Supramolecular chemistry is an emerging field of chemistry which has attracted much attention in recent years as a result of its broad applicability in many areas. Thus, the design of functional supramolecular systems is strongly in demand in this field. For this purpose, we have developed ratiometric fluorescent chemosensors for ion sensing and mechanically interlocked structures for their application in molecular logic. In the first part, we report a novel dimeric boradiazaindacene dye which can be converted in one step to an efficient resonance energy transfer (RET) dyad. In addition, if this modification is done with appropriate ligands, RET can be coupled to ion sensing. The utility of this approach is demonstrated in a highly selective, emission ratiometric chemosensor for Ag(I). In the second part, boradiazaindacene dyads designed as energy transfer casettes were modified to signal cation concentrations ratiometrically. If the energy transfer efficiency is increased by changing spectral overlap on cation binding, an enhancement of emission signal ratios can be obtained. A larger range of ratios results in highly improved sensitivity to analyte concentrations. We demonstrate this approach in a de novo design of a novel and highly selective ratiometric chemosensor for Hg(II) ions. In the last part, we synthesized a two-station [2]catenane composed of an &amp / #960 / -electron rich bis-1,5-dihydroxynapthalene[38]-crown-10 (1/5DNPC10) ring interlocked with a second macrocycle containing two &amp / #960 / -electron deficient unit, namely, napthodiimide (NpI) and bipyridinium (BIPY)2+ unit using the Cu(I)-catalyzed Huisgen 1,3-cycloaddition reaction. The resulting bistable [2]catenane is isolated as a single co-conformation which is comprised of the 1/5DNP[38]C10 ring around the NpI unit. Thermal activation of the pure NpI-isomer at 70&amp / #730 / C for 60 h leads to the formation of the BIPY2+-isomer by virtue of the circumrotation of the crown-ether ring along the backbone of the other macrocycle over the steric barrier of the tetra-aryl methane units. The energy barrier for the circumrotation is 28.5&plusmn / 0.3 kcal/mol. Electrochemistry of a 1:1 mixture of the two possible isomers shows that the [2]catenane cannot be switched mechanically on account of the large steric barriers presented by the tetra-aryl methane groups on the electron-accepting ring.

Rational design of fluorescent chemosensors is an active area of supramolecular chemistry, photochemistry and photophysics. Ratiometric chemosensors are even more important, as they have an internal system for selfcalibration. In order to develop a new methodology for a ratiometric chemosensor design, we proposed coupling of energy transfer phenomenon to ion sensing. In this study, we targeted energy transfer cassette type chemosensors, where the efficiency of transfer is modulated on the donor side, by metal ion binding which changes the spectral overlap. This work involves the synthesis of a number of EET systems with varying degrees of EET efficiency. The results suggest that this strategy for ratiometric ion sensing is a promising one, enabling a modular approach in chemosensor design.

Theoretical modeling of biological response to radiation describes qualitatively and quantitatively the results of radiobiological effects at the molecular, chromosomal, and cellular level. The repair-misrepair (RMR) model is the radiobiological model chosen for our study. It models deoxyribonucleic acid (DNA) damage formation and lesion repair through linear and quadratic processes. Double strand breaks (DSB) are a critical lesion in DNA. With increasing LET, the number of DSB per track traversing the cell nucleus increases. Using a compound Poisson process (CPP), we describe DNA damage formation. Three models were considered: a simple CPP using constant LET, a CPP using a chord length distribution, and a CPP using specific energy distribution. In the two first cases, and for low LET radiation the initial distribution of DSB was well approximated by a Poisson distribution, while for high LET radiation the initial distribution of DSB deviated slightly from a Poisson distribution. In the last case, DSB distribution was much broader than a pure Poisson distribution. Datasets from the literature for seven human cell lines, exhibiting various sensitivities to radiation were analyzed. We compared stochastic, CPP, and CPP using chord length distribution, with deterministic RMR models. For low LET radiation and at high dose rates the stochastic survival results agree well with the deterministic survival results. Also the stochastic model allows for non-linearity at low doses due to the accumulation of sub-lethal damage. At low dose rates deterministic results overestimate the surviving fraction compared to stochastic results. For high LET radiation stochastic and deterministic survival results agree. Stochastic survival results using specific energy distribution diverged from deterministic results by underestimating the surviving fraction at low and high LET radiation. The dose rate sparing curve, representing surviving fraction at a dose of 10Gy vs. dose rate shows that deterministic survival results are consistent with stochastic survival results, using CPP, or CPP with chord length distribution, for low and high dose rate values. Compared to deterministic aspects of DNA damage formation we concluded that stochastic aspects of DNA damage formation and repair using CPP or CPP with chord length distribution are not as prominent as reported in the earlier studies.

In order to gain insights into the electronic interactions between metallic gold and self-assembled monolayers composed of π-conjugated thiols, a series of thiol-containing molecules based on a stilbene backbone were synthesized and assembled on gold surface. The resulted monolayers were characterized with a variety of surface-sensitive techniques and the electronic properties of the obtained surfaces were studied with the use of ultraviolet photoelectron spectroscopy. Work-function changes and alignment of the molecular energy levels with respect to the Fermi level of the metal were investigated and important insights regarding the electronic properties of the metal / organic interfaces were obtained. Another aspect of interactions between organic dyes and metallic gold was studied in the context of spectroscopic properties of systems incorporating gold nanoparticles with organic fluorophores covalently attached to the nanoparticle surface. Ultrafast dynamics of the excited-state deactivation of the organic fluorophores attached to the surface of gold nanoparticles were studied with the use of a fs transient absorption technique. It was found that the close proximity of a gold nanoparticle had a profound impact on the excited-state lifetime of the studied organic fluorophore. The influence of the structure of the studied systems on the excited-state deactivation dynamics of the organic fluorophores was described.

<p>The aim of this diploma work is to improve selectivity and sensitivity in DNA-chips by utilizing fluorescence resonance energy transfer (FRET) between conjugated polyelectrolytes (CPEs) and fluorophores.</p><p>Leclerc and co-workers have presented successful results from studies of super FRET between fluorophore tagged DNA and a CPE during hybridisation of the double strand. Orwar and co-workers have constructed a DNA-chip using standard photo lithography creating a pattern of the hydrophobic photoresist SU-8 and cholesterol tagged DNA (chol-DNA). This diploma work will combine and modify these two ideas to fabricate a improved DNA-chip.</p><p>Immobilizing of DNA onto surface has been done by using soft lithography. Hydrophobic pattern arises from the poly(dimethylsiloxane) (PDMS) stamp. The hydrophobic pattern will attract chol-DNA that is adsorbed to the chip. Different sets of fluorophores are covalently bound to the DNA and adding CPEs to the complex will make FRET occur between CPE and bound fluorophore.</p><p>We will here show that the specificity in DNA hybridization by using PDMS patterning was high. FRET clearly occurred, especially with the CPEs as donor to the fluorophore Cy5. The intensity of FRET was higher when the fluorophore and the CPE were conjugated to the same DNA strand. The largest difference in FRET intensity between double stranded and single stranded complexes was observed with the CPE tPOMT. Super FRET has been observed but not yet fully proved. The FRET efficiency was lower with the fluorophore Alexa350 as donor compared to the Cy5/CPE complex. Most of the energy transferred from Alexa350 was extinguished by quenching.</p>

Current military-grade rifle body armor technology uses hard ballistic plates positioned on top of flexible materials, such as woven Kevlar® to stop projectiles and absorb the energy of the impact. However, absorbing the impact energy and stopping a rifle projectile comes at a cost to the wearer - mobility. In this thesis, a new concept for personal body armor is proposed - a semi-flexible hybrid body armor. This hybrid armor is comprised of two components that work as a system to effectively balance the flexibility offered by a soft fabric based armor with the protection level of hard plated armor. This work demonstrates techniques used to analyze and design the hybrid armor to be compliant with National Institute of Justice guidelines. In doing so, finite element analysis is used to simulate the effect of a projectile impacting the armor at various locations, angles, and velocities, while design of experiments is used to study the effect of these various impact combinations on the ability of the armor component(s) (including the wearer) to absorb energy. The flexibility and protection offered by the two component armor system is achieved by the use of proven technique and innovative geometry. For the analytical design, the material properties, contact area(s), dwell duration, and energy absorption are all carefully considered. This yields a lightweight but yet effective armor, which is estimated to weigh 36% less than the current military grade hard body armor. Using ANSYS, several simulations were conducted using finite element analysis, including a direct center impact, along with various other impacts to investigate possible weak points in the armor. In doing so, it is determined that only one of these impact locations is indeed a potential weak point. The finite element analysis continues to show that a rifle projectile impacting at an oblique angle reduces the energy transferred to the wearer by about 25% (compared to a direct impact). A design of experiments approach was used to determine the influence of various input parameters, such as projectile impact velocity and impact location. It is shown that the projectile impact velocity contributes 36% to the ability of the wearer to absorb energy, whereas impact velocity contributes only 13% to the energy absorbed by the top armor component. Furthermore, the analysis shows that the impact location is a highly influential factor (with a 69% contribution) in the energy absorption by the top armor component.

Steady state reflectance and emission characteristics of anthracene adsorbed on silica gel and titania-silica mixed oxides have been investigated as a function of sample loading. Titania-silica mixed oxides with 1, 3, 5 and 10 wt. % TiO2 were prepared by two different methods: a dropwise method and a sol-gel route. Ground state diffuse reflectance and fluorescence emission spectra of anthracene adsorbed on titania-silica surfaces show a dependence on titania content. The absorption peaks of anthracene are difficult to resolve at higher titania content due to the increasing red-shift of the titania absorption edge. The absorption edge of titania is shifted to longer wavelengths and the band gap energy decreases with increasing the titania loading. Diffuse reflectance laser flash photolysis at 355 nm produces both the triplet and radical cation of anthracene and gives relevant information regarding the photochemical transients and the kinetics details of the surface photochemical processes. Energy dependence studies confirm the monophotonic nature of the triplet production, whereas the anthracene radical cation is formed by monophoton or multiphoton ionisation in the mixed titania-silica systems. Energy and electron transfer reactions of anthracene co-adsorbed with azulene as electron donor on silica sol-gel and titania-silica mixed oxides prepared by the sol-gel method with different titania content have been studied using the time-resolved diffuse reflectance laser flash photolysis technique. The fluorescence of excited anthracene adsorbed on silica sol-gel is quenched by the addition of azulene, while co-adsorption of azulene on titania-silica mixed oxides resulted in a decrease in the fluorescence intensity of the adsorbed anthracene due to the formation, at the same time, of anthracene radical cation and Ti3+ species on the titania-silica surface. Triplet-triplet energy transfer from the excited anthracene to ground state azulene and electron transfer from azulene to the anthracene radical cation have been investigated using a time-resolved diffuse reflectance laser flash photolysis technique following laser excitation at 355 nm. Bimolecular rate constants for energy and electron transfer between anthracene and azulene have been obtained. Kinetic analysis of the decay of the anthracene triplet state and radical cation show that the kinetic parameters depend on the titania content of the sample and the azulene concentration. This indicates that the rate of energy and electron transfer reactions increases as a function of azulene concentration and decreases with increasing titania content in titania-silica mixed oxides, whereas the observed rate of reaction on silica sol-gel is predominantly governed by the rate of diffusion of azulene. Electron transfer reactions in a ternary system using azulene for hole transfer between 9-anthracenecarboxylic acid radical cation as electron acceptor and perylene as electron donor were also studied in order to demonstrate the mobility of radical cations on the silica sol-gel and titania-silica surfaces. The co-adsorption of azulene as a molecule shuttle with 9-anthracenecarboxylic acid and perylene on both silica sol-gel and titania-silica systems has been shown to enhance the rate of electron transfer in this ternary system. Activation energies for energy and electron transfer on photoinduced bimolecular and termolecular processes on silica sol-gel and titania-silica mixed oxides have been measured. In bimolecular anthracene / azulene systems, at higher azulene loadings, the activation energies and the pre-exponential factors on titania-silica surfaces are the same for both energy and electron transfer and are comparable with the parameters extracted for azulene diffusion on silica Davisil suggesting that azulene diffuses across the silica Davisil and titania-silica mixed oxides surfaces, while at lower azulene loadings, ion-electron recombination dominates and the activation energy extracted is for this process. In a ternary 9-anthracenecarboxylic acid / azulene / perylene system, the activation energy for perylene diffusion is higher than that observed for the anthracene / azulene system, reflecting the lower mobility of the perylene molecule. In this study, a series of titania-silica samples with different loadings of titania (1 10 wt. %) prepared by the sol-gel method and also the pure TiO2 P25 Degussa have been used to study the photocatalytic degradation of 4-chlorophenol in aqueous solution under UV light irradiation. The absorption peak of 4-chlorophenol at 280 nm decreases with increasing titania content and finally disappeared suggesting that titania has a positive influence on the degradation of 4-chlorophenol. The investigated titania-silica mixed oxides prepared by the sol-gel method are less efficient photocatalysts for the degradation of 4-chlorophenol than TiO2 P25.

Mutations in BEST1, the gene encoding for Bestrophin-1 (Best1), cause five, clinically distinct inherited retinopathies: Best vitelliform macular dystrophy (BVMD), adult-onset vitelliform macular dystrophy (AVMD), autosomal recessive bestrophinopathy (ARB), autosomal dominant vitreoretinochoroidopathy (ADVIRC), and retinitis pigmentosa (RP). Little is known regarding how BEST1 mutations cause disease and why mutations cause multiple disease phenotypes. Within the eye, Best1 is a homo-oligomeric, integral membrane protein that is exclusively localized to the basolateral plasma membrane of the retinal pigment epithelium (RPE). Here, it regulates intracellular Ca2+ signaling and putatively mediates anion transport. Since defects in localization and oligomerization are known to underlie other channelopathies, we investigated how mutations causal for BVMD, AVMD, ARB, ADVIRC, and RP impact the localization and oligomerization of Best1. We generated replication-defective adenoviral vectors encoding for WT and 31 mutant forms of Best1 associated with these five diseases and expressed them in confluent, polarized Madin-Darby canine kidney and/or RPE cells. Localization was assessed via immunofluorescence and confocal microscopy. Oligomerization was examined using live-cell fluorescence resonance energy transfer (FRET) as well as reciprocal co-immunoprecipitation experiments. We report that all 31 BVMD, AVMD, ARB, ADVIRC, and RP mutants tested can reciprocally co-immunoprecipitate with and exhibit comparable FRET efficiencies to WT Best1, indicative of unimpaired oligomerization. While all RP and ADVIRC mutants were properly localized to the basolateral plasma membrane, many but not all AVMD, ARB, and BVMD mutants were mislocalized to intracellular compartments. When co-expressed with WT Best1, mislocalized mutants predominantly co-localized with WT Best1 in intracellular compartments. Studies involving four ARB truncation mutants reveal that the first 174 amino acids are sufficient to mediate oligomerization with WT Best1 and that amino acids 472-585 are not necessary for proper trafficking. We conclude that, although mislocalization is a common result of BEST1 mutation, it is not an absolute feature of any individual bestrophinopathy. Moreover, we show that some recessive mutants mislocalize WT Best1 when co-expressed, indicating that mislocalization cannot, on its own, generate a disease phenotype, and that the absence of Best1 at the plasma membrane is well tolerated.

Understanding energy transfer at the molecular scale is both essential for the design of novel molecular level devices and vital for uncovering the fundamental properties of non-equilibrium open quantum systems. In this thesis, we first establish the connection between molecular scale devices -- molecular electronics and phononics -- and open quantum system models. We then develop theoretical tools to study various properties of these models. We extend the standard master equation method to calculate the steady state thermal current and conductance coefficients. We then study the scaling laws of the thermal current with molecular chain size and energy, and apply this tool to investigate the onset of nonlinear thermal current - temperature characteristics, thermal rectification and negative differential conductance. Our master equation technique is valid in the ``on-resonance" regime, referring to the situation in which bath modes in resonance with the subsystem modes are thermally populated. In the opposite ``off-resonance" limit, we develop the Energy Transfer Born-Oppenheimer method to obtain the thermal current scaling without the need to solve for the subsystem dynamics. Finally, we develop a mapping scheme that allows the dynamics of a class of open quantum systems containing coupled subsystems to be treated by considering the separate dynamics in different subsections of the Hilbert space. We combine this mapping scheme with path integral numerical simulations to explore the rich phenomenon of entanglement dynamics within a dissipative two-qubit model. The formalisms developed in this thesis could be applied for the study of energy transfer in different realizations, including molecular electronic junctions, donor-acceptor molecules, artificial solid state qubits and cold-atom lattices.

Fluorescence-based techniques are widely used in bioscience, offering a high sensitivity and versatility. In this work, fluorescence electronic energy migration/ transfer is applied to measure intramolecular distances in two types of systems and under various conditions. The main part of the thesis utilizes the process of donor-acceptor energy transfer to probe distances within the ribosomal protein S16. Proteins are essential to all organisms. Therefore, it is of great interest to study protein structure and function in order to understand and prevent protein malfunction. Moreover, it is also important to try to study the proteins in an environment which resembles its natural habitat. Here two protein homologs were investigated; S16Thermo and S16Meso, isolated from a hyperthemophilic bacterium and a mesophilic bacterium, respectively. It was concluded that the chemically induced unfolded state ensemble of S16Thermo is more compact than the corresponding ensemble of S16Meso. This unfolded state compaction may be one reason for the increased thermal stability of S16Thermo as compared to S16Meso. The unfolded state of S16 was also studied under highly crowded conditions, mimicking the environment found in cells. It appears that a high degree of crowding, induced by 200 mg/mL dextran 20, forces the unfolded state ensemble of S16Thermo to become even more compact. Further, intramolecular distances in the folded state of five S16 mutants were investigated upon increasing amounts of dextran 20. We found that the probed distances in S16Thermo are unaffected by increasing degree of crowding. However, S16Meso shows decreasing intramolecular distances for all three studied variants, up to 100 mg/mL dextran. At higher concentrations, the change in distance becomes anisotropic. This suggests that marginally stable proteins like s16Meso may respond to macromolecular crowding by fine-tuning its structure. More stable proteins like S16Thermo however, show no structural change upon increasing degree of crowding. We also investigated the possibility of local specific interactions between the protein and crowding agent, by means of fluorescence quenching experiments. Upon increasing amounts of a tyrosine labelled dextran, a diverse pattern of fluorescence quantum yield and lifetime suggests that specific, local protein-crowder interactions may occur. In a second studied system, electronic energy migration between two donor-groups, separated by a rigid steroid, was studied by two-photon excitation depolarization experiments. Data were analysed by using recent advances, based on the extended Förster theory, which yield a reasonable value of the distance between the two interacting donor-groups. To the best of our knowledge, this is the first quantitative analysis of energy migration data, obtained from two-photon excited fluorescence.