Biological and Chemical Physics Commons^™

Hard-Sphere-Like Dynamics In Highly Concentrated Alpha-Crystallin Suspensions, Preeti Vodnala, Laurence Lurio, Michael C. Vega, Elizabeth Gaillard

Faculty Articles, Papers, and Other Scholarship

The dynamics of concentrated suspensions of the eye-lens protein alpha crystallin have been measured using x-ray photon correlation spectroscopy. Measurements were made at wave vectors corresponding to the first peak in the hard-sphere structure factor and volume fractions close to the critical volume fraction for the glass transition. Langevin dynamics simulations were also performed in parallel to the experiments. The intermediate scattering function f(q,τ) could be fit using a stretched exponential decay for both experiments and numerical simulations. The measured relaxation times show good agreement with simulations for polydisperse hard-sphere colloids.

A Machine Learning Algorithm For Identifying And Tracking Bacteria In Three Dimensions Using Digital Holographic Microscopy, Manuel Bedrossian, Marwan El-Kholy, Daniel Neamati, Jay Nadeau

Physics Faculty Publications and Presentations

Digital Holographic Microscopy (DHM) is an emerging technique for three-dimensional imaging of microorganisms due to its high throughput and large depth of field relative to traditional microscopy techniques. While it has shown substantial success for use with eukaryotes, it has proven challenging for bacterial imaging because of low contrast and sources of noise intrinsic to the method (e.g. laser speckle). This paper describes a custom written MATLAB routine using machine-learning algorithms to obtain three-dimensional trajectories of live, lab-grown bacteria as they move within an essentially unrestrained environment with more than 90% precision. A fully annotated version of the software used …

Information Content, Charge Transport Properties, And Computational Capacities Of Proteins, Joseph Murphy Brisendine Jr.

Dissertations, Theses, and Capstone Projects

This thesis is the beginning of an attempt to build a coherent theory of the properties of proteins based in information theory and the duality of information theory and nonequilibrium thermodynamics. Throughout, we will adopt the viewpoint that information can act as a thermodynamic potential, which is necessary to understand how biological processes are both enabled and constrained by the laws of thermodynamics. Understanding information as a form of thermodynamic potential also clarifies the description of proteins and other biological macromolecules as “molecular machines”: meso-scale structures with emergent causal powers which perform work on their environments by irreversibly dissipating energy …

Lanthanum-Mediated Dehydrogenation Of Butenes: Spectroscopy And Formation Of La(C4H6) Isomers, Wenjin Cao, Dilkrushi Hewage, Dong-Sheng Yang

Chemistry Faculty Publications

La atom reactions with 1-butene, 2-butene, and isobutene are carried out in a laser-vaporization molecular beam source. The three reactions yield the same La-hydrocarbon products from the dehydrogenation and carbon-carbon bond cleavage and coupling of the butenes. The dehydrogenated species La(C₄H₆) is the major product, which is characterized with mass-analyzed threshold ionization (MATI) spectroscopy and quantum chemical computations. The MATI spectrum of La(C₄H₆) produced from the La+1-butene reaction exhibits two band systems, whereas the MATI spectra produced from the La+2-butene and isobutene reactions display only a single band system. Each of these …

Detection And Characterization Of The Tin Dihydride (Snh2 And Snd2) Molecule In The Gas Phase, Tony C. Smith, Dennis J. Clouthier

Chemistry Faculty Publications

The SnH₂ and SnD₂ molecules have been detected for the first time in the gas phase by laser-induced fluorescence (LIF) and emission spectroscopic techniques through the ùB₁–X̃¹A₁ electronic transition. These reactive species were prepared in a pulsed electric discharge jet using (CH₃)₄Sn or SnH₄/SnD₄ precursors diluted in high pressure argon. Transitions to the electronic excited state of the jet-cooled molecules were probed with LIF, and the ground state energy levels were measured from single rovibronic level emission spectra. The LIF spectrum of SnD_{2 …}

Modulation Of The Navigational Strategy Of Insects In Controlled Temperature Environments, Joseph Shomar, Anggie Ferrer, Josh Forer, Tom Zhang, Mason Klein

2018 Entries

With its small size and limited motor tool set, the Drosophila larva is a good system to study how animals alter specific elements of their behavior to search and reach optimal environmental conditions. We aim to understand the larva’s response to temperature across development, in sensory gradients, and to distinguish behavioral modulations based on physical changes from those due to sensory input. PID-controlled instruments drive temporal or spatial temperature gradients; combined with a moat system to replenish gels at high temperature, we can explore the larva’s full behavioral profile. Many larvae are simultaneously observed during free navigation in three different …

Three-Dimensional Imaging Of Kndy Neurons In The Mammalian Brain Using Optical Tissue Clearing And Multiple-Label Immunocytochemistry, Aleisha M. Moore, Kathryn A. Lucas, Robert L. Goodman, Lique M. Coolen, Michael N. Lehman

Faculty & Staff Scholarship

Kisspeptin/Neurokinin B/Dynorphin (KNDy) neurons of the arcuate nucleus (ARC) play a key role in the regulation of fertility. The ability to detect features of KNDy neurons that are essential for fertility may require three-dimensional (3D) imaging of the complete population. Recently developed protocols for optical tissue clearing permits 3D imaging of neuronal populations in un-sectioned brains. However, these techniques have largely been described in the mouse brain. We report 3D imaging of the KNDy cell population in the whole rat brain and sheep hypothalamus using immunolabelling and modification of a solvent-based clearing protocol, iDISCO. This study expands the use of …

Macrophage Sensing Of Single- Walled Carbon Nanotubes Via Toll- Like Receptors, Sourav P. Mukherjee, Olesja Bondarenko, Pekka Kohonen, Fernando T. Andon, Tana Brzicova, Isabel Gessner, Sanjay Mathur, Massimo Bottini, Paolo Calligari, Lorenzo Stella, Elena Kisin, Anna Shvedova, Reija Autio, Heli Salminen-Mankonen, Ritta Lahesmaa, Bengt Fadeel

Faculty & Staff Scholarship

Carbon-based nanomaterials including carbon nanotubes (CNTs) have been shown to trigger

inflammation. However, how these materials are ‘sensed’ by immune cells is not known. Here we compared the effects of two carbon-based nanomaterials, single-walled CNTs (SWCNTs) and graphene oxide (GO), on primary human monocyte-derived macrophages. Genome-wide transcriptomics assessment was performed at sub-cytotoxic doses. Pathway analysis of the microarray data revealed pronounced effects on chemokine-encoding genes in macrophages exposed to SWCNTs, but not in response to GO, and these results were validated by multiplex array-based cytokine and chemokine profiling. Conditioned medium from SWCNT-exposed cells acted as a chemoattractant for dendritic cells. …

Learning From Disorder And Noise In Physical Biology, Taylor Emil Firman

Electronic Theses and Dissertations

Stochasticity, disorder, and noise play crucial roles in the functioning of many biological systems over many different length scales. On the molecular scale, most proteins are envisioned as pristinely folded structures, but intrinsically disordered proteins (IDPs) have no such folded state and still serve distinct purposes within the cell. At the scale of gene regulation, realistic in vivo conditions produce stochastic fluctuations in gene expression that can lead to advantageous bet-hedging strategies, but can be difficult to characterize using a deterministic framework. Even at the organismal scale, germband extension (GBE) in Drosophila melanogaster embryos systematically elongates the epithelial tissue using …

Can A Comprehensive Transition Plan To Barefoot Running Be The Solution To The Injury Epidemic In American Endurance Runners?, Michael A. Scarlett

CMC Senior Theses

Fossils belonging to the genus Homo, dating as far back as two million years ago, exhibit uniquely efficient features suggesting that early humans had evolved to become exceptional endurance runners. Although they did not have the cushion or stability-control features provided in our modern day running shoes, our early human ancestors experienced far less of the running-related injuries we experience today. The injury rate has been estimated as high as 90% annually for Americans training for a marathon and as high as 79% annually for all American endurance runners. There is an injury epidemic in conventionally shod populations that …

Comparison Between The Water Activation Effects By Pulsed And Sinusoidal Helium Plasma Jets, Han Xu, Dingxin Liu, Wenjie Xia, Chen Chen, Weitao Wang, Zhijie Liu, Xiaohua Wang, Michael G. Kong

Bioelectrics Publications

Comparisons between pulsed and sinusoidal plasma jets have been extensively reported for the discharge characteristics and gaseous reactive species, but rarely for the aqueous reactive species in water solutions treated by the two types of plasma jets. This motivates us to compare the concentrations of aqueous reactive species induced by a pulsed and a sinusoidal plasma jet, since it is widely reported that these aqueous reactive species play a crucial role in various plasma biomedical applications. Experimental results show that the aqueous H₂O₂, OH/O₂⁻, and O₂⁻/ONOO⁻ induced by the …

Compositional And Topographical Characterization Of Carbonaceous Chondritic Meteorites Moss And Murray Using Micro-Raman Spectroscopy And Sem/Eds, Aaron Stokke

All Graduate Theses, Dissertations, and Other Capstone Projects

Carbonaceous chondritic meteorites are considered some of the most primitive surviving materials from the formation of our solar system. Thus, these objects can provide information about planet formation through their physical properties (such as structure, composition, and morphology) which can be characterized using microscopy and spectroscopy techniques. In this work, the analytical methods of Raman spectroscopy, scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), and optical microscopy are applied to determine the mineralogical, topographical, and elemental compositions of two carbonaceous chondritic fragments: Moss and Murray. Both samples were comprised of chondrules and matrix while Moss contained chondrule rims and Murray …

First-Principles Investigation Of The Interfacial Properties Of Boron Nitride, Kevin Waters

Dissertations, Master's Theses and Master's Reports

The interactions of nanomaterial surfaces with biological compounds, e.g. proteins, DNA, etc., unites the biological regime and nanomaterial world. Hybrid systems of boron-nitride nanotubes (BNNTs) and biological compounds are well-suited for a broad range of applications. First-principles methods are used to characterize the interface of these hybrid systems. Previous work has shown that the sensing capabilities of pristine BNNT are limited by long-ranged interactions. In this study the surfaces of pristine and functionalized BNNTs are investigated. The surfaces of the functionalized BNNTs give new properties to the tubes, which may enhance their sensing capabilities, while retaining their stability and chemical …

Hyperthermia As A Cancer Treatment- From Theory To Practice, Graham Fullerton

CMC Senior Theses

Using iron super-paramagnetic and ferromagnetic nanoparticles composed of Fe₃O₄ molecules, scientists analyze the effectiveness and practicality of this new treatment theory, hyperthermia. The problems of magnetic particle density, isothermal barriers/cellular cooling thresholds, and nanoparticle specific targeting are addressed in this review.

Iron magnetic nanoparticles were chosen due to their relatively low biological reactivates and lack of subsequent cellular toxicity. However, there are significant heating problems associated with these magnetic nanoparticles due to their relative size and short thermal time constants or thermal half-lives. Effectively, these aforementioned issues create a phenomenon where cancerous cells, surrounded by unheated healthy …

Regulation Of Cytoplasmic Dynein By Lis1 And Adenomatous Polyposis Coli, Timothy Joshua Hines

Theses and Dissertations

Cytoplasmic dynein 1 (dynein) is a microtubule motor that plays a role in mitosis, cell migration, and minus-end directed microtubule-based transport. The lissencephaly protein, Lis1, and its binding partner, Ndel1, are critical regulators of cytoplasmic dynein (Niethammer et al., 2000). In humans, haploinsufficiency of Lis1 leads to lissencephaly, a devastating developmental neurological disorder characterized by severe brain malformation, leading to cognitive and motor defects, and progressively worsening seizures (Dobyns et al., 1993). While Lis1 is known to play a role in regulating dynein-dependent functions such as neuronal migration and mitotic spindle orientation during development, the protein is still highly expressed …

Ecology And Virulence Capabilities Of Vibrios Isolated From The Pristine North Inlet Estuary, Savannah Leigh Klein

Theses and Dissertations

Vibrio bacteria are Gram negative, motile organisms that occur naturally in most coastal and estuarine ecosystems. Some vibrios are important human pathogens, including Vibrio parahaemolyticus and Vibrio vulnificus. The CDC estimates that vibrios cause 80,000 cases of disease each year in the United States alone. Most cases are caused by V. parahaemolyticus, which infects humans after the consumption of contaminated raw or undercooked seafood, primarily oysters. V. parahaemolyticus causes mild gastroenteritis that is self-limiting unless the patient is immunocompromised. V. vulnificus has a much lower incidence of disease (100 cases in the USA yr-1); however, this organism causes much more …

Evaluation And Adaptation Of Live-Cell Interferometry For Applications In Basic, Translational, And Clinical Research, Kevin A. Leslie

Theses and Dissertations

Cell mass is an important indicator of cell health and status. A diverse set of techniques have been developed to precisely measure the masses of single cells, with varying degrees of technical complexity and throughput. Here, the development of a non-invasive, label-free optical technique, termed Live-Cell Interferometry (LCI), is described. Several applications are presented, including an evaluation of LCI’s utility for assessing drug response heterogeneity in patient-derived melanoma lines and the measurement of CD3+ T cell kinetics during hematopoietic stem cell transplantation. The characterization of mast cells during degranulation, the measurement of viral reactivation kinetics in Kaposi’s Sarcoma, and drug …

An Application Of M-Matrices To Preserve Bounded Positive Solutions To The Evolution Equations Of Biofilm Models, Richard S. Landry Jr.

LSU New Orleans Theses and Dissertations

In this work, we design a linear, two step implicit finite difference method to approximate the solutions of a biological system that describes the interaction between a microbial colony and a surrounding substrate. Three separate models are analyzed, all of which can be described as systems of partial differential equations (PDE)s with nonlinear diffusion and reaction, where the biological colony grows and decays based on the substrate bioavailability. The systems under investigation are all complex models describing the dynamics of biological films. In view of the difficulties to calculate analytical solutions of the models, we design here a numerical technique …

Untangling The Mechanics Of Co-Entangled Cytoskeletal Networks, Shea Ricketts

Undergraduate Honors Theses

Active networks of interlinked protein filaments comprising the cytoskeleton largely control cellular mechanics and cell architecture. By forming cytoskeleton networks that combine motile, semiflexible actin with rigid, supportive microtubules, cells maintain structural integrity and shape while being able to flow and move. To elucidate the complex mechanical processes that arise between interacting networks of actin and microtubules within cells, we create a suite of randomly-oriented, well mixed networks of actin and microtubules by co-polymerizing varying ratios of both proteins in situ. We use optical tweezer microrheology in order to characterize the nonlinear mesoscale mechanics of in vitro co-entangled actin-microtubule composites. …

An Experiment-Based Model Quantifying Antimicrobial Activity Of Silver Nanoparticles On Escherichia Coli, Mohammad A. Haque, Riku Imamura, George A. Brown, Venkata R. Krishnamurthi, Isabelle I. Niyonshuti, Tiffany Marcelle, Leanne E. Mathurin, Jingyi Chen, Yong Wang

Physics Faculty Publications and Presentations

Silver nanoparticles (AgNPs) are well known to exhibit antimicrobial effects through plausible interactions with proteins and/or deoxyribonucleic acid inside the bacteria. Yet a quantitative understanding on the antimicrobial activities of AgNPs remains obscure. Here we conducted in-depth kinetic growth assays and colony-forming unit (CFU) assays on Escherichia coli (E. coli) cultured in AgNPs or Ag ion-containing growth media. Compared to the Ag-absent culture medium, it was found that the growth rate of the bacteria remained unaffected but the lag time of the bacterial growth was extended due to the presence of AgNPs or Ag ions. From the CFU-based time-kill curves, …