Neural representation of auditory temporal structure

Neurons in the songbird forebrain nucleus HVc are highly sensitive to auditory temporal context and have some of the most complex auditory tuning properties yet discovered. HVc is crucial for learning, perceiving, and producing song, thus it is important to understand the neural circuitry and mechanisms that give rise to these remarkable auditory response properties. This thesis investigates these issues experimentally and computationally.

Extracellular studies reported here compare the auditory context sensitivity of neurons in HV c with neurons in the afferent areas of field L. These demonstrate that there is a substantial increase in the auditory temporal context sensitivity from the areas of field L to HVc. Whole-cell recordings of HVc neurons from acute brain slices are described which show that excitatory synaptic transmission between HVc neurons involve the release of glutamate and the activation of both AMPA/kainate and NMDA-type glutamate receptors. Additionally, widespread inhibitory interactions exist between HVc neurons that are mediated by postsynaptic GABA_A receptors. Intracellular recordings of HVc auditory neurons in vivo provides evidence that HV c neurons encode information about temporal structure using a variety of cellular and synaptic mechanisms including syllable-specific inhibition, excitatory post-synaptic potentials with a range of different time courses, and burst-firing, and song-specific hyperpolarization.

The final part of this thesis presents two computational approaches for representing and learning temporal structure. The first method utilizes comput ational elements that are analogous to temporal combination sensitive neurons in HVc. A network of these elements can learn using local information and lateral inhibition. The second method presents a more general framework which allows a network to discover mixtures of temporal features in a continuous stream of input.

Analysis of temporal structure in spike trains of visual cortical area MT

The temporal structure of neuronal spike trains in the visual cortex can provide detailed information about the stimulus and about the neuronal implementation of visual processing. Spike trains recorded from the macaque motion area MT in previous studies (Newsome et al., 1989a; Britten et al., 1992; Zohary et al., 1994) are analyzed here in the context of the dynamic random dot stimulus which was used to evoke them. If the stimulus is incoherent, the spike trains can be highly modulated and precisely locked in time to the stimulus. In contrast, the coherent motion stimulus creates little or no temporal modulation and allows us to study patterns in the spike train that may be intrinsic to the cortical circuitry in area MT. Long gaps in the spike train evoked by the preferred direction motion stimulus are found, and they appear to be symmetrical to bursts in the response to the anti-preferred direction of motion. A novel cross-correlation technique is used to establish that the gaps are correlated between pairs of neurons. Temporal modulation is also found in psychophysical experiments using a modified stimulus. A model is made that can account for the temporal modulation in terms of the computational theory of biological image motion processing. A frequency domain analysis of the stimulus reveals that it contains a repeated power spectrum that may account for psychophysical and electrophysiological observations.

Some neurons tend to fire bursts of action potentials while others avoid burst firing. Using numerical and analytical models of spike trains as Poisson processes with the addition of refractory periods and bursting, we are able to account for peaks in the power spectrum near 40 Hz without assuming the existence of an underlying oscillatory signal. A preliminary examination of the local field potential reveals that stimulus-locked oscillation appears briefly at the beginning of the trial.

Identification of thermally-tagged coherent structures in the zero pressure gradient turbulent boundary layer

A zero pressure gradient boundary layer over a flat plate is subjected to step changes in thermal condition at the wall, causing the formation of internal, heated layers. The resulting temperature fluctuations and their corresponding density variations are associated with turbulent coherent structures. Aero-optical distortion occurs when light passes through the boundary layer, encountering the changing index of refraction resulting from the density variations. Instantaneous measurements of streamwise velocity, temperature and the optical deflection angle experienced by a laser traversing the boundary layer are made using hot and cold wires and a Malley probe, respectively. Correlations of the deflection angle with the temperature and velocity records suggest that the dominant contribution to the deflection angle comes from thermally-tagged structures in the outer boundary layer with a convective velocity of approximately 0.8U∞. An examination of instantaneous temperature and velocity and their temporal gradients conditionally averaged around significant optical deflections shows behavior consistent with the passage of a heated vortex. Strong deflections are associated with strong negative temperature gradients, and strong positive velocity gradients where the sign of the streamwise velocity fluctuation changes. The power density spectrum of the optical deflections reveals associated structure size to be on the order of the boundary layer thickness. A comparison to the temperature and velocity spectra suggests that the responsible structures are smaller vortices in the outer boundary layer as opposed to larger scale motions. Notable differences between the power density spectra of the optical deflections and the temperature remain unresolved due to the low frequency response of the cold wire.

Cooperative properties of lipid bilayers : collective director fluctuations and the effects of hydrophobic mismatch in protein/lipid membrane systems

Cooperative director fluctuations in lipid bilayers have been postulated for many years. ^2H-NMR T_1^(-1), T_(1P)^(-1) , and T_2^(-1); measurements have been used identify these motions and to determine the origin of increased slow bilayer motion upon addition of unlike lipids or proteins to a pure lipid bilayer.

The contribution of cooperative director fluctuations to NMR relaxation in lipid bilayers has been expressed mathematically using the approach of Doane et al.^1 and Pace and Chan.^2 The T_2^(-1)’s of pure dimyristoyllecithin (DML) bilayers deuterated at the 2, 9 and 10, and all positions on both lipid hydrocarbon chains have been measured. Several characteristics of these measurements indicate the presence of cooperative director fluctuations. First of all, T_2^(-1) exhibits a linear dependence on S2/CD. Secondly, T_2^(-1) varies across the ^2H-NMR powder pattern as sin^2 (2, β), where , β is the angle between the average bilayer director and the external magnetic field. Furthermore, these fluctuations are restricted near the lecithin head group suggesting that the head group does not participate in these motions but, rather, anchors the hydrocarbon chains in the bilayer.

T_2^(-1)has been measured for selectively deuterated liquid crystalline DML hilayers to which a host of other lipids and proteins have been added. The T_2^(-1) of the DML bilayer is found to increase drastically when chlorophyll a (chl a) and Gramicidin A' (GA') are added to the bilayer. Both these molecules interfere with the lecithin head group spacing in the bilayer. Molecules such as myristic acid, distearoyllecithin (DSL), phytol, and cholesterol, whose hydrocarbon regions are quite different from DML but which have small,neutral polar head groups, leave cooperative fluctuations in the DML bilayer unchanged.

The effect of chl a on cooperative fluctuations in the DML bilayer has been examined in detail using ^2H-NMR T_1^(-1), T_(1P)^(-1) , and T_2^(-1); measurements. Cooperative fluctuations have been modelled using the continuum theory of the nematic state of liquid crystals. Chl a is found to decrease both the correlation length and the elastic constants in the DML bilayer.

A mismatch between the hydrophobic length of a lipid bilayer and that of an added protein has also been found to change the cooperative properties of the lecithin bilayer. Hydrophobic mismatch has been studied in a series GA' / lecithin bilayers. The dependence of 2H-NMR order parameters and relaxation rates on GA' concentration has been measured in selectively deuterated DML, dipalmitoyllecithin (DPL), and DSL systems. Order parameters, cooperative lengths, and elastic constants of the DML bilayer are most disrupted by GA', while the DSL bilayer is the least perturbed by GA'. Thus, it is concluded that the hydrophobic length of GA' best matches that of the DSL bilayer. Preliminary Raman spectroscopy and Differential Scanning Calorimetry experiments of GA' /lecithin systems support this conclusion. Accommodation of hydrophobic mismatch is used to rationalize the absence of H_(II) phase formation in GA' /DML systems and the observation of H_(II) phase in GA' /DPL and GA' /DSL systems.

1. J. W. Doane and D. L. Johnson, Chem. Phy3. Lett., 6, 291-295 (1970). 2. R. J. Pace and S. I. Chan, J. Chem. Phy3., 16, 4217-4227 (1982).

Control of dynamical systems with temporal logic specifications

This thesis is motivated by safety-critical applications involving autonomous air, ground, and space vehicles carrying out complex tasks in uncertain and adversarial environments. We use temporal logic as a language to formally specify complex tasks and system properties. Temporal logic specifications generalize the classical notions of stability and reachability that are studied in the control and hybrid systems communities. Given a system model and a formal task specification, the goal is to automatically synthesize a control policy for the system that ensures that the system satisfies the specification. This thesis presents novel control policy synthesis algorithms for optimal and robust control of dynamical systems with temporal logic specifications. Furthermore, it introduces algorithms that are efficient and extend to high-dimensional dynamical systems.

The first contribution of this thesis is the generalization of a classical linear temporal logic (LTL) control synthesis approach to optimal and robust control. We show how we can extend automata-based synthesis techniques for discrete abstractions of dynamical systems to create optimal and robust controllers that are guaranteed to satisfy an LTL specification. Such optimal and robust controllers can be computed at little extra computational cost compared to computing a feasible controller.

The second contribution of this thesis addresses the scalability of control synthesis with LTL specifications. A major limitation of the standard automaton-based approach for control with LTL specifications is that the automaton might be doubly-exponential in the size of the LTL specification. We introduce a fragment of LTL for which one can compute feasible control policies in time polynomial in the size of the system and specification. Additionally, we show how to compute optimal control policies for a variety of cost functions, and identify interesting cases when this can be done in polynomial time. These techniques are particularly relevant for online control, as one can guarantee that a feasible solution can be found quickly, and then iteratively improve on the quality as time permits.

The final contribution of this thesis is a set of algorithms for computing feasible trajectories for high-dimensional, nonlinear systems with LTL specifications. These algorithms avoid a potentially computationally-expensive process of computing a discrete abstraction, and instead compute directly on the system's continuous state space. The first method uses an automaton representing the specification to directly encode a series of constrained-reachability subproblems, which can be solved in a modular fashion by using standard techniques. The second method encodes an LTL formula as mixed-integer linear programming constraints on the dynamical system. We demonstrate these approaches with numerical experiments on temporal logic motion planning problems with high-dimensional (10+ states) continuous systems.

Temporal and spacial control of RNA stability in the early embryo of Drosophila melanogaster

Early embryogenesis in metazoa is controlled by maternally synthesized products. Among these products, the mature egg is loaded with transcripts representing approximately two thirds of the genome. A subset of this maternal RNA pool is degraded prior to the transition to zygotic control of development. This transfer of control of development from maternal to zygotic products is referred to as the midblastula transition (or MBT). It is believed that the degradation of maternal transcripts is required to terminate maternal control of development and to allow zygotic control of development to begin. Until now this process of maternal transcript degradation and the subsequent timing of the MBT has been poorly understood. I have demonstrated that in the early embryo there are two independent RNA degradation pathways, either of which is sufficient for transcript elimination. However, only the concerted action of both pathways leads to elimination of transcripts with the correct timing, at the MBT. The first pathway is maternally encoded, is triggered by egg activation, and is targeted to specific classes of mRNAs through cis-acting elements in the 3' untranslated region (UTR}. The second pathway is activated 2 hr after fertilization and functions together with the maternal pathway to ensure that transcripts are degraded by the MBT. In addition, some transcripts fail to degrade at select subcellular locations adding an element of spatial control to RNA degradation. The spatial control of RNA degradation is achieved by protecting, or masking, transcripts from the degradation machinery. The RNA degradation and protection events are regulated by distinct cis-elements in the 3' untranslated region (UTR). These results provide the first systematic dissection of this highly conserved process in development and demonstrate that RNA degradation is a novel mechanism used for both temporal and spatial control of development.

High fidelity probe and mitigation of mirror thermal fluctuations

Thermal noise arising from mechanical loss in high reflective dielectric coatings is a significant source of noise in precision optical measurements. In particular, Advanced LIGO, a large scale interferometer aiming to observed gravitational wave, is expected to be limited by coating thermal noise in the most sensitive region around 30–300 Hz. Various theoretical calculations for predicting coating Brownian noise have been proposed. However, due to the relatively limited knowledge of the coating material properties, an accurate approximation of the noise cannot be achieved. A testbed that can directly observed coating thermal noise close to Advanced LIGO band will serve as an indispensable tool to verify the calculations, study material properties of the coating, and estimate the detector’s performance.

This dissertation reports a setup that has sensitivity to observe wide band (10Hz to 1kHz) thermal noise from fused silica/tantala coating at room temperature from fixed-spacer Fabry–Perot cavities. Important fundamental noises and technical noises associated with the setup are discussed. The coating loss obtained from the measurement agrees with results reported in the literature. The setup serves as a testbed to study thermal noise in high reflective mirrors from different materials. One example is a heterostructure of Al_xGa_1−xAs (AlGaAs). An optimized design to minimize thermo–optic noise in the coating is proposed and discussed in this work.

Cosmological consequences of dark matter interactions and vacuum fluctuations

This thesis is divided into two parts: interacting dark matter and fluctuations in cosmology. There is an incongruence between the properties that dark matter is expected to possess between the early universe and the late universe. Weakly-interacting dark matter yields the observed dark matter relic density and is consistent with large-scale structure formation; however, there is strong astrophysical evidence in favor of the idea that dark matter has large self-interactions. The first part of this thesis presents two models in which the nature of dark matter fundamentally changes as the universe evolves. In the first model, the dark matter mass and couplings depend on the value of a chameleonic scalar field that changes as the universe expands. In the second model, dark matter is charged under a hidden SU(N) gauge group and eventually undergoes confinement. These models introduce very different mechanisms to explain the separation between the physics relevant for freezeout and for small-scale dynamics.

As the universe continues to evolve, it will asymptote to a de Sitter vacuum phase. Since there is a finite temperature associated with de Sitter space, the universe is typically treated as a thermal system, subject to rare thermal fluctuations, such as Boltzmann brains. The second part of this thesis begins by attempting to escape this unacceptable situation within the context of known physics: vacuum instability induced by the Higgs field. The vacuum decay rate competes with the production rate of Boltzmann brains, and the cosmological measures that have a sufficiently low occurrence of Boltzmann brains are given more credence. Upon further investigation, however, there are certain situations in which de Sitter space settles into a quiescent vacuum with no fluctuations. This reasoning not only provides an escape from the Boltzmann brain problem, but it also implies that vacuum states do not uptunnel to higher-energy vacua and that perturbations do not decohere during slow-roll inflation, suggesting that eternal inflation is much less common than often supposed. Instead, decoherence occurs during reheating, so this analysis does not alter the conventional understanding of the origin of density fluctuations from primordial inflation.

Fluctuations in a tokamak plasma

An experimental investigation of low frequency floating potential fluctuations (f ≤ 200 kHz) in a research tokamak plasma using two spatially separated electrostatic probes has been performed. The spectra, correlation length, and the phase velocity of the fluctuations in both the radial and azimuthal direction have been determined. The propagation velocity in the toroidal direction was also measured and was found to be in the direction of electron current flow. The waves traveled azimuthally in the ion diamagnetic drift direction, even after the usual E x B rotation was taken into account. The electron density fluctuations associated with these oscillations were large, δn/n ≃ 0.35 - 0.50.

The spectra were found to have regularly spaced peaks which seemed to be related to specific azimuthal modes (m =1,2,3,...,etc. ) A parametric study was made to determine what effect plasma parameters had on these peaks. During periods of high electron density in the first 2 msec of the plasma lifetime, strong sawtooth type oscillations were observed. These oscillations typically had frequencies of approximately 10 kHz and were also present when large amounts of neutral gas were added during the discharge by a process called "gas puffing."

The results are compared with experimental observations made on other plasma devices with electric and magnetic probes and with microwave and CO₂ laser scattering techniques. (The scattering measurements are complimentary to the probe measurements since, in the former case, the wavelength is fixed by the scattering angle, but the oscillations could not be spatially localized.) The oscillations in the Caltech torus were probably related to a drift-tearing type instability which is thought to play a major role in the anomalous particle and energy flux observed in tokamaks. Comparisons are made between current theory and the experimental results. However, the theory for the observed oscillations is still in a rudimentary stage of development, and it is hoped that the present investigation will stimulate future analytical work.

A theory of strong and weak scintillations with applications to astrophysics

The propagation of waves in an extended, irregular medium is studied under the "quasi-optics" and the "Markov random process" approximations. Under these assumptions, a Fokker-Planck equation satisfied by the characteristic functional of the random wave field is derived. A complete set of the moment equations with different transverse coordinates and different wavenumbers is then obtained from the characteristic functional. The derivation does not require Gaussian statistics of the random medium and the result can be applied to the time-dependent problem. We then solve the moment equations for the phase correlation function, angular broadening, temporal pulse smearing, intensity correlation function, and the probability distribution of the random waves. The necessary and sufficient conditions for strong scintillation are also given.

We also consider the problem of diffraction of waves by a random, phase-changing screen. The intensity correlation function is solved in the whole Fresnel diffraction region and the temporal pulse broadening function is derived rigorously from the wave equation.

The method of smooth perturbations is applied to interplanetary scintillations. We formulate and calculate the effects of the solar-wind velocity fluctuations on the observed intensity power spectrum and on the ratio of the observed "pattern" velocity and the true velocity of the solar wind in the three-dimensional spherical model. The r.m.s. solar-wind velocity fluctuations are found to be ~200 km/sec in the region about 20 solar radii from the Sun.

We then interpret the observed interstellar scintillation data using the theories derived under the Markov approximation, which are also valid for the strong scintillation. We find that the Kolmogorov power-law spectrum with an outer scale of 10 to 100 pc fits the scintillation data and that the ambient averaged electron density in the interstellar medium is about 0.025 cm^-3. It is also found that there exists a region of strong electron density fluctuation with thickness ~10 pc and mean electron density ~7 cm^-3 between the PSR 0833-45 pulsar and the earth.

Incremental Control Synthesis for Robotics in the Presence of Temporal Logic Specifications

This thesis presents methods for incrementally constructing controllers in the presence of uncertainty and nonlinear dynamics. The basic setting is motion planning subject to temporal logic specifications. Broadly, two categories of problems are treated. The first is reactive formal synthesis when so-called discrete abstractions are available. The fragment of linear-time temporal logic (LTL) known as GR(1) is used to express assumptions about an adversarial environment and requirements of the controller. Two problems of changes to a specification are posed that concern the two major aspects of GR(1): safety and liveness. Algorithms providing incremental updates to strategies are presented as solutions. In support of these, an annotation of strategies is developed that facilitates repeated modifications. A variety of properties are proven about it, including necessity of existence and sufficiency for a strategy to be winning. The second category of problems considered is non-reactive (open-loop) synthesis in the absence of a discrete abstraction. Instead, the presented stochastic optimization methods directly construct a control input sequence that achieves low cost and satisfies a LTL formula. Several relaxations are considered as heuristics to address the rarity of sampling trajectories that satisfy an LTL formula and demonstrated to improve convergence rates for Dubins car and single-integrators subject to a recurrence task.