Dans ce travail de thèse, on s’intéresse aux applications des concepts d’antenne pour la manipulation de la lumière. Aux fréquences optiques, les antennes métalliques font intervenir des modes de surfaces dit plasmoniques permettant une forte interaction lumière/matière dans des volumes hautement confinés. Pour tirer partie de cette propriété, on s’intéressera à trois applications des antennes plasmoniques. D’abord dans le cadre des sources de photons uniques, on présentera une étude théorique et expérimentale des performances d’émetteurs uniques en présence d’une antenne planaire métallique. Nous proposerons ensuite une stratégie pour améliorer les performances de l’antenne. Puis dans le cadre de la génération électrique de lumière par effet tunnel inélastique, on analysera la modification des propriétés de rayonnement en présence d’un petit cylindre métallique. Cette analyse ouvre la voie à la conception de sources électriques intégrées de plasmons de surface. Enfin dans le cadre de la détection de molécules en faible quantité, on étudiera théoriquement l’interaction d’un faisceau infrarouge avec une couche de molécules résonnantes déposées sur un miroir métallique nanostructuré. / The work of this thesis has been devoted to a few applications of antenna concepts for the manipulation of light. In the optical range, surface modes called surface plasmon polaritons take place in the vicinity of metallic antennas, enabling a strong light/matter interaction within highly confined volumes. In order to take advantage of this property, three applications of plasmonic antennas will be investigated. First, in the case of single-photon sources, both theoretical and experimental studies of single-emitters performance when coupled to a planar metallic antenna will be presented. A strategy to enhance its performance will be studied theoretically. Then, in the case of electrical generation of light by inelastic electron tunneling, we will analyse the modification of radiation properties close to a metallic nano-rod. This analysis paves the way towards the design of integrated, compact electrical sources of surface plasmons. Finally, in the case of detecting a weak quantity of molecules, the interaction between an infrared light beam and a sub-nanometric layer of resonant molecules deposited on a nanostructured metallic mirror will be studied.

Les foldamères sont des architectures moléculaires synthétiques repliées, inspirées par les structures et les fonctions des biopolymères naturels. Le repliement est un processus sélectionné par la nature pour contrôler la conformation de sa machinerie moléculaire afin de réaliser des tâches chimiques ou mécaniques. Durant les dix dernières années de recherche sur les foldamères, des oligomères synthétiques, capables d'adopter des conformations repliées bien définies et prévisibles, comme des hélices, ont été proposés. Les progrès récents ont montré que la synthèse chimique par étapes et le design moléculaire basé sur un squelette oligoamide aromatique permettaient de produire des architectures moléculaires repliées de manière hélicoïdale. La forme du squelette et sa rigidité, des préférences conformationnelles locales, des interactions spécifiques entre monomères éloignés dans une séquence, ainsi que l'action de paramètres externes comme le solvant, ou la présence d'ions peuvent être combinés pour induire une tendance au repliement. Ces architectures sont remarquables car elles peuvent donner lieu à des motifs de repliement qui n'ont pas d'équivalent dans les structures des biopolymères naturels. Par exemple, des hélices dont le diamètre varie le long de la séquence, ou des hélices possédant un centre d'inversion du pas, des hélices en chevrons,... ont été rapportées. Alors que les structures de ces molécules hélicoïdales ont été abondamment caractérisées à l'état solide par cristallographie des rayons X, leur comportement en solution, et surtout le comportement dynamique, est très peu connu. Leurs propriétés mécano-chimiques sont quant à elles inconnues à ce jour. L'objectif du projet est de synthétiser différentes molécules synthétiques hélicoïdales de type oligoamide aromatique et d'obtenir une description détaillée de leur conformation dynamique en solution, ainsi que de leurs propriétés mécano-chimiques, par spectroscopie de force sur molécule unique basée sur l'AFM. / Foldamers are artificial folded molecular architectures inspired by the structures and functions of natural biopolymers. Folding is the process selected by nature to control the conformation of its molecular machinery to carry out chemical functions and mechanical tasks, such as en-zyme catalysis, duplication in nucleic acids, force generation,... During the last decade of research on foldamers, synthetic oligomers able to adopt well- defined and predictable folded conformations, such as helices, have been proposed. Recent progress has shown that stepwise chemical synthesis and molecular design based on aromatic oligoamide backbones enable to produce large helically folded molecular architectures. The shape and stiffness of the backbone, local conformational preferences, specific interactions between distant monomers in sequences, as well as the action of external parameters such as the solvent or the presence of ions, can be combine to induce folding tendency. A remarkable aspect of these architectures is that they can give rise to folded patterns that have no in natural counterparts biopolymer structures. For instance, helices whose diameter varies along the se-quence, helices possessing a handedness inversion centre, herringbone helices have been reported. While the structures of these helical molecules have been well characterized in the solid state by X-ray crystallography, much less is known about their dynamic behavior in solution. Their mechanochemical properties are unknown. The objective of the project is to synthesize various helical nanorchitectures based on an oli-goamide aromatic backbone and to obtain a detailed picture of their dynamical conformation in solution, as well as, their mechanochemical properties, by AFM-based single molecule force spectroscopy.

L’interaction de molécules organiques avec les surfaces semiconductrices permet de contrôler les propriétés physiques de ces dernières et ce, soit à travers une modification locale en utilisant des molécules individuelles, soit par la passivation de la surface par une mono-couche complète. Aussi, le contrôle de l’interaction moléculaire nous permet de modifier les propriétés intrinsèques des molécules à travers un découplage électronique partiel ou complet entre les orbitales moléculaires et la surface. Pour atteindre ces objectifs, cette thèse présente l’étude expérimentale de l’adsorption de molécules sur la surface semiconductrice à large gap de 6H-SiC(0001)-3x3. Les expériences ont été réalisées à l’aide d’un microscope à effet tunnel opérant dans les conditions d’Ultra-Haut Vide et de température ambiante (UHV RT-STM). Les résultats ont été comparés à des études théoriques employant des calculs selon la théorie de la fonctionnelle de la densité (DFT). Trois molécules on été étudié durant ce travail de thèse : C60, Caltrope et Trima. Les études STM et DFT montre que les molécules individuelles de C60 sont chimisorbé à la surface de carbure de silicium SiC(0001)-3x3 à travers la formation d’une seule liaison Si-C avec un seul adatome de silicium, contrairement aux autres surfaces semiconductrices où la molécule se chimisorbe en formant plusieurs liaisons. Trois sites d’adsorption par rapport à l’adatome de Si de la maille de surface ont été observés. Pour expliquer les observations STM, les forces de Van der Waals entre la molécule de C60 et les atomes de la surface voisins ont du être pris en compte dans les calculs DFT. Il a été observé aussi que les molécules de C60 forment de petits clusters même à de faibles taux de couverture ce qui indique la présence d’un état précurseur de la molécule et des interactions intermoléculaires non négligeable. La molécule de Caltrope, nouvellement synthétisée, a été étudié aussi bien sur la surface de Silicium que celle de SiC. Le dépôt de cette molécule complexe ne peut être réalisé selon la méthode d’évaporation classique sans induire sa dissociation et a donc nécessité l'emploi de techniques d’évaporation spécifiques. Nos résultats expérimentaux montrent un comportement remarquable: le dépôt de molécule individuelle est induit sur la surface de manière efficace par la pointe du STM démontrant ainsi l’idée d’imprimerie moléculaire. Suite à son adsorption sur la surface de silicium à travers une seule liaison, la molécule de Caltrope se comporte comme un moteur moléculaire activé thermiquement. La troisième molécule a être étudié est la molécule de Trima. Elle a été sélectionnée à cause de sa taille comparable à la distance des ad-atomes de silicium de la surface de SiC. La structure chimique de la molécule qui se termine par un groupement cétone rend possible la fonctionnalisation de la surface. Ceci est révélé par les calculs DFT de la densité de charge. La distribution de charge montre qu’il n’y a pas de partage entre les atomes d’oxygènes de la molécule et les ad-atomes de la surface et donc nous avons un évidence claire pour la formation d’une liaison dative. / The interaction of organic molecules with a semiconductor surface enables the physical properties of the surface to be controlled, from a local modification using individual isolated molecules to passivation using a complete monolayer. Controlling the molecular interaction also allows us to modify the intrinsic properties of the molecules by partial or complete electronic decoupling between the molecular orbitals and the surface. To this end, this thesis presents experimental studies of the adsorption of molecules on the wide band gap 6H-SiC(0001)-3×3 substrate. The experiments were performed using Ultra-High Vacuum Room Temperature Scanning Tunneling Microscopy (UHV RT STM) and the results were compared with comprehensive theoretical Density Functional Theory (DFT) calculations. Three different molecules were studied in this thesis: C60, Caltrop and Trima. The STM and DFT studies show that individual C60 fullerene molecules are chemisorbed on the silicon carbide SiC(0001)-3×3 surface through the formation of a single Si-C bond to one silicon adatom, in contrast to multiple bond formation on other semiconducting surfaces. We observed three stable adsorption sites with respect to the Si adatoms of the surface unit cell. To explain the STM observations, Van der Waals forces between the C60 molecule and the neighboring surface atoms had to be included in the DFT calculations. The C60 molecules are also observed to form small clusters even at low coverage indicating the presence of a mobile molecular precursor state and non negligible intermolecular interactions. The second newly designed Caltrop molecule was studied on both the Si and SiC surfaces. Intact adsorption of this complex organic molecule cannot be realized using classical adsorption methods and requires the use of specific evaporation techniques. Our experimental results show remarkable behavior: The STM tip efficiently deposits single molecules one at a time, demonstrating the concept of single molecule printing. After adsorption on the Si surface through one bond, the Caltrop operates as a thermally activated molecular rotor. The third molecule to be studied is the Trima molecule. This molecule was chosen because it is commensurable in size with the surface Si adatom distance. The chemical termination of the molecule with a ketone group enables the successful functionalization of the SiC surface. The Trima molecule provides a rare and clear-cut example of the formation of two dative bonds between the oxygen atoms of the carbonyl groups and the Si adatoms of the SiC surface. This is revealed by the DFT calculations of the charge density. The charge distribution shows that there is no sharing of electrons between the oxygen atoms of the molecule and the surface which is clear evidence for the formation of a dative bond.

Small devices capable of self-propulsion have potential application in areas of nanoscience where autonomous locomotion and programmability are needed. The specific base-pairing interactions that arise from DNA hybridisation permit the programmed assembly of matter and also the creation of controllable dynamical systems. The aim of this thesis is to use the tools of DNA nanotechnology to design synthetic active matter at the micro and nano scales. In the first section, DNA was used as an active medium capable of transporting information faster than diffusion in the form of chemical waves. DNA waves were generated experimentally using a DNA autocatalytic reaction in a microfluidic channel. The propagation velocity of DNA chemical waves was slowed down by creating concentration gradients that changed the reaction kinetics in space. The second section details the synthesis of chemically-propelled particles and the use of DNA as a 'programmable glue' to mediate their interactions. Janus micromotors were fabricated by physical vapour deposition and a wet-chemical approach was demonstrated to synthesise asymmetrical catalytic Pt-Au nanoparticles that function as nanomotors. Dynamic light scattering measurements showed nanomotor activity that depends on H₂O₂ concentration, consistent with chemical propulsion. Gold nanoparticles/Origami hybrids were assembled in 2D lattices of different symmetries arranged by DNA linkers. The third section details the design process and synthesis of nanomotors using DNA as a structural scaffold. 3D DNA Origami rectangular prisms were functionalised site-specifically with bioconjugated catalysts, i.e. Pt nanoparticles and catalase. Enzymatic nanomotors were also conjugated to various cargoes and their motor activity was demonstrated by Fluorescence Correlation Spectroscopy. In the final section, control mechanisms for autonomous nanomotors are studied, which includes the conformational change of DNA aptamers in response to chemical signals, as well as a design for an adaptive dynamical system based on DNA/enzyme reaction networks.

Ce travail porte sur l’étude de la fidélité de la traduction chez les eucaryotes d’un point de vue mécanistique et génomique. Au cours de ma thèse j'ai développé trois approches :Le premier projet porte sur l’étude du rôle du facteur de l’élongation eEF2 dans le maintien du cadre de lecture. La stratégie associe une mutagénèse aléatoire du gène EFT2 à un criblage phénotypique, elle permet d’isoler des mutants capables d’augmenter ou diminuer l’efficacité de recodage d’une séquence de décalage du cadre de lecture en -1.Le second projet décrit la mise au point d’un système de traduction en molécule unique qui permet d’étudier le ribosome eucaryote. La traduction est initiée grâce à l’IRES CrPV qui a pour caractéristique d’être totalement indépendante des facteurs d’initiation et de l’ARNt initiateur. L’élongation de la traduction est détectée grâce au départ d’un oligonucléotide fluorescent qui est décroché par l’activité hélicase du ribosome. Les résultats de ces expériences constituent une preuve de principe démontrant que l’étude de la traduction eucaryote en molécule unique est possible.Le troisième projet est une étude de génomique comparative qui permet de rechercher des événements de recodage ainsi que d’autres événements non-conventionnels de la traduction dans le génome de la levure Saccharomyces cerevisiae. L’approche est basée sur une recherche d’organisations génomiques conservées au sein de 19 génomes de levures. Les gènes candidats sont testés in vivo grâce à un vecteur double rapporteur. Cette étude a permis de mettre en évidence le gène VOA1 qui a été ensuite caractérisé plus en détails. / This report describes a study of translation fidelity in Eukarya. Two aspects are tested: the molecular mechanism of recoding and the research of recoding events at the genomic level. During my PhD I have developed three projects:The first project deals with the role of the elongation factor eEF2 in reading frame maintenance. The strategy is based on a random mutagenesis of EFT2 and a phenotypic screening in order to isolate mutants increasing or reducing -1 frameshifting efficiency.The second project describes the development of a single molecule translational system to study the eukaryotic ribosome. Translation initiation is mediated by the CrPV IRES which is initiation factor and initiation tRNA independent. Elongation is monitored with the dissociation of a fluorescent oligonucleotide by the helicase activity of the ribosome. This work is a proof of principle that studying eukaryotic ribosome with single molecule techniques is now feasible.The third project is a comparative genomic approach to search for recoding and unconventional translational events in the genome of yeast Saccharomyces cerevisiae. The approach is based on the detection of conserved genomic organization among 19 Fungi genomes. The candidate genes are then tested in vivo with a dual reporter system. This study allowed the characterization of VOA1 which was further analysed.

As the microelectronics industry pushes microfabrication processes further, the lab-on-a-chip field has continued to piggy-back off the industry's fabrication capabilities with the goal of producing total chemical and biological systems on small chip-size platforms. One important function of such systems is the ability to perform single molecule detection. There are currently many methods being researched for performing single molecule detection, both macro and micro in scale. This dissertation focuses on an optofluidic, lab-on-a-chip platform called the ARROW biosensor, which possesses several advantages over macro-scale single molecule detection platforms. These advantages include an amplification-free detection scheme, cheap parallel fabrication techniques, rapid single molecule detection results, and extremely low volume sample probing, which leads to ultra-sensitive detection. The ARROW biosensor was conceived in the early 2000s; however, since then it has undergone many design changes to improve and add new functionality to the lab-on-a-chip; however, water absorption in the plasma enhanced chemical vapor deposited silicon dioxide has been a problem that has plagued the biosensor platform for some time. Moisture uptake in the oxide layer of the ARROWs leads to loss of waveguiding confinement and drastically decreases the overall sensitivity of the ARROW biosensors. New ARROW designs were investigated to alleviate the negative water absorption effects in the ARROWs. The new waveguide designs were tested for resiliency to water absorption and the buried ARROW (bARROW) design was determined to be the most successful at preventing negative water absorption effects from occurring in the PECVD oxide waveguides. The bARROWs were integrated into the full biosensor platforms and used to demonstrate high sensitivity single molecule detection without any signs of water absorption affecting the bARROWs' waveguiding capabilities. The bARROW biosensors are not only water resistant, they also proved to be the most sensitive biosensors yet fabricated with average signal-to-noise ratios around 80% higher than any previously fabricated ARROW biosensors.

Ce travail de thèse a été dédié à l’élaboration et l’étude de nouveaux matériaux hybrides obtenus par la fonctionnalisation de molécule-aimants (en anglais single-molecule magnets, SMMs) et de complexes à transfert d’électron. Le premier chapitre fait un état de l’art des deux classes de composés magnétiques utilisées dans ce travail : les molécule-aimants et les systèmes à transfert d’électrons. Une brève description des systèmes magnétiques hybrides présents dans la littérature est ensuite présentée dans le but d’illustrer les motivations qui ont conduit à ce travail. Le chapitre II décrit la fonctionnalisation des molécule-aimants de type [Mn12] dans le but d’obtenir des systèmes cristaux liquides hybrides. Deux approches ont été étudiées : (a) la fonctionnalisation des ligands périphériques avec des groupements fortement lipophiles (longues chaines alkyle) ou (b) le greffage de promoteurs mésogènes par l’intermédiaire d’espaceurs aliphatiques flexibles. Les chapitres III à V présentent les études sur des carrés moléculaires à ponts cyanure {Fe2Co2} qui montrent un transfert d’électron thermo- et photo-induit. Le chapitre III discute de la possibilité de moduler le processus de transfert d’électron de ces carrés moléculaires via le changement du contre anion. La fonctionnalisation du carré moléculaire {Fe2Co2} avec de chaines aliphatiques et son impact induit sur les propriétés physiques à l’état solide et en solutions sont décrits dans le chapitre IV. Le chapitre V discute de l’effet de la fonctionnalisation avec des groupements fortement électrodonneurs, tels que les groupements méthoxy, sur le processus de transfert d’électron des carrés moléculaires {Fe2Co2}. / The work presented in this thesis was focused on the design and investigation of novel hybrid materials via ligand functionalization of the single-molecule magnets (SMMs) and electron transfer complexes. Chapter I contains general information about these two classes of the magnetic systems. In order to illustrate the motivation behind our work, a brief review on previously reported soft hybrid magnetic systems, is presented. Chapter II is dedicated to the functionalization of [Mn12]-based SMMs towards hybrid liquid crystalline systems via two different approaches: (a) the functionalization of peripheral ligands with strongly lipophilic groups (long alkyl chains), or (b) the grafting of mesogenic promoters through flexible aliphatic spacers. Chapters III – V are focused on cyanido-bridged molecular {Fe2Co2} squares that exhibit thermally or photo-induced electron transfer. Thus, in Chapter III, the possibility to modulate the electron transfer properties in {Fe2Co2} molecular squares via the use of different counter-anion is discussed. The functionalization with long aliphatic chains and its influence over the properties of {Fe2Co2} molecular squares in solid state and solutions are discussed in Chapter IV. Finally, the effect of the ligand functionalization with strongly electron density donating groups (methoxy) over the electron transfer properties of {Fe2Co2} molecular squares is investigated in Chapter V.

<p>Information about protein structures is important in many areas of life sciences, including structure-based drug design. Gas phase methods, like electrospray ionization and mass spectrometry are powerful tools for the analysis of molecular interactions and conformational changes which complement existing solution phase methods. Novel techniques such as single particle imaging with X-ray free electron lasers are emerging as well. A requirement for using gas phase methods is that we understand what happens to proteins when injected into vacuum, and what is the relationship between the vacuum structure and the solution structure.</p><p>Molecular dynamics simulations in combination with experiments show that protein structures in the gas phase can be similar to solution structures, and that hydrogen bonding networks and secondary structure elements can be retained. Structural changes near the surface of the protein happen quickly (ns-µs) during transition from solution into vacuum. The native solution structure results in a reasonably well defined gas phase structure, which has high structural similarity to the solution structure. </p><p>Native charge locations are in some cases also preserved, and structural changes, due to point mutations in solution, can also be observed in vacuo. Proteins do not refold in vacuo: when a denatured protein is injected into vacuum, the resulting gas phase structure is different from the native structure.</p><p>Native structures can be protected in the gas phase by adjusting electrospray conditions to avoid complete evaporation of water. A water layer with a thickness of less than two water molecules seems enough to preserve native conditions.</p><p>The results presented in this thesis give confidence in the continued use of gas phase methods for analysis of charge locations, conformational changes and non-covalent interactions, and provide a means to relate gas phase structures and solution structures.</p>

In this thesis we have developed electronic and spin model Hamiltonians to understand magnetism in molecule based magnets like photomagnets, high-nuclearity transition metal complexes and single molecule magnets. In chapter 1, we provide an overview of molecular magnets. Here, we present a survey on the literature available on molecule based magnets. The chapter throws light on various phenomena found in molecular magnetic systems that range in dimensions from 3D down to molecular dimension. This is followed by a brief introduction to high-nuclearity transition metal complexes and single molecule magnets (SMMs). In the last two sections of this chapter, we discuss Light Induced Excited Spin State Trapping (LIESST) and photomagnetism in some molecular systems. Chapter 2 discusses various theoretical models that have been developed for magnetism. We begin with an introduction to the spin Hamiltonian and the origin of direct and kinetic exchange in simple systems and extend it to larger systems. Then we introduce the concept of superexchange proposed by Goodenough and Kanamori, followed by introduction to anisotropic Dzyalashinskii-Moria (DM) exchange and Ruderman-Kittel-Kasuya-Yosida (RKKY) interactions. We also discuss molecular magnetic anisotropy, long-range magnetic interactions and higher order exchange interactions. These are effective model Hamiltonians that do not provide microscopic origin of magnetism, hence electronic model Hamiltonians need to be invoked. We introduce electronic model Hamiltonians like Huckel, Hubbard and Pariser-Parr-Popple (PPP) models and then present numerical techniques like valencebond (VB) and constant MS techniques that are used to exactly solve these model Hamiltonians. We present a many-body electronic model involving the active orbitals on the transition metal ions for photomagnetism in MoCu6 cluster, in chapter 3. The model is exactly solved using a valence bond approach. The ground state solution of the model is highly degenerate and is spanned by five S=0 states, nine S=1 states, five S=2 states and one S=3 state. The orbital occupancies in all these states correspond to six Cu(II) ions and one diamagnetic Mo(IV ) ion. The optically excited chargetransfer (CT) state in each spin sector occurs at nearly the same excitation energy of 2.993 eV for physically reasonable parameter values. We find that the excitation cross sections in different spin manifolds are similar in magnitude. The lifetime of the S=3 excited states is expected to be the largest as the number of states below that energy is very sparse in this spin sector compared to other spin sectors. This shows that photomagnetism is not due to preferential excitation to the S = 3 state. The inputs from the electronic model allows us to develop a kinetic model. In this model, photomagnetism is attributed to a long lived S=3 charge transfer excited state for which there appears to be sufficient experimental evidence. Based on this postulate, we model photomagnetism by including internal conversions and intersystem crossings. The key feature of the model is the assumption of existence of two kinds of S=3 states; one of which has no direct pathway for internal conversion and the other characterized by slow kinetics for internal conversion to the lowenergy states. The trapped S=3 state can decay via a thermally activated barrier to the other S = 3 state. The experimental XMT vs. T variation for two different irradiation times are fitted using Arrhenius dependence of the rate constants in the model. Conventional superexchange rules predict ferromagnetic exchange interaction between Ni(II) and M (M = MoV ,WV , NbIV ). Recent experiments show that in some systems this superexchange is antiferromagnetic. To understand this feature, in chapter 4 we develop a microscopic model for Ni(II) - M systems and solve it exactly using a valence bond approach. We identify direct exchange coupling, splitting of the magnetic orbitals and interorbital electron repulsions, on the M site as the parameters which control the ground state spin of various clusters of the Ni(II) - M system. We present quantum phase diagrams which delineate the high-spin and low-spin ground states in the parameter space. We fit the spin gap to a spin Hamiltonian and extract the effective exchange constant within the experimentally observed range, for reasonable parameter values. We also find a region in the parameter space where an intermediate spin state is the ground state. These results indicate that the spin spectrum of the microscopic model cannot be reproduced by a simple Heisenberg exchange Hamiltonian. The electronic model for A − B systems has been employed to reproduce the experimental magnetic data of the { NiW }2 system. In chapter 5, we present a theoretical approach to calculate the molecular magnetic anisotropy parameters, DM and EM for single molecule magnets in any eigenstate of the exchange Hamiltonian, treating the anisotropy Hamiltonian as a perturbation. Neglecting inter-site dipolar interactions, we calculate molecular magnetic anisotropy in a given total spin state from the known single-ion anisotropies of the transition metal centers. The method is applied to Mn12Ac and Fe8 in their ground and first few excited eigenstates, as an illustration. We have also studied the effect of orientation of local anisotropies on the molecular anisotropy in various eigenstates of the exchange Hamiltonian. We find that, in case of Mn12Ac, the molecular anisotropy depends strongly on the orientation of the local anisotropies and the spin of the state. The DM value of Mn12Ac is almost independent of the orientation of the local anisotropy of the core Mn(IV ) ions. In the case of Fe8, the dependence of molecular anisotropy on the spin of the state in question is weaker. We have also calculated the anisotropy constants for several sets of exchange parameters and find that in Mn12Ac the anisotropy increases with spin excitation gap while in Fe8, the anisotropy is almost independent of the gap. We have modeled the magnetic property of Nb6Ni12 cluster using a spin Hamiltonian in chapter 6. From Goodenough-Kanamori rules we should expect a ferromagnetic exchange between Nb and Ni ions. However, the magnetic studies indicate that the interaction is antiferromagnetic. We give reasons for the anomaly and fit the XMT data using an antiferromagnetic Heisenberg model. The observed XMT value at 2 K however does not correspond to ferrimagnetic ground state of Stot=9 and we invoke intermolecular interaction to explain this feature.

Fundamental to all biological processes is the interplay between biomolecules such as proteins and nucleic acids. Studies of interactions should therefore be more informative than mere detection of expressed proteins. Preferably, such studies should be performed in material that is as biologically and clinically relevant as possible, i.e. in primary cells and tissues. In addition, to be able to take into account the heterogeneity of such samples, the analyses should be performed in situ to retain information on the sub-cellular localization where the interactions occur, enabling determination of the activity status of individual cells and allowing discrimination between e.g. tumor cells and surrounding stroma. This requires assays with an utmost level of sensitivity and selectivity. Taking these issues into consideration, the in situ proximity-ligation assay (in situ PLA) was developed, providing localized detection of proteins, protein-protein interactions and post-translational modifications in fixed cells and tissues. The high sensitivity and selectivity afforded by the assay's requirement for dual target recognition in combination with powerful signal amplification enables visualization of single protein molecules in intact single cells and tissue sections. To further increase the usefulness and application of in situ PLA, the assay was adapted to high content analysis techniques such as flow cytometry and high content screening. The use of in situ PLA in flow cytometry offers the possibility for high-throughput analysis of cells in solution with the unique characteristics offered by the assay. For high content screening, it was demonstrated that in situ PLA can enable cell-based drug screening of compounds affecting post-translational modifications and protein-protein interactions in primary cells, offering superior abilities over current assays. The methods presented in this thesis provide powerful new tools to study proteins in genetically unmodified cells and tissues, and should offer exciting new possibilities for molecular biology, diagnostics and drug discovery.