Simulations of droplet dispersion in the wakes of cylinders and icing tunnel spray bars

Simulations of droplet dispersion behind cylinder wakes and downstream of icing tunnel spray bars were conducted. In both cases, a range of droplet sizes were investigated numerically with a Lagrangian particle trajectory approach while the turbulent air flow was investigated with a hybrid Reynolds-Averaged Navier-Stokes/Large-Eddy Simulations approach scheme. In the first study, droplets were injected downstream of a cylinder at sub-critical conditions (i.e. with laminar boundary layer separation). A stochastic continuous random walk (CRW) turbulence model was used to capture the effects of sub-grid turbulence. Small inertia droplets (characterized by small Stokes numbers) were affected by both the large-scale and small-scale vortex structures and closely followed the air flow, while exhibiting a dispersion consistent with that of a scalar flow field. Droplets with intermediate Stokes numbers were centrifuged by the vortices to the outer edges of the wake, yielding an increased dispersion. Large Stokes number droplets were found to be less responsive to the vortex structures and exhibited the least dispersion. Particle concentration was also correlated with vorticity distribution which yielded preferential bias effects as a function of different particle sizes. This trend was qualitatively similar to results seen in homogenous isotropic turbulence, though the influence of particle inertia was less pronounced for the cylinder wake case. A similar study was completed for droplet dispersion within the Icing Research Tunnel (IRT) at the NASA Glenn Research Center, where it is important to obtain a nearly uniform liquid water content (LWC) distribution in the test section (to recreate atmospheric icing conditions).. For this goal, droplets are diffused by the mean and turbulent flow generated from the nozzle air jets, from the upstream spray bars, and from the vertical strut wakes. To understand the influence of these three components, a set of simulations was conducted with a sequential inclusion of these components. Firstly, a jet in an otherwise quiescent airflow was simulated to capture the impact of the air jet on flow turbulence and droplet distribution, and the predictions compared well with experimental results. The effects of the spray bar wake and vertical strut wake were then included with two more simulation conditions, for which it was found that the air jets were the primary driving force for droplet dispersion, i.e. that the spray bar and vertical strut wake effects were secondary.

Studies of Protein-Protein and Protein-Water Interactions by Small Angle X-Ray Scattering, Terahertz Spectroscopy, ASMOS, And Computer Simulation

The protein folding problem has been one of the most challenging subjects in biological physics due to its complexity. Energy landscape theory based on statistical mechanics provides a thermodynamic interpretation of the protein folding process. We have been working to answer fundamental questions about protein-protein and protein-water interactions, which are very important for describing the energy landscape surface of proteins correctly. At first, we present a new method for computing protein-protein interaction potentials of solvated proteins directly from SAXS data. An ensemble of proteins was modeled by Metropolis Monte Carlo and Molecular Dynamics simulations, and the global X-ray scattering of the whole model ensemble was computed at each snapshot of the simulation. The interaction potential model was optimized and iterated by a Levenberg-Marquardt algorithm. Secondly, we report that terahertz spectroscopy directly probes hydration dynamics around proteins and determines the size of the dynamical hydration shell. We also present the sequence and pH-dependence of the hydration shell and the effect of the hydrophobicity. On the other hand, kinetic terahertz absorption (KITA) spectroscopy is introduced to study the refolding kinetics of ubiquitin and its mutants. KITA results are compared to small angle X-ray scattering, tryptophan fluorescence, and circular dichroism results. We propose that KITA monitors the rearrangement of hydrogen bonding during secondary structure formation. Finally, we present development of the automated single molecule operating system (ASMOS) for a high throughput single molecule detector, which levitates a single protein molecule in a 10 µm diameter droplet by the laser guidance. I also have performed supporting calculations and simulations with my own program codes.

Growth and Characterization of III-V Semiconductor Materials for MOCVD Reactor Qualification and Process Control

Metalorganic chemical vapor deposition is examined as a technique for growing compound semiconductor structures. Material analysis techniques for characterizing the quality and properties of compound semiconductor material are explained and data from recent commissioning work on a newly installed reactor at the University of Illinois is presented.

Investigating wetting characteristics on microstructured surfaces for superhydrophobicity and metal microcasting

The engineering of liquid behavior on surfaces is important for infrastructure, transportation, manufacturing, and sensing. Surfaces can be rendered superhydrophobic by microstructuring, and superhydrophobic devices could lead to practical corrosion inhibition, self-cleaning, fluid flow control, and surface drag reduction. To more fully understand how liquid interacts with microstructured surfaces, this dissertation introduces a direct method for determining droplet solid-liquid-vapor interfacial geometry on microstructured surfaces. The technique performs metrology on molten metal droplets deposited onto microstructured surfaces and then frozen. Unlike other techniques, this visualization technique can be used on large areas of curved and opaque microstructured surfaces to determine contact line. This dissertation also presents measurements and models for how curvature and flexing of microstructured polymers affects hydrophobicity. Increasing curvature of microstructured surfaces leads to decreased slide angle for liquid droplets suspended on the surface asperities. For a surface with regularly spaced asperities, as curvature becomes more positive, droplets suspended on the tops of asperities are suspended on fewer asperities. Curvature affects superhydrophobicity because microscopic curvature changes solid-liquid interaction, pitch is altered, and curvature changes the shape of the three phase contact line. This dissertation presents a model of droplet interactions with curved microstructured surfaces that can be used to design microstructure geometries that maintain the suspension of a droplet when curved surfaces are covered with microstructured polymers. Controlling droplet dynamics could improve microfluidic devices and the shedding of liquids from expensive equipment, preventing corrosion and detrimental performance. This dissertation demonstrates redirection of dynamic droplet spray with anisotropic microstructures. Superhydrophobic microstructured surfaces can be economically fabricated using metal embossing masters, so this dissertation describes casting-based microfabrication of metal microstructures and nanostructures. Low melting temperature metal was cast into flexible silicone molds which were themselves cast from microfabricated silicon templates. The flexibility of the silicone mold permits casting of curved surfaces, which this dissertation demonstrates by fabricating a cylindrical metal roller with microstructures. The metal microstructures can be in turn used as a reusable molding tool. This dissertation also describes an industrial investment casting process to produce aluminum molds having integrated microstructures. Unlike conventional micromolding tools, the aluminum mold was large and had complex curved surfaces. The aluminum was cast into curved microstructured ceramic molds which were themselves cast from curved microstructured rubber. Many structures were successfully cast into the aluminum with excellent replication fidelity, including circular, square, and triangular holes. This dissertation demonstrates molding of large, curved surfaces having surface microstructures using the aluminum mold. This work contributes a more full understanding of the phenomenon of superhydrophobicity and techniques for the economic fabrication of superhydrophobic microstructures.

Measurements of small ice crystals in arctic cirrus: observations from the Indirect and Semi-Direct Aerosol Campaign (ISDAC)

In-situ observations on the size and shape of particles in arctic cirrus are less common than those in mid-latitude and tropical cirrus with considerable uncertainty about the contributions of small ice crystals (maximum dimension D<50 µm) to the mass and radiative properties that impact radiative forcing. In situ measurements of small ice crystals in arctic cirrus were made during the Indirect and Semi-Direct Aerosol Campaign (ISDAC) in April 2008 during transits of the National Research Council of Canada Convair-580 between Fairbanks and Barrow, Alaska and during Mixed Phase Arctic Cloud Experiment (MPACE) in October 2004 with the University of North Dakota (UND) Citation over Barrow, Alaska. Concentrations of small ice crystals with D < 50 μm from a Cloud and Aerosol Spectrometer (CAS), a Cloud Droplet Probe (CDP), a Forward Scattering Spectrometer Probe (FSSP), and a two-dimensional stereo probe (2DS) were compared as functions of the concentrations of crystals with D > 100 μm measured by a Cloud Imaging Probe (CIP) and two-dimensional stereo probe (2DS) in order to assess whether the shattering of large ice crystals on protruding components of different probes artificially amplified measurements of small ice crystal concentrations. The dependence of the probe comparison on other variables as CIP N>100 (number concentrations greater than diameter D>100 μm),temperature, relative humidity respect to ice (RHice), dominant habit from the Cloud Particle Imager (CPI), aircraft roll, pitch, true air speed and angle of attack was examined to understand potential causes of discrepancies between probe concentrations. Data collected by these probes were also compared against the data collected by a CAS, CDP and CIP during the Tropical Warm Pool-International Cloud Experiment (TWP-ICE) and by a CAS and 2DS during the Tropical Composition, Cloud and Climate Coupling (TC4) missions. During ISDAC, the CAS and FSSP both overestimated measurements of small ice crystals compared to both the CDP and 2DS by 1-2 orders of magnitude. Further, the amount of overestimation increased with the concentrations from the CIP2 (N>100 > 0.1 L-1). There was an unexplained discrepancy in concentrations of small crystals between the CDP and 2DS during ISDAC. In addition, there was a strong dependence on RHice of the average ratios of the N3-50, CAS/N3-50,CDP, N3-50, FSSP096/N3-50,CDP, N3-50, CAS/N3-50,FSSP096, N10-50, CDP/N3-50,2DS, N10-50, FSSP096/N10-50,2DS. Continued studies are needed to understand the discrepancy of these probes.

Microfluidic platforms for the characterization of in meso membrane protein crystallization

Membrane proteins, which reside in the membranes of cells, play a critical role in many important biological processes including cellular signaling, immune response, and material and energy transduction. Because of their key role in maintaining the environment within cells and facilitating intercellular interactions, understanding the function of these proteins is of tremendous medical and biochemical significance. Indeed, the malfunction of membrane proteins has been linked to numerous diseases including diabetes, cirrhosis of the liver, cystic fibrosis, cancer, Alzheimer's disease, hypertension, epilepsy, cataracts, tubulopathy, leukodystrophy, Leigh syndrome, anemia, sensorineural deafness, and hypertrophic cardiomyopathy.1-3 However, the structure of many of these proteins and the changes in their structure that lead to disease-related malfunctions are not well understood. Additionally, at least 60% of the pharmaceuticals currently available are thought to target membrane proteins, despite the fact that their exact mode of operation is not known.4-6 Developing a detailed understanding of the function of a protein is achieved by coupling biochemical experiments with knowledge of the structure of the protein. Currently the most common method for obtaining three-dimensional structure information is X-ray crystallography. However, no a priori methods are currently available to predict crystallization conditions for a given protein.7-14 This limitation is currently overcome by screening a large number of possible combinations of precipitants, buffer, salt, and pH conditions to identify conditions that are conducive to crystal nucleation and growth.7,9,11,15-24 Unfortunately, these screening efforts are often limited by difficulties associated with quantity and purity of available protein samples. While the two most significant bottlenecks for protein structure determination in general are the (i) obtaining sufficient quantities of high quality protein samples and (ii) growing high quality protein crystals that are suitable for X-ray structure determination,7,20,21,23,25-47 membrane proteins present additional challenges. For crystallization it is necessary to extract the membrane proteins from the cellular membrane. However, this process often leads to denaturation. In fact, membrane proteins have proven to be so difficult to crystallize that of the more than 66,000 structures deposited in the Protein Data Bank,48 less than 1% are for membrane proteins, with even fewer present at high resolution (< 2Å)4,6,49 and only a handful are human membrane proteins.49 A variety of strategies including detergent solubilization50-53 and the use of artificial membrane-like environments have been developed to circumvent this challenge.43,53-55 In recent years, the use of a lipidic mesophase as a medium for crystallizing membrane proteins has been demonstrated to increase success for a wide range of membrane proteins, including human receptor proteins.54,56-62 This in meso method for membrane protein crystallization, however, is still by no means routine due to challenges related to sample preparation at sub-microliter volumes and to crystal harvesting and X-ray data collection. This dissertation presents various aspects of the development of a microfluidic platform to enable high throughput in meso membrane protein crystallization at a level beyond the capabilities of current technologies. Microfluidic platforms for protein crystallization and other lab-on-a-chip applications have been well demonstrated.9,63-66 These integrated chips provide fine control over transport phenomena and the ability to perform high throughput analyses via highly integrated fluid networks. However, the development of microfluidic platforms for in meso protein crystallization required the development of strategies to cope with extremely viscous and non-Newtonian fluids. A theoretical treatment of highly viscous fluids in microfluidic devices is presented in Chapter 3, followed by the application of these strategies for the development of a microfluidic mixer capable of preparing a mesophase sample for in meso crystallization at a scale of less than 20 nL in Chapter 4. This approach was validated with the successful on chip in meso crystallization of the membrane protein bacteriorhodopsin. In summary, this is the first report of a microfluidic platform capable of performing in meso crystallization on-chip, representing a 1000x reduction in the scale at which mesophase trials can be prepared. Once protein crystals have formed, they are typically harvested from the droplet they were grown in and mounted for crystallographic analysis. Despite the high throughput automation present in nearly all other aspects of protein structure determination, the harvesting and mounting of crystals is still largely a manual process. Furthermore, during mounting the fragile protein crystals can potentially be damaged, both from physical and environmental shock. To circumvent these challenges an X-ray transparent microfluidic device architecture was developed to couple the benefits of scale, integration, and precise fluid control with the ability to perform in situ X-ray analysis (Chapter 5). This approach was validated successfully by crystallization and subsequent on-chip analysis of the soluble proteins lysozyme, thaumatin, and ribonuclease A and will be extended to microfluidic platforms for in meso membrane protein crystallization. The ability to perform in situ X-ray analysis was shown to provide extremely high quality diffraction data, in part as a result of not being affected by damage due to physical handling of the crystals. As part of the work described in this thesis, a variety of data collection strategies for in situ data analysis were also tested, including merging of small slices of data from a large number of crystals grown on a single chip, to allow for diffraction analysis at biologically relevant temperatures. While such strategies have been applied previously,57,59,61,67 they are potentially challenging when applied via traditional methods due to the need to grow and then mount a large number of crystals with minimal crystal-to-crystal variability. The integrated nature of microfluidic platforms easily enables the generation of a large number of reproducible crystallization trials. This, coupled with in situ analysis capabilities has the potential of being able to acquire high resolution structural data of proteins at biologically relevant conditions for which only small crystals, or crystals which are adversely affected by standard cryocooling techniques, could be obtained (Chapters 5 and 6). While the main focus of protein crystallography is to obtain three-dimensional protein structures, the results of typical experiments provide only a static picture of the protein. The use of polychromatic or Laue X-ray diffraction methods enables the collection of time resolved structural information. These experiments are very sensitive to crystal quality, however, and often suffer from severe radiation damage due to the intense polychromatic X-ray beams. Here, as before, the ability to perform in situ X-ray analysis on many small protein crystals within a microfluidic crystallization platform has the potential to overcome these challenges. An automated method for collecting a "single-shot" of data from a large number of crystals was developed in collaboration with the BioCARS team at the Advanced Photon Source at Argonne National Laboratory (Chapter 6). The work described in this thesis shows that, even more so than for traditional structure determination efforts, the ability to grow and analyze a large number of high quality crystals is critical to enable time resolved structural studies of novel proteins. In addition to enabling X-ray crystallography experiments, the development of X-ray transparent microfluidic platforms also has tremendous potential to answer other scientific questions, such as unraveling the mechanism of in meso crystallization. For instance, the lipidic mesophases utilized during in meso membrane protein crystallization can be characterized by small angle X-ray diffraction analysis. Coupling in situ analysis with microfluidic platforms capable of preparing these difficult mesophase samples at very small volumes has tremendous potential to enable the high throughput analysis of these systems on a scale that is not reasonably achievable using conventional sample preparation strategies (Chapter 7). In collaboration with the LS-CAT team at the Advanced Photon Source, an experimental station for small angle X-ray analysis coupled with the high quality visualization capabilities needed to target specific microfluidic samples on a highly integrated chip is under development. Characterizing the phase behavior of these mesophase systems and the effects of various additives present in crystallization trials is key for developing an understanding of how in meso crystallization occurs. A long term goal of these studies is to enable the rational design of in meso crystallization experiments so as to avoid or limit the need for high throughput screening efforts. In summary, this thesis describes the development of microfluidic platforms for protein crystallization with in situ analysis capabilities. Coupling the ability to perform in situ analysis with the small scale, fine control, and the high throughput nature of microfluidic platforms has tremendous potential to enable a new generation of crystallographic studies and facilitate the structure determination of important biological targets. The development of platforms for in meso membrane protein crystallization is particularly significant because they enable the preparation of highly viscous mixtures at a previously unachievable scale. Work in these areas is ongoing and has tremendous potential to improve not only current the methods of protein crystallization and crystallography, but also to enhance our knowledge of the structure and function of proteins which could have a significant scientific and medical impact on society as a whole. The microfluidic technology described in this thesis has the potential to significantly advance our understanding of the structure and function of membrane proteins, thereby aiding the elucidation of human biology, the development of pharmaceuticals with fewer side effects for a wide range of diseases. References (1) Quick, M.; Javitch, J. A. P Natl Acad Sci USA 2007, 104, 3603. (2) Trubetskoy, V. S.; Burke, T. J. Am Lab 2005, 37, 19. (3) Pecina, P.; Houstkova, H.; Hansikova, H.; Zeman, J.; Houstek, J. Physiol Res 2004, 53, S213. (4) Arinaminpathy, Y.; Khurana, E.; Engelman, D. M.; Gerstein, M. B. Drug Discovery Today 2009, 14, 1130. (5) Overington, J. P.; Al-Lazikani, B.; Hopkins, A. L. Nat Rev Drug Discov 2006, 5, 993. (6) Dauter, Z.; Lamzin, V. S.; Wilson, K. S. Current Opinion in Structural Biology 1997, 7, 681. (7) Hansen, C.; Quake, S. R. Current Opinion in Structural Biology 2003, 13, 538. (8) Govada, L.; Carpenter, L.; da Fonseca, P. C. A.; Helliwell, J. R.; Rizkallah, P.; Flashman, E.; Chayen, N. E.; Redwood, C.; Squire, J. M. J Mol Biol 2008, 378, 387. (9) Hansen, C. L.; Skordalakes, E.; Berger, J. M.; Quake, S. R. P Natl Acad Sci USA 2002, 99, 16531. (10) Leng, J.; Salmon, J.-B. Lab Chip 2009, 9, 24. (11) Zheng, B.; Gerdts, C. J.; Ismagilov, R. F. Current Opinion in Structural Biology 2005, 15, 548. (12) Lorber, B.; Delucas, L. J.; Bishop, J. B. J Cryst Growth 1991, 110, 103. (13) Talreja, S.; Perry, S. L.; Guha, S.; Bhamidi, V.; Zukoski, C. F.; Kenis, P. J. A. The Journal of Physical Chemistry B 2010, 114, 4432. (14) Chayen, N. E. Current Opinion in Structural Biology 2004, 14, 577. (15) He, G. W.; Bhamidi, V.; Tan, R. B. H.; Kenis, P. J. A.; Zukoski, C. F. Cryst Growth Des 2006, 6, 1175. (16) Zheng, B.; Tice, J. D.; Roach, L. S.; Ismagilov, R. F. Angew Chem Int Edit 2004, 43, 2508. (17) Li, L.; Mustafi, D.; Fu, Q.; Tereshko, V.; Chen, D. L. L.; Tice, J. D.; Ismagilov, R. F. P Natl Acad Sci USA 2006, 103, 19243. (18) Song, H.; Chen, D. L.; Ismagilov, R. F. Angew Chem Int Edit 2006, 45, 7336. (19) van der Woerd, M.; Ferree, D.; Pusey, M. Journal of Structural Biology 2003, 142, 180. (20) Ng, J. D.; Gavira, J. A.; Garcia-Ruiz, J. M. Journal of Structural Biology 2003, 142, 218. (21) Talreja, S.; Kenis, P. J. A.; Zukoski, C. F. Langmuir 2007, 23, 4516. (22) Hansen, C. L.; Quake, S. R.; Berger, J. M. US, 2007. (23) Newman, J.; Fazio, V. J.; Lawson, B.; Peat, T. S. Cryst Growth Des 2010, 10, 2785. (24) Newman, J.; Xu, J.; Willis, M. C. Acta Crystallographica Section D 2007, 63, 826. (25) Collingsworth, P. D.; Bray, T. L.; Christopher, G. K. J Cryst Growth 2000, 219, 283. (26) Durbin, S. D.; Feher, G. Annu Rev Phys Chem 1996, 47, 171. (27) Talreja, S.; Kim, D. Y.; Mirarefi, A. Y.; Zukoski, C. F.; Kenis, P. J. A. J Appl Crystallogr 2005, 38, 988. (28) Yoshizaki, I.; Nakamura, H.; Sato, T.; Igarashi, N.; Komatsu, H.; Yoda, S. J Cryst Growth 2002, 237, 295. (29) Anderson, M. J.; Hansen, C. L.; Quake, S. R. P Natl Acad Sci USA 2006, 103, 16746. (30) Hansen, C. L.; Sommer, M. O. A.; Quake, S. R. P Natl Acad Sci USA 2004, 101, 14431. (31) Lounaci, M.; Rigolet, P.; Abraham, C.; Le Berre, M.; Chen, Y. Microelectron Eng 2007, 84, 1758. (32) Zheng, B.; Roach, L. S.; Ismagilov, R. F. J Am Chem Soc 2003, 125, 11170. (33) Zhou, X.; Lau, L.; Lam, W. W. L.; Au, S. W. N.; Zheng, B. Anal. Chem. 2007. (34) Cherezov, V.; Caffrey, M. J Appl Crystallogr 2003, 36, 1372. (35) Qutub, Y.; Reviakine, I.; Maxwell, C.; Navarro, J.; Landau, E. M.; Vekilov, P. G. J Mol Biol 2004, 343, 1243. (36) Rummel, G.; Hardmeyer, A.; Widmer, C.; Chiu, M. L.; Nollert, P.; Locher, K. P.; Pedruzzi, I.; Landau, E. M.; Rosenbusch, J. P. Journal of Structural Biology 1998, 121, 82. (37) Gavira, J. A.; Toh, D.; Lopez-Jaramillo, J.; Garcia-Ruiz, J. M.; Ng, J. D. Acta Crystallogr D 2002, 58, 1147. (38) Stevens, R. C. Current Opinion in Structural Biology 2000, 10, 558. (39) Baker, M. Nat Methods 2010, 7, 429. (40) McPherson, A. In Current Topics in Membranes, Volume 63; Volume 63 ed.; DeLucas, L., Ed.; Academic Press: 2009, p 5. (41) Gabrielsen, M.; Gardiner, A. T.; Fromme, P.; Cogdell, R. J. In Current Topics in Membranes, Volume 63; Volume 63 ed.; DeLucas, L., Ed.; Academic Press: 2009, p 127. (42) Page, R. In Methods in Molecular Biology: Structural Proteomics - High Throughput Methods; Kobe, B., Guss, M., Huber, T., Eds.; Humana Press: Totowa, NJ, 2008; Vol. 426, p 345. (43) Caffrey, M. Ann Rev Biophys 2009, 38, 29. (44) Doerr, A. Nat Methods 2006, 3, 244. (45) Brostromer, E.; Nan, J.; Li, L.-F.; Su, X.-D. Biochemical and Biophysical Research Communications 2009, 386, 634. (46) Li, G.; Chen, Q.; Li, J.; Hu, X.; Zhao, J. Anal Chem 2010, 82, 4362. (47) Jia, Y.; Liu, X.-Y. The Journal of Physical Chemistry B 2006, 110, 6949. (48) RCSB Protein Data Bank. http://www.rcsb.org/ (July 11, 2010). (49) Membrane Proteins of Known 3D Structure. http://blanco.biomol.uci.edu/Membrane_Proteins_xtal.html (July 11, 2010). (50) Michel, H. Trends Biochem Sci 1983, 8, 56. (51) Rosenbusch, J. P. Journal of Structural Biology 1990, 104, 134. (52) Garavito, R. M.; Picot, D. Methods 1990, 1, 57. (53) Kulkarni, C. V. 2010; Vol. 12, p 237. (54) Landau, E. M.; Rosenbusch, J. P. P Natl Acad Sci USA 1996, 93, 14532. (55) Pebay-Peyroula, E.; Rummel, G.; Rosenbusch, J. P.; Landau, E. M. Science 1997, 277, 1676. (56) Cherezov, V.; Liu, W.; Derrick, J. P.; Luan, B.; Aksimentiev, A.; Katritch, V.; Caffrey, M. Proteins: Structure, Function, and Bioinformatics 2008, 71, 24. (57) Cherezov, V.; Rosenbaum, D. M.; Hanson, M. A.; Rasmussen, S. G. F.; Thian, F. S.; Kobilka, T. S.; Choi, H. J.; Kuhn, P.; Weis, W. I.; Kobilka, B. K.; Stevens, R. C. Science 2007, 318, 1258. (58) Cherezov, V.; Yamashita, E.; Liu, W.; Zhalnina, M.; Cramer, W. A.; Caffrey, M. J Mol Biol 2006, 364, 716. (59) Jaakola, V. P.; Griffith, M. T.; Hanson, M. A.; Cherezov, V.; Chien, E. Y. T.; Lane, J. R.; IJzerman, A. P.; Stevens, R. C. Science 2008, 322, 1211. (60) Rosenbaum, D. M.; Cherezov, V.; Hanson, M. A.; Rasmussen, S. G. F.; Thian, F. S.; Kobilka, T. S.; Choi, H. J.; Yao, X. J.; Weis, W. I.; Stevens, R. C.; Kobilka, B. K. Science 2007, 318, 1266. (61) Wacker, D.; Fenalti, G.; Brown, M. A.; Katritch, V.; Abagyan, R.; Cherezov, V.; Stevens, R. C. J Am Chem Soc 2010, 132, 11443. (62) Höfer, N.; Aragão, D.; Caffrey, M. Biophys J 2010, 99, L23. (63) Li, L.; Ismagilov, R. F. Ann Rev Biophys 2010. (64) Pal, R.; Yang, M.; Lin, R.; Johnson, B. N.; Srivastava, N.; Razzacki, S. Z.; Chomistek, K. J.; Heldsinger, D. C.; Haque, R. M.; Ugaz, V. M.; Thwar, P. K.; Chen, Z.; Alfano, K.; Yim, M. B.; Krishnan, M.; Fuller, A. O.; Larson, R. G.; Burke, D. T.; Burns, M. A. Lab Chip 2005, 5, 1024. (65) Jayashree, R. S.; Gancs, L.; Choban, E. R.; Primak, A.; Natarajan, D.; Markoski, L. J.; Kenis, P. J. A. J Am Chem Soc 2005, 127, 16758. (66) Wootton, R. C. R.; deMello, A. J. Chem Commun 2004, 266. (67) McPherson, A. J Appl Crystallogr 2000, 33, 397.

Low temperature magneto-photoluminescence characterization of high purity gallium arsenide and indium phosphide

Low-temperature magneto-photoluminescence is a very powerful technique to characterize high purity GaAs and InP grown by various epitaxial techniques. These III-V compound semiconductor materials are used in a wide variety of electronic, optoelectronic and microwave devices. The large binding energy differences of acceptors in GaAs and InP make possible the identification of those impurities by low-temperature photoluminescence without the use of any magnetic field. However, the sensitivity and resolution provided by this technique rema1ns inadequate to resolve the minute binding energy differences of donors in GaAs and InP. To achieve higher sensitivity and resolution needed for the identification of donors, a magneto-photoluminescence system 1s installed along with a tunable dye laser, which provides resonant excitation. Donors 1n high purity GaAs are identified from the magnetic splittings of "two-electron" satellites of donor bound exciton transitions 1n a high magnetic field and at liquid helium temperature. This technique 1s successfully used to identify donors 1n n-type GaAs as well as 1n p-type GaAs in which donors cannot be identified by any other technique. The technique is also employed to identify donors in high purity InP. The amphoteric incorporation of Si and Ge impurities as donors and acceptors in (100), (311)A and (3ll)B GaAs grown by molecular beam epitaxy is studied spectroscopically. The hydrogen passivation of C acceptors in high purity GaAs grown by molecular beam epitaxy (MBE) and metalorganic chemical vapor deposition (MOCVD) 1s investigated using photoluminescence. Si acceptors ~n MBE GaAs are also found to be passivated by hydrogenation. The instabilities in the passivation of acceptor impurities are observed for the exposure of those samples to light. Very high purity MOCVD InP samples with extremely high mobility are characterized by both electrical and optical techniques. It is determined that C is not typically incorporated as a residual acceptor ~n high purity MOCVD InP. Finally, GaAs on Si, single quantum well, and multiple quantum well heterostructures, which are fabricated from III-V semiconductors, are also measured by low-temperature photoluminescence.

Chemical and physical effects of ultrasound: sonoluminescence and materials

When a liquid is irradiated with ultrasound, acoustic cavitation (the formation, growth, and implosive collapse of bubbles in liquids irradiated with ultrasound) generally occurs. This is the phenomenon responsible for the driving of chemical reactions (sonochemistry) and the emission of light (sonoluminescence). The implosive collapse of bubbles in liquids results in an enormous concentration of sound energy into compressional heating of the bubble contents. Therefore, extreme chemical and physical conditions are generated during cavitation. The study of multibubble sonoluminescence (MBSL) and single-bubble sonoluminescence (SBSL) in exotic liquids such as sulfuric acid (H2SO4) and phosphoric acid (H3PO4) leads to useful information regarding the intracavity conditions during bubble collapse. Distinct sonoluminescing bubble populations were observed from the intense orange and blue-white emissions by doping H2SO4 and H3PO4 with sodium salts, which provides the first experimental evidence for the injected droplet model over the heated-shell model for cavitation. Effective emission temperatures measured based on excited OH• and PO• emission indicate that there is a temperature inhomogeneity during MBSL in 85% H3PO4. The formation of a temperature inhomogeneity is due to the existence of different cavitating bubble populations: asymmetric collapsing bubbles contain liquid droplets and spherical collapsing bubbles do not contain liquid droplets. Strong molecular emission from SBSL in 65% H3PO4 have been obtained and used as a spectroscopic probe to determine the cavitation temperatures. It is found that the intracavity temperatures are dependent on the applied acoustic pressures and the thermal conductivities of the dissolved noble gases. The chemical and physical effects of ultrasound can be used for materials synthesis. Highly reactive species, including HO2•, H•, and OH• (or R• after additives react with OH•), are formed during aqueous sonolysis as a consequence of the chemical effects of ultrasound. Reductive species can be applied to synthesis of water-soluble fluorescent silver nanoclusters in the presence of a suitable stabilizer or capping agent. The optical and fluorescent properties of the Ag nanoclusters can be easily controlled by the synthetic conditions such as the sonication time, the stoichiometry of the carboxylate groups to Ag+, and the polymer molecular weight. The chemical and physical effects of ultrasound can be combined to prepare polymer functionalized graphenes from graphites and a reactive solvent, styrene. The physical effects of ultrasound are used to exfoliate graphites to graphenes while the chemical effects of ultrasound are used to induce the polymerization of styrene which can then functionalize graphene sheets via radical coupling. The prepared polymer functionalized graphenes are highly stable in common organic solvents like THF, CHCl3, and DMF. Ultrasonic spray pyrolysis (USP) is used to prepare porous carbon spheres using energetic alkali propiolates as the carbon precursors. In this synthesis, metal salts are generated in situ, introducing porous structures into the carbon spheres. When different alkali salts or their mixtures are used as the precursor, carbon spheres with different morphologies and structures are obtained. The different precursor decomposition pathways are responsible for the observed structural difference. Such prepared carbon materials have high surface area and are thermally stable, making them potentially useful for catalytic supports, adsorbents, or for other applications by integrating other functional materials into their pores.

Core-level photoemission investigations of the CDTE(100) and INSB(100) surface and interfacial structures

Photoemission techniques, utilizing a synchrotron light source, were used to analyze the clean (100) surfaces of the zinc-blende semiconductor materials CdTe and InSb. Several interfacial systems involving the surfaces of these materials were also studied, including the CdTe(lOO)-Ag interface, the CdTe(lOO)-Sb system, and the InSb(lOO)-Sn interface. High-energy electron diffraction was also employed to acquire information about of surface structure. A one-domain (2xl) structure was observed for the CdTe(lOO) surface. Analysis of photoemission spectra of the Cd 4d core level for this surface structure revealed two components resulting from Cd surface atoms. The total intensity of these components accounts for a full monolayer of Cd atoms on the surface. A structural model is discussed commensurate with these results. Photoemission spectra of the Cd and Te 4d core levels indicate that Ag or Sb deposited on the CdTe(l00)-(2xl) surface at room temperature do not bound strongly to the surface Cd atoms. The room temperature growth characteristics for these two elements on the CdTe(lOO)-(2xl) are discussed. The growth at elevated substrate temperatures was also studied for Sb deposition. The InSb(lOO) surface differed from the CdTe(lOO) surface. Using molecular beam epitaxy, several structures could be generated for the InSb(lOO) surface, including a c(8x2), a c(4x4), an asymmetric (lx3), a symmetric (lx3), and a (lxl). Analysis of photoemission intensities and line shapes indicates that the c(4x4) surface is terminated with 1-3/4 monolayers of Sb atoms. The c(8x2) surface is found to be terminated with 3/4 monolayer of In atoms. Structural models for both of these surfaces are proposed based upon the photoemission results and upon models of the similar GaAs(lOO) structures. The room temperature growth characteristics of grey Sn on the lnSb(lOO)-c(4x4) and InSb(l00)-c(8x2) surfaces were studied with photoemission. The discontinuity in the valence band maximum for this semiconductor heterojunction system is measured to be 0.40 eV, independent of the starting surface structure and stoichiometry. This result is reconciled with theoretical predictions for heterostructure behavior.

Solid-liquid interactions in microscale structures and devices

Liquid-solid interactions become important as dimensions approach mciro/nano-scale. This dissertation focuses on liquid-solid interactions in two distinct applications: capillary driven self-assembly of thin foils into 3D structures, and droplet wetting of hydrophobic micropatterned surfaces. The phenomenon of self-assembly of complex structures is common in biological systems. Examples include self-assembly of proteins into macromolecular structures and self-assembly of lipid bilayer membranes. The principles governing this phenomenon have been applied to induce self-assembly of millimeter scale Si thin films into spherical and other 3D structures, which are then integrated into light-trapping photovoltaic (PV) devices. Motivated by this application, we present a generalized analytical study of the self-folding of thin plates into deterministic 3D shapes, through fluid-solid interactions, to be used as PV devices. This study consists of developing a model using beam theory, which incorporates the two competing components — a capillary force that promotes folding and the bending rigidity of the foil that resists folding into a 3D structure. Through an equivalence argument of thin foils of different geometry, an effective folding parameter, which uniquely characterizes the driving force for folding, has been identified. A criterion for spontaneous folding of an arbitrarily shaped 2D foil, based on the effective folding parameter, is thus established. Measurements from experiments using different materials and predictions from the model match well, validating the assumptions used in the analysis. As an alternative to the mechanics model approach, the minimization of the total free energy is employed to investigate the interactions between a fluid droplet and a flexible thin film. A 2D energy functional is proposed, comprising the surface energy of the fluid, bending energy of the thin film and gravitational energy of the fluid. Through simulations with Surface Evolver, the shapes of the droplet and the thin film at equilibrium are obtained. A critical thin film length necessary for complete enclosure of the fluid droplet, and hence successful self-assembly into a PV device, is determined and compared with the experimental results and mechanics model predictions. The results from the modeling and energy approaches and the experiments are all consistent. Superhydrophobic surfaces, which have unique properties including self-cleaning and water repelling are desired in many applications. One excellent example in nature is the lotus leaf. To fabricate these surfaces, well designed micro/nano- surface structures are often employed. In this research, we fabricate superhydrophobic micropatterned Polydimethylsiloxane (PDMS) surfaces composed of micropillars of various sizes and arrangements by means of soft lithography. Both anisotropic surfaces, consisting of parallel grooves and cylindrical pillars in rectangular lattices, and isotropic surfaces, consisting of cylindrical pillars in square and hexagonal lattices, are considered. A novel technique is proposed to image the contact line (CL) of the droplet on the hydrophobic surface. This technique provides a new approach to distinguish between partial and complete wetting. The contact area between droplet and microtextured surface is then measured for a droplet in the Cassie state, which is a state of partial wetting. The results show that although the droplet is in the Cassie state, the contact area does not necessarily follow Cassie model predictions. Moreover, the CL is not circular, and is affected by the micropatterns, in both isotropic and anisotropic cases. Thus, it is suggested that along with the contact angle — the typical parameter reported in literature quantifying wetting, the size and shape of the contact area should also be presented. This technique is employed to investigate the evolution of the CL on a hydrophobic micropatterned surface in the cases of: a single droplet impacting the micropatterned surface, two droplets coalescing on micropillars, and a receding droplet resting on the micropatterned surface. Another parameter which quantifies hydrophobicity is the contact angle hysteresis (CAH), which indicates the resistance of the surface to the sliding of a droplet with a given volume. The conventional methods of using advancing and receding angles or tilting stage to measure the resistance of the micropatterned surface are indirect, without mentioning the inaccuracy due to the discrete and stepwise motion of the CL on micropillars. A micronewton force sensor is utilized to directly measure the resisting force by dragging a droplet on a microtextured surface. Together with the proposed imaging technique, the evolution of the CL during sliding is also explored. It is found that, at the onset of sliding, the CL behaves as a linear elastic solid with a constant stiffness. Afterwards, the force first increases and then decreases and reaches a steady state, accompanied with periodic oscillations due to regular pinning and depinning of the CL. Both the maximum and steady state forces are primarily dependent on area fractions of the micropatterned surfaces in our experiment. The resisting force is found to be proportional to the number of pillars which pin the CL at the trailing edge, validating the assumption that the resistance mainly arises from the CL pinning at the trailing edge. In each pinning-and-depinning cycle during the steady state, the CL also shows linear elastic behavior but with a lower stiffness. The force variation and energy dissipation involved can also be determined. This novel method of measuring the resistance of the micropatterned surface elucidates the dependence on CL pinning and provides more insight into the mechanisms of CAH.