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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

All 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 ...


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.


Physics 516: Electromagnetic Phenomena (Spring 2020), Philip C. Nelson 2020 University of Pennsylvania

Physics 516: Electromagnetic Phenomena (Spring 2020), Philip C. Nelson

Department of Physics Papers

These course notes are made publicly available in the hope that they will be useful. All reports of errata will be gratefully received. I will also be glad to hear from anyone who reads them, whether or not you find errors: pcn@upenn.edu.


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 ...


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 ...


Application Of Optical Trapping To Obtain Single-Source Str Profiles From Forensically Relevant Body Fluid Mixtures With Modified Dna Analysis Workflow, Benjamin J. O'Brien 2020 Virginia Commonwealth University

Application Of Optical Trapping To Obtain Single-Source Str Profiles From Forensically Relevant Body Fluid Mixtures With Modified Dna Analysis Workflow, Benjamin J. O'Brien

Theses and Dissertations

Current methods of mixture separation in forensic DNA laboratories typically deconvolute the mixture after analysis using statistical analysis or probabilistic genotyping. To save time and effort of labs already backlogged, a method to separate mixtures on a cellular level before analysis needs to be developed. Optical trapping is a method that uses a focused 1064 nm laser to manipulate cells. Previous research has shown that approximately 50 spermatozoa or 15 leukocytes from a liquid sample are required to produce a full STR DNA profile. It was found that the number of spermatozoa required remains constant when the method of sample ...


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.


Characterization Of The Anomalous Ph Of Aqueous Nanoemulsions, Kieran P. Ramos 2019 University of Massachusetts Amherst

Characterization Of The Anomalous Ph Of Aqueous Nanoemulsions, Kieran P. Ramos

Doctoral Dissertations

Aqueous water-in-oil nanoemulsions have emerged as a versatile tool for use in microfluidics, drug delivery, single-molecule measurements, and other research. Nanoemulsions are often prepared with perfluorocarbons which are remarkably biocompatbile due to their stability, low surface tension, lipophobicity, and hydrophobicity. Therefore it is often assumed that droplet contents are unperturbed by the perfluorinated surface. However, in microemulsions, which are similar to nanoemulsions, it is known that either the pH of the aqueous phase or the ionization constants of encapsulated molecules are different from bulk solution. There is also recent evidence of low pH in perfluorinated aqueous nanoemulsions. The current underlying ...


Analog Implementation Of The Hodgkin-Huxley Model Neuron, Zachary D. Mobille, George H. Rutherford, Jordan Brandt-Trainer, Rosangela Follmann, Epaminondas Rosa 2019 Illinois State University

Analog Implementation Of The Hodgkin-Huxley Model Neuron, Zachary D. Mobille, George H. Rutherford, Jordan Brandt-Trainer, Rosangela Follmann, Epaminondas Rosa

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Period Drift In A Neutrally Stable Stochastic Oscillator, Kevin Sanft 2019 Illinois State University

Period Drift In A Neutrally Stable Stochastic Oscillator, Kevin Sanft

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Exploring The Complex Folding Free Energy Landscapes Of A Series Of Β-Rich Proteins, Noah R. Cohen 2019 University of Massachusetts Medical School

Exploring The Complex Folding Free Energy Landscapes Of A Series Of Β-Rich Proteins, Noah R. Cohen

GSBS Dissertations and Theses

Protein aggregation is deleterious to human health and detrimental to therapeutic shelf-life. The physical processes that induce aggregation are the same processes that drive productive folding reactions. As such, protein aggregation is a non-productive form of protein folding. To gain insight into the steps that serve as a partition between the folding and aggregation reactions, the folding mechanisms of several β-rich proteins with links to human disease or medicine were examined.

In the ALS-linked protein, SOD1, a subpopulation of the unfolded ensemble is found to be a common source of both nonnative structure and frustrated folding. These behaviors are only ...


Impact Of Excitation-Inhibition Balance/Imbalance On Dynamics Of Cortical Neural Networks, Vidit Agrawal 2019 University of Arkansas, Fayetteville

Impact Of Excitation-Inhibition Balance/Imbalance On Dynamics Of Cortical Neural Networks, Vidit Agrawal

Theses and Dissertations

The purpose of this research is to study the implications of Excitation/Inhibition balance and imbalance on the dynamics of ongoing (spontaneous) neural activity in the cerebral cortex region of the brain.

The first research work addresses the question that why among the continuum of Excitation-Inhibition balance configurations, particular configuration should be favored? We calculate the entropy of neural network dynamics by studying an analytically tractable network of binary neurons. Our main result from this work is that the entropy maximizes at regime which is neither excitation-dominant nor inhibition-dominant but at the boundary of both. Along this boundary we see ...


Modeling Proton Relative Biological Effectiveness Using Monte Carlo Simulations Of Microdosimetry, Mark A. Newpower 2019 The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences

Modeling Proton Relative Biological Effectiveness Using Monte Carlo Simulations Of Microdosimetry, Mark A. Newpower

The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access)

Proton therapy is a radiotherapy modality that can offer a better physical dose distribution when compared to photon radiotherapy by taking advantage of the Bragg peak, a narrow region of rapid energy loss. Proton therapy is also known to offer an enhanced relative biological effectiveness (RBE) compared to photons. In the current clinical standard, RBE is fixed at 1.1 at all points along the proton beam, meaning protons are assumed to require 10% less dose than photons to achieve target coverage and organ at risk (OAR) sparing. However, there is mounting clinical evidence, and a significant number of in ...


Commissioning Of Micro-Cube Thermoluminescent Dosimeters For Small Field Dosimetry Quality Assurance In Radiotherapy, Brandon Luckett 2019 The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences

Commissioning Of Micro-Cube Thermoluminescent Dosimeters For Small Field Dosimetry Quality Assurance In Radiotherapy, Brandon Luckett

The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access)

Small field dosimetry presents complications and uncertainties that could be circumvented by using detectors which are smaller than the radiation field. This study evaluates the reproducibility and accuracy of TLD micro-cubes for use in stereotactic radiosurgery (SRS) remote auditing quality assurance (QA) for treatment centers participating in clinical trials. This study tested the hypothesis that TLD micro-cubes could be commissioned to evaluate small field dosimetry, and provide reproducibility within 3%, as well as assure agreement between measured dose and calculated doses to within 5%.

The aims of this thesis were to characterize and commission TLD micro-cubes as well as to ...


Quantifying Uncertainty In A Measurement-Based Assessment Of Relative Biological Effectiveness In Carbon Ion Radiotherapy, Shannon Hartzell 2019 The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences

Quantifying Uncertainty In A Measurement-Based Assessment Of Relative Biological Effectiveness In Carbon Ion Radiotherapy, Shannon Hartzell

The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access)

One of the largest inconsistencies in dose delivered during carbon ion therapy is due to uncertainties in relative biological effectiveness (RBE), a value that is calculated via one of several clinically implemented algorithms. This study investigates the uncertainty in measured microdosimetric parameters for RBE calculation by the Microdosimetric Kinetic Model (MKM), Repair Misrepair Fixation model (RMF), and Local Effect Model I (LEM) using a Tissue Equivalent Proportional Counter (TEPC).

Microdosimetric spectra, kinetic energy spectra, and dose fragment contributions were calculated using Monte Carlo (GEANT IV) for monoenergetic and SOBP carbon beams of clinical energy. From microdosimetric spectra, lineal energy values ...


Reactive And Stimuli-Responsive Sulfonium-Based Polymer Zwitterions, Cristiam Santa Chalarca 2019 University of Massachusetts Amherst

Reactive And Stimuli-Responsive Sulfonium-Based Polymer Zwitterions, Cristiam Santa Chalarca

Doctoral Dissertations

This dissertation describes the synthesis and characterization of novel monomers and (co)polymer zwitterions that incorporate trialkylsulfonium cations. The novel materials presented herein constitute a unique type of polymer zwitterions that exhibit salt- and temperature-dependent water solubility as well as inherent reactivity. The behavior of these polymers in aqueous solutions, as nanostructures, and at liquid-liquid interfaces was studied; in all cases, the inherent reactivity of the polymers was harnessed towards the fabrication of novel polymers and soft materials.

Following an introductory chapter, Chapter 2 describes the synthesis of sulfonium sulfonate monomers and polymer zwitterions. Both styrenic and methacrylic monomers were ...


Quantifying Complex Systems Via Computational Fly Swarms, Troy Taylor 2019 Linfield College

Quantifying Complex Systems Via Computational Fly Swarms, Troy Taylor

Senior Theses

Complexity is prevalent both in natural and in human-made systems, yet is not well understood quantitatively. Qualitatively, complexity describes a phenomena in which a system composed of individual pieces, each having simple interactions with one another, results in interesting bulk properties that would otherwise not exist. One example of a complex biological system is the bird flock, in particular, a starling murmuration. Starlings are known to move in the direction of their neighbors and avoid collisions with fellow starlings, but as a result of these simple movement choices, the flock as a whole tends to exhibit fluid-like movements and form ...


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