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Publication Developing Reactive Molecular Dynamics for Understanding Polymer Chemical Kinetics(2009-05) Smith, Kenneth D.One of the challenges in understanding polymer flammability is the lack of information about microscopic events that lead to macroscopically observed species, and Reactive Molecular Dynamics is a promising approach to obtain this crucially needed information. The development of a predictive method for condensed-phase reaction kinetics can provide significant insight into polymer ammability, thus helping guide future synthesis of fire-resistant polymers. Through this dissertation, a new reactive forcefield, RMDff, and Reactive Molecular Dynamics program, RxnMD, have been developed and used to simulate such material chemistry. It is necessary to have accurate description of chemical kinetics to describe quantitative chemical kinetics. Typical equilibrium forcefields are inadequate for describing chemical reactions due to the inability to represent bonding transformations. This issue was resolved by developing a new method, RMDff, that allows standard equilibrium forcfields to describe reactive transitions. The chemical reactions are described by employing switching functions that permit smooth transitions between the reactant and product descriptions available from traditional forcefields. Because all of the chemical motions are described, a complete potential energy surface is obtained for the course of the reaction. Descriptions of scission, addition/beta-scission, and abstraction reactions were developed for hydrocarbon species. Reactive potentials were developed using a representative reaction involving small molecules. It is shown that the overall geometric and energetic changes are transferable to larger and substituted molecules. The main source of error found in RMDff resulted from errors within the equilibrium forcefield descriptions. In order to simulate the chemical kinetics, it was necessary to create a molecular dynamics program that could implement the reactions from RMDff. RxnMD was developed as a new C++-based Reactive Molecular Dynamics code to simulate the dynamics using RMDff. Polymer kinetics were predicted for high-density polyethylene and used to test the method and code. Conformational changes and polymer length in the initial polyethylene molecules did not significantly alter the backbone decomposition kinetics. The results also revealed that the backbone carbon-carbon bonds could break with an activation energy approximately 100 kJ/mol below the carbon-carbon bond dissociation energy. This decrease was believed to occur from intramolecular polymer stress, which is relieved via backbone scission. Such stress was also observed to increase the beta-scission reaction rate at high temperatures, apparently because the scission reaction alone is not always sufficient to remove the energy associated with the polymer stress concentrated near the scission location. Finally, the RMD method was also shown to be transferable and applicable in describing the decomposition of novel fire-resistant polymers.Publication Dynamic Modeling of Synthetic Microbial Consortia to Optimize the Co-fermentation of Glucose and Xylose(2013-09) Hanly, Timothy JosephSecond-generation biofuels have the potential to replace fossil fuels in the energy economy without negatively impacting the food supply. An effective biocatalyst must be able to convert all sugars found in lignocellulosic hydrolysates to biofuels. Few microbes exist in that have both a wide substrate range and high ethanol yields necessary for this process. Mixed culture biotechnology is a promising alternative to the use of single organisms in the production of fuels from lignocellulosic biomass. These systems mimic natural processes for the degradation of lignocellulose and exploit the native capabilities of each microbe. The segregation of metabolic pathways allows for the individual optimization of each step in the process. Preliminary work with a consortium capable of saccharification and fermentation showed promise, but the dynamics were poorly understood. Metabolic modeling is a powerful tool for understanding the interactions between microbes in mixed cultures. The development of accurate models of mixed culture metabolism will help drive the engineering of these systems for industrial applications. In this dissertation, dynamic flux balance analysis is applied to mixed culture systems by combining mathematical reconstructions of pure culture metabolism. By tuning the inoculum to sugar concentration, simulations of Saccharomyces cerevisiae and Escherichia coli mutants engineered to ferment a specific substrate display the potential for improved ethanol production over pure cultures. A framework for translating model predictions to experimental systems was developed for a co-culture of S. cerevisiae and xylose-specific E. coli. The consumption of sugar mixtures was optimized through this method, but the inability of the predicted gains in ethanol production to be replicated in experimental systems reveals the importance of selecting microbes with similar optimal growth conditions. The more compatible microbes S. cerevisiae and Scheffersomyces stipitis were modeled under microaerobic conditions to optimize ethanol production from a mixture of glucose and xylose. To further demonstrate the ability of these systems to ferment lignocellulosic hydrolysates, the effect of furan inhibitors on pure and co-cultures was assessed through modeling and experiment. The work presented here represents the first steps towards engineering and optimizing a microbial consortium for the production of ethanol from lignocellulosic biomass.Publication Discriminatory Bio-Adhesion Over Nano-Patterned Polymer Brushes(2013-09) Gon, SaugataSurfaces functionalized with bio-molecular targeting agents are conventionally used for highly-specific protein and cell adhesion. This thesis explores an alternative approach: Small non-biological adhesive elements are placed on a surface randomly, with the rest of the surface rendered repulsive towards biomolecules and cells. While the adhesive elements themselves, for instance in solution, typically exhibit no selectivity for various compounds within an analyte suspension, selective adhesion of targeted objects or molecules results from their placement on the repulsive surface. The mechanism of selectivity relies on recognition of length scales of the surface distribution of adhesive elements relative to species in the analyte solution, along with the competition between attractions and repulsions between various species in the suspension and different parts of the collecting surface. The resulting binding selectivity can be exquisitely sharp; however, complex mixtures generally require the use of multiple surfaces to isolate the various species: Different components will be adhered, sharply, with changes in collector composition. The key feature of these surface designs is their lack of reliance on biomolecular fragments for specificity, focusing entirely on physicochemical principles at the lengthscales from 1 – 100 nm. This, along with a lack of formal patterning, provides the advantages of simplicity and cost effectiveness. This PhD thesis demonstrates these principles using a system in which cationic poly-L-lysine (PLL) patches (10 nm) are deposited randomly on a silica substrate and the remaining surface is passivated with a bio-compatible PEG brush. TIRF microscopy revealed that the patches were randomly arranged, not clustered. By precisely controlling the number of patches per unit area, the interfaces provide sharp selectivity for adhesion of proteins and bacterial cells. For instance, it was found that a critical density of patches (on the order of 1000/m2) was required for fibrinogen adsorption while a greater density comprised the adhesion threshold for albumin. Surface compositions between these two thresholds discriminated binding of the two proteins. The binding behavior of the two proteins from a mixture was well anticipated by the single- protein binding behaviors of the individual proteins. The mechanism for protein capture was shown to be multivalent: protein adhesion always occurred for averages spacings of the adhesive patches smaller than the dimensions of the protein of interest. For some backfill brush architectures, the spacing between the patches at the threshold for protein capture clearly corresponded to the major dimension of the target protein. For more dense PEG brush backfills however, larger adhesion thresholds were observed, corresponding to greater numbers of patches involved with the adhesion of each protein molecule. . The thesis demonstrates the tuning of the position of the adhesion thresholds, using fibrinogen as a model protein, using variations in brush properties and ionic strength. The directions of the trends indicate that the brushes do indeed exert steric repulsions toward the proteins while the attractions are electrostatic in nature. The surfaces also demonstrated sharp adhesion thresholds for S. Aureus bacteria, at smaller concentrations of adhesive surfaces elements than those needed for the protein capture. The results suggest that bacteria may be captured while proteins are rejected from these surfaces, and there may be potential to discriminate different bacterial types. Such discrimination from protein-containing bacterial suspensions was investigated briefly in this thesis using S. Aureus and fibrinogen as a model mixture. However, due to binding of fibrinogen to the bacterial surface, the separation did not succeed. It is still expected, however, that these surfaces could be used to selectively capture bacteria in the presence of non-interacting proteins. The interaction of these brushes with two different cationic species PLL and lysozyme were studied. The thesis documents rapid and complete brush displacement by PLL, highlighting a major limitation of using such brushes in some applications. Also unanticipated, lysozyme, a small cationic protein, was found to adhere to the brushes in increasing amounts with the PEG content of the brush. This finding contradicts current understanding of protein-brush interactions that suggests increases in interfacial PEG content increase biocompatibility.Publication Particle-Collector Interactions In Nanoscale Heterogeneous Systems(2013-02) Bendersky, MarinaParticle-surface interactions govern a myriad of interface phenomena, that span from technological applications to naturally occurring biological processes. In the present work, particle-collector DLVO interactions are computed with the grid-surface integration (GSI) technique, previously applied to the computation of particle colloidal interactions with anionic surfaces patterned with O(10 nm) cationic patches. The applicability of the GSI technique is extended to account for interactions with collectors covered with topographical and chemical nanoscale heterogeneity. Surface roughness is shown to have a significant role in the decrease of the energy barriers, in accordance with experimental deposition rates that are higher than those predicted by the DLVO theory for smooth surfaces. An energy- and force-averaging technique is presented as a reformulation of the GSI technique, to compute the mean particle interactions with random heterogeneous collectors. A statistical model based on the averaging technique is also developed, to predict the variance of the interactions and the particle adhesion thresholds. An excellent agreement is shown between the models' predictions and results obtained from GSI calculations for large number of random heterogeneous collectors. Brownian motion effects for particle-collector systems governed by nanoscale heterogeneity are analyzed by introducing stochastic Brownian displacements in particle trajectory equations. It is shown that for the systems under consideration and particle sizes usually used in experiments, it is reasonable to neglect the effects of Brownian motion entirely. Computation of appropriately defined P ́eclet numbers that quantify the relative importance of shear, colloidal and Brownian forces validate that conclusion. An algorithm for the discretization of spherical surfaces into small equal-area elements is implemented in conjunction with the GSI technique and mobility matrix calculations of particle velocities, to obtain interactions and dynamic behaviors of patchy particles in the vicinity of uniform flat collectors. The patchy particle and patchy collector systems are compared in detail, through the computation of statistical measures that include adhesion probabilities and maximum residence times per patch. The lessened tendency of the patchy particle to adhere on the uniform collector is attributed to a larger maximum residence time per patch, which precludes interactions with multiple surface nano-features at a given simulated time. Also briefly described are directions for future work, that involve the modeling of two heterogeneous surfaces, and of surfaces covered with many types of heterogeneity, such as patches, pillars and spring-like structures that resemble polymer brushes or cellular receptors.Publication Determining Detailed Reaction Kinetics for Nitrogen-and Oxygen-Containing Fuels(2013-02) Labbe, Nicole JeanneWith the emergence of new biorenewable transportation fuels, the role of heteroatoms in combustion has increased tremendously. While petroleum-based fuels are primarily hydrocarbons, many biorenewable fuels contain heteroatoms such as oxygen and nitrogen, introducing new challenges associated with toxic emissions. A fundamental understanding of the chemical kinetics of combustion of these heteroatomic fuels is necessary to elucidate the pathways by which these toxic emissions are formed and may be achieved through the development of combustion models. Reaction sets, the core of these combustion models, may be assembled for individual fuels through a balance of employing vetted rate constants from prior publications, quantum chemistry calculations, and rate constant estimations. For accuracy, reaction sets should be tested against experimental combustion studies such as low-pressure flame experiments using molecular-beam mass spectrometry (MBMS) or chemiluminescence and high-pressure shock-tube experiments. This dissertation presents the development of a new reaction set to describe gas-phase combustion chemistry of fuels containing only hydrogen, carbon, oxygen, and nitrogen. The foundation of this model was a reaction set to describe combustion of ammonia flames. This reaction set contains only H/N/O chemistry for simplicity. The new reaction set was tested against a pyrolysis shock-tube study, as well as 12 MBMS flame experiments under a variety of conditions, including different mixtures of fuels and oxidizers (NH3, N2O, H2, NO, O2), fuel equivalence ratios (lean to rich), pressures, and concentrations of diluent gas. Additionally, the base H/N/O mechanism was expanded to include carbon chemistry and was tested against flames of dimethylamine, ethylamine, and a methane/ammonia mixture. This reaction set was employed to study heterocyclic biofuels including a fuel-rich flame of tetrahydropyran, the monoether analogue to cyclohexane and the basic ring in cellulose. Additionally, the model was used in a study of morpholine, a 6-membered ring with both ether and amine functionalities, testing the model against fuel-rich flame studies using both MBMS and chemiluminescence techniques and high-pressure shock-tube studies for both oxidation and pyrolysis at elevated temperatures and pressures. Lastly, the model was used to study the combustion of hypergolic rocket fuels, specifically monomethyl hydrazine and tetramethylethyldiamine with red fuming nitric acid.Publication Molecular and Population Level Approaches to Understand Taxus Metabolism in Cell Suspension Cultures(2013-02) Patil, Rohan AnilPlant cell culture is an attractive platform technology for production and supply of important plant derived medicinals. A unique characteristic of plant cells is the ability to grow as multicellular aggregates in suspension. The presence of these non-uniform aggregates results in creation of distinct microenvironments, which can induce variations in cellular metabolism (e.g., growth, oxygen consumption and secondary metabolite synthesis). This heterogeneity can lead to unpredictable and suboptimal performance in large scale bioprocesses. One example is the Taxus cell culture system, which produces a widely used chemotherapeutic drug - paclitaxel (Taxol ®). Despite extensive process engineering efforts which have led to increased yields of paclitaxel, Taxus cells exhibit variability in productivity that is poorly understood. Elicitation of Taxus cultures with methyl jasmonate (MeJA) induces the accumulation of paclitaxel, but to varying extents in culture. A significant negative correlation was observed between paclitaxel level and mean aggregate size of the culture, demonstrating the relevance of measuring, and potentially controlling aggregate size during long term subculture. Understanding the regulation of gene expression can provide rational engineering strategies to control variability and optimize performance of Taxus cell cultures. Biosynthetic pathway gene analyses revealed upregulation of genes upon elicitation with MeJA; results also suggested additional molecular regulatory points outside of the biosynthetic pathway. In order to fully understand Taxus molecular regulation and the relationship to paclitaxel production variability, a transcriptome-wide analysis using next generation sequencing (454 and Illumina) methods was performed. Several pathways outside of paclitaxel biosynthesis were found active upon MeJA elicitation. Global comparison of gene expression amongst cultures accumulating different levels of paclitaxel is being performed to completely understand the interactions amongst the paclitaxel biosynthetic pathway and other complimentary and competing pathways to suggest effective targets for metabolic engineering. This work collectively represents the first molecular studies to understand metabolic regulation in Taxus cell cultures. Apart from inducing paclitaxel biosynthesis, MeJA decreases cell growth in Taxus cell cultures. The MeJA-mediated repression of cell growth was shown to correlate with inhibition of cell cycle progression as evident both at the culture level through flow cytometric analyses and at the transcriptional level by repression of key cell cycle-associated genes. Results from this study provide valuable insight into the mechanisms governing MeJA perception and subsequent events leading to repression of Taxus cell growth.Publication Effect of Colloidal Interactions on Formation of Glasses, Gels, Stable Clusters and Structured Films(2013-02) Atmuri, Anand KumarColloidal suspensions are ubiquitous because of their vast industrial and household usage. We demonstrate that interactions between colloidal particles play a crucial role in manipulating the phase behavior and thereby the macroscopic properties of a variety of colloidal materials, including structured films, gels, glasses and stable clusters. First, we examined films comprised of two different colloidal particles and investigated the impact of colloidal interactions in manipulating the extent of segregation in the dried films. A transport model was used to predict the volume fraction profiles of the particles as a function of film thickness, which showed that segregation could be altered by changing the particle interactions. Experimental studies were carried out using different charged latex particles and varying the pH to change the interactions, and the results from experiments and model show a very good agreement to capture the extent of segregation. Second, we studied the effect of adding low molecular weight adsorbing and non-adsorbing polymers to suspensions to modify the interparticle interactions. We studied the structural dynamics and bulk rheology of a disk-shaped clay colloid, laponite® , and polymer. Under basic conditions laponite® forms a repulsive colloidal glass. We show that low concentrations of an adsorbing polymer retards glass formation, whereas at higher concentrations an attractive glass is formed. Thus, we obtain a type of re-entrant glass transition, which is a first of its kind observed in anisotropic colloids with adsorbing polymer. On the other hand addition of a non-adsorbing polymer to laponite® suspensions triggers the formation of particle clusters, and increasing the concentration of polymer increases the strength of attraction between the particles and the size of the clusters. To further understand formation of stable clusters, we utilized population balance equations (PBE) models to study aggregation of charged colloids under quiescent conditions. We considered particles with a DLVO-type potential, where the interactions are a sum of van der Waals attraction and electrostatic repulsion. Under certain conditions, the net repulsion between large aggregates and a single particle acts as a barrier against further aggregation, and clusters reach a stable size. The PBE model was used to map out regimes of uncontrolled aggregation, controlled aggregation, and no aggregation as a function of ionic strength and colloid weight fraction. The model was tested using experimental data on charged latex particles with different colloid weight fractions and ionic strengths. The model was able to predict the regime of controlled aggregation and final size of aggregates very well. However, the rate of aggregation predicted by the model was much faster than observed experimentally. Finally, we explored aggregation of latex particles in a shear environment similar to that used in industrial toner production processes. We studied the effect of temperature, pH and coagulant concentration on aggregation and showed that there is a optimum variable space to have aggregates of controlled size and distribution.Publication Modeling the Self-Assembly of Ordered Nanoporous Materials(2012-09) Jin, LinPorous materials have long been a research interest due to their practical importance in traditional chemical industries such as catalysis and separation processes. The successful synthesis of porous materials requires further understanding of the fundamental physics that govern the formation of these materials. In this thesis, we apply molecular modeling methods and develop novel models to study the formation mechanism of ordered porous materials. The improved understanding provides an opportunity to rational control pore size, pore shape, surface reactivity and may lead to new design of tailor-made materials. To attain detailed structural evolution of silicate materials, an atomistic model with explicitly representation of silicon and oxygen atoms is developed. Our model is based on rigid tetrahedra (representing SiO4) occupying the sites of a body centered cubic (bcc) lattice. The model serves as the base model to study the formation of silica materials. We first carried out Monte Carlo simulations to describe the polymerization process of silica without template molecules starting from a solution of silicic acid in water at pH 2. We predicted Qn evolutions during silica polymerization and good agreement was found compared with experimental data, where Qn is the fraction of Si atoms with n bridging oxygens. The model captures the basic kinetics of silica polymerization and provides structural evolution information. Next we generalize the application of this atomic lattice model to materials with tetrahedral (T) and bridging (B) atoms and apply parallel tempering Monte Carlo methods to search for ground states. We show that the atomic lattice model can be applied to silica and related materials with a rich variety of structures including known chalcogenides, zeolite analogs, and layered materials. We find that whereas canonical Monte Carlo simulations of the model consistently produce the amorphous solids studied in our previous work, parallel tempering Monte Carlo gives rise to ordered nanoporous solids. The utility of parallel tempering highlights the existence of barriers between amorphous and crystalline phases of our model. The role of template molecules during synthesis of ordered mesoporous materials was investigated. Implemented surfactant lattice model of Larson, together with atomic tetrahedral model for silica, we successfully modeled the formation of surfactant-templated mesoporous silica (MCM-41), with explicit representation of silicic acid condensation and surfactant self-assembly. Lamellar and hexagonal mesophases form spontaneously at different synthesis conditions, consistent with published experimental observations. Under conditions where silica polymerization is negligible, reversible transformation between hexagonal and lamellar phases were observed by changing synthesis temperatures. Upon long-time simulation that allows condensation of silanol groups, the inorganic phases of mesoporous structures were found with thicker walls that are amorphous and lack of crystallinity. Compared with bulk amorphous silica, the wall-domain of mesoporous silicas are less ordered withlarger fractions of three- and four-membered rings and wider ring-size distributions. It is the first molecular simulation study of explicit representations of both silicic acid condensation and surfactant self-assembly.Publication Modeling the Relaxation Dynamics of Fluids in Nanoporous Materials(2012-09) Edison, John R.Mesoporous materials are being widely used in the chemical industry in various environmentally friendly separation processes and as catalysts. Our research can be broadly described as an effort to understand the behavior of fluids confined in such materials. More specifically we try to understand the influence of state variables like temperature and pore variables like size, shape, connectivity and structural heterogeneity on both the dynamic and equilibrium behavior of confined fluids. The dynamic processes associated with the approach to equilibrium are largely unexplored. It is important to look into the dynamic behavior for two reasons. First, confined fluids experience enhanced metastabilities and large equilibration times in certain classes of mesoporous materials, and the approach to the metastable/stable equilibrium is of tremendous interest. Secondly, understanding the transport resistances in a microscopic scale will help better engineer heterogeneous catalysts and separation processes. Here we present some of our preliminary studies on dynamics of fluids in ideal pore geometries. The tool that we have used extensively to investigate the relaxation dynamics of fluids in pores is the dynamic mean field theory (DMFT) as developed by Monson[P. A. Monson, J. Chem. Phys., 128, 084701 (2008) ]. The theory is based on a lattice gas model of the system and can be viewed as a highly computationally efficient approximation to the dynamics averaged over an ensemble of Kawasaki dynamics Monte Carlo trajectories of the system. It provides a theory of the dynamics of the system consistent with the thermodynamics in mean field theory. The nucleation mechanisms associated with confined fluid phase transitions are emergent features in the calculations. We begin by describing the details of the theory and then present several applications of DMFT. First we present applications to three model pore networks (a) a network of slit pores with a single pore width; (b) a network of slit pores with two pore widths arranged in intersecting channels with a single pore width in each channel; (c) a network of slit pores with two pore widths forming an array of ink-bottles. The results illustrate the effects of pore connectivity upon the dynamics of vapor liquid phase transformations as well as on the mass transfer resistances to equilibration. We then present an application to a case where the solid-fluid interactions lead to partial wetting on a planar surface. The pore filling process in such systems features an asymmetric density distribution where a liquid droplet appears on one of the walls. We also present studies on systems where there is partial drying or drying associated with weakly attractive or repulsive interactions between the fluid and the pore walls. We describe the symmetries exhibited by the lattice model between pore filling for wetting states and pore emptying for drying states, for both the thermodynamics and dynamics. We then present an extension of DMFT to mixtures and present some examples that illustrate the utility of the approach. Finally we present an assessment the accuracy of the DMFT through comparisons with a higher order approximation based on the path probability method as well as Kawasaki dynamics.Publication Catalytic Fast Pyrolysis of Furan Over Zsm-5 Catalysts: A Model Biomass Conversion Reaction(2012-09) Cheng, Yu-TingDue to its low cost and availability, lignocellulosic biomass is receiving significant attention worldwide as a feedstock for renewable liquid bio-fuels. We have recently shown that zeolites can be added to a pyrolysis reactor to directly make aromatics from solid biomass in one single step in a process called catalytic fast pyrolysis (CFP). The advantage of this approach is that valuable petrochemicals can be made directly from solid biomass in a single catalytic step using zeolite catalysts. However, little is known about the conversion chemistry that occurs within the zeolites during CFP. The objective of this thesis is to identify the key catalytic reactions that occur for conversion of biomass inside ZSM-5 zeolite catalysts using furan and its derivatives as model biomass compounds. The kinetic data and chemistry was obtained by using a continuous flow fixed-bed reactor, and an in-situ temperature-programmed reactor system. Furan adsorbs as oligomers at room temperature. These oligomers are converted into CO, CO2, H2O, olefins, monocyclic aromatics, and undesired polycyclic aromatics and coke at 400 - 600°C. An important route to form aromatics at 600°C is Diels-Alder reaction/dehydration where furan reacts with produced olefins and forms aromatics and water. The Diels-Alder reaction can be further utilized by co-feeding olefins with furanic compounds to tune the aromatics distribution. For example, in our experiments we were able to double toluene and triple xylenes selectivity for furan and 2-methylfuran CFP, respectively. Moreover, we synthesized a series of Ga-promoted catalysts to increase the rate of aromatics production. The aromatics selectivity obtained from furan conversion over Ga-containing ZSM-5 was 40% higher than unpromoted ZSM-5. The promotion was also observed in a bubbled fluidized-bed reactor used for pinewood CFP, where the aromatics yield was increased by 50% using a Ga-promoted ZSM-5 FCC catalyst. We finally fine-tuned ZSM-5 pores to impose more space confinement on aromatic products. These modified ZSM-5 increased p-xylene selectivity in xylenes from 32% to greater than 90% for conversion of 2-methylfuran and propylene while the overall p-xylene selectivity was increased from 5% to 15%. The Ga promotional effect was also observed on a spray-dried ZSM-5 catalyst. This study addresses the catalytic chemistry that occurs inside zeolites during CFP of biomass into aromatics using furan as a model biomass compound. Understanding this reaction chemistry can give us insight into how to design more effective zeolite catalysts and reactors for the efficient utilization of our biomass resources.Publication Modeling Material Transformations in Biorefinement(2012-09) Agarwal, VishalLignocellulosic biomass is a significant pool of energy resource, which can be harnessed to supplement or replace the dwindling fossil fuel reserves. This requires development of economically viable means to efficiently convert biomass to biofuels. A major requirement in biofuel industry is to develop highly active, selective and stable catalysts. Zeolites are an important class of micro-porous crystalline solids, and have proven to be effective and stable acid catalysts for a variety of petrochemical and fine-chemical processes. Nitrided zeolites -- i.e., those with Si-O-Si and Si-OH-Al groups substituted by Si-NH-Si and Si-NH2-Al -- have shown promise as shape-selective basic catalysts, and are potential candidates for biofuel production catalysts. In the first part of this dissertation, the stability and base characteristics of nitrided zeolites have been explored. The nitridation mechanism in HY and silicate type zeolites is computed by first time implementation of embedded-cluster procedure with nudged-elastic-band method of finding elusive transition states. The stability of nitrided sites is investigated by modeling the kinetics of nitridation in reverse, going back to untreated zeolite plus ammonia. Our calculations suggest that nitrided silicalite and HY zeolites require high temperatures to form, but once formed, they remain relatively stable, auguring well for their use as shape-selective base catalysts. In addition, a systematic study of base strength versus aluminium content or alkali cation of nitrided zeolites is also performed. Our studies suggest that K-N-Y (Si:Al = 11) optimizes the balance of activity, stability and cost. Pyrolysis of lignocellulosic biomass is a burgeoning technology to obtain renewable fuels. Commercializing pyrolysis would require efficient process design, especially reactors as they are one of the most energy intensive units in the whole process. This would in turn require detailed understanding of complex pyrolysis chemistries. Biomass is mainly composed of the biopolymer cellulose; therefore, understanding cellulose pyrolysis chemistries is important for efficiently modeling and optimizing pyrolysis reactors. In the second part of this dissertation, the mechanism(s) of conversion of crystalline cellulose to precursors of major products in cellulose pyrolysis have been explored. As the first step, the transformation of cellulose Iβ to a high-temperature (550 K) structure is modeled by computing infrared (IR) spectra as a probe of hydrogen bonding using constant-pressure classical molecular-dynamics simulations. To assist in the analysis of IR spectra, a novel synthesis of normal mode analysis and power spectrum methods is developed to assign the O-H stretches. Simulated IR spectra at elevated temperatures suggests a structural transformation above 450 K, a result in agreement with experimental IR results. The low-temperature (300-400 K) structure is found to be dominated by intrachain hydrogen bonds, whereas in the high-temperature structure (450- 550 K), many of these intrachain hydrogen bonds transform to longer, weaker interchain hydrogen bonds. Next, the subsequent decomposition of cellulose is modeled at 600 and 873 K using Car-Parrinello molecular- dynamics simulations and the metadynamics method. The computed nascent processes can explain the formation of precursors to major products observed during cellulose pyrolysis such as levoglucosan (LGA), hydroxy-methylfurfurral (HMF) and fragmentation products such as formic acid. LGA is found to be kinetically and thermodynamically favorable in comparison to other products, which explains why LGA is the major product observed during cellulose pyrolysis. The molecular insights presented in this part of the study will be helpful in developing detailed kinetic models for optimizing pyrolysis reactors.Publication Enhanced Mechanical Performance of Low Dielectric Constant Thin Films Synthesized in Supercritical Co2, and Sans Studies of Microemulsions Induced or Destabilized by Compressed Co2(2012-05) Romang, Alvin HoratioBlock copolymer (BCP) phase segregation and self-assembly into two or more distinct domains are primarily dictated by two parameters: the block volume fraction, f, and the product of the segment-segment interaction parameter and the length of polymer chain, XN. The volume fraction determines a block copolymer's phase segregated morphology, whereas XN dictates its overall segregation strength, or phase stability. In order to achieve smaller domain sizes, the interaction parameter must be increased to compensate for the decrease in chain length. In the melt, PEO-b-PPO-b-PEO (Pluronic) triblock copolymer surfactants do not phase segregate primarily due to their low molecular weights and insufficient segregation strength, or low XN. Strong hydrogen bonding and selective interactions of PEO chains with homopolymers capable of hydrogen bonding, such as poly(acrylic acid) were shown to increase the effective segregation strength of the blend. Small angle X-ray scattering demonstrated highly ordered sub-10 nm domains resulting from phase segregation of the blends. The strong hydrogen bonding interaction between PEO and H-bonding homopolymers was also utilized to incorporate polyhedral oligomeric silsesquioxanes (POSS) into silicate films. In order to improve the compatibility between hydrophobic POSS with hydrophilic Pluronic copolymers, POSS-decorated acrylate monomer was copolymerized with acrylic acid. This eliminated the macrophase segregation between the BCP templates and POSS molecules. The inclusion of POSS is shown to increase the mechanical performance of the low-k films. A supercritical CO2 synthesis route enables the transport of silica precursors into the polymer blends. An increase of hardness of up to 1.8 GPa at k = 2.4 and 1.2 GPa for k = 2.1 was observed for these mesoporous organosilicate films. Finally, this work has also focused on the formation of ordered domains of the Pluronic surfactants into a ternary solvent system consisting of two liquid solvents and compressed CO2. Compressed CO2 can influence the compatibility of liquid solvents, inducing phase separation or phase mixing. CO2-induced phase separation of acetone and water and phase mixing of tetradecane and methanol were studied for the formation and breaking of nanoscale domains in the presence of Pluronic surfactants. Long-range ordered structures were observed using small angle neutron scattering.Publication Production of Green Aromatics and Olefins from Lignocellulosic Biomass by Catalytic Fast Pyrolysis: Chemistry, Catalysis, and Process Development(2012-05) Jae, JunghoDiminishing petroleum resources combined with concerns about global warming and dependence on fossil fuels are leading our society to search for renewable sources of energy. In this respect, lignocellulosic biomass has a tremendous potential as a renewable energy source, once we develop the economical processes converting biomass into useful fuels and chemicals. Catalytic fast pyrolysis (CFP) is a promising technology for production of gasoline range aromatics, including benzene, toluene, and xylenes (BTX), directly from raw solid biomass. In this single step process, solid biomass is fed into a catalytic reactor in which the biomass first thermally decomposes to form pyrolysis vapors. These pyrolysis vapors then enter the zeolite catalysts and are converted into the desired aromatics and olefins along with CO, CO2, H2O, and coke. The major challenge with the CFP process is controlling the complicated homogeneous and heterogeneous reaction chemistry. The focus of this thesis is to study the reaction chemistry, catalyst design, and process development for CFP to advance the CFP technology. To gain a fundamental understanding of the underlying chemistry of the process, we studied the reaction chemistry for CFP of glucose (i.e. biomass model compound). Glucose is thermally decomposed in a few seconds and produce dehydrated products, including anhydrosugars and furans. The dehydrated products then enter into the zeolite catalyst pore where they are converted into aromatics, CO, CO2, H2O and coke. The zeolite catalyzed step is far slower than the initial decomposition step (>2 min). Isotopic labeling studies revealed that the aromatics are formed from random hydrocarbon fragments composed of the dehydrated products. The major competing reaction to aromatic production is the formation of coke. The main coking reaction is the polymerization of the furan intermediates on the catalyst surface. CFP is a shape selective reaction where the product selectivity is related to the zeolite pore size and structure. The shape selectivity of the zeolite catalysts in the CFP of glucose was systematically studied with different zeolites. The aromatic yield is a function of the pore size and internal pore space of the zeolite catalyst. Medium pore zeolites with pore sizes in the range of 5.2 to 5.9 √Ö and moderate pore intersection size, such as ZSM-5 and ZSM-11 produced the highest aromatic yield and least amount of coke. The kinetic diameter estimation of the aromatic products and the reactants revealed that the majority of these molecules can fit inside the zeolite pores of the medium pore zeolites. The ZSM-5 catalyst, the best catalyst for aromatic production, was modified further to improve its catalytic performance. These modifications include: (1) adjusting the concentration of acid sites inside the zeolites catalyst; (2) incorporation of mesoporosity into the ZSM-5 framework to enhance its diffusion characteristics, and (3) addition of Ga to the ZSM-5. Mesoporous ZSM-5 showed high selectivity for heavier alkylated monoaromatics. Ga promoted ZSM-5 increased the aromatic yield over 40%. A process development unit was designed and built for continuous operation of the CFP process in a pilot scale. The effects of process variables such as temperature, biomass weight hourly space velocity, catalyst to biomass ratio, catalyst static bed height, and fluidization gas velocity were studied to optimize the reactor performance. It was demonstrated that CFP could produce liter quantities of aromatic products directly from solid biomass.Publication On the Effect of Elasticity on Drag Reduction Due to Polymer Additives Using a Hybrid D.N.S. and Langevin Dynamics Approach(2012-05) Boelens, ArnoutIn this work the effect of elasticity on turbulent drag reduction due to polymers is investigated using a hybrid Direct Numerical Simulation (D.N.S) and Langevin dynamics approach. Simulations are run at a friction Reynolds number of Re_&tau = 560 for 960.000 dumbbells with Deborah numbers of De = 0, De = 1, and De = 10. The conclusions are that it is possible to simulate a drag reduced flow using hybrid D.N.S. with Langevin dynamics, that polymers, like other occurrences of drag reduction, reduce drag through streak stabilization, and that the essential property of polymers and fibers in having a drag reducing effect is their ability to exert a torqueon the solvent when they orientate in the boundary layer of the turbulent flow.Publication Microtechnologies for Mimicking Tumor-Imposed Transport Limitations and Developing Targeted Cancer Therapies(2012-02) Toley, Bhushan JayantIntravenously delivered cancer drugs face transport limitations at the tumor site and cannot reach all parts of tumors at therapeutically effective concentrations. Transport limitations also prevent oxygen from distributing evenly in tumors resulting in hypoxia, which plays a critical role in cancer progression. In this dissertation, I present the development of micro-devices that mimic transport limitations of drugs and nutrients on three dimensional tumor tissues, enable visualization and quantification of the ensuing gradients, and enable simple analysis and mathematical modeling of obtained data. To measure the independent effects of oxygen gradients on tumor tissues, an oxygen delivery device that used microelectrodes to generate oxygen directly underneath three-dimensional tumor cylindroids was developed. Supplying oxygen for 60 hours eliminated the necrotic region typically found in the center of cylindroids. Dead cells were observed moving away from the location of oxygen delivery. These measurements show that oxygen gradients are an important determinant of cell viability and rearrangement. Another micro-device was developed to mimic the delivery and systemic clearance of therapeutic agents. This microfluidic device consisted of cuboidal tumor tissue subjected to continuous medium perfusion along one face. The device was used to measure the spatiotemporal dynamics of the accumulation of therapeutic bacteria in tumors. Suspensions of Salmonella typhimurium and Escherichia coli strains were delivered to tumor tissues for 1 hour. Bacterial motility strongly correlated (R2 = 99.3%) with the extent of tissue accumulation. Based on spatio-temporal profiles and a mathematical model of motility and growth, bacterial dispersion was found to be necessary for deep penetration into tissue. These results show that motility is critical for effective distribution of bacteria in tumors. The microfluidic device was further used to mimic the delivery and clearance of equal concentrations of doxorubicin and liposome-encapsulated doxorubicin (Doxil). A pharmacokinetic/pharmacodynamic model incorporating mechanisms of tissue-level diffusion and binding was developed and experimental data was fit to this model. Doxorubicin was found to have the optimal diffusivity and binding for maximizing therapeutic effect. Doxil was severely limited by low intratumor drug release. These results show that in-vitro models mimicking tissue-level transport limitations more accurately predict the therapeutic response of drugs.Publication Modeling the Free Energy Functional at the Fluid-Solid Transition in Classical Many-Particle Systems(2012-02) Verma, AnuragThe problem of phase equilibrium in colloidal and classical atomistic systems is of great interest in modern micro/nano fabrication and self-assembly processes. Systems with specific potential interactions are increasingly being developed and knowledge of their phase diagrams would aid in their use in materials applications. The conventional methods of using simulations and experiments to evaluate phase equilibrium are costly, especially for fluid-solid equilibrium. One way to address this problem is to improve the accuracy of theories, such as classical density functional theory (cDFT), that predict thermodynamic properties at the fluid-solid transition with modest computational cost. In such a program the challenges are of two kinds, viz. (1) the development of a new cDFT formulation to treat fluid-solid equilibrium, especially with regard to the higher order multi-body interaction terms in the free energy expression and (2) finding a more accurate numerical method to solve the cDFT equations. In our work we develop several numerical and inversion methodologies to meet these challenges, including closure relations that capture the higher order terms in the free energy expansion. We find that these closures are qualitatively and quantitatively very different from their liquid state analogs found in the Ornstein-Zernike integral equation theory. Specifically, we discover new closure relations applicable to the fluid-solid transition in hard-sphere, soft-repulsive and Lennard-Jones potentials. We further discuss the universal nature of these closures for different interaction potentials and explore the breadth of their applicability and future prospects.Publication Separation of Carboxylic Acids From Aqueous Fraction of Fast Pyrolysis Bio-Oils Using Nanofiltration and Reverse Osmosis Membranes(2011-09) Teella, Achyuta Vara Prasada RaoThere has been a growing interest in renewable sources of energy due to an increase in demand and potential shortages and environmental problems associated with fossil fuels. Bio-oils, complex liquid fuels produced from fast pyrolysis of biomass, have been recognized as one potential source of renewable energy. However, they cannot be utilized directly due to their high viscosity, corrosiveness, and high char content. Bio-oils readily phase separate into aqueous phase and organic phase upon addition of water. The aqueous fraction of bio oil (AFBO) is convenient to process and contains sugars, organic acids, hydroxyacetone, hydroxyacetaldehyde, furfural, phenols and other organic species that can potentially be converted to hydrogen, alkanes, aromatics, or olefins. However, the acidity of AFBO (pH ~2.5) is relatively high due to the presence of organic acids which can impose more demands on construction equipment of the vessels and the upgrading process. Removal of acids is essential to use AFBO as a commercial fuel or further upgrading into fuels or chemicals. Traditional separation techniques for the removal of acids from AFBO, like ion exchange and distillation are not attractive due to practical limitations. Membrane-based separations have been increasingly employed due to their inherent advantages over conventional separations methods. Pressure driven membrane processes like nanofiltration (NF) and reverse osmosis (RO) have been used in chemical, electronics, textile, petrochemical, pulp and paper, and food industries as well as for the treatment of municipal wastewater and landfill leachates. However, these processes are targeted for aqueous systems containing little or no organic solvents. The use of membranes to separate organic solvent solutions or organic-rich aqueous solutions is still at a very early stage. The feasibility of removing small organic acids from the AFBO using NF and RO membranes was studied. Experiments were conducted with commercially available polymeric NF and RO membranes and aqueous solutions of increasing complexity, i.e. single solute solutions of acetic acid and glucose, binary solute solutions containing both acetic acid and glucose, and a model AFBO containing acetic acid, glucose, formic acid, hydroxyacetone, furfural, guaiacol, and catechol. Feed concentrations (up to 34 % solute by weight) close to those in real AFBO were chosen. These were generally at least an order of magnitude higher than previously studied in the literature for related membrane separations. Retention factors for single and binary solutions of acetic acid and glucose were promising so that the separation was expected to be feasible. However, all the membranes were irreversibly damaged when experiments were conducted with the model AFBO due to the presence of guaiacol in the feed solution. Experiments with model AFBO excluding guaiacol were also conducted. NF membranes showed retention factors of glucose greater than 80% and of acetic acid less than -15% when operated at transmembrane pressures near 60 bar. Finally, the solution-diffusion (SD) model was applied to predict the permeate flux and solute retention and compared to the experimental results. In another study, we explored the potential of nanocomposite membranes in gas separations. Solubility based membrane gas separation, in which the more soluble (and perhaps slower-diffusing) species preferentially permeates through the membranes, has received considerable attention due to both economic and environmental concerns. In this work, we synthesized organic-inorganic nanocomposite membranes by decorating the surfaces of commercially available alumina substrates with a selective organic material that is physically or chemically anchored to the porous surfaces. Hyperbranched melamine-based dendrimers and polydimethylsiloxane (PDMS) were used as filling agents. Separation factors for propane/nitrogen and carbon dioxide/methane were obtained for modified membranes. The separation performance of PDMS-alumina composite membranes was comparable to the currently best known polymers being used for this type of application.Publication Development of Plant Cell Culture Processes to Produce Natural Product Pharmaceuticals: Characterization, Analysis, and Modeling of Plant Cell Aggregation(2011-09) Kolewe, MartinPlant derived natural products represent some of the most effective anti-cancer and anti-infectious disease pharmaceuticals available today. However, uncertainty regarding the feasibility of commercial supply due to the limited availability of many plants in nature has resulted in a dramatic reduction in the use of natural products as leads in modern drug discovery. Plant cell suspension culture, consisting of dedifferentiated plant cells grown in vitro and amenable to large scale industrial biotechnology processes, is a production alternative which promises renewable and economical supply of these important drugs. The widespread application of this technology is limited by low product yields, slow growth rates, challenges in scale-up, and above all, variability in these properties, which is poorly understood. Plant cells grow as aggregates in suspension cultures ranging from two to thousands of cells (less than 100 micron to well over 2 mm). Aggregates have long been identified as an important feature of plant cell culture systems, as they create microenvironments for individual cells with respect to nutrient limitations, cell-cell signaling, and applied shear in the in vitro environment. Despite its purported significance, a rigorous engineering analysis of aggregation has remained elusive. In this thesis, aggregation was characterized, analyzed, and modeled in Taxus suspension cultures, which produce the anti-cancer drug paclitaxel. A technique was developed to reliably and routinely measure aggregate size using a Coulter counter. The analysis of aggregate size as a process variable was then used to evaluate the effect of aggregation on process performance, and the analysis of single cells isolated from different sized aggregates was used to understand the effect of aggregation on cellular metabolism and heterogeneity. Process characterization studies indicated that aggregate size changed over a batch cycle as well as from batch to batch, so a population balance equation model was developed to describe and predict these changes in the aggregate size distribution. This multi-scale engineering approach towards understanding plant cell aggregation serves as an important step in the development of rational strategies aimed at controlling the process variability which has heretofore limited the application of plant cell culture technology.Publication Modeling and Simulation of Nanoparticle Formation in Microemulsion Droplets(2011-09) Kuriyedath, Sreekumar R.Semiconductor nanocrystals, also known as quantum dots (QDs), are an important class of materials that are being extensively studied for a wide variety of potential applications, such as medical diagnostics, photovoltaics, and solid-state lighting. The optical and electronic properties of these nanocrystals are different from their bulk properties and depend on the size of the QDs. Therefore an important requirement in their synthesis is a proper control on the final nanoparticle size. Recently, a technique has been developed for synthesizing zinc selenide (ZnSe) QDs using microemulsion droplets as templates. In these systems, a fixed amount of a reactant is dissolved in each droplet and a second reactant is supplied by diffusion through the interface. Spontaneous reaction between the two reactants at the droplet interface forms ZnSe nuclei, whose subsequent diffusion and coalescence into clusters ultimately leads to the formation of a single particle in each droplet. The size of the final particle can be adjusted by changing the initial concentration of the reactant that is dissolved in the dispersed phase of the microemulsion. In this thesis we use a modeling and simulation approach to study the phenomena underlying the formation of QDs in the droplets of a microemulsion. A Lattice Monte-Carlo model was developed to describe Brownian diffusion of a Zn-containing precursor (reactant) inside a droplet, formation of ZnSe nuclei via an irreversible reaction with a Se-containing precursor at the droplet interface, Brownian diffusion and coalescence of nuclei into clusters ultimately leading to the formation of a single nanoparticle inside the droplet. The time required for forming a single particle was found to initially increase as the final particle size was increased by increasing the initial concentration of the reactant in the droplet, but it quickly passed through a maximum, and subsequently decreased. The simulations revealed that this seemingly anomalous result can be explained by studying the intermediate cluster populations that show the formation of a large intermediate "sweeper" cluster. This sweeper cluster is a more effective collision partner to smaller ones and accelerates the coalescence process that eventually leads to the formation of a single particle. A generalized dimensionless equation was obtained that relates the formation time of the final particle to its size for various droplet sizes and diffusivities of the reactant and clusters in the droplet. A parametric study revealed that the final particle formation time is more sensitive to changes in the cluster coalescence probability than in the probability of nucleation. We subsequently compared these results with those obtained by simulating the coalescence of nuclei that are assumed to be formed spontaneously inside a droplet and to be initially uniformly dispersed in it. Comparison of the time required for forming a single final particle for the two cases revealed that for ZnSe particles with diameter smaller than 3.5 nm the predicted formation times were approximately the same. Surprisingly, for particles larger than 3.5 nm, the scenario that required diffusion of a reactant to the interface and formation of nuclei via a reaction at the interface led to the formation of a single particle faster than the scenario that started with nuclei uniformly dispersed in the droplet. Analysis of intermediate cluster populations indicates that the "sweeper" clusters are more effective in accelerating cluster coalescence when the nuclei are supplied gradually, as in the first scenario, compared to spontaneous nucleation throughout the domain. Generalized equations were obtained that describe the evolution of the number of different cluster sizes during coalescence starting from an initially monodispersed population of nuclei thus extending the classical theory of coalescence of monodisperse aerosols in an infinite domain to include coalescence in finite spherical domains with reflective boundaries. Finally, a generalized phenomenological model describing an energy balance during coalescence of two nanoparticles was developed. The reduction in the surface area of the coalescing system was modeled to be the source of thermal energy released due to the formation of additional bonds in the bulk of the coalesced particles. The temperature rise of the coalescing system was predicted for adiabatic coalescence and for coalescence with energy dissipation to a surrounding medium. Generalized equations were developed by scaling the temperature rise with its maximum value that corresponds to adiabatic conditions and the time with a characteristic time for coalescence obtained from the literature that depends on the mechanism (e.g., viscous flow, bulk diffusion, or surface diffusion). As a case study, the effects of the size of coalescing ZnSe nanoparticles on the temperature evolution of the coalescing system were studied by assuming that surface diffusion is the predominant mechanism for coalescence in this system. This modeling and simulation study of nanoparticle nucleation and coalescence presented in this thesis has revealed new phenomena and led to generalized models that can be used for studying such systems. Our work extended the classical theory for coalescence in an infinite domain to include finite spherical domains with reflective boundaries and provided a generalized approach for the analysis of transient thermal effects occurring during coalescence of two nanoparticles.Publication Role of Strongly Interacting Additives in Tuning the Structure and Properties of Polymer Systems(2011-09) Daga, Vikram KumarBlock copolymer (BCP) nanocomposites are an important class of hybrid materials in which the BCP guides the spatial location and the periodic assembly of the additives. High loadings of well-dispersed nanofillers are generally important for many applications including mechanical reinforcing of polymers. In particular the composites shown in this work might find use as etch masks in nanolithography, or for enabling various phase selective reactions for new materials development. This work explores the use of hydrogen bonding interactions between various additives (such as homopolymers and non-polymeric additives) and small, disordered BCPs to cause the formation of well-ordered morphologies with small domains. A detailed study of the organization of homopolymer chains and the evolution of structure during the process of ordering is performed. The results demonstrate that by tuning the selective interaction of the additive with the incorporating phase of the BCP, composites with significantly high loadings of additives can be formed while maintaining order in the BCP morphology. The possibility of high and selective loading of additives in one of the phases of the ordered BCP composite opens new avenues due to high degree of functionalization and the proximity of the additives within the incorporating phase. This aspect is utilized in one case for the formation of a network structure between adjoining additive cores to derive mesoporous inorganic materials with their structures templated by the BCP. The concept of additive-driven assembly is extended to formulate BCP-additive blends with an ability to undergo photo-induced ordering. Underlying this strategy is the ability to transition a weakly interacting additive to its strongly interacting form. This strategy provides an on-demand, non-intrusive route for formation of well-ordered nanostructures in arbitrarily defined regions of an otherwise disordered material. The second area explored in this dissertation deals with the incorporation of additives into photoresists for next generation extreme ultra violet (EUV) photolithography applications. The concept of hydrogen bonding between the additives and the polymeric photoresist was utilized to cause formation of a physical network that is expected to slow down the diffusion of photoacid leading to better photolithographic performance (25-30 nm resolution obtained).