Proteins containing selenocysteine (selenoproteins) have been found to exist in organisms from all domains of life. Selenoproteins are important for many in vivo processes such as the removal of reactive oxygen containing species (ROS), redox disulfide shuffling reactions, and pro-hormone activation. Structurally and functionally analogous to cysteine, selenocysteine's lower pKa appears to be the defining chemical difference between these two amino acids. Using a single-molecule electrical recording technique, rate constants for the reaction of selenocysteine with small molecule disulfides were obtained over a pH range of 6 - 10. Analogous single molecule ~riments carried out ~ .. - using cysteine, revealed that, after correcting for the ratio of selenolate to selenol and thiolate to thiol based on the pKa of each amino acid, the nuc1eophilicity of selenocysteine was comparable to that of cysteine. The selenium atom of the selenylsulfide bond was found to be substantially more electrophilic than a sui fur atom of the analogous disulfide bond and the leaving group ability of the selenolate of selenocysteine compared to the thiolate of cysteine were found to be comparable. Another biologically relavant interaction that occurs in vivo is the reaction between selenocysteine and organoarsenic (Ill) molecules. It is known that arsenic (Ill) compounds are toxic to organisms, and that this toxicity stems from the ability to coordinate to the thiol and selenol groups of the cysteine and selenocysteine residues within proteins. The reaction of selenocysteine with an organoarsenic species was investigated at the single molecule level over the pH range 6.5 - 8.5. By carrying out an analogous reaction between cysteine and the organoarsenic (Ill) species, it was found that selenocysteine and cysteine exhibit similar reaction rates. The organoarsenic reagent could exist in a range of different protonation states in solution and it was concluded that the rate of reaction was governed by the equilibrium of the arsenic molecule, where only some of the forms were reactive towards the selenocysteine and cysteine groups.

Thesis advisor: Peter Clote / RNA folding pathways play an important role in various biological processes, such as 1) the conformational switch in spliced leader RNA from Leptomonas collosoma, which controls transsplicing of a portion of the 5’ exon, and 2) riboswitches–portions of the 5’ untranslated region of mRNA that regulate genes by allostery. Since RNA folding pathways are determined by the thermodynamic landscape, we have developed a number of novel algorithms—including FFTbor and FFTbor2D—which efficiently compute the coarse-grained energy landscape for a given RNA sequence. These energy landscapes can then be used to produce a model for RNA folding kinetics that can compute both the mean first passage time (MFPT) and equilibrium time in a deterministic and efficient manner, using a new software package we call Hermes. The speed of the software provided within Hermes—namely FFTmfpt and FFTeq—present what we believe to be the first suite of kinetic analysis tools for RNA sequences that are suitable for high throughput usage, something we believe to be of interest in the field of synthetic design. / Thesis (PhD) — Boston College, 2015. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

The search for an alternative clean and renewable energy source has become an urgent matter. One such energy-saving technology is a fuel cell; it uses fuel as the source of energy to produce electricity directly and the byproducts formed are not as voluminous and environmentally harmful. The conventional low temperature fuel cells use hydrogen as the fuel which is produced from conventional fuels via reforming. However, developing reformers for hydrocarbon fuels requires AN understanding of the fundamental mechanisms and kinetics studies. In this study, simple hydrocarbon fuel, namely methane, in external reforming or internal reforming within a solid oxide fuel cell has been studied because of its importance and with the hope that it will ultimately lead to an understanding of reforming of higher hydrocarbons, such as logistic fuels like JP-8. For this purpose, methane was used the starting point and building block for the progressive understanding of reforming of complex hydrocarbons. Methane steam reforming (MSR), CH4 + 2H2O = CO2 + 4H2 is, in fact, the most common method of producing commercial bulk hydrogen along with the hydrogen used in ammonia plants. United States alone produces 9 million tons of hydrogen per year. The overall MSR reaction CH4 + 2H2O = CO2 + 4H2 is in fact composed of two reactions, the water gas shift reaction, CO + H2O = CO2 + H2, which has recently been investigated by a former Ph.D. student in our group, Caitlin Callaghan. Here, the first reaction CH4 + H2O = CO + 3H2, i.e., methane reforming, is analyzed using a reaction route network approach to obtain the overall methane steam reforming network and kinetics. Kinetics providing detailed information of elementary reaction steps for this system, namely micro-kinetics, has not yet been fully addressed. Employing the theory of Reaction Route Network Theory, recently developed by Fishtik and Datta, and using the Unity Bond Index-Quadratic Exponential Potential (UBI-QEP) method of Shustorovich to predict elementary step kinetics coupled with transition-state theory, a detailed microkinetic model of steam and dry reforming of methane has been developed for Rh(111) and Ni(111) in this thesis. While there is extensive literature on it, the standard reference on the mechanism and kinetics of MSR is that of Xu and Froment, who proposed a 13 step mechanism. Based on the assumption of rate limiting steps for these overall reactions, Xu and Froment derived rate expressions for overall kinetics with fitted parameters. Here a more detailed micro-kinetic model of steam reforming of methane has been developed by adding 3 steps pertinent to carbon formation on the catalyst to Xu and Froment's mechanism. The complete set as well as the dominant reaction routes has been identified. This was accomplished first by enumerating the list of reaction routes and drawing this network. A program was written in Maple and was used to assist in creating the list of full routes, empty routes and intermediate nodes. This program reduces the amount of repetitive work that was needed in an earlier Matlab program when computing the list. After drawing the complete reaction network it was than converted into an equivalent electrical circuit and Multisim analysis was performed. Further, the resistances of various reaction steps were compared. From the reduced graph, it was determined that reaction steps pertaining to desorption of carbon dioxide, i.e., step s4, and intermediate methylene forming intermediate methylidyne, s11, are the rate limiting steps. Further, through simulation with Multisim, it was determined that in fact only 2 overall reactions are needed. Adding a third overall reaction results in a nodal balance error. A rate expression was developed based on assuming the above two rate determining steps, with remaining steps at pseudo equilibrium along with the quasi-steady state approximation. The rate expression however produced a substantial error in conversion when compared to the overall microkinetic model. In addition to computing the micro-kinetic model, experimental work for methane steam reforming was conducted. A steam to carbon ratio of 2:1 was fed to the packed bed reactor, where experimental conversion data were obtained. These data points for Ni and Rh catalyst were plotted against the model to see how well the simulation predicted the experimental results. Reasonable agreement was obtained.

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1979. / MICROFICHE COPY AVAILABLE IN ARCHIVES AND SCIENCE. / Bibliography: leaves 252-265. / Ph.D.

Fe-B熔體可鑄造成網絡狀合金的微觀結構。研究顯示，熔融狀態的Fe₈₄B₁₆在275 K 過冷時將發生形態轉變。實驗結果指出熔融狀態的Fe-B合金存在一亞穏液態互溶區。該互溶區範圍為Fe₈₄B₁₄.到Fe₈₂B₁₈.。Fe-B網絡狀合金的微觀結構，由一個易碎的Fe₃B子網絡和一個具延展性的αFe子網絡組成。因此Fe-B網絡狀合金擁有具吸引性的物理性能。 / 由於Fe₈₄B₁₆網絡狀合金並不存在任何微孔，因此我們可推斷合金在結晶的過程中，兩個子網絡的固體/液體界面將一起生長。而且，在固體/液體界面前並不具有硼原子的濃度梯度。因此我們提出了一個生長模型來分析Fe-B網絡狀合金來自掃瞄電子顯微鏡和透射電子顯微鏡的檢測結果。Fe-B網絡狀合金的結晶動力學和微觀結構均得到解釋。研究顯示，合金中的兩個子網絡均擁有特定的生長方向，並且以樹枝晶的方式來生長。 / Molten Fe₁₀₀-{U+2093}B{U+2093} melts, where x = 14 to 18, can be cast into ingots of network morphology. It was found that there is a morphological transition in molten Fe₈₄B₁₆.with undercooling of 275 K. The experimental results indicate that there is a metastable liquid miscibility gap in undercooled Fe-B melts. The network morphology consists of two interconnected subnetworks, which are αFe subnetwork and Fe₃B subnetwork respectively. The Fe-B network alloys have attractive mechanical properties. / As micropore does not exist in the Fe₈₄B₁₆ network ingot, it is proposed that the solid/liquid interfaces of the two subnetworks advance together during solidification. In addition, there is no composition gradient of boron atoms at the growth front. A growth model is proposed to explain the results by scanning electron microscopy and transmission electron microscopy. It was found that there is special crystallinity in Fe₈₄B₁₆ network ingots. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Wong, Tak Cheung = 鐵硼網狀合金的形成和結晶動力學 / 黃德彰. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2012. / Includes bibliographical references. / Abstracts also in Chinese. / Wong, Tak Cheung = Tie peng wang zhuang he jin de xing cheng he jie jing dong li xue / Huang Dezhang. / Abstract --- p.ii / Acknowledge --- p.iv / List of Table --- p.vii / List of Figures --- p.viii / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Phase diagram --- p.1 / Chapter 1.1.1 --- Undercooling --- p.1 / Chapter 1.2 --- Nucleation and Growth --- p.2 / Chapter 1.2.1 --- Homogeneous Nucleation --- p.3 / Chapter 1.2.2 --- Heterogeneous Nucleation --- p.3 / Chapter 1.2.3 --- Growth --- p.6 / Chapter 1.2.3.1 --- Growth of Pure Metal --- p.6 / Chapter 1.2.3.2 --- Solid/Liquid interface stability --- p.7 / Chapter 1.2.3.3 --- Solidification of Single Phase Binary Alloys --- p.8 / Chapter 1.2.3.3.1 --- Equilibrium Solidification --- p.8 / Chapter 1.2.3.3.2 --- Non-Equilibrium Solidification --- p.8 / Chapter 1.2.3.3.3 --- Morphology Change --- p.9 / Chapter 1.2.3.4 --- Solidification of the Binary Eutectic Alloy --- p.10 / Chapter 1.2.3.4.1 --- Growth of Lamellar Eutectics --- p.10 / Chapter 1.2.3.4.2 --- Off-Eutectic Alloys --- p.11 / Chapter 1.3 --- Binary Systems with a Solid Miscibility Gap --- p.11 / Chapter 1.4 --- Phase Separation Mechanisms in a Solid Miscibility Gap --- p.12 / Chapter 1.4.1 --- Nucleation and Growth --- p.12 / Chapter 1.4.2 --- Spinodal Decomposition --- p.13 / Chapter 1.4.4.1 --- The initiation of Spinodal Decomposition --- p.13 / Chapter 1.4.4.2 --- Diffusion Equation of Spinodal Decomposition --- p.14 / Chapter 1.4.4.3 --- Solution to the Modified Diffusion Equation --- p.17 / Figures --- p.18 / References / Chapter Chapter 2 --- Experimental --- p.29 / Chapter 2.1 --- Preparation of fused silica tube --- p.29 / Chapter 2.2 --- Alloying and fluxing --- p.29 / Chapter 2.3 --- Undercooling --- p.30 / Chapter 2.4 --- Sample Preparation --- p.31 / Chapter 2.4.1 --- Cutting, Grinding and Polishing --- p.31 / Chapter 2.4.2 --- Sample preparation for Scanning Electron Microscopy (SEM) --- p.32 / Chapter 2.4.3 --- Sample preparation for Transmission Electron Microscopy (TEM) --- p.32 / Chapter 2.5 --- Microhardness Test --- p.33 / Chapter 2.6 --- Compression Test --- p.33 / Chapter 2.7 --- Microstructure Analysis --- p.34 / Chapter 2.7.1 --- Scanning Electron Microscopy Analysis --- p.34 / Chapter 2.7.2 --- Transmission Electron Microscopy Analysis --- p.34 / Chapter 2.7.3 --- Indexing Diffraction Patterns --- p.34 / Figures --- p.36 / Chapter Chapter 3 --- Formation of Fe-B network alloys --- p.38 / Chapter 3.1 --- Abstract --- p.38 / Chapter 3.2 --- Introduction --- p.39 / Chapter 3.3 --- Experimental --- p.40 / Chapter 3.4 --- Results --- p.42 / Chapter 3.5 --- Discussion --- p.47 / Chapter 3.6 --- Conclusions --- p.48 / Figures --- p.50 / References --- p.69 / Chapter Chapter 4 --- SEM and TEM studies of Fe84B16 70 alloys of network morphology --- p.70 / Chapter 4.1 --- Abstract --- p.70 / Chapter 4.2 --- Introduction --- p.71 / Chapter 4.3 --- Background --- p.71 / Chapter 4.4 --- Experimental --- p.73 / Chapter 4.5 --- Results --- p.74 / Chapter 4.6 --- Discussions --- p.81 / Chapter 4.7 --- Conclusions --- p.85 / Figures --- p.87 / References --- p.106

Cheng, Lai Fung. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2009. / Includes bibliographical references (leaf 79). / Abstracts in English and Chinese. / Cheng, Lai Fung. / Chapter Chapter1 --- Introduction --- p.1 / Chapter 1.1 --- Phase diagram determination --- p.1 / Chapter 1.2 --- Formation of a hump in the free energy curve of L in a eutectic alloy --- p.2 / Chapter 1.3 --- Spinodal decomposition --- p.2 / Chapter 1.4 --- Early experience --- p.3 / Chapter 1.5 --- Bulk metallic glasses (BMG) --- p.5 / Chapter 1.6 --- Metal matrix composites (MMC) --- p.6 / Chapter 1.7 --- Liquid state phase separation and the formation of metal matrix comosites by fluxing --- p.6 / Chapter Chapter2 --- Experimental --- p.15 / Chapter 2.1 --- Introduction --- p.15 / Chapter 2.2 --- Preparation of fused silica tube --- p.15 / Chapter 2.3 --- Sample Preparation --- p.16 / Chapter 2.3.1 --- Alloying --- p.16 / Chapter 2.3.2 --- Fluxing --- p.16 / Chapter 2.4 --- Liquidus of Fe-C-Si specimens --- p.16 / Chapter 2.5 --- Microstructure Analysis --- p.17 / Chapter 2.6 --- Mechanical properties --- p.18 / Chapter 2.6.1 --- Hardness test --- p.18 / Chapter 2.6.2 --- Compressive strength --- p.18 / Chapter Chapter3 --- Formation and mechanical properties of Fe86Si14 network alloys --- p.23 / Chapter 3.1 --- Abstract --- p.23 / Chapter 3.2 --- Introduction --- p.24 / Chapter 3.3 --- Experimental --- p.25 / Chapter 3.4 --- Results --- p.27 / Chapter 3.5 --- Discussion --- p.33 / Chapter Chapter4 --- Dependence of mechanical behavior on C concentration in Fe-C-Si network alloys --- p.63 / Chapter 4.1 --- Abstract --- p.63 / Chapter 4.2 --- Introduction --- p.64 / Chapter 4.3 --- Experimental --- p.66 / Chapter 4.4 --- Results --- p.68 / Chapter 4.5 --- Discussions --- p.76

This thesis details four consecutive research investigations which were designed to examine the effect of age on the pulmonary oxygen uptake (VO2)and muscle oxygenation (mOxy) responses to exercise in well-trained cyclists. (Abridged)

Graduation date: 1999

Widespread tetracycline resistance (TcR) has limited the clinical use of Tc for the treatment of bacterial infections. Tet(O) protein is present in many bacteria and is the major transmissible TcR determinant in Campylobacter jejuni, a common cause of acute bacterial diarrhea worldwide. Tet(O) protects ribosomes against the inhibition of protein synthesis by Tc. Tet(O) binds to the ribosome at a similar site as EF-G, a structural homologue of Tet(O) with GTPase activity that is required for protein elongation. EF-G interfered with the kinetics of Tet(O)-mediated Tc release suggesting that EF-G competes with Tet(O) for ribosome binding. Indirect assessment of EF-G and Tet(O) binding to 70S ribosomes by GTP hydrolysis was unable to clearly demonstrate competition for binding. This thesis contributed to the further understanding of the kinetics of Tc release by Tet(O), and may facilitate the development of novel strategies to overcome Tet(O)-mediated TcR in bacteria which cause human infections.

Success in baseball batting is fundamental to the sport, however it remains one of, if not the most, challenging skills in sports to master. Batters utilize the kinetic chain to transfer energy from the lower body to the upper body to the bat, hoping to impart the maximum amount of energy into the ball. Scientists and coaches have researched the swing and developed theories on the keys for successful batting, but most of this research has been inadequate in attempting to fully describe the biomechanics of batting. The purposes of this study were to improve upon the methodology of previous researchers, provide a full biomechanical description of the swing, and compare swings against pitches thrown to different locations and at different speeds. AA-level Minor League Baseball players (n=43) took extended rounds of batting practice in an indoor laboratory against a pitcher throwing a mixture of fastballs and changeups. An eight camera motion analysis system and two force plates recording at 300 Hz captured the biomechanical data. The swing was divided into six phases (stance, stride, coiling, swing initiation, swing acceleration, and follow-through) by five key events (lead foot off, lead foot down, weight shift commitment, maximum front foot vertical ground reaction force, and bat-ball contact). Twenty-eight kinematic measurements and six ground reaction force measurements were computed based on the marker and force plate data, and all were assessed throughout the phases. First, a comprehensive description of a composite of the batters’ swings against fastballs “down the middle” was provided. Second, successful swings against fastballs thrown to one of five pitch locations (HIGH IN, HIGH OUT, LOW IN, LOW OUT, MIDDLE) were compared in terms of selected kinematics at the instant of bat-ball contact, timing and magnitude of peak kinematic velocities, and timing and magnitude of peak ground reaction forces. Third, these variables were once again compared for swings against fastballs and changeups. A large number of biomechanical differences were seen among the swings against various pitch locations. More fully rotated positions, particularly of the pelvis and bat were critical to the batters’ successes on inside pitches while less rotated positions keyed successes against outside pitches. The trail and lead arms worked together as part of a closed chain to drive the hand path. Successful swings had the trail elbow extended more for HIGH IN and flexed more for LOW OUT, though batters often struggled to execute this movement properly. A distinct pattern among successful swings against fastballs, successful swings against changeups, and unsuccessful swings against changeups was witnessed; namely a progressive delay in which the batter prematurely initiated the events of the kinetic chain, especially when unsuccessful in hitting a changeup. It was believed that this study was much more effective in capturing the essence of baseball batting than previous scientific works. Some recommendations to batting coaches would be to get batters to take a consistent approach in the early phases of every swing (particularly for the lower body), identify both pitch type and location as early as possible, use the rotation of the pelvis to propagate the energy transfer of the kinetic chain from the group to the upper body, and use the pelvis, and subsequently, the upper body, to orient the trunk and hands to an optimal position to drive the ball to the desired field. Limitations of the current study and ideas for future work were also presented to better interpret the findings of this research and further connect science and sport.