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Proton Pumping Mechanism In Cytochrome C Oxidase, Xiuhong Cai 2020 The Graduate Center, City University of New York

Proton Pumping Mechanism In Cytochrome C Oxidase, Xiuhong Cai

Dissertations, Theses, and Capstone Projects

Cytochrome c Oxidase (CcO), is the terminal electron acceptor in the membrane bound aerobic respiratory chain. It reduces O2 to water. The energy released by this reaction is stored by pumping protons from the high pH, N-side of the membrane to the low pH, P-side. The generated proton gradient provides the motive force for synthesis of ATP by the ATP synthase.

Building a proton gradient across the membrane requires that proton transport must occur along controllable proton pathways to prevent proton leakage to the N-side. It has been suggested that CcO function requires proton transfer channels in both the ...


Mechanochemical Recovery Of Co And Li From Lco Cathode Of Lithium-Ion Battery, Oleksandr Dolotko, Ihor Z. Hlova, Yaroslav Mudryk, Shalabh Gupta, Viktor Balema 2020 Ames Laboratory

Mechanochemical Recovery Of Co And Li From Lco Cathode Of Lithium-Ion Battery, Oleksandr Dolotko, Ihor Z. Hlova, Yaroslav Mudryk, Shalabh Gupta, Viktor Balema

Ames Laboratory Accepted Manuscripts

Increasing demand for lithium-ion batteries (LIBs) that serve as power source for diverse electronic devices, electrical propulsion systems and other applications, calls for economical and environmentally benign recycling of spent LIBs and recovery of critical elements such as Co and Li from rapidly growing volumes of battery wastes. The presented study explores mechanochemical extraction of Co and Li from lithium cobaltate (LiCoO2), which serves as cathode material in commercial LIBs. Our investigation reveals that solvent-free mechanochemical processing can successfully convert pure, reagent grade LiCoO2 into metallic Co and Li-derivatives that are suitable for the further recovery of Li. We also ...


Emergence, Mechanics, And Development: How Behavior And Geometry Underlie Cowrie Seashell Form, Michael G. Levy, Michael R. DeWeese 2020 University of California Berkeley

Emergence, Mechanics, And Development: How Behavior And Geometry Underlie Cowrie Seashell Form, Michael G. Levy, Michael R. Deweese

Biology and Medicine Through Mathematics Conference

No abstract provided.


Additive Modulation Of Dna-Dna Interactions By Interstitial Ions, Wei Meng, Raju Timsina, Abby Bull, Kurt Andresen, Xiangyun Qiu 2020 Hefei University / George Washington University

Additive Modulation Of Dna-Dna Interactions By Interstitial Ions, Wei Meng, Raju Timsina, Abby Bull, Kurt Andresen, Xiangyun Qiu

Physics and Astronomy Faculty Publications

Quantitative understanding of biomolecular electrostatics, particularly involving multivalent ions and highly charged surfaces, remains lacking. Ion-modulated interactions between nucleic acids provide a model system in which electrostatics plays a dominant role. Using ordered DNA arrays neutralized by spherical cobalt3+ hexammine and Mg2+ ions, we investigate how the interstitial ions modulate DNA-DNA interactions. Using methods of ion counting, osmotic stress, and x-ray diffraction, we systematically determine thermodynamic quantities, including ion chemical potentials, ion partition, DNA osmotic pressure and force, and DNA-DNA spacing. Analyses of the multidimensional data provide quantitative insights into their interdependencies. The key finding of this study is that ...


Determining The Kinetic Isotope Effect Of Ruthenium Compound Ru(Bpy)₂(Bpyno)(Pf₆)₂ Using Artificial Photosynthesis, Alexandra I. Kirkvold 2020 University of South Dakota

Determining The Kinetic Isotope Effect Of Ruthenium Compound Ru(Bpy)₂(Bpyno)(Pf₆)₂ Using Artificial Photosynthesis, Alexandra I. Kirkvold

Honors Thesis

The world’s demand for energy is ever-increasing, but its fuel resources are being depleted at an alarming rate. A potential solution for this crisis lies in using ruthenium-based compounds to produce hydrogen for use in fuel cells. This research uses the process of artificial photosynthesis to learn more about a promising ruthenium-based compound, Ru(bpy)₂(bpyNO)(PF₆)₂. The experiment tests the reaction for oxygen production in both H2O and D2O to determine the Kinetic Isotope Effect of the compound and, thus, aid future research working to understand the reaction mechanisms. The analysis shows ...


Vibration Overtone Hyperpolarizability Measured For H2, Rachel M. Ellis, David P. Shelton 2020 University of Nevada, Las Vegas

Vibration Overtone Hyperpolarizability Measured For H2, Rachel M. Ellis, David P. Shelton

Physics & Astronomy Faculty Publications

The second hyperpolarizability (γ) of the H2 molecule was measured by gas-phase electric field induced second harmonic generation at the frequencies of the one-photon resonance for the 3–0 Q(J) overtone transitions (v, J = 0, J → 3, J for J = 0, 1, 2, and 3). The magnitude of the resonant contribution to γ was measured with 2% accuracy using the previously determined non-resonant γ for calibration. Pressure broadening and frequency shift for the transitions were also measured. A theoretical expression for the resonant vibrational γ contribution in terms of transition polarizabilities is compared to the observations. The measured γ ...


Origin Of Short- And Medium-Range Order In Supercooled Liquid Ge3sb2te6 Using Ab Initio Molecular Dynamics Simulations, Chong Qiao, Y. R. Guo, Songyou Wang, Yu Jia, Cai-Zhuang Wang, Kai-Ming Ho 2020 Fudan University

Origin Of Short- And Medium-Range Order In Supercooled Liquid Ge3sb2te6 Using Ab Initio Molecular Dynamics Simulations, Chong Qiao, Y. R. Guo, Songyou Wang, Yu Jia, Cai-Zhuang Wang, Kai-Ming Ho

Ames Laboratory Accepted Manuscripts

Phase-change materials such as Ge–Sb–Te compounds have attracted much attention due to their potential value in electrical data storage. In contrast to the amorphous and crystalline phases, supercooled liquids are far from being deeply understood despite their inevitable role in both amorphization and crystallization processes. To this end, we have studied the dynamics properties and structural characteristics of liquid and supercooled liquid Ge3Sb2Te6 during the fast cooling process. As the temperature decreases, chemical bonds become more homogeneous, but coordination numbers of Ge, Sb and Te atoms change very little. Meanwhile, the structural order of short-range configuration is obviously ...


Sulfur Dioxide From The Atmospheric Chemistry Experiment Satellite, Doug Cameron 2020 Old Dominion University

Sulfur Dioxide From The Atmospheric Chemistry Experiment Satellite, Doug Cameron

College of Sciences Posters

The version 4.0 dataset from the Atmospheric Chemistry Experiment – Fourier Transform Spectrometer (ACE-FTS) on SCISAT, released in March of 2019, has sulfur dioxide (SO2) volume mixing ratio (VMR) profiles as a routine data product. From this dataset, global SO2 distributions between the altitudes of 10.5 km and 23.5 km are analyzed. The global distribution of all SO2 VMR data by altitude is broken down into 30° and 5° latitude zones. Seasonality of the global SO2 distribution is explored. Volcanic SO2 plumes are isolated in the dataset and compared with extinction data from ...


Inertial Focusing In Triangular Microchannels With Various Apex Angles, Jeong-ah Kim, Aditya Kommajosula, Yo-han Choi, Je-Ryung Lee, Eun-chae Jeon, Baskar Ganapathysubramanian, Wonhee Lee 2020 Korea Advanced Institute of Science and Technology (KAIST)

Inertial Focusing In Triangular Microchannels With Various Apex Angles, Jeong-Ah Kim, Aditya Kommajosula, Yo-Han Choi, Je-Ryung Lee, Eun-Chae Jeon, Baskar Ganapathysubramanian, Wonhee Lee

Mechanical Engineering Publications

We consider inertial focusing of particles in channels with triangular cross sections. The number and the location of inertial focusing positions in isosceles triangular channels can change with varying blockage ratios (a/H) and Reynolds numbers (Re). In triangular channels, asymmetric velocity gradient induced by the sloped sidewalls leads to changes in the direction and the strength of the inertial lift forces. Therefore, varying the configuration (specifically, angle) of the triangular cross section is expected to lead to a better understanding of the nature of the inertial lift forces. We fabricated triangular microchannels with various apex angles using channel molds ...


Similarities Between Insect Swarms And Isothermal Globular Clusters, Dan Gorbonos, Kasper van der Vaart, Michael Sinhuber, James G. Puckett, Andrew M. Reynolds, Nicholas T. Ouellette, Nir S. Gov 2020 The Weizmann Institute of Science

Similarities Between Insect Swarms And Isothermal Globular Clusters, Dan Gorbonos, Kasper Van Der Vaart, Michael Sinhuber, James G. Puckett, Andrew M. Reynolds, Nicholas T. Ouellette, Nir S. Gov

Physics and Astronomy Faculty Publications

Previous work has suggested that disordered swarms of flying insects can be well modeled as self-gravitating systems, as long as the “gravitational” interaction is adaptive. Motivated by this work, we compare the predictions of the classic, mean-field King model for isothermal globular clusters to observations of insect swarms. Detailed numerical simulations of regular and adaptive gravity allow us to expose the features of the swarms' density and velocity profiles that are due to long-range interactions and are captured by the King model phenomenology, and those that are due to adaptivity and short-range repulsion. Our results provide further support for adaptive ...


Fundamentals Of Au(111) Surface Dynamics: Coarsening Of 2d Au Islands, Peter M. Spurgeon, King C. Lai, Yong Han, James W. Evans, Patricia A. Thiel 2020 Iowa State University

Fundamentals Of Au(111) Surface Dynamics: Coarsening Of 2d Au Islands, Peter M. Spurgeon, King C. Lai, Yong Han, James W. Evans, Patricia A. Thiel

Chemistry Publications

Au(111) surfaces play a central role in many applications, yet studies of fundamental aspects of their dynamics are limited. Thus, using Scanning Tunneling Microscopy (STM) at 300 K, we analyze the coarsening of first-layer 2D Au islands directly on the Au(111) substrate, and also of second-layer 2D Au islands. Specifically, we monitor the decay of Au first-layer islands with areas of about 100-500 nm^2 in the vicinity of larger islands or extended step edges over a period of approximately 40 hours - the relevant time scale for this process. Experimentally observed behavior is captured by analytic theory for ...


Adsorption, Intercalation, Diffusion, And Adhesion Of Cu At The 2h−Mos2 (0001) Surface From First-Principles Calculations, Yong Han, Michael C. Tringides, James W. Evans, Patricia A. Thiel 2020 Iowa State University and Ames Laboratory

Adsorption, Intercalation, Diffusion, And Adhesion Of Cu At The 2h−Mos2 (0001) Surface From First-Principles Calculations, Yong Han, Michael C. Tringides, James W. Evans, Patricia A. Thiel

Chemistry Publications

Study of the adsorption of a transition metal on the surface of a layered material and the possible subsequent intercalation into that layered material is of fundamental interest and potential technological importance. In the present work, we choose the transition metal Cu as the adsorbate or intercalant and 2H-MoS2 as the layered material. Energetics are calculated characterizing four of the most basic surface and interfacial phenomena: adsorption, intercalation, diffusion, and adhesion. Using first-principles density functional theory (DFT), we find that intercalating a Cu atom into the van der Waals (vdW) gap below the MoS2 (0001) surface is 0.665 eV ...


Unusual Effect Of Iodine Ions On The Self-Assembly Of Poly(Ethylene Glycol)-Capped Gold Nanoparticles, Wenjie Wang, Hyeong Jin Kim, Wei Bu, Surya Mallapragada, David Vaknin 2020 Ames Laboratory

Unusual Effect Of Iodine Ions On The Self-Assembly Of Poly(Ethylene Glycol)-Capped Gold Nanoparticles, Wenjie Wang, Hyeong Jin Kim, Wei Bu, Surya Mallapragada, David Vaknin

Chemical and Biological Engineering Publications

We use synchrotron X-ray reflectivity and grazing incidence small-angle X-ray scattering to investigate the surface assembly of the polyethylene glycol (PEG) grafted gold nanoparticles (PEG-AuNPs) induced by different salts. We find that NaCl and CsCl behave as many other electrolytes, namely drive the PEG-AuNPs to the vapor/suspension interface to form a layer of single particle depth and organize them into very high quality two-dimensional (2D) hexagonal crystals. By contrast, NaI induces the migration of PEG-AuNPs to the aqueous surface at much higher surface densities than the other salts (at similar concentrations). The resulting 2D ordering at moderate NaI concentrations ...


Agenda, Revised, Shubha Tewari 2020 University of Massachusetts Amherst

Agenda, Revised, Shubha Tewari

Science and Engineering Saturday Seminars

Materials from the seminars. The agenda was revised to include online sessions due to the Covid-19 pandemic.


Examining Artifacts Of The Watershed Segmentation, Emily Jo Armitage 2020 University of Denver

Examining Artifacts Of The Watershed Segmentation, Emily Jo Armitage

Electronic Theses and Dissertations

The watershed segmentation is an algorithm used to systematically track cell intercalary behaviors during germ band extension of the Drosophila embryo. Neighboring cells share a contracting vertical interface, called a T1, which continues contracting to a single point, a T2, and extending in the horizontal direction to create what is called a T3 interface (Fig. 1). Additionally, higher order vertices called rosettes occur when five or more cells meet at a common vertex. Simulated T2 events demonstrate that cell angle and not noise level in the image contributes to the incorrect detection of artifactual T1s in more acute angled cells ...


Sensitivity Of Radical Sam Enzyme Mftc To Molecular Oxygen, Vishnu Govindarajan 2020 University of Denver

Sensitivity Of Radical Sam Enzyme Mftc To Molecular Oxygen, Vishnu Govindarajan

Electronic Theses and Dissertations

MftC is a radical S-adenosyl L-methionine (SAM) enzyme that catalyzes the first step in the production of mycofactocin. It is a ribosomally synthesized post-translationally modified (RiPP) redox cofactor shown to be essential for the survival of bacteria in the Mycobacterium genus in the presence of cholesterol as a carbon source and for the sequestration of ethanol. MftC catalyzes the C – terminal decarboxylation of tyrosine and the subsequent cross-linking of tyrosine to the penultimate valine on the precursor peptide MftA. The product formed out of the reaction is processed into mycofactocin in downstream processes. The bacteria in the Mycobacterium tuberculosis complex ...


Quantification Of Dynamic Epithelial Sheet Architecture In Botryllus Schlosseri Using 2-D & 3-D Image Analysis, Roopa Madhu 2020 University of Denver

Quantification Of Dynamic Epithelial Sheet Architecture In Botryllus Schlosseri Using 2-D & 3-D Image Analysis, Roopa Madhu

Electronic Theses and Dissertations

Epithelial tubules form critical structures in various body tissues; how- ever, since they are difficult to access experimentally, their architecture and dynamics are not well understood. Here we examine the dynamic remodeling of epithelial tubes in vivo using a novel and uniquely accessible model system: the extracorporeal vasculature of Botryllus schlosseri (sea squirt). In Botryllus, massive retraction of blood vessels can be triggered without loss of barrier function, through (i) disrupting collagen crosslinking in the basement membrane using β-aminopropionitrile (BAPN); or (ii) disrupting the integrin pathway through inhibition of focal adhesion kinase (FAK). We performed stereographic projections of 3-dimensional high-resolution ...


A Framework Of Multi-Dimensional And Multi-Scale Modeling With Applications, Zilong Li 2020 Louisiana Tech University

A Framework Of Multi-Dimensional And Multi-Scale Modeling With Applications, Zilong Li

Doctoral Dissertations

In this dissertation, a framework for multi-dimensional and multi-scale modeling is proposed. The essential idea is based on oriented space curves, which can be represented as a 3D slender object or 1D step parameters. SMILES and Masks provide functionalities that extend slender objects into branched and other objects. We treat the conversion between 1D, 2D, 3D, and 4D representations as data unification. A mathematical analysis of different methods applied to helices (a special type of space curves) is also provided. Computational implementation utilizes Model-ViewController design principles to integrate data unification with graphical visualizations to create a dashboard. Applications of multi-dimensional ...


A Vibrational Spectroscopic Based Approach For Diagnosing Babesia Bovis Infection, Anja Ruther, David Perezguaita, William Poole, Brian Cooke, Carlos Suarez, Philip Heraud, Bayden Wood 2020 Monash University

A Vibrational Spectroscopic Based Approach For Diagnosing Babesia Bovis Infection, Anja Ruther, David Perezguaita, William Poole, Brian Cooke, Carlos Suarez, Philip Heraud, Bayden Wood

Articles

Babesia bovis parasites present a serious and significant health concern for the beef and dairy industries in many parts of the world. Difficulties associated with the current diagnostic techniques include they are prone to human error (microscopy) or expensive and time consuming (Polymerase Chain Reaction) to perform. Little is known about the biochemical changes in blood that are associated with Babesia infections. The discovery of new biomarkers will lead to improved diagnostic outcomes for the cattle industry. Vibrational spectroscopic technologies can record a chemical snapshot of the entire organism and the surrounding cell thereby providing a phenotype of the organism ...


Crystal Structure Of Thermus Thermophilus Methylenetetrahydrofolate Dehydrogenase And Determinants Of Thermostability, Fernando Maiello, Gloria Gallo, Camila Coelho, Fernanda Sucharski, Leon Hardy, Martin Würtele 2020 University of South Florida St. Petersburg

Crystal Structure Of Thermus Thermophilus Methylenetetrahydrofolate Dehydrogenase And Determinants Of Thermostability, Fernando Maiello, Gloria Gallo, Camila Coelho, Fernanda Sucharski, Leon Hardy, Martin Würtele

Faculty Publications

The elucidation of mechanisms behind the thermostability of proteins is extremely important both from the theoretical and applied perspective. Here we report the crystal structure of methylenetetrahydrofolate dehydrogenase (MTHFD) from Thermus thermophilus HB8, a thermophilic model organism. Molecular dynamics trajectory analysis of this protein at different temperatures (303 K, 333 K and 363 K) was compared with homologous proteins from the less temperature resistant organism Thermoplasma acidophilum and the mesophilic organism Acinetobacter baumannii using several data reduction techniques like principal component analysis (PCA), residue interaction network (RIN) analysis and rotamer analysis. These methods enabled the determination of important residues for ...


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