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.

Time-Domain TeraHertz Spectroscopy and Observational Probes of Prebiotic Interstellar Gas and Ice Chemistry

Understanding the origin of life on Earth has long fascinated the minds of the global community, and has been a driving factor in interdisciplinary research for centuries. Beyond the pioneering work of Darwin, perhaps the most widely known study in the last century is that of Miller and Urey, who examined the possibility of the formation of prebiotic chemical precursors on the primordial Earth [1]. More recent studies have shown that amino acids, the chemical building blocks of the biopolymers that comprise life as we know it on Earth, are present in meteoritic samples, and that the molecules extracted from the meteorites display isotopic signatures indicative of an extraterrestrial origin [2]. The most recent major discovery in this area has been the detection of glycine (NH₂CH₂COOH), the simplest amino acid, in pristine cometary samples returned by the NASA STARDUST mission [3]. Indeed, the open questions left by these discoveries, both in the public and scientific communities, hold such fascination that NASA has designated the understanding of our "Cosmic Origins" as a key mission priority.

Despite these exciting discoveries, our understanding of the chemical and physical pathways to the formation of prebiotic molecules is woefully incomplete. This is largely because we do not yet fully understand how the interplay between grain-surface and sub-surface ice reactions and the gas-phase affects astrophysical chemical evolution, and our knowledge of chemical inventories in these regions is incomplete. The research presented here aims to directly address both these issues, so that future work to understand the formation of prebiotic molecules has a solid foundation from which to work.

From an observational standpoint, a dedicated campaign to identify hydroxylamine (NH₂OH), potentially a direct precursor to glycine, in the gas-phase was undertaken. No trace of NH₂OH was found. These observations motivated a refinement of the chemical models of glycine formation, and have largely ruled out a gas-phase route to the synthesis of the simplest amino acid in the ISM. A molecular mystery in the case of the carrier of a series of transitions was resolved using observational data toward a large number of sources, confirming the identity of this important carbon-chemistry intermediate B11244 as l-C₃H⁺ and identifying it in at least two new environments. Finally, the doubly-nitrogenated molecule carbodiimide HNCNH was identified in the ISM for the first time through maser emission features in the centimeter-wavelength regime.

In the laboratory, a TeraHertz Time-Domain Spectrometer was constructed to obtain the experimental spectra necessary to search for solid-phase species in the ISM in the THz region of the spectrum. These investigations have shown a striking dependence on large-scale, long-range (i.e. lattice) structure of the ices on the spectra they present in the THz. A database of molecular spectra has been started, and both the simplest and most abundant ice species, which have already been identified, as well as a number of more complex species, have been studied. The exquisite sensitivity of the THz spectra to both the structure and thermal history of these ices may lead to better probes of complex chemical and dynamical evolution in interstellar environments.

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.

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.

On Ultrafast Time-Domain TeraHertz Spectroscopy in the Condensed Phase: Linear Spectroscopic Measurements of Hydrogen-Bond Dynamics of Astrochemical Ice Analogs and Nonlinear TeraHertz Kerr Effect Measurements of Vibrational Quantum Beats

Much of the chemistry that affects life on planet Earth occurs in the condensed phase. The TeraHertz (THz) or far-infrared (far-IR) region of the electromagnetic spectrum (from 0.1 THz to 10 THz, 3 cm^-1 to 300 cm^-1, or 3000 μm to 30 μm) has been shown to provide unique possibilities in the study of condensed-phase processes. The goal of this work is to expand the possibilities available in the THz region and undertake new investigations of fundamental interest to chemistry. Since we are fundamentally interested in condensed-phase processes, this thesis focuses on two areas where THz spectroscopy can provide new understanding: astrochemistry and solvation science. To advance these fields, we had to develop new instrumentation that would enable the experiments necessary to answer new questions in either astrochemistry or solvation science. We first developed a new experimental setup capable of studying astrochemical ice analogs in both the TeraHertz (THz), or far-Infrared (far-IR), region (0.3 - 7.5 THz; 10 - 250 cm^-1) and the mid-IR (400 - 4000 cm^-1). The importance of astrochemical ices lies in their key role in the formation of complex organic molecules, such as amino acids and sugars in space. Thus, the instruments are capable of performing variety of spectroscopic studies that can provide especially relevant laboratory data to support astronomical observations from telescopes such as the Herschel Space Telescope, the Stratospheric Observatory for Infrared Astronomy (SOFIA), and the Atacama Large Millimeter Array (ALMA). The experimental apparatus uses a THz time-domain spectrometer, with a 1750/875 nm plasma source and a GaP detector crystal, to cover the bandwidth mentioned above with ~10 GHz (~0.3 cm^-1) resolution.

Using the above instrumentation, experimental spectra of astrochemical ice analogs of water and carbon dioxide in pure, mixed, and layered ices were collected at different temperatures under high vacuum conditions with the goal of investigating the structure of the ice. We tentatively observe a new feature in both amorphous solid water and crystalline water at 33 cm^-1 (1 THz). In addition, our studies of mixed and layered ices show how it is possible to identify the location of carbon dioxide as it segregates within the ice by observing its effect on the THz spectrum of water ice. The THz spectra of mixed and layered ices are further analyzed by fitting their spectra features to those of pure amorphous solid water and crystalline water ice to quantify the effects of temperature changes on structure. From the results of this work, it appears that THz spectroscopy is potentially well suited to study thermal transformations within the ice.

To advance the study of liquids with THz spectroscopy, we developed a new ultrafast nonlinear THz spectroscopic technique: heterodyne-detected, ultrafast THz Kerr effect (TKE) spectroscopy. We implemented a heterodyne-detection scheme into a TKE spectrometer that uses a stilbazoiumbased THz emitter, 4-N,N-dimethylamino-4-N-methyl-stilbazolium 2,4,6-trimethylbenzenesulfonate (DSTMS), and high numerical aperture optics which generates THz electric field in excess of 300 kV/cm, in the sample. This allows us to report the first measurement of quantum beats at terahertz (THz) frequencies that result from vibrational coherences initiated by the nonlinear, dipolar interaction of a broadband, high-energy, (sub)picosecond THz pulse with the sample. Our instrument improves on both the frequency coverage, and sensitivity previously reported; it also ensures a backgroundless measurement of the THz Kerr effect in pure liquids. For liquid diiodomethane, we observe a quantum beat at 3.66 THz (122 cm^-1), in exact agreement with the fundamental transition frequency of the υ4 vibration of the molecule. This result provides new insight into dipolar vs. Raman selection rules at terahertz frequencies.

To conclude we discuss future directions for the nonlinear THz spectroscopy in the Blake lab. We report the first results from an experiment using a plasma-based THz source for nonlinear spectroscopy that has the potential to enable nonlinear THz spectra with a sub-100 fs temporal resolution, and how the optics involved in the plasma mechanism can enable THz pulse shaping. Finally, we discuss how a single-shot THz detection scheme could improve the acquisition of THz data and how such a scheme could be implemented in the Blake lab. The instruments developed herein will hopefully remain a part of the groups core competencies and serve as building blocks for the next generation of THz instrumentation that pushes the frontiers of both chemistry and the scientific enterprise as a whole.

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.

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.

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.

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.

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.

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.