Seventeen Cree anti-diabetic herbal medicines and eight Traditional Chinese Medicines have been examined for their potential to cause interactions with drugs, which is considered as a major reason for adverse drug effects. Specifically, the effect of these natural health products was examined on major Phase I drug metabolism enzymes including cytochrome P450, human carboxylesterase-1 and flavin-containing monooxygenases. Several of these natural health products have the potential to cause adverse drug effect through the inhibition of major drug metabolism enzymes. The results indicated that 7 Cree medicines plant extracts inhibited CYP3A4 activity, and 3 of them have been proven to cause potent mechanism-based inactivation of CYP3A4. Seven of eight Traditional Chinese Medicines have been identified as strong CYP3A4 inhibitors; the ethanol extract of Goji has identified as a potent inhibitor for CYP2C9 and 2C19. Goji juice showed universal inhibitory effects on most of the tested enzymes except flavin-containing monooxygenases 3.

Seventeen Cree anti-diabetic herbal medicines and eight Traditional Chinese Medicines have been examined for their potential to cause interactions with drugs, which is considered as a major reason for adverse drug effects. Specifically, the effect of these natural health products was examined on major Phase I drug metabolism enzymes including cytochrome P450, human carboxylesterase-1 and flavin-containing monooxygenases. Several of these natural health products have the potential to cause adverse drug effect through the inhibition of major drug metabolism enzymes. The results indicated that 7 Cree medicines plant extracts inhibited CYP3A4 activity, and 3 of them have been proven to cause potent mechanism-based inactivation of CYP3A4. Seven of eight Traditional Chinese Medicines have been identified as strong CYP3A4 inhibitors; the ethanol extract of Goji has identified as a potent inhibitor for CYP2C9 and 2C19. Goji juice showed universal inhibitory effects on most of the tested enzymes except flavin-containing monooxygenases 3.

The work presented in this thesis was aimed to investigate the structure-function relationship of several photosynthetic Light-Harvesting Complexes (LHCs) including Chlorophyll Protein 29 (CP29) and Light-Harvesting Complex II (LHCII) of green plants, and Fenna-Matthews-Olson (FMO) complex of green sulfur bacterium Chlorobium tepidum. Based on the exciton calculations, a model was proposed to the electronic excited states (EES) of both CP29 and LHCII complexes by incorporating a considerable part of the current information offered by structure determination, mutagenesis analysis and spectroscopy in the modeling. The essential parameters for characterizing the excited states, Qy dipole orientations and site energies were assigned by suggesting a model that can explain both the key features of the linear (polarized) absorption spectra and the time scales of the energy transfer processes in CP29 and LHCII. The idea of offering structural information through setting connection between the spectroscopy and the spectral simulations were supported by the presented results on CP29 and LHCII. New spectroscopic measurements (absorption, linear dichroism (LD) and circular dichroism), carried out at 4 K on the FMO complex were presented, and also the LD spectrum was corrected for the degree of orientation of the sample, in order to provide comparison of not only the shape but also the size of the simulated and experimental spectra. The EES structure of the FMO complex was studied by simulating the measured optical spectra with more realistic model than the previously applied models. Simulations have been carried out with a computer program based on exciton model, which includes inhomogeneous, homogeneous and lifetime broadenings explicitly.

Seventeen Cree anti-diabetic herbal medicines and eight Traditional Chinese Medicines have been examined for their potential to cause interactions with drugs, which is considered as a major reason for adverse drug effects. Specifically, the effect of these natural health products was examined on major Phase I drug metabolism enzymes including cytochrome P450, human carboxylesterase-1 and flavin-containing monooxygenases. Several of these natural health products have the potential to cause adverse drug effect through the inhibition of major drug metabolism enzymes. The results indicated that 7 Cree medicines plant extracts inhibited CYP3A4 activity, and 3 of them have been proven to cause potent mechanism-based inactivation of CYP3A4. Seven of eight Traditional Chinese Medicines have been identified as strong CYP3A4 inhibitors; the ethanol extract of Goji has identified as a potent inhibitor for CYP2C9 and 2C19. Goji juice showed universal inhibitory effects on most of the tested enzymes except flavin-containing monooxygenases 3.

Photosynthesis involves the absorption of photons by light-harvesting pigments and the subsequent transfer of excitation from the absorption centre to the reaction centre. This highly efficient phenomenon of excitation transfer has traditionally been explained by the Forster mechanism of incoherent hopping of excitation from one chromophore to another. Recently 2D electronic spectroscopic evidences were gathered by Fleming and coworkers on the photosynthetic Fenna-Matthews-Olson (FMO) complex in green sulfur bacteria [1]. Subsequent simulation studies by the same group [2] led to the proposition of a quantum-mechanical, coherent, wave-like transfer of excitation among the chromophores. However, Fleming's conclusions regarding retention of coherence appeared surprising because, the complex would interact with the numerous degrees of freedom of the protein scaffold surrounding it, leading to decoherence, which is expected to be rapid. Thus, we were interested in proposing an analytical treatment to rationalize the excitation transfer. Traditional approaches employed for studying excitation energy transfer involve the master equation techniques where the system-bath coupling is perturbative and is truncated after a few orders. It is important to note that the system-bath coupling causes both decoherence and population relaxation. Such a perturbative approximation is difficult to justify for the photosystem, as the system-bath coupling and the interchromophoric electronic coupling have comparable values. Also, these treatments are largely numerical studies and demand involved calculations. Thus, exact calculations for such a system (7-level) are very difficult. Consequently, we were interested in developing an analytical approach where the coupling is treated as non-perturbative. We devised a novel analytical treatment which employs a unitary transformation analogous to the one used for the theory of nonadiabatic effects in chemical reactions [3]. Our treatment rests on an adiabatic basis which are eigenstates calculated at each nuclear position (i.e. at each configuration of the bath) bearing a parametric dependence in Qi, where Qi denotes the shift of the exciton at site `i' due to the environment. The treatment is justified because in the case of coherent transfer, the excitation would travel mostly amongst the adiabatic states and the effects of non-adiabaticity are small. We observed that the system-bath coupling, after the unitary transformation, could be decoupled at the lowest order into two parts: a) an adiabatic contribution, which accounts solely for decoherence (this is evaluated almost exactly in our approach) and b) a non-adiabatic contribution which accounts for population relaxation from one adiabatic state to another (treated by a Markovian master equation). When we applied our technique to the FMO complex, our prediction for population evolution at the chromophores showed excellent correspondence with those obtained by Nalbach and coworkers using path-integral calculations [4], which are exact. These were calculations where the environment was modelled using a Drude spectral density. Our method allowed the calculations to be readily performed for different temperatures as well. It should be specifically emphasized that, unlike the involved and cumbersome path-integral calculations by Nalbach and coworkers [4] or the hierarchical equation calculations by Ishizaki et al. [2], our method is simple, easy to apply and computationally expedient. Further it became evident that the ultra-efficiency of energy transfer in photosynthetic complexes is not completely captured by coherence alone but is the result of an interplay of coherence and the dissipative influence of the environment (also known as ENAQT or Environment Assisted Quantum Transport [5]). An added advantage of our analytical treatment was the flexibility it offered. Thus, we could use our formalism to perform expedient analyses on the behavior of the system under various conditions. For example, we may wish to evaluate the consequences of introducing correlations among the bath degrees of freedom on the efficiency of transfer to the reaction centre. To this end, we applied our formalism by introducing correlations among the bath degrees of freedom and then by introducing anticorrelations among the bath degrees of freedom. The conclusions were interesting, for they suggested that the efficiency of transfer to the reaction centre was enhanced by the presence of anti-correlations, when compared with an uncorrelated bath. Uncorrelated baths, in turn, had a higher efficiency of energy transfer than correlated baths [6]. Thus, the population evolution is fastest for the anti-correlated bath, followed by the uncorrelated bath and is slowest for the correlated bath. Similar conclusions have been reached at by Tiwari et al. [7]. We could also extend the formalism for studying the system under different spectral densities for the environment, apart from just the Drude spectral density which is popularly used in literature associated with FMO calculations. For instance, the FMO system could be analyzed for the Adolphs-Renger spectral density [3, 8]. Once again our results showed excellent agreement with those reported by Nalbach. We also analyzed the FMO system under the spectral density proposed by Kleinekathofer and coworkers [9]. It was found that these latter spectral densities had more profound participation from the environment, therefore coherences were destroyed more effectively and population relaxation was faster. The excitation transfer to the final site (site closest to the reaction centre in the FMO complex) was found to be faster for the Adolphs and Renger spectral density and the spectral density proposed by Kleinekathofer and coworkers, when compared to the Drude spectral density. Also, the excitation transfer was fastest when we modelled the environment using the Kleinekathofer spectral density. This reinforced the previous conclusions that the dissipative effects of the environment promote a faster energy transport. Being an almost analytical approach, our technique could be applied to systems with larger number of levels as well. A good example of such a case is the MEH-PPV polymer. 2D electronic-spectroscopic experiments performed on this polymer in solution speculate that the excitation energy transfer might be coherent even at physiological temperatures [10]. A prototype for studying this system might be a conjugated polymer with around 80-100 chromophores. Linewidths and Lineshapes in the vicinity of Graphene It has been reported that a vibrating dipole may de-excite by transferring energy non-radiatively to a neighboring metal surface [11]. It is also understood that due to its delocalized pi-cloud, graphene has a continuum of energy states and can behave like a metal sheet and accept energies. Thus, we proposed that if a vibrationally excited dipole de-excites in the vicinity of a graphene sheet, graphene may get electronically excited and thus serve as an effective quencher for such vibrational excitations. Depending on the distance of the dipole from the graphene sheet, the transfer might be intense enough to be spectroscopically probed. We have investigated the rate of such an energy transfer. We use the Dirac cone approximation for graphene, as this enables us to obtain analyt-ical results. The Fermi Golden rule was used to evaluate the rate of energy transfer from the excited dipole to the graphene sheet [12]. The calculations were performed for both the instances: a) energy transfer from a dipole to undoped graphene and, b) energy trans-fer from a dipole to doped graphene. For undoped graphene, the carrier (electron) charge density in the conduction band is zero and we would only have transitions from the valence band to the conduction band. As a consequence of absence of carrier charge density in CB (conduction band), the screening of Coulombic interactions in the graphene plane is ineffective. Thus, one could use the non-interacting polarizability for undoped graphene in the rate expression [13]. However, when we consider the case of doped graphene where EF is shifted upwards into CB, the conduction band electrons will contribute to screening. In this case, we have two sets of transitions: a) from ki in VB (valence band) to kf in CB and b) ki in CB to kf in CB, where ki and kf are the wavevectors which correspond to the initial and final electronic states in graphene. So we have used the polarizability propagator in the random phase approximation [14] to calculate the rate following the approach of [13]. It is also known that the imaginary part of the frequency domain dipole-dipole corre-lation function is a measure of the lineshape [15]. We were, thus, interested in evaluating the lineshape for these transitions. For evaluating the correlation function, we used the partitioning technique developed by L•owdin [16] and subsequently extracted the lineshape from its imaginary part. Using this method, we calculated lineshape for the vibrational excitation of CO molecule in the vicinity of an undoped graphene lattice. The linewidth for this system also was obtained. It could be seen that the vibrational linewidth for 1 CO in the vicinity (5 A) of undoped graphene (EF = 0:00eV ) is small (0:012 cm ) but could be observed experimentally. The lineshape calculations were also extended to cases where it is possible to have atomic transitions by placing an electronically excited atom in the vicinity of the graphene sheet. We considered the following two cases: a) 3p ! 2s transition in hydrogen atom, at a distance of 12 A from the graphene sheet and, b) 4p ! 3s transition in hydrogen atom, at a distance of 20 A from the graphene sheet. The linewidths for atomic transitions could be easily probed in these cases ( 55 cm 1 for 3p ! 2s and 56 cm 1 for 4p ! 3s). In the preceding calculations, the transi-tion dipoles were considered perpendicular to the graphene surface. It is worthwhile to note that if the transition dipoles are considered parallel to the graphene surface, the respective linewidths would be half of those obtained for the case where the transition dipoles are perpendicular. Another interesting possibility would be to consider a lanthanide metal complex placed within a few nanometers from graphene. Lanthanides are known to have sharp f-f transitions [17] and consequently, one could easily observe the effects of broadening due to energy transfer to the electronic system of graphene. Energy Eigenmodes for arrays of Metal Nanoparticles In the final part of the thesis we consider organized assemblies of metal nanoparti-cles, specifically helical and cylindrical assemblies and investigate the plasmonic excitation transfer across these assemblies. These were motivated by recent studies which reported growth of chiral asymmetric assemblies of nanoparticles on D and L- isomers of dipheny-lalanine peptide nanotubes [18]. The plasmons in the helical/cylindrical assemblies are expected to couple with each other via electromagnetic interactions. We construct the Hamiltonian for such systems and evaluate the eigenmodes and energies pertaining to these modes in the wave vector space. We also perform calculations for the group velocity for each eigenmode as this gives us an idea of which eigenmode transports excitation the fastest.

Organic solar cells (OSCs) based on non-fullerene acceptors (NFAs) have attracted a great deal of attention in recent years due to their rapidly increasing efficiency and enormous potential. In this work, the optical and electronic properties of systems containing the very promising non-fullerene acceptor PYT have been thoroughly studied with the use of the density functional theory (DFT) and the time-dependent density functional theory (TDDFT). By changing the electron linker from thiophene to furan and selenophene, respectively, the PYT was divided into three variants, each of which was studied independently. In addition, these three systems were combined with the donor PBDB-T to generate two distinct interface conformations. The properties studied in this work include the optimized geometries, HOMO-LUMO levels, UV-Vis spectra, frontier molecular orbitals (FMOs), natural transition orbitals (NTOs), density of states (DOS), dipole moments, open-circuit voltages, exciton binding energies, and local exciton (LE) and charge transfer (CT) energies. The calculations were performed in chlorobenzene solution utilizing the polarizable continuum model (PCM). It was discovered that PBDB-T/PY-Se exhibited remarkable flatness employing the π-π stacking conformation which corresponds well with the excellent D/A compatibility observed experimentally. All interfaces displayed appropriate positioning of the HOMO-LUMO levels, with the acceptor dominating the LUMO and the donor dominating the HOMO, with HOMO-LUMO gaps ranging between 1.34 and 1.38 eV. The differences in the interchanging of the electron linker were not that significant, and neither was the change in interface conformation in terms of the HOMO-LUMO levels. This may indicate that the system can be effective even without the presence of a π-π stacking conformation. The first excited states for all interface systems were shown to be pure CT transitions, and on average, 80% of the states exhibit CT character. The remaining contributions consisted of transitions within the pure materials, with a larger contribution within the acceptor. The theoretical results of this study indicate that systems containing the novel polymer acceptor PYT and its variants PY-O and PY-Se exhibit very intriguing properties, and further development of OSCs containing these polymers might further aid in the development of high-performance OSCs. / Organiska solceller (OSC) baserade på icke-fullerenacceptorer (NFA) har väckt stor uppmärksamhet de senaste åren på grund av dess snabbt ökande effektivitet och enorma potential. I detta arbete har de optiska och elektroniska egenskaperna hos system innehållande den mycket lovande icke-fullerenacceptorn PYT studerats grundligt med användning av täthetsfunktionalteorin (DFT) och den tidsberoende täthetsfunktionalteorin (TDDFT). Genom att ändra elektronförbindelsen från tiofen till furan respektive selenofen så delades PYT upp i tre varianter som var och en studerades oberoende av varandra. Dessutom kombinerades dessa tre system med donatorn PBDB-T för att generera två distinkta gränssnittskonformationer. Egenskaperna som studeras i detta arbete inkluderar optimerade geometrier, HOMO-LUMO-nivåer, UV-vis spektra, gränsmolekylära orbitaler (FMO), naturliga övergångsorbitaler (NTO), tillståndstäthet (DOS), dipolmoment, tomgångsspänning, excitonbindningsenergi samt lokal exciton (LE) och laddningsöverförings (CT) energier. Beräkningarna utfördes i klorbensenlösning med användning av den polariserbara kontinuummodellen (PCM). I resultatet uppvisade PBDB-T/PY-Se en anmärkningsvärd planhet med användning av π-π staplingskonformationen som överensstämmer väl med den utmärkta D/A-kompatibiliteten som observerats experimentellt. Alla gränssnitt visade lämplig positionering av HOMO-LUMO-nivåerna, med acceptorn som dominerade LUMO och donatorn som dominerade HOMO, med HOMO-LUMO-gap mellan 1.34 och 1.38 eV. Skillnaderna i utbytet av elektronförbindelsen visade sig inte vara signifikanta och inte heller skillnaden i gränssnittskonformation när det gäller HOMO-LUMO-nivåerna. Detta kan indikera att systemet kan vara effektivt även utan förekomst av π-π staplingskonformation. De första exciterade tillstånden för alla gränssnittssystem visade sig vara rena CT-övergångar och i genomsnitt uppvisade 80% av tillstånden CT-karaktär. Resterande andel bestod av övergångar inom de rena materialen med en större andel inom acceptorn. De teoretiska resultaten av denna studie indikerar att system innehållande den nya polymeracceptorn PYT och dess varianter PY-O och PY-Se uppvisar mycket spännande egenskaper samt att vidareutveckling av OSC:er som innehåller dessa polymerer ytterligare kan hjälpa till i utvecklingen av högpresterande OSC:er.

Title: Image Deblurring in Demanding Conditions Author: Jan Kotera Department: Institute of Information Theory and Automation, Czech Academy of Sciences Supervisor: Doc. Ing. Filip Šroubek, Ph.D., DSc., Institute of Information Theory and Automation, Czech Academy of Sciences Abstract: Image deblurring is a computer vision task consisting of removing blur from image, the objective is to recover the sharp image corresponding to the blurred input. If the nature and shape of the blur is unknown and must be estimated from the input image, image deblurring is called blind and naturally presents a more difficult problem. This thesis focuses on two primary topics related to blind image deblurring. In the first part we work with the standard image deblurring based on the common convolution blur model and present a method of increasing robustness of the deblur- ring to phenomena violating the linear acquisition model, such as for example inten- sity clipping caused by sensor saturation in overexposed pixels. If not properly taken care of, these effects significantly decrease accuracy of the blur estimation and visual quality of the restored image. Rather than tailoring the deblurring method explicitly for each particular type of acquisition model violation we present a general approach based on flexible automatic...