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Micro gas chromatographs are miniaturized analytical instruments developed based on gas chromatography (GC) and Micro-Electro-Mechanical Systems technologies for fast, on-site, volatile compound analysis. The small footprint of these devices enables portability, low power consumption, and fast analysis time. Due to these features, micro gas chromatographs can be applied to environmental monitoring, homeland security, and online quality tracking. This dissertation describes the development of prototype instruments as well as studies of core components such as micro preconcentrators, microcolumns, Deans switches, and micro vapor detectors. Two nondestructive photoionization detectors have been developed and verified to have ultra-low detection limits (few pg) as well as rapid response rates. The micro flow-through photoionization detector (micro-PID) integrates microfluidic channels and ionization chambers on monolithic chips, providing ‘on column detection’ for analytes. The micro-PID can be used at fluidic interfaces between each dimension in multidimensional GC systems for obtaining additional information for gas routing control and signal reconstruction. Helium dielectric barrier discharge photoionization detectors use helium plasma as an ionization source to emit photons with energies up to 17.5 eV. Thus, these detectors can serve as universal vapor sensors and will expand the application scope of micro GC systems. These detectors were used in an application on formaldehyde detection, which was studied with a heart cutting two-dimensional (2D) micro GC. Target compounds can be transferred into the second-dimensional system for further precise separation and detection. Analysis of other air pollution-related, toxic compounds was performed by the first-dimensional column and micro-PID simultaneously. The formaldehyde low detection limit of the novel 2D system was tested to be sub-ppb (V/V) level with 6 min of sampling. The design, fabrication, and evaluation of separation microcolumns are also discussed in this dissertation. A stationary phase thickness gradient coated microcolumn was developed to generate high-resolution chromatograms by introducing a peak focusing effect. Additionally, a hybrid adhesive connection method was developed for high-temperature applications and evaluated to be leak free and volatile compound free up to 350 °C even after thermal cycling. By integrating all miniaturized components, including micro preconcentrators, microcolumns, and micro-PIDs, an ultra-compact micro GC system (147 g in weight and 0.14 L in volume) was constructed. By scaling down the system, we achieved high separation performance and low power consumption, which clearly separated 14 compounds in 3 minutes.

MMFF94 is implemented for molecular mechanics calculation in the quantum chemistry polarizable force field program (QuanPol). As a general force field for organic molecules, the availability of MMFF94 expends the capability of the QuanPol program. The MMFF94 force field atom type determination and parameter matching methods are established and corresponding program routines are written in the FORTRAN language. In this implementation, the MMFF94 atom types can be determined automatically from the connectivity of the input atoms with no or minimum information of formal charges. This implementation of MMFF94 is validated using the 761 standard tests, thus is a complete implementation. MMFF94 molecular dynamics (MD) simulation is used to study the stability of a 21-residue antimicrobial peptide named MSI-78, which is an amphipathic alpha-helical peptide designed as a synthetic analog to the Magainin family peptides. The MD simulation shows that the MSI-78 peptide exhibits random coil structure in aqueous solvent, but alpha-helical structure in the 2,2,2-trifluoroethanol/water (50:50 V/V) solvent. These results are in good agreement with experiments. The MD simulation also suggests that the preferential stabilization of the folded alpha-helical structure of MSI-78 in the 2,2,2-trifluoroethanol/water solvent is due to its lower dielectric constant as compared to aqueous solvent. Advisor: Hui Li

Protein structural models provide essential information for the research on protein-protein interactions. In this dissertation, we describe two projects on the analysis of protein interactions using structural information. The focus of the first is to characterize and classify different types of interactions. We discriminate between biological obligate and biological non-obligate interactions, and crystal packing contacts. To this end, we defined six interface properties and used them to compare the three types of interactions in a hand-curated dataset. Based on the analysis, a classifier, named NOXclass, was constructed using a support vector machine algorithm in order to generate predictions of interaction types. NOXclass was tested on a non-redundant dataset of 243 protein-protein interactions and reaches an accuracy of 91.8%. The program is benecial for structural biologists for the interpretation of protein quaternary structures and to form hypotheses about the nature of proteinprotein interactions when experimental data are yet unavailable. In the second part of the dissertation, we present Galinter, a novel program for the geometrical comparison of protein-protein interfaces. The Galinter program aims at identifying similar patterns of different non-covalent interactions at interfaces. It is a graph-based approach optimized for aligning non-covalent interactions. A scoring scheme was developed for estimating the statistical signicance of the alignments. We tested the Galinter method on a published dataset of interfaces. Galinter alignments agree with those delivered by methods based on interface residue comparison and backbone structure comparison. In addition, we applied Galinter on four medically relevant examples of protein mimicry. Our results are consistent with previous human-curated analysis. The Galinter program provides an intuitive method of comparative analysis and visualization of binding modes and may assist in the prediction of interaction partners, and the design and engineering of protein interactions and interaction inhibitors.