This thesis presents various integrated antenna solutions for different types of systems and applications, e.g. wireless sensors, broadband handsets, advanced base stations, MEMS-based reconfigurable front-ends, automotive anti-collision radars, and large area electronics. For wireless sensor applications, a T-matched dipole is proposed and integrated in an electrically small body-worn sensor node. Measurement techniques are developed to characterize the port impedance and radiation properties. Possibilities and limitations of the planar inverted cone antenna (PICA) for small handsets are studied experimentally. Printed slot-type and folded PICAs are demonstrated for UWB handheld terminals. Both monolithic and hybrid integration are applied for electrically steerable array antennas. Compact phase shifters within a traveling wave array antenna architecture, on single layer substrate, is investigated for the first time. Radio frequency MEMS switches are utilized to improve the performance of reconfigurable antennas at higher frequencies. Using monolithic integration, a 20 GHz switched beam antenna based on MEMS switches is implemented and evaluated. Compared to similar work published previously, complete experimental results are here for the first time reported. Moreover, a hybrid approach is used for a 24 GHz switched beam traveling wave array antenna. A MEMS router is fabricated on silicon substrate for switching two array antennas on a LTCC chip. A concept of nano-wire based substrate integrated waveguides (SIW) is proposed for millimeter-wave applications. Antenna prototypes based on this concept are successfully demonstrated for automotive radar applications. W-band body-worn nonlinear harmonic radar reflectors are proposed as a means to improve automotive radar functionality. Passive, semi-passive and active nonlinear reflectors consisting of array antennas and nonlinear circuitry on flex foils are investigated. A new stretchable RF electronics concept for large area electronics is demonstrated. It incorporates liquid metal into microstructured elastic channels. The prototypes exhibit high stretchability, foldability, and twistability, with maintained electrical properties. / wisenet

This thesis investigates the use of high-power lasers for synchrotron radiation sources with high brilliance, from the EUV to the hard X-ray spectral range. Hereby lasers accelerate electrons by laser-wakefield acceleration (LWFA), act as optical undulators, or both. Experimental evidence shows for the first time that LWFA electron bunches are shorter than the driving laser and have a length scale comparable to the plasma wavelength. Furthermore, a first proof of principle experiment demonstrates that LWFA electrons can be exploited to generate undulator radiation. Building upon these experimental findings, as well as extensive numerical simulations of Thomson scattering, the theoretical foundations of a novel interaction geometry for laser-matter interaction are developed. This new method is very general and when tailored towards relativistically moving targets not being limited by the focusability (Rayleigh length) of the laser, while it does not require a waveguide. In a theoretical investigation of Thomson scattering, the optical analogue of undulator radiation, the limits of Thomson sources in scaling towards higher peak brilliances are highlighted. This leads to a novel method for generating brilliant, highly tunable X-ray sources, which is highly energy efficient by circumventing the laser Rayleigh limit through a novel traveling-wave Thomson scattering (TWTS) geometry. This new method suggests increases in X-ray photon yields of 2-3 orders of magnitudes using existing lasers and a way towards efficient, optical undulators to drive a free-electron laser. The results presented here extend far beyond the scope of this work. The possibility to use lasers as particle accelerators, as well as optical undulators, leads to very compact and energy efficient synchrotron sources. The resulting monoenergetic radiation of high brilliance in a range from extreme ultraviolet (EUV) to hard X-ray radiation is of fundamental importance for basic research, medical applications, material and life sciences and is going to significantly contribute to a new generation of radiation sources and free-electron lasers (FELs).

Die vorliegende Arbeit beschäftigt sich in Experiment und Theorie mit Laser-Plasma beschleunigten Elektronen und optischen Undulatoren zur Erzeugung von brillianter Synchrotronstrahlung. Zum ersten Mal wird experimentell nachgewießen, dass laserbeschleunigte Elektronenpulse kürzer als 30 fs sind. Ferner werden solche Elektronenpulse erstmalig in einem Demonstrationsexperiment durch einen magnetischen Undulator als Synchrotronstrahlenquelle genutzt. Aufbauend auf diesen experimentellen Erkenntnissen, sowie umfangreichen numerischen Simulationen zur Thomsonstreuung, werden die theoretischen Grundlagen einer neuartigen Interaktionsgeometrie für Laser-Materie Wechselwirkungen entwickelt. Diese neue, in der Anwendbarkeit sehr allgemeine Methode basiert auf raum-zeitlicher Laserpulsformung durch nichtlineare Winkeldispersion wie diese durch VLS- (varied-line spacing) Gitter erzeugt werden kann und hat den Vorteil nicht durch die Fokussierbarkeit des Lasers (Rayleighlänge) begrenzt zu sein. Zusammen mit laserbeschleunigten Elektronen ermöglicht dieser traveling-wave Thomson scattering (TWTS) benannte Ansatz neuartige, nur auf optischer Technologie basierende Synchrotronstrahlenquellen mit Zentimeter bis Meter langen optische Undulatoren. Die hierbei mit existierenden Lasern erzielbaren Brillianzen übersteigen diese bestehender Thomsonquellen-Designs um 2-3 Größenordnungen. Die hier vorgestellten Ergebnisse weisen weit über die Grenzen der vorliegenden Arbeit hinaus. Die Möglichkeit Laser als Teilchenbeschleuniger und auch optischen Undulator zu verwenden führt zu bauartbedingt sehr kompakten und energieeffizienten Synchrotronstrahlungsquellen. Die hieraus resultierende monochromatische Strahlung hoher Brillianz in einem Wellenlängenbereich von extremen ultraviolett (EUV) zu harten Röntgenstrahlen ist für die Grundlagenforschung, medizinische Anwendungen, Material- und Lebenswissenschaften von fundamentaler Bedeutung und wird maßgeblich zu einer neuen Generation ultrakurzer Strahlungsquellen und freien Elektronenlasern (FELs) beitragen. / This thesis investigates the use of high-power lasers for synchrotron radiation sources with high brilliance, from the EUV to the hard X-ray spectral range. Hereby lasers accelerate electrons by laser-wakefield acceleration (LWFA), act as optical undulators, or both. Experimental evidence shows for the first time that LWFA electron bunches are shorter than the driving laser and have a length scale comparable to the plasma wavelength. Furthermore, a first proof of principle experiment demonstrates that LWFA electrons can be exploited to generate undulator radiation. Building upon these experimental findings, as well as extensive numerical simulations of Thomson scattering, the theoretical foundations of a novel interaction geometry for laser-matter interaction are developed. This new method is very general and when tailored towards relativistically moving targets not being limited by the focusability (Rayleigh length) of the laser, while it does not require a waveguide. In a theoretical investigation of Thomson scattering, the optical analogue of undulator radiation, the limits of Thomson sources in scaling towards higher peak brilliances are highlighted. This leads to a novel method for generating brilliant, highly tunable X-ray sources, which is highly energy efficient by circumventing the laser Rayleigh limit through a novel traveling-wave Thomson scattering (TWTS) geometry. This new method suggests increases in X-ray photon yields of 2-3 orders of magnitudes using existing lasers and a way towards efficient, optical undulators to drive a free-electron laser. The results presented here extend far beyond the scope of this work. The possibility to use lasers as particle accelerators, as well as optical undulators, leads to very compact and energy efficient synchrotron sources. The resulting monoenergetic radiation of high brilliance in a range from extreme ultraviolet (EUV) to hard X-ray radiation is of fundamental importance for basic research, medical applications, material and life sciences and is going to significantly contribute to a new generation of radiation sources and free-electron lasers (FELs).

This research investigates the realization of parametric amplification in superconducting circuits and structures where nonlinearity is provided by Josephson junction (JJ) elements. We aim to develop a systematic analysis over JJ-based devices toward design of novel traveling-wave Josephson parametric amplifiers (TW-JPA). Chapters of this thesis fall into three categories: lumped JPA, superconducting periodic structures and discrete Josephson transmission lines (DJTL). The unbiased Josephson junction (JJ) is a nonlinear element suitable for parametric amplification through a four-photon process. Two circuit topologies are introduced to capture the unique property of the JJ in order to efficiently mix signal, pump and idler signals for the purpose of signal amplification. Closed-form expressions are derived for gain characteristics, bandwidth determination, noise properties and impedance for this kind of parametric power amplifier. The concept of negative resistance in the gain formulation is observed. A design process is also introduced to find the regimes of operation for gain achievement. Two regimes of operation, oscillation and amplification, are highlighted and distinguished in the result section. Optimization of the circuits to enhance the bandwidth is also carried out. Moving toward TW-JPA, the second part is devoted to modelling the linear wave propagation in a periodic superconducting structure. We derive closed-form equations for dispersion and s-parameters of infinite and finite periodic structures, respectively. Band gap formation is highlighted and its potential applications in the design of passive filters and resonators are discussed. The superconducting structures are fabricated using YBCO and measured, illustrating a good correlation with the numerical results. A novel superconducting Transmission Line (TL), which is periodically loaded by Josephson junctions (JJ) and assisted by open stubs, is proposed as a platform to realize a traveling-wave parametric device. Using the TL model, this structure is modeled by a system of nonlinear partial differential equations (PDE) with a driving source and mixed-boundary conditions at the input and output terminals, respectively. This model successfully emulates parametric and nonlinear microwave propagation when long-wave approximation is applicable. The influence of dispersion to sustain three non-degenerate phased-locked waves through the TL is highlighted. A rigorous and robust Finite Difference Time Domain (FDTD) solver based on the explicit Lax-Wendroff and implicit Crank-Nicolson schemes has been developed to investigate the device responses under various excitations. Linearization of the wave equation, under small-amplitude assumption, dispersion and impedance analysis is performed to explore more aspects of the device for the purpose of efficient design of a traveling-wave parametric amplifier. Knowing all microwave characteristics and identifying different regimes of operation, which include impedance properties, cut-off propagation, dispersive behaviour and shock-wave formation, we exploit perturbation theory accompanied by the method of multiple scale to derive the three nonlinear coupled amplitude equations to describe the parametric interaction. A graphical technique is suggested to find three waves on the dispersion diagram satisfying the phase-matching conditions. Both cases of perfect phase-matching and slight mismatching are addressed in this work. The incorporation of two numerical techniques, spectral method in space and multistep Adams-Bashforth in time domain, is employed to monitor the unilateral gain, superior stability and bandwidth of this structure. Two types of functionality, mixing and amplification, with their requirements are described. These properties make this structure desirable for applications ranging from superconducting optoelectronics to dispersive readout of superconducting qubits where high sensitivity and ultra-low noise operation is required.

The aim of this thesis is to investigate the dynamical behaviors of spatially extended systems with fluctuating time delays. In recent years, the study of spatially extended systems and systems with fluctuating delays has experienced a fast growth. In ubiquitous natural and laboratory situations, understanding the action of time-delayed signals is a crucial for understanding the dynamical behavior of these systems. Frequently, the length of the delay is found to change with time. Spatially extended systems are widely studied in many fields, such as chemistry, ecology, and biology. Self-organization, turbulence, and related nonlinear dynamic phenomena in spatially extended systems have developed into one of the most exciting topics in modern science. The first part of this thesis considers the discrete system. Diffusively coupled map lattices with a fluctuating delay are used in the study. The uncoupled local dynamics of the considered system are represented by the delayed logistic map. In particular, the influences of diffusive coupling and fluctuating delay are studied. To observe and understand the influences, the results for the considered system are compared with coupled map lattices without delay and with a constant delay as well as with the uncoupled logistic map with fluctuating delays. Identifying different patterns, determining the existence of traveling wave solutions, and specifying the fully synchronized stable state are the focus of this part of the study. The Lyapunov exponent, the master stability function, spectrum analysis, and the structure factor are used to characterize the different states and the transitions between them. The second part examines the continuous system. The delay is introduced into the reactionterm of the Fisher-KPP equation. The focus of this part of study is the time-delay-induced Turing instability in one-component reaction-diffusion systems. Turing instability has previously only been found in multiple-component reaction-diffusion systems. However, this work demonstrates with the help of the stability exponent that fluctuating delay can result in Turing instability in one-component reaction-diffusion systems as well. / Ziel der vorliegenden Arbeit ist die Untersuchung der Einflüsse der zeitlich fluktuierenden Verzögerungen in räumlich ausgedehnten diffusiven Systemen. Durch den Vergleich von Systemen mit konstanter Verzögerung bzw. Systemen ohne räumliche Kopplung erhält man ein tieferes Verständnis und eine bessere Beschreibungsweise der Dynamik des räumlich ausgedehnten diffusiven Systems mit fluktuierenden Verzögerungen. Im ersten Teil werden diskrete Systeme in Form von diffusiven Coupled Map Lattices untersucht. Als die lokale iterierte Abbildung des betrachteten Systems wird die logistische Abbildung mit Verzögerung gewählt. In diesem Teil liegt der Fokus auf Musterbildung, Existenz von Multiattraktoren und laufenden Wellen sowie der Möglichkeit der vollen Synchronisation. Masterstabilitätsfunktion, Lyapunov Exponent und Spektrumsanalyse werden benutzt, um das dynamische Verhalten zu verstehen. Im zweiten Teil betrachten wir kontinuierliche Systeme. Hier wird die Fisher-KPP Gleichung mit Verzögerungen im Reaktionsteil untersucht. In diesem Teil liegt der Fokus auf der Existenz der Turing Instabilität. Mit Hilfe von analytischen und numerischen Berechnungen wird gezeigt, dass bei fluktuierenden Verzögerungen eine Turing Instabilität auch in 1-Komponenten-Reaktions-Diffusionsgleichungen gefunden werden kann

This thesis investigates the use of high-power lasers for synchrotron radiation sources with high brilliance, from the EUV to the hard X-ray spectral range. Hereby lasers accelerate electrons by laser-wakefield acceleration (LWFA), act as optical undulators, or both. Experimental evidence shows for the first time that LWFA electron bunches are shorter than the driving laser and have a length scale comparable to the plasma wavelength. Furthermore, a first proof of principle experiment demonstrates that LWFA electrons can be exploited to generate undulator radiation. Building upon these experimental findings, as well as extensive numerical simulations of Thomson scattering, the theoretical foundations of a novel interaction geometry for laser-matter interaction are developed. This new method is very general and when tailored towards relativistically moving targets not being limited by the focusability (Rayleigh length) of the laser, while it does not require a waveguide. In a theoretical investigation of Thomson scattering, the optical analogue of undulator radiation, the limits of Thomson sources in scaling towards higher peak brilliances are highlighted. This leads to a novel method for generating brilliant, highly tunable X-ray sources, which is highly energy efficient by circumventing the laser Rayleigh limit through a novel traveling-wave Thomson scattering (TWTS) geometry. This new method suggests increases in X-ray photon yields of 2-3 orders of magnitudes using existing lasers and a way towards efficient, optical undulators to drive a free-electron laser. The results presented here extend far beyond the scope of this work. The possibility to use lasers as particle accelerators, as well as optical undulators, leads to very compact and energy efficient synchrotron sources. The resulting monoenergetic radiation of high brilliance in a range from extreme ultraviolet (EUV) to hard X-ray radiation is of fundamental importance for basic research, medical applications, material and life sciences and is going to significantly contribute to a new generation of radiation sources and free-electron lasers (FELs).

Die vorliegende Arbeit beschäftigt sich in Experiment und Theorie mit Laser-Plasma beschleunigten Elektronen und optischen Undulatoren zur Erzeugung von brillianter Synchrotronstrahlung. Zum ersten Mal wird experimentell nachgewießen, dass laserbeschleunigte Elektronenpulse kürzer als 30 fs sind. Ferner werden solche Elektronenpulse erstmalig in einem Demonstrationsexperiment durch einen magnetischen Undulator als Synchrotronstrahlenquelle genutzt. Aufbauend auf diesen experimentellen Erkenntnissen, sowie umfangreichen numerischen Simulationen zur Thomsonstreuung, werden die theoretischen Grundlagen einer neuartigen Interaktionsgeometrie für Laser-Materie Wechselwirkungen entwickelt. Diese neue, in der Anwendbarkeit sehr allgemeine Methode basiert auf raum-zeitlicher Laserpulsformung durch nichtlineare Winkeldispersion wie diese durch VLS- (varied-line spacing) Gitter erzeugt werden kann und hat den Vorteil nicht durch die Fokussierbarkeit des Lasers (Rayleighlänge) begrenzt zu sein. Zusammen mit laserbeschleunigten Elektronen ermöglicht dieser traveling-wave Thomson scattering (TWTS) benannte Ansatz neuartige, nur auf optischer Technologie basierende Synchrotronstrahlenquellen mit Zentimeter bis Meter langen optische Undulatoren. Die hierbei mit existierenden Lasern erzielbaren Brillianzen übersteigen diese bestehender Thomsonquellen-Designs um 2-3 Größenordnungen. Die hier vorgestellten Ergebnisse weisen weit über die Grenzen der vorliegenden Arbeit hinaus. Die Möglichkeit Laser als Teilchenbeschleuniger und auch optischen Undulator zu verwenden führt zu bauartbedingt sehr kompakten und energieeffizienten Synchrotronstrahlungsquellen. Die hieraus resultierende monochromatische Strahlung hoher Brillianz in einem Wellenlängenbereich von extremen ultraviolett (EUV) zu harten Röntgenstrahlen ist für die Grundlagenforschung, medizinische Anwendungen, Material- und Lebenswissenschaften von fundamentaler Bedeutung und wird maßgeblich zu einer neuen Generation ultrakurzer Strahlungsquellen und freien Elektronenlasern (FELs) beitragen. / This thesis investigates the use of high-power lasers for synchrotron radiation sources with high brilliance, from the EUV to the hard X-ray spectral range. Hereby lasers accelerate electrons by laser-wakefield acceleration (LWFA), act as optical undulators, or both. Experimental evidence shows for the first time that LWFA electron bunches are shorter than the driving laser and have a length scale comparable to the plasma wavelength. Furthermore, a first proof of principle experiment demonstrates that LWFA electrons can be exploited to generate undulator radiation. Building upon these experimental findings, as well as extensive numerical simulations of Thomson scattering, the theoretical foundations of a novel interaction geometry for laser-matter interaction are developed. This new method is very general and when tailored towards relativistically moving targets not being limited by the focusability (Rayleigh length) of the laser, while it does not require a waveguide. In a theoretical investigation of Thomson scattering, the optical analogue of undulator radiation, the limits of Thomson sources in scaling towards higher peak brilliances are highlighted. This leads to a novel method for generating brilliant, highly tunable X-ray sources, which is highly energy efficient by circumventing the laser Rayleigh limit through a novel traveling-wave Thomson scattering (TWTS) geometry. This new method suggests increases in X-ray photon yields of 2-3 orders of magnitudes using existing lasers and a way towards efficient, optical undulators to drive a free-electron laser. The results presented here extend far beyond the scope of this work. The possibility to use lasers as particle accelerators, as well as optical undulators, leads to very compact and energy efficient synchrotron sources. The resulting monoenergetic radiation of high brilliance in a range from extreme ultraviolet (EUV) to hard X-ray radiation is of fundamental importance for basic research, medical applications, material and life sciences and is going to significantly contribute to a new generation of radiation sources and free-electron lasers (FELs).

The aim of this thesis is to investigate the dynamical behaviors of spatially extended systems with fluctuating time delays. In recent years, the study of spatially extended systems and systems with fluctuating delays has experienced a fast growth. In ubiquitous natural and laboratory situations, understanding the action of time-delayed signals is a crucial for understanding the dynamical behavior of these systems. Frequently, the length of the delay is found to change with time. Spatially extended systems are widely studied in many fields, such as chemistry, ecology, and biology. Self-organization, turbulence, and related nonlinear dynamic phenomena in spatially extended systems have developed into one of the most exciting topics in modern science. The first part of this thesis considers the discrete system. Diffusively coupled map lattices with a fluctuating delay are used in the study. The uncoupled local dynamics of the considered system are represented by the delayed logistic map. In particular, the influences of diffusive coupling and fluctuating delay are studied. To observe and understand the influences, the results for the considered system are compared with coupled map lattices without delay and with a constant delay as well as with the uncoupled logistic map with fluctuating delays. Identifying different patterns, determining the existence of traveling wave solutions, and specifying the fully synchronized stable state are the focus of this part of the study. The Lyapunov exponent, the master stability function, spectrum analysis, and the structure factor are used to characterize the different states and the transitions between them. The second part examines the continuous system. The delay is introduced into the reactionterm of the Fisher-KPP equation. The focus of this part of study is the time-delay-induced Turing instability in one-component reaction-diffusion systems. Turing instability has previously only been found in multiple-component reaction-diffusion systems. However, this work demonstrates with the help of the stability exponent that fluctuating delay can result in Turing instability in one-component reaction-diffusion systems as well. / Ziel der vorliegenden Arbeit ist die Untersuchung der Einflüsse der zeitlich fluktuierenden Verzögerungen in räumlich ausgedehnten diffusiven Systemen. Durch den Vergleich von Systemen mit konstanter Verzögerung bzw. Systemen ohne räumliche Kopplung erhält man ein tieferes Verständnis und eine bessere Beschreibungsweise der Dynamik des räumlich ausgedehnten diffusiven Systems mit fluktuierenden Verzögerungen. Im ersten Teil werden diskrete Systeme in Form von diffusiven Coupled Map Lattices untersucht. Als die lokale iterierte Abbildung des betrachteten Systems wird die logistische Abbildung mit Verzögerung gewählt. In diesem Teil liegt der Fokus auf Musterbildung, Existenz von Multiattraktoren und laufenden Wellen sowie der Möglichkeit der vollen Synchronisation. Masterstabilitätsfunktion, Lyapunov Exponent und Spektrumsanalyse werden benutzt, um das dynamische Verhalten zu verstehen. Im zweiten Teil betrachten wir kontinuierliche Systeme. Hier wird die Fisher-KPP Gleichung mit Verzögerungen im Reaktionsteil untersucht. In diesem Teil liegt der Fokus auf der Existenz der Turing Instabilität. Mit Hilfe von analytischen und numerischen Berechnungen wird gezeigt, dass bei fluktuierenden Verzögerungen eine Turing Instabilität auch in 1-Komponenten-Reaktions-Diffusionsgleichungen gefunden werden kann

Metabolomics is the methodical scientific study of biochemical processes associated with the metabolome—which comprises the entire collection of metabolites in any biological entity. Metabolome changes occur as a result of modifications in the genome and proteome, and are, therefore, directly related to cellular phenotype. Thus, metabolomic analysis is capable of providing a snapshot of cellular physiology. Untargeted metabolomics is an impartial, all-inclusive approach for detecting as many metabolites as possible without a priori knowledge of their identity. Hence, it is a valuable exploratory tool capable of providing extensive chemical information for discovery and hypothesis-generation regarding biochemical processes. A history of metabolomics and advances in the field corresponding to improved analytical technologies are described in Chapter 1 of this dissertation. Additionally, Chapter 1 introduces the analytical workflows involved in untargeted metabolomics research to provide a foundation for Chapters 2 – 5. Part I of this dissertation which encompasses Chapters 2 – 3 describes the utilization of mass spectrometry (MS)-based untargeted metabolomic analysis to acquire new insight into cancer detection. There is a knowledge deficit regarding the biochemical processes of the origin and proliferative molecular mechanisms of many types of cancer which has also led to a shortage of sensitive and specific biomarkers. Chapter 2 describes the development of an in vitro diagnostic multivariate index assay (IVDMIA) for prostate cancer (PCa) prediction based on ultra performance liquid chromatography-mass spectrometry (UPLC-MS) metabolic profiling of blood serum samples from 64 PCa patients and 50 healthy individuals. A panel of 40 metabolic spectral features was found to be differential with 92.1% sensitivity, 94.3% specificity, and 93.0% accuracy. The performance of the IVDMIA was higher than the prevalent prostate-specific antigen blood test, thus, highlighting that a combination of multiple discriminant features yields higher predictive power for PCa detection than the univariate analysis of a single marker. Chapter 3 describes two approaches that were taken to investigate metabolic patterns for early detection of ovarian cancer (OC). First, Dicer-Pten double knockout (DKO) mice that phenocopy many of the features of metastatic high-grade serous carcinoma (HGSC) observed in women were studied. Using UPLC-MS, serum samples from 14 early-stage tumor DKO mice and 11 controls were analyzed. Iterative multivariate classification selected 18 metabolites that, when considered as a panel, yielded 100% accuracy, sensitivity, and specificity for early-stage HGSC detection. In the second approach, serum metabolic phenotypes of an early-stage OC pilot patient cohort were characterized. Serum samples were collected from 24 early-stage OC patients and 40 healthy women, and subsequently analyzed using UPLC-MS. Multivariate statistical analysis employing support vector machine learning methods and recursive feature elimination selected a panel of metabolites that differentiated between age-matched samples with 100% cross-validated accuracy, sensitivity, and specificity. This small pilot study demonstrated that metabolic phenotypes may be useful for detecting early-stage OC and, thus, supports conducting larger, more comprehensive studies. Many challenges exist in the field of untargeted metabolomics. Part II of this dissertation which encompasses Chapters 4 – 5 focuses on two specific challenges. While metabolomic data may be used to generate hypothesis concerning biological processes, determining causal relationships within metabolic networks with only metabolomic data is impractical. Proteins play major roles in these networks; therefore, pairing metabolomic information with that acquired from proteomics gives a more comprehensive snapshot of perturbations to metabolic pathways. Chapter 4 describes the integration of MS- and NMR-based metabolomics with proteomics analyses to investigate the role of chemically mediated ecological interactions between Karenia brevis and two diatom competitors, Asterionellopsis glacialis and Thalassiosira pseudonana. This integrated systems biology approach showed that K. brevis allelopathy distinctively perturbed the metabolisms of these two competitors. A. glacialis had a more robust metabolic response to K. brevis allelopathy which may be a result of its repeated exposure to K. brevis blooms in the Gulf of Mexico. However, K. brevis allelopathy disrupted energy metabolism and obstructed cellular protection mechanisms including altering cell membrane components, inhibiting osmoregulation, and increasing oxidative stress in T. pseudonana. This work represents the first instance of metabolites and proteins measured simultaneously to understand the effects of allelopathy or in fact any form of competition. Chromatography is traditionally coupled to MS for untargeted metabolomics studies. While coupling chromatography to MS greatly enhances metabolome analysis due to the orthogonality of the techniques, the lengthy analysis times pose challenges for large metabolomics studies. Consequently, there is still a need for developing higher throughput MS approaches. A rapid metabolic fingerprinting method that utilizes a new transmission mode direct analysis in real time (TM-DART) ambient sampling technique is presented in Chapter 5. The optimization of TM-DART parameters directly affecting metabolite desorption and ionization, such as sample position and ionizing gas desorption temperature, was critical in achieving high sensitivity and detecting a broad mass range of metabolites. In terms of reproducibility, TM-DART compared favorably with traditional probe mode DART analysis, with coefficients of variation as low as 16%. TM-DART MS proved to be a powerful analytical technique for rapid metabolome analysis of human blood sera and was adapted for exhaled breath condensate (EBC) analysis. To determine the feasibility of utilizing TM-DART for metabolomics investigations, TM-DART was interfaced with traveling wave ion mobility spectrometry (TWIMS) time-of-flight (TOF) MS for the analysis of EBC samples from cystic fibrosis patients and healthy controls. TM-DART-TWIMS-TOF MS was able to successfully detect cystic fibrosis in this small sample cohort, thereby, demonstrating it can be employed for probing metabolome changes. Finally, in Chapter 6, a perspective on the presented work is provided along with goals on which future studies may focus.