Spinal cord injury therapy through active learning

Therapy employing epidural electrostimulation holds great potential for improving therapy for patients with spinal cord injury (SCI) (Harkema et al., 2011). Further promising results from combined therapies using electrostimulation have also been recently obtained (e.g., van den Brand et al., 2012). The devices being developed to deliver the stimulation are highly flexible, capable of delivering any individual stimulus among a combinatorially large set of stimuli (Gad et al., 2013). While this extreme flexibility is very useful for ensuring that the device can deliver an appropriate stimulus, the challenge of choosing good stimuli is quite substantial, even for expert human experimenters. To develop a fully implantable, autonomous device which can provide useful therapy, it is necessary to design an algorithmic method for choosing the stimulus parameters. Such a method can be used in a clinical setting, by caregivers who are not experts in the neurostimulator's use, and to allow the system to adapt autonomously between visits to the clinic. To create such an algorithm, this dissertation pursues the general class of active learning algorithms that includes Gaussian Process Upper Confidence Bound (GP-UCB, Srinivas et al., 2010), developing the Gaussian Process Batch Upper Confidence Bound (GP-BUCB, Desautels et al., 2012) and Gaussian Process Adaptive Upper Confidence Bound (GP-AUCB) algorithms. This dissertation develops new theoretical bounds for the performance of these and similar algorithms, empirically assesses these algorithms against a number of competitors in simulation, and applies a variant of the GP-BUCB algorithm in closed-loop to control SCI therapy via epidural electrostimulation in four live rats. The algorithm was tasked with maximizing the amplitude of evoked potentials in the rats' left tibialis anterior muscle. These experiments show that the algorithm is capable of directing these experiments sensibly, finding effective stimuli in all four animals. Further, in direct competition with an expert human experimenter, the algorithm produced superior performance in terms of average reward and comparable or superior performance in terms of maximum reward. These results indicate that variants of GP-BUCB may be suitable for autonomously directing SCI therapy.

Part 1: Longitudinal static and dynamic effects in semiconductor lasers. Part II: Spectral characteristics of passively mode-locked quantum well lasers

In the first part of this thesis a study of the effect of the longitudinal distribution of optical intensity and electron density on the static and dynamic behavior of semiconductor lasers is performed. A static model for above threshold operation of a single mode laser, consisting of multiple active and passive sections, is developed by calculating the longitudinal optical intensity distribution and electron density distribution in a self-consistent manner. Feedback from an index and gain Bragg grating is included, as well as feedback from discrete reflections at interfaces and facets. Longitudinal spatial holeburning is analyzed by including the dependence of the gain and the refractive index on the electron density. The mechanisms of spatial holeburning in quarter wave shifted DFB lasers are analyzed. A new laser structure with a uniform optical intensity distribution is introduced and an implementation is simulated, resulting in a large reduction of the longitudinal spatial holeburning effect.

A dynamic small-signal model is then developed by including the optical intensity and electron density distribution, as well as the dependence of the grating coupling coefficients on the electron density. Expressions are derived for the intensity and frequency noise spectrum, the spontaneous emission rate into the lasing mode, the linewidth enhancement factor, and the AM and FM modulation response. Different chirp components are identified in the FM response, and a new adiabatic chirp component is discovered. This new adiabatic chirp component is caused by the nonuniform longitudinal distributions, and is found to dominate at low frequencies. Distributed feedback lasers with partial gain coupling are analyzed, and it is shown how the dependence of the grating coupling coefficients on the electron density can result in an enhancement of the differential gain with an associated enhancement in modulation bandwidth and a reduction in chirp.

In the second part, spectral characteristics of passively mode-locked two-section multiple quantum well laser coupled to an external cavity are studied. Broad-band wavelength tuning using an external grating is demonstrated for the first time in passively mode-locked semiconductor lasers. A record tuning range of 26 nm is measured, with pulse widths of typically a few picosecond and time-bandwidth products of more than 10 times the transform limit. It is then demonstrated that these large time-bandwidth products are due to a strong linear upchirp, by performing pulse compression by a factor of 15 to a record pulse widths as low 320 fs.

A model for pulse propagation through a saturable medium with self-phase-modulation, due to the a-parameter, is developed for quantum well material, including the frequency dependence of the gain medium. This model is used to simulate two-section devices coupled to an external cavity. When no self-phase-modulation is present, it is found that the pulses are asymmetric with a sharper rising edge, that the pulse tails have an exponential behavior, and that the transform limit is 0.3. Inclusion of self-phase-modulation results in a linear upchirp imprinted on the pulse after each round-trip. This linear upchirp is due to a combination of self-phase-modulation in a gain section and absorption of the leading edge of the pulse in the saturable absorber.

Synthetic molecular machines for active self-assembly : prototype algorithms, designs, and experimental study

Computer science and electrical engineering have been the great success story of the twentieth century. The neat modularity and mapping of a language onto circuits has led to robots on Mars, desktop computers and smartphones. But these devices are not yet able to do some of the things that life takes for granted: repair a scratch, reproduce, regenerate, or grow exponentially fast–all while remaining functional.

This thesis explores and develops algorithms, molecular implementations, and theoretical proofs in the context of “active self-assembly” of molecular systems. The long-term vision of active self-assembly is the theoretical and physical implementation of materials that are composed of reconfigurable units with the programmability and adaptability of biology’s numerous molecular machines. En route to this goal, we must first find a way to overcome the memory limitations of molecular systems, and to discover the limits of complexity that can be achieved with individual molecules.

One of the main thrusts in molecular programming is to use computer science as a tool for figuring out what can be achieved. While molecular systems that are Turing-complete have been demonstrated [Winfree, 1996], these systems still cannot achieve some of the feats biology has achieved.

One might think that because a system is Turing-complete, capable of computing “anything,” that it can do any arbitrary task. But while it can simulate any digital computational problem, there are many behaviors that are not “computations” in a classical sense, and cannot be directly implemented. Examples include exponential growth and molecular motion relative to a surface.

Passive self-assembly systems cannot implement these behaviors because (a) molecular motion relative to a surface requires a source of fuel that is external to the system, and (b) passive systems are too slow to assemble exponentially-fast-growing structures. We call these behaviors “energetically incomplete” programmable behaviors. This class of behaviors includes any behavior where a passive physical system simply does not have enough physical energy to perform the specified tasks in the requisite amount of time.

As we will demonstrate and prove, a sufficiently expressive implementation of an “active” molecular self-assembly approach can achieve these behaviors. Using an external source of fuel solves part of the the problem, so the system is not “energetically incomplete.” But the programmable system also needs to have sufficient expressive power to achieve the specified behaviors. Perhaps surprisingly, some of these systems do not even require Turing completeness to be sufficiently expressive.

Building on a large variety of work by other scientists in the fields of DNA nanotechnology, chemistry and reconfigurable robotics, this thesis introduces several research contributions in the context of active self-assembly.

We show that simple primitives such as insertion and deletion are able to generate complex and interesting results such as the growth of a linear polymer in logarithmic time and the ability of a linear polymer to treadmill. To this end we developed a formal model for active-self assembly that is directly implementable with DNA molecules. We show that this model is computationally equivalent to a machine capable of producing strings that are stronger than regular languages and, at most, as strong as context-free grammars. This is a great advance in the theory of active self- assembly as prior models were either entirely theoretical or only implementable in the context of macro-scale robotics.

We developed a chain reaction method for the autonomous exponential growth of a linear DNA polymer. Our method is based on the insertion of molecules into the assembly, which generates two new insertion sites for every initial one employed. The building of a line in logarithmic time is a first step toward building a shape in logarithmic time. We demonstrate the first construction of a synthetic linear polymer that grows exponentially fast via insertion. We show that monomer molecules are converted into the polymer in logarithmic time via spectrofluorimetry and gel electrophoresis experiments. We also demonstrate the division of these polymers via the addition of a single DNA complex that competes with the insertion mechanism. This shows the growth of a population of polymers in logarithmic time. We characterize the DNA insertion mechanism that we utilize in Chapter 4. We experimentally demonstrate that we can control the kinetics of this re- action over at least seven orders of magnitude, by programming the sequences of DNA that initiate the reaction.

In addition, we review co-authored work on programming molecular robots using prescriptive landscapes of DNA origami; this was the first microscopic demonstration of programming a molec- ular robot to walk on a 2-dimensional surface. We developed a snapshot method for imaging these random walking molecular robots and a CAPTCHA-like analysis method for difficult-to-interpret imaging data.

Tissue engineering active biological machines : bio-inspired design, directed self-assembly, and characterization of muscular pumps simulating the embryonic heart

Biological machines are active devices that are comprised of cells and other biological components. These functional devices are best suited for physiological environments that support cellular function and survival. Biological machines have the potential to revolutionize the engineering of biomedical devices intended for implantation, where the human body can provide the required physiological environment. For engineering such cell-based machines, bio-inspired design can serve as a guiding platform as it provides functionally proven designs that are attainable by living cells. In the present work, a systematic approach was used to tissue engineer one such machine by exclusively using biological building blocks and by employing a bio-inspired design. Valveless impedance pumps were constructed based on the working principles of the embryonic vertebrate heart and by using cells and tissue derived from rats. The function of these tissue-engineered muscular pumps was characterized by exploring their spatiotemporal and flow behavior in order to better understand the capabilities and limitations of cells when used as the engines of biological machines.

Frictional properties of faults : from observation on the Longitudinal Valley Fault, Taiwan, to dynamic simulations

Faults can slip either aseismically or through episodic seismic ruptures, but we still do not understand the factors which determine the partitioning between these two modes of slip. This challenge can now be addressed thanks to the dense set of geodetic and seismological networks that have been deployed in various areas with active tectonics. The data from such networks, as well as modern remote sensing techniques, indeed allow documenting of the spatial and temporal variability of slip mode and give some insight. This is the approach taken in this study, which is focused on the Longitudinal Valley Fault (LVF) in Eastern Taiwan. This fault is particularly appropriate since the very fast slip rate (about 5 cm/yr) is accommodated by both seismic and aseismic slip. Deformation of anthropogenic features shows that aseismic creep accounts for a significant fraction of fault slip near the surface, but this fault also released energy seismically, since it has produced five M_w>6.8 earthquakes in 1951 and 2003. Moreover, owing to the thrust component of slip, the fault zone is exhumed which allows investigation of deformation mechanisms. In order to put constraint on the factors that control the mode of slip, we apply a multidisciplinary approach that combines modeling of geodetic observations, structural analysis and numerical simulation of the "seismic cycle". Analyzing a dense set of geodetic and seismological data across the Longitudinal Valley, including campaign-mode GPS, continuous GPS (cGPS), leveling, accelerometric, and InSAR data, we document the partitioning between seismic and aseismic slip on the fault. For the time period 1992 to 2011, we found that about 80-90% of slip on the LVF in the 0-26 km seismogenic depth range is actually aseismic. The clay-rich Lichi M\'elange is identified as the key factor promoting creep at shallow depth. Microstructural investigations show that deformation within the fault zone must have resulted from a combination of frictional sliding at grain boundaries, cataclasis and pressure solution creep. Numerical modeling of earthquake sequences have been performed to investigate the possibility of reproducing the results from the kinematic inversion of geodetic and seismological data on the LVF. We first investigate the different modeling strategy that was developed to explore the role and relative importance of different factors on the manner in which slip accumulates on faults. We compare the results of quasi dynamic simulations and fully dynamic ones, and we conclude that ignoring the transient wave-mediated stress transfers would be inappropriate. We therefore carry on fully dynamic simulations and succeed in qualitatively reproducing the wide range of observations for the southern segment of the LVF. We conclude that the spatio-temporal evolution of fault slip on the Longitudinal Valley Fault over 1997-2011 is consistent to first order with prediction from a simple model in which a velocity-weakening patch is embedded in a velocity-strengthening area.

Active interaction control for civil structures

This thesis presents a civil engineering approach to active control for civil structures. The proposed control technique, termed Active Interaction Control (AIC), utilizes dynamic interactions between different structures, or components of the same structure, to reduce the resonance response of the controlled or primary structure under earthquake excitations. The primary control objective of AIC is to minimize the maximum story drift of the primary structure. This is accomplished by timing the controlled interactions so as to withdraw the maximum possible vibrational energy from the primary structure to an auxiliary structure, where the energy is stored and eventually dissipated as the external excitation decreases. One of the important advantages of AIC over most conventional active control approaches is the very low external power required.

In this thesis, the AIC concept is introduced and a new AIC algorithm, termed Optimal Connection Strategy (OCS) algorithm, is proposed. The efficiency of the OCS algorithm is demonstrated and compared with two previously existing AIC algorithms, the Active Interface Damping (AID) and Active Variable Stiffness (AVS) algorithms, through idealized examples and numerical simulations of Single- and Multi-Degree-of Freedom systems under earthquake excitations. It is found that the OCS algorithm is capable of significantly reducing the story drift response of the primary structure. The effects of the mass, damping, and stiffness of the auxiliary structure on the system performance are investigated in parametric studies. Practical issues such as the sampling interval and time delay are also examined. A simple but effective predictive time delay compensation scheme is developed.

The application of trimethylsilyl diazomethane to the synthesis of optically active pyrazolines and related studies

The 1,3-dipolar cycloadditions of trimethylsilyl diazomethane with camphorsultam-derived acrylates are reported as a means for the efficient synthesis of optically active pyrazolines. Trimethylsilyl diazomethane is a safe, commercially available diazoalkane which provides Δ¹-pyrazolines 1n good yield and diastereoselectivity when camphorsultam-derived acrylates are used as the reaction dipolarophiles . These initial cycloadducts are subsequently converted to stable, characterizable Δ²-pyrazolines upon desilylation.

A manifold of reactions that can be applied to these Δ²-pyrazolines has been developed which includes pyrazoline reduction, N-N bond reduction, addition to the pyrazoline C=N by mild carbon nucleophiles, and both solvolytic and reductive chiral auxiliary removal. Additionally, it has been demonstrated that the pyrazoline reduction products can take part in peptide coupling reactions that allow for the pyrazolidines to serve as proline-like molecules. The development of this methodology is a general solution to the problem of highly substituted, functionalized pyrazoline synthesis. Importantly, the pyrazolines thus provided have been demonstrated to be amenable to reactions that add to their value as synthetic intermediates.

Transition metal clusters supported by multinucleating ligand frameworks as models of biological active sites

This dissertation describes efforts to model biological active sites with small molecule clusters. The approach used took advantage of a multinucleating ligand to control the structure and nuclearity of the product complexes, allowing the study of many different homo- and heterometallic clusters. Chapter 2 describes the synthesis of the multinucleating hexapyridyl trialkoxy ligand used throughout this thesis and the synthesis of trinuclear first row transition metal complexes supported by this framework, with an emphasis on tricopper systems as models of biological multicopper oxidases. The magnetic susceptibility of these complexes were studied, and a linear relation was found between the Cu-O(alkoxide)-Cu angles and the antiferromagnetic coupling between copper centers. The triiron(II) and trizinc(II) complexes of the ligand were also isolated and structurally characterized.

Chapter 3 describes the synthesis of a series of heterometallic tetranuclear manganese dioxido complexes with various incorporated apical redox-inactive metal cations (M = Na⁺, Ca²⁺, Sr²⁺, Zn²⁺, Y³⁺). Chapter 4 presents the synthesis of heterometallic trimanganese(IV) tetraoxido complexes structurally related to the CaMn₃ subsite of the oxygen-evolving complex (OEC) of Photosystem II. The reduction potentials of these complexes were studied, and it was found that each isostructural series displays a linear correlation between the reduction potentials and the Lewis acidities of the incorporated redox-inactive metals. The slopes of the plotted lines for both the dioxido and tetraoxido clusters are the same, suggesting a more general relationship between the electrochemical potentials of heterometallic manganese oxido clusters and their “spectator” cations. Additionally, these studies suggest that Ca²⁺ plays a role in modulating the redox potential of the OEC for water oxidation.

Chapter 5 presents studies of the effects of the redox-inactive metals on the reactivities of the heterometallic manganese complexes discussed in Chapters 3 and 4. Oxygen atom transfer from the clusters to phosphines is studied; although the reactivity is kinetically controlled in the tetraoxido clusters, the dioxido clusters with more Lewis acidic metal ions (Y³⁺ vs. Ca²⁺) appear to be more reactive. Investigations of hydrogen atom transfer and electron transfer rates are also discussed.

Appendix A describes the synthesis, and metallation reactions of a new dinucleating bis(N-heterocyclic carbene)ligand framework. Dicopper(I) and dicobalt(II) complexes of this ligand were prepared and structurally characterized. A dinickel(I) dichloride complex was synthesized, reduced, and found to activate carbon dioxide. Appendix B describes preliminary efforts to desymmetrize the manganese oxido clusters via functionalization of the basal multinucleating ligand used in the preceding sections of this dissertation. Finally, Appendix C presents some partially characterized side products and unexpected structures that were isolated throughout the course of these studies.

Multilayer Active Shell Mirrors

This thesis presents a novel active mirror technology based on carbon fiber composites and replication manufacturing processes. Multiple additional layers are implemented into the structure in order to provide the reflective layer, actuation capabilities and electrode routing. The mirror is thin, lightweight, and has large actuation capabilities. These features, along with the associated manufacturing processes, represent a significant change in design compared to traditional optics. Structural redundancy in the form of added material or support structures is replaced by thin, unsupported lightweight substrates with large actuation capabilities.

Several studies motivated by the desire to improve as-manufactured figure quality are performed. Firstly, imperfections in thin CFRP laminates and their effect on post-cure shape errors are studied. Numerical models are developed and compared to experimental measurements on flat laminates. Techniques to mitigate figure errors for thicker laminates are also identified. A method of properly integrating the reflective facesheet onto the front surface of the CFRP substrate is also presented. Finally, the effect of bonding multiple initially flat active plates to the backside of a curved CFRP substrate is studied. Figure deformations along with local surface defects are predicted and characterized experimentally. By understanding the mechanics behind these processes, significant improvements to the overall figure quality have been made.

Studies related to the actuation response of the mirror are also performed. The active properties of two materials are characterized and compared. Optimal active layer thicknesses for thin surface-parallel schemes are determined. Finite element simulations are used to make predictions on shape correction capabilities, demonstrating high correctabiliity and stroke over low-order modes. The effect of actuator saturation is studied and shown to significantly degrade shape correction performance.

The initial figure as well as actuation capabilities of a fully-integrated active mirror prototype are characterized experimentally using a Projected Hartmann test. A description of the test apparatus is presented along with two verification measurements. The apparatus is shown to accurately capture both high-amplitude low spatial-frequency figure errors as well as those at lower amplitudes but higher spatial frequencies. A closed-loop figure correction is performed, reducing figure errors by 94%.

Kinetics and mechanisms of adsorption of Escherichia coli bacteriophage T_4 to activated carbon

A study was conducted on the adsorption of Escherichia coli bacteriophage T₄ to activated carbon. Preliminary adsorption experiments were also made with poliovirus Type III. The effectiveness of such adsorbents as diatomaceous earth, Ottawa sand, and coconut charcoal was also tested for virus adsorption.

The kinetics of adsorption were studied in an agitated solution containing virus and carbon. The mechanism of attachment and site characteristics were investigated by varying pH and ionic strength and using site-blocking reagents.

Plaque assay procedures were developed for bacteriophage T₄ on Escherichia coli cells and poliovirus Type III on monkey kidney cells. Factors influencing the efficiency of plaque formation were investigated.

The kinetics of bacteriophage T₄ adsorption to activated carbon can be described by a reversible second-order equation. The reaction order was first order with respect to both virus and carbon concentration. This kinetic representation, however, is probably incorrect at optimum adsorption conditions, which occurred at a pH of 7.0 and ionic strength of 0.08. At optimum conditions the adsorption rate was satisfactorily described by a diffusion-limited process. Interpretation of adsorption data by a development of the diffusion equation for Langmuir adsorption yielded a diffusion coefficient of 12 X 10^-8 cm²/sec for bacteriophage T₄. This diffusion coefficient is in excellent agreement with the accepted value of 8 X 10^-8 cm²/sec. A diffusion-limited theory may also represent adsorption at conditions other than the maximal. A clear conclusion on the limiting process cannot be made.

Adsorption of bacteriophage T₄ to activated carbon obeys the Langmuir isotherm and is thermodynamically reversible. Thus virus is not inactivated by adsorption. Adsorption is unimolecular with very inefficient use of the available carbon surface area. The virus is probably completely excluded from pores due to its size.

Adsorption is of a physical nature and independent of temperature. Attraction is due to electrostatic forces between the virus and carbon. Effects of pH and ionic strength indicated that carboxyl groups, amino groups, and the virus's tail fibers are involved in the attachment of virus to carbon. The active sites on activated carbon for adsorption of bacteriophage T₄ are carboxyl groups. Adsorption can be completely blocked by esterifying these groups.

Heterometallic Complexes as Models of Enzymatic Active Sites

This dissertation describes studies on two multinucleating ligand architectures: the first scaffold was designed to support tricopper complexes, while the second platform was developed to support tri- and tetrametallic clusters.

In Chapter 2, the synthesis of yttrium (and lanthanide) complexes supported by a tripodal ligand framework designed to bind three copper centers in close proximity is described. Tricopper complexes were shown to react with dioxygen in a 1:1 [Cu₃]/O₂ stoichiometry to form intermediates in which the O–O bond was fully cleaved, as characterized via UV-Vis spectroscopy and determination of the reaction stoichiometry. Pre-arrangement of the three Cu centers was pivotal to cooperative O₂ activation, as mono-copper complexes reacted differently with dioxgyen. The reactivity of the observed intermediates was studied with various substrates (reductants, O-atom acceptors, H-atom donors, Brønsted acids) to determine their properties. In Chapter 3, the reactivity of the same yttrium-tricopper complex with nitric oxide was explored. Reductive coupling to form a trans-hyponitrite complex (characterized by X-ray crystallography) was observed via cooperative reactivity by an yttrium and a copper center on two distinct tetrametallic units. The hyponitrite complex was observed to release nitrous oxide upon treatment with a Brønsted acid, supporting its viability as an intermediate in nitric oxide reduction to nitrous oxide.

In Chapter 4, a different multinucleating ligand scaffold was employed to synthesize heterometallic triiron clusters containing one oxide and one hydroxide bridges. The effects of the redox-inactive, Lewis acidic heterometals on redox potential was studied by cyclic voltammetry, unveiling a linear correlation between redox potential and heterometal Lewis acidity. Further studies on these complexes showed that the Lewis acidity of the redox-inactive metals also affected the oxygen-atom transfer reactivity of these clusters. Comparisons of this reactivity with manganese systems, collaborative efforts to reassign the structures of related manganese oxo-hydroxo clusters, and synthetic attempts to access related dioxo clusters are also described.

In Appendix A, ongoing efforts to synthesize new clusters supported by the same multinucleating ligand platform are described. Studies of novel approaches towards ligand exchange in tetrametallic clusters and incorporation of new supporting and bridging ligand motifs in trinuclear complexes are presented.