Physics Doctoral Work

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Biophysical Characterization of Living Cells and Membrane Receptors by Atomic Force Spectroscopy
(North Dakota State University, 2021) Alhalhooly, Lina
Cellular biomechanics and cellular communication via receptor-ligand interactions play an important role in controlling cell development and maintaining cellular functions. Atomic force spectroscopy (AFM) technique has been widely used to characterize the changes in cellular biomechanics and quantify the receptor-ligand interactions. In this dissertation, we introduce working principles of AFM-based force spectroscopy, visualize cross-communications between membrane mechanics and cellular signaling, and identify quantitative relationship between receptor-ligand binding dynamics and multivalent interactions. First, by exploiting force spectroscopy methods, we probed biomechanical kinetics (stiffness, morphology, roughness, adhesion) of the brain, breast, prostate, and pancreatic cancer cells with standard chemotherapeutic drugs in normoxia and hypoxia over 12 – 24 hours. After exposure to the drugs, we found that brain, breast, and pancreatic cancer cells became approximately 20 – 50% less stiff, while prostate cancer cells became more stiff, due to either drug-induced disruption or reinforcement of cytoskeletal structure. However, the rate of the stiffness change decreased up to 2-folds in hypoxia, suggesting a correlation between cellular stiffness and drug resistance of cancer cells in hypoxic tumor microenvironment. Our results show that a degree of chemotherapeutic drug effects on biomechanical and biophysical properties of cancer cells is distinguishable in normoxia and hypoxia, which are correlated with alteration of cytoskeletal structure and integrity during a drug-induced apoptotic process. Second, we probed the binding strength of ligand-receptor interactions on live pancreatic cancer cells using single-molecule force spectroscopy methods, in which the peptides (cyclic arginine-glycine-aspartic acid: cRGD) was functionalized on a force probe tip through the polyethylene glycol-based bifunctional linker molecules. Although the density of integrin heterodimer receptors on the cell surface of each cell differs from cell to cell, the individual cRGD-integrin complexes exhibited a cell type-independent, monovalent bond strength. The load-dependent, bond strength of multivalent cRGD-integrin interactions scaled sublinearly with increasing bond number, consistent with the noncooperative, parallel bond model. Comparison of energy landscapes of the bond number revealed a substantial decrease of kinetic off rates for multivalent bonds, along with the widened width of the potential well and the increased potential barrier height between bound and unbound state, enhancing the stability of multivalent bonds between them.
Buckling Instabilities of Nanoscale Polymer Films and Colloidal Particle Layers
(North Dakota State University, 2015) Gurmessa, Bekele Jemama
Nanoscale polymer films have numerous potential applications such as protective coatings, flexible electronics, energy harvesting devices, and drug delivery systems. For realization of these potential applications, the mechanical properties of these materials and the underlying physics need to be understood. This dissertation focuses on understanding the responses of nanoscale films to mechanical deformations. In this regard, an elastic instability was exploited to locally bend and impart a local tensile stress in a nanoscale polystyrene film, and directly measure the resulting residual stress caused by the bending. Our results indicate that the onset of permanent deformation for thin polystyrene films is an order of magnitude smaller than what has been reported for the bulk value. In addition, not only is the onset of failure strain found to be small but also it increases with increased confinement. Using similar processing techniques, the yield strain of a more complex material - poly(styrene-b-divinylpyridine) - was studied. Similar to the polystyrene films, failure in polystyrene-b-poly(2-vinylpyridine) is also initiated at extremely low strain and is influenced by thin film confinement effects. In addition, we have demonstrated that internal nanostructure of self-assembled polystyreneb- poly(2-vinylpyridine) affects the onset of failure strain. Having introduced an idealized heterogeneity to a sample through ultraviolet/ozone treatment, we have created samples ranging from continuous thin films to sets of isolated plates. We demonstrated that, when subjected to mechanical deformation, the unbounded plates form isotropic undulations that persist even beyond high strain. In contrast, isolated plates undergo non-isotropic undulations in the range of high strains. The non-isotropic undulation shape has been described through a simple numerical modeling subjected to controlled boundary conditions. The agreement between experiment and numerical modeling is remarkable. Finally, through an integrated experimental methods and theoretical modeling, the response of discrete colloidal layers to mechanical deformations have been exploited. The buckling profiles measured experimentally demonstrate a great insight that the continuum model may not be able to predict the response of discrete systems. Theoretically, a granular model was constructed and structural stability analysis was investigated to predict the experimental observations. The overall agreement of the experiment and the modeling was good.
Electrostatic Interactions at Dielectric Interfaces: From Colloids to Membranes
(North Dakota State University, 2017) Volpe Bossa, Guilherme
In this thesis we have investigated electrostatic interactions at dielectric interfaces using theoretical models based on the non-linear Poisson-Boltzmann theory and its extensions. We have focused on three major topics: (1) modeling the energetics and interactions of charged nanoparticles trapped at the air-water interface; (2) calculation of the line tension between domains in charged lipid membranes, lipid-lipid correlations, and how membrane curvature is influenced by charged peptides; and (3) extensions of the classical Poisson-Boltzmann theory by accounting for the influence of ion-specific solvent-mediated interactions. More precisely, ion-specificity has been accounted for using the Poisson-Helmholtz-Boltzmann formalism, which adds to the bare Coulombic interactions a Yukawa-like potential that accounts for the interacting hydration shells of ions. Motivated by recent experimental and computational results, all projects present here aim to provide a deeper understanding of fundamental physical properties of charged dielectric interfaces.
Fluctuations in the Lattice Boltzmann Method
(North Dakota State University, 2012) Kaehler, Goetz August
The implementation of fluctuations in the lattice Boltzmann method has made significant progress in the last 10 years. The significance of incorporating noise to all non-conserved degrees of freedom was a significant recent discovery that was based on a simplified Langevin treatment of the linarized Boltzmann equation. However, for non-vanishing mean velocities significant deviations in the correlation functions were observed. In this thesis we show how we can largely alleviate these deviations by incorporating fully velocity dependent moment transforms and thus recover a fluctuation dissipation theorem that is valid for a larger range of velocities. Furthermore we show that the remaining deviations can be attributed to the collision operator of the linearized Boltzmann equation not being identical to the one of the BGK collision which forms the basis of most modern lattice Boltzmann applications. Finally we show that the locally velocity dependent transforms significantly improve the stability of fluctuating lattice Boltzmann simulations at low particle densities.
Fundamental Studies of Interfacial Forces Acting on Thin Films
(North Dakota State University, 2021) Twohig, Timothy John
A thin film is a material that is many orders of magnitude thinner than it is long or wide. They are commonly found in many forms and have been adapted to a wide variety of uses. The art of origami uses thin films(sheets of paper) and precise folding to create complex, three-dimensional shapes out of flat, quasi two-dimensional sheets, and has emerged as a unique way to solve problems in engineering and science. As technology and devices are scaled to smaller sizes new understanding of origami methods are required to work at these small scales. The interactions between thin films and liquids, substrates that films exist on, and other thin films is the focus of this dissertation. Capillary interactions are used to manipulate and fold thin films that are too thin to be actuated with hands or everyday tools. The relation between the macroscopic and the microscopic interactions at the point where the capillary liquid and the film meet is explored. We show how films can be manipulated by capillary drops and how exactly the force is applied to the film. The adhesive interactions of the film were studied as a method of precisely placing folds for elastic film origami. The capillary peel of a film from a substrate drove folds to desired locations. Adhesion of a film to itself was used to lock these bends in place in lieu of the permanent creases commonly used in plastic systems such as paper. The combination of these two methods enabled the creation of stable, multi-step origami systems from reusable elastic films. This research culminates in the discussion of fundamentally new origami-like designs that rely only on adhesion of the film to itself, which we call kuttsukugami (sticky+paper from Japanese). This new form allows for the creation of shapes that are nearly impossible to create with traditional origami methods such as loops, tubes, and cones. Advances made in capillary and adhesive thin film studies allow for kuttsukugami shapes to be scaled down to microscopic sizes for a huge array of applications including drug delivery, thin electronics, encapsulation, and more.
Lattice Gas and Lattice Boltzmann Methods for Fluctuating Systems, Barrier Coatings, and Overrelaxation
(North Dakota State University, 2022) Strand, Kyle
In the field of computational fluid dynamics, lattice gas and lattice Boltzmann methods are powerful simulation methods derived from kinetic theory. These methods are renowned for their simplicity of implementation and computational speed. In recent years, lattice Boltzmann has risen in popularity for modeling hydrodynamic flows, diffusion, and more. However, a limitation of these methods is the lack of fluctuations due to the continuous nature of the model. Fluctuations arise from the discreteness found in nature, so including fluctuations presents difficulties. This dissertation explores new and novel ways of improving lattice Boltzmann and lattice gas methods. First, we present a new derivation for a fluctuating lattice Boltzmann method in a diffusive system. Fluctuations are absent lattice Boltzmann since they were derived as a Boltzmann average of discrete lattice gases. This lattice Boltzmann method is exact and includes density dependent noise which models fluctuations to high accuracy. Second, we extend diffusive lattice Boltzmann methods to apply to physical systems for diffusion through barrier coatings. We found that these models were able to reproduce the behavior from previous experiments and provided a simple tool for analyzing such systems. Higher order corrections to lattice Boltzmann methods are explored for extending the range for successful lattice Boltzmann implementations. Recently, the implementation of an integer lattice gas with a Monte Carlo collision operator by Blommel et al. provided a template for incorporating fluctuations through the discrete nature of lattice gases. A sampling collision operator for integer lattice gases by Seekins et al. was able to reproduce the fluctuating diffusion equation in the Boltzmann limit similar to the diffusive fluctuating lattice Boltzmann. However, lattice gases have a more limited range of transport coefficients than lattice Boltzmann methods, since lattice Boltzmann collisions are deterministic and allow for the implementation of over-relaxation and lattice gas collisions are probabilistic and overrelaxation in a lattice gas requires a probability greater than 1. The final section of this dissertation presents a simple method for including overrelaxation into an integer lattice gas using the sampling collision operator. It will be shown that this is possible through a permutation of occupation numbers.
Multi-Scale Simulation Methods of Crosslinked Polymer Networks and Degradation
(North Dakota State University, 2018) Feickert, Aaron James
Crosslinked thermoset polymers are used heavily in industrial and consumer products, as well as in infrastructure. When used as a protective coating, a thermoset's net-like structure can act as a barrier to protect an underlying substrate from permeation of moisture, salt, or other chemicals that otherwise weaken the coating or lead to substrate corrosion. Understanding how such coatings degrade, both at microscopic and macroscopic scales, is essential for the development and testing of materials for optimal service life. Several numerical and computational techniques are used to analyze the behavior of model crosslinked polymer networks under changing conditions at a succession of scales. Molecular dynamics is used to show the effects of cooling and constraints on cavitation behavior in coarse-grained bulk thermosets, as well as to investigate dynamical behavior under varying degradation conditions. Finite-element analysis is applied to examine strain distributions and loci of failure in several macroscopic coated test panel designs, discussing the effects of flexure and coating stack moduli. Finally, the transport of moisture through model coatings under cycled conditions is examined by lattice Boltzmann numerical techniques, considering several common concentration-dependent diffusivity models used in the literature and suggesting an optimal behavior regime for non-constant diffusivity.
The Nature of Single-Wall Carbon Nanotube-Silicon Heterojunction Solar Cells
(North Dakota State University, 2015) Harris, John Michael
Since their inception in 2007, nanotube-silicon heterojunction solar cells have experienced rapid improvement due to the diligent work of several research groups. These devices have quickly reached a point where they might begin to possibly compete with current well-established silicon solar technologies; however the development of industrial-scale nanotube synthesis and purification capabilities remains problematic. Although there has been significant recent progress in improving performance, the precise classification of nanotube-silicon heterojunctions has remained ambiguous. In this thesis, I use type, chirality and length purified single-wall carbon nanotubes to clarify the nature of this particular class of solar cell. The junctions that I assembled were made from freestanding nanotube sheets that showed remarkable stability in response to repeated crumpling and folding during fluid processing, which suggests that the films could be well suited to flexible device platforms. Despite modest ideality factors, the best diodes created in this study met or exceeded state-of-the-art device characteristics, but with a surprising lack of any significant dependence on sample type. The data further suggest that these devices might be simultaneously categorized as either Schottky or p-n junctions. More importantly, the results of this study demonstrate the manner in which band-gap engineering can optimize these devices while emphasizing the important role of the junction morphology.
A Numerical and Analytical Analysis of the Physics of Phase-Separation Fronts
(North Dakota State University, 2012) Foard, Eric Merlin
My dissertation is an investigation into the basic Physics of phase separation fronts. Such phase-separation fronts occur in many practical applications, like the formation of immersion precipitation membranes, Temperature induced phase-separation of polymeric blends, or the formation of steel. Despite the fact that these phenomena are ubiquitous no generally acceptable theory of phase-separation front exists. I believe the reason lies in the complexity of many of these material systems where a large number of physical effects (like phase-separation, crystallization, hydrodynamics, etc) cooperate to generate these structures. As a Physicist, I was driven to develop an understanding of these systems, and we choose to start our investigation with the simplest system that would incorporate a phase-separation front. So we initially limited our study to systems with a purely diffusive dynamics. The phase-separation front is induced by a control-parameter front that is a simple step function advancing with a prescribed velocity. We investigated these systems numerically using a lattice Boltzmann method and also investigated them analytically as much as possible. Starting from a one-dimensional front moving with a constant velocity we then extended the complexity of the systems by increasing the number of dimensions, examining a variable front velocity, and finally by including hydrodynamics.
Properties of Reinfoced Carbon Nanotube and Laser-Crystallized Silicon Films
(North Dakota State University, 2016) Semler, Matthew Roy
Flexible electronics are anticipated to be one of the next technological advancements of electronic devices. The enhanced durability, light-weight nature, and conformity of flexible electronics are desired properties in a variety of fields and are anticipated to reduce production costs. Two promising materials for use in flexible electronics are carbon nanotube (CNT) films and laser-crystallized thin silicon films. CNTs are in their infancy in respect to their presence in electronic devices; however their superb mechanical and electronic properties make them ideal candidates for flexible electronics. Thin silicon films are a natural transition from bulk silicon as bulk silicon has been the preferred material in electronics since the dawn of the transistor. Thin-film silicon retains the well-studied electronic properties of bulk silicon; however, it becomes flexible as it is thinned. Obstacles to the application of both these materials in flexible electronics nonetheless exist. Compressed CNT films undergo strain softening – a mechanism in which the CNT film restructures itself in response to an applied strain, which reduces the Young’s modulus and electronic conductivity. In this dissertation, thin CNT films are capped with a thin polymer layer, with the aim to mitigate strain softening through excluded volume interactions in a bilayer format that serves as a paradigm for more sophisticated device relevant settings. More specifically, metallic and semiconducting CNT films of different thicknesses are capped with a polystyrene film of comparable thickness, and the mechanical and electronic strain response of the capped CNT film is examined and discussed. Ultrathin silicon films cannot be grown as monocrystalline silicon, so amorphous silicon films must be deposited and crystallized. Laser crystallization is an alternative to oven annealing and has a faster throughput. In this dissertation, amorphous silicon films of various thicknesses were deposited on several substrates via plasma enhanced chemical vapor deposition. The films were crystallized with a pulsed Nd:YVO4 laser operating at the third harmonic of 355 nm, and the structural and electronic properties were characterized to determine the effects of film thickness and substrate composition.
Single-Molecule Studies of Intermolecular Kinetics Using Nano-Electronics Circuits
(North Dakota State University, 2020) Froberg, James Steven
As science and medicine advance, it becomes ever more important to be able to control and analyze smaller and smaller bioparticles all the way down to single molecules. In this dissertation several studies aimed at improving our ability to manipulate and monitor single biomolecules will be discussed. First, we will discuss a study on developing a way to map dielectrophoresis with nanoscale resolution using a novel atomic force microscopy technique. Dielectrophoresis can be applied on nanoparticles through micron-scale electrodes to separate and control said particles. Therefore, this new method of mapping this force will greatly improve our ability to manipulate single biomolecules through dielectrophoresis. The next two studies discussed will be aimed at using carbon nanotube nanocircuits to monitor single protein kinetics in real time. Drug development and delivery methods rely on the precise understanding of protein interactions, thus creating the need for information on single protein dynamics that our techniques provides. The proteins studied in these sections are MMP1 and HDAC8, both of which are known targets of anti-cancer drugs. Finally, we developed a new strategy for diagnosing pancreatic cancer. Our strategy involves using graphene nanotransistors to detect exosomes released from the pancreatic tumor. The ability to reliably diagnose pancreatic cancer before it reaches metastasis would greatly improve the life expectancy of patients who develop this condition. We were able to test our technique on samples from a number of patients and were successfully able to distinguish patients with pancreatic cancer from noncancerous patients.
Thermodynamic and Kinetic Modeling of Mixed Lipid Membranes and their Interaction with Macromolecules
(North Dakota State University, 2015) Loew, Stephan
Mixed lipid membranes play a crucial role in numerous cellular processes and pharmaceutical applications. Fully understanding the interactions between membranes and biomacromolecules is not possible without gaining insight into underlying physical concepts. In this thesis we develop theoretical models that aim to rationalize a number of experimental findings, all involving lipid layers and their interaction with macromolecules. Our models are phenomenological and employ a minimal set of order parameters, thus focusing on essential physical interactions. We address four major subjects: First, certain mixed model membranes containing cholesterol are able to undergo macroscopic phase separation. Based on a previously suggested thermodynamic model we demonstrate that peripherally adsorbed membrane proteins tend to further facilitate phase separation, especially when they exhibit attractive interactions. Second, we show that the coupling between the two leaflets of a mixed lipid bilayer can influence its phase behavior. To this end, we calculate detailed phase diagrams and argue that their predictions are in principal agreement with experimental observations. Specifically, the coupling can trigger or inhibit phase separation, depending on lipid compositions in each leaflet and coupling strength. Third, we investigate the fundamental question if physiological pH-changes are sufficient -- and can this be employed by cellular processes -- to trigger the adsorption of peripheral proteins. Proposing a model for the previously suggested electrostatic-hydrogen bond switch mechanism, we show that protein adsorption based on electrostatic interactions alone has a weak pH dependence but is rendered pH sensitive by the electrostatic-hydrogen bond switch. Finally, the transfer of hydrophobic drug molecules in model systems from donor liposomes to a target carrier is known from experimental work to typically exhibit a first-order kinetics, sometimes also sigmoidal behavior. We develop a detailed kinetic model for drug transfer that is based on a statistical description of drug occupation numbers in liposomes and includes both drug diffusion and liposome collision mechanisms.
The Thiol-ene Encapsulation and Photo-physical Characterization of Colloidal Silicon Nanocrystals Synthesized with Si6H12 Using Non-thermal Plasma Reactor
(North Dakota State University, 2021) Sefannaser, Mahmud Ayad
Silicon nanocrystals (SiNCs) are nanometer-sized semiconducting materials. Their small size endows them with unique photophysical properties. Efficient photoluminescence (PL) from silicon nanocrystal (SiNC) composites has important implications for emerging solar-energy collection technologies, yet a detailed understanding of PL relaxation in non-colloidal SiNCs is still materializing. In this dissertation, we examine the photophysical properties of silicon nanocrystal/off-stoichiometry thiol-ene composites (SiNCs/OSTE hybrids). The dissertation begins with an introduction to the photophysical properties of SiNCs, their photophysical properties, how SiNC/polymer composites are made, the various SiNC preparation techniques, and the most likely application areas for these nanocrystals. A description of experimental methods such as PL spectroscopy and transmission electron microscopy (TEM) follows, and SiNC/OSTE polymer preparation methods are then explained in detail. In the first study, TEM and photophysical characterization were performed on selected polydisperse SiNCs samples. These samples were synthesized in a nonthermal plasma reactor, using Si6H12 as precursor, and functionalized with R (where R is 1-dodecene). These SiNCs were dispersed in mesitylene:1-dodecene (5:1) as a colloid. Optical absorption, quantum efficiency, and PL lifetime of SiNCs were then investigated, as well as the relationship between quantum yield, lifetime, and PL peak. In the second study, we selected samples for size separation via the density gradient ultracentrifugation method (DGU). We successfully applied this technique to separate silicon nanocrystals with sizes from 2 nm to 4 nm from the ensemble samples using an engineered density medium layer stack, and photophysical characterization was performed on the DGU size–separated SiNCs. Lastly, we explored details of PL relaxation in photo-polymerized off-stoichiometric polymer/nanocrystal hybrids. We found time- and air-stable emission from dilute composites with up to 70% QY, and we investigated PL relaxation in the parameter space of nanocrystal size and temperature. In light of previous work, our results reveal similarities between the impacts of crosslinking and cooling to cryogenic temperature, but of which are characterized by a relative reduction in the available of phonons.

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