Environment plays an important role in the evolution of galaxies. In particular, denser environments, such as galaxy clusters and large-scale field filaments of the cosmic web have been found to reduce star formation in galaxies. The intersection of these environments provides an interesting regime of study. We investigate how cosmic filaments impact the quenching of galaxies within one virial radius of 324 simulated clusters. We use hydrodynamic runs from The Three Hundred Project along with the cosmic web extractor DisPerSE to track filaments and the structure finder VELOCIraptor to identify halos hosting galaxies. Limited by the resolution of the simulation, we examine star formation indirectly by way of galaxy colour and cold gas fraction. We find that cluster galaxies residing closer to filaments tend to be star-forming, bluer, and contain more cold gas than their counterparts further away from filaments. This is in stark contrast with galaxies residing outside of clusters, where galaxies close to filaments show clear signs of density related pre-processing. Careful examination of flows around and into cluster galaxies strongly suggests that the colder, dynamically coherent hydrodynamic streams along intra-cluster filaments partially shield galaxies close to them from strangulation by the hot, dense intra-cluster medium. These streams, in addition to the reduced density contrast of intra-cluster filaments with the intra-cluster medium, also limit the ram pressure stripping experienced by cluster galaxies. We further examine stripping in the context of gas disturbances in phase space to create a classification for wet and dry galaxies. / Thesis / Master of Science (MSc)

The overall goal of this work is to expand the materials library for the fused filament fabrication (FFF) material extrusion additive manufacturing (AM) process through innovations in the FFF process, post-process, and polymer composition. This research was conducted at two opposing ends of the FFF-processing temperature: low processing temperature (<100 °C) for pharmaceutical applications and high processing temperatures (>300 °C) for high-performance structural polymer applications. Both applications lie outside the typical range for FFF (190-260 °C). To achieve these goals, both the material and process were modified. Due to the low processing temperature requirements for pharmaceutical active ingredients, a water-soluble, low melting temperature material (sulfonated poly(ethylene glycol)) series was used to explore how different counterions affect FFF processing. The strong ionic interaction within poly(PEG8k-co-CaSIP) resulted in the best print quality due to the higher viscosity (105 Pa∙s) allowing the material to hold shape in the melt and the high-nucleation producing small spherulites mitigating the layer warping. Fillers were then explored to observe if an ionic filler would produce a similar effect. The ionic filler (calcium chloride) in poly(PEG8k-co-NaSIP) altered the crystallization kinetics, by increasing the nucleation density and viscosity, resulting in improved printability of the semi-crystalline polymer. A methodology for embedding liquids and powders into thin-walled capsules was developed for the incorporation of low-temperature active ingredients into water-soluble materials that uses a higher processing temperature than the actives are compatible with. By tuning the thickness of the printed walls, the time of internal liquid release was controlled during dissolution. This technique was used to enable the release of multiple liquids and powders at different times during dissolution. To enable the printing of high-temperature, high-performance polymers, an inverted desktop-scale heated chamber with the capability of reaching over 300 °C was developed for FFF. The design was integrated onto a FFF machine and was used to successfully print polyphenylsulfone which resulted in a 48% increase in tensile strength (at 200 °C) when compared to printing at room temperature. Finally, the effects of thermal processing conditions for printing ULTEM® 1010 were studied by independently varying the i) nozzle temperature, ii) environment temperature, and iii) post-processing conditions. The nozzle temperature primarily enables flow through the nozzle and needs to be set to at least 360 °C to prevent under extrusion. The environment temperature limits the part warping, as it approaches Tg (217 °C), and improves the layer bonding by decreasing the rate of cooling that allows more time for polymer chain entanglement. Post-processing for a longer time above Tg (18 hrs at 260 °C) promotes further entanglement, which increases the part strength (50% increase in yield strength); however, the part is susceptible to deformation. A post-processing technique was developed to preserve the parts' shape by packing solid parts into powdered salt. / Doctor of Philosophy / Fused filament fabrication (FFF) is the most widely used additive manufacturing (also referred to as 3D printing) process in industry, education, and for hobbyists. However, there is a limited number of materials available for FFF, which limits the potential of using FFF to solve engineering problems. This work focuses on material and machine modifications to enable FFF for use in both pharmaceutical and structural applications. Specifically, many pharmaceutical active ingredients require processing temperatures lower than what FFF typically uses. A low-temperature water-soluble material was altered by incorporating salt ions and ionic fillers separately. The differences in the printability were directly correlated to the measured variations in the viscosity and crystallization material properties. Alternatively, a technique is presented to embed liquids and powders into thin-walled, water-soluble printed parts that are processed using typical FFF temperatures, where the embedded material remains cool. The release time of the embedded material during dissolution is controlled by the thickness of the capsule structure. For structural applications, a machine was developed to allow for the processing of high-performance, high-temperature polymers on a desktop-scale system. This system uses an inverted heated chamber that uses natural convection to be able to heat the air around the part and not the electric components of the machine. The heated environment allows the part to remain at a higher temperature for a longer time, which enables a better bond between printed layers to achieve high-strength printed parts using high-performance materials. This machine was used to characterize the thermal processing effect for printing the high-performance polymer ULTEM® 1010. The nozzle temperature, environment temperature, and post-processing were tested where i) a higher nozzle temperature (360 °C) increases strength and prevents under extrusion, ii) a higher environment temperature (≥200 °C) increases the strength by slowing cooling and decreases warping by limiting the amount of shrinkage the occurs during printing, and iii) post-processing in powdered salt (18 hrs at 260 °C) increases part strength (50%) by allowing the printed roads to fuse.

Thermoplastic composite filament winding is an on-line consolidation process, where the composite experiences a complex temperature history and undergoes a number of temperature history affected microstructural changes that influence the structure's subsequent properties. These changes include melting, crystallization, void formation, degradation and consolidation. In the present study, models of the thermoplastic filament winding process were developed to identify and understand the relationships between process variables and the structure quality. These include models that describe the heat transfer, consolidation and crystallization processes that occur during fabrication of a filament wound composites structure. A comprehensive thermal model of the thermoplastic filament winding process was developed to calculate the temperature profiles in the composite substrate and the towpreg temperature before entering the nippoint. A two-dimensional finite element heat transfer analysis for the composite-mandrel assembly was formulated in the polar coordinate system, which facilitates the description of the geometry and the boundary conditions. A four-node 'sector element' was used to describe the domain of interest. Sector elements were selected to give a better representation of the curved boundary shape which should improve accuracy with fewer elements compared to a finite element solution in the Cartesian-coordinate system. Hence the computational cost will be reduced. The second thermal analysis was a two-dimensional, Cartesian coordinate, finite element model of the towpreg as it enters the nippoint. The results show that the calculated temperature distribution in the composite substrate compared well with temperature data measured during winding and consolidation. The analysis also agrees with the experimental observation that the melt region is formed on the surface of the incoming towpreg in the nippoint and not on the substrate. Incorporated with the heat transfer analysis were the consolidation and crystallization models. These models were used to calculate the degree of interply bonding and the crystallinity achieved during composite manufacture. Bonding and crystallinity developments during the winding process were investigated using the model. It is concluded that lower winding speed, higher hot-air heater nozzle temperature, and higher substrate preheating temperature yield higher nippoint temperature, better consolidation and a higher degree of crystallization. Complete consolidation and higher matrix crystallization will result in higher interlaminar strength of the wound composite structure. / Master of Science

Homologous recombination (HR) is an essential mechanism for accurate repair of DNA double-strand breaks (DSBs). However, HR must be tightly controlled because excessive or unwanted HR events can lead to genome instability, which is a prerequisite for premature aging and cancer development. A critical step of HR is the loading of RAD51 molecules onto single-stranded DNA regions generated in the vicinity of the DSB, leading to the formation of a nucleoprotein filament. Several DNA helicases have been involved in the regulation of the HR process. One of these is human FBH1 (F-box DNA helicase 1) that is a member of SF1 superfamily of helicases. As a unique DNA helicase, FBH1 additionally possesses a conserved F-box motif that allows it to assemble into an SCF complex, an E3 ubiquitin ligase that targets proteins for degradation. FBH1 has been implicated in the restriction of nucleoprotein filament stability. However, the exact mechanism of how FBH1 controls the RAD51 action is still not certain. In this work, we revealed that FBH1 actively disassembles RAD51 nucleoprotein filament. We also show that FBH1 interacts with RAD51 and RPA physically in vitro. Based on these data, we propose a potential mechanism of FBH1 antirecombinase function.

Na busca pela substituição dos materiais convencionais por materiais com alto desempenho estrutural nos mais variados setores do mercado, os materiais compósitos têm recebido cada vez mais a confiança dos engenheiros projetistas. Isto devido às características, comparadas com materiais convencionais como: baixa densidade associada à excelente rigidez e resistência estrutural, alta resistência à corrosão, resistência à temperaturas elevadas e ótimos resultados estéticos. Um dos processos de fabricação bastante utilizado para a produção de peças nestes materiais é o processo conhecido como Filament Winding ou \"Enrolamento Filamentar\". Essa técnica consiste em revestir a superfície de um mandril, através do enrolamento de fibras contínuas impregnadas por um banho de resina. As fibras utilizadas nesse processo, geralmente de vidro ou de carbono são posicionadas em uma trajetória calculada por algoritmos matemáticos que determinam o seu posicionamento adequado, o que está diretamente relacionado às propriedades mecânicas desejadas na peça final. Desta forma, este trabalho tem por objetivo desenvolver um sistema computacional para o cálculo da trajetória de deposição da fibra sobre o mandril e seu seqüenciamento durante o processo de Filament Winding. Foram desenvolvidas e implementadas computacionalmente estratégias para os revestimentos circular, helicoidal e polar utilizando trajetórias geodésicas, o que abrange a grande maioria das peças fabricadas por este processo. Os resultados foram validados com exemplo da literatura e, também através de interface com sistema CAD. / ln the search for the replacement of conventional materials by those with high structural performance, the reinforced composite materials have increasingly used by engineers during the product development process. The main reasons lies in their excellent characteristics compared to conventional materials such as: low-density associated with high stiffness and strength, good tolerance to corrosion, resistance to high temperatures and good aesthetic results. One of the manufacturing processes most used to produce composite parts is the Filament Winding. This technique consists in winding continuous impregnated fiber by a bath of resin along a mandrel. The fibers used are generally of glass or carbon, guided through a trajectory calculated by mathematical algorithms. Because of the importance of this study, this work proposes and develops a computational system to calculate the trajectories and sequences of the fiber in the Filament Winding process, considering geodesic trajectories during the hoop, helical and polar winding, which cover the majority of parts produced by this process. The routines and system are validated with the literature as well as in the CAD system.

Na busca pela substituição dos materiais convencionais por materiais com alto desempenho estrutural nos mais variados setores do mercado, os materiais compósitos têm recebido cada vez mais a confiança dos engenheiros projetistas. Isto devido às características, comparadas com materiais convencionais como: baixa densidade associada à excelente rigidez e resistência estrutural, alta resistência à corrosão, resistência à temperaturas elevadas e ótimos resultados estéticos. Um dos processos de fabricação bastante utilizado para a produção de peças nestes materiais é o processo conhecido como Filament Winding ou \"Enrolamento Filamentar\". Essa técnica consiste em revestir a superfície de um mandril, através do enrolamento de fibras contínuas impregnadas por um banho de resina. As fibras utilizadas nesse processo, geralmente de vidro ou de carbono são posicionadas em uma trajetória calculada por algoritmos matemáticos que determinam o seu posicionamento adequado, o que está diretamente relacionado às propriedades mecânicas desejadas na peça final. Desta forma, este trabalho tem por objetivo desenvolver um sistema computacional para o cálculo da trajetória de deposição da fibra sobre o mandril e seu seqüenciamento durante o processo de Filament Winding. Foram desenvolvidas e implementadas computacionalmente estratégias para os revestimentos circular, helicoidal e polar utilizando trajetórias geodésicas, o que abrange a grande maioria das peças fabricadas por este processo. Os resultados foram validados com exemplo da literatura e, também através de interface com sistema CAD. / ln the search for the replacement of conventional materials by those with high structural performance, the reinforced composite materials have increasingly used by engineers during the product development process. The main reasons lies in their excellent characteristics compared to conventional materials such as: low-density associated with high stiffness and strength, good tolerance to corrosion, resistance to high temperatures and good aesthetic results. One of the manufacturing processes most used to produce composite parts is the Filament Winding. This technique consists in winding continuous impregnated fiber by a bath of resin along a mandrel. The fibers used are generally of glass or carbon, guided through a trajectory calculated by mathematical algorithms. Because of the importance of this study, this work proposes and develops a computational system to calculate the trajectories and sequences of the fiber in the Filament Winding process, considering geodesic trajectories during the hoop, helical and polar winding, which cover the majority of parts produced by this process. The routines and system are validated with the literature as well as in the CAD system.

The biological function and the technological applications of semiflexible polymers, such as DNA, actin filaments and carbon nanotubes, strongly depend on their rigidity. Semiflexible polymers are characterized by their persistence length, the definition of which is the subject of the first part of this thesis. Attractive interactions, that arise e.g.~in the adsorption, the condensation and the bundling of filaments, can change the conformation of a semiflexible polymer. The conformation depends on the relative magnitude of the material parameters and can be influenced by them in a systematic manner. In particular, the morphologies of semiflexible polymer rings, such as circular nanotubes or DNA, which are adsorbed onto substrates with three types of structures, are studied: (i) A topographical channel, (ii) a chemically modified stripe and (iii) a periodic pattern of topographical steps. The results are compared with the condensation of rings by attractive interactions. Furthermore, the bundling of two individual actin filaments, whose ends are anchored, is analyzed. This system geometry is shown to provide a systematic and quantitative method to extract the magnitude of the attraction between the filaments from experimentally observable conformations of the filaments. / Die biologische Funktion und die technologischen Anwendungen semiflexibler Polymere, wie DNA, Aktinfilamente und Nanoröhren aus Kohlenstoff, werden wesentlich von deren Biegesteifigkeit bestimmt. Semiflexible Polymere werden charakterisiert durch ihre Persistenzlänge, mit deren Definition sich der erste Teil dieser Arbeit befasst. Anziehende Wechselwirkungen, wie sie z.B. bei der Adsorption, der Kondensation und der Bündelung von Filamenten auftreten, können die Konformation eines semiflexiblen Polymers verändern. Die Konformation ist dabei abhängig von der relativen Größe der Materialparameter und kann durch diese gezielt beeinflusst werden. Im Einzelnen werden hier die Morphologien semiflexibler Polymerringe, wie z.B. DNA oder ringförmiger Nanoröhren, untersucht, die auf drei verschieden strukturierten Substraten adsorbieren: (i) Ein topographischer Kanal, (ii) ein chemisch modifizierter Streifen und (iii) ein periodisches Muster topographischer Oberflächenstufen. Die Ergebnisse werden mit der Kondensation von Ringen durch anziehende Wechselwirkungen verglichen. Des Weiteren wird die Bündelung zweier Aktinfilamente, deren Enden verankert sind, untersucht. Diese Systemgeometrie liefert eine systematische Methode, um die Stärke der Anziehung zwischen den Filamenten aus experimentell beobachtbaren Konformationen zu berechnen.

The filament-winding process produces quality consistent composite parts for many industries. Filament winding allows for consistent quality parts by automating the winding process. A recent development of filament winding is the Lotus process. The Lotus process reverses conventional filament winding by leaving the mandrel stationary and winding composite fiber around the mandrel. The automated Lotus filament-winding machine is controlled by four-axis control manipulating the Lotus ring around a fixed mandrel. This allows Lotus filament winding to wind parts that do not have a linear axis. Lotus filament winding is in its early stages of development. As a second step in the development of Lotus filament winding a method of automatic part-to-machine manipulation has been developed. Parts wound on the new automatic-manipulated Lotus machine have comparable quality and appearance to those made by conventional winding.

Im Laufe der Evolution haben Bakterienarten äußerst vielfältige und ausgeklügelte extrazelluläre Strukturen entwickelt, die es ihnen ermöglichen, Substrate in ihre Umgebung abzugeben oder Wirtszellen während einer Invasion anzugreifen. Diese Sekretionssysteme sind an vielen bakteriellen Mechanismen wie Biofilmbildung, Zellmotilität, Virulenz oder Gentransfer und Verbreitung von Antibiotikaresistenzen beteiligt. Das Verständnis des Aufbaus und der Regulierung dieser Strukturen ist angesichts der zunehmenden Entwicklung multiresistenter Bakterien von entscheidender Bedeutung. Darüber hinaus geht der Aufbau solcher Strukturen unweigerlich auf Kosten wertvoller zellulärer Energieressourcen, was einen spannenden Parameter darstellt, um zu untersuchen, wie Bakterien den optimalen Mechanismus zum Ausgleich zwischen zellulären Mechanismen und Energieverbrauch wählen. Diese Arbeit konzentriert sich auf den Aufbau und die Regulierung bakterieller extrazellulärer Filamente, insbesondere des flagellaren Typ-III-Sekretionssystems (T3SS). Im ersten Kapitel werden Defekte in der Zellmorphologie aufgezeigt, die durch die Deletion des FlhE-Proteins während des Zusammenbaus der Flagellen verursacht werden, was die Bedeutung der Regulierung des Membranpotentials verdeutlicht. Das zweite Kapitel zeigt, dass der Assemblierungsmechanismus der Flagellen-Filamente, welcher dem Injektions-Diffusions-Modell entspricht, im Vergleich zu anderen Sekretionssystemen schneller ist und für die Energieerhaltung optimiert ist. Das dritte Kapitel untersucht die Rolle des Pilus beim Plasmid-Transfer, der mit einem Typ-IV-Sekretionssystem (T4SS) assoziiert ist, und liefert zusätzliche Hinweise darauf, dass der Pilus als Kanal für den Plasmid-DNA-Transfer dienen kann. Im letzten Kapitel wird ein neuer Biosensor zur Messung des Gehalts an bis-(3'-5')-zyklischem Diguanosinmonophosphat (c-di-GMP) entwickelt, einem entscheidenden Molekül in bakteriellen Mechanismen, die Zellmotilität und Biofilmbildung miteinander verbinden. Insgesamt bietet diese Arbeit Einblicke in die Regulation des flagellaren T3SS und des T4SS-Pilus, ein neues Werkzeug zur Untersuchung von c-di-GMP und Einblicke, wie Bakterien entscheidende Überlebensparameter und die Optimierung eines energiesparenden Aufbaus abwägen. / Through evolution, bacterial species have developed highly diverse and sophisticated extracellular structures enabling them to secrete substrates in their environment or to target host cells during invasion. Those secretion systems are involved in many bacterial mechanisms such as biofilm formation, cell motility, virulence or gene transfer and antibiotic resistance dissemination. Understanding the assembly and regulation of these structures is crucial due to the increasing development of multi-drug resistant bacteria. Moreover, the assembly of such structures inevitably comes at the cost of valuable cellular energy resources, representing an exciting parameter to study how bacteria selected the optimal mechanism to balance cellular mechanisms and energy consumption. This thesis focuses on the assembly and regulation of bacterial extracellular filaments, notably the flagellar type III secretion system (T3SS) flagellum . The first chapter reveals cell morphology defects caused by the deletion of the FlhE protein during flagellum assembly, highlighting the importance of membrane potential regulation . Chapter two illustrates that the flagellar filament assembly mechanism, following the injection-diffusion model, is faster compared to other secretion systems and optimized for energy conservation. The third chapter investigates the role of the pilus in plasmid transfer, associated with a type IV secretion system (T4SS), and gives additional evidence that the pilus may also act as a channel for plasmid DNA transfer. The final chapter develops a new biosensor for measuring bis-(3’-5’)-cyclic diguanosine monophosphate (c-di-GMP) levels, a crucial molecule in bacterial mechanisms linking cell motility and biofilm formation. Overall, this thesis provides insights into the regulation of the flagellar T3SS and the T4SS pilus, a new tool to study c-di-GMP, and how bacteria balance crucial survival parameters and energy-conserving assembly optimization .

Additive manufacturing (AM) is a rapidly growing and evolving form of product development that has the potential to revolutionize both the industrial and academic spheres. For example, AM offers much greater freedom of design while producing significantly less waste than most traditional manufacturing techniques such as injection and blow molding. Filament-based material extrusion AM, commonly referred to as fused filament fabrication (FFF), is one of the most well-known AM modalities using a polymeric feedstock; however, several obstacles currently prohibit widespread use of this manufacturing technique to produce end-use products, which will be discussed in this dissertation. Specifically, a severely limited material catalog restricts tailored product development and the variety of applications. Additionally, poor interlayer adhesion results in anisotropic mechanical properties which can lead to failure, an issue not often observed in traditional manufacturing techniques. A review of the current state of the art research in the field of FFF, focusing on the multiphysics-based modeling of the system and exploring some empirically determined relationships, is presented herein to provide a more thorough understanding of FFF and its complexities. This review further guides the work discussed in this dissertation. The primary focus of this dissertation is to expand the fundamental understanding of the FFF process, which has proven difficult to measure directly. On this size scale, introduction of measurement devices such as thermocouples and pressure transducers can significantly alter the behavior of the process or require major changes to the geometry of the system, leading to spurious measurements, incorrect outcomes, and/or conclusions. Therefore, the research presented in this dissertation focuses on the development and validation of predictive models based on first principles approaches that can provide information leading to the optimization of printing parameters and exploration of novel and/or modified materials without an exhaustive and inefficient trial-and-error process. The first potential issue a novel material may experience in FFF is an inability to extrude from the heated nozzle. Prior to this work, no efforts were focused on the molten material inside the liquefier and its propensity to flow in the reverse direction through the annular region between the filament and the nozzle wall, referred to as annular backflow. The study presented in this dissertation explores this phenomenon, determining its cause and sensitivity to processing parameters and material properties. A dimensionless number, named the "Flow Identification Number" or FIN, is defined that can predict the propensity to backflow based on the material's shear thinning behavior, the filament diameter, the nozzle diameter, and the filament feed rate and subsequent pressure inside the nozzle. An analysis of the FIN suggested that the backflow potential of a given material is most sensitive to the filament diameter and its shear thinning behavior (power law index). The predictive model and FIN were explored using three materials with significantly different onsets of shear thinning. The experiments validated both the backflow model and a previously derived buckling model, leading to the development of a rapid screening technique to efficiently estimate the extrudability of a material in FFF. Following extrusion from the nozzle, the temperature profile of the deposited filament will determine nearly all of the mechanical properties of the printed part as well as the geometry of the individual roads and layers because of its temperature dependent viscoelastic behavior. Therefore, to better understand the influence of the temperature profile on the evolution of the road geometry and subsequent interlayer bonding, a three-dimensional finite element heat transfer analysis was developed. The focus of this study is the high use temperature engineering thermoplastic polymer polyetherimide, specifically Ultem™ 1010, which had not been studied in prior modeling analyses but presents significant challenges in terms of large thermal gradients and challenging AM machine requirements. Through this analysis, it was discovered that convective cooling dominated the heat transfer (on the desktop FFF scale) producing a significant cross-sectional temperature gradient, whereas the gradient along the axis was observed to be significantly smaller. However, these results highlighted a primary limitation in computer modeling based on computational time requirements. This study, utilizing a well-defined three-dimensional model based on a geometry measured empirically, produced results describing 0.5 s of printing time in the printing process and elucidated great details in the road shape and thermal profile, but required more than a week of computation time, suggesting a need for to modify the modeling approach while still accurately capturing the physics of the FFF layer deposition process. The determination of the extensive time required to converge the three-dimensional model, as well as the identification of a relative lack of axial thermal transfer, led to the development of a two-dimensional, cross-sectional heat transfer analysis based on a finite difference approach. This analysis was coupled with a diffusion model and a stress development model to estimate the recovery of the bulk strength and warping potential of a printed part, respectively. Through this analysis, it was determined that a deposited road may remain above Tg for 2-10 s, depending on the layer time, or time required for the nozzle to pass a specific point in the x-y plane between each layer. The predicted strength recovery was significantly overestimated, leading to the discovery of the extreme sensitivity of the predictive models to the relaxation time of a material, particularly at long layer times. When the deposited filament has enough time to attain an equilibrium temperature, small changes in the relaxation time of the material resulted in significant changes in the predicted healing results. These results highlight the need for exact estimations of the material parameters to accurately predict the properties of the final print. / Doctor of Philosophy / Additive manufacturing (AM), particularly filament-based material extrusion additive manufacturing, commonly known as fused filament fabrication (FFF), has recently become the subject of much study with the goal of utilizing it to produce parts tailored to specific purposes quickly and cheaply. AM is especially suited to this purpose due to its ability to produce highly complex parts with the ability to change design very easily. Furthermore, AM typically produces less waste than many traditional manufacturing techniques due to the process building a part layer by layer rather than removing unneeded material from a larger piece, resulting in a cheaper process. These freedoms make AM, and FFF in particular, highly prized among industrial producers. However, numerous challenges prevent the adoption of FFF by these companies. Particularly, a lack of available material options and anisotropic material properties lead to issues when attempting to produce a part targeted for use in a specific field. FFF is primarily commercially limited to two materials: polylactic acid (PLA) and acrylonitrile-butadiene-styrene (ABS) with a few other materials available in more specialized fields. However, essentially all these materials are limited to low use temperatures (less than 300 °C) and are primarily amorphous or with nearly negligible amounts of crystallinity. This severely limits the ability to tailor a printed part to a specific purpose and restricts the use of printed parts to applications requiring very low strengths. This is one reason why FFF, and most types of AM, is limited to the prototyping field rather than end-use applications. The other reason, anisotropic mechanical properties, is caused by the building methodology of AM. Creating a part layer by layer naturally introduces potential areas of weakness at the joining of the layers. If bulk properties are not recovered, the interlayer bond acts as a stress concentrator under load and will break before the bulk material. The work presented in this dissertation proposes methods to better understand the FFF system in order to address these two issues, leading to the optimization of the printing process and ability to expand the material catalog, particularly in the direction of high use temperature materials. The research discussed herein attempts to develop predictive models that may allow exploration into the FFF system which can be difficult to do experimentally, and by predicting the properties of a printed part, the models can guide future experimentation in FFF without the need for an extensive trial-and-error process. The work presented in this dissertation includes exploring the flow phenomena inside the FFF nozzle to determine extrudability as well as two-dimension and three-dimension heat transfer models with the goal of describing the viscoelastic, flow, diffusion, and stress development phenomena present in FFF.