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In this thesis we develop a molecular modeling toolkit that models the conformation space of proteins and allows easy prototyping of algorithms on the conformation space models, by extending an existing molecular modeling tool. Our toolkit creates a factor graph to represent the conformation space model and links it with an inference framework. This enables execution of statistical inference tasks and implementation of algorithms that work on graphical models. As an application of our toolkit, we study estimating free energy changes after mutations. We show that it is possible to represent molecular dynamics trajectories using graphical models and free energy perturbation calculations can be done efficiently on these models.

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Chromosomal DNA of A. vinelandii thought to carry multiple gene copies was examined in efforts to visualize its chromosomal structure using electron microscopy. The chromosomal DNA of A. vinelandii may have multiple circular genomic units carrying multiple copies of genes. Three possible branch construction schemes and their replication modes are postulated in this study.

This document only includes an excerpt of the corresponding thesis or dissertation. To request a digital scan of the full text, please contact the Ruth Lilly Medical Library's Interlibrary Loan Department (rlmlill@iu.edu).

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The objectives of these two studies were to characterize normal growth and resultant changes in conformation and walk kinematics of warmblood foals. The first study quantified linear and angular conformation changes of 13 warmblood foals during the first 9 mo of growth. An objective photographic method of evaluating conformation was used to obtain all data. All linear measurements increased significantly over the investigated ages and growth rates were highest in the first 2 mo of growth. Total percentage of growth during the study was greatest for neck and back length. Distal limb growth was minimal over the investigated ages. Metacarpal growth slowed earlier than many other traits. Length of the metatarsus increased minimally during the studied ages with significant growth occurring only between 23 wk and post-weaning measurements. Increasing wither heights were positively associated with increases in scapula, humerus, radius, ilium, femur, tibia and metatarsal and metacarpal lengths. Angular conformation also changed significantly during growth. Trends in angular changes were generally less clear than those for linear variables. Scapula, femur and hock angles significantly increased and humerus angle decreased with age. Utilizing a plumb line from the hock upward, the distance of the hindlimb behind the body was quantified. The distance out behind decreased significantly between 1 and 15 wk. Distance out behind was positively correlated with tibia angle at all ages. The second study quantified linear and temporal kinematics of the walk in growing foals. Nine warmblood foals from the first study were filmed as they walked over a uniform concrete surface covered in 13mm thick rubber matting. Speed was controlled through the use of a uniform handler with a metronome. Trait means at ages 3, 11, 21 wk and post-weaning were compared. Length variables were standardized to percent of total stride length. Temporal variables were standardized to percent of stride duration. Stride length and duration increased significantly with age. Step lengths, stance duration and protraction and retraction durations did not change across ages. Over-stride decreased significantly with age, potentially due to increased back length in older foals. Linear distance between diagonal hooves during stance increased with age, and was negatively correlated to the decrease in over-stride. While older foals appeared to display a more regular, 4-beat walk rhythm, timing between lateral and diagonal footfalls remained significantly different at all ages. Both conformation and kinematics changed during growth. Characterizing conformational changes due to growth can allow a better understanding of how foal conformation and gait change during growth and may predict these traits in adults, thus allowing selection of top performance prospects at a younger age. / Master of Science

The potential energy surface of naphtho (1,8-b,c) -1,5-dithiocin and its mono-, di-, tri-, and tetraoxides was analyzed by dynamic ¹H NMR spectroscopy, AM1 semiempirical calculations, and x-ray crystallography. The lowest energy conformers of these compounds in the solid state, the gas state, and in solution, as well as the energy barriers for the interconversion between their conformers are reported. The electronic structure of naphtho (1,8-b,c) -1,5-dithiocin was analyzed by the AM1 semiempirical method. An experimental method was developed to verify these calculations. Comparison of the relative intensities of the bands observed in the He I and He II photoelectron spectra of aromatic thioethers provides an effective means for assigning bands to ionizations from specific molecular orbitals. Such methodology confirmed the calculations which showed that naphtho (1,8-b,c) -1,5-dithiocin has a large sulfur-sulfur lone pair splitting of 1.6-2.0 eV. Dissolution of naphtho (1,8-b,c) -1,5-dithiocin-1-oxide in concentrated sulfuric acid produced the corresponding disulfide dication, which upon hydrolysis regenerated the sulfoxide. The mechanism of this reaction sequence was investigated using 2-monodeuterated naphtho (1,8-b,c) -1,5-dithiocin-1-oxide. This stereochemical probe showed that both the formation of the disulfide dication and its hydrolysis occurred with retention of stereochemistry at the sulfoxide sulfur. The molecular structure of naphtho (1,8-b,c) -1,5-dithiocin-1-oxide, determined by x-ray crystallographic methods, showed evidence of transannular interaction between the sulfur atoms. Vibronic analysis on naphtho (1,8-b,c) -1,5-dithiocin and naphtho (1,8-b,c) -1,5-dithiocin-1-oxide using the Hartree-Fock method with the STO-3G basis set showed no evidence of bond formation in naphtho (1,8-b,c) -1,5-dithiocin-1-oxide compared with naphtho (1,8-b,c) -1,5-dithiocin. Thus this transannular interaction in the sulfoxide must be due to electrostatic interaction and not incipent sulfurane formation. The mechanism of the photodecompositions of perester and aldehyde compounds with β substituted sulfur moieties was investigated. The photodecomposition of these compounds produced their corresponding alkenes without stereocontrol. These results suggest that the decompositions occur via a stepwise non-stereoselective mechanism. Flash photolysis of peresters β substituted with sulfonium salt groups was shown to produce thioether cation radicals, e.g., the 1,5-dithiocane cation radical. This demonstrated that the photodecomposition of β sulfonium salt peresters is potentially a powerful and novel method for making cation radicals.