectrometer. Absorptions from 1.3 THz to 2.0 THz were compared to JPL catalog data for methanol and the spectrometer achieved an RMS error of 402 kHz, improving to 303 kHz when excluding low signal-to-noise absorptions. This level of accuracy compares favorably with the ~100 kHz accuracy achieved by JPL frequency multiplier submillimeter spectrometers. Additionally, the relative intensity performance of the THz frequency comb spectrometer is linear across the entire decade-spanning bandwidth, making it the preferred instrument for recovering lineshapes and taking absolute intensity measurements in the THz region. The data acquired by the Terahertz Frequency Comb Spectrometer for methanol-OD is of comparable accuracy to the methanol data and may be used to refine the fit parameters for the predicted spectrum of methanol-OD.