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In this dissertation, the central objective is to achieve fairness in bandwidth sharing amongst selfish users in a distributed system. Because of the inherent contention-based nature of the distributed medium access and the selfishness of the users, the distributed medium access is modeled as a non-cooperative game; designated as the Access Game. A p-CSMA type medium access scenario is proposed for all the users. Therefore, in the Access Game, each user has two actions to choose from: "transmit" and "wait". The outcome of the Access Game and payoffs to each user depends on the actions taken by all the users. Further, the utility function of each user is constructed as a function of both Quality of Service (QoS) and Battery Power (BP). Various scenarios involving the relative importance of QoS and BP are considered. It is observed that, in general the Nash Equilibrium of the Access Game does not result into fairness. Therefore, Constrained Nash Equilibrium is proposed as a solution. The advantage of Constrained Nash Equilibrium is that it can be predicated on the fairness conditions and the solution will be guaranteed to result in fair sharing of bandwidth. However, Constrained Nash Equilibrium is that it is not self-enforcing. Therefore, two mechanisms are proposed to design the Access Game in such a way that in each case the Nash Equilibrium of the Access Game satisfies fairness and maximizes throughput. Hence, with any of these mechanisms the solution of the Access Game becomes self-enforcing.

Our ability to sense small molecules with high specificity, over a broad range of concentrations, is limited and difficult to accomplish in a way that is inexpensive and continuous. The most commercially successful biosensor is the enzyme-based blood glucose electrochemical biosensor, yet for nearly all other biomolecules, detection and monitoring require specialized equipment, trained personnel, and long lead times, and are not amenable to continuous monitoring. Industries in need of enzyme-based small-molecule biosensors, including medical diagnostics, industrial production, environmental monitoring, food safety analysis, and international security, would benefit greatly from the development of new devices capable of measuring biomolecules of interest. Environmental microbes have been gaining attention because of the vast array of biomolecules that they are capable of sensing and degrading. These microbes do so, in part, through redox enzymes with diverse substrate specificities that represent an immense resource for developing electrochemical biosensors. However, the development of new enzyme biosensors has largely been limited by the lack of a general high-throughput method to identify these redox enzymes, making discovery slow, laborious, and ad hoc. To address this need, a high-throughput functional screening approach has been developed to isolate microbial oxidase enzymes from complex metagenomic DNA libraries based solely on the enzyme-mediated degradation of any target analyte. The approach can be applied to DNA isolated from any complex microbial sample, including unidentified or unculturable bacteria. In this research, I first describe the development of a general assay to capture the activity of oxidase enzymes expressed in E. coli cells. I then demonstrate how the assay can be used to screen for the nicotine degrading oxidase NicA2 from a genomic DNA library generated from the microbe P. putida. Lastly, I describe the use of this screen to identify a new hydrocortisone-responsive oxidase from a pooled genomic DNA library of eight microbes, representing over 43 Mb of DNA sequence space. This hydrocortisone oxidase represents the first of many new enzymes that can be discovered leveraging our screening platform, which is poised to revolutionize the electrochemical biosensing field and substantially broaden the number of molecules these electrochemical biosensors can detect continuously and quantitatively. / 2023-02-17T00:00:00Z

Thesis advisor: Charles Hoffman / The second messenger cyclic 3’-5’ adenosine monophosphate (cAMP) signaling pathway plays an important physiological role in many organisms. Cyclic nucleotide phosphodiesterases (PDEs) regulate signal transduction by catalyzing the hydrolysis of cAMP and cGMP allowing for the downregulation of cyclic nucleotide levels. Human PDEs are encoded by 21 genes grouped into 11 families. The biological role of the most recently discovered PDE family (PDE11) remains poorly understood partly due to the lack of selective inhibitors. Mutations in the PDE11A gene have been linked to a wide range of diseases, such as Cushing Syndrome, which is a result of inactivating mutations expressed in adrenocortical tumors. Meanwhile, PDE11 levels are seen to increase in the ventral hippocampus as a function of aging, and is associated with a loss of social memory. Thus, the development of a selective PDE11 inhibitor could provide a potential therapeutic benefit to patients receiving long-term corticosteroid treatment by stimulating cortisol production by the adrenal gland, as well as to aging adults to maintain social memory. To address these needs, candidate PDE11 inhibitors related to a compound discovered by the Hoffman lab in a high throughput screen for PDE11 inhibitors are being synthesized by the Rotella laboratory. I have been evaluating these compounds using two fission yeast-based growth assays in complement with in vitro enzyme assays carried out by Dr. Jeremy Eberhard. Here I describe my role in the project, leading to the identification of a compound, SMQ2-57, which is a selective inhibitor of the PDE11 enzyme whose potency has been confirmed through both yeast-based assays and in vitro enzyme assays. In addition, I have taken both a forward and reverse genetic approach to identify PDE11A4 mutant alleles that confer resistance to inhibitor compounds as such knowledge could guide a rational drug design approach to produce more effective PDE11 inhibitors. Based on our results, SMQ2-57 could serve as a useful tool in understanding the biological role of PDE11. Meanwhile, data from my study of compound resistant mutant PDE11 alleles should allow for the characterization of the physical interaction between PDE11 and its inhibitors in an effort to guide a medicinal chemistry program to develop a more potent and drug-like PDE11 inhibitor. / Thesis (BS) — Boston College, 2023. / Submitted to: Boston College. College of Arts and Sciences. / Discipline: Scholar of the College. / Discipline: Biology.

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京都大学 / 新制・課程博士 / 博士(生命科学) / 甲第24052号 / 生博第478号 / 新制||生||63(附属図書館) / 京都大学大学院生命科学研究科高次生命科学専攻 / (主査)教授 朝長 啓造, 教授 野田 岳志, 教授 今吉 格 / 学位規則第4条第1項該当 / Doctor of Philosophy in Life Sciences / Kyoto University / DFAM

Wireless network for connecting the devices and sensors to communicate and sense is quite attractive nowadays for a wide range of applications. The scaling of the wireless network to millions of nodes currently is impractical if the process is supplied by battery energy. The batteries need to be periodically replaced or recharged due to the limited battery size. One solution is harvesting ambient energy to power the network. In this thesis, we consider a battery-limited energy harvesting communication system with online power control. Assuming independent and identically distributed (i.i.d.) energy arrivals and the harvest-store-use architecture, it is shown that the greedy policy achieves the maximum throughput if and only if the battery capacity is below a certain positive threshold that admits a precise characterization. Simple lower and upper bounds on this threshold are established. The asymptotic relationship between the threshold and the mean of the energy arrival process is analyzed for several examples. Furthermore, value iteration method is applied for solving the Bellman equation to obtain the optimal power allocation policy. The optimal policy is analyzed for several examples. / Thesis / Master of Applied Science (MASc)