In the first part of the dissertation, we develop a theoretical approach to analyze nonlinear spectroscopy experiments based on the formalism of quantum state (QST) and process tomography (QPT). In it, a quantum system is regarded as a black box which can be systematically tested in its performance, very much like an electric circuit is tested by sending a series of inputs and measuring the corresponding outputs, but in the quantum sense. We show how to collect a series of pump-probe or photon-echo experiments, and by varying polarizations and frequency components of the perturbations, reconstruct the quantum state (density matrix) of the probed system for a set of different initial conditions, hence simultaneously achieving QST and QPT. Furthermore, we establish the conditions under which a set of two-dimensional optical spectra also yield the desired results. Simulations of noisy experiments with inhomogeneous broadening show the feasibility of the protocol. A spin-off of this work is our suggestion of a witness that distinguishes between spectroscopic time-oscillations corresponding to vibronic only coherences against their electronic counterparts. We conclude by noting that the QST/QPT approach to nonlinear spectroscopy sheds light on the amount of quantum information contained in the output of an experiment, and hence, is a convenient theoretical and experimental paradigm even when the goal is not to perform a full QPT. In the second part of the thesis, we discuss a methodology to study the electronic dynamics of complex molecular systems, such as photosynthetic units, in the framework of time-dependent density functional theory (TD-DFT). By treating the electronic degrees of freedom as the system and the nuclear ones as the bath, we develop an open quantum systems (OQS) approach to TD-DFT. We formally extend the theoretical backbone of TD-DFT to OQS, and suggest a Markovian bath functional which can be readily included in electronic structure codes.

Zusammenfassung in PostScript In dieser Arbeit wird die photoinduzierte Dynamik offener Molekularsysteme unter dem Einfluß intensiver und ultrakurzer Laserpulse untersucht. Die Anregung eines Moleküls durch einen optischen ultrakurzen Laserpuls führt zu Übergängen zwischen verschiedenen elektronischen Zuständen. Dieser Anregungsprozeß wird begleitet von dissipativen Vorgängen wie Energie-- und Phasenrelaxation. Die Beschreibung dieser photoinduzierten Dynamik erfolgt mit Hilfe der Methode der Dichtematrixtheorie. Dabei zeigt die Ableitung der Quanten--Master--Gleichung im Rahmen des Projektionsoperator--Formalismus, daß die wirkenden äußeren Felder einmal direkt im reversiblen Anteil der Bewegungsgleichung auftreten, aber auch einen indirekten Einfluß über den die Dissipation beschreibenden Dissipations--Superoperator ausüben. In dieser Arbeit wird zum ersten Mal die durch ultrakurze Laserpulse induzierte Feldabhängigkeit des Dissipations--Superoperators berücksichtigt. Im Rahmen der Darstellung der Quanten--Master--Gleichung im Floquetbild kann eine anschauliche Deutung dieses feldabhängigen Effektes gegeben werden: die die Dissipation beschreibende frequenzabhängige Spektraldichte der Umgebungsmoden wird feldabhängig bei verschiedenen Frequenzen abgefragt. Analytische Untersuchungen zum Zwei--Niveau--System zeigen, daß die Feldabhängigkeit dann relevant wird, wenn die Pulslänge vergleichbar ist mit der Zeitskala, auf der die Autokorrelationsfunktion der Umgebungsfreiheitsgrade abklingt. Um den Einfluß auf experimentelle Größen zu untersuchen, wird ein zweifarbiges Pump--Test--Experiment zum Laserfarbstoffmolekül IR 125 betrachtet, bei welchem die spektral und zeitlich aufgelöste Transmission auf einer Femtosekunden-- und Pikosekunden--Zeitskala gemessen wurde. Im Rahmen des Modells einer effektiven Schwingungsmode wird eine Anpassungsrechnung an das Experiment vorgenommen. Dabei wird zunächst die Standard-Redfield-Theorie verwendet, um ein Referenzmodell zu gewinnen. Es gelingt, eine gute Übereinstimmung mit dem Experiment zu erreichen. Die exakte Berücksichtigung des Einflusses der internen Konversion zwischen den angeregten elektronischen Zuständen führt zu einem Anstieg der Transmission innnerhalb einer Pikosekunde. Es ist notwendig, die Dichtematrixgleichungen exakt zu lösen, da eine vergleichende Untersuchung mit Hilfe der nichtlinearen Suszeptibilität dritter Ordnung eine deutliche Abweichung zum exakten Resultat zeigt. Ausgehend vom Referenzfall feldunabhängiger Dissipation wird dann die Feldabhängigkeit der Relaxationsraten bestimmt sowie der Einfluß auf Observablen wie der relativen Transmission untersucht. In Übereinstimmung mit den analytischen Ergebnissen zeigt sich, daß der feldabhängige Effekt am größen ausgeprägt ist, wenn die Pulslänge kleiner als die Korrelationszeit der Umgebungsfreiheitsgrade wird und die wirkenden Felder hinreichend intensiv sind.Damit wird eine Kontrolle von Dissipation möglich. Ein Einfluß des feldabhängigen Effektes auf experimentelle Observablen wird vorhergesagt. / abstract in PostScript This thesis investigates the influence of intense and ultrashort laser pulses on the photoinduced dynamics of open molecular systems. The excitation of a molecule by an optical ultrashort laser pulse induces transitions between different electronic states. This excitation process is accompanied by the dissipative processes of energy and vibrational relaxation. This excitation process is described within the method of the density matrix theory. Thereby, the derivation of the quantum master equation in the framework of the projection operator formalism demonstrates that the external fields are present in the reversible part of the equation of motion and also exert an indirect influence by acting on the dissipation superoperator which accounts for dissipation. In this thesis the field--dependency of the dissipation superoperator which is induced by the external fields is considered for the first time. By a representation of the quantum master equation in the Floquet picture, an interpretation of this field--dependent effect can be given: the frequency--dependent spectral density of the environmental modes which describe dissipation is determined at different field--dependent frequencies. Analytical investigations for the two level system demonstrate that the field dependence becomes relevant if the pulse length is comparable with the time scale on which the autocorrelation function of the environmental degrees of freedom decays.To investigate the influence on experimental quantities, a two--color pump--probe experiment for the laser dye molecule IR 125 is considered for which the spectrally and temporally resolved transmission on a femtosecond and picosecond time scale has been measured. Within the model of one effective vibrational mode the experimental data is fitted. The standard Redfield theory is used to provide a reference model. A high degree of concurrence between the theory and the results of the experiment is achieved. The exact treatment of internal conversion between the excited electronic states leads to a rise in transmission within one picosecond. It is necessary to solve the density matrix equations exactly because a comparative investigation with the nonlinear susceptibility of third order leads to a clear viation from the exact result. Starting from the reference case of field--independent dissipation, the field--dependency of the relaxation rates is determined and the influence on observables for example the relative transmission is investigated. The analytical results show that the field--dependent effect is strongest if the pulse length becomes smaller than the correlation time of the environmental modes and if the acting fields are sufficiently strong. Thereby, a control of dissipation becomes possible. An influence of the field--dependent effect on experimental observables is predicted.

L'objectiu del treball presentat en aquesta tesi va ser el desenvolupament i l'aplicació de metodologies computacionals que integren l’anàlisis de informació sobre seqüències proteiques, informació funcional i genòmica per a la reconstrucció, anotació i organització de proteomes complets, de manera que els resultats es poden comparar entre qualsevol nombre d'organismes amb genomes completament seqüenciats. Metodològicament, m'he centrat en la identificació de l'organització molecular dins d'un proteoma complet d'un organisme de referència i comparació amb proteomes d'altres organismes, en espacial, estructural i funcional, el teixit cel • lular de desenvolupament, o els nivells de la fisiologia. La metodologia es va aplicar per abordar la qüestió de la identificació de organismes model adequats per a estudiar diferents fenòmens biològics. Això es va fer mitjançant la comparació d’un conjunt de proteines involucrades en diferents fenòmens biològics en Saccharomyces cerevisiae i Homo sapiens amb els conjunts corresponents d'altres organismes amb genomes. La tesi conclou amb la presentació d'un servidor web, Homol-MetReS, en què s'implementa la metodologia. Homol-MetReS proporciona un entorn de codi obert a la comunitat científica en què es poden realitzar múltiples nivells de comparació i anàlisi de proteomes. / El objetivo del trabajo presentado en esta tesis fue el desarrollo y la aplicación de metodologías computacionales que integran el análisis de la secuencia y de la información funcional y genómica, con el objetivo de reconstruir, anotar y organizar proteomas completos, de tal manera que estos proteomas se puedan comparar entre cualquier número de organismos con genomas completamente secuenciados. Metodológicamente, I centrado en la identificación de organización molecular dentro de un proteoma completo de un organismo de referencia, vinculando cada proteína en que proteoma a las proteínas de otros organismos, de tal manera que cualquiera puede comparar los dos proteomas en espacial, estructural, funcional tejido, celular, el desarrollo o los niveles de la fisiología. La metodología se aplicó para abordar la cuestión de la identificación de organismos modelo adecuados para estudiar diferentes fenómenos biológicos. Esto se hizo comparando conjuntos de proteínas involucradas en diferentes fenómenos biológicos en Saccharomyces cerevisiae y Homo sapiens con los conjuntos correspondientes de otros organismos con genomas completamente secuenciados. La tesis concluye con la presentación de un servidor web, Homol-MetReS, en el que se implementa la metodología. Homol-MetReS proporciona un entorno de código abierto a la comunidad científica en la que se pueden realizar múltiples niveles de comparación y análisis de proteomas. / The aim of the work presented in this thesis was the development and application of computational methodologies that integrate sequence, functional, and genomic information to provide tools for the reconstruction, annotation and organization of complete proteomes in such a way that the results can be compared between any number of organisms with fully sequenced genomes. Methodologically, I focused on identifying molecular organization within a complete proteome of a reference organism and comparing with proteomes of other organisms at spatial, structural, functional, cellular tissue, development or physiology levels. The methodology was applied to address the issue of identifying appropriate model organisms to study different biological phenomena. This was done by comparing the protein sets involved in different biological phenomena in Saccharomyces cerevisiae and Homo sapiens. This thesis concludes by presenting a web server, Homol-MetReS, on which the methodology is implemented. It provides an open source environment to the scientific community on which they can perform multi-level comparison and analysis of proteomes.

Les recherches menées dans le cadre de cette thèse avaient un double objectif. Premièrement, le développement d’une nouvelle méthode de chimie quantique à croissance linéaire basée sur le concept d’Orbitales Moléculaires Extrêmement Localisées (ELMOs) et adaptée à l’étude de très gros systèmes moléculaires. Deuxièmement, il s’agit d’évaluer le potentiel des méthodes de calcul utilisant de fonctions d’ondes contraintes et leur capacité à reproduire des données de diffraction aux rayons-X. En ce qui concerne le premier objectif, notre approche se base sur le principe de transférabilité, à savoir l’observation que les systèmes moléculaires sont composés par des unités fonctionnelles récurrentes qui conservent leurs caractéristiques lorsqu’elles se trouvent dans un même environnement chimique. Malheureusement, les orbitales moléculaires traditionnellement employées en chimie théorique dans des modèles de particule indépendante (Hartree-Fock, Kohn-Sham) sont complètement délocalisées sur le système étudié et, par conséquent, ne peuvent pas être transférées d’une molécule à une autre. Ce problème peut être résolu en ayant recours à des orbitales moléculaires déterminées de manière variationnelle sous la contrainte d’être exprimées à partir des fonctions de base centrées sur des atomes de fragments présélectionnés : les ELMOs. En fait, puisqu’elles sont strictement localisées, ces orbitales sont en principe transférables d’une molécule à une autre. L’objectif à terme est d’exploiter cette transférabilité en construisant une base de données d’ELMOs permettant de calculer quasiment instantanément, de manière approximative, des fonctions d’ondes et des densités électroniques de macromolécules. Dans la première partie de cette thèse, nous avons évalué le degré de transférabilité des orbitales moléculaires extrêmement localisées et nous avons proposé une approximation appropriée pour les molécules modèles servant à la détermination des ELMOs qui seront stockées dans la future base de données. Nous avons également comparé la transférabilité des ELMOs avec celle de densités électroniques atomiques asphériques (pseudo-atomes) qui sont largement répandues en cristallographie pour le raffinement de structure cristallographique de grands systèmes. La seconde partie de la thèse se focalise sur les méthodes quantiques utilisant des fonctions d’ondes contraintes. Dans ces méthodes, on cherche à déterminer des fonctions d’ondes qui minimisent l’énergie électronique des systèmes étudiés, mais qui en même temps doivent reproduire un jeu d’amplitudes de facteurs de structure expérimentaux. Cette technique, initialement proposée par Jayatilaka, a récemment été étendue à la théorie des orbitales moléculaires extrêmement localisées. Dans ce contexte, nous avons tout d’abord étudié les effets d’une localisation stricte sur la structure électronique dans des calculs de la fonction d’onde contrainte. Puis, nous avons déterminé si la fonction d’onde contrainte (et la densité associée) est capable de capturer des effets de la corrélation électronique. Enfin, en utilisant une nouvelle technique dite Valence Bond "expérimentale", basée sur les ELMOs, nous avons effectué une étude théorique sur le syn-1,6:8,13- Biscarbonyl[14] annulène (BCA) pour expliquer la rupture partielle de son aromaticité à haute pression observée expérimentalement. Cette dernière étude illustre positivement la potentialité du concept d’orbitale moléculaire strictement localisée en chimie quantique, qui ouvre des perspectives très larges notamment pour l’étude statique ou dynamique de systèmes moléculaires complexes. / The goal of the present work was dual. At first, this thesis aimed at proposing new lin- ear scaling quantum chemistry methods based on Extremely Localized Molecular Orbitals (ELMOs) and, secondly, it focused on the assessment of the capabilities of the X-ray con- strained wave function approaches. Concerning the first target, our approach is based on the transferability principle, namely the observation that molecular systems are composed by recurrent functional units that generally keep their features when they are in a similar chemical environment. In this context, it is possible to take advantage of the intrinsic trans- ferability of molecular orbitals strictly localized on small molecular subunits to recover wave functions and electron densities of large systems. Unfortunately, the molecular or- bitals traditionally used in quantum chemistry are completely delocalized on the system in exam and, therefore, are not transferable from a molecule to another. This problem can be solved only considering molecular orbitals variationally determined under the constraint of expanding them on local basis sets associated with pre-determined molecular fragments: the ELMOs. In fact, since they are strictly localized, these orbitals are in principle transfer- able from molecule to molecule and our final goal is to construct databanks of ELMOs that will enable to recover almost instantaneously approximate wave functions and electron densities of macromolecules at a very low computational cost. In the first part of this the- sis, we have evaluated the transferability of the Extremely Localized Molecular Orbitals and we have defined a suitable model molecule approximation for the computation of the ELMOs to be stored in the future databases. We have also compared the transferability of the ELMOs to the one of the aspherical atomic electron densities (pseudoatoms), which are largely used in crystallography to refine crystallographic structures of large systems. The second part of this work focuses on the X-ray constrained wave function approach. This method consists in determining wave functions that not only minimize the electronic energy of the systems under exam, but that also reproduce sets of experimental structure factor amplitudes within a desired accuracy. The technique, initially proposed by Jayatilaka has been recently extended to the theory of the Extremely Localized Molecular Orbitals. In this context, we have first studied the effects of introducing a strict a priori localization on the electronic structure in X-ray constrained wave function calculations. Then, we have determined if the X-ray constrained wave function is intrinsically able to capture the elec- tron correlation effects on the electron densities. Finally, also exploiting a novel X-ray con- strained ELMO-based Valence Bond technique, we have reported theoretical studies on the syn-1,6:8,13-Biscarbonyl[14] annulene (BCA) to explain the partial rupture of the aromatic character of the molecule occurring at high-pressure

Organic conjugated systems are attractive because of wide range of applications, which includes stimulated emission from -conjugated polymers, optical switches, organic solar cells and organic light emitting diodes, to name a few. They have the advantage of low cost, ease of processing and tunability of their linear and nonlinear optical properties by functionalization with donor or acceptor groups. In chapter 1, we provide an introduction to the π-conjugated systems and various interesting phenomena observed in these systems, This is followed by a brief description of the application of the above mentioned -conjugated systems for organic light emitting diodes, and organic photovoltaic cells. In the last section of this chapter, we give an introduction to magnetism due to π-electron systems. In chapter 2, we begin with energy band theory in one-dimension and its drawbacks. We introduce various model Hamiltonians which incorporate electron-electron inter-actions like Hubbard model, and Pariser-Parr-Pople (PPP) model. We present numerical techniques like valence-bond (VB) and constant MS techniques that are used to exactly solve the above model Hamiltonian. This is followed by an introduction to density matrix renormalization group method (DMRG) employed for the above model Hamiltonian for larger system in one-dimension and quasi-one-dimension. We give description of linear and nonlinear optical properties followed by the oriented gas model for ensemble of molecules. Various methods for computing polarizabilities and hyperpolarizibilities of molecules includes such as Finite-Field method, Sum-Over-State Method, and Correction Vector (CV) Methods are described in detail. In chapter 3, we look into fused azulene systems as a possible organic multiferroics. Azulene molecule with fused five and seven membered π-conjugated rings has a dipole moment, and the π-framework has geometric frustration. Hence in fused azulenes we can expect both ferroelectric and magnetic ground state. To explore this, we study low-lying correlated electronic states of fused azulenes using the long-range interacting PPP model and the finite DMRG method. The ground state is a singlet for oligomers up to 5 azulene units. For oligomers with more than 5 azulene units and up to 11 azulene units the oligomers have a triplet ground state. From the excitation gaps between the lowest MS = 0 state and the lowest states in MS=1, 2, and 3 sectors we predict that the ground-state spin of the fused azulene increases with the number of azulene units. In the thermodynamic limit, we expect the fused azulene to be a ferromagnet. Charge density calculations show that the ground state of the system has ferroelectric alignment of the dipoles of the monomeric units. Thus, a fused azulene system could be the first example of an organic molecule which is both ferromagnetic and ferroelectric, in the ground state. In chapter 4, we study the linear and nonlinear optical properties of diradical systems. We have studied linear and non-linear optical properties of π-conjugated diradicals because they are expected to exhibit large non-linear responses. The system studied are oligomers of dicyclopenta-fused acenes (DPA) and the s-indaceno[1,2,3-cd;5,6,7-c'd']diphenalene (IDPL) molecule. Spin-spin correlation functions within a correlated PPP model Hamiltonian, using exact diagonalization method, are used to characterize the diradical nature of DPA-2 and similar calculations on Anthracene have been performed to contrast this with a singlet character. The diradical character of DPA-2 is also manifest as low optical gap, low spin gap and large THG coefficients compared to Anthracene molecule. Larger DPA-k, k > 2, oligomers as well as the IDPL molecule have been studied within the DMRG technique. In the DPA-4, we nd a very small spin gap (0.04 eV), while in the oligomers with k > 4, we nd that the ground state is degenerate with the lowest triplet state. The energy of the second excited triplet state decreases with increasing size k and seems to saturate at ~0.36 eV in the thermodynamic limit. The lowest optical gap in DPA-4 is at 1.94 eV and has large transition dipoles, while for DPA-k, 4 < k ≥ 28, we have not been able to access states with large transition dipoles. The weak low-energy excitations seem to saturate at 0.5 eV and the two-photon gap also seems to be saturating at~ 0.3 eV in the thermodynamic limit. These polymers will not be IR uorescent by Kasha rule. The dominant component of the THG coefficient, γxxxx, is highest for DPA-4 which reduces almost by an order of magnitude in DPA-8; for k > 8 it increases up to the largest system with k=20 for which we have computed the coe cient. The variation of the charge gap of DPA oligomer with the increase in system size is small and in the polymer limit the charge gap is 4:24 eV. For IDPL molecule spin gap is 0.20 eV and next excited triplet state is at 1.48 eV. Two lowest singlet states in B space are nearly degenerate and have large transition dipole moments. Optical gaps to the above states are 2.20 eV and 2.22 eV. Two-photon gap in this system is 1.29 eV, hence this system is also non- uorescent. We calculated the dispersion of the major component of the THG coefficient, γxxxx, over a wide frequency range for this molecule, and we observe resonances corresponding to the 21Ag and 11Bu states. Extrapolated value of γxxxx at zero frequency is 15:58 x 106 a.u which is very large and the system does not have any donor or acceptor substituent groups. In chapter 5, we study absorption spectra and two photon absorption coefficient of expanded porphyrins (EPs). We nd that in the 4n+2 EPs there are two prominent low-lying one-photon excitations while in 4n systems there is only one such excitation. The two-photon gaps in both these types of systems are at energies close to the one-photon excitations. The spin gap in 4n+2 EPs are very small although the spin-1/2 Heisenberg calculations show that a pure spin system in this geometry will not have vanishing spin-gap. The charge density rearrangement in the one-photon excited state is most at the aza nitrogen site and at the meso carbon sites. In the two-photon states also the charge density rearrangement occurs mostly at the aza-ring sites. The bond order changes in these states is much more striking. In the one-photon state, the C-C bond length in the aza rings show a tendency to become uniform. Similar qualitative trend is also observed for the two-photon state. In chapter 6, we study linear and nonlinear optical properties of two push-pull polyenes stacked in head to head (HtH) and head to tail con gurations (HtT), at different stacking angles, exactly within the PPP model. Varying the stacking angle between polyenes, we nd that the optical gap varies slightly, but transition dipoles show large variation. The dominant component of first-order hyperpolarizability, βxxx for HtH and βyyy for HtT arrangement strongly depend on the distance between molecules. The βxxx for HtH configuration shows a maximum at a nonzero stacking angle, which varies with inter polyene distance. ZINDO study on two monomers, (4-hydroxy-40-nitro-azobenzene) connected by a conjugated bridge shows that βav is more than twice the monomer value and with a red-shift in the optical gap. In chapter 7, we have calculated the shifts in optical gaps and band edges as a function of the distance between two monomers within a correlated PPP model Hamiltonian for various stacking geometries. We have used as model monomers, both unsubstituted polyenes and push-pull substituted polyenes. We have carried out calculations with and without inter-chain hopping between sites on different molecules. We note that in the absence of inter-chain hopping, the energy level shifts are almost independent of the distances between the chains in all stacking geometries. It is also interesting to note that only electron-electron interactions yield a blue shift in the optical gaps for parallel stacking, but red shift in the gap for all other stacking geometries. We note that most of the shift in the gap is due to shifts in the excited state energy and the ground-state energy remains almost the same. With interchain transfer the shift in the optical gap increases with decrease in the interchain distance. We observe red-shifts in parallel stacking geometry when inter-chain electron hopping is turned on, at small interchain separations. In general interchain hopping increases significantly the red shift in the optical gaps for all geometries. Even for push-pull polyenes of | e| =2.0 eV, we observe the same trend in the shift in the optical gap for various stacking geometries. In this case the shift in optical gap is an order of magnitude higher when interchain hopping is turned on compared to that in the absence of interchain hopping. We find that the optical gap shifts are largest for the parallel stacking geometry, and it also shows stronger distance dependence. This is in close conformity with experimental observation of red-shift in absorption maxima when hydrostatic pressure is applied on the system. The shift in the HOMO (LUMO) level is small in the absence of t?, and the largest shift is in the case of parallel stacking compared to other stacking geometries. The distance dependence of the HOMO shifts is also rather weak. When t? is turned on, the level shifts become large by a factor of five or more. When we have push-pull groups electron-hole symmetry is broken and the shift is different for the HOMO and the LUMO level. Depending upon stacking geometry, the HOMO shifts vary from 0:1 ~ eV to 0.3 eV, which is larger than the shifts observed in unsubstituted polyenes. This large shift in the LUMO reduces the efficiency of exciton dissociation.

[ES] Las proteínas DELLA son elementos centrales de la ruta de señalización por giberelinas (GAs), donde actúan como represores de las respuestas a GAs. En angiospermas, se ha observado que las DELLAs interaccionan con cientos de factores de transcripción y otros reguladores transcripcionales, modulando de este modo la expresión génica. Por lo tanto, la participación generalizada de las GAs a lo largo del ciclo vital de las plantas es una consecuencia directa de la promiscuidad de las proteínas DELLA y de su rol como reguladores transcripcionales clave. Aunque las DELLAs se encuentran en todas las plantas terrestres, solo son reguladas por GAs en traqueofitas, en las cuales se han centrado la mayoría de los estudios previos. El trabajo aquí presentado pretende descifrar en qué punto de la evolución las DELLAs adquirieron las características moleculares que las convierten en "hubs", y qué ventajas biológicas podrían estar relacionadas con la evolución de las DELLAs. En el primer capítulo, describimos análisis comparativos de redes de co-expresión génicas asociadas a DELLA en especies vasculares y no vasculares, y proponemos que las DELLAs tienen un papel crítico en la conformación de panoramas transcripcionales. Desde su aparición en el ancestro de las plantas terrestres, conectaron múltiples programas transcripcionales que serían independientes sin ellas, mejoraron la eficiencia de la transmisión de información y aumentaron el nivel de complejidad en la regulación transcripcional. También observamos que este efecto se incrementó tras su integración en la señalización por GAs. En el segundo capítulo, proporcionamos pruebas experimentales más sólidas que extienden esta conclusión. Usando una combinación de rastreos de doble híbrido en levadura dirigidos, con DELLAs de diferentes posiciones en el linaje vegetal, y complementación heteróloga en plantas de Arabidopsis y Marchantia, mostramos que la promiscuidad es una característica conservada en todas las proteínas DELLA examinadas; lo cual sugiere que esta propiedad puede haber estado codificada en la DELLA ancestral, y después se mantuvo a lo largo de la evolución, con episodios de co-evolución entre las DELLAs y sus interactores. Finalmente, la comparación de dianas transcripcionales de las DELLAs en diferentes especies muestra la llamativa conservación de un pequeño conjunto de funciones reguladas por DELLAs en plantas vasculares y no vasculares -incluyendo la respuesta a factores de estrés-, mientras que análisis comparativos de promotores indican que las dianas específicas de cada especie aparecen mediante al menos dos mecanismos: el establecimiento de nuevas interacciones de la DELLA, y el acceso a nuevos promotores diana a través de interactores conservados. En resumen, proponemos que las DELLAs son proteínas intrínsecamente promiscuas, con propiedades de "hub" en virtualmente todas las plantas, y la conservación de sus dianas transcripcionales depende en gran medida de la evolución de sus interactores. La conservación de las propiedades de "hub" de las proteínas DELLA las convierte en dianas biotecnológicas ideales, ya que la mayoría del conocimiento generado en una especie podría ser fácilmente adaptado a otras especies relativamente lejanas. / [CA] Les proteïnes DELLA són elements centrals de la ruta de senyalització per gibberel·lines (GAs), on actuen com a repressors de les respostes a GAs. En angiospermes, s'ha observat que les DELLAs interaccionen amb centenars de factors de transcripció i altres reguladors transcripcionals, modulant d'aquesta manera l'expressió gènica. Per tant, la participació generalitzada de les GAs al llarg del cicle vital de les plantes és una conseqüència directa de la promiscuïtat de les proteïnes DELLA i del seu rol com a reguladors transcripcionals clau. Tot i que les DELLAs es troben en totes les plantes terrestres, només són regulades per GAs en traqueofites, en les quals s'han centrat la majoria dels estudis anteriors. El treball ací presentat pretén desxifrar en quin punt de l'evolució les DELLAs van adquirir les característiques moleculars que les converteixen en "hubs", i quins avantatges biològics podrien estar relacionats amb l'evolució de les DELLAs. En el primer capítol, descrivim anàlisis comparatius de xarxes de co-expressió gèniques associades a DELLA en espècies vasculars i no vasculars, i proposem que les DELLAs tenen un paper crític en la conformació de panorames transcripcionals. Des de la seua aparició en l'ancestre de les plantes terrestres, van connectar múltiples programes transcripcionals que serien independents sense elles, van millorar l'eficiència de la transmissió d'informació i augmentar el nivell de complexitat en la regulació transcripcional. També observem que aquest efecte es va incrementar després de la seua integració en la senyalització per GAs. En el segon capítol, proporcionem proves experimentals més sòlides que estenen aquesta conclusió. Usant una combinació de rastrejos de doble híbrid en rent dirigits, amb DELLAs de diferents posicions en el llinatge vegetal, i complementació heteròloga en plantes d'Arabidopsis i Marchantia, vam mostrar que la promiscuïtat és una característica conservada en totes les proteïnes DELLA examinades; la qual cosa suggereix que aquesta propietat pot haver estat codificada en la DELLA ancestral, i després es va mantenir al llarg de l'evolució, amb episodis de co-evolució entre les DELLAs i els seus interactors. Finalment, la comparació de dianes transcripcionals de les DELLAs en diferents espècies mostra la cridanera conservació d'un petit conjunt de funcions regulades per DELLAs en plantes vasculars i no vasculars -incloent la resposta a factors de estrès-, mentre que anàlisis comparatius de promotors indiquen que les dianes específiques de cada espècie apareixen mitjançant al menys dos mecanismes: l'establiment de noves interaccions de la DELLA, i l'accés a nous promotors diana a través d'interactors conservats. En resum, proposem que les DELLAs són proteïnes intrínsecament promíscues, amb propietats de "hub" en virtualment totes les plantes, i la conservació de les seues dianes transcripcionals depèn en gran mesura de l'evolució dels seus interactors. La conservació de les propietats de "hub" de les proteïnes DELLA les converteix en dianes biotecnològiques ideals, ja que la majoria del coneixement generat en una espècie podria ser fàcilment adaptat a altres espècies relativament llunyanes. / [EN] DELLA proteins are central elements of the gibberellin (GA) signaling pathway, where they act as repressors of GA responses. In angiosperms, DELLAs have been shown to interact with hundreds of transcription factors and other transcriptional regulators, thereby modulating gene expression. Hence, the widespread involvement of GAs along the plant life cycle is a direct consequence of the promiscuity of DELLA proteins and their role as key transcriptional regulators. Although DELLAs can be found in all land plants, they are only regulated by GAs in tracheophytes, where most of the previous studies have been focused. The work presented here aims to decipher at which point in evolution did DELLAs acquired the molecular features that render them as 'hubs', and what biological advantages could be related with DELLA evolution. In the first chapter, we describe comparative analyses of DELLA-associated gene co-expression networks in vascular and non-vascular species and propose that DELLAs have a critical role in the conformation of transcriptional landscapes. Upon their emergence in the ancestor of land plants, they connected multiple transcriptional programs that would be independent without them, improved the efficiency of information transmission and increased the level of complexity in transcriptional regulation. We also observed that this effect was enhanced after their integration in GA signaling. In the second chapter, we provide stronger experimental evidence that extends this conclusion. Using a combination of targeted yeast two-hybrid screenings with DELLAs from different positions in the plant lineage, and heterologous complementation in Arabidopsis and Marchantia plants, we show that promiscuity is a conserved feature in all the examined DELLA proteins, which suggests that this property might have been encoded in the ancestral DELLA, and then maintained along evolution, with episodes of co-evolution between DELLAs and their partners. Finally, comparison of DELLA transcriptional targets in different species shows a striking conservation of a small set of functions regulated by DELLAs in vascular and non-vascular plants -including the response to stress factors-, while comparative promoter analysis indicates that species-specific DELLA targets emerge through at least two mechanisms: establishment of novel DELLA interactions, and the access by conserved partners to new target promoters. In summary, we propose that DELLAs are intrinsically promiscuous proteins, with hub properties in virtually all land plants, and the conservation of their transcriptional targets largely depends on the evolution of their interactors. The conservation of the hub properties of DELLA proteins makes them ideal biotechnological targets, as most of the knowledge generated in one species could be readily adapted to other relatively distant species. / Esta tesis doctoral ha sido posible gracias a un contrato predoctoral FPU del Ministerio de Educación (FPU2014-01941). / Briones Moreno, A. (2020). Evolution of DELLA proteins as transcriptional hubs in plants [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/159378 / TESIS

In the last few years, considerable efforts have been given to develop sensitive and effective sensors for explosive materials and to generate systems which exhibit high luminescence in both solution and solid-state. The increasing number of terrorist activities around the world have prompted scientists to design effective ways to detect and disarm even the trace amount of explosives. The nitroaromatics (NACs) are the common constituents of most of the explosives due to high explosive velocity and ease of availability. The NACs were extensively used as the main constituents in landmines until World War II. Apart from their explosive behavior, the NACs are well-known environmental pollutants. The industrial waste and the leakages from unexploded landmines are the major contributors towards the soil and ground water contamination. Presently for effective detection of trace amount of explosives, skilled canines and metal based detectors are commonly used. The canines are trained for a specific type of explosives which limit their ability to detect different types of substrates. The chemical sensors that work on the principle of colorimetric and/or fluorimetric detection techniques have emerged as suitable alternative due to cheap production cost, portability and sensitivity. Different types of materials including conjugated polymers, metal-organic frameworks (MOFs), and quantum-dots have been reported as efficient chemosensors for NACs. However, poor solubility in the common organic solvents, low solid-state fluorescence, very high molecular weight and lack of signal amplification have restricted the application of these material for in-field testing. Renewed interests have been invested in small molecule based systems; and metal-organic discrete molecular architectures due to precise control over their photophysical properties and the supramolecular interaction among neighboring molecules that facilitates energy migration among the molecular backbone. On the other hand, recently post-synthetic modification of different molecular systems including MOFs and polymers has emerged as a potential technique to incorporate desired functional groups into the system and to tune their properties with the retention of basic structures. Reports on the post-synthetic modification of discrete metal-organic architectures are rare due to the delicate nature of the metal-organic bonds that ruptures on mild environmental changes. Therefore, post-synthetic functionalization of discrete molecular systems using mild reaction conditions will open up a myriad of possibilities to generate new systems with desired characteristics. Chapter 1 of the thesis will briefly discuss the history of different explosive materials including different detection methodologies that are widely used. It will also include a brief discussion on different small molecular systems with high solid-state luminescence. In Chapter 2, design and synthesis of triphenylamine-based two Platinum(Pt)(II) molecules functionalized with carboxylic acid and ester groups including their organic analogues have been discussed. The triphenylamine core was chosen due its unique non-planarity and luminescence. On the other hand, Pt(II) center was incorporated to increase intermolecular spacing in solid-state that can induce high luminescence. Scheme 1. Schematic representation of fluorescence quenching using small molecules. All the four molecules were found to be highly sensitive towards NACs including picric acid and dinitrophenol. Although the molecules exhibited similar sensitivity in solution, the carboxylic acid analogues demonstrated superior sensitivity in solid-state. Careful observation of the crystal structures of the systems revealed the acid analogues were oriented in a 2-D grid-like pattern that facilitated energy migration among neighboring molecules (Scheme 1.). Chapter 3 describes design, synthesis, and NACs sensing behavior of anthracene-based four purely organic small molecules. The molecules exhibited high selectivity towards picric acid only. All the molecules were found to be highly emissive in both solution and solid-state due to the vinylanthracene backbone (Scheme 2.). Scheme 2. Schematic representation of fluorescence quenching and solid-state sensing behavior. Chapter 4 discusses the strategy to develop mechano-fluorochromic and AIE active triphenylamine-based Pt(II) complex and its organic analogue. The twisted triphenylamine backbone restricted molecular close packing in solid-state; and weak C-H-- interactions were utilized to hinder the motion of the phenyl rings. As a result, the molecules were highly emissive in solid-state. Grinding disrupted the intermolecular interactions and thus mechano-fluorochromic behavior was observed. Due to twisted backbone, the molecules were also found to be AIE active. Both the systems containing terminal aldehyde groups were finally utilized for selective detection of biomolecule cysteine (Scheme 3.). Scheme 3. Mechano-fluorochromic and AIE behavior of the triphenylamine based Pt(II) complex. In Chapter 5 vinylanthracene-based linear donor was used in combination with carbazole-based 90° and triphenylamine-based 120° Pt(II) acceptors to generate (4+4) and (6+6) molecular squares and hexagons, respectively. The vinylanthracene backbone imparts high solution and solid-state luminescence to the system as well as made them AIE active. The molecules were further investigated for the solution and solid-state sensing for NACs and found to be effective for trinitrotoluene (TNT) and dinitrotoluene (DNT) (Scheme 4.). Scheme 4. Schematic representation of AIE active molecular square and its NACs sensing. Chapter 6 describes the formation of Pd3 self-assembled molecular trinuclear barrels containing triphenylamine imidazole donors and Pd(II) acceptors. Using Knoevenagel condensation the aldehyde group present in the barrel was post-synthetically functionalized with Meldrum’s acid. From spectroscopic characterization, it was proved that the structural integrity remained intact after the post-modification treatment (Scheme 6.). Surprisingly, pre-synthetic modification of the donor alone with Meldrum’s acid followed by self-assembly treatment with the Pd(II) ion did not yield trigonal barrel 6.8. Scheme 6. Post-synthetic functionalization of trinuclear barrels using Knoevenagel condensation.(For colour pictures pl see the abstract pdf file)