+publisher:"Penn State University" +contributor:("James David Kubicki, Committee Member")

Penn State University

1. Cruz-uribe, Alicia Marie. Assessment and implications of (dis)equilibrium in metamorphic rocks.

Degree: 2014, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/22896

► The ability to quantify the rates at which metamorphic reactions occur is critical to assessing the extent to which equilibrium is achieved and maintained in… (more)

▼ The ability to quantify the rates at which metamorphic reactions occur is critical to assessing the extent to which equilibrium is achieved and maintained in a variety of dynamic settings. Here I investigate the kinetics of rutile replacement by titanite during amphibolite-facies overprinting of eclogite, garnet amphibolite and anorthosite from Catalina Island, CA, the Tromsø Nappe, Norway, the North Qaidam terrane, China, and the Guichicovi Complex, Mexico. Trace element concentration profiles across rutile rimmed by titanite, as determined by laser ablation (LA) ICP-MS, reveal Nb zoning in rutile that are interpreted to be the result of Nb back-diffusion from the rutile-titanite boundary. I present new field-based reaction rates calculated from grain boundary velocities, which in turn were calculated using a 1-D diffusion model for Nb back-diffusion into rutile during titanite replacement over the temperature range 670–770 °C. These data are consistent with or slightly faster than previous estimates of regional metamorphic reaction rates, and extend the temperature and composition range over which regional metamorphic reaction rates are known. Further investigation of the kinetics of all metamorphic reactions reveals a strong correlation between heating rate (dT/dt) and net reaction rate for regional, contact, and subduction zone metamorphic settings. This relationship is used to formulate a new expression relating net reaction rate (Rnet) temperature (T) and heating rate (dT/dt): Rnet=(4.24*10^-11)*((dT/dt)¹.25)*exp(0.00668T) This expression provides a universal prediction of metamorphic reaction kinetics at the tectonic scale and accounts for the 4-7 orders of magnitude range in metamorphic reaction rates observed in natural systems. Based on this analysis, the dynamic nature of subduction zones (high dT/dt) may result in conditions that are far from equilibrium (large ΔGrxn), which drives faster reaction rates in these systems. Examination of the relative abundances of trace elements in rutile and titanite reveal striking differences between high temperature (amphibolite-facies) and low temperature (blueschist-facies) overprinting. I find that trace element distributions approach equilibrium partition coefficients in rocks from amphibolite-facies overprinted terranes, whereas trace element distributions did not approach equilibrium in rocks that experienced blueschist-facies overprinting. Calculated Zr-in-titanite temperatures for amphibolite-facies overprinted rocks are consistent with those reported in the literature, while Zr-in-titanite temperatures for blueschist-facies overprinting consistently overestimate temperature by 50-250 °C, suggesting that Zr does not approach equilibrium distributions during blueschist-facies overprinting. I conclude that single phase thermometers that rely upon slow-diffusing high field strength elements should not be applied to rocks equilibrated at ≤550 °C unless attainment of trace element equilibrium can be demonstrated. In situations where trace element… Advisors/Committee Members: Maureen Feineman, Dissertation Advisor/Co-Advisor, James David Kubicki, Committee Member, David H Eggler, Committee Member, John Richard Hellmann Jr., Committee Member.

Subjects/Keywords: metamorphism; kinetics

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APA (6^th Edition):

Cruz-uribe, A. M. (2014). Assessment and implications of (dis)equilibrium in metamorphic rocks. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/22896

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Cruz-uribe, Alicia Marie. “Assessment and implications of (dis)equilibrium in metamorphic rocks.” 2014. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/22896.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Cruz-uribe, Alicia Marie. “Assessment and implications of (dis)equilibrium in metamorphic rocks.” 2014. Web. 22 Jan 2021.

Vancouver:

Cruz-uribe AM. Assessment and implications of (dis)equilibrium in metamorphic rocks. [Internet] [Thesis]. Penn State University; 2014. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/22896.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Cruz-uribe AM. Assessment and implications of (dis)equilibrium in metamorphic rocks. [Thesis]. Penn State University; 2014. Available from: https://submit-etda.libraries.psu.edu/catalog/22896

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

2. Fleeger, Claire Rene. Contaminant sequestration and phase transformation properties of birnessite-like phases (delta-mno2).

Degree: 2012, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/12688

► For the first time, time-resolved X-ray diffraction (TR-XRD) and inductively coupled plasma-mass spectrometry (ICP-MS) have been coupled to monitor contaminant (e.g., Cs and Mn) cation… (more)

▼ For the first time, time-resolved X-ray diffraction (TR-XRD) and inductively coupled plasma-mass spectrometry (ICP-MS) have been coupled to monitor contaminant (e.g., Cs and Mn) cation exchange reactions into two birnessite-like phases, which exhibit triclinic and hexagonal symmetry. Cs is a principal contaminant at several nuclear waste sites, including the DOE Hanford Site, where high-level, high pH nuclear waste is leaking from tens of underground storage tanks. Our results indicate that Cs uptake by hexagonal H-birnessite increases as pH increases from pH 3 to pH 11; the increase in Cs uptake (wt%) correlates to an incremental increase in unit-cell volume as a function of pH. As Cs adsorption increases and pH increases, the rate of Cs cation exchange reaction decreases. On the other hand, triclinic Na-birnessite adsorbs less Cs at a neutral pH than at high or low pH. Again, greater uptake of Cs correlates to a decrease in Cs cation exchange rate as the pH becomes more acidic or basic. During the course of these variable pH reactions, we observed that a phase transformation occurred between the triclinic and hexagonal phases as a function of pH even in the presence of competing cations (i.e., Cs). At pH 3, triclinic Na-birnessite transformed to hexagonal H- or Cs-birnessite, and at pH 13, hexagonal H-birnessite transformed to triclinic Na- or Cs-birnessite. At both low and high pH, cation exchange with the dissolved cation (H, Na, or Cs) preceded the symmetry-changing transformation. The interlayer cation remained within the structure during the phase transformations, indicating that these materials act as sequestering agents no matter the pH or crystalline phase. For the last set of experiments, we exchanged Mn2+ into triclinic Na-birnessite to assess the possibility of a redox-driven phase transformation to hexagonal H-birnessite. We determined that aqueous Mn2+ catalyzed the phase transformation at pH 3, and the rate of phase transformation increased as [Mn2+] increased. However, at pH 4.5 and 6, Mn2+(aq) promoted the breakdown of the manganese oxide octahedral sheets. Initially the Mn2+ exchanged into the interlayer region, indicated by a decrease in unit-cell volume, followed by an increase in the Mnoct-Ooct bond distances to 2.01 Å, suggesting that the octahedral Mn4+(s) was reduced to Mn3+(s). We supported this observation by completing the same reaction in a batch reactor, where the final solid-state products were a mixture of triclinic birnessite, hausmannite, and three Mn3+OOH products (manganite, groutite, and feitknechtite). This investigation reveals the adaptability of birnessite as a function of chemical environment. Mn oxides control heavy metal mobility not only by high sorption and cation exchange capacities but by redox reactivity, and these properties vary with the particular phase of Mn oxide. Thus, each phase needs to be characterized individually to fully understand how mixtures will interact in natural systems. Advisors/Committee Members: Peter J Heaney, Dissertation Advisor/Co-Advisor, James David Kubicki, Committee Member, Matthew Scott Fantle, Committee Member, William D Burgos, Committee Member.

Subjects/Keywords: birnessite; cesium sequestration; phase transformation; manganese oxide

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APA (6^th Edition):

Fleeger, C. R. (2012). Contaminant sequestration and phase transformation properties of birnessite-like phases (delta-mno2). (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/12688

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Fleeger, Claire Rene. “Contaminant sequestration and phase transformation properties of birnessite-like phases (delta-mno2).” 2012. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/12688.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Fleeger, Claire Rene. “Contaminant sequestration and phase transformation properties of birnessite-like phases (delta-mno2).” 2012. Web. 22 Jan 2021.

Vancouver:

Fleeger CR. Contaminant sequestration and phase transformation properties of birnessite-like phases (delta-mno2). [Internet] [Thesis]. Penn State University; 2012. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/12688.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Fleeger CR. Contaminant sequestration and phase transformation properties of birnessite-like phases (delta-mno2). [Thesis]. Penn State University; 2012. Available from: https://submit-etda.libraries.psu.edu/catalog/12688

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

3. Harouaka, Khadouja. Experimental and theoretical effects of microorganisms, organic molecules, and atom exchange rates on the Ca isotopic composition of gypsum: Implications for the use of Ca isotopes as a geochemical proxy.

Degree: 2016, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/28895

► The Ca isotopic composition of minerals in the geologic rock record is a valuable proxy used to understand the processes that shaped the physical, chemical… (more)

▼ The Ca isotopic composition of minerals in the geologic rock record is a valuable proxy used to understand the processes that shaped the physical, chemical and biological evolution of our planet. However, correctly applying the Ca isotope proxy requires an in depth knowledge of how Ca isotopes fractionate during mineral precipitation. The mechanisms that control Ca isotopic fractionation during abiotic mineral precipitation are not yet clearly understood, and there is very little known about the mechanisms that govern biologically induced Ca isotopic fractionation during biomineralization. The main goal of this dissertation is to determine how biology can control Ca isotopic fractionation by quantifying the effect microbial life has on the Ca isotopic composition of gypsum and determining the underlying mechanisms that produce the measured Ca isotopic composition. The results of the work will be used to evaluate the viability of Ca isotopes as a biosignature of microbial life, as well as the extent to which the presence of organics can impact the Ca isotope record. The presence of Acidithiobacillus thiooxidans microbes in the gypsum precipitation solution resulted in a Ca isotopic fractionation factor that was 0.3 permil lighter than gypsum precipitated from abiotic controls. The change in tge fractionation factor due to the presence of microbes was strongly correlated with crystal morphology, such that biotic precipitates have smaller aspect ratios than abiotic precipitates produced under the same conditions. The change in morphology led to the hypothesis that microbially produced soluble and insoluble organic molecules inhibit gypsum precipitation rate, altering the fractionation factor. Simple gypsum precipitation experiments in the presence of basic amino acids confirmed this hypothesis, as amino acid inhibition resulted in lowering the fractionation factor by 0.2 permil relative to controls. Further, the difference in the energy of a surface upon which an amino acid is detached and attached, as determined by DFT theory, can vary up to 3 eV between multiple gypsum faces, which implies that organic molecule inhibition of gypsum precipitation is a surface selective process. It was also found, based on Gaussian frequency calculations of the same faces, that the fractionation factor associated with growth on the individual faces can vary by as much as 1.4 permil. Hence, surface selective inhibition of gypsum can allow for a greater expression of the fractionation factor of uninhibited faces relative to the inhibited faces, resulting in an isotopically distinct crystal. The empirical and theoretical evidence presented in this dissertation lead to the hypothesis that the presence of organic molecules can influence the fractionation factor of minerals by surface selective inhibition of a growing particle. Each crystal face is theorized to have a distinct fractionation factor, and surface selective inhibition results in compensatory growth on alternate faces, allowing for their distinct fractionation factor to be… Advisors/Committee Members: Matthew Scott Fantle, Dissertation Advisor/Co-Advisor, Jennifer Macalady, Committee Member, James David Kubicki, Committee Member, Christopher Aaron Gorski, Special Member.

Subjects/Keywords: Calcium isotopes; gypsum; surface selective inhibition; exchange rates; morphology

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APA (6^th Edition):

Harouaka, K. (2016). Experimental and theoretical effects of microorganisms, organic molecules, and atom exchange rates on the Ca isotopic composition of gypsum: Implications for the use of Ca isotopes as a geochemical proxy. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/28895

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Harouaka, Khadouja. “Experimental and theoretical effects of microorganisms, organic molecules, and atom exchange rates on the Ca isotopic composition of gypsum: Implications for the use of Ca isotopes as a geochemical proxy.” 2016. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/28895.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Harouaka, Khadouja. “Experimental and theoretical effects of microorganisms, organic molecules, and atom exchange rates on the Ca isotopic composition of gypsum: Implications for the use of Ca isotopes as a geochemical proxy.” 2016. Web. 22 Jan 2021.

Vancouver:

Harouaka K. Experimental and theoretical effects of microorganisms, organic molecules, and atom exchange rates on the Ca isotopic composition of gypsum: Implications for the use of Ca isotopes as a geochemical proxy. [Internet] [Thesis]. Penn State University; 2016. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/28895.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Harouaka K. Experimental and theoretical effects of microorganisms, organic molecules, and atom exchange rates on the Ca isotopic composition of gypsum: Implications for the use of Ca isotopes as a geochemical proxy. [Thesis]. Penn State University; 2016. Available from: https://submit-etda.libraries.psu.edu/catalog/28895

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

4. Hanoian, Philip. Computer Simulations Of Enzymes.

Degree: 2014, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/22078

► Enzymes are proteins that perform the essential function of facilitating chemical reactions within living organisms, and the rate enhancements provided by enzymes are so significant… (more)

Subjects/Keywords: molecular dynamics simulations; enzymes; computational; ketosteroid isomerase; dihydrfolate reductase; empirical valence bond

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APA (6^th Edition):

Hanoian, P. (2014). Computer Simulations Of Enzymes. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/22078

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Hanoian, Philip. “Computer Simulations Of Enzymes.” 2014. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/22078.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Hanoian, Philip. “Computer Simulations Of Enzymes.” 2014. Web. 22 Jan 2021.

Vancouver:

Hanoian P. Computer Simulations Of Enzymes. [Internet] [Thesis]. Penn State University; 2014. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/22078.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Hanoian P. Computer Simulations Of Enzymes. [Thesis]. Penn State University; 2014. Available from: https://submit-etda.libraries.psu.edu/catalog/22078

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

5. Raju, Muralikrishna. Applications of Molecular Dynamics, Monte Carlo and Metadynamics Simulations using ReaxFF Reactive Force Fields to Fluid/Solid Interfaces.

Degree: 2015, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/23853

► The interaction of dense fluids (water, polar organic solvents, room temperature ionic liquids, etc.) with solid substrates controls many chemical processes encountered in nature and… (more)

▼ The interaction of dense fluids (water, polar organic solvents, room temperature ionic liquids, etc.) with solid substrates controls many chemical processes encountered in nature and industry. The key features of fluid-solid interfaces (FSIs) are the high mobility and often reactivity of the fluid phase, and the structural control provided by the solid phase. In this dissertation we apply molecular modeling methods to study FSIs in the following systems: 1. Dissociation of water on titania surfaces We studied the adsorption and dissociation of water at 300 K on the following TiO2 surfaces: anatase (101), (100), (112), (001) and rutile (110) at various water coverages, using a recently developed ReaxFF reactive force field. The molecular and dissociative adsorption configurations predicted by ReaxFF for various water coverages agree with previous theoretical studies and experiment. ReaxFF predicts a complex distribution of water on these surfaces depending on an intricate balance between the spacing of the adsorption sites (under-coordinated Ti and O surface atoms), water-surface interactions, and water-water interactions. Using molecular dynamics simulations to quantify water dissociation over the TiO2 surfaces at various water coverages, we find that the extent of water dissociation predicted by the ReaxFF reactive force field is in general agreement with previous density-functional theory studies and experiments. We demonstrate a correlation between the extent of water dissociation on different TiO2 surfaces and the strength of hydrogen bonding between adsorbed water molecules and water outside the adsorbed layer, as evidenced by the red shift of the O-H vibrational stretching mode of adsorbed water. 2. Mechanisms of Oriented Attachment in TiO2 nanocrystals Oriented attachment (OA) of nanocrystals is now widely recognized as a key process in the solution-phase growth of hierarchical nanostructures. However, the microscopic origins of OA remain unclear. Using the same ReaxFF Ti/O/H reactive force field employed in the previous study, we perform molecular dynamics simulations to study the aggregation of various titanium dioxide (anatase) nanocrystals in vacuum and humid environments. In vacuum, the nanocrystals merge along their direction of approach, resulting in a polycrystalline material. By contrast, in the presence of water vapor, the nanocrystals reorient themselves and aggregate via the OA mechanism to form a single or twinned crystal. They accomplish this by creating a dynamic network of hydrogen bonds between surface hydroxyls and surface oxygens of aggregating nanocrystals. We determine that OA is dominant on surfaces that have the greatest propensity to dissociate water. Our results are consistent with experiment, are likely to be general for aqueous oxide systems, and demonstrate the critical role of solvent in nanocrystal aggregation. This work opens up new possibilities for directing nanocrystal growth to fabricate nanomaterials with desired shapes and sizes. 3. Li interactions in carbon based… Advisors/Committee Members: Kristen Ann Fichthorn, Committee Chair/Co-Chair, Adrianus C Van Duin, Committee Chair/Co-Chair, Jorge Osvaldo Sofo, Committee Member, Milton Walter Cole, Committee Member, James David Kubicki, Committee Member.

Subjects/Keywords: Computational Chemistry; ReaxFF Reactive Force Fields; Fluid/Solid Interfaces; Titania-Water Interactions; Li/C ReaxFF

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APA (6^th Edition):

Raju, M. (2015). Applications of Molecular Dynamics, Monte Carlo and Metadynamics Simulations using ReaxFF Reactive Force Fields to Fluid/Solid Interfaces. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/23853

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Raju, Muralikrishna. “Applications of Molecular Dynamics, Monte Carlo and Metadynamics Simulations using ReaxFF Reactive Force Fields to Fluid/Solid Interfaces.” 2015. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/23853.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Raju, Muralikrishna. “Applications of Molecular Dynamics, Monte Carlo and Metadynamics Simulations using ReaxFF Reactive Force Fields to Fluid/Solid Interfaces.” 2015. Web. 22 Jan 2021.

Vancouver:

Raju M. Applications of Molecular Dynamics, Monte Carlo and Metadynamics Simulations using ReaxFF Reactive Force Fields to Fluid/Solid Interfaces. [Internet] [Thesis]. Penn State University; 2015. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/23853.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Raju M. Applications of Molecular Dynamics, Monte Carlo and Metadynamics Simulations using ReaxFF Reactive Force Fields to Fluid/Solid Interfaces. [Thesis]. Penn State University; 2015. Available from: https://submit-etda.libraries.psu.edu/catalog/23853

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

6. Pandey, Jyotsna Lavanya. Investigation of lignin interactions and deposition in plant cell walls.

Degree: 2015, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/24769

► Lignin is a natural cell wall polymer found in land plants and is a major component of lignocellulosic biomass. The presence of lignin in the… (more)

▼ Lignin is a natural cell wall polymer found in land plants and is a major component of lignocellulosic biomass. The presence of lignin in the plant cell walls provides recalcitrance to plant biomass, making it difficult to convert lignocellulosic biomass to sugars and other reactive intermediates during the production of biochemical and biofuels. Even though lignin is the second most abundant biopolymer on earth after cellulose, the structure and formation of lignin is very poorly understood; a better understanding of how lignin if formed is required in order to develop methods to effectively degrade it. It is quite well understood how lignin monomers or monolignols are synthesized in the cytoplasm of plant cells. However, not much is understood about how these monolignols are transported from the cytoplasm and deposited into the cell wall, cell corners and middle lamella and polymerized into lignin. This dissertation aims at understanding some of these aspects of lignification by developing methods to visualize lignin monomer deposition in plant cell walls. Lignin localization and visualization have also been attempted using fluorescent dyes and other markers, but their specificity has been a topic of contention. In this dissertation, a different approach to visualize the process of lignification was developed. Monolignol analogs that accurately imitate natural monolignols but contain a bioorthogonal alkynyl functional group were developed. These monolignols could be labeled with various tags containing an azide group using a simple click chemistry reaction. The tags explored in this dissertation include fluorescent-azide dyes, which can be visualized using fluorescence microscopy. Other tags that could be used include gold nanoparticles functionalized with an azide group, which can be visualized using electron microscopy. Monolignol analogs were fed to plant tissue and were successfully incorporated into cell walls, which is attributed to the flexibility with which multiple lignin monomers are known to be deposited into the walls. These versatile monolignol analogs provide several approaches to visualize lignin deposition, as the characteristic Raman signal for the alkyne group enables its visualization using Raman microscopy without requiring an additional labeling step that kills the plant cells. In addition to exploring the deposition of the monolignols in plant cell walls, the nature of their interactions with another wall component were explored using computational chemistry. Methods based on Density Functional Theory (DFT) were developed to study the nature and strength of non-covalent interactions between lignin dimers and individual amino acids. This computational analysis is not only helpful in understanding the nature of lignin-protein interactions that occur in cell walls but could also be helpful in developing force fields to model larger lignin-protein interactions at the molecular level in the future, and aid in designing protein modifications to lignin in the cell wall to improve degradability,… Advisors/Committee Members: Thomas Lehman Richard, Dissertation Advisor/Co-Advisor, Thomas Lehman Richard, Committee Chair/Co-Chair, Nicole Robitaille Brown, Committee Member, Charles T Anderson, Committee Member, James David Kubicki, Committee Member, Ming Tien, Committee Member.

Subjects/Keywords: lignin; density function theory; amino acid; non-covalent interaction; monolignol; click chemistry

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Pandey, J. L. (2015). Investigation of lignin interactions and deposition in plant cell walls. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/24769

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Pandey, Jyotsna Lavanya. “Investigation of lignin interactions and deposition in plant cell walls.” 2015. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/24769.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Pandey, Jyotsna Lavanya. “Investigation of lignin interactions and deposition in plant cell walls.” 2015. Web. 22 Jan 2021.

Vancouver:

Pandey JL. Investigation of lignin interactions and deposition in plant cell walls. [Internet] [Thesis]. Penn State University; 2015. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/24769.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Pandey JL. Investigation of lignin interactions and deposition in plant cell walls. [Thesis]. Penn State University; 2015. Available from: https://submit-etda.libraries.psu.edu/catalog/24769

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

7. Peterson, Kristina Marie. nucleation, growth, and phase transformation mechanisms of the iron (oxy)hydroxides.

Degree: 2015, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/24811

► The precipitation of akaganeite and its transformation to hematite under hydrothermal conditions was monitored using a combination of in situ and ex situ experimental techniques.… (more)

▼ The precipitation of akaganeite and its transformation to hematite under hydrothermal conditions was monitored using a combination of in situ and ex situ experimental techniques. Using synchrotron time-resolved X-ray diffraction (TRXRD), in situ experiments between 100 and 200 °C revealed that akaganeite was the first phase to form, and hematite was the final phase between 150 and 200 °C. A transient Fe-poor, OH-rich hematite phase with a chemical formula consistent with “hydrohematite” was identified in our in situ TRXRD experiments at 150, 175, and 200 °C. Rietveld analyses revealed that water concentrations in the first-formed crystals of hydrohematite were comparable to water contents of FeOOH phases, such as akaganeite and goethite. Distinct peak splitting was observed in the 200 °C hydrohematite diffraction patterns, indicating a violation of the 3-fold rotational symmetry of S.G. R-3c. We present a new structure refinement for hydrohematite using a monoclinic space group (I2/a). To our knowledge, this is the first lower symmetry hematite-like phase captured with XRD. Kinetic analyses using phase abundances derived from Rietveld calculations of TRXRD data demonstrated that the rates of akaganeite crystallization and dissolution, hematite nucleation and crystallization increased with temperature. However, in experiments with target temperatures between 150 and 200 °C, akaganeite nucleated instantaneously once experimental temperatures reached ~123 °C. Thus, the activation energy for akaganeite nucleation over the temperature range of 150 to 200 °C was 0 kJ/mol. The activation energy for the crystal growth and dissolution of akaganeite was 74 ± 8 kJ/mol and 125 ± 7 kJ/mol, respectively. Our calculated activation energies for hematite nucleation and crystal growth was 80 ± 13 kJ/mol and 110 ± 21 kJ/mol, respectively. iii iv FESEM and TEM characterization of samples heated to 150 °C revealed that two akaganeite morphologies – rectangular rods and spherulites – developed simultaneously. The first hematite crystals that we detected adopted the spherulitic morphology of the precursor akaganeite. These observations suggest that hematite nucleated heterogeneously within the akaganeite spherulites in our system. We propose that the transformation from akaganeite to hematite proceeded via short-range dissolution and reprecipitation leading to pseudomorphic replacement. The akaganeite rods persisted during the first stages of pseudomorphism, and in the final stage of transformation, the growth of hematite spherulites proceeded at the expense of the akaganeite rectangular rods. Advisors/Committee Members: Peter J Heaney, Dissertation Advisor/Co-Advisor, Peter J Heaney, Committee Chair/Co-Chair, James David Kubicki, Committee Member, Christopher Gorski, Committee Member, Matthew Scott Fantle, Committee Member, Demian Saffer, Special Member.

Subjects/Keywords: akaganeite; hematite; Rietveld; synchrotron; time-resolved X-ray diffraction

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APA (6^th Edition):

Peterson, K. M. (2015). nucleation, growth, and phase transformation mechanisms of the iron (oxy)hydroxides. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/24811

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Peterson, Kristina Marie. “nucleation, growth, and phase transformation mechanisms of the iron (oxy)hydroxides.” 2015. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/24811.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Peterson, Kristina Marie. “nucleation, growth, and phase transformation mechanisms of the iron (oxy)hydroxides.” 2015. Web. 22 Jan 2021.

Vancouver:

Peterson KM. nucleation, growth, and phase transformation mechanisms of the iron (oxy)hydroxides. [Internet] [Thesis]. Penn State University; 2015. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/24811.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Peterson KM. nucleation, growth, and phase transformation mechanisms of the iron (oxy)hydroxides. [Thesis]. Penn State University; 2015. Available from: https://submit-etda.libraries.psu.edu/catalog/24811

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

8. Fan, Bingxin. Molecular Dynamics Simulation of Solvated Cell Wall Polysaccharides: a Structual and Dynamic Study.

Degree: 2015, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/25081

► We investigate behavior of cell wall polysaccharides using computational approaches. Research on cell wall has become an increasingly emphasized topic due to the lignocellulosic biomass… (more)

▼ We investigate behavior of cell wall polysaccharides using computational approaches. Research on cell wall has become an increasingly emphasized topic due to the lignocellulosic biomass is a great candidate for biofuel production. Understanding the cell wall hierarchical structure is not only beneficial for fundamental understanding. It also provides a scientific basis for developing more effective methods for the conversion process. In this thesis, we focus on both the structural behavior of the polysaccharides and the dynamic properties of their surrounding water. The load-bearing network of cell wall is the cellulose/xyloglucan network. In order to avoid harsh chemical extraction treatment and to simulate the polysaccharides in the length scale that close to that in plant cell walls, we developed a coarse-grained force field for both cellulose and (XXXG) xyloglucan, and combined these two force fields for studying the network structure. The force field for cellulose is built based on atomistic simulation of a 6x6x40 microfibril. The force sites are defined as the geometric average of the six member glucose ring. The force field is parameterized such that the chain configuration, intermolecular packing, and hydrogen bonding of the two levels of modeling are consistent. To retain the directionality of the interfibril interactions, we define pair-wised interactions between the interchain neighbors, and add the potentials sequentially until the crystal structure of the coarse-grained fibril matches that of the atomistic target. The coarse-grained simulation shows that microfibrils longer than 100nm tend to form kinks along their longitudinal direction. The kink structure may be linked to the periodic disorder of the microfibril observed based on small angle neutron scattering measurements. The xyloglucan force field is build based on atomistic simulation of 15 (XXXG)3 segments, which is the shortest length of xyloglucan that shows significant interaction on cellulose microfibril surfaces. In order to make the two force fields compatible, we also define the xyloglucan force sites as the geometric average of the glucose rings or xylose rings. Thus, there are two types of beads in the xyloglucan chains. The coarse-grained simulation uses the atomistic chain configuration and intermolecular spacings as the target. Upon completion, we performed a simulation combining the two force fields. The simulation box in this case contains one 6x6x200 microfibril surrounded by 20 randomly placed (XXXG)50 xyloglucan chains. The coarse-grained simulation shows three types of xyloglucan based on their interaction with cellulose chains: the bridge chains (that interact with both the microfibril and its periodic image), the single chains (that only interacts with the microfibril), and the isolated chains (that do not directly interact with the microfibril). We also see that some of the isolated chains may bind to the other two types of xyloglucan and participating indirectly in bridging the microfibrils. Therefore, even though some… Advisors/Committee Members: Janna Kay Maranas, Dissertation Advisor/Co-Advisor, Janna Kay Maranas, Committee Chair/Co-Chair, James David Kubicki, Committee Member, Seong Han Kim, Committee Member, Scott Thomas Milner, Committee Member.

Subjects/Keywords: plant cell wall; cellulose; hemicellulose; coarse-grained simulation

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Fan, B. (2015). Molecular Dynamics Simulation of Solvated Cell Wall Polysaccharides: a Structual and Dynamic Study. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/25081

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Fan, Bingxin. “Molecular Dynamics Simulation of Solvated Cell Wall Polysaccharides: a Structual and Dynamic Study.” 2015. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/25081.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Fan, Bingxin. “Molecular Dynamics Simulation of Solvated Cell Wall Polysaccharides: a Structual and Dynamic Study.” 2015. Web. 22 Jan 2021.

Vancouver:

Fan B. Molecular Dynamics Simulation of Solvated Cell Wall Polysaccharides: a Structual and Dynamic Study. [Internet] [Thesis]. Penn State University; 2015. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/25081.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Fan B. Molecular Dynamics Simulation of Solvated Cell Wall Polysaccharides: a Structual and Dynamic Study. [Thesis]. Penn State University; 2015. Available from: https://submit-etda.libraries.psu.edu/catalog/25081

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

9. Guo, Jing. CELLULOSE NANOSTRUCTURE AND BINDING CHARACTERISTICS .

Degree: 2011, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/12637

► Cellulases are important enzymes both for the photosynthetically fixed carbon recycling on earth and for biotechnical applications. The physical parameters of cellulose such as surface… (more)

▼ Cellulases are important enzymes both for the photosynthetically fixed carbon recycling on earth and for biotechnical applications. The physical parameters of cellulose such as surface area and porosity are important in the development of cellulose composites which may contain valuable additives which bind to cellulose. In this area, the use of acid hydrolyzed nano-dimensional cellulose nanowhiskers (CNWs) has attracted significant interest, yet the surface area and porosity of these materials have not been explored experimentally. The objective of this work was to characterize the surface area and porosity of CNWs from different origins (plant cotton/bacterium Gluconacetobacter xylinus) and different acid treatments (H2SO4/HCl) by N2 adsorption; as well as to compare surface area and porosity of bacterial cellulose synthesized by static and agitated cultures. Our results showed that CNWs produced from H2SO4/HCl exhibited significantly increased surface area and porosity relative to starting material cotton fiber CF11. Micropores were generated in HCl hydrolyzed CNWs but not in H2SO4 hydrolyzed CNWs. Bacterial CNWs exhibited larger surface area and porosity compared to plant CNWs. Cellulose synthesized by G. xylinus ATCC 700178 from agitated cultures also exhibited less surface area and porosity than those from static cultures. Phage display technology was used to screen peptides that selectively bind to crystalline cellulose nanowhiskers (CNWs) from a library of a number of different polypeptides. These peptides were selected on immobilized CNWs by biopanning, by which all possible heptapeptides were screened based on the binding affinity to the crystalline CNWs. A consensus peptide of WHWTYYW was identified to efficiently bind to CNWs. Binding affinities of isolated phage particles were quantitatively analyzed by single-phage biopanning assay and enzyme-linked immunesorbent assay (ELISA). This consensus peptide was synthesized and exhibited a binding affinity of ~105 M-1 towards CNWs as measured by isothermal titration calorimetry (ITC), in good agreement with ELISA results. In addition, the affinities of this peptide to cello-oligosaccharides were also measured with UV spectroscopy and fluorescence quenching experiments. The molecular details of the interaction of this heptapeptide with cellohexaose were determined by nuclear magnetic resonance (NMR). The interaction with crystalline cellulose was investigated by molecular modeling (MM) studies. Both NMR and MM experiments suggest that this heptapeptide has adopted a bended structure for binding and Y5 can form CH/ð stacking and hydrogen bond with glucose ring of cellulose. Family I cellulose binding modules CBMCel7A and CBMCel6A were heterologously expressed and purified from Escherichia coli, and the binding properties between these CBMs and cellulose substrates were studied. Cellulose nanowhiskers (CNWs), the crystalline portions of cellulose, microcrystalline cellulose Avicel PH101 (partially crystalline cellulose), and phosphoric acid swollen cellulose (PASC,… Advisors/Committee Members: Jeffrey M Catchmark, Dissertation Advisor/Co-Advisor, Jeffrey M Catchmark, Committee Chair/Co-Chair, Teh Hui Kao, Committee Member, Ming Tien, Committee Member, James David Kubicki, Committee Member.

Subjects/Keywords: cellulose binding modules; cellulose nanowhiskers; Cellulose nanostructure

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Guo, J. (2011). CELLULOSE NANOSTRUCTURE AND BINDING CHARACTERISTICS . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/12637

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Guo, Jing. “CELLULOSE NANOSTRUCTURE AND BINDING CHARACTERISTICS .” 2011. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/12637.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Guo, Jing. “CELLULOSE NANOSTRUCTURE AND BINDING CHARACTERISTICS .” 2011. Web. 22 Jan 2021.

Vancouver:

Guo J. CELLULOSE NANOSTRUCTURE AND BINDING CHARACTERISTICS . [Internet] [Thesis]. Penn State University; 2011. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/12637.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Guo J. CELLULOSE NANOSTRUCTURE AND BINDING CHARACTERISTICS . [Thesis]. Penn State University; 2011. Available from: https://submit-etda.libraries.psu.edu/catalog/12637

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

10. Qian, Yufeng. Microbes Breathe Iron: Characterization of Dissimilatory Iron Reduction by Shewanella oneidensis MR-1.

Degree: 2011, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/12448

► This dissertation concerns the biological process of dissimilatory iron reduction (DIR) by a model iron-reducing microorganism: Shewanella oneidensis MR-1. Biochemical studies were performed to probe… (more)

▼ This dissertation concerns the biological process of dissimilatory iron reduction (DIR) by a model iron-reducing microorganism: Shewanella oneidensis MR-1. Biochemical studies were performed to probe the iron binding site on a small tetraheme cytochrome and to elucidate the electron transfer network in the periplasm. An outer membrane (OM)-localized TonB-dependent receptor was identified as a putative iron transport protein involved in DIR. A periplasm-localized small tetraheme cytochrome (STC) was heterologously expressed and purified from Escherichia coli. Kinetic studies have been performed to probe the electron flow on STC. Chemical modifications followed by site-directed mutagenesis along with isothermal titration calorimetry (ITC) and stopped flow measurements were performed to identify the iron binding site on STC. Chemical modification of STC revealed that carboxyl groups are involved in iron binding. Scanning mutagenesis on Asp and Glu was carried out to probe the putative iron binding site on STC. Two STC mutants (D21N; D80N) showed approximately 70% decrease in observed electron transfer rate constant with EDTA-Fe3+ from transient-state kinetic measurements. The impaired reactivity of STC (D80N/D21N) with EDTA-Fe3+ was further confirmed by a significant decrease (>10 fold) in iron binding affinity. Metal-catalyzed protein oxidation was used to identify membrane proteins which bind iron, acting either as an iron transporter or as a terminal iron reductase. This oxidation system catalyzed the modification of amino acids in close proximity to the iron binding site. The carbonyl groups formed from this oxidation can then be labeled with fluoresceinamine (FLNH2). The peptide containing the FLNH2 can then be proteolytically digested, purified by HPLC and then identified by MALDI-TOF tandem MS. A predominant peptide was identified to be part of SO2907 that encodes a putative TonB dependent receptor. Compared to wild type (wt), the so2097 gene deletion (∆SO2907) mutant has impaired ability to reduce soluble Fe(III). In vitro iron binding assay demonstrated that a truncated form of heterologous-expressed SO2907 that contains the Fe(III) binding site, is capable of binding soluble Fe(III) forms with a Kd of approximate 50 μM. Biochemical studies were carried out to investigate the electron transfer network in the periplasm. In vitro protein-protein interactions were conducted between three important electron transfer components: cytoplamic-membrane-localized CymA, soluble periplamsic-localized STC and OM associated MtrA in S. oneidensis MR-1. The specific interaction was found between CymA and MtrA while no apparent interaction was observed between CymA and STC. Through the in vitro membrane-catalyzed (formate-dehydrogenase-dependent) MtrA reduction, the direct electron transfer was demonstrated between CymA with MtrA. A proposed electron transfer route in the periplasm is presented. Advisors/Committee Members: Ming Tien, Dissertation Advisor/Co-Advisor, Ming Tien, Committee Chair/Co-Chair, Carsten Krebs, Committee Member, Squire J Booker, Committee Member, James David Kubicki, Committee Member, B Tracy Nixon, Committee Member.

Subjects/Keywords: Shewanella; Iron reduction

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Qian, Y. (2011). Microbes Breathe Iron: Characterization of Dissimilatory Iron Reduction by Shewanella oneidensis MR-1. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/12448

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Qian, Yufeng. “Microbes Breathe Iron: Characterization of Dissimilatory Iron Reduction by Shewanella oneidensis MR-1.” 2011. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/12448.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Qian, Yufeng. “Microbes Breathe Iron: Characterization of Dissimilatory Iron Reduction by Shewanella oneidensis MR-1.” 2011. Web. 22 Jan 2021.

Vancouver:

Qian Y. Microbes Breathe Iron: Characterization of Dissimilatory Iron Reduction by Shewanella oneidensis MR-1. [Internet] [Thesis]. Penn State University; 2011. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/12448.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Qian Y. Microbes Breathe Iron: Characterization of Dissimilatory Iron Reduction by Shewanella oneidensis MR-1. [Thesis]. Penn State University; 2011. Available from: https://submit-etda.libraries.psu.edu/catalog/12448

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

11. Regberg, Aaron Benjamin. THE EFFECT OF DISSIMILATORY IRON REDUCTION, NITRATE REDUCTION AND MICROBIAL GROWTH ON ELECTRICAL CONDUCTIVITY .

Degree: 2011, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/11734

► Changes in measured electrical conductivity are related to measured changes in aqueous concentrations of ions. In previous work anomalous increases in electrical conductivity measured in… (more)

▼ Changes in measured electrical conductivity are related to measured changes in aqueous concentrations of ions. In previous work anomalous increases in electrical conductivity measured in and around contaminated aquifers have been associated with biogeochemical activity. The respiration and growth of micro-organisms has been suggested as a possible cause of these conductivity signals. However, a quantitative link between the activity of micro-organisms and electrical conductivity has not been established. In this dissertation changes in the fluid electrical conductivity (σf) and σb are related to changes in chemical concentrations at multiple scales. Changes in σf can be interpreted as reaction rates if the stoichiometry of the reaction is understood. Results from batch experiments demonstrate that measured changes in σf over time document rates of abiotic and biotic reduction of goethite. In two column reactors packed with sediments from Oyster Virginia and fed with an input containing dissolved acetate, measured changes in σb initially document biogeochemical reaction rates of iron reduction or nitrate reduction. Eventually, σb becomes decoupled from changes in chemical concentrations and increases significantly. Fe(II) adsorption does not cause σb to become decoupled from aqueous chemistry. Instead, this decoupling is attributed to the growth and presence of an electrically conductive biofilm. Reactive transport modeling is used to constrain the amount of biomass produced in each reactor. A value for electrical conductivity is estimated that depends on the calculated growth in biomass and the assumed density of that biomass. For iron-reducing conditions biofilms, the model is consistent with values of biofilm conductivity > 2.2 S/m, and for nitrate reducing conditions, with conductivity > 300 S/m. These values are the first estimates for biofilm electrical conductivity based on column reactor experiments. The results of a field-scale tracer test involving nitrate reduction are also presented. The results suggest that electrical conductivity may be able to track biogeochemical activity if the tracers are large enough and conductive enough to be detectable. Finally, results of preliminary electrochemical experiments designed to directly measure the conductivity of biofilms are presented. Methods for improving the accuracy of these experiments are proposed. Advisors/Committee Members: Susan Louise Brantley, Dissertation Advisor/Co-Advisor, Susan Louise Brantley, Committee Chair/Co-Chair, Kamini Singha, Committee Chair/Co-Chair, James David Kubicki, Committee Member, Ming Tien, Committee Member.

Subjects/Keywords: Biofilms; Kinetics; Electrical Conductivity; Reactive Transport Modeling; Dissimilatory Iron Reduction; Nitrate Reduction

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Regberg, A. B. (2011). THE EFFECT OF DISSIMILATORY IRON REDUCTION, NITRATE REDUCTION AND MICROBIAL GROWTH ON ELECTRICAL CONDUCTIVITY . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/11734

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Regberg, Aaron Benjamin. “THE EFFECT OF DISSIMILATORY IRON REDUCTION, NITRATE REDUCTION AND MICROBIAL GROWTH ON ELECTRICAL CONDUCTIVITY .” 2011. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/11734.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Regberg, Aaron Benjamin. “THE EFFECT OF DISSIMILATORY IRON REDUCTION, NITRATE REDUCTION AND MICROBIAL GROWTH ON ELECTRICAL CONDUCTIVITY .” 2011. Web. 22 Jan 2021.

Vancouver:

Regberg AB. THE EFFECT OF DISSIMILATORY IRON REDUCTION, NITRATE REDUCTION AND MICROBIAL GROWTH ON ELECTRICAL CONDUCTIVITY . [Internet] [Thesis]. Penn State University; 2011. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/11734.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Regberg AB. THE EFFECT OF DISSIMILATORY IRON REDUCTION, NITRATE REDUCTION AND MICROBIAL GROWTH ON ELECTRICAL CONDUCTIVITY . [Thesis]. Penn State University; 2011. Available from: https://submit-etda.libraries.psu.edu/catalog/11734

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

12. Sanders, Rebecca L. CLAY MINERAL REACTIVITY ACROSS SCALES UTILIZING SOLID-STATE NUCLEAR MAGNETIC RESONANCE.

Degree: 2011, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/11716

► An understanding of the surface reactivity of minerals is crucial for characterizing and scaling numerous environmental processes. For instance, the release rate of ions during… (more)

▼ An understanding of the surface reactivity of minerals is crucial for characterizing and scaling numerous environmental processes. For instance, the release rate of ions during dissolution is scaled to remove differences in the available surface area. Typically, BET or geometric surface area measurements are the convention to calculate surface area. However, these methods do not necessarily report on the reactive surface area of a mineral, which provides a chemically-sensitive measure of surface area. The reactive surface area of clay minerals can be particularly challenging to quantify as they have a layered structure with two distinct surfaces: edge sites and basal planes. The edge sites dissolve preferentially compared to basal planes. When clay minerals are weathered, the reactive surface area decreases as edge sites are depleted. Throughout this thesis, the objective was to develop and demonstrate that advanced experimental tools can be used to predict reactive surface area across spatial scales for clay minerals. To measure reactive surface area, the probe molecule (3,3,3-trifluoropropyl) dimethylchlorosilane (TFS) is attached to lone Q3Si hydroxyl sites and the 19F spins in the TFS-treated samples are then quantified using 19F magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy. The quantification of the number of reactive hydroxyl sites per gram of sample is proportional to the reactive surface area of each mineral, particularly the edge sites for clay minerals. Batch dissolution experiments of kaolinite were conducted at 21 °C and pH 3. During the course of three months, dissolution rate decreased over time. BET specific surface area measurements did not reflect changes in dissolution rate. However, the selective nature of TFS attachment has been utilized to demonstrate the changes in reactive surface area are tied to a concomitant decrease in the rates of Si and Al release into solution. Similar studies were conducted with bentonite, a montmorillonite-rich clay that contained an amorphous silica phase. The silica phase was identified to be opal-CT and was not observed to contribute the dissolution rate of bentonite. Similar results to the kaolinite experiments were obtained in which the decreasing dissolution rate was correlated with changes in reactive surface area. The quantity of reactive sites can be used to predict the dissolution rates of kaolinite and montmorillonite. Dissolution rates in the field can be several orders of magnitude slower than rates for the same mineral when dissolved in the laboratory. Several factors including reactive surface area can account for the differences in dissolution rates. The solid-state NMR proxy for reactive surface area was used to determine how surface reactivity impacts the rates of mineral transformations at the Shale Hills catchment, a Critical Zone Observatory located in central Pennsylvania. The reactive surface area was quantified for a series of soils collected along a downslope planar transect at Shale Hills. Variables that were… Advisors/Committee Members: Karl Todd Mueller, Dissertation Advisor/Co-Advisor, Karl Todd Mueller, Committee Chair/Co-Chair, Barbara Jane Garrison, Committee Member, John B Asbury, Committee Member, James David Kubicki, Committee Member.

Subjects/Keywords: reactive surface area; clay minerals; NMR; dissolution; kaolinite; montmorillonite; Shale Hills; TFS

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Sanders, R. L. (2011). CLAY MINERAL REACTIVITY ACROSS SCALES UTILIZING SOLID-STATE NUCLEAR MAGNETIC RESONANCE. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/11716

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Sanders, Rebecca L. “CLAY MINERAL REACTIVITY ACROSS SCALES UTILIZING SOLID-STATE NUCLEAR MAGNETIC RESONANCE.” 2011. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/11716.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Sanders, Rebecca L. “CLAY MINERAL REACTIVITY ACROSS SCALES UTILIZING SOLID-STATE NUCLEAR MAGNETIC RESONANCE.” 2011. Web. 22 Jan 2021.

Vancouver:

Sanders RL. CLAY MINERAL REACTIVITY ACROSS SCALES UTILIZING SOLID-STATE NUCLEAR MAGNETIC RESONANCE. [Internet] [Thesis]. Penn State University; 2011. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/11716.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Sanders RL. CLAY MINERAL REACTIVITY ACROSS SCALES UTILIZING SOLID-STATE NUCLEAR MAGNETIC RESONANCE. [Thesis]. Penn State University; 2011. Available from: https://submit-etda.libraries.psu.edu/catalog/11716

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

13. Fischer, Timothy B. STRUCTURAL TRANSFORMATIONS OF BIRNESSITE (δ-MnO2) DURING BIOLOGICAL AND ABIOLOGICAL REDUCTION .

Degree: 2011, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/11319

► Time-resolved structural analyses of synthetic birnessite (δ-MnO2) during reaction with both biological and abiological reactants confirmed that the evolution of the mineral’s crystal structure during… (more)

▼ Time-resolved structural analyses of synthetic birnessite (δ-MnO2) during reaction with both biological and abiological reactants confirmed that the evolution of the mineral’s crystal structure during reduction and dissolution depended upon the nature of the reactant and the fate of the reduced Mn. The first-ever real-time X-ray diffraction (XRD) analysis of a biological-mineral reaction demonstrated that the reductive dissolution of birnessite during direct electron transfer by total-membrane fractions of the facultative anaerobe Shewanella oneidensis was characterized by a collapse of the birnessite structure due to a decrease in the c unit-cell parameter. The observed structural collapse was verified by analysis of the reaction products of batch reactions between whole-cell cultures of S. oneidensis and birnessite. A combined XRD and X-ray absorption spectroscopy (XAS) examination indicated that the unit-cell collapse was caused by reduction of structural Mn4+ to Mn3+, which increased the net negative charge on birnessite’s octahedral sheets, followed by an inferred increase in the interlayer Na:H2O ratio. The reduced Mn2+ precipitated as rhodochrosite (MnCO3). The reduction, chelation, and removal of Mn from the birnessite crystal structure by bacterial siderophores did not result in a structural collapse of the mineral, despite the large amount of Mn removed from the MnO6 octahedral sheets (up to 20 mol%). Rather, the unit-cell parameters remained constant throughout the complete dissolution of birnessite. A third structural pathway was revealed during the reduction of birnessite in the presence of dissolved transition metals. When aqueous Cr3+ was oxidized to Cr6+ by reduction of octahedral Mn, the birnessite crystal structure experienced a phase transformation from triclinic to hexagonal. During this abiological reduction, the reduced Mn remained part of the hexagonal crystal structure, occupying positions above or below octahedral vacancies. The specialized nature of birnessite’s transformations in response to alternative reduction/dissolution mechanisms presents the possibility that crystallographic analysis of birnessite may serve as a useful biomarker in studies of environments where it is desirable to know whether life forms participated in mineral redox processes. Advisors/Committee Members: Peter J Heaney, Dissertation Advisor/Co-Advisor, Peter J Heaney, Committee Chair/Co-Chair, Maryann Victoria Bruns, Committee Chair/Co-Chair, James David Kubicki, Committee Member, Christopher Howard House, Committee Member, William D Burgos, Committee Member.

Subjects/Keywords: birnessite; bioreduction; manganese oxides; chromium; shewanella; time-resolved XRD; siderophores

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Fischer, T. B. (2011). STRUCTURAL TRANSFORMATIONS OF BIRNESSITE (δ-MnO2) DURING BIOLOGICAL AND ABIOLOGICAL REDUCTION . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/11319

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Fischer, Timothy B. “STRUCTURAL TRANSFORMATIONS OF BIRNESSITE (δ-MnO2) DURING BIOLOGICAL AND ABIOLOGICAL REDUCTION .” 2011. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/11319.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Fischer, Timothy B. “STRUCTURAL TRANSFORMATIONS OF BIRNESSITE (δ-MnO2) DURING BIOLOGICAL AND ABIOLOGICAL REDUCTION .” 2011. Web. 22 Jan 2021.

Vancouver:

Fischer TB. STRUCTURAL TRANSFORMATIONS OF BIRNESSITE (δ-MnO2) DURING BIOLOGICAL AND ABIOLOGICAL REDUCTION . [Internet] [Thesis]. Penn State University; 2011. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/11319.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Fischer TB. STRUCTURAL TRANSFORMATIONS OF BIRNESSITE (δ-MnO2) DURING BIOLOGICAL AND ABIOLOGICAL REDUCTION . [Thesis]. Penn State University; 2011. Available from: https://submit-etda.libraries.psu.edu/catalog/11319

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

14. Murphy, Kelly Ann. Characterizing the Alteration Layers on Nuclear Waste Glasses by Solid-State Nuclear Magnetic Resonance.

Degree: 2014, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/20489

► One of the most promising options for long-term storage of radioactive waste is vitrification, or immobilization in a glass matrix. The viability of this storage… (more)

▼ One of the most promising options for long-term storage of radioactive waste is vitrification, or immobilization in a glass matrix. The viability of this storage method is evaluated by exposure of the glass to corrosive conditions. Previous work has indicated that alteration layers, which may be protective in nature, form on the glass surface. Solid-state nuclear magnetic resonance (NMR) spectroscopy is an ideal tool to study the alteration layers because this technique provides structural and (indirectly) compositional information. Moreover, inherent properties of the glass can be exploited to differentiate between the alteration layers and bulk glass via cross-polarization magic angle spinning (CP-MAS) NMR. Initial characterization suggested the alteration layers formed on two glass compositions were comprised of a hydrated glass layer (barrier between pristine glass and gel layer) and a nano-porous gel layer (directly in contact with solution). The former contained hydrated versions of all components in the pristine, non-corroded glass. Only certain components such as silicon and aluminum, however, were retained in the gel layer. Experimental conditions such as glass composition and form (powder versus fiber) have been shown to influence the composition and structure of the alteration layers. After formation, the alteration layers continue to interact with solution species due to an established dynamic equilibrium. Through isotopic labeling and solution swapping experiments, recondensation of aqueous silicon onto the powder surface was observed at short and long equilibration periods. Boron sorption after release to solution was also observed for one glass composition. The questions probed in these studies suggest that the solution-surface interface is constantly evolving. Therefore, future work in the field should continue to strive towards mimicking environmental conditions and attempting to answer fundamental questions about water-glass interactions. Advisors/Committee Members: Karl Todd Mueller, Dissertation Advisor/Co-Advisor, Karl Todd Mueller, Committee Chair/Co-Chair, Carlo G Pantano, Dissertation Advisor/Co-Advisor, Miriam Arak Freedman, Committee Member, Danny Glynn Sykes, Committee Member, James David Kubicki, Committee Member.

Subjects/Keywords: NMR; Alteration layers; Surface structure; Nuclear waste glasses; Corrosion

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Murphy, K. A. (2014). Characterizing the Alteration Layers on Nuclear Waste Glasses by Solid-State Nuclear Magnetic Resonance. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/20489

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Murphy, Kelly Ann. “Characterizing the Alteration Layers on Nuclear Waste Glasses by Solid-State Nuclear Magnetic Resonance.” 2014. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/20489.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Murphy, Kelly Ann. “Characterizing the Alteration Layers on Nuclear Waste Glasses by Solid-State Nuclear Magnetic Resonance.” 2014. Web. 22 Jan 2021.

Vancouver:

Murphy KA. Characterizing the Alteration Layers on Nuclear Waste Glasses by Solid-State Nuclear Magnetic Resonance. [Internet] [Thesis]. Penn State University; 2014. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/20489.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Murphy KA. Characterizing the Alteration Layers on Nuclear Waste Glasses by Solid-State Nuclear Magnetic Resonance. [Thesis]. Penn State University; 2014. Available from: https://submit-etda.libraries.psu.edu/catalog/20489

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

15. Alimohammadi Zanjani, Mozhgan. Molecular Dynamics Simulations of Aggregation of Anatase (Titanium Dioxide) Nanocrystals .

Degree: 2011, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/12106

► A quantitative understanding of the forces between colloidal nanoparticles would benefit numerous applications in sensing, nanoelectronics, composite materials, nanofluids, optics, and catalysis, which could exploit… (more)

▼ A quantitative understanding of the forces between colloidal nanoparticles would benefit numerous applications in sensing, nanoelectronics, composite materials, nanofluids, optics, and catalysis, which could exploit the unique properties associated with their small sizes. In applications involving crystallization, the aggregation of nanoparticles can be important. Recent experiments on specific materials, including anatase-TiO₂, have documented the phenomenon of oriented attachment, in which nanocrystals approach one another and merge along specific crystallographic directions to form twinned or single-crystalline structures. The ability to direct crystallization through oriented attachment is an exciting prospect that could allow for the creation of new nanostructures with well-defined sizes and shapes. To realize the full potential of oriented attachment for achieving the controlled synthesis of anatse nanocrystals, insight into its origins, which are not currently clear in all cases, would be beneficial. This dissertation employs molecular dynamics simulations to resolve the issues regarding anatse nanoparticle aggregation in a vacuum and in aqueous environments. By utilizing both symmetric and asymmetric nanocrystals, the majority of the observed synthesized anatase shapes have been covered. MD simulations have been carried out to determine the aggregation pathway of such nanocrystals, and by repeating the simulation with different initial configurations, the directional alignment of these nanocrystals has been discovered in vacuum environment. Also, by performing force, energy, dipole-dipole interactions, and other sorts of calculations, the origins of the preferred alignment of anatase nanocrystals in vacuum has been discovered. Oriented attachment was first discovered in experimental studies for the crystallization of anatase nanocrystals under hydrothermal aqueous conditions. For the aqueous anatase nanoparticles, the Bandura-Kubicki force field has been tested against results from first-principles calculations based on density-functional theory and refined to describe the binding of H₂O, H⁺, and OH^- to various crystal faces. Hence, the parameters for the available force fields have been modified to be used for anatase nanocrystals. Since MD is a very strong tool that allows solving larger systems with many water molecules, it has become possible to study the aggregation mechanism of anatase nanocrystals in an aqueous environment. Also, the difference in water adsorption on anatase surfaces under ambient and hydrothermal conditions has been studied, while hydration effects have been quantified. Advisors/Committee Members: Kristen Ann Fichthorn, Dissertation Advisor/Co-Advisor, James David Kubicki, Committee Member, Darrell Velegol, Committee Member, Michael John Janik, Committee Member, Kristen Ann Fichthorn, Committee Chair/Co-Chair.

Subjects/Keywords: rutile; anatase; titanium dioxide; oriented attachment; aggregation

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Alimohammadi Zanjani, M. (2011). Molecular Dynamics Simulations of Aggregation of Anatase (Titanium Dioxide) Nanocrystals . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/12106

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Alimohammadi Zanjani, Mozhgan. “Molecular Dynamics Simulations of Aggregation of Anatase (Titanium Dioxide) Nanocrystals .” 2011. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/12106.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Alimohammadi Zanjani, Mozhgan. “Molecular Dynamics Simulations of Aggregation of Anatase (Titanium Dioxide) Nanocrystals .” 2011. Web. 22 Jan 2021.

Vancouver:

Alimohammadi Zanjani M. Molecular Dynamics Simulations of Aggregation of Anatase (Titanium Dioxide) Nanocrystals . [Internet] [Thesis]. Penn State University; 2011. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/12106.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Alimohammadi Zanjani M. Molecular Dynamics Simulations of Aggregation of Anatase (Titanium Dioxide) Nanocrystals . [Thesis]. Penn State University; 2011. Available from: https://submit-etda.libraries.psu.edu/catalog/12106

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

16. Karra, Murthy Dakshina. SOLID-STATE NMR STUDIES OF BRONSTED ACID SITES IN ZEOLITES UTILIZING THE PROBE MOLECULE TRIMETHYLPHOSPHINE OXIDE .

Degree: 2008, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/6016

► Zeolites are extremely efficient catalysts for a wide variety of industrial processes such as fluid cracking and xylene isomerization. It is well established that acid… (more)

▼ Zeolites are extremely efficient catalysts for a wide variety of industrial processes such as fluid cracking and xylene isomerization. It is well established that acid forms of zeolites are the most active in these reactions and the excellent catalytic abilities are thought to be due to the presence of Brønsted and Lewis acid centers or sites in the zeolite structure. The purpose of this study is to characterize these acid sites by using the 31P solid-state NMR of the probe molecule trimethylphosphine oxide adsorbed onto these zeolites. The 31P nucleus possesses excellent sensitivity and more importantly a large chemical shift range. This characteristic property of the 31P nucleus is essential to resolve the different acid sites in a zeolite based on their strength or ‘proton donating ability’. When a TMPO molecule is complexed to an acid site, there is a loss of electron density near the oxygen atom, which is relayed back to the 31P nucleus and is seen as a deshielding effect. The NMR resonances of the 31P nucleus are then shifted downfield and there have been suggestions in literature that this shift can be used as an indicator of acid strength. This study undertakes to prove, through the use of double- and triple-resonance NMR techniques that the resonances seen in the 31P spectrum of TMPO complexed to acid zeolites are either due to Brønsted or Lewis sites. The differences in structure between these two complexes are exploited to assign the acid sites. In particular since a Brønsted site is defined by the presence of a proton, dipolar connectivity experiments such as cross-polarization and rotational echo double resonance between protons and 31P nuclei are used to verify the nature of these resonances. Since TMPO contains three methyl groups, it is critical to replace the protons with deuterium hence ensuring that the source of the 1H magnetization is from the zeolite. The deuterated version of the probe molecule, TMPO-d9 has been synthesized and used extensively to study the acid sites in two very important zeolites, HY and HZSM-5 with varying Si/Al ratios. In HY, two types of acid sites have been resolved and identified as Brønsted sites. One resonance in the 31P spectrum is assigned to protons associated with bridging hydroxyl groups pointing into the supercages while the other to protons in the smaller sodalite cages. In the zeolite HZSM-5, three Brønsted resonances have been confirmed and agree with recent reports in literature, which identify three cation positions in this zeolite. As the Si/Al ratio is increased (and the overall acid site concentration decreases), it is found that the relative amounts of the stronger acid sites increases. On comparing the chemical shifts of the probe molecule bound to HY and HZSM-5, it also found that the resonances in HZSM-5 show a greater downfield shift. This result is in qualitative agreement with the general thinking that HZSM-5 contains stronger acid sites. The resonances of the probe molecule bound to zeolite H- appear at positions intermediate to HY… Advisors/Committee Members: James David Kubicki, Committee Member, Anne M Andrews, Committee Member, Karl Todd Mueller, Committee Chair/Co-Chair, Alan James Benesi, Committee Member.

Subjects/Keywords: zeolite; hy; trimethylphosphine oxide; zsm-5; faujasite; acid sites; nmr

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Karra, M. D. (2008). SOLID-STATE NMR STUDIES OF BRONSTED ACID SITES IN ZEOLITES UTILIZING THE PROBE MOLECULE TRIMETHYLPHOSPHINE OXIDE . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/6016

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Karra, Murthy Dakshina. “SOLID-STATE NMR STUDIES OF BRONSTED ACID SITES IN ZEOLITES UTILIZING THE PROBE MOLECULE TRIMETHYLPHOSPHINE OXIDE .” 2008. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/6016.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Karra, Murthy Dakshina. “SOLID-STATE NMR STUDIES OF BRONSTED ACID SITES IN ZEOLITES UTILIZING THE PROBE MOLECULE TRIMETHYLPHOSPHINE OXIDE .” 2008. Web. 22 Jan 2021.

Vancouver:

Karra MD. SOLID-STATE NMR STUDIES OF BRONSTED ACID SITES IN ZEOLITES UTILIZING THE PROBE MOLECULE TRIMETHYLPHOSPHINE OXIDE . [Internet] [Thesis]. Penn State University; 2008. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/6016.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Karra MD. SOLID-STATE NMR STUDIES OF BRONSTED ACID SITES IN ZEOLITES UTILIZING THE PROBE MOLECULE TRIMETHYLPHOSPHINE OXIDE . [Thesis]. Penn State University; 2008. Available from: https://submit-etda.libraries.psu.edu/catalog/6016

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

17. Van Essendelft, Dirk Thomas. KINETICS OF THE ACID DIGESTION OF SERPENTINE WITH CONCURRENT GRINDING FOR THE PURPOSE OF CARBON DIOXIDE SEQUESTRATION .

Degree: 2008, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/9211

► The kinetics of the acid digestion of serpentine is an important scientific and industrial issue as pertains to carbon dioxide sequestration. Serpentine contains approximately 25%… (more)

▼ The kinetics of the acid digestion of serpentine is an important scientific and industrial issue as pertains to carbon dioxide sequestration. Serpentine contains approximately 25% magnesium by weight and is prolific near most major population centers. These two properties make serpentine an ideal mineral carbonation feedstock. However, serpentine is a highly ordered ultramafic magnesium silicate structure consisting of alternating sheets of brucite-like material and silica-like material. This highly ordered structure causes the formation of a silica barrier around the mineral particles that can slow or even stop the kinetics as the particles dissolve. The physical behavior of this layer causes a shift in kinetic behavior from surface limited kinetics to diffusion limited kinetics. However, it has been shown that both behaviors are important at the same time and vary by particle size. Further, it has been shown that the kinetics can be greatly accelerated by incorporating concurrent, low energy, attrition-type grinding during the chemical reaction. A computational model based on surface kinetics, surface species distribution, surface charge, the electrical double layer, gel layer diffusion, solution thermodynamics, and particle size and shape was developed to describe the kinetics. It was demonstrated that the computational model can describe the experimental fractional magnesium extraction of magnesium from serpentine within ~3% in every case and within ~1% in most cases with reasonable understanding and characterization of the materials going into the system. It was found that particle shape as well as size plays a critical role in the kinetics. However, the tools to quickly and adequately characterize particle shape were not available during this study and represent a great opportunity for future research. The experiments performed in this study allowed the model to be predictive and be used to size and design of large scale industrial equipment and estimate the upper bound of the energy consumption for the system. It was found that the total parasitic energy loss for the large scale digestion system would be less than 6.1%, which is much less than competing technologies. Advisors/Committee Members: Harold Harris Schobert, Committee Chair/Co-Chair, Derek Elsworth, Committee Member, Mark Stephen Klima, Committee Member, James David Kubicki, Committee Member, Sridhar Komarneni, Committee Member.

Subjects/Keywords: Chemical Kinetics; Computational Modeling; Serpentine; Carbon Dioxide Sequestration; Mineral Carbonation; Strong Acid Dissolution

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Van Essendelft, D. T. (2008). KINETICS OF THE ACID DIGESTION OF SERPENTINE WITH CONCURRENT GRINDING FOR THE PURPOSE OF CARBON DIOXIDE SEQUESTRATION . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/9211

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Van Essendelft, Dirk Thomas. “KINETICS OF THE ACID DIGESTION OF SERPENTINE WITH CONCURRENT GRINDING FOR THE PURPOSE OF CARBON DIOXIDE SEQUESTRATION .” 2008. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/9211.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Van Essendelft, Dirk Thomas. “KINETICS OF THE ACID DIGESTION OF SERPENTINE WITH CONCURRENT GRINDING FOR THE PURPOSE OF CARBON DIOXIDE SEQUESTRATION .” 2008. Web. 22 Jan 2021.

Vancouver:

Van Essendelft DT. KINETICS OF THE ACID DIGESTION OF SERPENTINE WITH CONCURRENT GRINDING FOR THE PURPOSE OF CARBON DIOXIDE SEQUESTRATION . [Internet] [Thesis]. Penn State University; 2008. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/9211.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Van Essendelft DT. KINETICS OF THE ACID DIGESTION OF SERPENTINE WITH CONCURRENT GRINDING FOR THE PURPOSE OF CARBON DIOXIDE SEQUESTRATION . [Thesis]. Penn State University; 2008. Available from: https://submit-etda.libraries.psu.edu/catalog/9211

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

18. Tai, Yuan-Liang. KINETIC AND MECHANISTIC STUDY FOR THE ABIOTIC OXIDATION OF Fe(II) CATALYZED AT THE FERRIC (OXYHYDR)OXIDE AND SOLUTION INTERFACE .

Degree: 2009, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/10218

► This research dealt with the heterogeneous oxidation of Fe(II) by some environmentally significant contaminants including nitrite, uranium, and arsenate using Hydrous Ferric Oxide (HFO) as… (more)

▼ This research dealt with the heterogeneous oxidation of Fe(II) by some environmentally significant contaminants including nitrite, uranium, and arsenate using Hydrous Ferric Oxide (HFO) as the catalytical solid phase in anoxic soil medium and sediments. It is the first study of the Fe(II)/Fe(III)/HFO system in which mass balance has been performed for both Fe(II) and all the oxidant species using a strictly anoxic environment at circumneutral pH. Fe(II) and HFO were used as the electron donor and catalytical solid phase because Fe(II)/Fe(III) redox couple is often dominant in controlling the redox potential in anoxic groundwater system and HFO is ubiquitous in soils and sediments, and it is an important adsorbent for a wide range of chemicals. The results showed that the reaction between Fe(II) and either NO2- or U(VI) was fast in the presence of HFO. The rate for the oxidation of Fe(II) and the reduction of either NO2- or U(VI) was found to be a function of dissolved Fe(II), solid-bound Fe(II) and oxidant concentration, and can be described by Rate = - koverall • [Fe(II)diss] • [Fe(II)solid-bound] • [Oxidant]. However, the reaction rate for Fe(II)/HFO/U(VI) was an order of magnitude faster than for nitrite, possibly due to high affinity of U(VI) to the HFO surface which could provide a shorter pathway for electron-transfer. Conservation of solid-bound Fe(II) was observed for either oxidant throughout the reaction with Fe(II)/HFO, therefore solid-bound Fe(II) functioned as a catalyst for the reduction of either oxidant by Fe(II). In experiments with nitrite or no oxidant in Fe(II)/HFO, concentration of Fe(II)solid-bound first increased less than 100% and then decreased coincident with partial conversion of HFO to goethite. When U(VI) was used as an oxidant, Fe(II)solid-bound increased and then remained constant such that solid-bound Fe(II) density was increased by 3 to 5 times compared to absence of U(VI). The significant increase of solid-bound Fe(II) in Fe(II)/U(VI) reaction could be due to the newly formed sorption sites created by the sorption and reductive precipitation of U(VI) and oxidative precipitation of Fe(II). The characterization of Fe(II)/Fe(III) systems from this study is consistent with several other recent studies that have supported the hypothesis that Fe(II) is incorporated into the bulk phase of Fe(III) oxides, rather than remaining at the interface, and that this unusual behavior results in apparently unique redox reactivity. Interestingly, overall rate constants declined when Fe(II)solid-bound exceeded 0.02 mol Fe(II) per mol Fe(III), similar to results from previous studies using O2 and NO2- as oxidants. We also investigated the effectiveness of two extractants, bicarbonate and phosphoric acid, on the quantification of U(VI) species during Fe(II)/U(VI) reaction in HFO suspension. Higher phosphate extractable U(VI) (U(VI)phosphate) than bicarbonate extractable U(VI) ( U(VI)bicarbonate ) was observed in all experiments. Interestingly, consumed U(VI)bicarbonate /consumed U(VI)phosphate ratios… Advisors/Committee Members: Brian Dempsey, Dissertation Advisor/Co-Advisor, Brian Dempsey, Committee Chair/Co-Chair, William D Burgos, Committee Member, James David Kubicki, Committee Member, Richard Charles Stehouwer, Committee Member.

Subjects/Keywords: reaction kinetics; ferrihydrite; uranium; nitrite; Solid-bound Fe(II); HFO; abiotic redox reaction

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Tai, Y. (2009). KINETIC AND MECHANISTIC STUDY FOR THE ABIOTIC OXIDATION OF Fe(II) CATALYZED AT THE FERRIC (OXYHYDR)OXIDE AND SOLUTION INTERFACE . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/10218

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Tai, Yuan-Liang. “KINETIC AND MECHANISTIC STUDY FOR THE ABIOTIC OXIDATION OF Fe(II) CATALYZED AT THE FERRIC (OXYHYDR)OXIDE AND SOLUTION INTERFACE .” 2009. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/10218.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Tai, Yuan-Liang. “KINETIC AND MECHANISTIC STUDY FOR THE ABIOTIC OXIDATION OF Fe(II) CATALYZED AT THE FERRIC (OXYHYDR)OXIDE AND SOLUTION INTERFACE .” 2009. Web. 22 Jan 2021.

Vancouver:

Tai Y. KINETIC AND MECHANISTIC STUDY FOR THE ABIOTIC OXIDATION OF Fe(II) CATALYZED AT THE FERRIC (OXYHYDR)OXIDE AND SOLUTION INTERFACE . [Internet] [Thesis]. Penn State University; 2009. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/10218.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Tai Y. KINETIC AND MECHANISTIC STUDY FOR THE ABIOTIC OXIDATION OF Fe(II) CATALYZED AT THE FERRIC (OXYHYDR)OXIDE AND SOLUTION INTERFACE . [Thesis]. Penn State University; 2009. Available from: https://submit-etda.libraries.psu.edu/catalog/10218

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

19. Hummer, Daniel Robert. Mechanisms of Aqueous Crystallization and Phase Transformation in Titanium Oxide Minerals.

Degree: 2010, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/10644

► The sequence of mineral phases that appear during the crystallization of titanium oxides from aqueous solutions was examined using a variety of experimental and theoretical… (more)

▼ The sequence of mineral phases that appear during the crystallization of titanium oxides from aqueous solutions was examined using a variety of experimental and theoretical techniques. Time-resolved X-ray diffraction experiments showed that the traditionally metastable phase anatase was the first TiO2 polymorph to crystallize for all conditions, and anatase converted to rutile over many hours. Thus, the reversal of thermodynamic phase stability for particles with large surface area to volume ratios can be attributed to increased surface energies at the nanoscale. Quantum energy calculations on model anatase and rutile nanoparticles and surfaces revealed that the energy of under-bonded atoms on various crystallographic surfaces, and especially defects at the edges and corners of nanocrystals, were responsible for the stability reversal rather than surface-induced perturbations to the crystal structure. Kinetic modeling of mineral abundance data from the XRD experiments, using a self-authored kinetic fitting program, demonstrated that minerals precipitate from and re-dissolve into solution without undergoing solid state phase transitions. Time-resolved small-angle X-ray scattering (TR-SAXS) revealed that nanoparticles nucleate and grow rapidly into broad, Gaussian-type particle size distributions, and also showed evidence of oriented aggregation. An analysis of the in situ pH data and XRD data for the co-existing particles revealed the counterintuitive conclusion that precipitation is slower at high Ti4+ concentrations. A crystallization model is proposed based on classical nucleation theory, in which different interfacial energies between the mineral surface and the fluid cause each polymorph to have different activation energies of precipitation. These activation energies scale positively with the saturation state of the fluid. Advisors/Committee Members: Peter J Heaney, Dissertation Advisor/Co-Advisor, Peter J Heaney, Committee Chair/Co-Chair, James David Kubicki, Committee Member, Lee Kump, Committee Member, Kwadwo Osseo Asare, Committee Member.

Subjects/Keywords: anatase; rutile; titanium oxide; titanium dioxide; crystallization; precipitation; time-resolved X-ray diffraction; time-resolved small angle X-ray scattering; nanoparticles; phase stability reversal; surface energy; nucleation; crystal growth; hydrolysis; global optimization; kinetic fitting; kinetic modeling

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Hummer, D. R. (2010). Mechanisms of Aqueous Crystallization and Phase Transformation in Titanium Oxide Minerals. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/10644

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Hummer, Daniel Robert. “Mechanisms of Aqueous Crystallization and Phase Transformation in Titanium Oxide Minerals.” 2010. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/10644.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Hummer, Daniel Robert. “Mechanisms of Aqueous Crystallization and Phase Transformation in Titanium Oxide Minerals.” 2010. Web. 22 Jan 2021.

Vancouver:

Hummer DR. Mechanisms of Aqueous Crystallization and Phase Transformation in Titanium Oxide Minerals. [Internet] [Thesis]. Penn State University; 2010. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/10644.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Hummer DR. Mechanisms of Aqueous Crystallization and Phase Transformation in Titanium Oxide Minerals. [Thesis]. Penn State University; 2010. Available from: https://submit-etda.libraries.psu.edu/catalog/10644

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

20. Swalina, Chet W. Dynamical electron-proton correlation in the nuclear-electronic orbital framework.

Degree: 2008, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/7332

► Methods for including dynamical electron-proton correlation within the nuclear-electronic orbital (NEO) framework are explored. In the NEO approach, nuclear quantum effects are incorporated directly within… (more)

▼ Methods for including dynamical electron-proton correlation within the nuclear-electronic orbital (NEO) framework are explored. In the NEO approach, nuclear quantum effects are incorporated directly within electronic structure calculations by treating specified nuclei quantum mechanically on the same level as the electrons. Mixed nuclear electronic wavefunctions are calculated by solving the time independent nuclear-electronic Schrodinger equation using molecular orbital techniques. A formulation of nuclear-electronic orbital many-body perturbation theory (NEO-MP2) for recovering electron-proton correlation is presented. The molecular structures for a series of bihalides and the hydrogen fluoride (HF) dimer are calculated at the NEO-MP2 level and compared to vibrationally averaged structures obtained using conventional Born-Oppenheimer based approaches and to experimental values. The bihalide X-X distances are similar for all methods. For the HF dimer, the NEO-MP2 F-F distance is in excellent agreement with the distance obtained experimentally for a model which removes the large amplitude bending motions. The NEO-MP2 approach does not include these large amplitude bending motions because it does not recover enough dynamical electron-proton orrelation. A method which incorporates explicit electron-proton correlation directly into the nuclear-electronic orbital self consistent-field framework is presented. This nuclear-electronic orbital explicitly correlated Hartree-Fock (NEO-XCHF) scheme is formulated using Gaussian basis functions for the electrons and the quantum nuclei in conjunction with Gaussian type geminal functions. The description of the nuclear wavefunction is significantly improved by the inclusion of explicit electron-proton correlation. The NEO-XCHF method leads to hydrogen vibrational stretch frequencies that are in excellent agreement with those calculated from grid-based methods. Overall, these findings demonstrate that dynamical electron proton correlation significantly impacts the qualitative characteristics of nuclear wavefunctions. Moreover, in the NEO framework, dynamical electron-proton correlation is even more important than dynamical electron-electron correlation. Methods based on orbital expansions for recovering dynamical electron proton correlation suffer from slow convergence reminiscent of that found for precise treatments of electron-electron correlation. Therefore, an explicit treatment of electron-proton correlation is required. Advisors/Committee Members: Sharon Hammes Schiffer, Committee Chair/Co-Chair, Barbara Jane Garrison, Committee Member, James David Kubicki, Committee Member, Karl Todd Mueller, Committee Member.

Subjects/Keywords: dynamical correlation; electron; proton

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APA (6^th Edition):

Swalina, C. W. (2008). Dynamical electron-proton correlation in the nuclear-electronic orbital framework. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/7332

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Swalina, Chet W. “Dynamical electron-proton correlation in the nuclear-electronic orbital framework.” 2008. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/7332.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Swalina, Chet W. “Dynamical electron-proton correlation in the nuclear-electronic orbital framework.” 2008. Web. 22 Jan 2021.

Vancouver:

Swalina CW. Dynamical electron-proton correlation in the nuclear-electronic orbital framework. [Internet] [Thesis]. Penn State University; 2008. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/7332.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Swalina CW. Dynamical electron-proton correlation in the nuclear-electronic orbital framework. [Thesis]. Penn State University; 2008. Available from: https://submit-etda.libraries.psu.edu/catalog/7332

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

21. Washton, Nancy Maurer. DETERMINATION OF OXIDE SURFACE REACTIVITY VIA SOLID-STATE NUCLEAR MAGNETIC RESONANCE AND AB INITIO METHODS .

Degree: 2008, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/7720

► Although a mature field, the study of oxide surface speciation and reactivity is still open to scientific investigations endeavoring to elucidate the chemical species involved… (more)

▼ Although a mature field, the study of oxide surface speciation and reactivity is still open to scientific investigations endeavoring to elucidate the chemical species involved in various forms of reactivity. Silicates, aluminosilicates, and aluminas are unarguably the most important oxide materials for industrial uses, in addition to comprising a large percentage of environmentally important oxides, e.g., quartz, feldspars, clays, gibbsite, etc. We have used solid-state Nuclear Magnetic Resonance (NMR) and ab initio computational methods to probe the surface reactivity of several [alumino]silicate materials. Cohesion for this work is provided by studying the effects of chemically modifying oxide surfaces with a monochlorosilane, either experimentally through the use of NMR, or computationally, through the use of Density Functional Theory (DFT) investigations of the reaction pathways. For two suites of natural aluminosilicate glasses, the number of accessible and reactive sites for covalent attachment of a fluorine containing chlorosilane probe molecule was determined by quantitative 19F nuclear magnetic resonance (NMR) spectroscopy. The first set of samples consists of six rhyolitic and dacitic glasses originating from volcanic activity in Iceland and one rhyolitic glass from the Bishop Tuff, CA. For this suite of samples the rate of acid-mediated dissolution (pH approximately 4) does not correlate to geometric surface area or BET measured surface area, but does depend directly on the number of reactive sites as measured by solid-state NMR. These data imply that the M-OH species bonded to (3,3,3-trifluoropropyl)dimethyl-chlorosilane (TFS) represent loci accessible to proton-mediated dissolution. The chemisorption site for TFS on silicates is known to be non-hydrogen bonded Q3 groups, and therefore these sites are implicated as regions that control or influence the rate of acid-mediated dissolution. The second suite of rhyolites, from Kozushima Japan, constitutes a chronosequence, and is comprised of four rhyolites that have weathered for 1.1, 1.8, 26, and 52 thousand years. For both suites of samples the number of reactive sites on a per gram basis is shown to increase as a function of laboratory and field weathering time. These new data provide a chemically specific and quantifiable proxy for reactive surface area, and our interpretations offer a testable hypothesis for the mechanism of acid-mediated dissolution for aluminosilicate minerals and glasses. The implication that the chlorosilane binding site on aluminosilicate glasses was potentially the rate-determining site for dissolution led to an investigation of the surface species involved in chlorosilane binding. The low surface area of the volcanic glasses precluded their use as samples for detailed surface characterization via NMR, and therefore a set of six [alumino]silicate gels with high surface area were used as models for the natural glasses. This set of six samples included pure silica gel, pure mesoporous alumina, and four aluminosilicate samples… Advisors/Committee Members: Karl Todd Mueller, Committee Chair/Co-Chair, Barbara Jane Garrison, Committee Member, James David Kubicki, Committee Member, John B Asbury, Committee Member, Susan Louise Brantley, Committee Member.

Subjects/Keywords: chlorosilane; surface modification; reaction pathways; ab initio; aluminosilicates; reactive surface area; NMR

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APA (6^th Edition):

Washton, N. M. (2008). DETERMINATION OF OXIDE SURFACE REACTIVITY VIA SOLID-STATE NUCLEAR MAGNETIC RESONANCE AND AB INITIO METHODS . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/7720

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Washton, Nancy Maurer. “DETERMINATION OF OXIDE SURFACE REACTIVITY VIA SOLID-STATE NUCLEAR MAGNETIC RESONANCE AND AB INITIO METHODS .” 2008. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/7720.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Washton, Nancy Maurer. “DETERMINATION OF OXIDE SURFACE REACTIVITY VIA SOLID-STATE NUCLEAR MAGNETIC RESONANCE AND AB INITIO METHODS .” 2008. Web. 22 Jan 2021.

Vancouver:

Washton NM. DETERMINATION OF OXIDE SURFACE REACTIVITY VIA SOLID-STATE NUCLEAR MAGNETIC RESONANCE AND AB INITIO METHODS . [Internet] [Thesis]. Penn State University; 2008. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/7720.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Washton NM. DETERMINATION OF OXIDE SURFACE REACTIVITY VIA SOLID-STATE NUCLEAR MAGNETIC RESONANCE AND AB INITIO METHODS . [Thesis]. Penn State University; 2008. Available from: https://submit-etda.libraries.psu.edu/catalog/7720

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

22. Lopano, Christina Lynn. Time-Resolved Structural Analyses of Cation Exchange Reactions in Synthetic Birnessite .

Degree: 2008, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/7477

► Rietveld refinements of time-resolved synchrotron X-ray diffraction data have documented real-time changes in unit-cell parameters in response to cation substitution in synthetic Na-birnessite. K-, Cs-,… (more)

▼ Rietveld refinements of time-resolved synchrotron X-ray diffraction data have documented real-time changes in unit-cell parameters in response to cation substitution in synthetic Na-birnessite. K-, Cs-, and Ba-birnessite, like Na-birnessite, were all found to have a triclinic unit-cell. Rietveld analyses of the X-ray diffraction patterns for K- and Ba-exchanged birnessite revealed decreases in the a, c, and  unit-cell parameters in unit-cell volume relative to Na-birnessite. Cs-exchange resulted in increases in c and unit-cell volume. Fourier electron difference syntheses revealed that the changes in the configuration of the interlayer species, and the charge, size, and hydration of the substituting cations, serve as the primary controls on changes in unit-cell parameters. Further TEM, SEM, and EDS analyses of batch Cs-exchange samples suggests that Na-birnessite and Cs-birnessite may co-exist in individual grains of birnessite, with both Na+ and Cs+ homogeneously distributed throughout individual incompletely exchanged grains. This suggests that the Cs-exchange reaction pathway likely occurred as part of a diffusion process, possibly aided by partial delamination of the Mn-O octahedral layers. Cation exchange rates for K-, Cs-, and Ba-exchange in birnessite were calculated for the first time from the time-resolved XRD results. The exchange rates for Na in birnessite decreased in the order: Cs >> K > Ba. These results are likely a function of hydration energy differences of the cations and the preference of the solution phase for the more readily hydrated cation. The kinetic modeling supports a two-stage reaction pathway for cation exchange, and these kinetic steps correlate with changes in crystal structure. Upon variation of solution pH, the K-exchange results quantitatively demonstrate that decreasing pH leads to faster cation exchange reaction kinetics. It is hypothesized that the enhanced K+ exchange with increased H+ concentration is caused mechanistically by the role that H+ plays during the diadochic substitution. These state-of-the-art time-resolved synchrotron studies have revealed for the first time reaction rates and possible mechanisms for cation exchange in birnessite, a prominent Mn-oxide soil constituent. Advisors/Committee Members: Peter J Heaney, Committee Chair/Co-Chair, Sridhar Komarneni, Committee Member, Susan Louise Brantley, Committee Member, James David Kubicki, Committee Member, C Enid Martinez, Committee Member.

Subjects/Keywords: birnessite; cation exchange; X-ray diffraction; synchrotron; manganese oxides

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APA (6^th Edition):

Lopano, C. L. (2008). Time-Resolved Structural Analyses of Cation Exchange Reactions in Synthetic Birnessite . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/7477

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Lopano, Christina Lynn. “Time-Resolved Structural Analyses of Cation Exchange Reactions in Synthetic Birnessite .” 2008. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/7477.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Lopano, Christina Lynn. “Time-Resolved Structural Analyses of Cation Exchange Reactions in Synthetic Birnessite .” 2008. Web. 22 Jan 2021.

Vancouver:

Lopano CL. Time-Resolved Structural Analyses of Cation Exchange Reactions in Synthetic Birnessite . [Internet] [Thesis]. Penn State University; 2008. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/7477.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Lopano CL. Time-Resolved Structural Analyses of Cation Exchange Reactions in Synthetic Birnessite . [Thesis]. Penn State University; 2008. Available from: https://submit-etda.libraries.psu.edu/catalog/7477

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

23. Kumarasiri, Malika Dhananjaya. Anharmonic Effects of Small Clusters of Molecules and Ranking Activity of Protein Mutants .

Degree: 2008, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/9276

► This thesis is presented in two parts. In part 1, anharmonic effects of small molecules are investigated using theoretical methods. In part 2, mutants of… (more)

▼ This thesis is presented in two parts. In part 1, anharmonic effects of small molecules are investigated using theoretical methods. In part 2, mutants of enzymes are ranked according to their activation energy barriers. Anharmonic effects are required to describe vital processes such as bond breaking or bond forming, and they significantly affect properties such as geometries and vibrational frequencies. Despite their importance, anharmonic effects are typically overlooked due to the high computational cost associated with calculating them. In part 1 of this thesis, anharmonic effects of small clusters of ammonium nitrate and hydroxylammonium nitrate are investigated. We compare the structures and vibrational modes against their harmonic counterparts using a vibrational perturbation theory approach within the density functional theory framework. Anharmonic effects significantly alter the structures and vibrational frequencies of ammonium nitrate and hydroxylammonium nitrate clusters. In part 2 of the thesis, we implement an efficient procedure to rank many mutants of enzymes or protein designs according to the free energy barrier of the catalyzed reaction. Escherichia coli dihydrofolate reductase (DHFR) and its mutants are used in this study, and the mutant structures are generated based on the wild type enzyme structure. Different methods are investigated to calculate the free energy barrier of hydride transfer in DHFR. The hydride transfer reaction is investigated using empirical valence bond molecular dynamics simulations followed by a weighted histogram analysis or umbrella integration to generate the free energy distribution along the reaction coordinate. Fifteen single mutants of DHFR are used in this study. Our results indicate a promising correlation between experimentally determined reaction rates and calculated free energy barriers. The procedures are mostly automated and can easily be adapted for other enzymatic mutants or designs. Advisors/Committee Members: Prof Sharon Hammes Schiffer, Dissertation Advisor/Co-Advisor, Sharon Hammes Schiffer, Committee Chair/Co-Chair, Will Castleman, Committee Member, Philip C. Bevilacqua, Committee Member, James David Kubicki, Committee Member.

Subjects/Keywords: Molecular Dynamics; Mutant Studies

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APA (6^th Edition):

Kumarasiri, M. D. (2008). Anharmonic Effects of Small Clusters of Molecules and Ranking Activity of Protein Mutants . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/9276

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Kumarasiri, Malika Dhananjaya. “Anharmonic Effects of Small Clusters of Molecules and Ranking Activity of Protein Mutants .” 2008. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/9276.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Kumarasiri, Malika Dhananjaya. “Anharmonic Effects of Small Clusters of Molecules and Ranking Activity of Protein Mutants .” 2008. Web. 22 Jan 2021.

Vancouver:

Kumarasiri MD. Anharmonic Effects of Small Clusters of Molecules and Ranking Activity of Protein Mutants . [Internet] [Thesis]. Penn State University; 2008. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/9276.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Kumarasiri MD. Anharmonic Effects of Small Clusters of Molecules and Ranking Activity of Protein Mutants . [Thesis]. Penn State University; 2008. Available from: https://submit-etda.libraries.psu.edu/catalog/9276

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

24. Bazilevskaya, Ekaterina. IRON AND ALUMINUM HYDROXIDE NANOPARTICLES IN THE ENVIRONMENT: FROM NANO-SCALE TO THE FIELD PROCESSES.

Degree: 2009, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/10329

► The objective of this doctoral research was to increase scientific understanding of the behavior of Fe and Al hydroxide nanoparticles in soils. These particles are… (more)

▼ The objective of this doctoral research was to increase scientific understanding of the behavior of Fe and Al hydroxide nanoparticles in soils. These particles are of great environmental importance due to their ability to retain and transport nutrients and contaminants. Three studies were undertaken at different scales, which are documented in three manuscripts included in this dissertation The first study examined the rate constants for goethite (á-FeOOH) crystallization from nano-particulate Fe hydroxide suspensions in the absence (0% Al) and presence (2% Al) of aluminum. One of the merits of this study was the application of a multivariate curve resolution analysis (MCR) of infrared spectra to environmentally important mixed Fe-Al hydroxide colloids in order to quantify goethite content in poorly-crystalline mixtures. Obtained rate constants were found to be equal to (7.64±0.67)*10-7 s-1 for 0% Al and (4.5±0.21)*10-7 s-1 for 2% Al hydroxides. Dissolution-precipitation mechanism was dominant in the process of goethite transformation to ferrihydrite. Further growth of goethite crystals took place either by aggregation mechanism to form polycrystalline agglomerates or alternatively by Oswald ripening to form large single crystals. The presence of aqueous Al species „poisoned“ goethite’s surface by disrupting the formation of hydrogen bonds thus increasing the number of non-stoichiometric hydroxyls. The second study addressed changes of mineral composition in mixed Fe-Al hydroxide nanoparticles as a function of Al-substitution and reaction time. It was found that low Al concentrations (2-8 mol. %) lead to formation of moderately crystalline Al-goethite upon ageing, while at medium Al concentrations (10-20%) colloidal suspensions remained stable for the duration of the whole experiment (54 days), goethite formation was completely retarded, and less crystalline intermediate structure were formed. At 25% Al substitution, gibbsite Al(OH)3 microcrystalline structures appeared within the first days of experiment. In addition, to understand the mechanism of Al substitution in goethite, we explored the most energetically favorable arrangement of Al atoms within goethite by ab initio periodic density functional theory (DFT) calculations. These calculations showed that Al may form Al-O-Al clusters as opposed to evenly distributed isolated Al atoms (Al-O-Fe) in goethite structure. The third study was conducted to investigate the relative importance of Fe and Al hydroxide nanoparticles in migration and accumulation of these elements in soils. I approached this goal by studying soil water and coatings on mineral grains from Spodosol soil, which is characterized by intensive leaching of Fe, Al, and organic matter (OM) and their accumulation in Spodosol profile. While Fe, Al and Si were mostly transported as inorganic colloids, Al also showed close association with organic matter. Fe, Al, and Si have the highest mobility in organic-rich A and Bh horizons of the spodosol profile, which suggests that the presence of organic… Advisors/Committee Members: Carmen Enid Martinez, Dissertation Advisor/Co-Advisor, Carmen Enid Martinez, Committee Chair/Co-Chair, Douglas Archibald, Committee Member, Edward John Ciolkosz, Committee Member, James David Kubicki, Committee Member, Kwadwo Osseo Asare, Committee Member.

Subjects/Keywords: nanoparticles; iron and aluminum hydroxides; rate constants of goethite crystallization; ATR-FTIR; Spodosols; colloidal transport

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APA (6^th Edition):

Bazilevskaya, E. (2009). IRON AND ALUMINUM HYDROXIDE NANOPARTICLES IN THE ENVIRONMENT: FROM NANO-SCALE TO THE FIELD PROCESSES. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/10329

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Bazilevskaya, Ekaterina. “IRON AND ALUMINUM HYDROXIDE NANOPARTICLES IN THE ENVIRONMENT: FROM NANO-SCALE TO THE FIELD PROCESSES.” 2009. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/10329.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Bazilevskaya, Ekaterina. “IRON AND ALUMINUM HYDROXIDE NANOPARTICLES IN THE ENVIRONMENT: FROM NANO-SCALE TO THE FIELD PROCESSES.” 2009. Web. 22 Jan 2021.

Vancouver:

Bazilevskaya E. IRON AND ALUMINUM HYDROXIDE NANOPARTICLES IN THE ENVIRONMENT: FROM NANO-SCALE TO THE FIELD PROCESSES. [Internet] [Thesis]. Penn State University; 2009. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/10329.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Bazilevskaya E. IRON AND ALUMINUM HYDROXIDE NANOPARTICLES IN THE ENVIRONMENT: FROM NANO-SCALE TO THE FIELD PROCESSES. [Thesis]. Penn State University; 2009. Available from: https://submit-etda.libraries.psu.edu/catalog/10329

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

25. Taron, Joshua. Geophysical and Geochemical Analyses of Flow and Deformation in Fractured Rock .

Degree: 2009, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/10135

► The following is a study of fluid flow and deformation in fractured rock, with particular emphasis on environments under thermal and chemical stress. Fractures are… (more)

▼ The following is a study of fluid flow and deformation in fractured rock, with particular emphasis on environments under thermal and chemical stress. Fractures are treated in the greatest detail, with constitutive modeling at pore and reservoir scale, and their impact explored with reservoir scale numerical simulation. Part I (Chapters I-IV) explores the behavior of engineered systems pushed far from equilibrium and highlights feedbacks between stress and chemistry on the evolution of the mechanical and transport properties of rocks; these observations and analyses are focused on the behavior of geothermal reservoirs. Part II (Chapters V-VI) examines the response to natural forcing and follows the complex interactions that shape processes in volcanic environments. Chapter I introduces a simulator to examine thermal, hydrologic, mechanical, and chemical processes (THMC) in deformable, fractured porous media. The combined influence of stress-enhanced dissolution, thermal-hydro-mechanical asperity strain, and mineral reaction alter the permeability of fractures during thermal, hydraulic, and chemical stimulation. Chapter II examines a prototypical enhanced geothermal system (EGS) for the relative, temporal arrival of hydro-mechanical vs. thermo-mechanical vs. chemical changes in fluid transmission as cold water is injected at geochemical disequilibrium within a heated reservoir. Chapter III develops a relationship to examine dissolution precipitation creep in crustal rocks with implicit coupling of the dissolution-diffusion-precipitation system. Long-term compaction, previously ill-constrained, is explored with two alternate methods. Chapter IV presents a model to represent these permeability change mechanisms as innately hysteretic and interlinked processes in rough contacting fractures. This model is incorporated into the numerical simulator of Chapters I and II and applied to a candidate engineered geothermal reservoir system (EGS). Utilizing a several year history of rainfall, seismic, and magma effux records, Chapter V presents a limit-equilibrium model for rainfall infiltration into a hot lava carapace to evolve stability of the dome at Soufrière Hills Volcano (SHV). Model predictions are compared to observed dome collapse events from 2000-2002. In Chapter VI histories of magma efflux and surface deformation are utilized to geodetically image magma transfer within the deep crustal plumbing system of SHV. Magma efflux is constrained with wide-aperture geodetic data to supplement a well-documented extrusion record, and these are used to explore the role of deeply sourced fluxes on short-term eruption periodicity. Advisors/Committee Members: Derek Elsworth, Dissertation Advisor/Co-Advisor, Derek Elsworth, Committee Chair/Co-Chair, James David Kubicki, Committee Member, Chris Marone, Committee Member, Demian Saffer, Committee Member, Barry Voight, Committee Member.

Subjects/Keywords: permeability; rock fracture; fractured reservoir simulation; geothermal; volcanic dome; chemical creep

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Taron, J. (2009). Geophysical and Geochemical Analyses of Flow and Deformation in Fractured Rock . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/10135

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Taron, Joshua. “Geophysical and Geochemical Analyses of Flow and Deformation in Fractured Rock .” 2009. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/10135.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Taron, Joshua. “Geophysical and Geochemical Analyses of Flow and Deformation in Fractured Rock .” 2009. Web. 22 Jan 2021.

Vancouver:

Taron J. Geophysical and Geochemical Analyses of Flow and Deformation in Fractured Rock . [Internet] [Thesis]. Penn State University; 2009. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/10135.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Taron J. Geophysical and Geochemical Analyses of Flow and Deformation in Fractured Rock . [Thesis]. Penn State University; 2009. Available from: https://submit-etda.libraries.psu.edu/catalog/10135

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

26. Strepka, Caleb. SOLID-STATE NMR STUDIES OF THE IMPACT OF TANK WASTE LEACHATES IN THE ENVIRONMENT .

Degree: 2010, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/10532

► Using a combination of analytical spectroscopy and wet chemistry techniques, we are investigating the coupling between mineral weathering from caustic waste release and contaminant fate/transport… (more)

Subjects/Keywords: NMR; montmorillonite; hanford; zeolite

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APA (6^th Edition):

Strepka, C. (2010). SOLID-STATE NMR STUDIES OF THE IMPACT OF TANK WASTE LEACHATES IN THE ENVIRONMENT . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/10532

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Strepka, Caleb. “SOLID-STATE NMR STUDIES OF THE IMPACT OF TANK WASTE LEACHATES IN THE ENVIRONMENT .” 2010. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/10532.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Strepka, Caleb. “SOLID-STATE NMR STUDIES OF THE IMPACT OF TANK WASTE LEACHATES IN THE ENVIRONMENT .” 2010. Web. 22 Jan 2021.

Vancouver:

Strepka C. SOLID-STATE NMR STUDIES OF THE IMPACT OF TANK WASTE LEACHATES IN THE ENVIRONMENT . [Internet] [Thesis]. Penn State University; 2010. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/10532.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Strepka C. SOLID-STATE NMR STUDIES OF THE IMPACT OF TANK WASTE LEACHATES IN THE ENVIRONMENT . [Thesis]. Penn State University; 2010. Available from: https://submit-etda.libraries.psu.edu/catalog/10532

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

27. Chakravorty, Dhruva Kumar. HYBRID QUANTUM/CLASSICAL MOLECULAR DYNAMICS SIMULATIONS OF HYDROGEN TRANSFER REACTIONS IN ENZYMES .

Degree: 2010, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/10699

► This thesis describes the study of hydrogen transfer reactions in enzymes. For this purpose the thesis is divided into two parts. The first part is… (more)

▼ This thesis describes the study of hydrogen transfer reactions in enzymes. For this purpose the thesis is divided into two parts. The first part is work undertaken in the development of new methods for the study of such reactions, while the second part of the thesis focuses on the study of the isomerization reaction in ketosteroid isomerase (KSI). In part one of this thesis, the implementation of the umbrella integration method for calculating the potential of mean force (PMF) for a chemical reaction within the empirical valence bond (EVB) framework is presented. The umbrella integration method is based on the derivative of the PMF with respect to the reaction coordinate. An analytical expression for this derivative applicable to certain types of EVB potentials is presented. The umbrella integration method reduces the statistical errors, converges efficiently, and does not require significantly overlapping windows compared to the Weighted Histogram Analysis method. A modified version of the weighted histogram analysis method that shares these advantages is also proposed and implemented. The second part of this thesis presents the study of proton transfer reactions in ketosteroid isomerase (KSI) using hybrid quantum/classical methodologies. The reaction requires two proton transfer reactions. Tyr14 and Asp99 form catalytically important hydrogen bonds that help stabilize the dienolate intermediate in these reactions. Chapter 3 describes the study of these proton transfer reactions in wild-type KSI. Chapter 4 extends this analysis to the Tyr14Phe, Asp99Leu and Tyr14Phe/Asp99Leu mutant varieties of KSI. Our simulations suggest a pre-organized active site in which relatively small changes occur to strengthen the hydrogen bonds that stabilize the intermediate, thereby facilitating the proton transfer reactions. Advisors/Committee Members: Prof Sharon Hammes Schiffer, Dissertation Advisor/Co-Advisor, Prof Sharon Hammes Schiffer, Committee Chair/Co-Chair, James Bernhard Anderson, Committee Member, Philip C. Bevilacqua, Committee Member, James David Kubicki, Committee Member.

Subjects/Keywords: DLPROTEIN; EVB; DHFR; ketosteroid isomerase; KSI; WHAM; Umbrella Integration; hydrogen transfer

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Chakravorty, D. K. (2010). HYBRID QUANTUM/CLASSICAL MOLECULAR DYNAMICS SIMULATIONS OF HYDROGEN TRANSFER REACTIONS IN ENZYMES . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/10699

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Chakravorty, Dhruva Kumar. “HYBRID QUANTUM/CLASSICAL MOLECULAR DYNAMICS SIMULATIONS OF HYDROGEN TRANSFER REACTIONS IN ENZYMES .” 2010. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/10699.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Chakravorty, Dhruva Kumar. “HYBRID QUANTUM/CLASSICAL MOLECULAR DYNAMICS SIMULATIONS OF HYDROGEN TRANSFER REACTIONS IN ENZYMES .” 2010. Web. 22 Jan 2021.

Vancouver:

Chakravorty DK. HYBRID QUANTUM/CLASSICAL MOLECULAR DYNAMICS SIMULATIONS OF HYDROGEN TRANSFER REACTIONS IN ENZYMES . [Internet] [Thesis]. Penn State University; 2010. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/10699.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Chakravorty DK. HYBRID QUANTUM/CLASSICAL MOLECULAR DYNAMICS SIMULATIONS OF HYDROGEN TRANSFER REACTIONS IN ENZYMES . [Thesis]. Penn State University; 2010. Available from: https://submit-etda.libraries.psu.edu/catalog/10699

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

28. Younker, Jarod Michael. Development and Application of Optimizations in Computational Chemistry .

Degree: 2010, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/10499

► <html> <body> Computational chemistry is broadly defined as the application of numerical methods to solve chemical problems. This field encompasses the microscopic world of quantum… (more)

▼ <html> <body> Computational chemistry is broadly defined as the application of numerical methods to solve chemical problems. This field encompasses the microscopic world of quantum mechanics to the macroscopic behavior observed when exploring the behavior of large ensembles of interacting molecules. The complexity of these problems requires, in most instances, the use of computers to simulate the physics of the phenomenon and model the dynamic behavior. For example, in quantum mechanics the only systems which can be solved exactly are those composed of only one or two particles. Nevertheless, high-level numerical approximations to the many-bodied problem can be achieved employing numerical methods. Other numerical methods enable researchers to understand large amounts of data, which modern-day instruments record, via decomposition and simulation. Each chapter of the thesis addresses an independent topic in computational chemistry. <h3>Chapter 1</h3> Deoxyribonucleotides are the building blocks of DNA. One of the last steps in their de novo synthesis is carried out by ribonucleotide reductase (RNR). RNR is ubiquitous in all living organisms and catalyzes the reduction of di- or triphosphate ribonucleoside to the respective deoxyribonucleoside. Recently a new subclass of RNR has been discovered. The class Ic RNR from the obligate parasite Chlamydia trachomatis (Ct) uses a stable Mn(IV)/Fe(III) cofactor to initiate nucleotide reduction by a free-radical mechanism. This novel cofactor may be a promising drug target. The generation of the Mn(IV)/Fe(III) active state begins with either a Mn(II)/Fe(II) or a Mn(III)/Fe(III) cofactor, which is oxidized via molecular oxygen or hydrogen peroxide to yield a Mn(IV)/Fe(IV) state. This latter state is quickly reduced by one electron. Ct RNR holds promise for new insights into the structures of high-valent dinuclear metal clusters. Unlike their analogues from E. coli RNR and methane monooxygenase (MMO), both complexes can be obtained in high yields. The presence of the two different metals in the cofactor could further our understanding of dinuclear metal clusters. Their presence allows researchers to study EPR-active oxidation states, that in the diiron E. coli RNR and MMO cofactors are EPR-inactive. In this chapter, extended X-ray absorption fine structure (EXAFS) spectroscopy and density functional theory (DFT) calculations are coupled with previous EPR and ⁵⁷Fe Mossbauer spectroscopy to postulate structures for the two cofactors. Fe and Mn K-edge EXAFS data yield intermetallic distances for the Mn(IV)/Fe(III) and Mn(IV)/Fe(IV) cofactors of ~2.9 and ~2.8 Angstrom, respectively. The Mn data also suggest the presence of a short 1.74 Angstrom Mn-O bond for the Mn(IV)/Fe(III) cofactor. These metrics are compared to the results of DFT calculations on 16 cofactor models derived from the crystal structure of the inactive Fe₂(III/III) form of the protein. Models are differentiated by the… Advisors/Committee Members: Michael Thomas Green, Dissertation Advisor/Co-Advisor, Michael Thomas Green, Committee Chair/Co-Chair, Joseph M Bollinger Jr., Committee Member, Carsten Krebs, Committee Member, Philip C. Bevilacqua, Committee Member, James David Kubicki, Committee Member.

Subjects/Keywords: Chloroperoxidase; P450; Rate Equations; Principal Components Analysis; Numerical Optimizations; Adomian Decomposition; Density Functional Theory; Ribonucleotide Reductase

Record Details Similar Records Cite « Share

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Younker, J. M. (2010). Development and Application of Optimizations in Computational Chemistry . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/10499

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Younker, Jarod Michael. “Development and Application of Optimizations in Computational Chemistry .” 2010. Thesis, Penn State University. Accessed January 22, 2021. https://submit-etda.libraries.psu.edu/catalog/10499.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Younker, Jarod Michael. “Development and Application of Optimizations in Computational Chemistry .” 2010. Web. 22 Jan 2021.

Vancouver:

Younker JM. Development and Application of Optimizations in Computational Chemistry . [Internet] [Thesis]. Penn State University; 2010. [cited 2021 Jan 22]. Available from: https://submit-etda.libraries.psu.edu/catalog/10499.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Younker JM. Development and Application of Optimizations in Computational Chemistry . [Thesis]. Penn State University; 2010. Available from: https://submit-etda.libraries.psu.edu/catalog/10499

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

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