Biological and Chemical Physics Commons^™

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 …

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 …

Generation & Kinetic Studies Of Porphyrin Chromium-Oxo Intermediates, Iyanu Olumide Ojo

Masters Theses & Specialist Projects

Recent emerging applications of chromium porphyrin complexes are generating increasing interest in oxidation chemistry and catalysis. Its recent application as metal-organic frames in spintronic devices supports the rich electronic system of chromium metal. Through the past decades, first-row transition metalloporphyrins have served as biomimetic oxidation catalysts and models of cytochrome P450 enzymes. However, the oxygen atom transfer mechanism of chromium porphyrin complexes, most especially in sulfide oxidation reactions, has been scarcely investigated.

In this study, high-valent chromium-oxo porphyrin species, namely Cr^IV-oxo and Cr^V-oxo species, with electron-donating tetramesitylporphyrin(TMP) ligand were successfully generated and characterized with UV-vis, ESI-MS, …

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 …

Optimization Of Modular, Long-Range, Ultra-Fast Optical Tweezers With Fluorescence Capabilities For Single-Molecule And Single-Cell Based Biophysical Measurements, Subash C. Godar

All Dissertations

An Optical tweezer is a tightly focused laser beam that applies and senses precise and localized optical force to a dielectric microsphere and offers a unique and effective tool for manipulating the single cell or cell components, including nucleotides and dynein motor proteins. Here, I used highly stabilized optomechanical components and ultra-sensitive detection modules to significantly improve the measurement capabilities over a wide range of temporal and spatial scales. I combined the optical tweezer-based force spectroscopy technique with fluorescence microscopy to develop an integrated high-resolution force-fluorescence system capable of measuring displacements at sub-nanometer, forces at sub-piconewton over a temporal range …

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.

Physics 422 (Biophysics), Ronald Koder

Open Educational Resources

No abstract provided.

Growth Kinetics Determine The Polydispersity And Size Of Pbs And Pbse Nanocrystals, Michael P. Campos, Jonathan De Roo, Matthew W. Greenberg, Brandon M. Mcmurtry, Mark P. Hendricks, Ellie Bennett, Natalie Saenz, Matthew Y. Sfeir, Benjamin Abecassis, Sanjit K. Ghose, Jonathan S. Owen

Advanced Science Research Center

A library of thio- and selenourea derivatives is used to adjust the kinetics of PbE (E = S, Se) nanocrystal formation across a 1000-fold range (kr = 10−1 to 10−4 s−1), at several temperatures (80–120 °C), under a standard set of conditions (Pb : E = 1.2 : 1, [Pb(oleate)2] = 10.8 mM, [chalcogenourea] = 9.0 mM). An induction delay (tind) is observed prior to the onset of nanocrystal absorption during which PbE solute is observed using in situ X-ray total scattering. Density functional theory models fit to the X-ray pair distribution function (PDF) support a Pb2(μ2-S)2(Pb(O2CR)2)2 structure. Absorption spectra …

Nanoscale Hybrid Electrolytes With Viscosity Controlled Using Ionic Stimulus For Electrochemical Energy Conversion And Storage, Sara T. Hamilton, Tony G. Feric, Sahana Bhattacharyya, Nelly M. Cantillo, Steven G. Greenbaum, Thomas A. Zawodzinski, Ah-Hyung Alissa Park

Publications and Research

As renewable energy is rapidly integrated into the grid, the challenge has become storing intermittent renewable electricity. Technologies including flow batteries and CO 2 conversion to dense energy carriers are promising storage options for renewable electricity. To achieve this technological advancement, the development of next generation electrolyte materials that can increase the energy density of flow batteries and combine CO 2 capture and conversion is desired. Liquid-like nanoparticle organic hybrid materials (NOHMs) composed of an inorganic core with a tethered polymeric canopy (e.g., polyetheramine (HPE)) have a capability to bind chemical species of interest including CO 2 and redox-active species. …

Post-Acquisition Hyperpolarized 29silicon Mr Image Processing For Visualization Of Colorectal Lesions Using A User-Friendly Graphical Interface, Caitlin V Mccowan, Duncan Salmon, Jingzhe Hu, Shivanand Pudakalakatti, Nicholas Whiting, Jennifer S Davis, Daniel D Carson, Niki M Zacharias, Pratip K Bhattacharya, Mary C Farach-Carson

College of Science & Mathematics Departmental Research

Medical imaging devices often use automated processing that creates and displays a self-normalized image. When improperly executed, normalization can misrepresent information or result in an inaccurate analysis. In the case of diagnostic imaging, a false positive in the absence of disease, or a negative finding when disease is present, can produce a detrimental experience for the patient and diminish their health prospects and prognosis. In many clinical settings, a medical technical specialist is trained to operate an imaging device without sufficient background information or understanding of the fundamental theory and processes involved in image creation and signal processing. Here, we …

Seizure Prediction In Epilepsy Patients, Gary Dean Cravens

NSU REACH and IPE Day

Purpose/Objective: Characterize rigorously the preictal period in epilepsy patients to improve the development of seizure prediction techniques. Background/Rationale: 30% of epilepsy patients are not well-controlled on medications and would benefit immensely from reliable seizure prediction. Methods/Methodology: Computational model consisting of in-silico Hodgkin-Huxley neurons arranged in a small-world topology using the Watts-Strogatz algorithm is used to generate synthetic electrocorticographic (ECoG) signals. ECoG data from 18 epilepsy patients is used to validate the model. Unsupervised machine learning is used with both patient and synthetic data to identify potential electrophysiologic biomarkers of the preictal period. Results/Findings: The model has shown states corresponding to …

A Microfluidic Approach For Synthesis And Kinetic Profiling Of Branched Gold Nanostructures, Qi Cai, Valentina Castagnola, Luca Boselli, Alirio Moura, Hender Lopez, Wei Zhang, João M. De Araújo, Kenneth A. Dawson

Articles

Automatized approaches for nanoparticle synthesis and characterization represent a great asset to their applicability in the biomedical field by improving reproducibility and standardization, which help to meet the selection criteria of regulatory authorities. The scaled-up production of nanoparticles with carefully defined characteristics, including intrinsic morphological features, and minimal intra-batch, batch-to-batch, and operator variability, is an urgent requirement to elevate nanotechnology towards more trustable biological and technological applications. In this work, microfluidic approaches were employed to achieve fast mixing and good reproducibility in synthesizing a variety of gold nanostructures. The microfluidic setup allowed exploiting spatial resolution to investigate the growth evolution …

Morphological Phenotypes, Cell Division, And Gene Expression Of Escherichia Coli Under High Concentration Of Sodium Sulfate, Khanh Nguyen, Pradeep Kumar

Physics Faculty Publications and Presentations

Sodium and sulfate ions are among the suggested abundant ions on Europa, a moon of Jupiter. In order to investigate the potential habitability of Europa, we study the effects of sodium sulfate (Na2SO4) on a non-halophilic bacterium by subjecting Escherichia coli (E. coli) to a wide range of Na2SO4 concentrations (0–1.0 m). We discover that, as the concentration of sodium sulfate increases, the biomass doubling time increases and the cell growth is completely inhibited at 1.0" role="presentation" style="box-sizing: border-box; max-height: none; display: inline; line-height: normal; font-size: 13.2px; text-align: left; word-spacing: normal; overflow-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: …

Spectroscopic Properties Relevant To Astronomical And Laboratory Detection Of Mch And Mch+ (M = Al, Mg), Vincent J. Esposito, Tarek Trabelsi, Joseph S. Francisco

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

New spectroscopic parameters have been calculated to aid in the laboratory and observational detection of AlCH, AlCH⁺, MgCH, MgCH⁺, and their deuterated analogs. All species exist in linear geometry except for AlCH+, which exhibits a bent structure. Rotational frequencies have been calculated and the transition with maximum intensity is discussed for three temperature regions present in space: 100 K for a central circumstellar envelope (CSE), 30 K for an outer CSE, and 3 K indicative of the interstellar medium. Pertinent frequencies range from 25 to 250 GHz, depending on the species. At 30 K, the most …

Inhibitors Of Alpha-Synuclein Aggregation, Jemil Ahmed

Electronic Theses and Dissertations

Alpha-Synuclein (αS) – a neuronal, disordered, presynaptic protein – aggregates into amyloid fibrils and accumulates in the substantia nigra pars compacta of Parkinson's Disease (PD) patients. The aggregation and accumulation of αS amyloid fibrils leads to death of dopaminergic neurons; a hallmark of PD. Although it’s not clear why αS aggregates, prior studies have found that intrastriatal injection of fibril alone is sufficient to cause PD pathology in mouse and non-human primates models. These observations implicate αS as a therapeutic target against PD.

Unfortunately, there are three caveats when attempting to target αS. First, αS is a neuronal protein expressed …

Examining Ecological Succession Of Diatoms In California Current System Cyclonic Mesoscale Eddies, Zuzanna M. Abdala, Sophie Clayton, Sveinn V. Einarsson, Kimberly Powell, Claire P. Till, Tyler H. Coale, P. Dreux Chappell

OES Faculty Publications

The California Current System is a diatom-dominated region characterized by seasonal coastal upwelling and additional elevated mesoscale activity. Cyclonic mesoscale eddies in the region trap productive coastal waters with their planktonic communities and transport them offshore with limited interaction with surrounding waters, effectively acting as natural mesocosms, where phytoplankton populations undergo ecological succession as eddies age. This study examines diatom community composition within two mesoscale cyclonic eddies that formed in the same region of the California Current System 2 months apart and in the California Current waters surrounding them. The diatom communities were analyzed in the context of shifting environmental …

Characterization Of Nanoparticles Using Inductively-Coupled Plasma Mass Spectrometry, Jabez D. Campbell

Graduate Theses/Dissertations

Nanomaterials are a relatively new class of materials that have many applications which span a wide host of fields from medical products to consumer products. The possible compositions and forms of nanomaterials are just as varied as the applications. Therefore, a versatile characterization method is needed for researchers and regulators alike to ensure nanomaterials are properly used. Single Particle Inductively Coupled Plasma Mass Spectrometry (SP-ICP-MS) is a functional method that could fill the characterization need in the nanomaterial research field. Using data from both SP-ICP-MS tests and data from literature established characterization methods, the viability of making SP-ICP-MS the standard …

Verification Of Electron Beam Production For Radiation Dosimetry Experimentation, Henri J. Lemieux

All Graduate Theses, Dissertations, and Other Capstone Projects

Radiation is a natural phenomenon in which energy is emitted in the form of waves or particles through a given medium. Radiation dosimetry is the method of analyzing and assessing this deposited emitted energy. How this emitted energy effects a given object when deposited has been a topic of interest in the fields of science and medicine. In this paper, a novel method is proposed for the verification of electrons in air and determining their delivered dose rate. Using a linear accelerator which had its polarity flipped from producing positive ions to producing electrons, work to verify the production of …

Stratospheric Aerosol Composition Observed By The Atmospheric Chemistry Experiment Following The 2019 Raikoke Eruption, Chris D. Boone, Peter F. Bernath, Keith Labelle, Jeff Crouse

Chemistry & Biochemistry Faculty Publications

Infrared aerosol spectra derived from Atmospheric Chemistry Experiment measurements following the June 2019 Raikoke volcanic eruption are used to evaluate the composition of stratospheric aerosols in the Arctic. A blanket of aerosols, spanning an altitude range from the tropopause (8–11 km) to 20 km, persisted in the stratosphere over northern latitudes for many months. The aerosols within this blanket were almost exclusively sulfates. The percentage of sulfuric acid in the aerosols decreased over time, dropping below 50% H₂SO₄ concentration at some altitudes by March 2020. Contrary to previous reports, the aerosol blanket was not comprised of smoke …

Quantitative Raman Analysis Of Carotenoid Protein Complexes In Aqueous Solution, Joy Udensi, Ekaterina Loskutova, James Loughman, Hugh Byrne

Datasets

Carotenoids are naturally abundant fat-soluble pigmented compounds, with dietary, antioxidant and vision protection advantages. The dietary carotenoids, Beta Carotene, Lutein and Zeaxanthin, complexed with in bovine serum albumin (BSA) in aqueous solution, were explored using Raman spectroscopy to differentiate and quantify their spectral signatures. UV visible absorption spectroscopy was employed to confirm the linearity of responses over the concentration range employed (0.05-1mg/ml) and, of the 4 source wavelengths, 785nm, 660nm, 532nm, 473nm, 532nm was chosen to provide the optimal response. After preprocessing to remove water and BSA contributions, and correct for self-absorption, a partial least squares model with R^{2 …}

Self-Assembly Of Black Cumin Oil-Based Nanoemulsion On Various Surfactants: A Molecular Dynamics Study, Aulia Fikri Hidayat, Taufik Muhammad Fakih

Makara Journal of Science

Black cumin is commonly used as traditional medicine due to its wide range of pharmacological potential. Black cumin oil (BCO) was often prepared as nanoemulsion to improve its solubility, stability, and bioavailability. This study was conducted to investigate the molecular behavior as well as structural evolution of BCO-surfactant systems during self-assembly micellization using molecular dynamics (MD) simulations. Several BCO constituents and variations of surfactants were employed to model BCO-surfactant systems. 50 ns of MD simulations were performed to elucidate their evolution of structures and physicochemical properties during formation. Results showed that BCO-tween20 and BCO-lecithin were able to form spherical-shaped micelles …

A Nanoscale Shape-Discovery Framework Supporting Systematic Investigations Of Shape-Dependent Biological Effects And Immunomodulation, Wei Zhang, Hender Lopez, Luca Boselli, Paolo Bigini, André Perez-Potti, Zengchun Xie, Valentina Castagnola, Qi Cai, Camila P. Silveira, Joao M. De Araujo, Laura Talamini, Nicolò Panini, Giuseppe Ristagno, Martina B. Violatto, Stéphanie Devineau, Marco P. Monopoli, Mario Salmona, Valeria A. Giannone, Sandra Lara, Kenneth A. Dawson, Yan Yan

Articles

Since it is now possible to make, in a controlled fashion, an almost unlimited variety of nanostructure shapes, it is of increasing interest to understand the forms of biological control that nanoscale shape allows. However, a priori rational investigation of such a vast universe of shapes appears to present intractable fundamental and practical challenges. This has limited the useful systematic investigation of their biological interactions and the development of innovative nanoscale shape-dependent therapies. Here, we introduce a concept of biologically relevant inductive nanoscale shape discovery and evaluation that is ideally suited to, and will ultimately become, a vehicle for machine …