In the master's thesis, there has been described and explained the principle of operation of the second generation coherence controlled holographic microscope (CCHM2) designed at the Brno University of Technology. There has also been listed theoretical description of the operation of the optical trap, together with the calculation of the forces acting on it, ways of measuring the stiffness of the optical trap and the principle of~creating a time-shared optical traps. The optical tweezers forming a separate module connectable to CCHM2 was designed. Simulation and optimization of parameters of the optical system, mechanical design, manufacturing documentation, current source to power the laser diode which allows to control the diode output power by the controller card connected to the PC was designed. The galvano-optics mirror angle is controlled by the PC card too. The optical tweezer has been designed, manufactured and tested in conjunction with the CCHM2.

Besides biochemical and molecular regulation, the migration and invasion of cells is controlled by the environmental mechanics and cellular mechanics. Hence, the mechanical phenotype of cells, such as fibroblasts, seems to be crucial for the migratory capacity in confined 3D extracellular matrices. Recently, we have shown that the migratory and invasive capacity of mouse embryonic fibroblasts depends on the expression of the Rho-GTPase Rac1, similarly it has been demonstrated that the Rho-GTPase Cdc42 affects cell motility. The p21-activated kinase (PAK) is an effector down-stream target of both Rho-GTPases Rac1 and Cdc42, and it can activate via the LIM kinase-1 its down-stream target cofilin and subsequently support the cell migration and invasion through the polymerization of actin filaments. Since Rac1 deficient cells become mechanically softer than controls, we investigated the effect of group I PAKs and PAK1 inhibition on cell mechanics in the presence and absence of Rac1. Therefore, we determined whether mouse embryonic fibroblasts, in which Rac1 was knockedout, and control cells, displayed cell mechanical alterations after treatment with group I PAKs or PAK1 inhibitors using a magnetic tweezer (adhesive cell state) and an optical cell stretcher (non-adhesive cell state). In fact, we found that group I PAKs and Pak1 inhibition decreased the stiffness and the Young’s modulus of fibroblasts in the presence of Rac1 independent of their adhesive state. However, in the absence of Rac1 the effect was abolished in the adhesive cell state for both inhibitors and in their nonadhesive state, the effect was abolished for the FRAX597 inhibitor, but not for the IPA3 inhibitor. The migration and invasion were additionally reduced by both PAK inhibitors in the presence of Rac1. In the absence of Rac1, only FRAX597 inhibitor reduced their invasiveness, whereas IPA3 had no effect. These findings indicate that group I PAKs and PAK1 inhibition is solely possible in the presence of Rac1 highlighting Rac1/PAK I (PAK1, 2, and 3) as major players in cell mechanics.

Όταν ηλεκρομαγνητική (ΗΜ) ακτινοβολία, προερχόμενη από κάποια πηγή, προσπίπτει σε σύνολο από σωμάτια τότε λαμβάνουν χώρα δύο φαινόμενα. Πρώτον, ασκούνται δυνάμεις στα σωμάτια οι οποίες οφείλονται αποκλειστικά στην σκέδαση της ΗΜ ακτινοβολίας της πηγής από αυτά. Οι δυνάμεις αυτές ονομάζονται Optical Trapping Forces. Δεύτερον, τα ίδια τα σωμάτια σκεδάζοντας την ΗΜ ακτινοβολία της πηγής, λειτουργούν και αυτά ως πηγές ακτινοβολίας. Έτσι ασκούν δυνάμεις το ένα στο άλλο. Οι δυνάμεις αυτές ονομάζονται Optical Binding Forces. H παράλληλη δράση των δύο αυτών ειδών δυνάμεων έχει ως αποτέλεσμα την δημιουργία ευσταθών δομών από τα σωμάτια. Προκειμένου την θεωρητική πρόβλεψη των δομών που αναπτύσσονται, χρειαζόμαστε έναν ταχύτατο αλγόριθμο υπολογισμού των δυνάμεων. Ο πιο ταχύς αλγόριθμος θα είναι το αποτέλεσμα της εύρεσης ενός αναλυτικού τύπου υπολογισμού των δυνάμεων. Η κατασκευή και η παρουσίαση του αναλυτικού τύπου αυτού είναι και το περιεχόμενο της εργασίας που ακολουθεί. / When the electromagnetic radiation, originating from a source, meets an ensemble of particles, there are two phenomena which take place. First, there are forces acting on these particles due exclusively to the scattering of the electromagnetic radiation from the particles. These are the so-called “Optical Trapping Forces”. Second, particles themselves act as sources of radiation since they scatter the radiation, and they exert forces one to another. These are the so-called “Optical Binding Forces”. The coexistence of these two different forces results in the creation of stable structures where the particles are self-organized. To achieve the theoretical prediction of these structures, we need a very efficient algorithm to calculate the forces. The fastest possible and thus more efficient algorithm originates from the analytical formula of the forces. The construction and the solution of the forces analytical formula is the content of this research work.

Au cours des vingt dernières années, la diffusion inélastique de la lumière par les modes propres de vibration des nanoparticules, appelés modes de Lamb, s’est avérée être une méthode très efficace pour caractériser la taille et les propriétés mécaniques des nano-objets. La fréquence de résonance d’une nano-sphère, dans la gamme du gigahertz, est donnée, en première approximation, par le ratio de la vitesse acoustique du matériau massif et la taille du confinement. Les raffinements du modèle théorique permettent d’obtenir, à partir de ces modes de vibration, des informations essentielles sur la géométrie et l’environnement local des nano-objets. L’objectif de cette thèse est de sonder le domaine de validité du modèle de Lamb, d’analyser les différents impacts de l’environnement sur ces modes de vibration et de développer de nouvelles méthodes pour les mesurer. Plusieurs aspects de l’interaction avec le milieu extérieur peuvent ainsi être pris en considération selon le type de système étudié. D’une part, la délocalisation de l’onde acoustique dans le cas de systèmes cœur-coquille, qui est gouvernée par les impédances acoustiques respectives du cœur et de la coquille, et qui se traduit par un couplage mécanique. D’autre part, l’effet de masse inertielle induite par la présence de ligands organiques à la surface de la particule qui modifie la fréquence de résonance. La validité de ces deux approches est ainsi discutée en fonction de la configuration des objets considérés, puis ces modèles théoriques sont appliqués à des cas réels tels que des nanoparticules cœur-coquille et des nano-plaquettes de semi-conducteurs ou des agrégats métalliques colloïdaux. L’effet de masse inertielle s’avère non négligeable pour des objets de petites tailles et il est ainsi montré la faisabilité de réaliser des nano-balances ultra-sensibles capable de sonder l’environnement proche des nano-objets. Par ailleurs, dans le cas des agrégats d’or, cette approche permet de discuter les limites du modèle de Lamb, basé sur la théorie des milieux continus, sur des vibrations n’impliquant que six atomes. Ainsi, grâce à la spectroscopie Raman basses fréquences, il apparait que les résultats expérimentaux des vibrations de ces objets s’accordent à la fois avec l’approche des milieux continus en considérant l’effet de masse inertielle et aussi avec les calculs de dynamique moléculaire. Finalement, le développement expérimental d’un montage optique capable de mesurer ces modes Raman basses fréquences sur une particule unique en milieu liquide est présenté. Cette approche nécessite de localiser une particule en milieu liquide à l’aide de nano-pinces plasmoniques puis d’exalter le signal Raman basses fréquences en stimulant les modes de vibration par électrostriction. Les perspectives étant d’appliquer cette méthode à l’étude de la dynamique vibrationnelle de nano-objet unique tel que des virus ou des protéines / Over the past twenty years, inelastic light scattering by vibrational eigenmodes of nanoparticles, called Lamb modes, has proven to be an effective method for characterizing the size and mechanical properties of nano-objects. The resonant frequency of a nano-sphere, in the gigahertz range, is given, as a first approximation, by the ratio of the acoustic velocity of the bulk material and the size of confinement. The refinements of the theoretical model allow to obtain, from these eigenmodes, information on the shape and local environment of nano-objects.The objective of this thesis is to probe the domain of validity of the Lamb model, to analyze the different impacts of the environment on eigenmodes and to develop a new strategy to measure them. Several aspects of interaction with the external medium can be considered depending on the system studied. On the one hand, the delocalization of the acoustic wave in the case of core shell systems is ruled by the acoustic impedance of the core and the shell and leads to a mechanical coupling. On the other hand, the inertial mass effect induced by the presence of organic ligands on the surface of the particle modifies the resonant frequency. The validity of both approaches is discussed according to the configuration and these models are applied to real cases, such as semiconductor core shell nanoparticles and nanoplatelets, or gold colloidal clusters. The inertial mass effect is significant for small objects and it is shown the feasibility to realize ultra-sensitive nano-balance capable of probing the local environment of nano-objects. Furthermore, in the case of gold clusters, this approach makes it possible to discuss the limit of the Lamb model, based on continuum mechanics, to interpret vibrations involving only six atoms. Thanks to low frequency Raman spectroscopy, it appears that the experimental results are in good agreement with both the continuum mechanics approach, by considering the inertial mass effect, and also with density functional theory (DFT) calculations. Finally, the experimental development of an optical set-up capable of measuring low frequency Raman modes on a single nanoparticle in a liquid medium is presented. This technic requires to localize a nanoparticle in a liquid medium with plasmonic tweezers and to enhance the low frequency Raman signal by stimulating vibrational modes with electrostriction. The perspectives are to apply this method to the dynamical study of a single object such as viruses or proteins.

F₁-ATPase, the sector of ATP synthase where the synthesis of cellular ATP occurs, is a rotary molecular motor in its own right. Driven by ATP hydrolysis, direct observation of the rotation of the central axis within single molecules of F₁ is possible. Operating at close to 100% efficiency, F₁ from thermophilic Bacillus has been shown to produce ~40pN˙nm of torque during rotation. This thesis details the groundwork required for the direct measurement of the torque produced by F₁ using a rotary angle clamp, an optical trapping system specifically designed for application to rotary molecular motors. Proof-of-concept experiments will be presented thereby demonstrating the ability to directly manipulate single F₁ molecules from Escherichia coli and yeast mitochondria (Saccharomyces cerevisiae), along with activation of F₁ out of its inhibited state by the application of external torque. Despite in-depth knowledge of the rotary mechanism of F₁ from thermophilic Bacillus, the rotation of F₁ from Escherichia coli is relatively poorly understood. A detailed mechanical characterization of E.coli F₁ will be presented here, with particular attention to the ground states within the catalytic cycle, notably the ATP-binding state, the catalytic state and the inhibited state. The fundamental mechanism of E.coli F₁ appears to depart little from that of F₁ from thermophilic Bacillus, although, at room temperature, chemical processes occur faster within the E.coli enzyme, in line with considerations regarding the physiological conditions of the different species. Also presented here is the verification of the rotary nature of yeast mitochondrial F₁. The torque produced by F₁ from thermophilic Bacillus, E.coli and yeast mitochondria is the same, within experimental error, despite their diverse evolutionary and environmental origins.