Polyurethane (PU) is an important commodity polymer with a broad range of applications. Increasing regulations on isocyanates have prompted investigations into alternative routes to PU. Cyclic carbonate aminolysis leading to polyhydroxyurethane (PHU) is a promising alternative. This dissertation describes the first fundamental investigation of the synthesis and properties of segmented,...
Advancements in nanotechnology have led to the production of devices with components with sub-100 nm size scales. Studies have investigated how properties of polymers change when confined to nanoscale dimensions. However, stiffness-confinement studies have reported increases, decreases, and invariance with confinement for different polymer/substrate pairs, making it difficult to obtain...
The genetic code, a set of rules by which mRNA codons are translated into the twenty standard amino acids used in protein synthesis, was once thought to be immutable. As we expanded our understanding of molecular biology more variations in this genetic code have been found across the animal kingdom....
Free radical polymerization has a wide range of applications and continues to attract research interest as the demand for tailored specialty polymers grows. Sequence distribution, tacticity and composition of copolymers play a key role in understanding the reaction kinetics and the properties of the polymers 1. One of the chief...
Contagion processes arise broadly in the social and biological sciences, manifested as, for example the spread of infectious and the diffusion of innovations. Depending on the network structure, the transmission dynamics can have different. However, when the structure is too complex (e.g. multipartite networks), understanding the properties of the network...
Phase separation in segmented polymers provides distinct challenges in regard to their chemical reaction kinetics and characterization. Well studied, it has been shown that structure, phase separation and non-covalent interactions are key factors in the design of elastomeric polyurethanes. Specifically, this dissertation is focused on two areas: the synthesis of...
Autoxidation is a primary route by which lubricants in working conditions undergo degradation. Degraded lubricants, if not replaced periodically, contribute to increased wear and product failure. Experimental studies of lubricant degradation have yielded useful results but have left important questions unanswered. While many computational studies of degradation have been carried...
The use of processes based on microorganisms to produce fuels, monomers, and pharmaceuticals from renewable feedstocks is increasing today due to their environmental and economic advantages over petrochemical-based processes. In order to unlock the full potential of microorganisms to produce a sustainable industry centered on biosynthesis, an improved understanding of...
Modeling and simulation at different scales were used to study mass transport, residence times and selective oxidation in nanostructured membranes. First, analytical equations of the possible mass transport mechanisms inside the pores were used to determine that diffusion dominates over convection under the conditions of interest for selective oxidation: 700...
Spontaneous regeneration in the adult mammalian central nervous system is rare, minimal, and generally does not lead to substantial functional recovery. Tissue engineering strategies to promote nerve regeneration aim to provide an environment that is physically and chemically engineered to enhance tissue formation. Strategic design of this environment is crucial...
The study of granular matter is both scientifically intriguing and industrially important, yet it presents several unique characteristics and challenges. The discrete nature of granular materials often precludes the use of the continuum descriptions that are so commonly used for fluids, so alternative methods must be developed. Particles interact via...
The emergence of antimicrobial resistance and the growing concern to produce new drugs have influenced an increase in the amount of research directed towards the engineering of novel polyketides. The polyketide carbon backbone is synthesized by a set of enzymes known as polyketide synthases (PKSs). These catalyze the formation of...
Nature often uses reaction-diffusion(RD) as a means of making structures and materials of unique properties or morphologies on scales from macro- (e.g., stripes in zebras, tigers, and seashells, and formations in trees, agates, and rocks) to microscopic (e.g., cellular growth, chemotaxis and biological waves). However, reaction-diffusion phenomena have not yet...
Structural dynamics in three polymer blend systems, differing largely with respect to morphology, have been investigated. The first system, composed of two immiscible homopolymers, exhibits a microstructure of micron-sized droplets dispersed in a matrix phase. We have examined small-angle x-ray scattering (SAXS) as a new approach for conducting in situ...
Little is known about the transcriptional events underlying megakaryocytic (Mk) differentiation from hematopoietic stem cells. We sought to identify genes and pathways not previously associated with megakaryopoiesis and to evaluate the CHRF-288-11 (CHRF) megakaryoblastic cell line as a model system for investigating megakaryopoiesis.
Using DNA microarrays, Q-RT-PCR, and protein-level assays,...
Megakaryocytic cells (Mks) are derived from hematopoietic stem cells (HSCs) and give rise to platelets. Ex vivo culture of HSCs under conditions that promote Mk differentiation has been proposed as a method for producing Mks and platelets for cell therapies. Mk maturation involves the development of polyploid cells via endomitosis,...
The physics of granular materials is one of the big questions in science. Granular materials serve as a prototype of collective systems far from equilibrium and fundamental questions remain. At the same time, an understanding of granular materials has tremendous practical importance. Among practical problems, granular mixing and its interplay...
The hematopoietic stem cell (HSC) niche is the site where HSCs reside in vivo. The HSC niche is formed by supporting cells that provide structure and appropriate environmental cues for HSCs. In this study, three components of the HSC niche were evaluated for their influence on HSC expansion ex vivo:...
Using a novel DNA-microarray hybridization protocol, the diffusion distance during static microarray hybridization was estimated for Cy3- and Cy5-labeled cDNA probes as 3.8 and 2.6 mm, respectively, despite having almost identical molecular masses. Continuous mixing during microarray hybridization resulted in a 15-20% increase in signal intensity over arrays hybridized statically....
Two subjects are the focus of this dissertation: Au/TiO2 catalyst used for oxidation of CO at low temperature and siloxane nanocages, a novel material (~2nm) recently developed in our group
While bulk gold is chemically inert, gold supported as nanoparticles is remarkably active for the oxidation of carbon monoxide at...
The task of designing porous materials for use in specific applications requires a detailed understanding of the adsorption process and how adsorption is affected by material properties. Applications of interest include maximizing gravimetric or volumetric adsorption capacity for hydrogen and carbon dioxide and increasing the selectivity for carbon dioxide in...
The recent tightening of permissible NOx release from diesel-powered engines has intensified the search for a catalytic system that can effectively remove NOx under challenging diesel exhaust conditions. Hydrogen-assisted selective catalytic reduction (H2-SCR) using supported palladium catalysts offers significant promise for lean NOx treatment due to its high activity at...
The prediction of multicomponent adsorption equilibria from pure component data alone has been an active research area for over forty years. The Ideal Adsorbed Solution theory (IAS) has been the standard method of doing so, but contains an embedded assumption of Langmuir mixing. This assumption causes its predictions to be...
Granular matter and living cells represent two extremes of what have come to be regarded as complex systems - systems characterized by a richness in global behavior that is not easily deduced from the interactions of their individual parts, even when those interactions are simple and well understood. On the...
Time-resolved in situ synchrotron x-ray scattering studies of particle orientation in polymer-clay nanocomposites under simple shear and complex flow were performed. Shear flow experiments used an annular cone and plate x-ray shear cell to allow measurement of platelet orientation within the flow-gradient plane.
Intercalated nanocomposites were made by dispersing organically...
Separation of DNA molecules by electrophoresis through entangled polymer solutions continues to be an important tool for genetic analysis, especially Sanger-based DNA sequencing. Separations of DNA on microfluidic devices are much more efficient than in capillary electrophoresis (CE) systems, such that the implementation of DNA sequencing onto microchips promises to...
The proper distribution of cellular organelles and protein complexes is important for maintaining cellular organization and function. Transport in eukaryotic cells requires three motor proteins, kinesin, dynein, and myosin, attached to specific cargoes mostly by adaptor proteins. This work focuses on the mechanism of microtubule-dependent organelle transport in vivo.
This...
The automobile coating industry is undergoing reformation driven by environmental regulations that demand low content of volatile organic compounds. Traditional solvent-borne acrylic resins
consisting of high molecular weight polymers that are produced at low temperatures (< 80 C) need high levels of organic solvent (70%) to be processed as coatings....
The average and local glass transition temperatures (Tgs) and physical aging behavior of various confined polymers were studied in order to gain an understanding of these surface/interface effects and their propagation into the polymer. Using a novel multilayer/fluorescence method, the Tgs of layers at the free surface, substrate-polymer interface, and...
The world's aquatic food webs are currently in crisis due to the cumulative, interacting effects of anthropogenic pressures including non-indigenous species invasions, chemical contamination, overfishing, habitat disruption and global climate change. Efforts to restore or protect the integrity and sustainability of these systems are limited by a lack of knowledge...
Natural tissues can have complex architectures characterized by the organization of multiple cells into structures, such as branching networks of the vascular or nervous systems. This cellular organization arises, in part, from spatial patterns in the expression of soluble factors, which create concentration gradients that direct cellular processes during morphogenesis....
Over the past decade and a half, there has been considerable interest in the effect confinement and interfaces have on the properties of glass forming materials. With the emergence of nanotechnology, some glass formers, in particular polymeric glass formers, will be used at increasingly smaller length scales. An understanding of...
The growing worldwide threat of antibiotic-resistant pathogens has necessitated a constant search for new classes of antibiotics. Antimicrobial peptides (AMPs) are integral components of innate immunity in virtually every living organism, and, due to their proven efficacy over millions of years of evolution, are considered promising leads for new antibiotic...
The de novo design of bio-inspired materials with precisely controlled properties is challenging, but has potential applications in nano-biotechnology. Applications range from nanometer scaled assemblies to three-dimensional scaffolds for tissue engineering. Genetic engineering of protein-based polymers offers distinct advantages over traditionally synthesized polymers, de novo proteins can be produced with...
Cells are regulated by a combination of soluble stimuli and adhesive interactions with other cells and the extracellular matrix (ECM). We are developing systems to present ECM and cytokine receptor ligands in a defined manner for applications in hematopoietic stem and progenitor cell (HSPC) culture. We hypothesize that the controlled,...
End-Labeled Free-Solution Electrophoresis, or ELFSE, is an alternative strategy for DNA sequencing that proposes to eliminate the need for a viscous sieving matrix for size-based DNA separation. In this bioconjugate method, a perturbing entity or "drag-tag" is attached to differently sized DNA fragments produced by the Sanger reaction. This drag-tag...
Resource recovery is a promising category of polymer recycling where polymeric waste is converted via thermal or chemical means to monomer and chemical feedstocks. Specifically, pyrolysis is an attractive method because of its simplicity and ability to handle a heterogeneous feedstock. Polymer pyrolysis is characterized by a complex free radical...
Tissue engineering offers a promising approach for the replacement of diseased or injured tissues, and is based upon the premise that cells can be induced to form new tissues when presented with the appropriate set of environmental cues. Polymer scaffolds play a central role in most tissue engineering strategies by...
The genetic information in DNA is transcribed to mRNA and then translated to proteins, which form the building blocks of life. Translation, or protein synthesis, is hence a central cellular process. Decades of experimentation have elucidated a vast wealth of molecular information about discrete translation steps, but the sheer complexity...
Improving cancer treatments are saving the lives of many young women, however these treatments often lead to premature infertility. The in vitro development of ovarian follicles would provide reproductive options to these women by supporting immature follicle growth following ovarian tissue cryobanking. In addition, the system provides a platform to...
T-cell activation is an essential step of the immune response, yet the cellular and molecular events underlying this complex process are not fully understood. Significantly, a comparative genome-scale transcriptional analysis of two T-cell subsets and the natural-mixed CD3+ population remains unexplored. Using microarrays, we investigated the temporal global transcriptional profile...
Nature has been evolving innovative solutions to complex design challenges for billions of years, the success of which is evidenced by the myriad of life-sustaining systems that operate with unparalleled simplicity, efficiency, and durability. Biomimetic researchers derive inspiration from principles underlying natural phenomena to solve design challenges. This work is...
Granular materials exhibit a wide variety of fascinating physical properties that can be observed both in nature and industry. The goal of this work is to better understand the flow, mixing, and segregation of granular materials in a prototypical system, the rotating tumbler, using numerical modeling, specifically, the Discrete Element...
To increase the butanol titers and selectivity in <em>Clostridium acetobutylicum</em> we replaced the promoter of the alcohol/aldehyde dehydrogenase (<em>aad</em>) gene with the phosphotranbutyrylase (<em>ptb</em>) promoter and combined this with CoAT downregulation to minimize acetone production. This led to early production of high alcohol (butanol plus ethanol) titers and overall solvent...
The adoption of surfactant replacement therapy (SRT) for the treatment of neonatal respiratory distress syndrome (nRDS) is one of the main contributors to the dramatic decline in infant mortality rates observed in the 1980s. Despite the significant efficacy of animal-derived surfactant preparations, there are still some concerns associated with their...
Growing concerns associated with global warming and the depletion of oil reserves have motivated significant research in support of sustainable polymers systems. In this thesis, biobased and biodegradable polymer blends and nanocomposites were created using a novel processing method, solid-state shear pulverization (SSSP). This process utilizes a modified twin-screw extruder...
Granular solids consisting of various particle sizes exhibit the tendency to de-mix, or segregate, when caused to shear by external forces such as gravity. This well-known phenomenon is of special practical interest to many industries involved in the handling and transportation of bulk solids, where segregation can lead to adverse...
The Escherichia coli ribosome is a 2.4 MDa molecular machine that consists of a large subunit and a small subunit, and is the key catalyst in gene expression, responsible for synthesizing proteins from amino acids in a sequence-defined fashion with impressive speed and accuracy. Expanding the repertoire of ribosome substrates...
There is a need for alternative biomanufacturing solutions to produce novel medicines and help solve long-standing issues regarding difficult-to-treat diseases. Cell-free protein synthesis (CFPS) provides scientists with a new paradigm for producing proteins with an unprecedented freedom and control over the biomolecular machinery involved. In this document, I describe my...
Individuals commonly engage in collaborative behavior to more easily produce works of high societal impact. The effect of many individual characteristics such as age or gender on the effectiveness of a team is still unclear. Gender is especially pertinent because many professional settings are still far from gender parity, despite...
Graphene and graphene oxide (GO), a highly oxidized form of graphene, are materials with incredibly interesting chemical and mechanical properties. These materials have high surface areas and electrical properties that can be tuned by reducing the amount of oxygenates on the surface. They have already demonstrated their importance in the...
Supported metal oxides are an important class of catalysts for chemical synthesis and manufacturing, particularly for selective oxidation reactions. This dissertation seeks to understand broad relationships among families of silica-supported Group 4 and 5 metal oxide catalysts for the synthesis of epoxides with hydrogen peroxide (H2O2) and to further extend...
MoS2 is a ubiquitous catalyst for hydrogenation and hydrogenolysis reactions for hydrotreating of petroleum sources for the removal of sulfur and nitrogen containing compounds. Through exploration of this activity, structural models for MoS2 as a series of stacked S-Mo-S platelets held together by Van der Waals forces has been developed....
Lewis acids are an important class of catalysts for chemical synthesis and manufacturing. Tris-(pentafluorophenyl)borane (FAB) catalyst has been discovered as an excellent Lewis acid catalyst for a great variety of reactions in organic and organometallic chemistry, particularly for alkoxylation reactions which is relevant to the industrial production of polyether alcohols....
Metabolic engineering of microorganisms to produce useful compounds from renewable substrates is a promising means for sustainable, on-demand production of chemicals. However, efforts to design and engineer microbial cell factories are constrained by costly and slow “build” times in which each genetic variation requires re-engineering a new strain for each...
The rational and deliberate assembly of functional materials from nanoscale building blocks requires a fundamental understanding of interactions between individual components as well as their collective behavior. This thesis investigates the hierarchical organization of nanoparticles using DNA into well-defined three-dimensional materials on the micrometer and millimeter length scales. This assembly...
Computational models greatly benefit metabolic engineering efforts by helping to elucidate experimental observations and predict engineering targets for improved cellular performance. Additionally, supplementing experimental efforts with computational modeling can reduce the loss of time and resources in the lab by narrowing down testing conditions. In optimal cases, computational models can...
The ability to efficiently sense and respond to molecular signals is crucial for any organism's survival. Sensitive, specific and timely, microbial sensing systems provide an excellent starting point for the engineering of single-celled organisms to detect new molecules of human interest. Towards this goal, our lab pursues the engineering of...
Mixed oxides including SiO2', 'and supported oxides on SiO2', 'comprise the majority of', 'heterogeneous catalysts employed in the chemical industry. SiO2', '-Al2O3', 'and microporous,', 'crystalline variants called zeolites have been used widely since the 1960s in petroleum', 'processing, commodity chemical production, and fine chemical synthesis [1]. SiO2', 'supported', 'TiOx catalysts...
The use of biomass as a feedstock for fuels and chemicals has been a long-standing challenge and opportunity for the chemical and basic materials industries. In order to unlock the value of biomass, it is necessary to first deconstruct its structural polymers, cellulose, hemicellulose, and lignin, into low molecular weight...
Pressure swing adsorption (PSA) is a promising technology for carbon capture and sequestration (CCS). However, while there has been much interest in PSA process development, the choice of adsorbent for the separation is just as important as the process configuration. Therefore, it is important to develop PSA processes in conjunction...
Oxidation processes play an integral role in many industries, but questions still remain regarding the mechanisms of carbon-hydrogen bond activation and oxidation in free-radical and catalyzed processes. Microkinetic modeling is a powerful tool capable of examining oxidation processes at the mechanistic level to gain understanding and guide catalyst applications. This...
Gene regulatory networks contain multiple components including microRNAs (miRNAs) that coordinate regulation of genes to produce higher level cell functions. miRNAs are small non-coding RNA molecules that modulate gene expression post-transcriptionally by binding to short target motifs on mRNA transcripts to down-regulate target genes. Because miRNA regulation of genes is...
The phase-field crystal (PFC) model is an exciting new method for simulating crystalline materials with atomic resolution over diffusional time scales. Unfortunately, applications of the model have been severely limited by the requirement that novel free energies must be constructed for each new material of interest. This thesis describes three...
Composites of metal nanoparticles encapsulated by metal-organic frameworks (NP@MOFs) have recently emerged as intriguing heterogeneous catalysts for regioselective reactions. Sharing qualities of both zeolites and enzymes, these catalysts employ the pore system of a MOF to direct reactant access to the surface of nanoparticles. This dissertation seeks to better understand...
Biology is entering the exciting world of big data. Modern high-throughput experimental techniques often produce large datasets that aim to capture complex relationships often found in biological systems. While these larger data sets contain vast amounts of useful information, the answers are often locked behind a wall of numbers. As...
Nanostructured semiconductors exhibit promising optoelectronic properties, such as high photoluminescence quantum yield and efficient charge separation, making them attractive materials for applications including photovoltaics, LEDs, and lasers. These superior properties are often due to improved crystallinity and reduced charge separation distance compared to bulk semiconductors. As a result, it is...
It is pertinent now more than ever that we find sustainable alternatives to produce chemicals. For decades, scientists and engineers have turned to biological systems to help meet societal needs in energy, medicine, materials, and moreespecially when chemical synthesis is untenable. Often, biologically-produced small molecules are insufficient for production at...
Supported metal oxides are an important class of heterogeneous catalysts active for many selective oxidation reactions including alkane oxidative dehydrogenation. Attempts to develop fundamental structure-function relationships for supported metal oxide catalysts for alkane oxidative dehydrogenation have been challenging, with many conflicting reports in literature. This has been in part due...