We present an autonomous, chemical logic gate based on a switchable metal–organic framework (MOF) composite, containing carbon nanoparticles and a Pt catalyst. The switchable MOF composite performs as AND logic gate. Hydrogen and oxygen gas streams serve as binary inputs. Catalytically formed water induces a structural transition (crystal volume expansion) of the MOF, and as a consequence, a detectable drop in conductance of the composite as a ‘true’ output only if both gases come in contact with the composite.

Polyzyklische organische Moleküle und deren Derivate sind eine Klasse von Nanostrukturen, die wegen diverser möglicher Anwendungen in molekularer und organischer Elektronik viel Aufmerksamkeit in der Wissenschaft erregt haben. Um ihre einzigartigen Eigenschaften in vollem Umfang auszunutzen, muss man das Verhalten von molekularen Systemen auf der Nanoskala verstehen und eine Reihe von Herstellungsverfahren entwickeln. In dieser Arbeit werden molekulare Nanostrukturen durch den Bottom-Up-Ansatz der Oberflächensynthese erzeugt. Als Untersuchungsmethode gilt Rastertunnelmikroskopie (STM) bei tiefen Temperaturen und im Ultrahochvakuum als Werkzeug der Wahl. Drei verschiedene molekulare Systeme werden ausführlich erforscht, mit dem Ziel organische Nanostrukturen mit gewünschten Eigenschaften und atomarer Präzision zu erzeugen. Im ersten Teil dieser Arbeit wird eine Cyclodehydrierungsreaktion erfolgreich für die Synthese von asymmetrischen Starphen verwendet. Es wird dann gezeigt, dass dieses Molekül als unimolekulares NAND-Logikgatter fungieren kann. Dabei wird die Positionierungsänderung der elektronischen Resonanz nach der Zufügung einzelner Goldatome an die Inputs des Moleküls gemessen. Eine Kombination aus atomarer und molekularer Lateralmanipulation mithilfe der Spitze des Rastertunnelmikroskops sowie Rastertunnelspektroskopie wird verwendet, um dieses Verhalten zu demonstrieren. Die steuerbare Verschiebung von molekularen Resonanzen entsteht wegen der asymmetrischen Form des Starphens und wurde theoretisch vorhergesagt. Molekulare Drähte werden im zweiten Teil der Arbeit durch die oberflächenassistierte Ullmann-Kupplung hergestellt. Ihr Baustein besteht aus abwechselnden Donor- und Akzeptorgruppen und wurde speziell vorgesehen, um leitfähige flexible molekulare Drähte herzustellen. Die Leitfähigkeit wird durch Ziehen einzelner Drähten von der Oberflächen mit der STM-Spitze gemessen. Theoretische Berechnungen der komplexen Bandstruktur der molekularen Drähte bestätigen die experimentellen Ergebnisse und unterstützen dabei die Wichtigkeit der Balance zwischen Akzeptor- und Donorgruppen für die Leitfähigkeit der Drähte. Basierend auf diesen Resultaten werden neue Strukturen zur Herstellung vorgeschlagen. Der letzte Teil befasst sich schließlich mit einer unimolekularen Reaktion, die zur Erzeugung einer anomalen Kombination von Pentagon- und Heptagonringen in einem einzelnen organischen Molekül führt. Solche 5-7-Einheiten sind analog zu Stone-Wales-Defekten in Graphen und können elektronische Eigenschaften beachtlich ändern. Die exakte intramolekulare Struktur der Reaktionsprodukte wird durch hochauflösende STM-Bildgebung mit funktionalisierter Spitze eindeutig zugeordnet und zusätzlich durch DFT-Rechnungen bestätigt. / Polycyclic organic molecules and their derivatives present the class of nanostructures that are currently in the focus of scientific research due to their perspectives for the versatile applications in molecular and organic electronics. To exploit their unique properties to full extent, one has to understand the behavior of molecular systems at the nanoscale and to develop a set of fabrication methods. In this work, molecular nanostructures are fabricated using the bottom-up on-surface synthesis approach, which allows precision of the desired products and control over their properties through careful precursors design. To study the reaction flow and the properties of the formed structures, scanning tunneling microscopy (STM) at low temperature and in ultra-high vacuum is the tool of choice. In this work, three molecular systems are studied in detail, with the focus of fabricating atomically precise nanostructures with tailored properties. A cyclodehydrogenation reaction is successfully applied to synthesize an asymmetric starphene molecule in the first part of the work. It is then shown that this molecule can function as a unimolecular NAND logic gate with its response to the attached single Au atoms measured as the position of the electronic resonance. A combination of the atomic and molecular lateral manipulation with the STM tip and scanning tunneling spectroscopy (STS) is used to demonstrate this behavior. The effect of the controllable shifting of the molecular resonances is due to the asymmetric shape of the starphene molecule and was initially predicted theoretically. More complex structures, molecular wires, are presented in the second part of the work by using the surface-assisted Ullmann coupling reaction. The monomer unit, consisting of the alternant donor and acceptor parts, was specifically designed to achieve highly-conductive flexible molecular wires. The conductance is measured by pulling the single wires with the STM tip off the surface. Theoretical calculations of the complex band structure of the wires confirm the obtained results and support the discussion of the importance of the balance between the strength of acceptor and donor units for the conductance of the resultant wires. Based on this, some model structures are proposed. Finally, the last part deals with a unimolecular reaction to create an anomalous combination of pentagon and heptagon rings in a single organic molecule. Such 5-7 moieties are analogous to the Stone-Wales defects in graphene and may significantly alter the electronic properties. The precise intramolecular structure of the reaction products is unambiguously assigned by high-resolution STM imaging with functionalized tips and further confirmed by DFT calculations.

A presente tese aborda dois problemas distintos e independentes: triangularização de sistemas não-lineares com duas entradas e controle de sistemas sem arrasto que evoluem no grupo especial unitário SU(n). Em relação ao primeiro, estabeleceu-se, através da generalização de resultados bem conhecidos, condições geométricas para que um sistema com duas entradas seja descrito por uma forma triangular específica após uma mudança de coordenadas e uma realimentação de estado estática regular. Para o segundo problema, desenvolveu-se uma estratégia de controle que força o estado do sistema a rastrear assintoticamente uma trajetória de referência periódica que passa por um estado objetivo arbitrário. O método de controle proposto utiliza os resultados de convergência de tipo- Lyapunov que foram estabelecidos pela presente pesquisa e que tiveram como inspiração uma versão periódica do princípio da invariância de LaSalle. Apresentou-se, ainda, os resultados de simulação obtidos com a aplicação da técnica de controle desenvolvida a um sistema quântico consistindo de duas partículas de spin-1/2, com o objetivo de gerar a porta lógica quântica C-NOT. / This thesis treats two distinct and independent problems: triangularization of nonlinear systems with two inputs and control of driftless systems which evolve on the special unitary group SU(n). Concerning the first, one has established, by means of the generalization of well-known results, geometric conditions for a system with two inputs to be described by a specific triangular form after a change of coordinates and a regular static state feedback. For the second problem, one has developed a control strategy that forces the state of the system to track in an asymptotic manner a periodic reference trajectory which passes by an arbitrary goal state. The proposed control method uses Lyapunovlike convergence results that were established in this research and which were inspired in a periodic version of LaSalles invariance principle. Furthermore, one has shown the simulation results obtained from the application of the developed control technique to a quantum system consisting of two spin-1/2 particles, with the aim of generating the C-NOT quantum logic gate.

L'imagerie de fluorescence s'est particulièrement développée au fil de ces dernières décennies notamment pour l'exploration des systèmes biologiques. De nombreux développements portant à la fois sur les instruments d'analyse et les agents de contraste (sondes) ont été entrepris pour améliorer cette technique de bioanalyse. Mes travaux de thèse avaient pour but d'explorer diverses plateformes moléculaires pro-fluorescentes pouvant générer, sous l'effet d'un stimulus biologique / chimique, un fluorophore organique. Cette approche de synthèse chimique in-situ met en jeu des réactions domino caractérisées par la formation et la rupture de liaisons covalentes. Ce processus devrait ouvrir la voie à des sondes fluorogéniques possédant des rapports signal sur bruit élevés. Cette étude avait aussi pour but d'étudier la synthèse in-situ de fluorophores déclenchée par plusieurs stimuli afin de concevoir des portes logiques moléculaires de type "AND", dans un but de détection "multi-analytes". Pour établir la preuve de principe, la formation d'un coeur 7-hydroxy-2-iminocoumarine fluorescent déclenchée par divers couples d'enzymes (hydrolase / nitroréductase) a été étudiée. L'ensemble de ces travaux sont décrits dans le chapitre I de ce manuscrit. Par la suite et comme présenté dans les chapitres II et III, notre intérêt s'est porté sur le développement des plateformes fluorogéniques libérant des fluorophores ayant des maxima d'absorption / émission décalés vers le rouge en comparaison de ceux des coumarines. Une première réalisation a concerné la conception d'un précurseur "cagé" agissant comme sonde à peptidases ou nitroréductase par libération d'un dérivé pyronine. Des travaux portant sur la formation in-situ d'une benzophénoxazine sont également en cours et sont présentés au chapitre III. Un dernier aspect de ce travail a concerné la chimie d'une nouvelle famille de fluorophores proche-IR (les hybrides dihydroxanthène-hémicyanine) dont la formation in-situ pourra être envisagée pour des applications in-vivo. / Fluorescence imaging is a growing field of biology over the past decades. Intensive works mainly focused on instrumental developments and chemistry of contrast agents (probes), were already done to improve such bioanalytical technique. The main goal of this Ph. D. thesis was to explore various fluorogenic molecular platforms responsive to various (bio)chemical stimuli and capable of releasing organic fluorophores in the biological medium to analyze. This approach named "in-situsynthesis" is based on domino reactions belonging to the repertoire of "covalent chemistry", triggered by the target (bio)analyte. This kind of process should provide advanced fluorogenic probes with high signal-to-noise ratio. Another purpose of this work was to investigate some dualtriggering events to access to fluorogenic molecules acting as "AND-type" molecular logic gates for dual-analytes detection applications. To establish this approach, the formation of highly fluorescent7-hydroxy-2-iminocoumarin scaffolds triggered by several enzyme pairs (hydrolase and nitroreductase) was studied and now described in the first chapter of this manuscript. The second part of this work, described in chapters II and III, was devoted to the development of original "caged" precursors able to release fluorophores whose absorption / emission maxima are dramatically redshifted compared to those of coumarin derivatives. The first achievement concerned the detection of protease or nitroreductase activities through in-situ formation of a pyronin scaffold. Further works, currently in progress, are focused on "caged" precursors whose the dual reaction with a model protease should lead to the release of a benzophenoxazine derivative. Finally, some chemistry aspects related to an emerging and promising class of NIR fluorophores (dihydroxanthene-hemicyanine hybrids) are presented and the opportunity to form them in biological media, upon enzymatic triggering is also discussed.

A presente tese aborda dois problemas distintos e independentes: triangularização de sistemas não-lineares com duas entradas e controle de sistemas sem arrasto que evoluem no grupo especial unitário SU(n). Em relação ao primeiro, estabeleceu-se, através da generalização de resultados bem conhecidos, condições geométricas para que um sistema com duas entradas seja descrito por uma forma triangular específica após uma mudança de coordenadas e uma realimentação de estado estática regular. Para o segundo problema, desenvolveu-se uma estratégia de controle que força o estado do sistema a rastrear assintoticamente uma trajetória de referência periódica que passa por um estado objetivo arbitrário. O método de controle proposto utiliza os resultados de convergência de tipo- Lyapunov que foram estabelecidos pela presente pesquisa e que tiveram como inspiração uma versão periódica do princípio da invariância de LaSalle. Apresentou-se, ainda, os resultados de simulação obtidos com a aplicação da técnica de controle desenvolvida a um sistema quântico consistindo de duas partículas de spin-1/2, com o objetivo de gerar a porta lógica quântica C-NOT. / This thesis treats two distinct and independent problems: triangularization of nonlinear systems with two inputs and control of driftless systems which evolve on the special unitary group SU(n). Concerning the first, one has established, by means of the generalization of well-known results, geometric conditions for a system with two inputs to be described by a specific triangular form after a change of coordinates and a regular static state feedback. For the second problem, one has developed a control strategy that forces the state of the system to track in an asymptotic manner a periodic reference trajectory which passes by an arbitrary goal state. The proposed control method uses Lyapunovlike convergence results that were established in this research and which were inspired in a periodic version of LaSalles invariance principle. Furthermore, one has shown the simulation results obtained from the application of the developed control technique to a quantum system consisting of two spin-1/2 particles, with the aim of generating the C-NOT quantum logic gate.

Diploma thesis deals with the basic description of cardiac muscle cells, the mechanism of its contraction and events associated with contractions. There are different types of methods which can be used for measuring of contractions and for evaluation of cell length. This work describe these methods and evaluate their pros and cons. Based on available information and technical possibilities is one of the methods chosen and used for the design of block diagram system for measuring of contraction of isolated heart cells in real time. The practical part of this diploma thesis deals with the designing of a system which allows processing the image of isolated cardiac muscle cells that facilitate the detection of the cells edge. For this purpose it was created a device that allows the user to select a single row from television signal containing the image information from a location where is the currently selected row. Thus obtained image information can be used for cells edge detection and measuring of its length and contractions.

The development of shape in multicellular organisms has intrigued human minds for millenia. Empowered by modern genetic techniques, molecular biologists are now striving to not only dissect developmental processes, but to exploit their modularity for the design of custom living systems used in bioproduction, remediation, and regenerative medicine. Currently, our capacity to harness this potential is fundamentally limited by a lack of spatiotemporal control over gene expression in multicellular systems. While several synthetic genetic circuits for control of multicellular patterning have been reported, hierarchical induction of gene expression domains has received little attention from synthetic biologists, despite its fundamental role in biological self-organization. In this thesis, I introduce the first synthetic genetic system implementing population-based AND logic for programmed hierarchical patterning of bacterial populations of Escherichia coli, and address fundamental prerequisites for implementation of an analogous genetic circuit into the emergent multicellular plant model Marchantia polymorpha. In both model systems, I explore the use of bacteriophage T7 RNA polymerase as a gene expression engine to control synthetic patterning across populations of cells. In E. coli, I developed a ratiometric assay of bacteriophage T7 RNA polymerase activity, which I used to systematically characterize different intact and split enzyme variants. I utilized the best-performing variant to build a three-color patterning system responsive to two different homoserine lactones. I validated the AND gate-like behavior of this system both in cell suspension and in surface culture. Then, I used the synthetic circuit in a membrane-based spatial assay to demonstrate programmed hierarchical patterning of gene expression across bacterial populations. To prepare the adaption of bacteriophage T7 RNA polymerase-driven synthetic patterning from the prokaryote E. coli to the eukaryote M. polymorpha, I developed a toolbox of genetic elements for spatial gene expression control in the liverwort: I analyzed codon usage across the transcriptome of M. polymorpha, and used insights gained to design codon-optimized fluorescent reporters successfully expressed from its nuclear and chloroplast genomes. For targeting of bacteriophage T7 RNA polymerase to these cellular compartments, I functionally validated nuclear localization signals and chloroplast transit peptides. For spatiotemporal control of bacteriophage T7 RNA polymerase in M. polymorpha, I characterized spatially restricted and inducible promoters. For facilitated posttranscriptional processing of target transcripts, I functionally validated viral enhancer sequences in M. polymorpha. Taking advantage of this genetic toolbox, I introduced inducible nuclear-targeted bacteriophage T7 RNA polymerase into M. polymorpha. I showed implementation of the bacteriophage T7 RNA polymerase/PT7 expression system accompanied by hypermethylation of its target nuclear transgene. My observations suggest operation of efficient epigenetic gene silencing in M. polymorpha, and guide future efforts in chassis engineering of this multicellular plant model. Furthermore, my results encourage utilization of spatiotemporally controlled bacteriophage T7 RNA polymerase as a targeted silencing system for functional genomic studies and morphogenetic engineering in the liverwort. Taken together, the work presented enhances our capacity for spatiotemporal gene expression control in bacterial populations and plants, facilitating future efforts in synthetic morphogenesis for applications in synthetic biology and metabolic engineering.