Master of Science / Department of Physics / Robert Szoszkiewicz / Proteins are involved in many of the essential cellular processes, such as cell adhesion, muscle function, enzymatic activity or signaling. It has been observed that the biological function of many proteins is critically connected to their folded conformation. Thus, the studies of the process of protein folding have become one of the central questions at the intersection of biophysics and biochemistry. We propose to use the changes of the nanomechanical properties of these biomolecules as a proxy to study how the single proteins fold. In the first steps towards this goal, the work presented in this thesis is concentrated on studies of unfolding forces and pathways of one particular multidomain protein, as well as on development of the novel method to study elastic spring constant and mechanical energy dissipation factors of simple proteins and peptides. In the first part of this thesis we present the results of the mean unfolding forces of the NRR region of the Notch1 protein. Those results are obtained using force spectroscopy techniques with the atomic force microscope (AFM) on a single molecule level. We study force-induced protein unfolding patterns and relate those to the conformational transitions within the protein using available crystal structure of the Notch protein and molecular dynamics simulations. Notch is an important protein, involved in triggering leukemia and breast cancers in metazoans, i.e., animals and humans. In the second part of this thesis we develop a model to obtain quantitative measurements of the molecular stiffness and mechanical energy dissipation factors for selected simple proteins and polypeptides from the AFM force spectroscopy measurements. We have developed this model by measuring the shifts of several thermally excited resonance frequencies of atomic force microscopy cantilevers in contact with the biomolecules. Next, we provided partial experimental validation of this model using peptide films. Ultimately, our results are expected to contribute in the future to the developments of medical sciences, which are advancing at a level, where human health and disease can be traced down to molecular scale.

La compréhension des mécanismes à l’origine de la progression métastatique des tumeurs mammaires reste une préoccupation constante en cancérologie et nécessite la découverte de nouveaux marqueurs prédictifs. Dans ce sens, le laboratoire a montré que la protéine DDB2 (Damaged-DNA Binding 2) était impliquée dans la tumorigenèse mammaire, en favorisant la prolifération et en réduisant le pouvoir invasif des cellules tumorales. Les propriétés invasives des cellules étant étroitement liées à leurs capacités d’adhérence, nous nous sommes intéressés au rôle de DDB2 dans l’adhérence des cellules tumorales mammaires. L’étude des propriétés d’adhérence et mécaniques a révélé une baisse de l’adhérence des cellules exprimant DDB2 sur des supports neutres ainsi qu’une augmentation de l’élasticité membranaire, associées une baisse du réseau d’actine corticale. Afin de comprendre les mécanismes mis en jeu, une analyse transcriptomique a été réalisée et révèle une diminution du niveau d’expression du gène codant le TGFß1 dans les cellules exprimant DDB2. Ainsi dans un second temps, nous avons étudié l’influence de DDB2 sur la voie du TGFß1. Nos résultats montrent que DDB2 inhibe transcriptionnelle des Smads en se fixant à proximité des éléments de réponse des Smads entraînant ainsi une diminution de leur présence sur le promoteur de leur gène cible. L’ensemble de ces résultats indique que DDB2 modulerait les propriétés nanomécaniques membranaires des cellules tumorales mammaires et la voie de signalisation induite par le TGFß1. Ce travail confirme donc l’importance clinique de la protéine DDB2 en tant que nouveau marqueur prédictif de la progression métastatique dans le cancer du sein / Understanding of mechanisms allowing metastatic progression remains a major issue in cancer research and requires discovery of new predictive markers. Thus, the laboratory has highlighted that DDB2 protein (Damaged-DNA Binding 2) is an important factor in breast tumorigenesis, by increasing proliferation and reducing invasive abilities of breast tumor cells. Migratory and invasive properties being closely related to adhesive properties, the aim of this work has been to study the involvement of DDB2 in breast cancer cell adhesion. First, adhesive and mechanical properties have been assessed, and reveal that DDB2 expression is associated with a decrease of adhesion on neutral surfaces, a decrease of cell stiffness in DDB2-expressing cells, related to the loss of cortical actin cytoskeleton. To understand molecular mechanisms involved in DDB2-dependent modulation of these properties, a transcriptomic study has been performed and shows the transcript level of gene encoding TGFß1 is modulated according to DDB2 expression level. Second, we have studied the influence of DDB2 on the TGFß signaling pathway. Our results show that DDB2, inhibits Smads transcriptional activity by binding near Smads responsive elements and decreasing so their binding on target genes promoter. Taken together, these data indicate that DDB2 could modulate nanomechanical properties of breast tumor cell membranes and the TGFß1 signaling pathway. The present work also confirms the clinical importance of DDB2 in breast tumorigenesis as a new predictive marker of metastatic progression of breast cancer

Coil coatings are durable  organic coatings used to protect metal sheets from corrosion and improve their aesthetic properties. Because of their extensive use, coil coatings have long been of interest for industrial and academic researchers. This interest has recently been furthered by a societal push towards the replacement of fossil-based raw materials with alternatives that are biobased and renewable. The aim of this licentiate thesis is to demonstrate how analyses on the macro-, micro-, and nanoscale can be used to better understand the degradation process of polyester-based coil coatings. The included manuscripts showcase methods for evaluating and comparing different coil coating formulations and for verifying accelerated weathering techniques. Multiple techniques, focusing on infrared (IR) spectroscopy and atomic force microscopy (AFM), were used to analyze coating systems before and after different types of weathering. IR data acquired from techniques without spatial resolution, such as attenuated total reflection (ATR) and photoacoustic spectroscopy (PAS) have been expanded upon with spatially resolved focal plane array (FPA) and s-SNOM  (scattering-type scanning near-field optical microscopy) measurements. Spatially resolved chemical data of coating cross sections were acquired and used to assess how the degradation at the surface and in the bulk was related. Additionally, differences between the degradation behavior of a standard fossil-based coating and a similar coating with biobased components as well as differences between the degradation caused by artificial and natural weathering was discussed. Nanoscale mechanical measurements of simplified coating surfaces showed that weathering increased nanomechanical stiffness and led to homogenization of mechanical properties on the local level. In addition, measurements with nanoscale FTIR correlated with macroscale FTIR. Even relatively minor changes in band intensities could be tracked on a local scale. Although the simplified samples were chemically homogeneous, nanoscale FTIR shows great promise for the assessment of local degradation of full systems. / Bandlackering är en process för att applicera stabila organiska beläggningar på metallytor för att skydda från korrosion och förbättra deras utseende. På grund av beläggningarnas omfattande användning så har utvärdering och analys av dem varit av intresse för både akademi och industri i flera årtionden. Detta långvariga intresse har ytterligare främjats av en ökade miljömedvetenhet och ett tryck att ersätta miljöfarliga och fossila råmaterial mot biobaserade och förnyelsebara alternativ. Målet med denna licentiatavhandling är att visa hur analysmetoder på makro-, mikro-, och nanonivå kan användas för att bättre förstå nedbrytning av bandlackerade beläggningar. Denna förståelse kan användas både för att utvärdera prestandan hos både nya redan befintliga system, men också för att kunna verifiera accelererade testmetoder vars mål är att minska tiden som krävs för utvärdering. Flera tekniker, med fokus på infraröd (IR) spektroskopi och atomkrafts-mikroskopi  (AFM) använts för att analysera beläggningar före och efter att de blivit utsatta för olika typer av aggressiva miljöer. Spektroskopiska data utan spatial upplösning som attenuerad totalreflektions FTIR (ATR) och fotoakustisk spektroskopi (PAS) har kompletterats med spatialt upplösta fokalplans array (FPA) och s-SNOM mätningar. Kemisk information med spatial upplösning har använts för att utvärdera hur nedbrytningen nära ytan relaterade till nedbrytningen längre ner i beläggningen. Likheter och skillnader i nedbrytningen som skedde i en standardbeläggning och ett system med biobaserade additiv jämfördes efter både väderbestendighets-testning som skedde utomhus och i labb. Skillnader mellan dessa exponeringsmetoder diskuterades också. Nanomekanisk analys med hjälp av atomkraftsmikroskopi användes för att bestämma lokala förändringar av mekaniska egenskaper i förenklade klarlacker. Mätningarna visade att exponeringar i aggressiva miljöer leder till en lokal homogenisering av mekaniska egenskaper och ökad styvhet. Utöver detta så utvärderades likheter och skillnader mellan FTIR spektra som tagits på makro- och nanonivå. Dessa mätningar gav lovande resultat för fortsatta ytanalyser. / <p>QC 2023-05-15</p>

Two technologies, namely Laser Technology and Surface Modification Technology, have made rapid strides in the last few decades. The lasers have evolved from a simple laboratory curiosity to a matured industrial tool and its applications are limited only by imagination. Intense, coherent and monochromatic laser sources with power outputs ranging over several orders of magnitude have found innumerable applications in the realm of materials engineering. Reactive Pulsed Laser Deposition (PLD) is a powerful technique that utilises the power of a nanosecond pulsed laser for materials synthesis. Unlike conventional PLD, which require high density targets that are difficult to synthesize at a reasonable cost, the RPLD circumvents the need for one such ceramic target. This thesis presents a detailed and judicious use of this technique for synthesis of hard ceramic multilayer coatings using elemental metal targets. Transition metal nitrides having rock salt structure are known to exhibit superior properties such as hardness and wear resistance and hence formed the basis for the development of first generation coatings. Further improvements through alloying of these binary compounds with metal or metalloid components lead to the development of second generation coatings. As the demand for functional materials increased, surface modification technology alias surface engineering, grew in leaps and bounds. As the large number of coating requirements for optimal performance could not be fulfilled by a single homogeneous material, third generation coatings, comprising multilayer coatings, were developed. It is this aspect of combining the advantages of RPLD process to synthesize ceramic multilayer coatings, provides the main motivation for the present research work. In this thesis, a systematic study presented for synthesis of nanocrystalline and stoichiometric TiN and NbN thin films using RPLD through ablation of high purity titanium and niobium targets, in the presence of low pressure nitrogen gas. A novel Secondary Ion Mass Spectrometry (SIMS) based analysis was developed to effectively deduce the important process parameters in minimum trials to arrive at desired composition. The validity of this SIMS based method, for optimization of process parameters to get stoichiometric nitride films, was proved beyond any speculation by corroborative Proton Elastic Backscattering Spectrometric (PEBS) analysis. SIMS was also used to characterize the [NbN/TiN] multilayers. The feasibility of growing nanocrystalline multilayers with varying thicknesses has been demonstrated. Nanomechanical properties including hardness and adhesion strength of monolithic TiN and NbN films and multilayers were evaluated. The thesis is organised into six chapters. The first chapter gives a brief account on the history and development of ‘surface engineering’. The second chapter provides a comprehensive description of the experimental facility developed in-house to pursue research on PLD grown ceramic thin films and multilayers. Thin film synthesis procedure for ex-situ SIMS and TEM analyses is described. Brief introduction is also presented on the characterization techniques used in this study to investigate the surface, interface and microstructural aspects of PLD grown films with underlying basic principles. The third and fourth chapter describes the synthesis and characterization of titanium nitride and niobium nitride thin films using RPLD technique, respectively. SIMS was used in depth profiling mode, for optimization of three important process parameters, viz., nitrogen gas pressure, substrate temperature and laser pulse energy, to get stoichiometric nitride films. Further, films were characterized using GIXRD, TEM, XPS and PEBS for their structure and composition. AFM measurements were made to elucidate the surface morphological features. PEBS was effectively used to estimate the nitrogen concentration in a quantitative manner and the results corroborate well with the SIMS measurements. Having succeeded in synthesizing stoichiometric TiN and NbN films, further studies on the nanomechanical properties of monolithic TiN and NbN films and their multilayers were carried out and these results form the contents of the fifth chapter. The findings of the work reported in this thesis are concluded in Chapter 6 and few possible suggestions were presented as future directions. Both the monolithic TiN and NbN coatings showed a deposition pressure dependent hardness variation. The hardness of these monolithic films was found to be around 30 GPa, higher than the hardness values obtained by other conventional techniques. Keeping total thickness of the multilayers constant at 1 μm, [NbN/TiN] multilayers having bilayer periods ranging from 50 nm to 1000 nm, were synthesized. A systematic enhancement in hardness upto ~ 40 GPa was observed for [NbN/TiN]10 with the modulus of the multilayer remaining almost constant. The pileup observed around the indentation edge is indicative of toughening in multilayers. The tribological properties of multilayer films showed a better performance in terms of low coefficient of friction and regeneration of coating surfaces as revealed from the nanotribological studies. Overall, the multilayer coatings exhibited better performance in terms of hardness, toughness and adhesion with the substrate material.