This work focuses on the emission processes of metal-organic clusters MmMen, (M is the organic molecule and Me the metal atom) ejected from self assembled monolayers (SAMs) of alkanethiols on gold after keV ion bombardment. These aggregates are often observed upon energetic ion bombardment of strongly bound molecules like SAMs. The explanation of this effect remains elusive, especially for large clusters as those observed in our study. The emission of these clusters is investigated using ToF-SIMS under 15 keV Ga+ bombardment. In particular, we have measured the energy distributions (KEDs), which are informative of the physical processes of sputtering. We have probed both the influence of the intermolecular forces and the adsorbate-metal bonding on the cluster ion emission. Importantly, our KEDs revealed that a significant fraction of MmMen clusters is formed via the metastable decay of larger aggregates in the acceleration section of the spectrometer. This is the experimental evidence that another cluster formation channel has to be considered in addition to the recombination mechanisms proposed by other groups. In parallel to these experiments, we have used classical molecular dynamics (MD) simulations to model an overlayer of octanethiols on gold. A realistic potential has been used including long-range forces between the hydrocarbon chains of the alkanethiols. Our key finding concerns the emission of large clusters which were not observed under sub-keV projectile impact. Statistically, they are predominantly formed in high yield events, where many fragments and (supra)molecular species are ejected. From the microscopic viewpoint, these events mostly stem from the confinement of the projectile and recoil atom energies in a finite nanovolume of the surface. As a result of the high local energy density, molecular aggregates desorb from an overheated liquid-like region surrounding the impact point. In summary, from a combined experimental and computational study we have shown that analytical models involving linear collision cascades and recombination processes are insufficient to describe metal-thiolate cluster emission from SAMs under keV ion bombardment. The detailed MD investigation have allowed us to obtain a general picture of the emission of these aggregates in which the mechanisms at play are reminiscent of those high yields events (megaevents) with non linear effects used usually to account for large (bio)molecule desorption.

I denna avhandling beskrivs tillverkning, karaktärisering och tillämpning av ett antal biomimetiska ytor. Biomimetik är att härma naturen och grundtanken är att titta på hur naturen löst liknande problemställningar. Två olika typer av modellsystem med inspiration från naturen har tagits fram för framtida tillämpningar inom bioanalys, biosensorer samt antifrysmaterial. Det ena typen av modellsystem innefattar fosforylerade ytor och det andra består av ytor som härmar antifrys(glyko)proteiner. Ytorna tillverkades av monolager av självorganiserande svavelorganiska molekyler och karaktäriserades före tillämpning med hjälp av ellipsometri, IR-spektroskopi, kontaktvinkelmätning och röntgenfotoelektronspektroskopi. Modellsystemen för att studera vattenfrysning på ytor inspirerades av antifrys(glyko)proteiner som bl.a. kan hittas i polarfiskar. Två modellsystem utvecklades och studerades med avseende på frysning av kondenserat vatten. Det ena designades att härma den aktiva domänen hos ett antifrysglykoproteiner (AFGP) och det andra härmade typ I antifrysproteiner (AFP I). Frysstudierna visade på signifi-kanta skillnader för AFGP-modellen jämfört med ett (OH/CH3) referenssystem med jämförbar vätbarhet, men inte för AFP Imodellen. Vattnet frös vid högre temperatur för AFGPmodellen. Modellsystemen med fosforylerade ytor inspirerades av fosforylering och biomineralisering. Två system utvecklades, ett med långa och ett med korta alkylkedjor på aminosyraanalogerna, både med och utan fosfatgrupp. En ny metod användes med skyddsgrupper på fosfaterna hos de långa analogerna innan bildandet av monolager. Skyddsgrupperna togs bort efter bildandet av monolager. Dessa monolager undersöktes också med elektrokemiska metoder och signifikant högre kapacitans observerades för de fosforylerade monolageren jämfört med de icke fosforylerade. / This thesis describes the preparation, characterization and application of a few biomimetic surfaces. Biomimetics is a modern development of the ancient Greek concept of mimesis, i.e. man-made imitation of nature. The emphasis has been on the preparation and characterization of two types of model systems with properties inspired by nature with future applications in bioanalysis, biosensors and antifreeze materials. One type of model system involves phosphorylated surfaces; the other consists of surfaces mimicking antifreeze (glyco)proteins. The surfaces were made by chemisorbing organosulfur substances to a gold surface into monomolecular layers, so called self-assembled monolayers (SAMs). The physicochemical properties of the SAMs were thoroughly characterized with null ellipsometry, contact angle goniometry, x-ray photoelectron spectroscopy and infrared spectroscopy prior to application. The work on antifreeze surfaces was inspired by the structural properties of antifreeze (glyco)proteins, which can be found in polar fish. Two model systems were developed and studied with respect to ice nucleation of condensed water layers. One was designed to mimic the active domain of antifreeze glycoproteins (AFGP) and the other mimicked type I antifreeze proteins (AFP I). Subsequent ice nucleation studies showed a significant difference between the AFGP model and a (OH/CH3) reference system displaying identical wetting properties, whereas the AFP I model was indistinguishable from the reference system. The model systems with phosphorylated surfaces were inspired from phosphorylations and biomineralization. Two systems were developed, short- and long-chained amino acid analogues, with and without a phosphate group. A novel approach with protected groups before attachment to gold were developed for the long-chained analogues. The protective groups could be removed successfully after assembly. The long-chained SAMs were evaluated with electrochemical methods and significantly higher capacitance values were observed for the phosphorylated SAMs compared to the non-phosphorylated.

Immobilization of different bio- and organic molecules on solid supports is fundamental within many areas of science. Sometimes, it is desirable to obtain a directed orientation of the molecule in the immobilized state. In this thesis, the copper (I) catalyzed Huisgen 1,3-dipolar cycloaddition, referred to as a “click chemistry” reaction, was explored as a means to perform directed immobilization of small molecule ligands on gold surfaces. The aim was to synthesize alkyne- and azide-terminated alkanethiols that would form well-organized self assembled monolayers (SAMs) on gold from the commercially available substances orthoethylene glycol and bromo alkanoic acid. N-(23-azido-3,6,9,12,15,18,21-heptaoxatricosyl)-n-mercaptododekanamide/hexadecaneamide (n = 12, 16) were successfully synthesized and allowed to form SAMs of different compositions to study how the differences in density of the functional groups on the surface would influence the structure of the monolayer and the click chemistry reaction. The surfaces were characterized by different optical methods: ellipsometry, contact angle goniometry and infrared reflection-absorption spectroscopy (IRAS). The click reaction was found to proceed at very high yields on all investigated surfaces. Finally, the biomolecular interaction between a ligand immobilized by click chemistry on the gold surfaces and a model protein (bovine carbonic anhydrase) was demonstrated by surface plasmon resonance using a Biacore system.

Cell adhesion is the first step of cell response to materials and the extracellular matrix (ECM), and is essential to all cell behaviours such as cell proliferation, differentiation, migration and apoptosis for anchor-dependent cells. Therefore, studies of cell attachment have important implications to control and study cell behaviours. During many developed techniques for cell attachment, the manipulation of surface chemistry is a very important method to control initial cell attachment. To control cell adhesion on a two-dimensional surface is a simple model to study cell behaviours, and is a fundamental topic for cell biology, tissue engineering, and the development of biosensors. From the engineering point of view, the preparation of a material with controllable surface chemistry can help studies of cell behaviours and help scientists understand how surface features and chemistry influence cell behaviours. During the fabrication, the challenge is to create a surface with heterogeneous surface properties in the micro scale and subsequently to guide cell initial adhesion. In order to control cell adhesion in a spatial and temporal manner, a photochemical method to control surface chemistry was employed to control the surface property for cell adhesion in this project. Two photocleavable derivatives of the nitrobenzyl group were tried on two types of surfaces: a model self-assembled monolayer (SAM) with alkanethiol-gold surface and biodegradable chitosan. Reactive functional groups on two different surfaces can be inactivated by covalent binding with these photocleavable molecules, and light can be further introduced into the system as a stimulus to recover their reactivity. By simply applying a photomask with diffe

We have investigated the conductance, g, of 1,4-butanedithiol linked Au nanoparticle films as a function of temperature, T, bias potential, V, and applied magnetic field, B. An interesting temperature dependence is observed for non-metallic films with thicknesses just below a critical film thickness: g ~ exp [-(T_0/T)^(1/2)] for 20 K < T < 300 K. We show that this temperature dependence is incompatible with an Efros-Shklovskii "variable range hopping" model, since "hopping distances" are too large to be consistent with tunneling processes, and tend to scale with size of super-clusters of molecularly-linked nanoparticles. We propose a "quasilocalized hopping" model based on competition between single-electron charging of super-clusters and electron backscattering within super-clusters to explain the observed temperature dependence. Various electron scattering time scales are extracted from magnetoconductance data using a modified "weak localization" model. Elastic scattering time scales are comparable to those required for an electron to traverse a nanoparticle, while inelastic and spin-orbit scattering time scales are consistent with those found in studies of conventionally-prepared granular Au films. At interfaces between metallic 1,4-butanedithiol-linked Au nanoparticle films and conventional superconductors, we find that g consistently exhibits peaks, as well as oscillations, that depend simultaneously on both V and B. Such peaks and correlated conductance oscillations are predicted by an enhanced Andreev reflection process due to disorder-driven elastic scattering and electron-hole interference in the nanoparticle film. While oscillations have been predicted by a so-called "reflectionless tunneling" model, they have not been observed at other normal-superconductor interfaces. We speculate that oscillations are observable in this system due to synthetically controlled uniformity of elastic scattering length (i.e., nanoparticle diameter) and a reduced number of current-carrying pathways, especially near the interface. Contrary to predictions of existing "reflectionless tunneling" models, we find that the periods of oscillation in B decrease as T increases. This suggests that the area of interfering pathways increases with T. We propose that this increasing area can be attributed to magnetic field penetration into the superconductor. Conductance data agrees remarkably well with known temperature dependence of penetration depth predicted by BCS theory. Our study shows that this additional region of flux must be considered in experimental and theoretical studies of "reflectionless tunneling", and underscores the utility of molecularly-linked nano\-particle films as a platform for studying charge transport.

We have investigated the conductance, g, of 1,4-butanedithiol linked Au nanoparticle films as a function of temperature, T, bias potential, V, and applied magnetic field, B. An interesting temperature dependence is observed for non-metallic films with thicknesses just below a critical film thickness: g ~ exp [-(T_0/T)^(1/2)] for 20 K < T < 300 K. We show that this temperature dependence is incompatible with an Efros-Shklovskii "variable range hopping" model, since "hopping distances" are too large to be consistent with tunneling processes, and tend to scale with size of super-clusters of molecularly-linked nanoparticles. We propose a "quasilocalized hopping" model based on competition between single-electron charging of super-clusters and electron backscattering within super-clusters to explain the observed temperature dependence. Various electron scattering time scales are extracted from magnetoconductance data using a modified "weak localization" model. Elastic scattering time scales are comparable to those required for an electron to traverse a nanoparticle, while inelastic and spin-orbit scattering time scales are consistent with those found in studies of conventionally-prepared granular Au films. At interfaces between metallic 1,4-butanedithiol-linked Au nanoparticle films and conventional superconductors, we find that g consistently exhibits peaks, as well as oscillations, that depend simultaneously on both V and B. Such peaks and correlated conductance oscillations are predicted by an enhanced Andreev reflection process due to disorder-driven elastic scattering and electron-hole interference in the nanoparticle film. While oscillations have been predicted by a so-called "reflectionless tunneling" model, they have not been observed at other normal-superconductor interfaces. We speculate that oscillations are observable in this system due to synthetically controlled uniformity of elastic scattering length (i.e., nanoparticle diameter) and a reduced number of current-carrying pathways, especially near the interface. Contrary to predictions of existing "reflectionless tunneling" models, we find that the periods of oscillation in B decrease as T increases. This suggests that the area of interfering pathways increases with T. We propose that this increasing area can be attributed to magnetic field penetration into the superconductor. Conductance data agrees remarkably well with known temperature dependence of penetration depth predicted by BCS theory. Our study shows that this additional region of flux must be considered in experimental and theoretical studies of "reflectionless tunneling", and underscores the utility of molecularly-linked nano\-particle films as a platform for studying charge transport.

A materials synthesis technique was recently developed to generate polymer/nanoparticles composite microcapsules in which synthetic polyamines such as polyallylamine and/or polylysine were crosslinked with multivalent anions to form polymer-salt aggregates, that then served as templates for deposition of nanoparticles (NPs) of various compositions to form micron-sized hollow spheres or "nanoparticle-assembled capsules" (NACs). This electrostatically-driven "polymer-salt aggregate" or "PSA" assembly route is attractive for encapsulation and scale-up because encapsulation and materials formation occur in water, at mild pH values, and at room temperature. NACs can potentially find wide-ranging applications in pharmaceutical, food, and consumer products. It is of crucial importance to address the physical property aspects of NACs in view of their use and applicability. While most applications may require that NACs not disassemble or deform under shear stress, some may require triggered release under specific conditions to release the encapsulated material (e.g., enzymes or drugs). Comparatively, little has been done to assess the physical properties of NACs. The behavior of NACs under varying p1-1 and ionic strength conditions were determined. The capsules were found to be structural intact in the pH range of 4-9 at an ionic strength of 10 mM. The pH range in which they were intact narrowed with increasing ionic strength; the capsules fragmented into smaller pieces at 500 mM. The NACs could be made stable at ionic strengths as high as 1M by the addition of multivalent anions to the suspending fluid. The structurally intact NACs were found to vary in compressive strength from 1 atm to > ∼25 atm, via osmotic pressure studies. The benign assembly conditions of NACs allowed for encapsulation studies of various molecules such as fluorescein, Gd[DOTP] 5- (MRI contrast agent), doxorubicin (an anticancer drug), and uracil (pharmaceutical drug with anticancer properties). X-ray irradiation was studied as a potential external trigger for cargo release. A thorough experimental analysis on diffusive release of a dye molecule (fluorescein) from NACs was carried out. Manipulation of the PSA assembly process was carried out in several studies to explore the generality of the synthesis method. Positively-charged aluminosilicate NPs were studied in place of negatively-charged silica NPs. Surprisingly, these led to solid microspheres instead of hollow microspheres. Following the diffusion-deposition model for microsphere formation, it is seems that the NPs, with positively charged alumina patches on top of a negatively charged silica surface, can fully penetrate into the polymer-salt aggregate to form the solid microspheres. The viscoelastic nature of polymer-salt aggregates was exploited to produce non-sphere-shaped NACs through the use of a high-shear flow instrument (Reynolds number of ∼21,000). A mathematical model was developed to understand the formation of elongated NACs, which indicated the shear and elongational stresses within the boundary layer zones along the flow channel walls were responsible for the observed formation of rod-like microparticles.

Plasmonic nanoparticles and their assembly have the potential to serve as a platform in practical applications such as photonics, sensing, and nano-medicine. To use plasmonic nanoparticles in these applications, it is important to understand their optical properties and find methods to control their optical response. Using polarization-sensitive dark-field spectroscopy to study self-assembled nanoparticle rings on substrates with different permittivities I show that the interaction between collective plasmon resonances and the substrate can control the spatial scattering image. Using liquid crystals as an active medium that can be controlled with an external electric field I show that the Fano resonance of an asymmetric plasmonic assembly can be actively controlled utilizing the polarization change of scattered light passing through the liquid crystal device. Furthermore, utilizing the strong electromagnetic field enhancement of coupled plasmonic “nanospikes” on the surface of gold nanoshells with a silica core, I show the use of single spiky nanoshells as surface-enhanced Raman spectroscopy substrates. Individual spiky nanoshells give surprisingly reproducible surface-enhanced Raman spectroscopy intensities with a low standard deviation compared to clusters of nanoparticles. In summary, the work presented here provides understanding of the plasmonic response for assembled nanoparticles on different substrates, illustrated a new method to actively control the optical response of plasmonic nanoparticles, and characterizes spiky nanoshells as surface-enhanced Raman scattering platform.

Utilizing self-assembled monolayer nanotechnology, micro-electro-mechanical systems (MEMS) and IC technologies, a novel flexural plate-wave (FPW) biosensor is developed in this dissertation for detecting the immunoglobulin-E (IgE) concentration of human serum. The acoustic waves of the proposed FPW devices are launched by the 25-pair inter-digital transducer (IDT) input electrodes and propagated through the 4.82 £gm-thick Si/SiO2/Si3N4/Cr/Au/ZnO floating thin-plate. Since the thickness of such floating thin-plate is much smaller than the designed wavelength of FPW device (80 £gm), most of the propagating wave energy will not be dissipated into outside of thin-plate and the mass sensitivity is very high. To further reduce the insertion loss of the proposed FPW devices, two 3 £gm-thick Al reflection grating electrodes (RGE) are designed beside the input and output IDTs. To implement a FPW-based IgE biosensor, a Cr/Au electrode layer has to be deposited on the backside of the floating thin-plate to serve as a substrate for further coating the cystamine SAM/glutaraldehyde/IgE antibody layers. Once the IgE antigens of human serum are bound to the IgE antibody layer, the small change in the mass of floating thin-plate will result in a shift of center frequency of the testing FPW-based biosensor. Compared to the reference FPW biosensors, the shift of center frequency generated by the testing FPW biosensor under different IgE antigen concentration can be detected by commercial network analyzer or the frequency-shift readout system developed by our collaboration laboratory (VLSI Design Lab. of NSYSU). Compared to commercial enzyme linked immunosorbent assay (ELISA) analyzer (sample volume >25 £gl/well, testing time >60 min, dimension>40 cm ¡Ñ30 cm¡Ñ10 cm), the implemented FPW-based IgE biosensor presents a smaller sample volume (<5 £gl), faster response (<10 min) and smaller size (<9 mm¡Ñ6 mm¡Ñ0.5 mm). In addition, a very low insertion loss (-9.2 dB), a very high mass sensitivity (-6.08¡Ñ109 cm2 g-1) and a very high sensing linearity (99.46 %) of the proposed IgE biosensor can be demonstrated at 6.6 MHz center frequency. This study successfully developed a novel FPW-based allergy biosensor by MEMS technology, which has great potential to be further applied into point-of-care testing (POCT) microsystem.

In this study we use AFM-based nanolithography technique to produce nanofeatures of the single strand DNA and LNA probe molecules which are prepared via thiolated nucleic acid self-assembled monolayers (SAMs) on gold substrates. The goal is to observe the topographic changes of the DNA film structures resulting from the formation of rigid double strand DNA when the target and probe DNAs bind together. The so-called hybridization depends strongly on the probe density on the substrate surface. To find the proper probe density for hybridization, we vary the concentration of the probe DNA and search for the optimal conditions for measuring the height changes of the nanofeatures. We also monitor the topographic changes of the DNA nanofeatures in the different target DNA concentrations as a function of time, and the binding isotherms are fitted with the Langmuir adsorption model to derive the equilibrium dissociation constant and maximum hybridization efficiency. In addition, we extend the nanoscale hybridization reaction detection to mismatched DNA:DNA and LNA:DNA hybridization, and observe that topographic change of mismatched hybridization is inconspicuous and rapidly reach equilibrium. The results reveal the apparent difference between the perfect match and mismatch conditions, and validate that this approach can be applied to differentiate the situations for both perfect match and mismatch cases, demonstrating its potentials in the gene chip technology.