Three-dimensional (3D) structural determination of biological macromolecules is not only critical to understanding their mechanisms, but also has practical applications. Combining the high resolution imaging of transmission electron microscopy (TEM) and efficient computer processing, protein structures in solution or in two-dimensional (2D) crystals can be determined. The lipid monolayer technique uses the high affinity binding of 6His-tagged proteins to a Ni-nitrilotriacetic (NTA) lipid to create high local protein concentrations, which facilitates 2D crystal formation. In this study, several proteins have been crystallized using this technique, including the SARS virus Nsp15 endonuclease and the human Toll-like receptor (TLR) 3 extracellular domain (ECD). Single particle analysis can determine protein structures in solution without the need for crystals. 3D structures of several protein complexes had been solved by the single particle method, including IniA from Mycobacterium tuberculosis, Nsp15 and TLR3 ECD. Determining the structures of these proteins is an important step toward understanding pathogenic microbes and our immune system.

Carbon Monoxide Dehydrogenase (CODH), also known as Acetyl-CoA synthase (ACS), is one of seven known Ni containing enzymes. CODH/ACS is a bifunctional enzyme which oxidizes CO to CO2 reversibly and synthesizes acetyl-CoA. Recently, X-ray crystal structures of homodimeric CODH from Rhodospirillum rubrum (CODHRr) and CODH from Carboxydothermus hydrogenoformans (CODHCh) have been published. These two enzymes catalyze only the reversible oxidation of CO to CO2 and have a protein sequence homologous to that of the β subunit of heterotetrameric α2β2 enzyme from Moorella thermoacetica (CODHMt), formerly Clostridium thermoaceticum. Neither CODHRr nor CODHCh contain an α-subunit as is found in CODHMt. The precise structure of the active site for acetyl-CoA synthase, called the A-cluster, is not known. Therefore, crystallization of the α subunit is required to solve the remaining structural features of CODH/ACS. Obtaining crystals and determining the X-ray crystal structure is a high-risk endeavor, and a second project was pursued involving the preparation, expression and analysis of various site-directed mutants of CODHMt. Mutational analysis of particular histidine residues and various other conserved residues of CODH from Moorella thermoacetica is discussed. Visual inspection of the crystal structure of CODHRr and CODHCh, along with sequence alignments, indicates that there may be separate pathways for proton and electron transfer during catalysis. Mutants of a proposed proton transfer pathway were characterized. Four semi-conserved histidine residues were individually mutated to alanine. Two (His116Mt and His122Mt) were essential to catalysis, while the other two (His113Mt and His119Mt) attenuated catalysis but were not essential. Significant activity was "rescued" by a double mutant where His116 was replaced by Ala and His was also introduced at position 115. Activity was also rescued in double mutants where His122 was replaced by Ala and His was simultaneously introduced at either position 121 or 123. Activity was also "rescued" by replacing His with Cys at position 116. Mutation of conserved Lys587 near the C-cluster attenuated activity but did not eliminate it. Activity was virtually abolished in a double mutant where Lys587 and His113 were both changed to Ala. Mutations of conserved Asn284 also attenuated activity. These effects suggest the presence of a network of amino acid residues responsible for proton transfer rather than a single linear pathway.

The high surface to volume ratio which is a property of nanoscale devices means the interfacial effects from these devices on the mass transport of analyte can be significant. Quartz nanopipette effect on the mass transport behavior of inorganic monovalent salts such as potassium chloride is shown to differ from those of conical nanopore. Quartz nanopipettes demonstrate a more significant interfacial impact on the mass transport behavior of inorganic salts. This is evidenced by significant impacts on ionic transport even at high electrolyte concentration where nanopore interfacial effects do not significantly impact the ion transport. Nanopipettes have been use to precipitate salts such as lithium chloride in bulk concentrations three orders of magnitude below the saturation concentration. These novel interfacial interactions have opened new avenues for crystallization of more complex organic biomolecules using inorganic systems as model systems on which to base the approach for these more complex systems.

Preservation of cells and tissues by freezing at temperatures below 70°C has led to new possibilities for the storage of germ cells for fertility preservation. During the freezing process problems might occur, the greatest being ice crystallization which can cause membrane destruction and thus cell death. To minimize this risk, solutions that reduce the freezing point can be added to reduce crystallization and increase survival rates. These solutions are called cryoprotectants. The best method for freezing is still not known.The aim of this study was to analyze the effect of various parameters on the survival rate of human semen frozen with liquid nitrogen. The parameters investigated were thawing method (incubator or water bath) and container choice (straw or ampoule). In addition, two different cryoprotectants were tested.The method used was the instruction for preservation with Sperm CryoProtec™ II from Nidacon. In total 16 samples were collected for the first test and 13 samples for the second test. Sperm concentration and motility was measured.There seem to be no significant differences depending on container choice or thawing method leading to the conclusion that the most cost effective method of storage and thawing may be used. A small but significant difference was found in survival after thawing dependent on cryoprotectant p=0.041. However the study sample was limited and further studies might be of value.

Controlling crystal size distribution (CSD) is important to downstream processing and to product quality. It is well-recognized that selective removal functions can be used to influence CSD, for example by manufacturing a product with a larger dominant size or narrower distribution. Early work on the use of feedback control to manipulate the residence time distribution functions of fines in a continuous crystallizer demonstrated the utility of such an approach in handling process upsets and cycling that resulted from system instability. These efforts were extended to batch crystallization, although there remained significant difficulty associated with on-line analysis of the size distribution. The development of new technologies, such as Focused Beam Reflectance Measurement (FBRM), provides a methodology for on-line monitoring of a representation of the crystal population in either batch or continuous crystallization systems. The FBRM technology is based on laser light scattering; properly installed, it allows on-line determination of the chord length distribution (CLD), which is statistically related to the CSD and depends on the geometry of the crystal. The purpose of the present study is to use the FBRM to monitor the evolution of CSD characteristics and to implement a feedback control scheme that provides the flexibility to move the CSD in a preferred direction. Cooling batch crystallizations of paracetamol has been chosen to investigate implementation of the control scheme. The work will show how fines removal and varying cooling rates provide reliable and practical control of crystal size distribution.

In this dissertation we used tunable particle-particle and particle-substrate attraction to achieve reversible two-dimensional crystallization of colloids on homogeneous and patterned substrates. Total internal reflection and video microscopy techniques were used to quantify the interparticle and particle-substrate interactions in these colloidal systems. Equilibrium and dynamic simulations were then utilized to link these colloidal interactions to the experimental colloidal phase behaviour. The importance of the nature of the attractive interaction in successfully crystallizing colloids has also been documented. The first set of experiments demonstrates the use of temperature and specific ion effects to reversibly control the net particle-substrate van der Waals (vdW) attraction. Colloidal stabilization was achieved via the use of adsorbed polymer brush layers. By using evanescent wave microscopy, we directly and precisely measured how temperature and specific ion effects control the dimensions of adsorbed polymer layers and hence the net van der Waals attraction in between the colloids and the substrate. However, the magnitude of the van der Waals attraction decays very rapidly with increasing surface separation and is therefore not conducive to the self assembly of colloidal crystals. We successfully used thermoresponsive polymer nanoparticles to control the depletion attraction between micron sized silica particles and thereby induced reversible crystallization of the micron sized silica colloids on homogeneous substrates. Video and evanescent wave microscopy techniques were used to measure the nanoparticle-induced attractive interaction as a function of temperature. The experimentally observed phase behaviour was verified via simulations that utilized knowledge of the measured colloidal depletion interactions. Finally, patterned surface topologies were used to position attractive colloidal crystals. Simulations were used to link the measured colloidal interactions to experimental phase behaviour as well as substrate topology. An extension of the concepts developed in this dissertation might suggest a general strategy to assemble colloidal particles into robust and annealable crystals contributing to the fabrication of photonic bandgap materials.

Zeolites are microporous crystalline materials, which are widely used in catalysis, adsorption, and ion-exchange processes. However, in most cases, the synthesis of novel zeolites as functional materials still relies on trial-and-error methods, which are time consuming and expensive. Therefore, the motivation for this thesis work is to understand the zeolite synthesis mechanismand further develop knowledge for manipulating zeolite properties and ultimately the rational design of porous materials. This work focused on formation of silicalite-1 (pure-silica ZSM-5) from basic aqueous solutions containing tetraorthosilicate (TEOS) as silica source, and tetrapropylammonium (TPA) cations as the organic structure-directing agent. The presence of silica precursor particles with size of 2-5 nm in these mixtures prior to and during hydrothermal treatments have been observed through dynamic light scattering (DLS), small-angle X-ray (SAXS) and transmission electron microscopy (TEM). However, to quantify composition and the molecular structure transformation of these silica precursor particles during zeolite synthesis is still a technical challenge. Another important yet unresolved question is how organocations interact with these nanoparticles and direct zeolite nuclei. Unlike many studies performed analyzing the inorganic phase (silica) present in synthesis mixtures, this study quantified the organocation-silica particle interaction and its ultimate effect on zeolite growth mainly through probing the behavior of the organocations. Pulsed-field gradient (PFG) NMR was used to capture the mobility change of organocations, and was complemented with scattering measurements (DLS, SAXS) on the silica nanoparticles. On the basis of the measurement results, the thermodynamic and kinetic properties of the organic-inorganic interaction were derived. Upon aging at room temperature, this interaction manifested as binding of TPA onto the silica particles due to electrostatic interactions, and such binding behavior can be well described by the Langmuir adsorption model. Upon hydrothermal treatment, a fraction of TPA adsorbed at room temperature dissociates from the growing silica nanoparticles and the corresponding desorption profiles were fitted well by the pseudo-second order kinetic model. The addition of tetramethylammonium (TMA) as "competitors" promoted TPA desorption kinetics and hindered silica nanoparticle growth due to stronger association of TMA with particles than that of TPA. Finally, the TPA adsorption strength increased via addition of monovalent salts with increasing ionic size whereas that of TMA shows an opposite trend. This suggests one potential route for tuning the organic-silica precursor particle interactions and thus possibly affecting some kinetics steps in the synthesis.

A small amount of poly(trimethylene succinate) (PTSu) were copolymerized or blended with poly(butylenes succinate) (PBSu) in this study. The range of intrinsic viscosity for PBSu and PBSu-enriched copolymers are between 1.62 and 0.97 dL/g; number-average molecular weights are in the range of 2.5x104 and 11.9x104 g/mol with polydispersity indices ranging from 1.52 to 3.94. Copolymer composition is calculated from 1H and 13C NMR spectra, and the distribution of BS and TS units in these copolymers are supported to be random from the evidence of a single glass transition temperature (Tg) and a randomness value close to 1.0. Tg of PBSu is -40.8 ¢XC. The Tg values of copolymers and blends increased with TS contents. The melting temperature (Tm) and the exothermic heat of crystallization of blends were not strongly affected by blending with PTSu. The values of Avrami exponent (n) for PBSu, copolymers and blends ranging from 2.3 to 3.1 indicate that heterogeneous nucleation with three-dimensional growth and homogeneous nucleation with two-dimensional growth might happen during the crystallization process. Multiple melting behavior was observed for PBSu, PBSu- enriched copolyesters and blends. Their peak temperatures are denoted as Tm1, Tm2 and Tm3 in order of increasing temperature. Tm1 corresponds to the melting temperature of the so-called annealing peak which might be resulted from the competition between continuous melting and re-crystallization. In contrast the peak at Tm2 is attributed to the melting of the primary crystals formed during isothermal crystallization. The peak at Tm3 may arise from the melting of re-crystallized primary crystals. Equilibrium melting temperatures were determined by the Hoffman-Weeks linear extrapolations which yield of 127.4 ¢XC for PBS, 125.7 ¢XC for PBTSA95/05, 120.6 ¢XC for PBTSu90/10, 128.6 ¢XC for PBSu/PTSu 98/02, 127.0 ¢XC for PBSu/PTSu 95/05 and 125.5 ¢XC for PBSu/PTSu 90/10. The thickness coefficient ( ) is located between 0.77 and 0.80. Three characteristics temperatures of thermal degradation, defined as temperature of thermal degradation at begining (Tstart), weight losses of 2% (Tloss2%) and maximum degradation rate (Tmax), were employed to characterize the thermal stability of polyesters and blends. The Tloss2% and Tstart values of PBTSu90/10 are higher than the values of the others because of its unusually high molecular weight. Wide-angle x-ray diffraction patterns were obtained after complete isothermal crystallization. Diffraction peaks are in the same positions, and these peaks become sharper and increase in intensity as the crystallization temperature increases. This indicates that during the heating process, only one crystal form appears and both of the crystallite size and perfect degree increase. The isothermal growth rate of PBSu spherulite increases from 0.01 £gm/sec at 103 ¢XC to 3.33 £gm/sec at 75 ¢XC. When the TS units increase, the spherulitic growth rates of PBTSu95/05 and PBTSu90/10 copolyesters decline dramatically. One of the reasons is that the incorporation of TS units into PBSu significantly inhibits the crystallization behavior of PBSu. Growth rates data were treated with Lauritzen-Hoffman secondary nucleation theory to find the regime transition. Using the Williams-Landel-Ferry (WLF) values, regime II to III transition is found at 95.1 ¢XC for PBSu, 84.4 ¢XC PBTSu95/05, and 77.1 ¢XC for PBTSu 90/10. All melt-crystallized specimens formed two dimensional axial-like spherulites with negative birefringence. Extinction bands were observed when PBSu, PBSu- enriched copolymers and blends specimens were crystallized at large undercooling.

Minor amounts of monomers or homopolymer of poly(butylene succinate) (PBS) were copolymerized or blended with monomers or homopolymer of poly(ethylene succinate) (PES). PEBSA 95/05 represents a copolymer synthesized from a feed ratio of 95 mol% ethylene glycol and 5 mol% 1,4-butanediol with 100 mol% succinic acid. Copolymers PEBSA 90/10 and 50/50 were also synthesized. Blends of PES and PBS were prepared in solution with ratios of PES/PBS: 98/02, 95/05 and 90/10. Molecular weights of homopolymers and copolymers were measured using capillary viscometer and gel permeation chromatography. The results indicate that polyesters used in this study have high molecular weights. The chemical composition and the sequence distribution of co-monomers in copolyesters were determined using 1H NMR and 13C NMR. The distribution of ES and BS units in these copolyesters was found to be random from the evidence of a single Tg and a randomness value close to 1.0 for a random copolymer. Thermal properties of polyesters and blends were characterized using differential scanning calorimeter (DSC), temperature-modulated DSC (TMDSC) and thermogravimeter. For copolymers, melting point of PES significantly decreases from 100.9 to 94.5 to 89.8 oC with an increasing in BS units from 0 to 5 to 10 mol%. Blends keep the intrinsic melting points of PES and PBS homopolymers. There is no significant difference or no trend about the thermal stability of these polyesters and blends. Wide-angle X-ray diffractograms (WAXD) were obtained for specimens after complete isothermal crystallization. Diffraction peaks indicate that the crystal structure of PES is dominated in PES-enriched copolymers. However, PEBSA 50/50 displays weak diffraction peaks of the characteristic peaks of PBS homopolymer. Isothermal crystallization of copolyesters and blends were performed using DSC. Their crystallization kinetics and melting behavior after complete crystallization were analyzed. The n1 values of the Avrami exponent for copolyesters increased from 2.54 to 2.84 as the isothermal temperature (Tc) increased. The Hoffman-Weeks linear plots yielded an equilibrium melting temperature of 111.1 and 107.0 oC, respectively, for PEBSA 95/05 and 90/10. Homopolymer PES has an equilibrium melting temperature of 112.7 oC. For blends, the n1 value has a minimum at Tc of 40 oC then it increases with an increase in Tc or in PBS. At the same Tc, n1 increases slightly and the rate constant (k1) decreases when the ratio of PBS in blends increases. All of these blends gave an equilibrium melting temperature of 113.1 oC. Multiple melting behavior involves melting-recrystallization-remelting and various lamellar crystals. As Tc or BS unit in copolymer increases, the contribution of recrystallization slowly declines. Acetophenone was used a diluent for PES homopolymer. Five concentrations were used to estimate the melting point depression, and the heat of fusion of PES was obtained to have a value of 163.3 J/g according to Flory equation. Spherulitic growth rates of copolymers were measured at Tc between 30 and 80 oC using polarized light microscope (PLM). Maximum growth rates occurred at Tc around 50 oC. It is found that the growth rate of copolymer decreases significantly after randomly incorporating BS units into PES. Non-isothermal method at a cooling rate of 2, 4 or 6 oC/min was used to calculate the isothermal growth rates of copolymers. These continuous data fit very well with the data points measured isothermally. Growth rates data are separately analyzed using the Hoffman-Lauritzen equation. A regime II-III transition is found at 59.4 and 52.4 oC, respectively, for copolyesters PEBSA 95/05 and PEBSA 90/10. The results of DSC and PLM indicate that blend PES/PBS 98/02 not only retains the melting point and the crystallinity of PES homopolymer, but also increases the nucleation rate of this blend. The effect of blending 2 mol% PBS with PES on the biodegradability of PES is deserved to be investigated furthermore.

The compositions of a series of poly (ethylene/trimethylene terephthalate) copolyesters were identified by 1H-NMR and 13C-NMR. The ethylene terephthalate (ET) units are 8.9, 33.7, 37.9, 50.1, 72.5, 77.8, and 90.8% in the copolyesters with sample codes of C2, C3, C4, C5, C6, C7, and C8, respectively. The triad sequence probabilities were determined from the normalized areas of aromatic quaternary carbons. The calculated average-number sequence lengths of ethylene- and trimethylene- terephthalate units range from 1.0 to 10.2 that depends on the relative ratio of both units in the copolymer. The values of randomness parameter for all of these copolyesters are between 0.96 and 1.1. Both values of sequence length and randomness parameter indicate that these copolyesters are random copolymers. Differential scanning calorimeter (DSC) was used to study the isothermal crystallization kinetics and the melting behaviors at heating rates of 10 and 50¢XC/min. The average enthalpy of isothermal crystallization (DH) decreased from 47 to 28 J/g when the ET units in the copolymer increased from 8.9% (C2) to 72.5% (C6), and then the enthalpy increased up to 42 J/g for the C8 copolymer with 90.8% of ET units. The results of Avrami analysis yielded one (n1) or two exponents. The n1 values of all of these copolymers were between 2.03 and 2.98. It suggests that the primary crystallization followed a heterogeneous nucleation with two-three dimensional form of growth. While investigating the isothermal crystallization, DSC specimens were crystallized for 9-14 times of the peak time to ensure the completion of crystallization. Both heating curves at 10 and 50¢XC/min showed multiple endothermic peaks. Triple-melting peaks were detected at lower crystallization temperature (Tc), then the medium and the highest temperature peaks merged gradually to form double-melting peaks with increase in Tc, finally, all three peaks merged together to become a single peak at higher Tc. The low temperature melting peak was associated with the last step of secondary crystallization. The middle temperature melting peak was considered to be characteristic of the melting of the crystals formed in the primary crystallization. The highest temperature melting peak may be due to the melting of crystallite formed by melting and recrystallization during the DSC heating scans. From the results of multiple melting behaviors at a heating rate of 50¢XC/min, the melting peak temperatures of primary crystals were plotted versus the crystallization temperature, Tc. The Hoffman-Weeks plot gave an equilibrium melting temperature, . Using the half-time of crystallization (t1/2) for analysis, regime II¡÷III transition was found for each copolyester. The pairs of ( , ) in unit of ¢XC are (237.1, 193.6), (198.9, 147.3), (187.9, 140.4), (226.6, 164.8), (230.1, 172.0), and (261.1, 208.4) for C2, C3, C4, C6, C7, and C8, respectively. Finally, the overall crystallization rates (1/ t1/2) were compared at equivalent supercooling, DT ( - Tc). The C2 copolyester crystallized the fastest and at lower supercooling. C3 and C4 copolyesters had very similar rates. The C6 copolyester crystallized the slowest and at higher supercooling. At DT = 50~60¢XC, the rates of C7 were close to those of C3 and C4 copolyesters, then the C7 copolyester crystallized faster at higher supercooling. The average value of DH or crystallinity decreased from ¡V47 to ¡V32 J/g when the minor component, ET unit, increasesd from 8.9% (C2) to 37.9% (C4), and then the crystallinity increased from ¡V28 to ¡V42 J/g as the ET unit increases from 72.5% (C6) to 90.8% (C8). It indicated that the number and the distribution of minor component in the main chain should affect the nucleation rate, the growth rate and the final crystallinity of the copolyesters.