Biological and Chemical Physics Commons^™

Crystallography And Magnetism Of Magnetocalorically Important Ni-Mn-X Based Heusler Alloys, Amila S. B. Madiligama

Dissertations

Ni-Mn-X Heusler alloys, demonstrating strong coupling between crystalline structure and magnetic state, were studied. They undergo field-induced, first-order transformations from a low symmetry martensite to a high-symmetry austenitic phase around room temperature. The substantial difference between the entropies of the two phases results in a large adiabatic temperature change, called “Giant Magnetocaloric Effect (GMCE)”. Consequently, these alloys are promising refrigerants for near-room temperature cooling systems. This magnetic cooling is an energy-efficient and eco-friendly technology.

Crystalline structures and magnetic states of these alloys, which determine their magnetocaloric performances, highly depend on their composition. To examine new paths to optimize their magnetocaloric …

Investigating High Speed Localization Microscopy Through Experimental Methods, Data Processing Methods, And Applications Of Localization Microscopy To Biological Questions, Andrew J. Nelson

Electronic Theses and Dissertations

Fluorescence Photoactivation Localization Microscopy(FPALM) and other super resolution localization microscopy techniques can resolve structures with nanoscale resolution. Unlike techniques of electron microscopy, they are also compatible with live cell and live animal studies, making FPALM and related techniques ideal for answering questions about the dynamic nature of molecular biology in living systems. Many processes in biology occur on rapid sub second time scales requiring the imaging technique to be capable of resolving these processes not just with a high enough spatial resolution, but with an appropriate temporal resolution. To that end, this Dissertation in part investigates high speed FPALM as …

Study Of Charge Transport Mechanism In Microbial Nanowires, Ramesh Adhikari

Doctoral Dissertations

Conductivity of an individual proteinaceous filaments, called pili or microbial nanowires, produced by wild type Geobacter sulfurreducens was measured using a low-noise electrical transport technique. It was shown that the conductivity is diminished if aromatic amino acid residues are removed from the pili. It was demonstrated that the conductivity of G. sulfurreducens pili is similar to that of synthetic organic polymers and is related to the respiration rate of the bacteria. Conductivity measurements were performed on microbial nanowires produced by other species of Geobacter with a different aromatic amino acid distribution along the wire. Also, measurements on a mutated pili …

A Quantitative Measurement Of Structural Changes Of Rna Kissing Complexes Using Fluorescence Resonance Energy Transfer, Sheema Rahmanseresht

Doctoral Dissertations

Many RNA interactions in cells occur in the form of loop-loop interactions, also known as a "kissing complex". In the bacterial and viral systems discussed here, there are transiently bound proteins involved that modulate the function of kissing complex. These proteins either stabilize the kissing complex or facilitate its conversion to extended duplex. I studied R1inv-R2inv kissing complex (KC), derivatived from RNAI-RNAII complex of E.Coli. Rop protein is known to stabilize the bent R1inv-R2inv KC against dissociation. The goal was to study structural change of this kissing complex after binding of the stabilizing Rop protein. In this work for …

Splitting Nodes And Linking Channels: A Method For Assembling Biocircuits From Stochastic Elementary Units, Cameron Ferwerda, Ovidiu Lipan

Physics Faculty Publications

Akin to electric circuits, we construct biocircuits that are manipulated by cutting and assembling channels through which stochastic information flows. This diagrammatic manipulation allows us to create a method which constructs networks by joining building blocks selected so that (a) they cover only basic processes; (b) it is scalable to large networks; (c) the mean and variance-covariance from the Pauli master equation form a closed system; and (d) given the initial probability distribution, no special boundary conditions are necessary to solve the master equation. The method aims to help with both designing new synthetic signaling pathways and quantifying naturally existing …

Heart Attack Physics, John Zwart

Faculty Work Comprehensive List

I recently had a first-hand opportunity to learn some interesting biomedical applications of physics which provide application examples for introductory classes. While there were many such applications, from X-rays to ultrasonic imaging, I’ll focus on fluid flow through clogged coronary arteries and the use of radioactive materials in a nuclear stress test.

Exposure Of Fibrinogen And Thrombin To Nitric Oxide Donor Prolinonoate Affects Fibrin Clot Properties, Christine C. Helms, Shannon Kapadia, Anne C. Gilmore, Zhexi Lu, Swati Basu, Daniel B. Kim-Shapiro

Physics Faculty Publications

Fibrin fibers form the structural backbone of blood clots. The structural properties of fibrin clots are highly dependent on formation kinetics. Environmental factors such as protein concentration, pH, salt, and protein modification, to name a few, can affect fiber kinetics through altered fibrinopeptide release, monomer association, and/or lateral aggregation. The objective of our study was to determine the effect of thrombin and fibrinogen exposed to nitric oxide on fibrin clot properties. ProliNONOate (5 [mu]mol/l) was added to fibrinogen and thrombin before clot initiation and immediately following the addition of thrombin to the fibrinogen solution. Resulting fibrin fibers were probed with …

Dealloying Behavior Of Nico And Nicocu Thin Films, Benjamin Peecher, Jennifer R. Hampton

Faculty Publications

Porous metals and alloys, such as those fabricated via electrochemical dealloying, are of interest for a variety of energy applications, ranging from their potential for enhanced catalytic behavior to their use as high surface area supports for pseudocapacitor materials. Here, the electrochemical dealloying process was explored for electrodeposited binary NiCo and ternary NiCoCu thin films. For each of the four different metal ratios, films were dealloyed using linear sweep voltammetry to various potentials in order to gain insight into the evolution of the film over the course of the linear sweep. Electrochemical capacitance, scanning electron microscopy, and energy dispersive X-ray …

Chlorhexidine-Induced Elastic And Adhesive Changes Of Escherichia Coli Cells Within A Biofilm, Anne E. Murdaugh, Nicole Rodgers

Faculty Publications

Chlorhexidine is a widely used, commercially available cationic antiseptic. Although its mechanism of action on planktonic bacteria has been well explored, far fewer studies have examined its interaction with an established biofilm. The physical effects of chlorhexidine on a biofilm are particularly unknown. Here, the authors report the first observations of chlorhexidine-induced elastic and adhesive changes to single cells within a biofilm. The elastic changes are consistent with the proposed mechanism of action of chlorhexidine. Atomic force microscopy and force spectroscopy techniques were used to determine spring constants and adhesion energy of the individual bacteria within an Escherichia coli biofilm. …

Retardation Of Bulk Water Dynamics By Disaccharide Osmolytes.Pdf, Nimesh Shukla

Nimesh Shukla

No abstract provided.

An Automated Syringe Pump System For Improving The Reproducibility Of Dynamic Hyperpolarized Mri Phantoms, Harlee G. Harrison

Dissertations & Theses (Open Access)

AN AUTOMATED SYRINGE PUMP SYSTEM FOR IMPROVING THE REPRODUCIBILITY OF DYNAMIC HYPERPOLARIZED MRI PHANTOMS

Harlee Grace Harrison, B.S.

Advisory Professor: James Bankson, Ph.D.

Magnetic Resonance Imaging (MRI) is a powerful tool in the diagnosis of cancer due to its ability to provide good soft tissue contrast and image resolution without the use of ionizing radiation. The use of hyperpolarized pyruvate as a contrast agent for tumor metabolism during MR scans has the potential to provide information about tumor metabolism in vivo that is not available from traditional imaging measurements or any other method. Hyperpolarization is achieved through dynamic nuclear polarization. …

In Vitro Monitoring Of Time And Dose Dependent Cytotoxicity Of Aminated Nanoparticles Using Raman Spectroscopy, Esen Efeoglu, Alan Casey, Hugh Byrne

Articles

No abstract provided.

Morphological And Material Effects In Van Der Waals Interactions, Jaime C. Hopkins

Doctoral Dissertations

Van der Waals (vdW) interactions influence a variety of mesoscale phenomena, such as surface adhesion, friction, and colloid stability, and play increasingly important roles as science seeks to design systems on increasingly smaller length scales. Using the full Lifshitz continuum formulation, this thesis investigates the effects of system materials, shapes, and configurations and presents open-source software to accurately calculate vdW interactions. In the Lifshitz formulation, the microscopic composition of a material is represented by its bulk dielectric response. Small changes in a dielectric response can result in substantial variations in the strength of vdW interactions. However, the relationship between these …

Synthesis And Characterization Of Polymeric Anion Exchange Membranes, Wenxu Zhang

Doctoral Dissertations

As alkaline anion exchange membrane fuel cells (AAEMFC) are regarded as promising and important energy devices, the development of high performance anion exchange membranes are in urgent need, as well as fundamental investigation on the structure-property relationship, which are the motivation of this dissertation. Three different polymer systems are presented and focused on polymer synthesis, material morphology, and ion transport phenomena. Crosslinked membranes are promising as practical materials, however, the understanding and further improvement of its performance is hindered by the lack of an ordered morphology or well-defined chemical structure. In Chapter 2, a series of crosslinked membranes were design …

Designing Active Granular Squares, Christopher C. Olson

Masters Theses

The goal of this thesis has been to find a means of i) designing an active square particle, and ii) continuously varying its degree of activity with the objective of understanding the effects of activity on the various phases of granular matter. The motivations, results and limitations of our methods of creating active particles are discussed in this thesis. The applicability of a stochastic model based on the Langevin equation in 2D as well as implications for future experiments are also discussed.

Wavelet Packet Analysis Of Amino Acid Chain Sequences In The Proteins Of Mesophile And Thermophile Bacteria, John B. Linehan

DePaul Discoveries

In this project, proteins from mesophile and thermophile bacteria with similar functions are compared. Initially it is assumed that the differences between these two bacteria are substantial to be recognized in the amino acid sequences of their proteins. These differences would then lead to the creation of a statistical measure, which would allow the classification of a protein to its corresponding bacteria. By assigning hydrophobicity values from three well-known scales, a discrete numeric signal is produced for each protein, which is analyzed using wavelet packets. The result of this method indicates that the overall hydrophobic tendencies of these two bacteria’s …

Simulation Model Of An Automatic Commercial Ice Machine, Haithem Murgham, David Myszka, Vijay Bahel, Rajan Rajendran, Kurt Knapke, Suresh Shivashankar, Kyaw Wynn

Mechanical and Aerospace Engineering Faculty Publications

Automatic commercial ice-making machines that produce a batch of cube ice at regular intervals are known as “cubers." Such machines are commonly used in food service, food preservation, hotel, and health service industries. The machines are typically rated for the weight of ice produced over a 24-hour period at ambient air temperatures of 90°F and water inlet temperature of 70°F.

These cubers typically utilize an air-cooled, vapor-compression cycle to freeze circulating water flowing over an evaporator grid. Once a sufficient amount ice is formed, a valve switches to enable a harvest mode, where the compressor’s discharge gas is routed into …

Using Zinc Finger Proteins As A Diagnostic Tool For The Detection Of A Cancer Biomarker, Anu Kini

Masters Theses & Specialist Projects

RASSF1A is a tumor suppressor gene which loses its function due to methylation of CpG islands on its promoter region. Detection of methylation leads to early diagnosis of cancer.

Zinc finger proteins are capable of detecting a specific DNA sequence and Methyl binding domain can bind to the methyl group on the CpG, using this idea mCpG SEER- Lac system makes use of a split protein, β-lactamase. Lac A attached to the ZFP and Lac B attached to the MBD protein. On binding to the DNA, the Lac A and Lac B come in close proximity with each other causing …

Communication: Visualization And Spectroscopy Of Defects Induced By Dehydrogenation In Individual Silicon Nanocrystals, Dmitry A. Kislitsyn, Jon M. Mills, Vancho Kocevski, Sheng-Kuei Chiu, William J.I. Debenedetti, Christian F. Gervasi, Benjamen N. Taber, Ariel E. Rosenfield, Olle Eriksson, Ján Rusz, Andrea Mitchell Goforth, George V. Nazin

Chemistry Faculty Publications and Presentations

We present results of a scanning tunneling spectroscopy (STS) study of the impact of dehydrogenation on the electronic structures of hydrogen-passivated silicon nanocrystals (SiNCs) supported on the Au(111)surface. Gradual dehydrogenation is achieved by injecting high-energy electrons into individual SiNCs, which results, initially, in reduction of the electronic bandgap, and eventually produces midgap electronic states. We use theoretical calculations to show that the STS spectra of midgap states are consistent with the presence of silicon dangling bonds, which are found in different charge states. Our calculations also suggest that the observed initial reduction of the electronic bandgap is attributable to the …

An Experimental And Theoretical Study Of Ã2A"Π–X~2A' Band System Of The Jet-Cooled Hbbr/Dbbr Free Radical, Mohammed Gharaibeh, Dennis J. Clouthier, Riccardo Tarroni

Chemistry Faculty Publications

The electronic spectra of the HBBr and DBBr free radicals have been studied in depth. These species were prepared in a pulsed electric discharge jet using a precursor mixture of BBr₃ vapor and H₂ or D₂ in high pressure argon. Transitions to the electronic excited state of the jet-cooled radicals were probed with laser-induced fluorescence and the ground state energy levels were measured from the single vibronic level emission spectra. HBBr has an extensive band system in the red which involves a linear-bent transition between the two Renner-Teller components of what would be a ²Π state …

Expanded Parameters In The Self-Organized Critical Forest Fire Model, Riley Self

Senior Theses

The forest fire model has been used to test the theory of Self-Organized Criticality as a model of complexity. The goal is to search for scale invariance in randomly generated forest fires using a computer simulation. In a previous model by B. Drossel and F. Schwabl,¹ power-law behavior was seen when the nearest neighbors to a tree on fire catch on fire, and it has been assumed that if further trees also catch fire, then it will still exhibit self-organized criticality, showing scale invariance. Testing this assumption aids to the exploration of the applicability of self-organized criticality because the …

Classical Transport In Disordered Systems, Antonios Papaioannou

Dissertations, Theses, and Capstone Projects

This thesis reports on the manifestation of structural disorder on molecular transport and it consists of two parts. Part I discusses the relations between classical transport and the underlying structural complexity of the system. Both types of molecular diffusion, namely Gaussian and non-Gaussian are presented and the relevant time regimes are discussed. In addition the concept of structural universality is introduced and connected with the diffusion metrics. One of the most robust techniques for measuring molecular mean square displacements is magnetic resonance. This method requires encoding and subsequently reading out after an experimentally controlled time, a phase ϕ to the …

A Comparison Of Catabolic Pathways Induced In Primary Macrophages By Pristine Single Walled Carbon Nanotubes And Pristine Graphene, Caroline More, Jennifer Mcintyre, Luke O'Neill, Hugh Byrne

Articles

Understanding the correlation between the physico-chemical properties of carbonaceous nanomaterials and how these properties impact on cells and subcelluar mechanisms is critical to their risk assessment and safe translation into newly engineered devices. Here the toxicity, uptake and catabolic response of primary human macrophages to pristine graphene (PG) and pristine single walled carbon nanotubes (pSWCNT) are explored, compared and contrasted. The nanomaterial toxicity was assessed using three complementary techniques (live-dead assay, real time impedance technique and confocal microscopic analysis), all of which indicated no signs of acute cytotoxicity in response to PG or pSWCNT. Transmission electron microscopy (TEM) demonstrated that …

Modeling The Behavior Of The Graphene To Liquid Interfaces In An Electrolytic Liquid, Caitlin Duffner

Senior Theses

Understanding the mechanism for charge transfer between a graphene biosensor and its electrodes within an electrolyte solution is vital to better understand the sources of electrical noise in the system. By measuring the effective resistance and capacitance of the system at different frequencies, it is possible to develop a circuit model of the system's electrical behavior. This model provides a deeper understanding of the fundamental interactions that occur in a top-­gated graphene device and provides opportunities to improve a signal. To reduce noise created at the liquid to graphene interface, a buffer layer of Yttrium Oxide was applied. While the …

Effect Of Electrolyte Concentration On The Capacitance And Mobility Of Graphene, Flint A. Martino

Senior Theses

The use of graphene field-effect transistors as a biosensor is increasingly being used to study biological phenomena, due to the sensitivity and low reactivity of graphene. To further improve sensitivity in biological environments, we examined how different salt concentrations affect the mobility of capacitance of the graphene. Samples were also measured after an annealing process. We report on the positive correlation between sensitivity and electrolyte concentration and speculate on methods to improve future detectors. Mobility of the device was found to change from 1.07*10³cm²/ (V*s) in de-ionized water to 2.78*10³cm²/ (V*s) in …

Modeling A Circuit That Represents An Electrolytic Solution At Different Concentrations, Daniel C. Miller Ii

Senior Theses

Electrodes are often placed within bio samples in order to measure the electrical changes that occur within a system. In order to understand the information provided through the microelectrodes, this paper will describe an experiment to measure the capacitance and the resistance between two micro electrodes as an electrolyte becomes more concentrated. This resulted in a capacitance and a resistance that increased and decreased exponentially, respectively, as an electrolyte concentration increased logarithmically.

Protein Folding & Self-Organized Criticality, Arun Bajracharya

Senior Theses

Proteins are known to fold into tertiary structures that determine their functionality in living organisms. However, the complex dynamics of protein folding and the way they consistently fold into the same structures is unknown. Experimental studies of the folding process are difficult as proteins are made of more than one subunit and possess a high degree of conformational flexibility. Theoretically, self-organized criticality (SOC) has provided a framework for understanding complex systems in various scientific disciplines through scale invariance and the associated "fractal" power law behavior. Evidence of this criticality phenomena has been found in neural systems, cell cultures, and anesthetized …

2016-01-A3dsrinp-Csc-Sta-Cmb-522-Bps-542, Raymond Pulver, Neal Buxton, Xiaodong Wang, John Lucci, Jean Yves Hervé, Lenore Martin

Bioinformatics Software Design Projects

Cholesterol is carried and transported through bloodstream by lipoproteins. There are two types of lipoproteins: low density lipoprotein, or LDL, and high density lipoprotein, or HDL. LDL cholesterol is considered “bad” cholesterol because it can form plaque and hard deposit leading to arteries clog and make them less flexible. Heart attack or stroke will happen if the hard deposit blocks a narrowed artery. HDL cholesterol helps to remove LDL from the artery back to the liver.

Traditionally, particle counts of LDL and HDL plays an important role to understanding and prediction of heart disease risk. But recently research suggested that …

Biophysical Studies Of Cell Division Protein Localization Mechanisms In Escherichia Coli, Matthew Wayne Bailey

Doctoral Dissertations

How nanometer-scale proteins position accurately within micron-scale bacteria has intrigued both biologists and physicists alike. A critical process requiring precise protein localization is cell division. In most bacteria, cell division starts with the self-assembly of the FtsZ proteins into filaments that form a ring-like structure encircling the cell at its middle, the Z-ring. The Z-ring is a scaffold for additional proteins that synthesize the lateral cell wall which separates the two daughter cells. If division planes are misplaced relative to bacterial chromosomes, also called nucleoids, daughter cells with incomplete genetic material can be produced. In Escherichia coli, research carried out …

Strategies Of Balancing: Regulation Of Posture As A Complex Phenomenon, Allison Leich Hilbun

Electronic Theses and Dissertations

The complexity of the interface between the muscular system and the nervous system is still elusive. We investigated how the neuromuscular system functions and how it is influenced by various perturbations. Postural stability was selected as the model system, because this system provides complex output, which could indicate underlying mechanisms and feedback loops of the neuromuscular system. We hypothesized that aging, physical pain, and mental and physical perturbations affect balancing strategy, and based on these observations, we constructed a model that simulates many aspects of the neuromuscular system. Our results show that aging changes the control strategy of balancing from …