Nanoscale materials have many potential advantages because of their quantum confinement, cost and producibility by low-temperature chemical methods. Advancement of theoretical methods as well as the availability of modern high-performance supercomputers allow us to control and exploit their microscopic properties at the atomic scale, hence making it possible to design novel nanoscale molecular devices with interesting features (e.g switches, rectifiers, negative differential conductance, and high magnetoresistance). In this thesis, state-of-the-art theoretical calculations have been performed for the quantum transport properties of nano-structured materials within the framework of Density Functional Theory (DFT) and the Nonequilibrium Green's Function (NEGF) formalism. The switching behavior of a dithiolated phenylene-vinylene oligomer sandwiched between Au(111) electrodes is investigated. The molecule presents a configurational bistability, which can be exploited in constructing molecular memories, switches, and sensors. We find that protonation of the terminating thiol groups is at the origin of the change in conductance. H bonding at the thiol group weakens the S-Au bond, and thus lowers the conductance. Our results allow us to re-interpret the experimental data originally attributing the conductance reduction to H dissociation. Also examined is current-induced migration of atoms in nanoscale devices that plays an important role for device operation and breakdown. We studied the migration of adatoms and defects in graphene and carbon nanotubes under finite bias. We demonstrate that current-induced forces within DFT are non-conservative, which so far has only been shown for model systems, and can lower migration barrier heights. Further, we investigated the quantum transport behavior of an experimentally observed diblock molecule by varying the amounts of phenyl (donor) and pyrimidinyl (acceptor) rings under finite bias. We show that a tandem configuration of two dipyrimidinyl-diphenyl molecules improves the rectification ratio, and tuning the asymmetry of the tandem set-up by rearranging the molecular blocks greatly enhances it. It has been recently demonstrated that the large band gap of boronitrene can be significantly reduced by carbon functionalization. We show that specific defect configurations can result in metallicity, raising interest in the material for electronic applications. In particular, we demonstrate negative differential conductance with high peak-to-valley ratios, depending on the details of the material, and identify the finite bias effects that are responsible for this behavior. Also, we studied the spin polarized transport through Mn-decorated topological line defects in graphene. Strong preferential bonding is found, which overcomes the high mobility of transition metal atoms on graphene and results in stable structures. Despite a large distance between the magnetic centers, we find a high magnetoresistance and attribute this unexpected property to very strong induced π magnetism. Finally, the results obtained herein advance the field of quantum electronic transport and provide significant insight on switches, rectification, negative differential conductance, magnetoresistance, and current-induced forces of novel nanoscale materials.

At present chemistry is undergoing an interesting change from the traditional preparation and investigation of single molecules to the construction and use of more complex functionalized architectures. Especially the better understanding of biological processes and the demand to create new materials with specific properties lead to a development of novel nanostructured assemblies that are held together by reversible weak interactions, that include coordination and hydrogen bonds, van der Waals forces as well as p-p and electrostatic interactions. Based on the smart use of Nature’s principles of molecular recognition and self-assembly, the supramolecular chemistry is now one of the pillars within the framework of nanotechnology. This contribution gives an overview on the basic concepts of supramolecular chemistry, the latter’s connections with biological systems and foreseeable applications. / Die Chemie erfährt gegenwärtig einen interessanten Übergang von der traditionellen Betrachtung der Einzelmoleküle hin zu großen komplexen Funktionseinheiten. Besonders das wachsende Verständnis biologischer Prozesse als auch die steigenden Forderungen nach neuen Werkstoffen mit einem spezifischen Eigenschaftsprofil führten zur gezielten Konstruktion definierter Baueinheiten auf der Nanometerskala. Dabei werden in intelligenter Weise reversible Bindungsprozesse auf Basis schwacher nichtkovalenter Wechselwirkungen, wie koordinative und Wasserstoffbrückenbindungen, Van-der-Waals- Kräfte sowie p−p- und elektrostatische Wechselwirkungen, genutzt. Aufbauend auf den natürlichen Prinzipien der molekularen Erkennung und Selbstorganisation ist die supramolekulare Chemie heute eine der Säulen in der Entwicklung der Nanotechnologie. Im Beitrag wird ein Überblick über wesentliche Aspekte der supramolekularen Chemie, ihre Anknüpfung an biologische Prinzipien und ausgewählte Nutzungsmöglichkeiten gegeben.

This thesis presents the development and application of nanoscale techniques to trap and / Chemistry and Chemical Biology

At present chemistry is undergoing an interesting change from the traditional preparation and investigation of single molecules to the construction and use of more complex functionalized architectures. Especially the better understanding of biological processes and the demand to create new materials with specific properties lead to a development of novel nanostructured assemblies that are held together by reversible weak interactions, that include coordination and hydrogen bonds, van der Waals forces as well as p-p and electrostatic interactions. Based on the smart use of Nature’s principles of molecular recognition and self-assembly, the supramolecular chemistry is now one of the pillars within the framework of nanotechnology. This contribution gives an overview on the basic concepts of supramolecular chemistry, the latter’s connections with biological systems and foreseeable applications. / Die Chemie erfährt gegenwärtig einen interessanten Übergang von der traditionellen Betrachtung der Einzelmoleküle hin zu großen komplexen Funktionseinheiten. Besonders das wachsende Verständnis biologischer Prozesse als auch die steigenden Forderungen nach neuen Werkstoffen mit einem spezifischen Eigenschaftsprofil führten zur gezielten Konstruktion definierter Baueinheiten auf der Nanometerskala. Dabei werden in intelligenter Weise reversible Bindungsprozesse auf Basis schwacher nichtkovalenter Wechselwirkungen, wie koordinative und Wasserstoffbrückenbindungen, Van-der-Waals- Kräfte sowie p−p- und elektrostatische Wechselwirkungen, genutzt. Aufbauend auf den natürlichen Prinzipien der molekularen Erkennung und Selbstorganisation ist die supramolekulare Chemie heute eine der Säulen in der Entwicklung der Nanotechnologie. Im Beitrag wird ein Überblick über wesentliche Aspekte der supramolekularen Chemie, ihre Anknüpfung an biologische Prinzipien und ausgewählte Nutzungsmöglichkeiten gegeben.

In dieser Arbeit wurden auf Substratoberflächen adsorbierte Polymermoleküle mit Rasterkraftmikroskopie (RKM) untersucht. Dabei war die Form der Moleküle (Konformation) von besonderem Interesse. Sie ist von zentralerer Bedeutung in der Polymerphysik und wird üblicherweise in Lösung und mit Streumethoden untersucht. Polymerkonformationen auf Oberflächen sind heutzutage noch wenig untersucht. Üblicherweise wird das Verhalten nach dem so genannten Wormlike-Chain Modell angenommen. Es basiert auf der Annahme, dass die Kettenbiegung nur aus thermischen Fluktuationen resultiert, so dass sich die Kettenform durch statistische Mechanik beschreiben lässt. Es wurden für verschiedene Modellsystem einzelne Moleküle hochaufgelöst abgebildet und die Konformation aus den Bildern bestimmt. Es hat sich gezeigt, dass die idealisierte Vorstellung des Wormlike-Chain Modells tatsächlich nur für wenige der untersuchten Systeme erfüllt ist. Abweichende Konformationen sind oft auffallend regelmäßig: entweder sinusartig mäandrierte oder spiralförmig gedrehte. Beide Charakteristika lassen sich aus dem Prozess der Adsorption erklären, was zeigt, dass die Moleküle auf dem Substrat immobil sind, so dass eine thermische Relaxation der Konformation verhindert ist. Konformtionen lassen sich mit RKM nicht nur beobachten, sondern auch gezielt verändern (Nanomanipulation). Für dendronisierte Polymere konnte so gezeigt werden, dass es einen glasartigen Zustand für das einzelne Molekül gibt. In diesem Zustand verhält sich das Molekül nicht mehr wie eine bewegliche Kette, sondern formstabil, ähnlich einem makroskopischen festen Körper. / In this work single polymer molecules adsorbed onto substrate surfaces were investigated by scanning force microscopy (SFM). The focus was on the shape (conformation) of the molecules, which is of central importance in polymer physics. It is commonly investigated in solutions and with scattering methods. Conformations on surfaces are only little investigated thus far. Often a behavior according to the so-called worm-like chain model is assumed. It is based on the assumption that chain bending results entirely from thermal fluctuations so that the overall chain shape can be described by statistical mechanics. For several model systems single molecules were imaged and the conformation was determined from the images. It was found that the idealistic wormlike chain behavior is only valid for a few systems. Deviations are often remarkable regular: either sine-like undulated or spiral wound. Both characteristics can be explained from the process of adsorption, indicating that molecules are immobile on the substrate so that thermal relaxation is inhibited. Conformations can not only be imaged using the SFM, but also changed in a defined way (nanomanipulation). Manipulation experiments with dendronized polymers the existence of a glassy state for the single polymer. In this state the molecule no longer behaves as a flexible chain but remains its shape, similar to a macroscopic solid body.

Ce travail de thèse est principalement axé sur le développement d’une nouvelle méthode de manipulation de vortex d’Abrikosov individuels dans les supraconducteurs de type II. Cette méthode, rapide, efficace et précise, est basée sur l’optique en champ lointain et repose sur l’échauffement local du supraconducteur sous l’action d’un faisceau laser focalisé. Elle apporte une excellente alternative aux techniques existantes de manipulation de vortex, toutes basées sur l’utilisation de sondes locales, et donc intrinsèquement lentes et difficiles à mettre en oeuvre dans un environnement cryogénique. La combinaison de cette méthode à une technique d’imagerie magnéto-optique performante permet de déplacer des vortex individuels avec un taux de réussite de 100% et sur de grandes échelles limitées uniquement par le champ de l’objectif de microscope. Les vitesses de manipulation atteintes sont élevées, de l’ordre de 10 mm.s-1, mais encore limitées par l’instrumentation utilisée et loin des limites fondamentales offertes par cette méthode, estimées au km.s-1. La méthode de manipulation optique permet aussi de mesurer la distribution des forces de piégeage de chaque vortex d’un échantillon. En utilisant des puissances de chauffage laser permettant de dépasser localement la température critique, nous avons également pu étudier la pénétration des vortex à l’interface entre une zone normale et une zone supraconductrice.Durant ces travaux, nous avons aussi eu l’opportunité de mettre en évidence, par spectroscopie de molécules uniques, l’effet flexomagnétoélectrique dans un matériau multiferroïque, en employant un supraconducteur de type I comme générateur de champ magnétique inhomogène. Enfin, nous proposons à la fin de ce mémoire un concept de jonction Josephson créée tout optiquement, et dont les propriétés seraient contrôlables en temps réel par laser. / This thesis focuses on the development of a new manipulation technique to handle single Abrikosov vortices in type II superconductors. This fast, efficient and precise method is based on far field optics and rests on the local temperature elevation produced by a focused laser beam. It brings an excellent alternative to the existing techniques which are all based on local probes and thus heavy to implement in a cryogenic environment. The combination of this method with an efficient magneto-optical imaging system allows us to manipulate single vortices with a 100% rate of success on a large scale only limited by the field of view of the microscope objective. Manipulation speeds are high, of the order of 10 mm.s-1, but still limited by our setup and far from the fundamental limits offered by this technique, estimated to the km.s-1. This manipulation technique also allows to measure the pinning force of any single vortex in a superconducting sample. By using a high enough laser power which locally pushes the temperature above the critical temperature, we could also study the vortex penetration at the interface between normal and superconducting areas.In the course of this work, we also evidenced, with single molecule spectroscopy, the flexomagnetoelectric effect in a multiferoic material, by using a type I superconductor as a source of inhomogeneous magnetic field. Finally, we propose at the end of the manuscript the new concept of an optically created Josephson junctions, whose properties could be controlled in real time just with a laser beam.

Proteins have been optimized by evolution for billions of years to work on a nanometer scale. Therefore, they are extremely promising for nanotechnological applications. Cytoskeletal filaments propelled by surface-attached motor proteins have been recently established as versatile transport platforms for nano-sized cargo in molecular sorting and nano-assembly devices. However, in this gliding motility setup, cargo and motors share the filament lattice as a common substrate for their activity. Therefore, it is important to understand the influence of cargo-loading on transport properties. By performing single molecule stepping assays on biotinylated microtubules, it was shown that kinesin-1 motors first stop and then detach when they encounter a streptavidin obstacle on their path along the microtubule. Consequently, the deceleration of streptavidin coated microtubules in gliding assays could be attributed to an obstruction of kinesin-1's path on the microtubule rather than to "frictional" streptavidin-surface interactions. The insights gained by studying kinesin-1's behavior at obstacles were then used to demonstrate a novel sensing application: Using a mixture of two distinct microtubule populations that each bind a different kind of protein, the presence of these proteins was detected via speed changes in the respective microtubule populations. In future applications, this detection scheme could be combined with other recent advancements in the field, creating highly integrated lab-on-a-chip devices that use microtubule based transport to detect, sort and concentrate analytes. It has been envisioned that the kinesin-1-microtubule system could be used for even more complex appliances like nano-assembly lines. However, currently available control mechanisms for kinesin-1 based transport are not precise enough. Therefore, improved temporal control mechanisms for kinesin-1 were investigated: Using a polymer that changes its size in solution with temperature, starting and stopping of gliding microtubules was demonstrated. In combination with local heating by light, this effect could be used to control the gliding of single microtubules. Finally, a strategy to create photo-switchable kinesin-1 was developed and tested for feasibility using molecular modeling.

La spectroscopie de perte d’énergie des électrons (EELS) et la cathodoluminescence (CL) dans un microscope électronique en transmission à balayage (STEM) sont des techniques puissantes pour l’étude des nanostructures isolées. Cependant, des électrons rapides peuvent endommager fortement des échantillons minces et fragiles, ce qui limite la résolution spatiale et l’intensité des signaux spectroscopiques. Pendant cette thèse, nous avons dépassé cette restriction par le développement de protocoles d’acquisition spécifiques pour l’étude de certains archétypes de nanosystèmes fragiles. Dans la première partie de cette thèse, nous avons caractérisé des flocons minces de graphène oxydé (GO) et GO réduit (RGO) par EELS dans le STEM. Grâce aux spécificités techniques de notre microscope et à la définition des conditions d’illumination optimales, nous avons dérivé des cartes du contenu d’oxygène dans le (R)GO à une résolution spatiale inédite. Aussi, par l’analyse des pics EELS de structure fine, nous avons révisé les modèles atomiques proposés dans la littérature. Des molécules isolées constituent une autre classe de nanomatériaux fortement sensibles à l’irradiation et aussi à l’environnement chimique et physique. Nous avons conduit des expériences de CL sur des molécules individuelles, grâce à un choix avisé du substrat. Le nitrure de bore hexagonal (h-BN) est un matériaux bidimensionnel chimiquement inerte, qui participe activement au processus de CL en absorbant l’énergie incidente. Le transfert de l’excitation aux molécules et l’utilisation d’une routine innovante d’acquisition par balayage aléatoire ont permis de réduire les effets d’illumination. Ensuite, l’intérêt porté aux propriétés optiques du h-BN ont inspiré l’étude de sa phase cubique (c-BN), qui a été peu caractérisé auparavant à cause d’impuretés dans les cristaux. Nous avons analysé des cristaux de c-BN de haute pureté par EELS, en identifiant une bande interdite d’énergie plus grande que précédemment rapportée et plus proche des calculs les plus récents. Dans des cristaux moins purs, nous avons identifié et analysé plusieurs émissions associées à des défauts, en termes d’énergie caractéristique, distribution spatiale et temps de vie, par CL et interférométrie en intensité de Hanbury-Brown et Twiss. / Electron energy loss spectroscopy (EELS) and cathodoluminescence(CL) in a scanning transmission electron microscope (STEM) are extremely powerful techniques for the study of individual nanostructures. Nevertheless, fast electrons damage extremely sensitive thin specimens, imposing strong limitations on the spatial resolution and the intensity of spectroscopic measurements. During this thesis we have overcome this restriction by developing material-specific acquisition protocols for the study of some archetypical fragile nanosystems. In the first part of this thesis we have characterized graphene oxide (GO) and reduced graphene oxide (RGO) thin flakes by EELS spectroscopy in the STEM. Thanks to the particular setup of our microscope and by experimentally defining the optimal illumination conditions, we have derived oxygen quantification maps of (R)GO at an unprecedented spatial resolution. On the basis also of EELS fine structures analysis, we have revised the existing proposed atomic models for these materials. Another class of exceedingly sensitive nanometric systems is represented by individual molecules, which are strongly affected by both illumination and chemical/physical environment. We have performed the first CL-STEM investigation on the luminescence of isolated molecules, thanks to a watchful choice of the substrate. Hexagonal boron nitride (h-BN) is a flat, chemically inert 2D material, that actively takes part in the CL process by absorbing the incident energy. Excitation transfer from h-BN to molecules and the use of an innovative random scan acquisition routine in the STEM have allowed to considerably lower illumination effects and improve CL intensity. Afterwards, the attractive optical properties of h-BN have led to the study of its cubic phase (c-BN), which has been up to now hindered by the poor quality of the crystals. By EELS in the STEM we have analysed c-BN crystals of the highest available purity, identifying a wider optical band-gap with respect to previous experimental studies and in better agreement with recent calculations. In commercial crystals, several defect-related emissions have been identified and analysed in terms of characteristic energy, spatial distribution and lifetime using CL and Hanbury-Brown and Twiss intensity interferometry.

In this thesis, the response of DNA and RNA to linear and torsional mechanical stress is studied using coarse-grained models. Inspired by single-molecule assays developed over the last two decades, the end-to-end extension, buckling and torque response behaviour of the stressed molecules is probed under conditions similar to experimentally used setups. Direct comparison with experimental data yields excellent agreement for many conditions. Results from coarse-grained simulations are also compared to the predictions of continuum models of linear polymer elasticity. A state diagram for supercoiled DNA as a function of twist and tension is determined. A novel confomational state of mechanically stressed DNA is proposed, consisting of a plectonemic structure with a denaturation bubble localized in its end-loop. The interconversion between this novel state and other, known structural motifs of supercoiled DNA is studied in detail. In particular, the influence of sequence properties on the novel state is investigated. Several possible implications for supercoiled DNA structures in vivo are discussed. Furthermore, the dynamical consequences of coupled denaturation and writhing are studied, and used to explain observations from recent single molecule experiments of DNA strand dynamics. Finally, the denaturation behaviour, topology and dynamics of short DNA minicircles is studies using coarse-grained simulations. Long-range interactions in the denaturation behaviour of the system are observed. These are induced by the topology of the system, and are consistent with results from recent molecular imaging studies. The results from coarse-grained simulations are related to modelling of the same system in all-atom simulations and a local denaturation model of DNA, yielding insight into the applicability of these different modelling approaches to study different processes in nucleic acids.

Improved analytical methods provide new opportunities for both biological research and medical applications. This thesis describes several novel molecular techniques for nucleic acid and protein analysis based on detection or sequencing of amplified single molecules (ASMs). ASMs were generated from padlock probe assay and proximity ligation assay (PLA) through a series of molecular processes. In Paper I, a simple colorimetric readout strategy for detection of ASMs generated from padlock probe assay was used for highly sensitive detection of RNA virus, showing the potential of using padlock probes in the point-of-care diagnostics. In Paper II, digital quantification of ASMs, which were generated from padlock probe assay and PLA through circle-to-circle amplification (C2CA), was used for rapid and sensitive detection of nucleic acids and proteins, aiming for applications in biodefense. In Paper III, digital quantification of ASMs that were generated from PLA without C2CA was shown to be able to improve the precision and sensitivity of PLA when compared to the conventional real-time PCR readout. In Paper IV, a non-optical approach for detection of ASMs generated from PLA was used for sensitive detection of bacterial spores. ASMs were detected through sensing oligonucleotide-functionalized magnetic nanobeads that were trapped within them. Finally, based on in situ sequencing of ASMs generated via padlock probe assay, a novel method that enabled sequencing of individual mRNA molecules in their natural context was established and presented in Paper V. Highly multiplex detection of mRNA molecules was also achieved based on in situ sequencing. In situ sequencing allows studies of mRNA molecules from different aspects that cannot be accessed by current in situ hybridization techniques, providing possibilities for discovery of new information from the complexity of transcriptome. Therefore, it has a great potential to become a useful tool for gene expression research and disease diagnostics.