Wavelet (valić) transformacija

Valić transformacija daje sofisticiranu vremensko-frekvencijsku analizu i koristi se u brojnim algoritmima u raznim područjima znanosti. Nakon teorijske pozadine i usporedbe sa frekvencijskom analizom, bit će prezentirane neke primjene u području sažimanja slike i uklanjanju šuma iz signala. Pojašnjen je i algoritam za prepoznavanje osoba pomoću očnog uzorka

Tuning of the transverse magneto-optical Kerr effect in magneto-plasmonic crystals

The spectral properties of the transverse magneto-optical Kerr effect (TMOKE) in periodic metal–dielectric hybrid structures are studied, in particular with respect to the achievable magnitude. It is shown that the TMOKE is sensitive to the magneto-optical activity of the bismuth-substituted rare-earth iron garnet, which is used as a dielectric material in the investigated structures. For samples with larger Bi substitution level and, consequently, larger gyration constant, the magnitude of the TMOKE increases and reaches 13% in the case of a Bi1.8Lu1.2Fe3.6Al1.4O12 magnetic film. Further, it is demonstrated that the TMOKE vanishes at the high-symmetry points of the Brillouin zone (at the Γ and X points). The main enhancement of the TMOKE takes place near the resonances of the surface plasmon polaritons (SPPs) at the metal/magnetic–dielectric interface. However, near the degenerate resonances of the SPPs at the air/metal and metal/magnetic–dielectric interfaces the TMOKE is increased by the air/metal SPPs as well. This phenomenon is explained in terms of a coupled oscillator model

Magnetophotonic intensity effects in hybrid metal-dielectric structures

The magneto-optical properties of a hybrid metal-dielectric structure consisting of a one-dimensional gold grating on top of a magnetic waveguide layer are studied experimentally and theoretically. It is demonstrated that a magnetic field applied in the longitudinal configuration (in the plane of the magnetic film and perpendicular to the slits in the gold grating) to the metal-dielectric structure modifies the field distribution of the optical modes and thus changes the mode excitation conditions. In the optical far field, this manifests in the alteration of the optical transmittance or reflectance when the structure becomes magnetized. This magneto-optical effect is shown to represent a novel class of effects related to the magnetic-field-induced modification of the Bloch modes of the periodic hybrid structure. That is why we define this effect as longitudinal magnetophotonic intensity effect (LMPIE). The LMPIE has two contributions, odd and even in magnetization. While the even LMPIE is maximal for the light polarized perpendicular to the grating slits (TM) and minimal for the orthogonal polarization (TE), the odd LMPIE takes maximum values at some intermediate polarization and vanishes for pure TM and TE polarizations. Two principal modes of the magnetic layer - TM and TE - acquire in the longitudinal magnetic field additional field components and thus turn into quasi-TM and quasi-TE modes, respectively. The largest LMPIE is observed for excitation of the antisymmetrical quasi-TE mode by TM-polarized light. The value of the LMPIE measured for the plasmonic structure with a magnetic film of Bi2Dy1Fe4Ga1O12 composition is about 1% for the even effect and 2% for the odd one. However, the plasmonic structure with a magnetic film with a higher concentration of bismuth (Bi2.97Er0.03Fe4Al0.5Ga0.5O12) gives significantly larger LMPIE: even LMPIE reaches 24% and odd LMPIE is 9%. Enhancement of the magneto-optical figure of merit (defined as the ratio of the specific Faraday angle of a magnetic film to its absorption coefficient) of the magnetic films potentially causes the even LMPIE to exceed 100% as is predicted by calculations. Thus, the nanostructured material described here may be considered as an ultrafast magnetophotonic light valve

Plasmon-mediated magneto-optical transparency

Magnetic field control of light is among the most intriguing methods for modulation of light intensity and polarization on sub-nanosecond timescales. The implementation in nanostructured hybrid materials provides a remarkable increase of magneto-optical effects. However, so far only the enhancement of already known effects has been demonstrated in such materials. Here we postulate a novel magneto-optical phenomenon that originates solely from suitably designed nanostructured metal-dielectric material, the so-called magneto-plasmonic crystal. In this material, an incident light excites coupled plasmonic oscillations and a waveguide mode. An in-plane magnetic field allows excitation of an orthogonally polarized waveguide mode that modifies optical spectrum of the magneto-plasmonic crystal and increases its transparency. The experimentally achieved light intensity modulation reaches 24%. As the effect can potentially exceed 100%, it may have great importance for applied nanophotonics. Further, the effect allows manipulating and exciting waveguide modes by a magnetic field and light of proper polarization

In silico-aided design, build and test of synthetic proteins

Since the discovery of proteins in 1838, the field of protein engineering and our understanding of proteins have improved exponentially. Synthetic proteins have found applications in various biomedical, food and material-based settings. This rise in synthetic proteins was complemented with the parallel expansion in the availability of in silico tools for protein modelling. The complexity in the composition and design of synthetic proteins requires careful in silico validation to screen for potential pitfalls in the design. In silico tools for protein modelling and design have been used extensively to computationally validate the structure and functioning of the synthetic proteins prior to wet-lab testing. In this thesis, the workflow of design-model-build-test of synthetic proteins with novel applications in imaging is described. The in silico-aided design, screening and the in vitro testing of synthetic proteins targeting S. aureus surface antigen Clumping factor A are discussed in Chapter 2. In this chapter, a suitable candidate worthy of examining in a future in vivo setting was identified. During the in silico-aided screening, the complexity of data obtained from various in silico tools posed new challenges. This was termed as ‘the in silico myriad problem’. In Chapter 3, a mathematical strategy (Function2Form bridge) was tested to address the in silico myriad problem, by combining the scores of different design parameters pertaining to the synthetic protein being analysed into a single easily interpreted output describing overall performance. The strategy comprises 1. A mathematical strategy combining data from a myriad of in silico tools into an Overall Performance-score (a singular score informing on a user-defined overall performance); 2. The F2F-Plot, a graphical means of informing the wet-lab biologist holistically on designed construct suitability in the context of multiple parameters, highlighting scope for improvement. F2F bridge was implemented during the design process of all the synthetic proteins in Chapter 4 and Chapter 5. The synthetic protein design strategy used in Chapter 2 was implemented to design synthetic proteins targeting cancer cells, and to assess their potential as in vivo imaging agents in Chapter 4. For both MUC1 and ClfA targeted proteins, in vivo luminescence imaging studies involving systemic intravenous administration of proteins, validated synthetic protein specific accumulation at target cell locations within mice as evidenced by localised luminescence. Dose response studies indicated that luminescence output was both target cell and administered protein quantity related. In Chapter 5, a self-assembling protein ‘cage’ was designed, built and tested in vitro. An accompanying novel fluorescence-based protein-protein interaction reporting strategy was introduced, involving incorporation of cysteine residues at the interaction interface of monomeric proteins of the self-assembling protein cage. In silico tools were used to ensure the conformational and functional stability. FlAsH EDT2 (fluorescin arsenical hairpin binder-ethanedithiol) mediated fluorescence was used to confirm the self-assembly. This demonstrates the level of accuracy and detail that can be incorporated into synthetic protein design using in silico tools. In Chapter 6, the scope of introducing miniaturised optical devices to aid biological experimentation was explored. A novel handheld device for monitoring continuous bacterial growth, with prospects of measuring biofluorescence was developed. The device was tested using different bacterial strains and showed accuracy levels similar to a standard benchtop spectrophotometer. This thesis demonstrates the use of computational methods and various in silico tools for protein design. Modern day biomedical science demands novel concepts with deployable technology to assist their translation into user-based settings. In this thesis, various interdisciplinary concepts have been applied to deliver on a holistic end-goal

Function2Form Bridge - Towards synthetic protein holistic performance-prediction

Protein engineering and synthetic biology stand to benefit immensely from recent advances in in silico tools for structural and functional analyses of proteins. In the context of designing novel proteins, current in silico tools inform the user on individual parameters of a query protein, with output scores/metrics unique to each parameter. In reality, proteins feature multiple â partsâ /functions, and modification of a protein aimed at altering a given part, typically has collateral impact on other protein parts. A system for prediction of the combined effect of design parameters on the overall performance of the final protein does not exist. Function2Form Bridge (F2F-Bridge), attempts to address this by combining the scores of different design parameters pertaining to the protein being analysed into a single easily interpreted output describing overall performance. The strategy comprises 1. A mathematical strategy combining data from a myriad of in silico tools into an OP-score (a singular score informing on a user-defined overall performance); 2. The F2F-Plot, a graphical means of informing the wetlab biologist holistically on designed construct suitability in the context of multiple parameters, highlighting scope for improvement. F2F predictive output was compared with wetlab data from a range of synthetic proteins designed, built and tested for this study. Statistical/machine learning approaches for predicting overall performance, for use alongside the F2F plot, were also examined. Comparisons between wetlab performance and F2F predictions demonstrated close and reliable correlations. This user-friendly strategy represents a pivotal enabler in increasing accessibility of synthetic protein building and de novo protein design