Owing to atomic force microscopy’s (AFM) high-resolution in both imaging and force spectroscopy, it is very successful in probing not only structures, but also nanomechanics of biological samples in solution. In this thesis, the nanomechanical properties of lipid bilayers of biological relevance and proteins of the barnacle adhesive were examined using AFM indentation, AFM-based force mapping, and single-molecule pulling experiments. Through high-resolution AFM-based force mapping, the self-organized structures exhibited in phase-segregated supported lipid bilayers consisting of dioleoylphosphatidylcholine / egg sphingomyelin / cholesterol (DEC) in the absence and presence of ceramide (DEC-Ceramide) were directly correlated with their breakthrough forces, elastic moduli, adhesion, and bilayer thickness. Results were presented as two-dimensional visual maps. The highly stable ceramide-enriched domains in DEC-Ceramide bilayers and the effect of different levels of cholesterol as well as of diblock copolymers, on the nanomechanical stability of the model systems studied were further examined. For the proteins of the barnacle adhesive, scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy, and chemical staining with amyloid-selective dyes, in addition to AFM imaging, indentation, and pulling experiments were performed to study the structure and nanomechanics of the polymerized barnacle glue. Nanoscale structures exhibiting rod-shaped, globular, and irregularly shaped morphologies were observed in the bulk barnacle cement by AFM. SEM coupled with energy dispersive x-ray (EDX) makes evident the organic nature of the rod-shaped nanoscale structures while FTIR spectroscopy on the bulk cement gave signatures of β-sheet and random coil conformations. Indentation data yielded higher elastic moduli for the rod-shaped structures as compared to the other structures in the bulk cement. Single molecule AFM force-extension curves on the matrix of the bulk cement often exhibited a periodic sawtooth-like profile, observed in both extend and retract portions of the force curve. Rod-shaped structures stained with amyloid protein-selective dyes (Congo Red and Thioflavin-T) revealed that about 5% of the bulk cement are amyloids.

The work presented here has a multidisciplinary character, having as a common factor the characterization of self-assembled nanostructures through force spectroscopy. Exploring AFM as a tool for characterizing self-assembly and interaction forces in soft matter nanostructures, three different Bio and nonbiological systems where investigated, all of them share the common characteristic of being soft matter molecular structures at the nanoscale. The studied systems in question are: a) Polyelectrolyte – lipid nanocomposites. Single polyelectrolyte adsorption-desorption from supported lipid bilayers, b) Polyelectrolyte brushes and c) Virus-Like particles (VLPs). The scientific interest and industrial applications for each of these different nanostructures is broad, and their potential uses in the near future ranges from smart nanocontainers for drug and gene delivery, surface platforms for molecular recognition to the development of new nanodevices with ultrasensitive external stimuli responsiveness. These nano-structures are constructed following assembly of smaller subunits and belong to representative examples of soft matter in modern nanotechnology. The stability, behavior, properties and long term durability of these self-organized structures depends strongly on the environmental conditions to which they are exposed since their building mechanism is a balance between attractive noncovalent interactions and momentum transmitted collisions due Brownian motion of the solvent molecules. For example a set of long chain molecules firmly attached to one end to a surface will alter their conformation as the space between them is reduced or the environmental conditions are modified (i.e. ionic strength, pH or temperature). For a highly packed condition, this fuzzy surface known as a polyelectrolyte brush will then behave as a responsive material with tunable responsiveness. Thus the objective in the present case was to investigate the change in morphology and the mechanical response of a polyelectrolyte brush to external forces by application of AFM nanoindentations under different ionic strength conditions. The degree of penetration of the AFM tip through the brush will provide insights into the forces exerted by the brush against the tip. Compressions on the brush should aid to characterize its changes in compressibility for different salt concentrations. For the second chosen system, the interaction between two assembled interfaces was investigated at the single molecular level. A multilayered film formed by the consecutive assembly of oppositely charged polyelectrolytes and subsequently coated with a lipid membrane represents a fascinating soft composite material resembling more than a few structural components emerging in living organisms. The fluid bilayer, thus provide a biocompatible interface where additional functionalities can further be integrated (fusion peptides for instance). The smooth polymer cushion confers not only structural flexibility but also adaptability of the chosen substrate properties to be coated. This type of interface could be useful in the development of novel molecular biosensors with single molecule recognition capacities or in the fabrication of assays against pathogenic agents. The aim of this project was to study the molecular binding mechanism between the last polyelectrolyte layer and the lipid head group of the lower lipid leaflet. Understanding this adsorption mechanism between both interfaces, should likewise contribute to improve the fabrication of lipid coated polymeric nano/micro capsules with targeting properties. For example this could be critical in the field of nonviral gene therapy, where the improvement in the design of condensates of nucleic acids and other polymers with lipids (lipoplexes) are of main interest for its posterior use as delivery vectors. Finally, viral capsids were investigated. These naturally occurring assembled nanocontainers within living organisms stand for a remarkable example of nature’s morphological designs. These structures self-assemble from a small number of different proteins occurring in identical copies. The capsid as a self-assembled structure carries multiple functions: compaction of the genome, protection against external chemical threats, target recognition, structural support and finally facilitating the release of the genome into the host cell. It is highly interesting how these different functions are organized within the capsid which consists, for example, in the case of the norovirus of 180 identical copies of one single protein. Therefore, the mechanical stability and elastic properties of virus-like particles of Rubella and Norovirus were investigated by external application of loading forces with an AFM tip. The measurements were performed under conditions relevant for the virus infection mechanism. The applied compressions on these protein shells at pH values mimicking the virus life cycle will aid to learn about possible internal transitions among proteins which may be important for switching between the various functions of the capsid. The choice of two unrelated viral systems with different entry pathways into the cell and with different morphological architectures is expected to reveal crucial information about the stability and mechanical resistance to deformation of these empty membrane-coated and bare viral capsids. This last might provide clues on the stage of particle disassembly and cargo release during the final step of the infection process.

Flexible electronics attract research and commercial interests in last 2 decades for its flexibility, low cost, light weight and etc. To develop and improve the electro-mechanical properties of flexible electrodes is the most critical and important step. In this work, we have performed nanomechanical and electro-mechanical characterization of materials for flexible electrode applications, including metallic nanowires (NWs), indium tin oxide (ITO)-based and carbon nanotube (CNT)-based electrodes. First, we designed and developed four different testing platforms for nanomechanical and electro-mechanical characterization purpose. For the nano/sub-micro size samples, the micro mechanical devices can be used for uni-axial and bi-axial loading tests. For the macro size samples, the micro tester will be used for in situ monotonic tensile test, while the fatigue tester can be used for in situ cyclic tensile or bending testing purpose. Secondly, we have investigated mechanical behaviors of single crystalline Ni nanowires and single crystalline Cu nanowires under uni-axial tensile loading inside a scanning electron microscope (SEM) chamber. We demonstrated both size and strain-rate dependence on yield stress of single-crystalline Ni NWs with varying diameters (from 100 nm to 300 nm), and themolecular dynamics (MD) simulation helped to confirm and understand the experimental phenomena. Also, two different fracture modes, namely ductile and brittle-like fractures, were found in the same batch of Cu nanowire samples. Finally, we studied the electro-mechanical behaviors of flexible electrodes in macro scale. We reported a coherent study integrating in situ electro-mechanical experiments and mechanics modeling to decipher the failure mechanics of ITO-based and CNT-based electrodes under tension. It is believed that our combined experimental and simulation results provide some further insights into the important yet complicated deformation mechanisms for nanoscale metals and fracture mechanism for flexible electrodes applications.

Nanomechanics emerged as chemists and physicists began fabricating nanoscale objects. However, there are some materials that have neither been fabricated nor mechanical investigated at the nanoscale, such as rhodium. Rhodium is used in many applications, especially in coatings and catalysis. To contribute to the understanding the nano-properties of this important material, rhodium was fabricated and mechanically investigated at the nanoscale. The nanopillars approach was employed to study size effects on mechanical properties. Nanopillars with different diameters were fabricated using electroplating followed by uniaxial compression tests. SEM was used as a quality control technique by imaging the pillars before and after compression to assure the absence of buckling, barrelling, or any other problems. Transmission electron microscopy (TEM) and SEM were used as microstructural characterization techniques, and the energy-dispersive X-ray spectroscopy (EDX) was used as the chemical characterization technique. Due to substrate induced effects, only the plastic region of the stress-strain curves were investigated, and it was revealed that rhodium softens with decreased nanopillar diameter. This softening/weakening effect was due to the nanocrystallinity of the fabricated pillars. This effect is consistent with the literature that demonstrates the reversed size effect of nanocrystalline metals, i.e., smaller is weaker. Further studies should focus on eliminating the substrate effect that was due to the adhesion layers between Rh and the silicon substrate being softer than Rh, consequently, causing Rh to sink into the adhesion layer when compressed and thus perturbing the stress-strain curve. Moreover, further investigation of other properties of Rh is required to achieve a comprehensive understanding of Rh at the nanoscale, and to render it suitable for specific, multivariable applications.

Nanowires are an exciting class of novel materials that have potential applications in areas including biological sensing, photonics, and electronics. The promise of these future applications relies on the production of nanowires of controlled size, shape, and crystal structure, in reasonable quantities, and further, ultimately requires that the nanowires be mechanically stable in the application environment. This research is aimed at understanding the mechanical behavior of metallic nanowires, through the use of atomistic simulations. At the nanometer scale, where the surface-area-to-volume ratio is substantial, the effects of free surfaces have a primary influence on the physical properties of a material. Surface energy arises from unsatisfied bond coordination at the surface of a solid and results in a surface stress as the surface atoms contract into the bulk of the material to increase their local electron density. The magnitude of surface energy and surface stress is dependent on the orientation of the surface and the compliance of the structure. In bulk materials, the effects of surfaces are negligible; however, at the nanometer scale, surface effects become quite significant. In metallic nanowires, these surface effects strongly influence mechanical properties, and the characteristics of plastic deformation. The mechanical testing of nanowires is precluded by the difficulties of accurately applying and measuring forces on the nanometer scale. For this reason, computational simulations are a primary tool for investigating the mechanical behavior of nanowires. In this work, we have performed atomistic simulations to examine the mechanical response of silver nanowires. We have conducted studies to determine the deformation characteristics of experimentally observed nanowire geometries subjected to tensile and bending loads. We have also developed a technique to probe the energetics of mechanical deformation, in order to elucidate the energetically favored deformation pathways in nanowires. Our results show that nanowires may be tailored for specific mechanical requirements based on geometry and free surface orientation and provide insight to the effect of free surfaces in the mechanical deformation of nanometer scale structures.

This thesis is concerned with employing the statistics of charge transfer in a conductor as a tool for quantum measurement. The physical systems studied are electronic devices made by nanoscale manufacturing techniques. In this context quantum measurement appears not as a postulate, but as physical process. In this thesis I am considering a quantum system, in particular a qubit or a nanomechanical resonator, interacting with a tunnel junction. The effect of coupling a quantum system to a tunnel junction is twofold: The state of the quantum system will be changed and there will be information about the quantum system in the statistics of charge transfer of the tunnel junction. As the first example a quantum measurement process of a qubit is considered. A common description of the system and charge dynamics is found by introducing a new quantity, the charge specific density matrix. By deriving and solving a Markovian master equation for this quantity the measurement process is analyzed. The measurement is shown to be a dynamical process, where correlations between the initial state of the qubit and the number of charges transferred in the tunnel junction arise on a typical timescale, the measurement time. As another example of a quantum system a nanomechanical oscillator is considered. It is found, that the biased tunnel junction, acting as a non-equilibrium environment to the oscillator, increases the temperature of the oscillator from its thermal equilibrium value. The current in the junction is modulated by the interaction with the oscillator, but the influence vanishes for bias voltages smaller than the oscillator frequency. For an asymmetric junction and non-vanishing oscillator momentum a current is shown to flow through the junction even at zero bias. The current noise spectrum induced by the oscillator in the tunnel junction consists of a noise floor and a peaked structure with peaks at zero frequency, the oscillator frequency and double the oscillator frequency. The peak heights are dependent on the coupling strength between oscillator and junction, the occupation number of the oscillator, the bias voltage and the junction temperature. I show how the peak height can be used as a measure of the oscillator temperature, demonstrating that the noise of a tunnel junction can be used for electronic thermometry of a nanomechanical oscillator.

Since performances of experimental and numerical tools have been largely improved, mechanics of materials can explore smaller and smaller scales. Thus, a better comprehension, or even a prediction, of local phenomena associated with macroscopic deformations are hoped. This dissertation focuses on the smallest scale involved in mechanical behavior of materials, i.e. interactions between nuclei due to electrons behavior and especially to valence electrons. The originality of this work is setting up the finite element method as numerical tool to solve this problem. This approach largely used to solve structural mechanics problems provides powerful numerical tools to tackle electronic structures. The Hartree-Fock and post-Hartree-Fock models are employed, and mechanical properties of electronic structures are estimated. These estimates are based on a set of approximations of both model and numerical origins. Error estimates are proposed to analyze the accuracy of the results.

Living organisms are made up of a multitude of individual cells that are surrounded by biomolecules and fluids. It is well known that cells are highly regulated by biochemical signals; however it is now becoming clear that cells are also influenced by the mechanical forces and mechanical properties of the local microenvironment. Extracellular forces causing cellular deformation can originate from many sources, such as fluid shear stresses arising from interstitial or blood flow, mechanical stretching during breathing or compression during muscle contraction. Cells are able to sense variations in the mechanical properties (elasticity) of their microenvironment by actively probing their surroundings by utilizing specialized proteins that are involved in sensing and transmitting mechanical information. The actin cytoskeleton and myosin-II motor proteins form a contractile (actomyosin) network inside the cell that is connected to the extracellular microenvironment through focal adhesion and integrin sites. The transmission of internal actomyosin strain to the microenvironment via focal adhesion sites generates mechanical traction forces. Importantly, cells generate traction forces in response to extracellular forces and also to actively probe the elasticity of the microenvironment. Many studies have demonstrated that extracellular forces can lead to rapid cytoskeletal remodeling, focal adhesion regulation, and intracellular signalling which can alter traction force dynamics. As well, cell migration, proliferation and stem cell fate are regulated by the ability of cells to sense the elasticity of their microenvironment through the generation of traction forces. In vitro studies have largely explored the influence of substrate elasticity and extracellular forces in isolation, however, in vivo cells are exposed to both mechanical cues simultaneously and their combined effect remains largely unexplored. Therefore, a series of experiments were performed in which cells were subjected to controlled extracellular forces as on substrates of increasing elasticity. The cellular response was quantified by measuring the resulting traction force magnitude dynamics. Two cell types were shown to increase their traction forces in response to extracellular forces only on substrates of specific elasticities. Therefore, cellular traction forces are regulated by an ability to sense and integrate at least two pieces of mechanical information - elasticity and deformation. Finally, this ability is shown to be dependent on the microtubule network and regulators of myosin-II activity.

Nanomechanics emerged as chemists and physicists began fabricating nanoscale objects. However, there are some materials that have neither been fabricated nor mechanical investigated at the nanoscale, such as rhodium. Rhodium is used in many applications, especially in coatings and catalysis. To contribute to the understanding the nano-properties of this important material, rhodium was fabricated and mechanically investigated at the nanoscale. The nanopillars approach was employed to study size effects on mechanical properties. Nanopillars with different diameters were fabricated using electroplating followed by uniaxial compression tests. SEM was used as a quality control technique by imaging the pillars before and after compression to assure the absence of buckling, barrelling, or any other problems. Transmission electron microscopy (TEM) and SEM were used as microstructural characterization techniques, and the energy-dispersive X-ray spectroscopy (EDX) was used as the chemical characterization technique. Due to substrate induced effects, only the plastic region of the stress-strain curves were investigated, and it was revealed that rhodium softens with decreased nanopillar diameter. This softening/weakening effect was due to the nanocrystallinity of the fabricated pillars. This effect is consistent with the literature that demonstrates the reversed size effect of nanocrystalline metals, i.e., smaller is weaker. Further studies should focus on eliminating the substrate effect that was due to the adhesion layers between Rh and the silicon substrate being softer than Rh, consequently, causing Rh to sink into the adhesion layer when compressed and thus perturbing the stress-strain curve. Moreover, further investigation of other properties of Rh is required to achieve a comprehensive understanding of Rh at the nanoscale, and to render it suitable for specific, multivariable applications.

This research focuses to develop some new techniques on statistical learning including methodology, computation and application. We also developed statistical quantification in nanomaterials. For a large number of random variables with temporal or spatial structures, we proposed shrink estimates of covariance matrix to account their Markov structures. The proposed method exploits the sparsity in the inverse covariance matrix in a systematic fashion. To deal with high dimensional data, we proposed a robust kernel principal component analysis for dimension reduction, which can extract the nonlinear structure of high dimension data more robustly. To build a prediction model more efficiently, we developed an active learning via sequential design to actively select the data points into the training set. By combining the stochastic approximation and D-optimal designs, the proposed method can build model with minimal time and effort. We also proposed factor logit-models with a large number of categories for classification. We show that the convergence rate of the classifier functions estimated from the proposed factor model does not rely on the number of categories, but only on the number of factors. It therefore can achieve better classification accuracy. For the statistical nano-quantification, a statistical approach is presented to quantify the elastic deformation of nanomaterials. We proposed a new statistical modeling technique, called sequential profile adjustment by regression (SPAR), to account for and eliminate the various experimental errors and artifacts. SPAR can automatically detect and remove the systematic errors and therefore gives more precise estimation of the elastic modulus.