From the point of view of the electromagnetic interaction, empirical descriptions of the nucleus involve only a few parameters, one of the most important being the nuclear charge radius. This has been well measured for ground state nuclei, but it is difficult to measure for excited states, since they decay too quickly for conventional methods to be used. We study the atomic transitions in muonic ^{90}Zr and find that the nuclear charge radius of the first excited state can be inferred by measuring the gamma emissions from certain transitions. We find that with 1keV photon resolution, we can infer a difference between the charge radius of the nuclear ground state and first excited state as small as 0.13%. We will work in units where h = c = 4\pi\epsilon_0 = 1 so that e^2 = \alpha \approx 1/137 (unless otherwise specified). Mass, momentum, and energy will have units of eV, whereas distances will be given in eV^{-1}. In qualitative discussion, we will sometimes revert to discussing distances in meters due to the familiarity of typical scales (e.g. nuclear radius, Bohr radius). When working with 4-vectors in Minkowski space, we use the metric convention (+,-,-,-). / Graduate

It is emerging that the brain’s vasculature consists of a highly spatially heterogeneous network; however, information on how various vascular characteristics differ between brain regions is still lacking. Furthermore, aging studies rarely acknowledge regional differences in the changes of vascular features. The density of the capillary bed is one vascular feature that is important for the adequate delivery of nutrients to brain tissue. Additionally, capillary density may influence regional cerebral blood flow, a parameter that has been repeatedly correlated to cognitive-behavioural performance. Age-related decline in capillary density has been widely reported in various animal models, yet important questions remain concerning whether there are regional vulnerabilities and what mechanisms could account for these regional differences, if they exist. Here we used confocal microscopy combined with a fluorescent dye-filling approach to label the vasculature, and subsequently quantified vessel length, tortuosity and diameter in 15 brain regions in young adult and aged mice. Our data indicate that vessel loss was most pronounced in white matter followed by cortical, then subcortical gray matter regions, while some regions (visual cortex, amygdala, insular cortex) showed little decline with aging. Changes in capillary density are determined by a balance of pruning and sprouting events. Previous research showed that capillaries are naturally prone to plugging and prolonged obstructions often lead to vessel pruning without subsequent compensatory vessel sprouting. We therefore hypothesized that regional susceptibilities to plugging could help predict vessel loss. By mapping the distribution of microsphere-induced capillary obstructions, we discovered that regions with a higher density of persistent obstructions were more likely to show vessel loss with aging and vice versa. Although the relationship between obstruction density and vessel loss was strong, it was clear obstruction rates were insufficient to explain vessel loss on their own. For that reason, we subsequently used in vivo two-photon microscopy to track microsphere-induced capillary obstructions and vascular network changes over 24 days in two areas of cortex that showed different magnitudes of vessel loss and obstruction densities: visual and retrosplenial cortex. Surprisingly, we did not find evidence for differences in vessel pruning rates between areas, as we would have expected. Instead, we observed brain region-specific differences in recanalization times and rates of angiogenesis. These findings indicate that age-related vessel loss is region specific and that regional susceptibilities to capillary plugging and angiogenesis must be considered to explain these differences. Altogether, this work supports the overarching hypothesis that regional differences in vascular structure and function contribute to a regionally heterogeneous phenotype in the aging brain. / Graduate

No description available.

Indiana University-Purdue University Indianapolis (IUPUI) / Introduction: Multiphoton fluorescence excitation microscopy (MPM) is an invaluable tool for studying processes in tissue in live animals by enabling biologists to view tissues up to hundreds of microns in depth. Unfortunately, imaging depth in MPM is limited to less than a millimeter in tissue due to spherical aberration, light scattering, and light absorption. Spherical aberration is caused by refractive index mismatch between the objective immersion medium and sample. Refractive index heterogeneities within the sample cause light scattering. We investigate the effects of refractive index mismatch on imaging depth in MPM. Methods: The effects of spherical aberration on signal attenuation and resolution degradation with depth are characterized with minimal light absorption and scattering using sub-resolution microspheres mounted in test sample of agarose with varied refractive index. The effects of light scattering on signal attenuation and resolution degradation with depth are characterized using sub-resolution microspheres in kidney tissue samples mounted in optical clearing media to alter the refractive index heterogeneities within the tissue. Results: The studies demonstrate that signal levels and axial resolution both rapidly decline with depth into refractive index mismatched samples. Interestingly, studies of optical clearing with a water immersion objective show that reducing scattering increases reach even when it increases refractive index mismatch degrading axial resolution. Scattering, in the absence of spherical aberration, does not degrade axial resolution. The largest improvements in imaging depth are obtained when both scattering and refractive index mismatch are reduced. Conclusions: Spherical aberration, caused by refractive index mismatch between the immersion media and sample, and scattering, caused by refractive index heterogeneity within the sample, both cause signal to rapidly attenuate with depth in MPM. Scattering, however, seems to be the predominant cause of signal attenuation with depth in kidney tissue. Kenneth W. Dunn, Ph.D., Chair

An inexpensive detector for proteins is described. The detection technique was based on two-photon excitation intrinsic protein fluorescence using a visible 532 nm diode-pumped nano laser as the excitation source. Proteins that exhibit intrinsic fluorescence must contain at least one tryptophan, tyrosine, or phenylalanine residue in their amino acid sequences. The detector was characterized and was found to have a detection limit of 4 micro-molar for tryptophan, 22 micro-molar for tyrosine and 500 micro-molar for phenylalanine. Bovine serum albumin, a serum protein with 3 tryptophan residues in its amino acid sequence was also used to characterize the detector. It was found that the detection limit for this protein was 0.9 micro-molar. The detector volume was determined based on a photon counting histogram - a technique in fluorescence fluctuation spectroscopy. From the results of this analysis, the excitation volume was found to be 2.9 fL. With such an excitation volume, the detection limits were either within or below the atto-mole range.

?-Conjugated systems have been the focus of study in recent years in order to understand their charge transport and optical properties for use in organic electronic devices, fluorescence bioimaging, sensors, and 3D optical data storage (ODS), among others. As a result, several molecular building blocks have been designed, allowing new frontiers to be realized. While various successful building blocks have been fine-tuned at both the electronic and molecular structure level to provide advanced photophysical and optoelectronic characteristics, the azulene framework has been under-appreciated despite its unique electronic and optical properties. Among several attributes, azulenes are vibrant blue naturally occurring hydrocarbons that exhibit large dipolar character, coupled with stimuli-responsive behavior in acidic environments. Additionally, the non-toxic nature and the accompanying eco-friendly feature of some azulenes, namely guaiazulene, may set the stage to further explore a more "green" route towards photonic and conductive materials. The first part of this dissertation focuses on exploiting guaiazulene as a natural building block for the synthesis of chromophores with varying stimuli-responsiveness. Results described in Chapter 1 show that extending the conjugation of guaiazulene through its seven-membered ring methyl group with aromatic substituents dramatically impacts the optical properties of the guaiazulenium carbocation. Study of these ?–stabilized tropilium ions enabled establishing photophysical structure-property trends for guaiazulene-terminated ?-conjugated analogs under acidic conditions, including absorption, emission, quantum yield, and optical band gap patterns. These results were exploited in the design of a photosensitive polymeric system with potential application in the field of three dimensional (3D) optical data storage (ODS). Chapter 2 describes the use of guaiazulene reactive sites (C-3 and C-4 methyl group) to generate a series of cyclopenta[ef]heptalenes that exhibit strong stimuli-responsive behavior. The approach presents a versatile route that allows for various substrates to be incorporated into the resulting cyclopenta[ef]heptalenes, especially after optimization that led to devising a one-pot reaction toward such tricyclic systems. Examining the UV-vis absorption profiles in neutral and acidic media showed that the extension of conjugation at C(4) of the cyclopenta[ef]heptalene skeleton results in longer absorption maxima and smaller optical energy gaps. Additionally, it was concluded that these systems act as sensitizers of a UV-activated (< 300 nm) photoacid generator (PAG), via intermolecular photoinduced electron transfer (PeT), upon which the PAG undergoes photodecomposition resulting in the generation of acid. In a related study, the guaiazulene methyl group at C-4 was employed to study the linear and nonlinear optical properties of 4-styrylguaiazulenes, having the same ?–donor with varying ?-spacer. It was realized that the conjugation length correlates with the extent of bathochromic shift of the protonated species. On the other hand, a trend of decreasing quantum yield was established for this set of 4-styrylguaiazulenes, which can be explained by the increasingly higher degree of flexibility. The second part of this dissertation presents a comprehensive investigation of the linear photophysical, photochemical, and nonlinear optical properties of diketopyrrolopyrrole (DPP)-based derivatives, including two-photon absorption (2PA), femtosecond transient absorption, stimulated emission spectroscopy, and superfluorescence phenomena. The synthetic feasibility, ease of modification, outstanding robustness, and attractive spectroscopic properties of DPPs have motivated their study for fluorescence microscopy applications, concluding that the prepared DPP's are potentially suitable chromophores for high resolution stimulated emission depletion (STED) microscopy.

Organic π-conjugated solids are promising candidates for new optoelectronic materials. The large body of evidence points at their advantageous properties such as high charge-carrier mobility, large nonlinear polarizability, mechanical flexibility, simple and low cost fabrication and superior luminescence. They can be used as nonlinear optical (NLO) materials with large two-photon absorption (2PA) and as electronic components capable of generating nonlinear neutral (excitonic) and charged (polaronic) excitations. In this work, we investigate the appropriate theoretical methods used for the (a) prediction of 2PA properties for rational design of organic materials with improved NLO properties, and (b) understanding of the essential electronic excitations controlling the energy-transfer and charge-transport properties in organic optoelectronics. Accurate prediction of these electro-optical properties is helpful for structureactivity relationships useful for technological innovations. In Chapter 1 we emphasize on the potential use of the organic materials for these two applications. The 2PA process is advantageous over one-photon absorption for deep-tissue fluorescence microscopy, photodynamic therapy, microfabrication and optical data storage owing to the three-dimensional spatial selectivity and improved penetration depth in the absorbing or scattering media. The design of the NLO materials with large 2PA cross-sections may reduce the optical damage due to the use of the high intensity laser beams for excitation. The organic molecules also possess self-localized excited states which can decay radiatively or nonradiatively to form excitonic states. This suggests the use of these materials in the electroluminescent devices such as light-emitting diodes and photovoltaic cells through the processes of exciton formation or dissociation, respectively. It is therefore necessary to understand ultrafast relaxation processes required in understanding the interplay between the iv efficient radiative transfer between the excited states and exciton dissociation into polarons for improving the efficiency of these devices. In Chapter 2, we provide the detailed description of the various theoretical methods applied for the prediction as well as the interpretation of the optical properties of a special class of substituted PPV [poly (p-phenylene vinylene)] oligomers. In Chapter 3, we report the accuracy of different second and third order time dependent density functional theory (TD-DFT) formalisms in prediction of the 2PA spectra compared to the experimental measurements for donor-acceptor PPV derivatives. We recommend a posteriori Tamm-Dancoff approximation method for both qualitative and quantitative analysis of 2PA properties. Whereas, Agren's quadratic response methods lack the double excitations and are not suitable for the qualitative analysis of the state-specific contributions distorting the overall quality of the 2PA predictions. We trace the reasons to the artifactual excited states above the ionization threshold. We also study the effect of the basis set, geometrical constraints and the orbital exchange fraction on the 2PA excitation energies and cross-sections. Higher exchange (BMK and M05-2X) and range-separated (CAM-B3LYP) hybrid functionals are found to yield inaccurate predictions both quantitatively and qualitatively. The failure of the exchangecorrelation (XC) functionals with correct asymptotic is traced to the inaccurate transition dipoles between the valence states, where functionals with low HF exchange succeed. In Chapter 4, we test the performance of different semiempirical wavefunction theory methods for the prediction of 2PA properties compared to the DFT results for the same set of molecules. The spectroscopic parameterized (ZINDO/S) method is relatively better than the general purpose parameterized (PM6) method but the accuracy is trailing behind the DFT methods. The poor performances of PM6 and ZINDO/S methods are attributed to the incorrect description of excited-to-excited state transition and 2PA energies, respectively. The different v semiempirical parameterizations can at best be used for quantitative analysis of the 2PA properties. The ZINDO/S method combined with different orders of multi-reference configuration interactions provide an improved description of 2PA properties. However, the results are observed to be highly dependent on the specific choice for the active space, order of excitation and reference configurations. In Chapter 5, we present a linear response TD-DFT study to benchmark the ability of existing functional models to describe the extent of self-trapped neutral and charged excitations in PPV and its derivative MEH-PPV considered in their trans-isomeric forms. The electronic excitations in question include the lowest singlet (S1) and triplet (T1 † ) excitons, positive (P+ ) and negative (P- ) polarons and the lowest triplet (T1) states. Use of the long-range-corrected DFT functional, such as LC-wPBE, is found to be crucial in order to predict the physically correct spatial localization of all the electronic excitations in agreement with experiment. The inclusion of polarizable dielectric environment play an important role for the charged states. The particlehole symmetry is preserved for both the polymers in trans geometries. These studies indicate two distinct origins leading to self-localization of electronic excitations. Firstly, distortion of molecular geometry may create a spatially localized potential energy well where the state wavefunction self-traps. Secondly, even in the absence of geometric and vibrational dynamics, the excitation may become spatially confined due to energy stabilization caused by polarization effects from surrounding dielectric medium. In Chapter 6, we aim to separate these two fundamental sources of spatial localization. We observe the electronic localization of P + and Pis determined by the polarization effects of the surrounding media and the character of the DFT functional. In contrast, the self-trapping of the electronic wavefunctions of S1 and T1(T1 † ) mostly follows their lattice distortions. Geometry vi relaxation plays an important role in the localization of the S1 and T1 † excitons owing to the nonvariational construction of the excited state wavefunction. While, mean-field calculated P + , Pand T1 states are always spatially localized even in ground state S0 geometry. Polaron P+ and Pformation is signified by the presence of the localized states for the hole or the electron deep inside the HOMO-LUMO gap of the oligomer as a result of the orbital stabilization at the LCwPBE level. The broadening of the HOMO-LUMO band gap for the T1 exciton compared to the charged states is associated with the inverted bond length alternation observed at this level. The molecular orbital energetics are investigated to identify the relationships between state localization and the corresponding orbital structure. In Chapter 7, we investigate the effect of various conformational defects of trans and cis nature on the energetics and localization of the charged P + and Pexcitations in PPV and MEHPPV. We observe that the extent of self-trapping for P+ and Ppolarons is highly sensitive on molecular and structural conformations, and distribution of atomic charges within the polymers. The particle-hole symmetry is broken with the introduction of trans defects and inclusion of the polarizable environment in consistent with experiment. The differences in the behavior of PPV and MEH-PPV is rationalized based on their orbital energetics and atomic charge distributions. We show these isomeric defects influence the behavior and drift mobilities of the charge carriers in substituted PPVs.

Time Dependent Density Functional Theory offers a good accuracy/computational cost ratio among different methods used to predict the electronic structure for molecules of practical interest. The Coupled Electronic Oscillator (CEO) formalism was recently shown to accurately predict Nonlinear Optical (NLO) properties of organic chromophores when combined with Time Dependent Density Functional Theory. Unfortunately, CEO does not lend itself easily to interpretation of the structure activity relationships of chromophores. On the other hand, the Sum Over States formalism in combination with semiempirical wavefunction methods has been used in the past for the design of simplified essential states models. These models can be applied to optimization of NLO properties of interest for applications. Unfortunately, TD-DFT can not be combined directly with SOS because state-to-state transition dipoles are not defined in the linear response TD approach. In this work, a second order CEO approach to TD-DFT is simplified so that properties of double excited states and state-to-state transition dipoles may be expressed through the combination of linear response properties. This approach is termed the a posteriori Tamm-Dancoff approximation (ATDA), and validated against high-level wavefunction theory methods. Sum over States (SOS) and related Two-Photon Transition Matrix formalism are then used to predict Two-Photon Absorption (2PA) profiles and anisotropy, as well as Second Harmonic Generation (SHG) properties. Numerical results for several conjugated molecules are in excellent agreement with CEO and finite field calculations, and reproduce experimental measurements well.

In this work, hydrophilic fluorene-based derivatives that contain ethylene oxide substituents, have been synthesized and characterized for potential use as new fluorophores for bioimaging applications and for fluorescence sensing of heavy metals. Symmetrical and unsymmetrical fluorene derivatives based on structural types of acceptor-pi-acceptor, acceptor-pi-donor, and donor-pi-donor were characterized by TGA, UV-vis absorption, fluorescence emission, lifetime, anisotropy, and two-photon absorption (2PA) cross section. They were found to possess high thermal stability, high photostability, high fluorescence quantum yields, and generally large two-photon absorption cross sections, making them quite suitable for new probes in single-photon absorption and two-photon absorption fluorescence microscopy imaging. Novel hydrophilic fluorene derivatives were synthesized from fluorene in multiple steps employing the metal-catalyzed Heck coupling reaction, the Stille reaction, the Sonogashira reaction, the Ullmann condensation reaction, and "click" chemistry. To increase the hydrophilicity of the new compounds, ethylene oxide substituents were utilized for to impart water solubility. An alternative alkylation methodology using ethyleneoxy tosylates was introduced for the synthesis of ethylene oxide-containing fluorene derivatives. Several of these hydrophilic derivatives were incubated into various cell lines as new probes for both conventional and two-photon absorption fluorescence bioimaging. These compounds were biocompatible, exhibiting low cytotoxicity as determined by cell viability studies, and displayed colocalization for selected cellular organelles. In addition, hydrophilic bis(1,2,3-triazolyl)fluorene derivatives were found to exhibit sensitive fluorescence responses in the presence of certain heavy metal, and were selective for sensing zinc and mercury over other a number of other metal ions relevant to living cells or other biological environments. The UV-vis absorption and fluorescence emission spectra of the complexes exhibited a blue-shifted absorption and emission for selective metal chelation upon binding to zinc and mercury(II) ions, resulting in an approximately two-fold enhanced fluorescence response. Fluorescence titration studies revealed that the complexes of 1:2 and 1:3 ligand to metal formed with binding constant values of 108 and 1014 for zinc and mercury ions, respectively. Finally, preliminary experiments were performed to explore the possibility of employing select hydrophilic fluorene-based derivatives in the synthesis of hydrophilic fluorescent gold nanoparticles. Although results are very preliminary, the aim is to use such materials for other biomedical applications, such as surface enhanced scattering resonance and noninvasive photothermal therapy to diagnose and to treat cancers. Thus, this research had led to the discovery of alternative methodologies for synthesis of hydrophilic fluorene derivatives by alkylation with alkyl tosylates and synthesis of hydrophilic fluorescent molecule capped gold nanoparticles. Furthermore, several novel hydrophilic fluorene-based derivatives were synthesized and characterized for their linear and nonlinear photophysical properties, and are now available for further examination of their bioimaging and sensing applications.

<p>The thesis consists of two main parts of nonlinear optical instrumentation development. </p> <p>Fluorescence-detected mid-infrared photothermal (F-PTIR) microscopy is demonstrated for sub-diffraction limited mid-infrared microspectroscopy of model systems and applied to probe phase transformations in amorphous solid dispersions. To overcome the diffraction limit in infrared imaging, a highly localized temperature-dependent photothermal effect is an attractive alternative indicator to infrared absorption. Photothermal atomic force microscopy infrared spectroscopy (AFM-IR) achieves nanometer resolution by monitoring heat caused expansion but only restricted on the surface. For 3D imaging, optically detected photothermal infrared (O-PTIR) combines an infrared laser with a visible probe source with to transduce photothermal refractive index changes (e.g., from changes in beam divergence or scattering). The sensitivity of O-PTIR is ultimately limited by the relatively weak dependence of refractive index with temperature, exhibiting changes of ~0.01% per oC. Fluorescence-detected photothermal mid-infrared (F-PTIR) spectroscopy (Fig. 1) is demonstrated herein to support 3D imaging with improved photothermal sensitivity. In F-FTIR, the sensitivity of fluorescence quantum efficiency to temperature change (~1-2% per oC) is used to transduce transient heat flux from localized IR absorption. The infrared spatial resolution of F-FTIR is defined by fluorescence microscopy and the thermal diffusivity of the sample instead of infrared wavelength. Initial F-PTIR proof of concept studies are described for microparticle assemblies of silica gel and polyethylene glycol, followed by applications of F-PTIR for analysis of localized composition within phase-separated domains induced by water vapor exposure of an amorphous solid dispersion (ritonavir in copovidone).</p> <p>Fluorescence recovery while photobleaching (FRWP) is demonstrated as a method for quantitative measurements of rapid diffusion mapping over the microsecond to millisecond time scale. Diffusion measurements are critical for molecular mobility assessment in cell biology, materials science and pharmacology. Fluorescence recovery after photobleaching (FRAP) is a well-known noninvasive optical microscopy method for measuring diffusion coefficients of macromolecules, such as proteins in cells and viscous solutions. However, conventional point-bleach FRAP is challenging to implement with multi-photon excitation and typically only supports diffusion analysis over millisecond time scales due to camera frame rate limitations. FRWP with patterned illumination addresses these limitations of FRAP by probing the fluorescence intensity changes while bleaching a comb pattern within a field of view (FoV). Fast-scanning of an ultrafast excitation beam distributes heat rapidly over multiple adjacent pixels, minimizing local heating effects that could complicate analogous diffusion measurements by point-bleach FRAP with multiphoton excitation. In FRWP, time-scales of the probed diffusion events are defined by a single line-pass time of a resonant scanning-mirror with a period of 125  s. In FRWP, the bleach pattern spans locations across the whole FoV, enabling diffusion mapping through image segmentation. More than a hundred bleaching and recovery events can be recorded during a single 10s measurement. Normal and anomalous diffusion of rhodamine-labeled bovine serum albumin (BSA) molecules was studied as a model system, with applications targeting rapid assessment of therapeutic macromolecule mobility within heterogeneous biological environments.</p>