Biological and Chemical Physics Commons^™

Biosynthesis Of Mgo Nanoparticles And Their Impact On The Properties Of The Pva/Gelatin Nanocomposites For Smart Food Packaging Applications, Mohamed Morsy

Nanotechnology Research Centre

No abstract provided.

Modelling Cell Population Growth, Mahmood Mazarei

Electronic Thesis and Dissertation Repository

The growth of biological matter, e.g., tumor invasion, depends on various factors, mainly the tissue’s mechanical properties, implying elasticity, stiffness, or apparent viscosity. These properties are impacted by the characteristics of the tissue’s extracellular matrix and constituent cells, including, but not limited to, cell membrane stiffness, cell cytoskeleton mechanical properties, and the intensity and distribution of focal adhesions over the cell membrane. To compute and study the mechanical properties of tissues during growth and confluency, a theoretical and computational framework, called CellSim3D, was developed in our group based on a three-dimensional kinetic division model.

In this work, CellSim3D is …

Modeling Excited State Processes In Molecular Aggregates By Constructing An Adaptive Basis For The Hierarchy Of Pure States, Leonel Varvelo

Chemistry Theses and Dissertations

Simulating excitation energy transfer (EET) in molecular materials is of crucial importance for the development of and understanding of materials such as organic photovoltaics and photosynthetic systems and further development of novel materials. The Hierarchy of Pure States (HOPS) is an exact framework for the time evolution of an open quantum system in which a hierarchy of stochastic wave functions are propagated in time. The adaptive HOPS (adHOPS) method achieves size-invariant scaling with the number of simulated molecules for sufficiently large aggregates by using an adaptive basis that moves with the excitation through the material. To demonstrate the power of …

Long-Range And Chaotic Active Mixing Of Swimming Microbes In A Vortex Chain Flow, Nghia Le

Honors Theses

We present experiments studying the motion and active mixing of swimming mi- crobes in laminar, vortex-dominated fluid flows. We are testing a theory that predicts the existence of swimming invariant manifolds (SwIMs) - invisible, one-way barriers blocking the paths of self-propelled tracers in the flow in one direction. We also pro- pose that the SwIMs together can form chute structures in three-dimensional phase space that facilitate cross-vortex transport of the microbes. We also observe evidence of how these structures promote long-range transport at different non-dimensional velocities (microbe’s velocity relative to flow velocity). Long-range transport is quan- tified by measuring the …

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 …

Stability Of Group Four Monochalcogenides In Water And Air, William Shattuck

Graduate Theses and Dissertations

Previously published works have simulated the behavior of monolayer group IV monochalcogenides and predicted them to have very useful electronic properties. These simulations have also predicted that monolayers of group IV monochalcogenides will degrade quickly when exposed to water, even in extremely low concentrations. We hypothesize that thin samples of these materials will show signs of degradation if left in air and in water for an extended period of time.

Samples of each of the four monochalcogenides (GeS, GeSe, SnS and SnSe) were exfoliated onto clean oxidized silicon substrates. Chemical analysis showed the SnSe samples were contaminated, so they were …

Multifunctional Nanopipette For Single Nanoparticles And Proteins Analysis, Popular Pandey

FIU Electronic Theses and Dissertations

Complex biological processes occur in the nanoscale (1-100 nm) regime. ‘DNA’ which is just 2 nm in dimension is a fundamental building block of all life. ‘Hemoglobin’, a blood protein that transports oxygen throughout our body is only 5 nm in diameter. Importantly, the structure, composition, and dynamics of these nanoscale entities determine their biological function. A slight alteration in the structure and composition can lead to the malfunction of the protein which is key to various diseases including cancer. Therefore, the single-molecule measurement approach is essential to characterize both the average properties and the rare …

The Structural Information Filtered Features Potential For Machine Learning Calculations Of Energies And Forces Of Atomic Systems., Jorge Arturo Hernandez Zeledon

Graduate Theses, Dissertations, and Problem Reports

In the last ten years, machine learning potentials have been successfully applied to the study of crystals, and molecules. However, more complex materials like clusters, macro-molecules, and glasses are out reach of current methods. The input of any machine learning system is a tensor of features (the most universal type are rank 1 tensors or vectors of features), the quality of any machine learning system is directly related to how well the feature space describes the original physical system. So far, the feature engineering process for machine learning potentials can not describe complex material. The current methods are highly inefficient …

Hyperpolarization Of Silicon Nanoparticles With Tempo Radicals, Jingzhe Hu, Nicholas Whiting, Pratip Bhattacharya

Nicholas Whiting

Analyses Of Densely Crosslinked Phenolic Systems Using Low Field Nmr, Jigneshkumar Patel

Doctoral Dissertations

A uniform dispersion of reactants is necessary to achieve a complete reaction involving multi-components, especially for the crosslinking of rigid high-performance materials. In these reactions, miscibility is crucial for curing efficiency. This miscibility is typically enhanced by adding a third component, a plasticizer. For the reaction of the highly crystalline crosslinking agent hexamethylenetetramine (HMTA) with a strongly hydrogen-bonded phenol formaldehyde resin, furfural has been traditionally used as the plasticizer. However, the reason for its effectiveness is not clear. In this doctoral thesis work, miscibility and crosslinking efficiency of plasticizers in phenolic curing reactions are studied by thermal analysis and spectroscopic …

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 …

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 …

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.

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 …

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 …

Characteristic Length Scales Of The Secondary Relaxations In Glass-Forming Glycerol, Sudipta Gupta, Eugene Mamontov, Niina Jalarvo, Laura Stingaciu, Michael Ohl

Faculty Publications

We investigate the secondary relaxations and their link to the main structural relaxation in glass-forming liquids using glycerol as a model system. We analyze the incoherent neutron scattering signal dependence on the scattering momentum transfer, Q , in order to obtain the characteristic length scale for different secondary relaxations. Such a capability of neutron scattering makes it somewhat unique and highly complementary to the traditional techniques of glass physics, such as light scattering and broadband dielectric spectroscopy, which provide information on the time scale, but not the length scales, of relaxation processes. The choice of suitable neutron scattering techniques depends …

Voltage Driven Translocation Of Polyelectrolytes Through Nanopores, Byoung-Jin Jeon

Doctoral Dissertations

Recently, translocations of polyelectrolyte molecules through membrane channel protein pores or solid-state nanopores have been actively studied. Although the polymer translocation researches emerged mainly due to technological demands in terms of genome sequencing, the detailed physics of the single molecule transport through a narrow channel remains fully understood. To obtain further understanding of common features of the translocation process, this thesis focuses on the effects of salt concentration, pore-polymer electrostatic interactions, and externally applied electric field on the voltage-driven polymer translocations. The study is carried out by performing a series of systematically designed experiments using alpha-hemolysin (αHL) protein pore to …

Hydrogen Bond-Mediated Structural Order In Hydroxylated Bis-Mpa Dendritic Polymers: Experimental And Molecular Dynamics Simulation Study, Maliha N. Syed

Dissertations

Dendritic architectures are echoed throughout nature. While the significance of these pervasive patterns is not entirely clear, connections between their structures and physical properties are fascinating to contemplate. Particular interest has been paid to a family of synthetically manufactured and commercially available dendritic polymers based on 2,2-bis(hydroxymethyl) propionic acid (bis-MPA) as a monomer. Composed of two hydroxyls and a carboxyl group, bis-MPA based structures hydrogen bond (H-bond) profusely. Given the high concentration and unique spatial orientation of end-groups, as well as the multitude of carbonyl, ester, and ether interior H-bond acceptors, a set of distinct H-bond organizations may be observed …

Distributions Of Long-Lived Radioactive Nuclei Provided By Star-Forming Environments, Marco Fatuzzo, Fred Adams

Faculty Scholarship

Radioactive nuclei play an important role in planetary evolution by providing an internal heat source, which affects planetary structure and helps facilitate plate tectonics. A minimum level of nuclear activity is thought to be necessary—but not sufficient—for planets to be habitable. Extending previous work that focused on short-lived nuclei, this paper considers the delivery of long-lived radioactive nuclei to circumstellar disks in star forming regions. Although the long-lived nuclear species are always present, their abundances can be enhanced through multiple mechanisms. Most stars form in embedded cluster environments, so that disks can be enriched directly by intercepting ejecta from supernovae …

Measuring Charge Carrier Mobility In Graphene, Christina A. Harmon

Senior Theses

This research reports measurements of electron mobility in Graphene Field Effect Transistors (GFET), gated with liquid. Mobility is a quantity describing how easily charge carriers move through a material. GFET biosensors have the greatest sensitivity when the mobility is high; therefore, increasing mobility should improve sensitivity of these and similar devices. An optimal method was established for preparing samples and taking measurements of a liquid-gate device. Sheet conductivity was measured using van der Pauw geometry and carrier density was determined from measurements of the liquid-gate capacitance. It is shown that mobility improves after the graphene surface is cleaned by an …

Sucralose Destabilization Of Protein Structure, Christina M. Othon

Christina M Othon

Sucralose is a commonly employed artificial sweetener that behaves very differently than its natural disaccharide counterpart, sucrose, in terms of its interaction with biomolecules. The presence of sucralose in solution is found to destabilize the native structure of two model protein systems: the globular protein bovine serum albumin and an enzyme staphylococcal nuclease. The melting temperature of these proteins decreases as a linear function of sucralose concentration. We correlate this destabilization to the increased polarity of the molecule. The strongly polar nature is manifested as a large dielectric friction exerted on the excited-state rotational diffusion of tryptophan using time-resolved fluorescence …

Temperature Dependent C-Axis Hole Mobilities In Rubrene Single Crystals Determined By Time-Of-Flight, Russell L. Lidberg, Tom J. Pundsack, Neale O. Haugen, Lucas R. Johnstone, C. Daniel Frisbie

Physics and Astronomy Faculty Publications

Hole mobilities (μ) in rubrene single crystals (space group Cmca) along the crystallographic c-axis have been investigated as a function of temperature and applied electric field by the time-of-fight method. Measurements demonstrate an inverse power law dependence on temperature, namely,μ=μ₀T⁻ⁿ with n = 1.8, from room temperature down to 180 K. At 296 K, the average value of μ was found to be 0.29 cm²/Vs increasing to an average value of 0.70 cm²/Vs at 180 K. Below 180 K a decrease in mobility is observed with further cooling. Overall, these results confirm the …

Multimode Analysis Of Nanoscale Biomolecular Interactions, Purushottam Babu Tiwari

FIU Electronic Theses and Dissertations

Biomolecular interactions, including protein-protein, protein-DNA, and protein-ligand interactions, are of special importance in all biological systems. These interactions may occer during the loading of biomolecules to interfaces, the translocation of biomolecules through transmembrane protein pores, and the movement of biomolecules in a crowded intracellular environment. The molecular interaction of a protein with its binding partners is crucial in fundamental biological processes such as electron transfer, intracellular signal transmission and regulation, neuroprotective mechanisms, and regulation of DNA topology. In this dissertation, a customized surface plasmon resonance (SPR) has been optimized and new theoretical and label free experimental methods with related analytical …

Charged Particle Dynamics In The Magnetic Field Of A Long Straight Current-Carrying Wire, M. Fatuzzo, A. Prentice, T. Toepker

Faculty Scholarship

The article discusses the concept behind motion of a charged particle in a non-uniform filed of a wire carrying current. Topics discussed include possible types of motion in a current carrying field, vector analysis of velocity and magnetic field of the particle and Coupled differential equations.

A Molecular Simulation Study On Micelle Fragmentation And Wetting In Nano-Confined Channels, Mona Habibi

Electronic Thesis and Dissertation Repository

We performed coarse-grained molecular-dynamics (MD) simulations to study the structural and dynamical properties of surfactant micelles in equilibrium and under Poiseuille-like flow in a nano-confined geometry. We used the MARTINI force-field to model the interactions between water molecules, counter-ions, and sodium dodecyl sulfate (SDS) surfactants. SDS surfactant was chosen as the standard model because of its potential application in drug delivery systems. First, we focused on the self-assembly of SDS in equilibrium. To form stable spherical mi- celles, we ran simulations in the isothermal-isobaric ensemble (NPT) on a system of free SDS surfactants, counter-ions and water molecules. We studied the …

Wave Function For Harmonically Confined Electrons In Time-Dependent Electric And Magnetostatic Fields, Hong-Ming Zhu, Jin-Wang Chen, Xiao-Yin Pan, Viraht Sahni

Publications and Research

We derive via the interaction “representation” the many-body wave function for harmonically confined electrons in the presence of a magnetostatic field and perturbed by a spatially homogeneous time-dependent electric field—the Generalized Kohn Theorem (GKT) wave function. In the absence of the harmonic confinement – the uniform electron gas – the GKT wave function reduces to the Kohn Theorem wave function. Without the magnetostatic field, the GKTwave function is the Harmonic Potential Theorem wave function. We further prove the validity of the connection between the GKT wave function derived and the system in an accelerated frame of reference. Finally, we provide …

A Numerical Assessment Of Cosmic-Ray Energy Diffusion Through Turbulent Media, M. Fatuzzo, F. Melia

Faculty Scholarship

No abstract provided.

Effects Of Turbulence On Cosmic Ray Propagation In Protostars And Young Stars, M. Fatuzzo, F. C. Adams

Faculty Scholarship

No abstract provided.

Structure And Dynamics Of Model Systems: From Ferrofluids To Brain Membranes, Matthew A. Barrett

Matthew J. Barrett

Soft condensed matter systems are a very diverse and challenging subject to study. To understand the complex macro-properties of such systems one approach is to characterize the microscopic structure and dynamics. A powerful technique for determining micro and nanoscale properties is scattering of radiation sources. Light, electron and neutron scattering techniques provide insight into the complicated molecular structures and the processes happening on these small scales. We have used neutron and x-ray scattering techniques to determine structural and dynamical information from two different types of soft condensed matter systems. The microscopic nature of a cobalt magnetic fluid was studied using …