Biological and Chemical Physics Commons^™

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 and Statistics 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 …

Cell Division Dynamics Of Escherichia Coli In Extreme Environments, Steven P. Murray

Graduate Theses and Dissertations

Life is remarkable in how resilient it can be. Many organism, classified as ex- tremophiles, can not only survive in extreme environments, but they can thrive in them. In the search for extraterrestrial life, the best candidates to harbor life exist with some kind of extreme condition. Europa, for example, is a favorite for the possibility of accommodating life as we know it within our solar system. Thought there is believed to be a liquid ocean under its icy surface, this habitat would be under immense pressures and high salinity. To best know where to look for extraterrestrial life, it …

Photoionization Energetics And Dissociation Pathways Of Hydroperoxyethyl Formate Produced In The Reaction Of Ch3Choo + Formic Acid, Vincent J. Esposito, Trent A. Mchenry, Marsha I. Lester

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The bimolecular reaction of Criegee intermediates, zwitterionic carbonyl oxide species produced in alkene ozonolysis, with organic acids leads to formation of functional hydroperoxides implicated in the generation of atmospheric aerosols. This theoretical study using high-level explicitly correlated coupled-cluster theory examines the low energy conformers of hydroperoxyethyl formate [HOOCH(CH₃)OCHO, HPEF] formed in the bimolecular reaction of CH₃CHOO, a simple alkyl-substituted Criegee intermediate, with formic acid, and the detection of HPEF via photoionization. The vertical and adiabatic ionization energies of HPEF are computed, along with the pathways for dissociative ionization that produce HO₂ or OCHO fragments with …

Spectroscopic Properties Of The Astrochemical Molecules [Al, O, Si]X (X = 0, +1), Jacqueline M. Friskey, Vincent J. Esposito, Tarek Trabelsi, Joseph S. Francisco

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Aluminum and silicon are present in large quantities in the interstellar medium, making the triatomic species consisting of both elements intriguing with regard to the foundations of astrochemistry. Spectroscopic parameters have been calculated via high-level ab initio methods to assist with laboratory and observational detection of [Al, O, Si]^x(x = 0,+1). All [Al, O, Si]M^x(x = 0,+1) isomers exist in the linear geometry, with linear AlOSi (X ²Π) and linear AlOSi⁺ (X¹Δ) being the most stable neutral and cationic species, respectively. Formation of the neutral species most likely occurs via reaction of …

High Water-Responsiveness Of Peptidoglycan And Its Water-Responsive Mechanism, Haozhen Wang

Dissertations, Theses, and Capstone Projects

Water-responsive materials that reversibly deform in response to humidity changes show great potential for developing muscle-like actuators for miniature and biomimetic robotics. This thesis demonstrates that peptidoglycan exhibits ultrahigh water-responsive actuation energy and power densities, which are orders of magnitude higher than those of frequently used actuators, such as piezoelectric actuators and dielectric elastomers. Surprisingly, peptidoglycan exhibits an energy conversion efficiency of ~66.8%, which could be attributed to its super-viscous nanoconfined water that efficiently translates water’s movement to peptidoglycan’s mechanical deformation. The systematic water-responsive characterizations of peptidoglycan from different microorganisms and peptide crystals indicate that enhanced H-bonding interactions in water-responsive …

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 …

The Interaction Of Different Primary Producers And Physical And Chemical Dynamics Of An Urban Shallow Lake, Majid Sahin

Dissertations, Theses, and Capstone Projects

An artificial urban shallow lake, Prospect Park Lake (PPL), is situated on a terminal moraine in Brooklyn New York, and supplied with municipal water treated with ortho-phosphates. The constant input of the phosphate nutrient is the primary source of eutrophication in the lake. The numerous pools along the water course houses various aquatic phototrophs, which influence the water quality and the state of the system, driving conditions into favoring the survival of their species. In the first half of the dissertation, the focus of the project is on analyzing how the different primary producers in different regions of PPL affect …

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 …

The Photoionization Dynamics, Electronic Spectroscopy, And Excited State Photochemistry Of Alco And Aloc, Vincent J. Esposito, Joseph S. Francisco

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The high cosmic abundance of carbon monoxide (CO) and the ubiquitous nature of aluminum-coated dust grains sets the stage for the production of weakly bound triatomic molecules AlCO (X ²Π) and AlOC (X ²Π) in circumstellar envelopes of evolved stars. Following desorption of cold AlCO and AlOC from the dust grain surface, incoming stellar radiation in the 2–9 eV wavelength range (visible to vacuum ultraviolet) will drive various photochemical processes. Ionization to the singlet cation state will cause an immediate Al–X (X = C, O) bond dissociation to form Al⁺ (¹S) and CO (X ^{1 …}

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 …

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 …

Insights Into Molecular Recognition And Reactivity From Molecular Simulations Of Protein-Ligand Interactions Using Md And Qm/Mm, Jerrano L. Bowleg

Theses and Dissertations

In this thesis, we have employed two computational methods, molecular dynamics (MD) and hybrid quantum mechanics/molecular mechanics (QM/MM) MD simulations with umbrella sampling (US), to gain insights into the molecular mechanism governing the molecular recognition and reactivity in several protein-ligand complexes. Three systems involving protein-ligand interactions are examined in this dissertation utilizing well-established computational methodologies and mathematical modeling. The three proteins studied here are acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1). These enzymes are known to interact with a variety of ligands. AChE dysfunction caused by organophosphorus (OP) chemicals is a severe hazard since AChE is …

Aloso: Spectroscopy And Structure Of A New Group Of Astrochemical Molecules, Vincent J. Esposito, Tarek Trabelsi, Joseph S. Francisco

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

No abstract provided.

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 …