Capturing protein dynamics with time-resolved luminescence spectroscopy

The presented doctoral research utilizes time-resolved spectroscopy to characterize protein dynamics and folding mechanisms. We resolve millisecond-timescale folding by coupling time-resolved fluorescence energy transfer (trFRET) to a continuous flow microfluidic mixer to obtain intramolecular distance distributions throughout the folding process. We have elucidated the folding mechanisms of two cytochromes---one that exhibits two-state folding (cytochrome cb₅₆₂) and one that has both a kinetic refolding intermediate ensemble and a distinct equilibrium unfolding intermediate (cytochrome c₅₅₂). Our data reveal that the distinct structural features of cytochrome c₅₅₂ contribute to its thermostability.

We have also investigated intrachain contact dynamics in unfolded cytochrome cb₅₆₂ by monitoring electron transfer, which occurs as the heme collides with a ruthenium photosensitizer, covalently bound to residues along the polypeptide. Intrachain diffusion for chemically denatured proteins proceeds on the microsecond timescale with an upper limit of 0.1 microseconds. The power-law dependence (slope = -1.5) of the rate constants on the number of peptide bonds between the heme and Ru complex indicate that cytochrome cb₅₆₂ is minimally frustrated.

In addition, we have explored the pathway dependence of electron tunneling rates between metal sites in proteins. Our research group has converted cytochrome b₅₆₂ to a c-type cytochrome with the porphyrin covalently bound to cysteine sidechains. We have investigated the effects of the changes to the protein structure (i.e., increased rigidity and potential new equatorial tunneling pathways) on the electron transfer rates, measured by transient absorption, in a series of ruthenium photosensitizer-modified proteins.

Quantitative, Time-Resolved Proteomic Analysis Using Bio-Orthogonal Non-Canonical Amino Acid Tagging

Bio-orthogonal non-canonical amino acid tagging (BONCAT) is an analytical method that allows the selective analysis of the subset of newly synthesized cellular proteins produced in response to a biological stimulus. In BONCAT, cells are treated with the non-canonical amino acid L-azidohomoalanine (Aha), which is utilized in protein synthesis in place of methionine by wild-type translational machinery. Nascent, Aha-labeled proteins are selectively ligated to affinity tags for enrichment and subsequently identified via mass spectrometry. The work presented in this thesis exhibits advancements in and applications of the BONCAT technology that establishes it as an effective tool for analyzing proteome dynamics with time-resolved precision.

Chapter 1 introduces the BONCAT method and serves as an outline for the thesis as a whole. I discuss motivations behind the methodological advancements in Chapter 2 and the biological applications in Chapters 2 and 3.

Chapter 2 presents methodological developments that make BONCAT a proteomic tool capable of, in addition to identifying newly synthesized proteins, accurately quantifying rates of protein synthesis. I demonstrate that this quantitative BONCAT approach can measure proteome-wide patterns of protein synthesis at time scales inaccessible to alternative techniques.

In Chapter 3, I use BONCAT to study the biological function of the small RNA regulator CyaR in Escherichia coli. I correctly identify previously known CyaR targets, and validate several new CyaR targets, expanding the functional roles of the sRNA regulator.

In Chapter 4, I use BONCAT to measure the proteomic profile of the quorum sensing bacterium Vibrio harveyi during the time-dependent transition from individual- to group-behaviors. My analysis reveals new quorum-sensing-regulated proteins with diverse functions, including transcription factors, chemotaxis proteins, transport proteins, and proteins involved in iron homeostasis.

Overall, this work describes how to use BONCAT to perform quantitative, time-resolved proteomic analysis and demonstrates that these measurements can be used to study a broad range of biological processes.

Chemical studies of viral entry mechanisms: I. Hydrophobic protein-lipid interactions during sendai virus membrane fusion. II. Kinetics of bacteriophage λ DNA injection.

Viruses possess very specific methods of targeting and entering cells. These methods would be extremely useful if they could also be applied to drug delivery, but little is known about the molecular mechanisms of the viral entry process. In order to gain further insight into mechanisms of viral entry, chemical and spectroscopic studies in two systems were conducted, examining hydrophobic protein-lipid interactions during Sendai virus membrane fusion, and the kinetics of bacteriophage λ DNA injection.

Sendai virus glycoprotein interactions with target membranes during the early stages of fusion were examined using time-resolved hydrophobic photoaffinity labeling with the lipid-soluble carbene generator3-(trifluoromethyl)-3-(m-^(125 )I] iodophenyl)diazirine (TID). The probe was incorporated in target membranes prior to virus addition and photolysis. During Sendai virus fusion with liposomes composed of cardiolipin (CL) or phosphatidylserine (PS), the viral fusion (F) protein is preferentially labeled at early time points, supporting the hypothesis that hydrophobic interaction of the fusion peptide at the N-terminus of the F_1 subunit with the target membrane is an initiating event in fusion. Correlation of the hydrophobic interactions with independently monitored fusion kinetics further supports this conclusion. Separation of proteins after labeling shows that the F_1 subunit, containing the putative hydrophobic fusion sequence, is exclusively labeled, and that the F_2 subunit does not participate in fusion. Labeling shows temperature and pH dependence consistent with a need for protein conformational mobility and fusion at neutral pH. Higher amounts of labeling during fusion with CL vesicles than during virus-PS vesicle fusion reflects membrane packing regulation of peptide insertion into target membranes. Labeling of the viral hemagglutinin/neuraminidase (HN) at low pH indicates that HN-mediated fusion is triggered by hydrophobic interactions, after titration of acidic amino acids. HN labeling under nonfusogenic conditions reveals that viral binding may involve hydrophobic as well as electrostatic interactions. Controls for diffusional labeling exclude a major contribution from this source. Labeling during reconstituted Sendai virus envelope-liposome fusion shows that functional reconstitution involves protein retention of the ability to undergo hydrophobic interactions.

Examination of Sendai virus fusion with erythrocyte membranes indicates that hydrophobic interactions also trigger fusion between biological membranes, and that HN binding may involve hydrophobic interactions as well. Labeling of the erythrocyte membranes revealed close membrane association of spectrin, which may play a role in regulating membrane fusion. The data show that hydrophobic fusion protein interaction with both artificial and biological membranes is a triggering event in fusion. Correlation of these results with earlier studies of membrane hydration and fusion kinetics provides a more detailed view of the mechanism of fusion.

The kinetics of DNA injection by bacteriophage λ. into liposomes bearing reconstituted receptors were measured using fluorescence spectroscopy. LamB, the bacteriophage receptor, was extracted from bacteria and reconstituted into liposomes by detergent removal dialysis. The DNA binding fluorophore ethidium bromide was encapsulated in the liposomes during dialysis. Enhanced fluorescence of ethidium bromide upon binding to injected DNA was monitored, and showed that injection is a rapid, one-step process. The bimolecular rate law, determined by the method of initial rates, revealed that injection occurs several times faster than indicated by earlier studies employing indirect assays.

It is hoped that these studies will increase the understanding of the mechanisms of virus entry into cells, and to facilitate the development of virus-mimetic drug delivery strategies.

Wide Field-of-view Microscopes and Endoscopes for Time-lapse Imaging and High-throughput Screening

Wide field-of-view (FOV) microscopy is of high importance to biological research and clinical diagnosis where a high-throughput screening of samples is needed. This thesis presents the development of several novel wide FOV imaging technologies and demonstrates their capabilities in longitudinal imaging of living organisms, on the scale of viral plaques to live cells and tissues.

The ePetri Dish is a wide FOV on-chip bright-field microscope. Here we applied an ePetri platform for plaque analysis of murine norovirus 1 (MNV-1). The ePetri offers the ability to dynamically track plaques at the individual cell death event level over a wide FOV of 6 mm × 4 mm at 30 min intervals. A density-based clustering algorithm is used to analyze the spatial-temporal distribution of cell death events to identify plaques at their earliest stages. We also demonstrate the capabilities of the ePetri in viral titer count and dynamically monitoring plaque formation, growth, and the influence of antiviral drugs.

We developed another wide FOV imaging technique, the Talbot microscope, for the fluorescence imaging of live cells. The Talbot microscope takes advantage of the Talbot effect and can generate a focal spot array to scan the fluorescence samples directly on-chip. It has a resolution of 1.2 μm and a FOV of ~13 mm². We further upgraded the Talbot microscope for the long-term time-lapse fluorescence imaging of live cell cultures, and analyzed the cells’ dynamic response to an anticancer drug.

We present two wide FOV endoscopes for tissue imaging, named the AnCam and the PanCam. The AnCam is based on the contact image sensor (CIS) technology, and can scan the whole anal canal within 10 seconds with a resolution of 89 μm, a maximum FOV of 100 mm × 120 mm, and a depth-of-field (DOF) of 0.65 mm. We also demonstrate the performance of the AnCam in whole anal canal imaging in both animal models and real patients. In addition to this, the PanCam is based on a smartphone platform integrated with a panoramic annular lens (PAL), and can capture a FOV of 18 mm × 120 mm in a single shot with a resolution of 100─140 μm. In this work we demonstrate the PanCam’s performance in imaging a stained tissue sample.

Growth and characterization of novel, III-V semiconductor heterostructures

The material presented in this thesis concerns the growth and characterization of III-V semiconductor heterostructures. Studies of the interactions between bound states in coupled quantum wells and between well and barrier bound states in AlAs/GaAs heterostructures are presented. We also demonstrate the broad array of novel tunnel structures realizable in the InAs/GaSb/AlSb material system. Because of the unique broken-gap band alignment of InAs/GaSb these structures involve transport between the conduction- and valence-bands of adjacent layers. These devices possess a wide range of electrical properties and are fundamentally different from conventional AlAs/GaAs tunnel devices. We report on the fabrication of a novel tunnel transistor with the largest reported room temperature current gains. We also present time-resolved studies of the growth fronts of InAs/GainSb strained layer superlattices and investigations of surface anion exchange reactions.

Chapter 2 covers tunneling studies of conventional AlAs/GaAs RTD's. The results of two studies are presented: (i) A test of coherent vs. sequential tunneling in triple barrier heterostructures, (ii) An optical measurement of the effect of barrier X-point states on Γ-point well states. In the first it was found if two quantum wells are separated by a sufficiently thin barrier, then the eigenstates of the system extend coherently across both wells and the central barriers. For thicker barriers between the wells, the electrons become localized in the individual wells and transport is best described by the electrons hopping between the wells. In the second, it was found that Γ-point well states and X-point barrier states interact strongly. The barrier X-point states modify the energies of the well states and increase the escape rate for carriers in the quantum well.

The results of several experimental studies of a novel class of tunnel devices realized in the InAs/GaSb/AlSb material system are presented in Chapter 3. These interband tunnel structures involve transport between conduction- and valence-band states in adjacent material layers. These devices are compared and contrasted with the conventional AlAs/GaAs structures discussed in Chapter 2 and experimental results are presented for both resonant and nonresonant devices. These results are compared with theoretical simulations and necessary extensions to the theoretical models are discussed.

In chapter 4 experimental results from a novel tunnel transistor are reported. The measured current gains in this transistor exceed 100 at room temperature. This is the highest reported gain at room temperature for any tunnel transistor. The device is analyzed and the current conduction and gain mechanisms are discussed.

Chapters 5 and 6 are studies of the growth of structures involving layers with different anions. Chapter 5 covers the growth of InAs/GainSb superlattices for far infrared detectors and time resolved, in-situ studies of their growth fronts. It was found that the bandgap of superlattices with identical layer thicknesses and compositions varied by as much as 40 meV depending on how their internal interfaces are formed. The absorption lengths in superlattices with identical bandgaps but whose interfaces were formed in different ways varied by as much as a factor of two. First the superlattice is discussed including an explanation of the device and the complications involved in its growth. The experimental technique of reflection high energy electron diffraction (RHEED) is reviewed, and the results of RHEED studies of the growth of these complicated structures are presented. The development of a time resolved, in-situ characterization of the internal interfaces of these superlattices is described. Chapter 6 describes the result of a detailed study of some of the phenomena described in chapter 5. X-ray photoelectron spectroscopy (XPS) studies of anion exchange reactions on the growth fronts of these superlattices are reported. Concurrent RHEED studies of the same physical systems studied with XPS are presented. Using the RHEED and XPS results, a real-time, indirect measurement of surface exchange reactions was developed.

Engineering multi-step electron tunneling systems in proteins

Multi-step electron tunneling, or “hopping,” has become a fast-developing research field with studies ranging from theoretical modeling systems, inorganic complexes, to biological systems. In particular, the field is exploring hopping mechanisms in new proteins and protein complexes, as well as further understanding the classical biological hopping systems such as ribonuclease reductase, DNA photolyases, and photosystem II. Despite the plethora of natural systems, only a few biologically engineered systems exist. Engineered hopping systems can provide valuable information on key structural and electronic features, just like other kinds of biological model systems. Also, engineered systems can harness common biologic processes and utilize them for alternative reactions. In this thesis, two new hopping systems are engineered and characterized.

The protein Pseudomonas aeruginosa azurin is used as a building block to create the two new hopping systems. Besides being well studied and amenable to mutation, azurin already has been used to successfully engineer a hopping system. The two hopping systems presented in this thesis have a histidine-attached high potential rhenium 4,7-dimethyl-1,10-phenanthroline tricarbonyl [Re(dmp)(CO)3] + label which, when excited, acts as the initial electron acceptor. The metal donor is the type I copper of the azurin protein. The hopping intermediates are all tryptophan, an amino acid mutated into the azurin at select sites between the photoactive metal label and the protein metal site. One system exhibits an inter-molecular hopping through a protein dimer interface; the other system undergoes intra-molecular multi-hopping utilizing a tryptophan “wire.” The electron transfer reactions are triggered by excitation of the rhenium label and monitored by UV-Visible transient absorption, luminescence decays measurements, and time-resolved Infrared spectroscopy (TRIR). Both systems were structurally characterized by protein X-ray crystallography.

Synthesis and spectroscopy of ruthenium-modified nucleic acids

Redox-active probes are designed and prepared for use in DNA-mediated electron transfer studies. These probes consist of ruthenium(II) complexes bound to nucleosides that possess metal-binding ligands. Low- and high-potential oxidants are synthesized from these modified nucleosides and display reversible one-electron electrochemical behavior. The ruthenium-modified nucleosides exhibit distinct charge-transfer transitions in the visible region that resemble those of appropriate model complexes. Resonance Raman and time-resolved emission spectroscopy are used to characterize the nature of these transitions.

The site-specific incorporation of these redox-active probes into oligonucleotides is explored using post-synthetic modification and solid-phase synthetic methods. The preparation of the metal-binding nucleosides, their incorporation into oligonucleotides, and characterization of the resulting oligonucleotides is described. Because the insertion of these probes into modified oligonucleotides using post-synthetic modification is unsuccessful, solid-phase synthetic methods are explored. These efforts lead to the first report of 3'-metallated oligonucleotides prepared completely by automated solid-phase synthesis. Preliminary efforts to prepare a bis-metallated oligonucleotide by automated synthesis are described.

The electrochemical, absorption, and emissive features of the ruthenium-modified oligonucleotides are unchanged from those of the precursor metallonucleoside. The absence of any change in these properties upon incorporation into oligonucleotides and subsequent hybridization suggests that the incorporated ruthenium(II) complex is a valuable probe for DNA-mediated electron transfer studies.

Functionalization of Si(111) surfaces and the formation of mixed monolayers for the covalent attachment of molecular catalysts in photoelectrochemical devices

The functionalization of silicon surfaces with molecular catalysts for proton reduction is an important part of the development of a solar-powered, water-splitting device for solar fuel formation. The covalent attachment of these catalysts to silicon without damaging the underlying electronic properties of silicon that make it a good photocathode has proven difficult. We report the formation of mixed monolayer-functionalized surfaces that incor- porate both methyl and vinylferrocenyl or vinylbipyridyl (vbpy) moieties. The silicon was functionalized using reaction conditions analogous to those of hydrosilylation, but instead of a H-terminated Si surface, a chlorine-terminated Si precursor surface was used to produce the linked vinyl-modified functional group. The functionalized surfaces were characterized by time-resolved photoconductivity decay, X-ray photoelectron spectroscopy (XPS), electro- chemical, and photoelectrochemical measurements. The functionalized Si surfaces were well passivated, exhibited high surface coverage and few remaining reactive Si atop sites, had a very low surface recombination velocity, and displayed little initial surface oxidation. The surfaces were stable toward atmospheric and electrochemical oxidation. The surface coverage of ferrocene or bipyridine was controllably varied from 0 up to 30% of a monolayer without loss of the underlying electronic properties of the silicon. Interfacial charge transfer to the attached ferrocene group was relatively rapid, and a photovoltage of 0.4 V was generated upon illumination of functionalized n-type silicon surfaces in CH₃CN. The immobilized bipyridine ligands bound transition metal ions, and thus enabled the assembly of metal complexes on the silicon surface. XPS studies demonstrated that [Cp∗Rh(vbpy)Cl]Cl, [Cp∗Ir(vbpy)Cl]Cl, and Ru(acac)₂vbpy were assembled on the surface. For the surface prepared with iridium, x-ray absorption spectroscopy at the Ir L_III edge showed an edge energy and post-edge features virtually identical to a powder sample of [Cp∗Ir(bipy)Cl]Cl (bipy is 2,2 ́-bipyridyl). Electrochemical studies on these surfaces confirmed that the assembled complexes were electrochemically active.

Electron tunneling in proteins and water

The subject of this thesis is electronic coupling in donor-bridge-acceptor systems. In Chapter 2, ET properties of cyanide-bridged dinuclear ruthenium complexes were investigated. The strong interaction between the mixed-valent ruthenium centers leads to intense metal-to-metal charge transfer bands (MMCT). Hush analysis of the MMCT absorption bands yields the electronic-coupling strength between the metal centers (H_(AB)) and the total reorganization energy (λ). Comparison of ET kinetics to calculated rates shows that classical ET models fail to account for the observed kinetics and nuclear tunneling must be considered.

In Chapter 3, ET rates were measured in four ruthenium-modified highpotential iron-sulfur proteins (HiPIP), which were modified at position His50, His81, His42 and His18, respectively. ET kinetics for the His50 and His81 mutants are a factor of 300 different, while the donor-acceptor separation is nearly identical. PATHWAY calculations corroborate these measurements and highlight the importance of structural detail of the intervening protein matrix.

In Chapter 4, the distance dependence of ET through water bridges was measured. Photoinduced ET measurements in aqueous glasses at 77 K show that water is a poor medium for ET. Luminescence decay and quantum yield data were analyzed in the context of a quenching model that accounts for the exponential distance dependence of ET, the distance distribution of donors and acceptors embedded in the glass and the excluded volumes generated by the finite sizes of the donors and acceptors.

In Chapter 5, the pH-dependent excited state dynamics of ruthenium-modified amino acids were measured. The [Ru(bpy)_(3)] ^(2+) chromophore was linked to amino acids via an amide linkage. Protonation of the amide oxygen effectively quenches the excited state. In addition. time-resolved and steady-state luminescence data reveal that nonradiative rates are very sensitive to the protonation state and the structure of the amino acid moiety.

Cavity Optomechanics at Millikelvin Temperatures

The field of cavity optomechanics, which concerns the coupling of a mechanical object's motion to the electromagnetic field of a high finesse cavity, allows for exquisitely sensitive measurements of mechanical motion, from large-scale gravitational wave detection to microscale accelerometers. Moreover, it provides a potential means to control and engineer the state of a macroscopic mechanical object at the quantum level, provided one can realize sufficiently strong interaction strengths relative to the ambient thermal noise. Recent experiments utilizing the optomechanical interaction to cool mechanical resonators to their motional quantum ground state allow for a variety of quantum engineering applications, including preparation of non-classical mechanical states and coherent optical to microwave conversion. Optomechanical crystals (OMCs), in which bandgaps for both optical and mechanical waves can be introduced through patterning of a material, provide one particularly attractive means for realizing strong interactions between high-frequency mechanical resonators and near-infrared light. Beyond the usual paradigm of cavity optomechanics involving isolated single mechanical elements, OMCs can also be fashioned into planar circuits for photons and phonons, and arrays of optomechanical elements can be interconnected via optical and acoustic waveguides. Such coupled OMC arrays have been proposed as a way to realize quantum optomechanical memories, nanomechanical circuits for continuous variable quantum information processing and phononic quantum networks, and as a platform for engineering and studying quantum many-body physics of optomechanical meta-materials.

However, while ground state occupancies (that is, average phonon occupancies less than one) have been achieved in OMC cavities utilizing laser cooling techniques, parasitic absorption and the concomitant degradation of the mechanical quality factor fundamentally limit this approach. On the other hand, the high mechanical frequency of these systems allows for the possibility of using a dilution refrigerator to simultaneously achieve low thermal occupancy and long mechanical coherence time by passively cooling the device to the millikelvin regime. This thesis describes efforts to realize the measurement of OMC cavities inside a dilution refrigerator, including the development of fridge-compatible optical coupling schemes and the characterization of the heating dynamics of the mechanical resonator at sub-kelvin temperatures.

We will begin by summarizing the theoretical framework used to describe cavity optomechanical systems, as well as a handful of the quantum applications envisioned for such devices. Then, we will present background on the design of the nanobeam OMC cavities used for this work, along with details of the design and characterization of tapered fiber couplers for optical coupling inside the fridge. Finally, we will present measurements of the devices at fridge base temperatures of T_f = 10 mK, using both heterodyne spectroscopy and time-resolved sideband photon counting, as well as detailed analysis of the prospects for future quantum applications based on the observed optically-induced heating.

Dynamic Stall on Vertical Axis Wind Turbines

In this study the dynamics of flow over the blades of vertical axis wind turbines was investigated using a simplified periodic motion to uncover the fundamental flow physics and provide insight into the design of more efficient turbines. Time-resolved, two-dimensional velocity measurements were made with particle image velocimetry on a wing undergoing pitching and surging motion to mimic the flow on a turbine blade in a non-rotating frame. Dynamic stall prior to maximum angle of attack and a leading edge vortex development were identified in the phase-averaged flow field and captured by a simple model with five modes, including the first two harmonics of the pitch/surge frequency identified using the dynamic mode decomposition. Analysis of these modes identified vortical structures corresponding to both frequencies that led the separation and reattachment processes, while their phase relationship determined the evolution of the flow.

Detailed analysis of the leading edge vortex found multiple regimes of vortex development coupled to the time-varying flow field on the airfoil. The vortex was shown to grow on the airfoil for four convection times, before shedding and causing dynamic stall in agreement with 'optimal' vortex formation theory. Vortex shedding from the trailing edge was identified from instantaneous velocity fields prior to separation. This shedding was found to be in agreement with classical Strouhal frequency scaling and was removed by phase averaging, which indicates that it is not exactly coupled to the phase of the airfoil motion.

The flow field over an airfoil undergoing solely pitch motion was shown to develop similarly to the pitch/surge motion; however, flow separation took place earlier, corresponding to the earlier formation of the leading edge vortex. A similar reduced-order model to the pitch/surge case was developed, with similar vortical structures leading separation and reattachment; however, the relative phase lead of the separation mode, corresponding to earlier separation, necessitated that a third frequency to be incorporated into the reattachment mode to provide a relative lag in reattachment.

Finally, the results are returned to the rotating frame and the effects of each flow phenomena on the turbine are estimated, suggesting kinematic criteria for the design of improved turbines.

Deep tissue fluorescence imaging with time-reversed light

Advances in optical techniques have enabled many breakthroughs in biology and medicine. However, light scattering by biological tissues remains a great obstacle, restricting the use of optical methods to thin ex vivo sections or superficial layers in vivo. In this thesis, we present two related methods that overcome the optical depth limit—digital time reversal of ultrasound encoded light (digital TRUE) and time reversal of variance-encoded light (TROVE). These two techniques share the same principle of using acousto-optic beacons for time reversal optical focusing within highly scattering media, like biological tissues. Ultrasound, unlike light, is not significantly scattered in soft biological tissues, allowing for ultrasound focusing. In addition, a fraction of the scattered optical wavefront that passes through the ultrasound focus gets frequency-shifted via the acousto-optic effect, essentially creating a virtual source of frequency-shifted light within the tissue. The scattered ultrasound-tagged wavefront can be selectively measured outside the tissue and time-reversed to converge at the location of the ultrasound focus, enabling optical focusing within deep tissues. In digital TRUE, we time reverse ultrasound-tagged light with an optoelectronic time reversal device (the digital optical phase conjugate mirror, DOPC). The use of the DOPC enables high optical gain, allowing for high intensity optical focusing and focal fluorescence imaging in thick tissues at a lateral resolution of 36 µm by 52 µm. The resolution of the TRUE approach is fundamentally limited to that of the wavelength of ultrasound. The ultrasound focus (~ tens of microns wide) usually contains hundreds to thousands of optical modes, such that the scattered wavefront measured is a linear combination of the contributions of all these optical modes. In TROVE, we make use of our ability to digitally record, analyze and manipulate the scattered wavefront to demix the contributions of these spatial modes using variance encoding. In essence, we encode each spatial mode inside the scattering sample with a unique variance, allowing us to computationally derive the time reversal wavefront that corresponds to a single optical mode. In doing so, we uncouple the system resolution from the size of the ultrasound focus, demonstrating optical focusing and imaging between highly diffusing samples at an unprecedented, speckle-scale lateral resolution of ~ 5 µm. Our methods open up the possibility of fully exploiting the prowess and versatility of biomedical optics in deep tissues.

Travel time tomographic studies of seismic structures around subducted lithospheric slabs

The nature of the subducted lithospheric slab is investigated seismologically by tomographic inversions of ISC residual travel times. The slab, in which nearly all deep earthquakes occur, is fast in the seismic images because it is much cooler than the ambient mantle. High resolution three-dimensional P and S wave models in the NW Pacific are obtained using regional data, while inversion for the SW Pacific slabs includes teleseismic arrivals. Resolution and noise estimations show the models are generally well-resolved.

The slab anomalies in these models, as inferred from the seismicity, are generally coherent in the upper mantle and become contorted and decrease in amplitude with depth. Fast slabs are surrounded by slow regions shallower than 350 km depth. Slab fingering, including segmentation and spreading, is indicated near the bottom of the upper mantle. The fast anomalies associated with the Japan, Izu-Bonin, Mariana and Kermadec subduction zones tend to flatten to sub-horizontal at depth, while downward spreading may occur under parts of the Mariana and Kuril arcs. The Tonga slab appears to end around 550 km depth, but is underlain by a fast band at 750-1000 km depths.

The NW Pacific model combined with the Clayton-Comer mantle model predicts many observed residual sphere patterns. The predictions indicate that the near-source anomalies affect the residual spheres less than the teleseismic contributions. The teleseismic contributions may be removed either by using a mantle model, or using teleseismic station averages of residuals from only regional events. The slab-like fast bands in the corrected residual spheres are are consistent with seismicity trends under the Mariana Tzu-Bonin and Japan trenches, but are inconsistent for the Kuril events.

The comparison of the tomographic models with earthquake focal mechanisms shows that deep compression axes and fast velocity slab anomalies are in consistent alignment, even when the slab is contorted or flattened. Abnormal stress patterns are seen at major junctions of the arcs. The depth boundary between tension and compression in the central parts of these arcs appears to depend on the dip and topology of the slab.

Innovations of wide-field optical-sectioning fluorescence microscopy : toward high-speed volumetric bio-imaging with simplicity

Optical microscopy has become an indispensable tool for biological researches since its invention, mostly owing to its sub-cellular spatial resolutions, non-invasiveness, instrumental simplicity, and the intuitive observations it provides. Nonetheless, obtaining reliable, quantitative spatial information from conventional wide-field optical microscopy is not always intuitive as it appears to be. This is because in the acquired images of optical microscopy the information about out-of-focus regions is spatially blurred and mixed with in-focus information. In other words, conventional wide-field optical microscopy transforms the three-dimensional spatial information, or volumetric information about the objects into a two-dimensional form in each acquired image, and therefore distorts the spatial information about the object. Several fluorescence holography-based methods have demonstrated the ability to obtain three-dimensional information about the objects, but these methods generally rely on decomposing stereoscopic visualizations to extract volumetric information and are unable to resolve complex 3-dimensional structures such as a multi-layer sphere.

The concept of optical-sectioning techniques, on the other hand, is to detect only two-dimensional information about an object at each acquisition. Specifically, each image obtained by optical-sectioning techniques contains mainly the information about an optically thin layer inside the object, as if only a thin histological section is being observed at a time. Using such a methodology, obtaining undistorted volumetric information about the object simply requires taking images of the object at sequential depths.

Among existing methods of obtaining volumetric information, the practicability of optical sectioning has made it the most commonly used and most powerful one in biological science. However, when applied to imaging living biological systems, conventional single-point-scanning optical-sectioning techniques often result in certain degrees of photo-damages because of the high focal intensity at the scanning point. In order to overcome such an issue, several wide-field optical-sectioning techniques have been proposed and demonstrated, although not without introducing new limitations and compromises such as low signal-to-background ratios and reduced axial resolutions. As a result, single-point-scanning optical-sectioning techniques remain the most widely used instrumentations for volumetric imaging of living biological systems to date.

In order to develop wide-field optical-sectioning techniques that has equivalent optical performance as single-point-scanning ones, this thesis first introduces the mechanisms and limitations of existing wide-field optical-sectioning techniques, and then brings in our innovations that aim to overcome these limitations. We demonstrate, theoretically and experimentally, that our proposed wide-field optical-sectioning techniques can achieve diffraction-limited optical sectioning, low out-of-focus excitation and high-frame-rate imaging in living biological systems. In addition to such imaging capabilities, our proposed techniques can be instrumentally simple and economic, and are straightforward for implementation on conventional wide-field microscopes. These advantages together show the potential of our innovations to be widely used for high-speed, volumetric fluorescence imaging of living biological systems.

Velocity resolved - scalar modeled simulations of high Schmidt number turbulent transport

The objective of this thesis is to develop a framework to conduct velocity resolved - scalar modeled (VR-SM) simulations, which will enable accurate simulations at higher Reynolds and Schmidt (Sc) numbers than are currently feasible. The framework established will serve as a first step to enable future simulation studies for practical applications. To achieve this goal, in-depth analyses of the physical, numerical, and modeling aspects related to Sc>>1 are presented, specifically when modeling in the viscous-convective subrange. Transport characteristics are scrutinized by examining scalar-velocity Fourier mode interactions in Direct Numerical Simulation (DNS) datasets and suggest that scalar modes in the viscous-convective subrange do not directly affect large-scale transport for high Sc. Further observations confirm that discretization errors inherent in numerical schemes can be sufficiently large to wipe out any meaningful contribution from subfilter models. This provides strong incentive to develop more effective numerical schemes to support high Sc simulations. To lower numerical dissipation while maintaining physically and mathematically appropriate scalar bounds during the convection step, a novel method of enforcing bounds is formulated, specifically for use with cubic Hermite polynomials. Boundedness of the scalar being transported is effected by applying derivative limiting techniques, and physically plausible single sub-cell extrema are allowed to exist to help minimize numerical dissipation. The proposed bounding algorithm results in significant performance gain in DNS of turbulent mixing layers and of homogeneous isotropic turbulence. Next, the combined physical/mathematical behavior of the subfilter scalar-flux vector is analyzed in homogeneous isotropic turbulence, by examining vector orientation in the strain-rate eigenframe. The results indicate no discernible dependence on the modeled scalar field, and lead to the identification of the tensor-diffusivity model as a good representation of the subfilter flux. Velocity resolved - scalar modeled simulations of homogeneous isotropic turbulence are conducted to confirm the behavior theorized in these a priori analyses, and suggest that the tensor-diffusivity model is ideal for use in the viscous-convective subrange. Simulations of a turbulent mixing layer are also discussed, with the partial objective of analyzing Schmidt number dependence of a variety of scalar statistics. Large-scale statistics are confirmed to be relatively independent of the Schmidt number for Sc>>1, which is explained by the dominance of subfilter dissipation over resolved molecular dissipation in the simulations. Overall, the VR-SM framework presented is quite effective in predicting large-scale transport characteristics of high Schmidt number scalars, however, it is determined that prediction of subfilter quantities would entail additional modeling intended specifically for this purpose. The VR-SM simulations presented in this thesis provide us with the opportunity to overlap with experimental studies, while at the same time creating an assortment of baseline datasets for future validation of LES models, thereby satisfying the objectives outlined for this work.