Biological and Chemical Physics Commons^™

Characterization Of Boreal-Arctic Vegetation Growth Phases And Active Soil Layer Dynamics In The High-Latitudes Of North America: A Study Combining Multi-Year In Situ And Satellite-Based Observations, Michael G. Brown

Dissertations, Theses, and Capstone Projects

This dissertation examined the seasonal freeze/thaw activity in boreal-Arctic soils and vegetation physiology in Alaska, USA and Alberta, Canada, using in situ environmental measurements and passive microwave satellite observations. The boreal-Arctic high-latitudes have been experiencing ecosystem changes more rapidly in comparison to the rest of Earth due to the presently warming climatic conditions having a magnified effect over Polar Regions. Currently, the boreal-Arctic is a carbon sink; however, recent studies indicate a shift over the next century to become a carbon source. High-latitude vegetation and cold soil dynamics are influenced by climatic shifts and are largely responsible for the regions …

Modelling Cell Population Growth, Mahmood Mazarei

Electronic Thesis and Dissertation Repository

The growth of biological matter, e.g., tumor invasion, depends on various factors, mainly the tissue’s mechanical properties, implying elasticity, stiffness, or apparent viscosity. These properties are impacted by the characteristics of the tissue’s extracellular matrix and constituent cells, including, but not limited to, cell membrane stiffness, cell cytoskeleton mechanical properties, and the intensity and distribution of focal adhesions over the cell membrane. To compute and study the mechanical properties of tissues during growth and confluency, a theoretical and computational framework, called CellSim3D, was developed in our group based on a three-dimensional kinetic division model.

In this work, CellSim3D is …

An Ab Initio Computation Of The Potential Energy Surfaces Of The Dna Bases, Anjali F. Filinovich, Vola Andrianarijaona

Campus Research Day

The potential energy surfaces of atoms in DNA can be analyzed and compared to show how their bonds break. This DNA potential energy reference data is very useful to understanding how DNA damage occurs, however, a dataset of relevant potential energy surfaces is not available for scientific use. We obtain the potential energy surfaces of various atoms in the four DNA bases adenine, thymine, guanine, and cytosine, by moving an atom in these molecules in three orthogonal directions using ORCA, an ab initio quantum chemistry software. Density functional theory is
used to compute potential energies as an atom is moved, …

Analysis And Methodology Of Helical And Flexible Homopolymer Monte Carlo Simulations, Nathan Roberts

Honors College Theses

The purpose of my work is to analyze the results of Monte Carlo simulations of various types of polymers: a helical homopolymer and a flexible homopolymer. Specific applications of Monte Carlo polymer simulations and parallel tempering replica exchanges are presented. Using temporal analysis, I aim to measure the efficiency of each type of simulation as it relates to equilibration time. For the helical homopolymer model, equilibration time is expanded upon to analyze the rate of structure generation and relevant hyper-phase diagram. Stable states for helical homopolymers will use data generated from parallel tempering replica exchange Monte Carlo simulations created by …

Modeling Excited State Processes In Molecular Aggregates By Constructing An Adaptive Basis For The Hierarchy Of Pure States, Leonel Varvelo

Chemistry Theses and Dissertations

Simulating excitation energy transfer (EET) in molecular materials is of crucial importance for the development of and understanding of materials such as organic photovoltaics and photosynthetic systems and further development of novel materials. The Hierarchy of Pure States (HOPS) is an exact framework for the time evolution of an open quantum system in which a hierarchy of stochastic wave functions are propagated in time. The adaptive HOPS (adHOPS) method achieves size-invariant scaling with the number of simulated molecules for sufficiently large aggregates by using an adaptive basis that moves with the excitation through the material. To demonstrate the power of …

Developing Carbon Quantum Dots As Multimodal Contrast Agents, Nicholas Whiting

Faculty Scholarship for the College of Science & Mathematics

No abstract provided.

Reconversion Of Parahydrogen Gas In Surfactant-Coated Glass Nmr Tubes, Robert V. Chimenti, James Daley, James Sack, Jennifer Necsutu, Nicholas Whiting

Faculty Scholarship for the College of Science & Mathematics

The application of parahydrogen gas to enhance the magnetic resonance signals of a diversity of chemical species has increased substantially in the last decade. Parahydrogen is prepared by lowering the temperature of hydrogen gas in the presence of a catalyst; this enriches the para spin isomer beyond its normal abundance of 25% at thermal equilibrium. Indeed, parahydrogen fractions that approach unity can be attained at sufficiently low temperatures. Once enriched, the gas will revert to its normal isomeric ratio over the course of hours or days, depending on the surface chemistry of the storage container. Although parahydrogen enjoys long lifetimes …

Minimal Expression Of Dysferlin Prevents Development Of Dysferlinopathy In Dysferlin Exon 40a Knockout Mice, Joe Yasa, Claudia E. Reed, Adam M. Bournazos, Frances J. Evesson, Ignatius Pang, Mark E. Graham, Jesse R. Wark, Brunda Nijagal, Kim H. Kwan, Thomas Kwiatkowski, Rachel Jung, Noah Weisleder, Sandra T. Cooper, Frances A. Lemckert

Chemistry Faculty Publications

Dysferlin is a Ca2+-activated lipid binding protein implicated in muscle membrane repair. Recessive variants in DYSF result in dysferlinopathy, a progressive muscular dystrophy. We showed previously that calpain cleavage within a motif encoded by alternatively spliced exon 40a releases a 72 kDa C-terminal minidysferlin recruited to injured sarcolemma. Herein we use CRISPR/Cas9 gene editing to knock out murine Dysf exon 40a, to specifically assess its role in membrane repair and development of dysferlinopathy. We created three Dysf exon 40a knockout (40aKO) mouse lines that each express different levels of dysferlin protein ranging from similar to 90%, similar to 50% and …

Analysis Of Biologically Effective Dose For Retroactive Yttrium-90 Trans-Arterial Radioembolization Treatment Optimization, Mj Lindsey

CMC Senior Theses

Trans-arterial radioembolization (TARE) is a protracted modality of radiation therapy where radionuclides labeled with Yttrium-90 (⁹⁰Y) are inserted inside a patient's hepatic artery to treat hepatocellular carcinoma (HCC). While TARE has been shown to be a clinically effective and safe treatment, there is little understanding of the radiobiological relationship between absorbed dose and tissue response, and thus there is no dosimetric standard for treatment planning. The Biologically Effective Dose (BED) formalism, derived from the Linear-Quadratic model of radiobiology, is used to weigh the absorbed dose by the time pattern of delivery. BED is a virtual dose that can …

Homopurine Guanine-Rich Sequences In Complex With N-Methyl Mesoporphyrin Ix Form Parallel G-Quadruplex Dimers And Display A Unique Symmetry Tetrad, Ming Ye, Erin V. Chen, Shawn H. Pfeil, Kailey N. Martin, Tamanaa Atrafi, Sara Yun, Zahara Martinez, Liliya A. Yatsunyk

Physics & Engineering Faculty Publications

DNA can fold into G-quadruplexes (GQs), non-canonical secondary structures formed by pi-pi stacking of G-tet-rads. GQs are important in many biological processes, which makes them promising therapeutic targets. We identified a 42-nucleotide long, purine-only G-rich sequence from human genome, which contains eight G- stretches connected by A and AAAA loops. We divided this sequence into five unique segments, four guanine stretches each, named GA1-5. In order to investigate the role of adenines in GQ structure formation, we per-formed biophysical and X-ray crystallographic studies of GA1-5 and their complexes with a highly selective GQ ligand, N-methyl mesoporphyrin IX (NMM). Our data …

Fabrication And Investigation Of Microfluidic Devices That Produce Non-Linear Chemical Gradients, Elijah L. Waters

Electronic Theses and Dissertations

Investigation of cell chemotaxis requires controlled chemical gradients. We investigated microfluidic devices that could enhance small populations' cell assays because of their ability to generate various chemical gradients. Our five designs generate different chemical concentration landscapes that we can easily convert into tools to study cell response to growth factors. Gradient landscapes occurred by splitting and mixing two input fluid concentrations using bifurcations, trifurcations, and Y-mixing junctions in three consecutive steps. Such fluid flow manipulations resulted in nine concentration streams entering a 0.54-mm-wide gradient chamber. The first design used a 1:1 ratio Y-mixer (unbiased) when blending two concentrations, resulting in …

Optical Tweezers: Exerting Force With Light, Gabriella Seifert

Scripps Senior Theses

Photons carry momentum. When a tightly-focused beam of photons hit a particle, they transfer some of their momentum to the particle, exerting a force. Optical tweezers take advantage of this phenomenon to trap (or “tweeze”) a spherical bead just after the focus of a diverging laser beam, creating a potential well that pulls in beads. In this thesis, I predict the force exerted on trapped beads and measure the actual force using an optical tweezers setup that I built. To predict the force, I follow the path of all possible rays from a diverging beam incident on a spherical bead …

Behaviors For Which Deinonychosaurs Used Their Feet, Alexander King

Honors Projects

This paper seeks to show for what purpose deinonychosaurs used their feet. Fowler et al., (2011) showed that D. antirrhopus’s feet were closest in function to accipitrids, as they found it was more built for grasping prey than running.

I answered this question by using 2D images of the feet of three modern birds (Buteo jamaicensis, Phasianus colchicus, and Gallus gallus domesticus), one eudromaeosaur (Deinonychus antirrhopus), and one troodontid (Borogovia gracilicrus). I used ImageJ to apply 73 landmarks to each foot, capturing the variation between species in the metatarsals and pedal phalanges. These data were then uploaded to the software …

A Method For Exploring The Habitability Of Earth-Like Exoplanets: Applications To Tess Objects Of Interest 203 B, 256 B, And 700 D, Paul Bonney

Graduate Theses and Dissertations

The Transiting Exoplanet Survey Satellite (TESS) has and is continuing to discover a multitude of potentially habitable planet candidates. As more planets are detected and confirmed, it becomes increasingly important to strategically search for signs of habitability with which to differentiate and prioritize them for further observation, in particular with the James Webb Space Telescope (JWST). To facilitate this, I have created a method for prioritizing TESS planet candidates based on parameters derived from their light curves and have applied the method to the TESS Candidate Target List (CTL). This data set uses preliminary fits to transit modeling which can …

Fluid-Structure Interaction Modelling Of Neighboring Tubes With Primary Cilium Analysis, Nerion Zekaj, Shawn D. Ryan, Andrew Resnick

Mathematics Faculty Publications

We have developed a numerical model of two osculating cylindrical elastic renal tubules to investigate the impact of neighboring tubules on the stress applied to a primary cilium. We hypothesize that the stress at the base of the primary cilium will depend on the mechanical coupling of the tubules due to local constrained motion of the tubule wall. The objective of this work was to determine the in-plane stresses of a primary cilium attached to the inner wall of one renal tubule subject to the applied pulsatile flow, with a neighboring renal tube filled with stagnant fluid in close proximity …

Physics 516: Electromagnetic Phenomena (Spring 2023), 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.

Using Protonation Microstates And Hydrogen Bond Networks To Track Proton Transfer Pathways In Complex I, Umesh Khaniya

Dissertations, Theses, and Capstone Projects

Complex I, NADH-ubiquinone oxidoreductase, is the first enzyme in the mitochondrial and bacterial aerobic respiratory chain. It pumps four protons through four transiently open pathways from the high pH, negative, N- side of the membrane to the positive, P-side driven by the exergonic transfer of electrons from NADH to a quinone. Three protons transfer through subunits descended from Mrp antiporters, while the fourth, E-channel is unique. Because of the complex possible paths thorough the many buried polar residues and lack of high-resolution crystal structure, the path for protons through the E-channel is elusive.

In this dissertation, the E-channel proton pumping …

Coupled Oscillators: Protein And Acoustics, Angelique N. Mcfarlane

Theses

This work encompassed three different vibrational energy transfer studies of coupled resonators (metal, topological, and microtubule comparison) inspired by the lattices of microtubules from regular and cancerous cells. COMSOL Multiphysics 5.4 was utilized to design the experiment. The simulation starts with an acoustic pressure study to examine the vibrational modes present in coupled cylinders, representing α-, β-tubulin heterodimers. The Metal Study consisted of 3 models (monomer, dimer, and trimer) to choose the correct height (40 mm) and mode (Mode 1) for study. The Topological Study was run to predict and understand how the lattice structure changes over a parametric sweep …

Mathematics For Biomedical Physics, Jogindra M. Wadehra

Open Textbooks

Mathematics for Biomedical Physics is an open access peer-reviewed textbook geared to introduce several mathematical topics at the rudimentary level so that students can appreciate the applications of mathematics to the interdisciplinary field of biomedical physics. Most of the topics are presented in their simplest but rigorous form so that students can easily understand the advanced form of these topics when the need arises. Several end-of-chapter problems and chapter examples relate the applications of mathematics to biomedical physics. After mastering the topics of this book, students would be ready to embark on quantitative thinking in various topics of biology and …

A Computational Model Of The Line-1 Retrotransposon Life Cycle And Visualization Of Metabolic Networks In 3-Dimensions., Michael D. Martin

Electronic Theses and Dissertations

Computational modeling of metabolic reactions and cellular systems is evolving as a tool for quantitative prediction of metabolic parameters and reaction pathway analysis. In this work, the basics of computational cell biology are presented as well as a summary of physical processes within the cell, and the algorithmic methods used to find time dependent solutions. Protein-protein and enzyme-substrate interactions are mathematically represented via mass action kinetics to construct sets of linear differential equations that describe reaction rates and formation of protein complexes. Using mass action methods, examples of reaction networks and their solutions are presented within the Virtual Cell simulation …