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Abu-Baker, ShadiSolid-State NMR Spectroscopic Studies on Phospholamban and Saposin C Proteins in Phospholipid Membranes
Doctor of Philosophy, Miami University, 2007, Chemistry
Solid-state NMR spectroscopic techniques were used to investigate two significant membrane proteins, phospholamban (PLB) and Saposin C (Sap C). For the first protein, analysis of the 2H and 31P solid-state NMR data of chemically synthesized WT-PLB and its phophorylated form (P-PLB) in 1-palmitoyl-2-oleoyl-sn-glycero-phosphocholine (POPC) multilamellar vesicles (MLVs) indicates that the interaction of P-PLB with POPC bilayers was less significant when compared to PLB. Moreover, the secondary structure using 13C=O site-specific isotopically labeled Ala15-PLB and Ala15-P-PLB in POPC bilayers suggests that this residue, located in the cytoplasmic domain, is a part of an ?-helical structure for both PLB and P-PLB. Also, 2H NMR spectra of site-specific CD3-labeled WT-PLB and P-PLB at Ala15 exhibit one strong isotropic spectral component indicating the presence of additional motions as well as faster side-chain reorientations when compared with Leu51 and Ala24 representing the transmembrane domain. Conversely, the 15N Ala11 NMR spectrum of WT-PLB located on the cytoplasmic domain yields two dynamic components (powder pattern component and isotropic component) implying that the backbone dynamics of this residue exists in two populations: one that is immobile, and another which is motionally averaged on the NMR timescale. Upon phosphorylation, the 15N mobile component contribution increases. The POPC 15N NMR spectra indicate that the transmembrane domain has a tilt angle of 13 ± 6° with respect to the mechanically oriented POPC bilayer normal and that the cytoplasmic domain of WT-PLB lies on the surface of the phospholipid bilayers. For the second protein, 2H and 31P solid-state NMR data of Sap C in dioleoylphosphatidylglycerol (DOPG) and dioleoylphosphatidylserine (DOPS) mixed bilayers indicates that Sap C is not inserting deep into the bilayers and that it has no preference to DOPS over DOPG. Finally, several other solid-state NMR spectroscopic experiments indicate that protonated Sap C disturbs 1-palmitoyl-2-oleoyl-sn-glycero-3-[phospho-L-serine] (POPS) lipid bilayers and not the neutral POPC lipids.

Committee:

Lorigan Dr. Gary (Advisor)

Keywords:

Phospholamban; Saposin C; Solid-state NMR spectroscopy ; Solid-phase peptide synthesis; Protein-membrane interaction; multilamellar vesicles; Protein side-chain and backbone dynamics; Structural topology.

Daniels, Michael W.Generalized ID/LP grammar: a formalism for parsing linearization-based HPSG grammars
Doctor of Philosophy, The Ohio State University, 2005, Linguistics
This dissertation motivates and describes the Generalized Immediate Dominance/Linear Precedence (GIDLP) formalism: a formalism capable of serving as a processing backbone for linearization-based grammars in the Head Driven Phrase Structure Grammar (HPSG) framework. Complementing the work on the formalism, the thesis defines and implements an efficient parsing algorithm for GIDLP grammars. Representing a prominent tradition within HPSG, linearization-based HPSG assumes that the domain of word order can be larger than the local tree. This supports elegant and general linguistic analyses for (relatively) free word order languages, including the possibility of licensing discontinuous constituents. For processing with an HPSG grammar, most systems depend on parsing algorithms that make use of a phrase structure backbone – a part of the grammar that has been set aside and given a distinguished role in the parsing process – thereby contrasting with those that view parsing as a general constraint solving task, where general methods for logical reasoning are to be applied to the constraints present in an HPSG grammar. Processing backbones support efficient parsing algorithms, but they restrict the class of HPSG theories that can be encoded to those employing a phrase structure backbone, which excludes linearization-HPSG grammars. The GIDLP formalism solves the dilemma between the desire to encode linguistically general and elegant linearization-HPSG analyses and the need for a processing backbone. GIDLP allows linguists to specify grammars with linear precedence constraints that operate within explicitly declared word order domains extending beyond the local tree as well as immediate dominance rules in which the grammar writer can arrange the right-hand side as to minimize the number of parsing hypotheses that must be explored. The GIDLP parsing algorithm developed in the thesis supports efficient processing by making direct use of linear precedence constraints during parsing.

Committee:

W. Detmar Meurers (Advisor)

Subjects:

Language, Linguistics

Keywords:

parsing; backbone; linearization; HPSG; free word order

Ruan, NingNetwork Backbone with Applications in Reachability and Shortest Path Computation
PHD, Kent State University, 2012, College of Arts and Sciences / Department of Computer Science

This dissertation focuses on developing novel techniques to help understand, analyze, and query large graphs by utilizing backbone structures. Network backbone depicts a core substructure which not only offers concise and highlighted topological view of original graph, but also carries a large amount of essential information, such as information flow. In this dissertation, we introduce a novel backbone structure “gate graph” to provide a simplified topological view of original graph while preserving its distance measure. A graph simplification algorithm based on set cover framework is proposed to extract gate graph. We show theoretically and empirically that both approaches considerably reduce the complexity of original graph in terms of the number of vertices.

In addition, we also examine how to efficiently answer reachability query and shortest path (distance) query on large graphs, by utilizing tailored backbone structures: 1) first, to address scalability challenge in reachability query answering on massive graphs, we extract a “reachability backbone” and then leverage it to help scale the existing reachability indexing algorithms and speed up online query processing approaches; 2) secondly, to efficiently answer distance queries on large directed graphs, we present a novel labeling scheme, referred to as Highway-Centric Labeling, utilizing a directed spanning tree as highway structure. We build an interesting connection between our labeling problem and Bipartite Set Cover problem and propose an elegant algorithm with non-trivial logarithmic bound to solve it; 3) finally, we introduce a novel Hub2-Labeling approach to compute the exact shortest path between two vertices with distance no more than 6 in large social networks. Our approach significantly extends the existing landmark approach by utilizing a large number of hubs to help estimate the distance and to help reduce the search space. We demonstrate these approaches using synthetic datasets and real-world datasets to show that they achieve much better performance than existing methods, in terms of either scalability or query efficiency.

Committee:

Ruoming Jin, Dr. (Advisor); Feodor Dragan, Dr. (Committee Member); Jonathan Maletic, Dr. (Committee Member); Robin Selinger, Dr. (Committee Member); Almut Schroeder, Dr. (Committee Member)

Subjects:

Computer Science

Keywords:

network backbone; graph simplification; reachability; shortest path computation; scalability

Prakash, AbhinavAnonymous and Secure Communication in a Wireless Mesh Network
MS, University of Cincinnati, 2012, Engineering and Applied Science: Computer Science

With the rapid advancement of different types of wireless technologies the problem arose of combining them together to provide improved bandwidth and enhanced throughput. The answer came out in the form of a Wireless Mesh Network (WMN). A typical WMN is made up of mesh routers and mesh clients where mesh routers have somewhat limited mobility and they form the backbone of the network whereas mesh clients are allowed to be highly mobile or completely stationary or somewhere in between. This forms a very versatile network which allows clients with different levels of mobility, interface and bandwidth requirements to be a part of the same network. The communication can be achieved by directly communicating with the router by being in its range or in an ad hoc fashion through several hops. A WMN is mainly designed to be self-configured and self-adjusting dynamically. This ensures large network coverage with minimum infrastructure requirements, hence low cost. Although a WMN gives multifold advantages it is also vulnerable to several security and privacy threats being a dynamic open medium. Different types of clients such as laptops, cell phones, smart devices can join or leave the network anytime they wish. This opens up issues like fake registrations and packet sniffing.

This work deals with the issues of security and privacy separately in two parts in great detail by simulating countermeasures for different kinds of attacks in a WMN. The first part mainly deals with creating a perfectly secure network for safe communication by using a bi-variate polynomial scheme for low overheads instead of a public-private key mechanism. The second part deals with making any communication in the network anonymous by hiding the node initiating the session by using redundancy at the cost of some associated overheads.

Committee:

Dharma Agrawal, DSc (Committee Chair); Yizong Cheng, PhD (Committee Member); Chia Han, PhD (Committee Member)

Subjects:

Computer Science

Keywords:

Mesh Networks; Security; Onion Routing; Bivariate Polynomial Function; Backbone; Hybrid Networks

Chakraborty, RubyDevelopment of Novel Cycloaliphatic Siloxanes for Thermal and UV-curable Applications
Doctor of Philosophy, University of Akron, 2008, Polymer Engineering

Siloxanes have been extensively used as additives to modulate surface properties such as surface tension, hydrophobicity/hydrophobicity, and adhesion, etc. Although, polydimethyl -siloxane and polydiphenylsiloxane are the most commonly used siloxanes, the properties are at extremes in terms of glass transition temperature and flexibility. It is proposed that the ability to control the properties in between the these extremes can be provided by cycloaliphatic substitutions at the siloxane backbone. It is expected that this substitution might work due to the intermediate backbone rigidity.

In order to achieve the above objectives, a synthetic route was developed to prepare cycloaliphatic (cyclopentane and cyclohexane) silane monomers followed by subsequent polymerization and functionalizations to obtain glycidyl epoxy, aliphatic amine and methacrylate telechelic siloxanes. The siloxanes were either thermally or UV- cured depending on end functionalizations. Chemical characterization of monomers, oligomers and polymers were performed using 1H, 13C, 29Si-NMR, FT-IR and GPC. The curing kinetics of photo-induced reactions were investigated through photo-differential scanning calorimetry (PDSC). The oxygen permeability, mechanical, coatings, and release properties of siloxanes were studied as a function of the backbone substitutions. The mechanical, coatings and released properties of cycloaliphatic siloxanes improved with respect to polydimethylsiloxanes. The thermal analysis of the cured films were carried out using differential scanning calorimetry (DSC). Viscoelastic properties of the cured siloxanes due to the variation of substitution at the siloxane backbone were measured using dynamic mechanical thermal analysis (DMTA). The cycloaliphatic substituted siloxanes showed an increased glass transition temperature and permeability but reduced crosslink density, conversion, and rate of curing with respect to polydimethylsiloxanes.

Hybrids of siloxanes were prepared with linseed oil based alkyds to study the effect of variation of alkyd oil lengths and cycloaliphatic substitutions on siloxane backbone. The oil length of an alkyd resin is defined as the number of grams of oil used to produce 100 grams of resin. Three linseed oil based alkyds representing long, medium, and short oil lengths were grafted with siloxanes substituted with methyl, cyclopentyl, and cyclohexyl groups. The reaction was monitored through FTIR and 1H-NMR. The hybrids were formulated with standard drier package and thermally cured for detailed film characterization. Improvement in crosslink density, flexibility, and reverse impact resistance were found as function of oil length. However, tensile modulus, elongation, glass transition temperature, drying time and fracture toughness decreased with increase in oil length. For hybrids, the cycloaliphatic substituents at the siloxane backbone showed enhanced mechanical and coating properties as compared to hybrids with polydimethylsiloxanes.

Random and block copolymer of polydimethylsiloxanes with polydicycloaliphatic- siloxanes were synthesized and compared with homopolymers of polydicycloaliphatic siloxanes. The chemical characterization of the copolymers and homopolymers were carried out through 1H, 13C, 29Si-NMR, and FT-IR. The glass transition temperatures (Tg) of the synthesized polymers were obtained through DSC and advanced rheometric expansion system (ARES). The Tg of random copolymers were found to be higher than the corresponding block copolymers. There was very small difference in Tg between cycloaliphaticsiloxanes homopolymers and corresponding random copolymers. From the above results, it can be inferred that the cycloaliphatic substitutions at the siloxane backbone can be used as a means to obtain properties intermediate to polydimethyl- and polydiphenyl siloxanes.

Committee:

Mark Soucek, PhD (Advisor); Sadhan C. Jana, PhD (Committee Member); Erol Sancaktar, PhD (Committee Member); George G. Chase, PhD (Committee Member); Chrys Wedemiotis, PhD (Committee Member)

Subjects:

Chemistry; Experiments; Materials Science; Polymers

Keywords:

cycloaliphatic; siloxanes; hybrids; backbone rigidity; hydrophobicity; thermal; UV; curable