Biological and Chemical Physics Commons^™

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 …

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 …

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 …

Revealing The Role Of Electrostatics In Molecular Recognition, Ion Binding And Ph-Dependent Phenomena, Mihiri Hewa Bosthanthirige

All Dissertations

In this dissertation, we study the role of electrostatics in molecular recognition, ion binding and pH-dependent phenomena. In this work that includes three different research projects, the Poisson-Boltzmann (PB) model is used to describe the biological system and Delphi (which is a popular tool for solving the PB equation (PBE)) to study the electrostatics of biomolecular systems.

Chapter two aims to investigate the role of electrostatic forces in molecular recognition. We calculated electrostatic forces between binding partners separated at various distances. To accomplish this goal, we developed a method to find an appropriate direction to move one chain of protein …

Symmetry-Inspired Analysis Of Biological Networks, Ian Leifer

Dissertations, Theses, and Capstone Projects

The description of a complex system like gene regulation of a cell or a brain of an animal in terms of the dynamics of each individual element is an insurmountable task due to the complexity of interactions and the scores of associated parameters. Recent decades brought about the description of these systems that employs network models. In such models the entire system is represented by a graph encapsulating a set of independently functioning objects and their interactions. This creates a level of abstraction that makes the analysis of such large scale system possible. Common practice is to draw conclusions about …

A Molecular Dynamics Study Of Polymer Chains In Shear Flows And Nanocomposites, Venkat Bala

Electronic Thesis and Dissertation Repository

In this work we study single chain polymers in shear flows and nanocomposite polymer melts extensively through the use of large scale molecular dynamics simulations through LAMMPS. In the single polymer chain shear flow study, we use the Lattice Boltzmann method to simulate fluid dynamics and also include thermal noise as per the \emph{fluctuation-dissipation} theorem in the system. When simulating the nanocomposite polymer melts, we simply use a Langevin thermostat to mimic a heat bath. In the single polymer in shear flow study we investigated the margination of a single chain towards solid surfaces and how strongly the shear flow …

Dr. Lawrence J. Berliner, Anit Tyagi

DU Undergraduate Research Journal Archive

An interview with Dr. Lawrence J. Berliner.

Contributions Of Vibrational Spectroscopy To Virology: A Review, Iqra Chaudhary, Naomi Jackson, Denise Denning, Luke O'Neill, Hugh Byrne

Articles

Vibrational spectroscopic techniques, both infrared absorption and Raman scattering, are high precision, label free analytical techniques which have found applications in fields as diverse as analytical chemistry, pharmacology, forensics and archeometrics and, in recent times, have attracted increasing attention for biomedical applications. As analytical techniques, they have been applied to the characterisation of viruses as early as the 1970s, and, in the context of the coronavirus disease 2019 (COVID-19) pandemic, have been explored in response to the World Health Organisation as novel methodologies to aid in the global efforts to implement and improve rapid screening of viral infection. This review …

Scale-Free Behavioral Dynamics Directly Linked With Scale-Free Cortical Dynamics, Sabrina Jones

Physics Undergraduate Honors Theses

In organisms, an interesting phenomenon occurs in both behavior and neuronal activity: organization with fractal, scale-free fluctuations over multiple spatiotemporal orders of magnitude (1,2). In regard to behavior, this sort of complex structure-- which manifests itself from small scale fidgeting to purposeful, full body movements-- may support goals such as foraging (3-6), visual search (4), and decision making (7,8). Likewise, the presence of this sort of structure in the cerebral cortex in the form of spatiotemporal cascades, coined “neuronal avalanches,” may offer optimal information transfer (9). Thus, when considering the functional relationship between the cerebral cortex and movements of the …

Ongoing Calculus In The Cerebral Cortex, Luke Long

Physics Undergraduate Honors Theses

Various modes of neuronal computations have long been theorized to be possible based on the structure and geometry of the brain. These computations also seem necessary for many of the integral functions of the brain, like information processing and regulatory processes in the body. However, experimental data directly supporting these claims have been rare.

In this study, data collected in mice from a large number of neurons over a long period of time provided the opportunity to search for some of these computations, specifically change detection and squaring calculations. Using Matlab, the goal of this analysis was to find statistically …

Combining Pharmacokinetics And Vibrational Spectroscopy: Mcr-Als Hard-And-Soft Modelling Of Drug Uptake In Vitro Using Tailored Kinetic Constraints, David Perez-Guaita, Guillermo Quintas, Zeineb Farhane, Roma Tauler, Hugh Byrne

Articles

Raman microspectroscopy is a label-free technique which is very suited for the investigation of pharmacokinetics of cellular uptake, mechanisms of interaction, and efficacies of drugs in vitro. However, the complexity of the spectra makes the identification of spectral patterns associated with the drug and subsequent cellular responses difficult. Indeed, multivariate methods that relate spectral features to the inoculation time do not normally take into account the kinetics involved, and important theoretical information which could assist in the elucidation of the relevant spectral signatures is excluded. Here, we propose the integration of kinetic equations in the modelling of drug uptake and …

Prediction Of Pathogenic Mutations In Spermine/Spermidine Synthases, Shannon Bonomi

All Theses

As genetic technology and information become continuously more sophisticated and applied to the prevention and treatment of diseases, the need to understand the effects of genetic variants becomes an important task with regards to assessing disease risk. In the specific case of intellectual disabilities, prenatal screenings is an important diagnostic tool that prepares families and health professionals for the arrival of a child who may need immediate, specialized care. Cell Free DNA screenings are routine for determining sex and provide the opportunity to discover genetic anomalies. However, this has little value unless mutations can be recognized as pathogenic and are …

Supertertiary Structural Dynamics Modulate Function In Postsynaptic Density Protein 95, George L. Hamilton Iii

All Dissertations

Proteins, RNA, and DNA serve as the primary sub-cellular machinery that give rise to the necessary functions of life. The long-standing paradigm has been that the structures of biomolecules, or the arrangement of the subunits that make up a biomolecule, determine biological function. However, biomolecules are not static objects. Instead, they often undergo structural rearrangements that are crucial to enabling and regulating their functions. In my thesis I present several studies of the interplay between the structures, dynamics, and functions of biomolecules that combine experimental fluorescence spectroscopy and computational methods to probe these systems at the single-molecule level. In particular, …

Estimating The Analytical Performance Of Raman Spectroscopy For Quantification Of Active Ingredients In Human Stratum Corneum, Hichem Kichou, Emilie Munnier, Yuri Dancik, Kamilia Kemel, Hugh Byrne, Ali Tfayli, Dominique Bertrand, Martin Soucé, Igor Chourpa, Franck Bonnier

Articles

Confocal Raman microscopy (CRM) has become a versatile technique that can be applied routinely to monitor skin penetration of active molecules. In the present study, CRM coupled to multivariate analysis (namely PLSR—partial least squares regression) is used for the quantitative measurement of an active ingredient (AI) applied to isolated (ex vivo) human stratum corneum (SC), using systematically varied doses of resorcinol, as model compound, and the performance is quantified according to key figures of merit defined by regulatory bodies (ICH, FDA, and EMA). A methodology is thus demonstrated to establish the limit of detection (LOD), precision, accuracy, sensitivity (SEN), and …

Azo-Dye-Functionalized Polycarbonate Membranes For Textile Dye And Nitrate Ion Removal, Carrie Cockerham, Ashton Caruthers, Jeremy Mccloud, Laura Fortner, Sungmin Youn, Sean P. Mcbride

Physics Faculty Research

Challenges exist in the wastewater treatment of dyes produced by the world’s growing textiles industry. Common problems facing traditional wastewater treatments include low retention values and breaking the chemical bonds of some dye molecules, which in some cases can release byproducts that can be more harmful than the original dye. This research illustrates that track-etched polycarbonate filtration membranes with 100-nanometer diameter holes can be functionalized with azo dye direct red 80 at 1000 µM, creating a filter that can then be used to remove the entire negatively charged azo dye molecule for a 50 µM solution of the same dye, …

Physics 315 (Medical Physics), Ronald Koder

Open Educational Resources

No abstract provided.