Doctor of Philosophy, The Ohio State University, 2023, Chemistry

In nature, metal containing proteins are found in all kingdoms of life and perform some of the most biologically important chemical reactions. One class of metallocofactors, the iron-sulfur cluster, is responsible for a wide array of biological processes from electron transfer to energy storage and conversion in biological metabolism. While homometallic iron-sulfur clusters are widely observed, there are fewer examples of heterometallic iron-sulfur clusters, which contain a unique heterometal coordinated within the cluster scaffold. These clusters typically have a singular function; to catalyze difficult chemical reactions such as nitrogen or carbon fixation. One such enzyme, carbon monoxide dehydrogenase (CODH), contains a heterometallic [NiFe4S4] cluster active site called the C-cluster. This enzyme is of great interest with respect to current energy challenges, as it performs the reduction of carbon dioxide (CO2) to the chemical feedstock carbon monoxide (CO) with perfect selectivity and negligible overpotential under ambient conditions, characteristics current anthropogenic catalysts have been unable to achieve. However, due to the complexity of the system, there are significant gaps in our knowledge of the mechanism. Moreover, previous attempts to model this system using synthetic analogous have not been shown to operate with any functionality. Alternatively, it is possible to model metalloenzymes by repurposing existing metalloproteins, thus providing accurate structural models within a biological scaffold. We have chosen a ferredoxin (Fd) from Pyrococcus furiosus which contains a site-differentiated [Fe4S4] cluster. This site-differentiation allows for facile substitution of the unique site with Ni2+ to structurally model the active site of the CODH. The [NiFe3S4] Fd (NiFd) cluster exhibits reversible electron transfer and the ability to bind both CO and cyanide (CN-), a substrate and inhibitor of CODH respectively. We have extensively characterized the el (open full item for complete abstract)

Committee: Hannah Shafaat (Advisor); Christine Thomas (Advisor) Subjects: Chemistry

Doctor of Philosophy (Ph.D.), University of Dayton, 2023, Materials Engineering

Additive manufacturing (AM) has evolved as a convenient technology for rapid fabrication of prototype tooling and complex geometry components. Among all AM techniques, FFF is the most widely used for making polymeric structures. However, the process consistency and control of properties in the manufactured articles remains a challenging issue. The current study aims to investigate physical changes in polylactic acid (PLA) during 3D printing. The correlations between porosity, crystallinity and mechanical properties of the printed parts were studied. Moreover, the effects of bed-plate temperature were investigated. Experimental results confirmed the anisotropy of printed objects due to the occurrence of orientation phenomena during filament deposition and the formation both of ordered and disordered crystalline structures (α and δ, respectively). A post-3D printing heat treatment cycle was demonstrated as an effective method to improve mechanical properties by optimizing the crystallinity (transforming the α form into the δ form) and overcoming the anisotropy of the 3D printed object. The second approach to enhance the physical and chemical properties of neat PLA is by using nano-additives such as carbon nanotubes (CNTs) and carbon black (CB). 4 As the concentration of carbon nanotubes increased the mechanical and electrical properties were improved even with low volume ratio of CNTs. In molten polymer and under shear force CNTs tended to align parallel to the shear direction leading to significant increase in electrical properties in the direction of alignment. Also, a change in the enthalpy of cold crystallization was observed. The enthalpy of cold crystallization of PLA/CNT samples was lower than pure PLA because of a change in the type of crystallites formed during cold crystallization. The presence of carbon nanotubes reduced the crystallization domain leading to the formation of unstable crystalline phase δ, which was remarkably disordered compared to that o (open full item for complete abstract)

Committee: Khalid Lafdi (Committee Chair); Youssef Raffoul (Committee Member); Donald Klosterman (Committee Member); Li Cao (Committee Member) Subjects: Materials Science

Master of Science (MS), Wright State University, 2020, Chemistry

Acid dissociation constants, often expressed as pKa values, afford vital information with regards to molecular behavior in various environments and are of significance in fields of organic, inorganic, and medicinal chemistry. Several quantitative structure-activity relationships (QSARs) were developed that correlate experimental pKas for a given class of compounds with a descriptor(s) calculated using density functional theory at the B3LYP/6-31+G** level utilizing the CPCM solvent model. A set of carbon acids provided a good final QSAR model of experimental aqueous pKas versus ΔEH2O (R2 = 0.9647) upon removal of three aldehydes as outliers. A study of saturated alcohols offered a final QSAR model with R2 = 0.9594, which was employed to confirm the behavior of the three aldehydes as hydrated species in aqueous solution. Finally, a study restricted to ketones was conducted to estimate their pKas in dimethyl sulfoxide solution. QSAR models of experimental pKas versus ΔEDMSO for the keto and enol tautomers were modest at best (R2 = 0.8477 and 0.7694, respectively). A binary linear regression was employed to incorporate descriptors representing both the keto and enol tautomers, improving the final R2 to 0.9670 upon removal of one outlier. The QSAR models presented may be utilized to estimate pKas for related compounds not offered in the existing literature or that are challenging to measure experimentally.

Committee: Paul Seybold Ph.D. (Advisor); Eric Fossum Ph.D. (Committee Member); David Dolson Ph.D. (Committee Member) Subjects: Chemistry; Organic Chemistry; Physical Chemistry

Doctor of Philosophy, University of Akron, 2017, Polymer Science

Geckos are intriguing creatures, adhering to ceilings, to leafs, to glass and cement, all without glue. Instead, their adhesion is dependent on surface interactions between their hierarchical adhesive structure and the contacting substrates. These interactions on the nanoscale have significant macroscale influences. Changing the conditions between substrate and the nanostructures of the gecko adhesive affects the ability of geckos to adhere. Improving our understanding of how these conditions affect the adhesion of the natural gecko system can then inform our synthetic adhesive design efforts. Here, I have investigated how geckos perform on 'soft' substrates and on rough underwater substrates. Taking inspiration from the hierarchical nanostructure of the gecko adhesive, and its interactions with water, hierarchical rough carbon nanotube substrates were used to investigate the roles of roughness and surface chemistry on superhydrophobic stability. The 3D structure of CNTs was further used to investigate the influence of surface interactions on the macroscale thermal conductivity properties.

Committee: Ali Dhinojwala Dr. (Advisor); Yu Zhu Dr. (Committee Chair); Gary Hamed Dr. (Committee Member); Mesfin Tsige Dr. (Committee Member); Peter Niewiarowski Dr. (Committee Member) Subjects: Condensation; Experiments; Nanoscience; Physics; Polymers; Zoology

Master of Science (M.S.), University of Dayton, 2015, Electrical Engineering

Detection of biomolecules in aqueous or vapor phase is a valuable metric in the assessment of health and human performance. For this purpose, resonant capacitive sensors are designed and fabricated. The sensor platform used is a resonant test structure (RTS) with a molecular recognition element (MRE) functionalized guanine dielectric layer used as the sensing layer. The sensors are designed such that the selective binding of the biomarkers of interest with the MREs is expected to cause a shift in the test structure's resonant frequency, amplitude, and phase thereby indicating the biomarker's presence. This thesis covers several aspects of the design and development of these biosensors. Guanine biopolymer is characterized using capacitive test structures (CTSs) and RTSs with guanine dielectric layers. From this characterization, the dielectric constant and loss tangent of guanine are found to be 5.345 ± 0.294 and 0.015 ± 0.001 respectively. The resonance of the RTS with guanine dielectric layer is 3.148 ± 0.079 GHz with a notch depth of 7.472 ± 0.330 dB. To further characterize guanine, contact angle measurements with water were performed to determine the hydrophobic/hydrophilic properties. The contact angle is 62.07° ± 3.029° indicating the guanine thin films are slightly hydrophobic in comparison to glass (contact angle is 41.4° ± 2.72°). Additionally, a chemical functionalization method for guanine is developed. In this method, a cross-linker is simultaneously and covalently bound to the surface of the guanine and to the biomolecule thereby creating a covalent tether. Tests employing a biotin-streptavidin model indicate the chemical functionalization method is viable. In addition to the resonant capacitive sensor, two radio frequency (RF) test structures are developed: an RF bridge and a half-wavelength resonator. Both of these test structures have gaps in the transmission lines that will be bridged with MRE functionalized carbon nanotubes (CNTs). Any b (open full item for complete abstract)

Committee: Guru Subramanyam Ph.D. (Committee Chair); Karolyn M. Hansen Ph.D. (Committee Member); Partha Banerjee Ph.D. (Committee Member) Subjects: Biology; Electrical Engineering

PhD, University of Cincinnati, 2014, Engineering and Applied Science: Environmental Engineering

Black carbon (BC) from vehicular emission in transportation is a principal component of particulate matters ≤ 2.5 μm (PM2.5). PM2.5 and other diesel emission pollutants (e.g., NOx) are regulated by the Clean Air Act (CAA) according to the National Ambient Air Quality standards (NAAQS). This doctoral dissertation details a study on transport behaviors of black carbon and PM2.5 from transportation routes, their relations with the atmospheric structure of an urban formation, and their relations with the use of biodiesel fuels. The results have implications to near-road risk assessment and to the development of sustainable transportation solutions in urban centers. The first part of study quantified near-roadside black carbon transport as a function of particulate matter (PM) size and composition, as well as microclimatic variables (temperature and wind fields) at the interstate highway I-75 in northern Cincinnati, Ohio. Among variables examined, wind speed and direction significantly affect the roadside transport of black carbon and hence its effective emission factor. Observed non-Gaussian dispersion occurred during low wind and for wind directions at acute angles or upwind to the receptors, mostly occurring in the morning hours. Meandering of air pollutant mass under thermal inversion is likely the driving force. In contrary, Gaussian distribution predominated in daytime of strong downwinds. The roles of urban atmospheric structure, wind fields, and the urban heat island (UHI) effects were further examined on pollutant dispersion and transport. Spatiotemporal variations of traffic flow, atmospheric structure, ambient temperature and PM2.5 concentration data from 14 EPA-certified NAAQS monitoring stations, were analyzed in relation to land-use in the Cincinnati metropolitan area. The results show a decade-long UHI effects with higher interior temperature than that in exurban, and a prominent nocturnal thermal inversion frequent in urban boundar (open full item for complete abstract)

Committee: Timothy Keener Ph.D. (Committee Chair); Eileen Birch Ph.D. (Committee Member); Mingming Lu Ph.D. (Committee Member); George Sorial Ph.D. (Committee Member) Subjects: Environmental Engineering

PhD, University of Cincinnati, 2014, Arts and Sciences: Biological Sciences

The broad goal of stream ecology is to understand and predict complex interactions between environmental factors and processes that occur within streams and rivers, such as biological community composition and their interactions, system metabolism (productivity and respiration), and nutrient sources and concentration. Multiple factors are thought to play important roles in these processes including regional environmental conditions (i.e., hydrology, geology, stream form/morphology) and longitudinal position within a stream network (defined by Strahler stream order). In the past, several theoretical concepts have been proposed to attempt to describe and explain how streams behave, and each concept uses various factors weighted differently to characterize streams and gain a better understanding of ecological processes and overall system functions. Here, two differing theories of stream ecology are compared – the River Continuum Concept (RCC) and the Riverine Ecosystem Synthesis (RES). Each of these theories has unique predictions based on either Strahler stream order (SSO; used by the RCC) or Functional Process Zone (FPZ; used by the RES) defined by hydrogeomorphic characteristics. Predictions from both theories were tested across sites representing multiple SSOs and FPZs within the Kanawha River Basin. Measures of environmental heterogeneity (an important concept for differentiating between FPZs) were also assessed. This project has shown that some predictions from both the RCC and the RES are valid. The physical character of the basin is variable; sampling of riverbed substratum at each site revealed that similarities within each FPZ in riverbed composition exist and that each FPZ is distinct. Hydrogeomorphic factors including underlying geology and valley floor width strongly influence the character of the riverbed substratum. The ratio of primary productivity to ecosystem respiration (i.e., a measure of metabolism) aligned with predictions from the RES where p (open full item for complete abstract)

Committee: Stephen Matter Ph.D. (Committee Chair); Joseph E. Flotemersch Ph.D. (Committee Member); Ishi Buffam Ph.D. (Committee Member); Eric Maurer Ph.D. (Committee Member); Amy Townsend-Small Ph.D. (Committee Member) Subjects: Ecology

PHD, Kent State University, 2013, College of Arts and Sciences / Department of Biological Sciences

It is important to understand fate of nutrients like nitrogen, in streams given that anthropogenic activity, such as agriculture, have increased inputs of biologically reactive nitrogen to the environment leading to deterioration of stream health and eutrophication. Bacteria play a crucial role in the driving essential biogeochemical transformations. The purpose of this research was to improve our understanding of organic and inorganic nitrogen utilization by bacterial isolates and complex bacterial communities. Role of bacterial diversity in resource utilization is mostly neglected in biogeochemical models. Identification of bacteria based on molecular methods, like 16S rDNA sequencing, yield a wealth of information related to prokaryotic diversity and its importance in driving essential biogeochemical cycles. In this research utilization of organic and inorganic forms of nitrogen by stream heterotrophic bacterial isolates were examined. Our results reveal differences in bacterial resource utilization not as a function of the different taxa involved but of the enrichments the isolates were obtained from, as immediate environment dictate bacterial response to different nutrients and exerts a selection pressure. Carbon availability also influences nitrogen dynamics. To examine the impact of carbon on bacterial uptake of organic and inorganic nitrogen, bacterial abundance and community composition were examined in controlled, laboratory microcosms. There was a strong influence of carbon availability on bacterial nitrogen utilization, with preferential uptake of organic forms under low carbon concentrations. Carbon and nitrogen treatments likely drove changes in bacterial community composition that, in turn, affected rates of nitrogen utilization under various carbon concentrations. Metabolic functions, such as particular biogeochemical reactions are catalyzed by microbial extracellular enzymes, which are likely linked to the constituting taxa in a given microbial comm (open full item for complete abstract)

Committee: Laura Leff (Advisor); Christopher Blackwood (Committee Member); Christopher Woolverton (Committee Member); Anne Jefferson (Committee Member); Michael Tubergen (Other) Subjects: Biology; Ecology; Microbiology

Master of Science in Engineering (MSEgr), Wright State University, 2010, Materials Science and Engineering

Carbon substrates have a wide variety of applications, many of which are enabled by appropriate surface modifications. In particular, the use of carbon-based substrates for biological devices can be quite advantageous due to their relative inertness and biocompatibility. Moreover, graphitic carbon can take many forms ranging from flat sheets to foams, fibers, and nanotubes. In this project, larger carbon substrates such as microcellular foam and flat graphite have been modified with carbon nanotubes, and their potential use in two types of biological applications was tested. The first study involved an investigation of the growth and proliferation of osteoblast cells on carbon, so that such structures can be evaluated for possible use as a scaffold for in-vivo tissue regeneration. The surface modifications that were compared are a collagen coating, a silica film, and a strongly adhered carbon nanotube layer. It was seen that the attachment of carbon nanotubes led to the highest density and viability of osteoblast cells on the surface indicating their potential benefit in implant and cell scaffolding applications. In the second study, carbon nanotubes were attached on the graphite, and subsequently decorated with gold nanoparticles and a ribonucleic acid (RNA) sequence. These nano-structures show advantages in detecting the DH5α E. coli bacterial strain, indicating potential use as a biosensor. Proof-of-concept results indicate increased attachment of gold nanoparticles coated with an RNA capture element compared to uncoated particles onto the E. coli. This demonstrates the potential use of this concept in creation of a multi-array sensor for fast and sensitive detection of many types of pathogens. These results clearly show that attachment of carbon nanotubes on larger carbon substrates can provide the basis for several unique biological devices.

Committee: Sharmila Mukhopadhyay PhD (Advisor); Saber Hussain PhD (Committee Member); Allen Jackson PhD (Committee Member) Subjects: Biomedical Engineering; Engineering; Materials Science; Nanotechnology

MS, University of Cincinnati, 2007, Engineering : Computer Science

Currently many researchers are working on comparing proteins by aligning their sequences of amino acids. But the structural alignment of proteins is very important. This is because the structure of a protein is believed to be more closely related to function than sequence. There have been a number of tools developed to study three-dimensional protein structure. These include DALI (developed at the European Molecular Biology Laboratory, Cambridge), CHIMERA (developed at the University of California at San Francisco), and CE (developed at the San Diego Supercomputer Center). Most of these tools are vector based or distance based and use the Euclidean distance measure. In this project we use a generalized distance measure, along with powerful pattern-matching heuristics, to understand the functional and structural similarities of proteins whose underlying amino acid sequences may be different. In our method we take the alignments obtained from traditional methods such as CHIMERA and refine them further using a heuristic to minimize the distance between the aligned a-carbon atoms. This method involves formulating a cost function and minimizing it, followed by computation of protein structure alignment and calculating the distance between the two aligned protein structures. Our datasets are taken from the protein structures available in the Protein Data Bank (PDB). The protein structures are represented by their PDB ids. This method uses the coordinates of the a-carbon atoms of the PDB structures as input. Our datasets consist of proteins of various lengths, structural classes and different levels of identities. Our method is compared against popular methods such as DALI, CE, and CHIMERA and we show that it gives better alignment compared to these traditional alignment methods.

Committee: Dr. Carla Purdy (Advisor) Subjects: Computer Science

Master of Arts, University of Toledo, 2004, College of Arts and Sciences

The burning of fossil fuel since 1845 has increased the amount of greenhouse gasses within the atmosphere resulting in global climate change (Townsend et al. 1996). An increased carbon dioxide level from pre-industrial period to the present is thought to contribute 60% of the observed global warming (Grace 2004). Therefore understanding how and where carbon is sequestered is essential for predicting future climatic change and CO2 concentration modeling. Current carbon models do not take area of edge influence (AEI) into consideration which can account for a significant portion of a forested landscape (Mlandenoff et al. 1994). Failing to take the AEI into consideration could cause substantial error at the landscape scale. In this study it was determined that aboveground tree carbon (AGTc) had a depth of edge influence (DEI) of 12 m in both the recent and old inner edge and 5 m for the old outer edge. In addition, down woody debris carbon (DWDc) had a DEI of 22 m for recent and old inner edge and 5 m for the old outer edge. Snag carbon (snagc) had no DEI in any edge; recent inner, old inner, recent outer or old outer. Litter carbon (litterc) had a DEI only in the old inner edge and it extended for 5 m. This study alludes to the possibility of a photosynthetic gradient through the differences in leaf mass per area (LMA) values across an edge to interior gradient. The differences in DWD and the possible photosynthetic gradient could cause substantial error in current landscape level carbon estimates. Understanding how edges effect carbon allocations will improve our ability to predict landscape level carbon storage for developing future management plans.

Committee: Jiquan Chen (Advisor) Subjects: Biology, Ecology

Master of Science, The Ohio State University, 2012, Environment and Natural Resources

The world's human population is expected to expand to nine billion by the year 2050, with 70% projected to be living in cities. As urban populations grow, cities are producing an ever-increasing intensity of ecological light pollution (ELP). At the individual and population levels, artificial night lighting has been shown to influence predator-prey relationships, migration patterns, and reproductive success of many aquatic and terrestrial species. With few exceptions, the effects of ELP on communities and ecosystems remain unexplored. My research investigated the potential influences of ELP on stream-riparian invertebrate communities and trophic dynamics, as well as the reciprocal aquatic-terrestrial exchanges that are critical to ecosystem function. From June 2010 to June 2011, I conducted bimonthly surveys of aquatic emergent insects, terrestrial arthropods, and riparian spiders of the family Tetragnathidae at nine Columbus, OH stream reaches of differing ambient ELP levels (low: 0 - 0.5 lux; moderate: 0.5 - 2 lux; high 2 - 4 lux). In August 2011, I experimentally increased light levels at the low and moderate treatment reaches to ~12 lux. I quantified invertebrate biomass, family richness, density (individuals m-2) of aquatic and terrestrial invertebrates, and measured reciprocal stream-terrestrial invertebrate fluxes. Using stable isotopes of carbon (δ13C) and nitrogen (δ15N), I estimated trophic position, variability in trophic position, food-chain length, and contribution of aquatic (i.e., epilithic algae) vs. terrestrial (i.e., leaf litter detritus) carbon. I found that light strongly influenced invertebrate family richness, biomass, and density for discrete time periods over the course of the year. The experimental addition of light resulted in a ~42% decrease in tetragnathid spider density, a ~54% decrease in aquatic emergent insect biomass, a ~ 16% decrease in aquatic emergent insect family richness, and a ~38% decrease in density of terrestrial arthropo (open full item for complete abstract)

Committee: Mazeika Sullivan PhD (Advisor); Mary Gardiner PhD (Committee Member); Paul Rodewald PhD (Committee Member) Subjects: Aquatic Sciences; Ecology; Freshwater Ecology

Doctor of Philosophy, The Ohio State University, 2012, Evolution, Ecology and Organismal Biology

At the University of Michigan Biological Station (UMBS) in northern lower Michigan, USA, I employed a combination of chronosequence observations and experimental forest manipulation to evaluate the potential of partial forest disturbances to facilitate resilience of carbon (C) storage over two centuries of succession. In 2008, I assisted in initiation of the Forest Accelerated Succession ExperimenT (FASET). All aspen and birch trees in the treatment area were stem girdled to induce mortality. I used lysimeters to characterize nitrogen (N) leaching losses from soil in response to widespread tree mortality. N export was significantly greater in treated than control stands and corresponded to increased fine roots mortality, but total N export was insufficient to limit long-term C storage rates in affected stands. From 2008 through 2011, I used a portable canopy LiDAR (PCL) system to monitor canopy structural changes following widespread mortality in FASET. I also measured leaf-level maximum C assimilation (Amax) rates in canopy co-dominant red oak, red maple, and white pine to evaluate physiological consequences of aspen and birch senescence. Canopies became shorter, more open, and more heterogeneous over time in canopies of treated but not control stands. Leaf Amax of successor canopy species did not change in response to canopy structural rearrangements or increased N availability. I also used the PCL system to characterize canopy structure in stands spanning two centuries of succession. I define a novel metric of canopy structural complexity: rugosity. Rugosity increased with stand age in and explained more variation in aboveground C storage than other known drivers of forest C storage. Forests with more structurally complex canopies used light and nitrogen resources more efficiently than forests with structurally simpler canopies. I present evidence of a mechanistic linkage between canopy structure and forest function that allows aging forests to maintain higher t (open full item for complete abstract)

Committee: Peter Curtis (Advisor); Gil Bohrer (Committee Member); James Bauer (Committee Member); Charles Goebel (Committee Member); Kathleen Knight (Committee Member) Subjects: Biogeochemistry; Biology; Ecology; Environmental Science; Forestry

Doctor of Philosophy, The Ohio State University, 2010, Environment and Natural Resources

A paradigm shift from maximum to sustainable agricultural production also applies to cultivation of bioenergy crops. Nitrogen (N) fertilization is needed to sustain the biomass yield of switchgrass as a biofuel feedstock and, consequently, may influence the potential for soil quality improvement through soil organic carbon (SOC) sequestration. Because changes in soil quality can feed back to affect the sustainability of biomass production, the impacts of N application on switchgrass biomass production and soil quality need to be evaluated together. Therefore, the overall objective of this study was to assess the effects of N fertilization on switchgrass biomass, changes in SOC concentration and pool, and soil structural properties. This objective was realized by conducting field experiments in Ohio and Tenessee, and a laboratory incubation study in Ohio. The aboveground biomass of switchgrass was more strongly influenced by N fertilization than the belowground biomass. Even when the aboveground biomass was harvested and removed, N fertilization led to an increase in SOC, both in Ohio and Tennessee. The data from laboratory incubation study showed that N additions could retard the decomposition of organic matter, which may contribute towards higher SOC pools in N fertilized plots. The results from the Tennessee experiments indicated the important role of roots in stabilizing soil structure. Despite higher SOC concentrations in plots receiving a high rate of N fertilization, higher soil structural stability was associated with greater root biomass and longer root length in plots receiving none or a low rate of N fertilizer. These data indicated that root growth is a crucial driver of surface soil structure.

Committee: Rattan Lal PhD (Advisor); Peter Curtis PhD (Committee Member); David Barker PhD (Committee Member); Julie Jastrow PhD (Committee Member) Subjects: Soil Sciences

Doctor of Philosophy, The Ohio State University, 2005, Soil Science

Soil organic carbon (SOC) retention results from climate, vegetation, drainage and management interactions, but also from texture, mineralogy and structure. In order to assess the controls that these three soil properties exert on SOC levels in the Brazilian Cerrado region, three native soils under similar climate and slope but of contrasting texture were sampled in triplicate to 1m depth. Soils were characterized by physical, chemical, mineralogical, wet sieving, and microscopic analyses, and SOC concentration was determined in bulk soils, particle size separates (clay, silt, sand) and water-stable aggregates (WSA). The basic assumption was that SOC particle size determines its retention mechanism: colloidal forms are sorbed to clays, and particulate organic matter (POM, >20im) occurs outside (free-POM) or inside aggregates (occluded-POM). These mechanisms are affected by soil texture, mineralogy and structure, which then control SOC retention. The three soils were classified as kaolinitic clayey, loamy and sandy Haplustox. Soil texture and depth strongly affected SOC concentrations, which were modeled (R2=0.92, n=126) based on clay+silt and depth. Soil specific surface area (SSA) was modeled as a function of clay, silt and SOC contents, but not depth. Thus, SOC increased with higher SSA and clay; but in a single soil profile SSA decreased in topsoil because of SOC-enhanced aggregation. SOC concentration in size separates was inversely related to the amount of that size fraction in soil (SOC dilution effect), but the clay-sized SOC pool could be modeled as a function of clay contents and depth. The bulk SOC and clay-sized SOC pool were better correlated with Fe-oxides in topsoil and amorphous Al oxides in the subsoil. Soil structure, as indicated by mean weight diameter (MWD) and percent of WSA>2 mm, was strongly correlated with clay+silt contents, but bulk SOC was poorly correlated structure, except for the 0-5 cm depth. Occluded-POM was strongly affected by soil (open full item for complete abstract)

Committee: Rattan Lal (Advisor) Subjects:

Doctor of Philosophy, The Ohio State University, 2002, Biochemistry

This research was focused on the structure determination of four metalloproteins by x-ray crystallography. The first target was E. coli peptide deformylase that is responsible for deformylation of the N-terminus of nascent bacterial proteins and represents a potential drug target. We have determined the first crystal structures of formate- and inhibitor-bound deformylase complexes in different metal forms (Fe2+, Co2+ and Zn2+). The different formate-binding modes between the Zn and the other two metallated forms provide a possible explanation for the low activity of Zn enzyme as compared to Fe and Co enzymes. The inhibitor-bound structures reveal that the bound transition-state analog, (S)-2-O-(H-phosphonoxy)-L-caproyl-L-leucyl-p-nitroanilide (PCLNA), adopts an extended conformation and forms an interaction network with the protein. Based on these structures, a mechanism for deformylation is proposed and guidelines for the design of high-affinity deformylase inhibitors are suggested. The second part of this research involved structural studies of the FixL heme domain from Bradyrhizobium japonicum (BjFixLH). FixL proteins are biological oxygen sensors that regulate nitrogen fixation gene expression in Rhizobia. In these proteins, the activity of the C-terminus kinase domain is regulated by the binding of O2 and other strong-field ligands to the N-terminus heme domain. We have determined eight BjFixLH structures including two unliganded and six ligand-bound forms. These structures reveal a novel heme-binding fold that has been conserved in PAS-domain sensor superfamily. Comparison of these structures has also revealed a heme-mediated conformational change that is distinct from that in classic globins. In BjFixLH, binding of O2 to the heme results in the flattening of the heme plane, the rotation of a critical heme-pocket arginine, and the shift of a FG loop. We have proposed that this arginine plays a central role in ligand discrimination of BjFixLH. The third project (open full item for complete abstract)

Committee: Michael Chan (Advisor) Subjects: Biophysics, General

Doctor of Philosophy, The Ohio State University, 2002, Soil Science

Research was conducted to determine how water table management affects select physical properties and carbon fractions of a Hoytville clay loam soil. The research took place at the Northwest Branch of the Ohio Agricultural Research and Development Center in Wood County, Ohio. Water table management treatments included subsurface drainage and subsurface drainage with subirrigation. Subirrigation was applied during the vegetative, flowering and seed fill stages of crop growth to maintain a constant water table at 0.25 m below the surface and prevent moisture stress in the crops. The cropping system was a corn soybean rotation with fall tillage with a chisel for both crops and spring leveling with a Roterra before planting soybeans. Results show a difference in water stable aggregates (WSA) at a depth of 0.4 – 0.75 meters with the subirrigated treatment having a lower percentage of WSA. The mean weight diameter of aggregates in the subirrigated treatment was smaller than in the subsurface drainage treatment at a depth of 0.3 – 0.75 meters. A shift in the pore size distribution toward smaller pores in the subirrigated treatment further supported “loss of stable soil structure” theory for the subirrigated treatment. Penetration resistance measurements also revealed a change in the structural stability of the soil at a depth of 0.30 – 0.45 meters. No differences were seen between water management treatments in the carbon fractions of the upper 0 – 0.20 meters of the soil. The CENTURY model was tested to determine if it could be used to predict levels of soil organic matter as a result of subirrigation. The model was unable to predict the amount of total SOM in the soil unless the starting value of carbon was lowered well below actual values. Subirrigation of the Hoytville soil led to a loss of stable structure at a depth of approximately 0.40 meters in the soil. The exact reason for the loss of soil structure is unclear but may be related to long periods of saturation res (open full item for complete abstract)

Committee: Norman Fausey (Advisor) Subjects:

PHD, Kent State University, 2012, College of Arts and Sciences / Department of Biological Sciences

Dissolved organic carbon (DOC) is the dominant form of organic matter in aquatic ecosystems and bacteria play a key role in its mobilization to higher trophic levels. The DOC pool is often divided into broad classes such as labile or recalcitrant, based on its ease of uptake by bacteria; or as autochthonous and allochthonous, based on its production within or outside the ecosystem. In this dissertation, I examined the relationship between the composition of the DOC pool and bacterial community structure and function. The three research chapters address this relationship in different freshwater ecosystems. In the first research chapter, the effect of presence or absence of Microcystis, a dominant primary producer in the western basin of Lake Erie as well as an autochthonous DOC source, on bacterial community structure and heterotrophic productivity was studied. This study revealed that bacterial responses were independent of the presence of the dominant primary producer. In second research chapter, the effect of compositional diversity of DOC within labile and recalcitrant categories, on stream bacterial community structure and denitrification rates was investigated. Use of different compounds within each category, administered individually and in mixtures, contributed to the heterogeneity. Results of this study suggest molecular heterogeneity of DOC can lead to differences in bacterial structure and denitrification potential. In my final research chapter, bacterial responses to differences in proportion of autochthonous and allochthonous DOC between a river and reservoir ecosystem were compared. The findings of this study demonstrated that, rather than the proportion of the two DOC sources, each source, considered individually, played a more important role in determining bacterial response. Regardless of the study, in all cases bacterial community structure was not linked to function, emphasizing the requirement to study both. The results indicate that differences i (open full item for complete abstract)

Committee: Dr. Laura Leff (Committee Chair); Dr. Adam Leff (Committee Member); Dr. Darren Bade (Committee Member); Dr. Elizabeth Griffith (Committee Member); Dr. Roger Gregory (Committee Member) Subjects: Ecology

Doctor of Philosophy, Case Western Reserve University, 1990, Physics

Hydrogenated amorphous carbon films (a-C:H) have been deposited on glass, fused silica, Si, Mo, Al, and 304 stainless steel at room temperature by plasma enhanced chemical vapor deposition (PECVD). The rf glow discharge and plasma kinetics of the deposition process were investigated. Negative self-bias voltage V b and gas pressure P were used as two major deposition parameters. The hydrogen concentration, internal stress, mass density, hardness, and thickness of the deposited films were measured. In the low energy deposition region, 0 > V b > -100 V, soft polymerlike films with high hydrogen concentration and low density were found. Hard diamondlike films with high stress were deposited in the bias voltage range, -100 V > V b > -1000 V. Dark graphitic films with low hydrogen concentration were grown at V b < -1000 V. The optical absorption of a series of a-C:H films have been measured. Optical energy gaps deduced from optical absorption data using the Tauc relation lie between 0.8 eV and 1.4 eV. Doping of a-C:H films by boron and sulfur is accompanied by an increasing number of gap states, i.e., the absorption coefficient is increased and the optical gap is reduced. The thermal stability was studied by thermal desorption spectroscopy and heat tre atment at atmospheric pressure. A structural study of a-C:H films was performed using data taken on our films and from literature sources. The relation between cluster size and the intensity ratio of Raman peaks was studied. A comparison of the films as described by the graphitic cluster two-phase (GCT) model, the random covalent network (RCN) model and the all-sp2 defect graphite (DG) model was made. The properties and structure of a-C:H films are sensitively dependent on the preparation conditions. Correlations between the deposition conditions, structure, and properties are determined.

Committee: R Hoffman (Advisor) Subjects: Physics, Condensed Matter

Doctor of Philosophy, University of Akron, 2011, Polymer Science

Evaporation and the associated solidification are important factors that affect the diameter of electrospun nanofibers. The evaporation and solidification of a charged jet were controlled by varying the partial pressure of water vapor during electrospinning of poly(ethylene oxide) from aqueous solution. As the partial pressure of water vapor increases, the solidification process of the charged jet becomes slower, allowing elongation of the charged jet to continue longer and thereby to form thinner fibers. The morphology and internal structure of electrospun poly(vinylidene fluorides) nanofibers were investigated. Low voltage high resolution scanning electron microscopy was used to study the surface of electrospun nanofibers. Control of electrospinning process produced fibers with various morphological forms. Fibers that were beaded, branched, or split were obtained when different instabilities dominated in the electrospinning process. The high ratio of stretching during electrospinning aligns the polymer molecules along the fiber axis. A rapid evaporation of solvent during electrospinning gives fibers with small and imperfect crystallites. These can be perfected by thermal annealing. Fibers annealed at elevated temperature form plate-like lamellar crystals tightly linked by tie molecules. Electrospinning can provide ultrafine nanofibers with cross-sections that contain only a few polymer molecules. Ultrafine polymer nanofibers are extremely stable in transmission electron microscope. Electrospun nanofibers suspended on a holey carbon film showed features of individual polymer molecules. Carbon fibers with diameters ranging from 100 nm to several microns were produced from mesophase pitch by a low cost gas jet process. The structure of mesophase pitch-based carbon fibers was investigated as a function of heat treatment temperatures. Submicron-sized graphene oxide flakes were prepared by a combination of oxidative treatment and ultrasonic radiation. Because pitch i (open full item for complete abstract)

Committee: Darrell Reneker Dr. (Advisor); Gary Hamad Dr. (Committee Member); Stephen Z. D. Cheng Dr. (Committee Member); Shi-Qing Wang Dr. (Committee Member); George Chase Dr. (Committee Member) Subjects: Polymers