Finite-Difference Time-Domain method (FDTD) is based on numerical solution of Maxwell's equations, nowadays widely used for simulating optical response of photonic structures. This paper provides brief introduction to the FDTD method and several important extensions which make the basic code much more versatile. In order to broaden analysis of photonic structures, transfer matrix method (TMM) is also involved. The code is firstly tested using simple model structures which optical response might be compared with different numerical or even analytical approaches. Debugged code is used to improve photonic crystals for enhanced sensitivity of biosensing devices based on refractive index changes of sensed medium. Last but not the least, properties (sensitivity and Q-factor of resonant peak) of holey waveguide are investigated in one-, two- and three-dimensional simulation. It is shown here, that even this simple structure may compete with complex photonic crystals in the field of biosensors. Powered by TCPDF (www.tcpdf.org)

Title: The study on interactions of functional surfaces with biological systems Author: Ivana Víšová Department: Institute of Physics of the Czech Academy of Sciences, Department of optical and biophysical systems. Supervisor: RNDr. Hana Vaisocherová-Lísalová, Ph.D., Institute of Physics of the Czech Academy of Sciences, Department of optical and biophysical systems. Abstract: This work is devoted to the study of processes influencing the performance of functional antifouling polymer brush coatings and their interactions with complex biological media. Specifically, both results of the fundamental and applied research on the i) functionalization processes influencing coating resistance, ii) tailoring of the physico-chemical properties of the antifouling coatings to minimize the nonspecific interactions with complex biological samples, and iii) behavior and performance of the polymer brush coatings in varying environments are presented. Acrylamide and methacrylamide-based polymer brushes with side hydroxyl, carboxybetaine, and sulfobetaine groups were studied, showing the great potential of their optimized copolymer structures as tunable antifouling functionalizable platforms for cell research or biosensor applications. Moreover, newly developed procedures for antifouling properties recovery after EDC/NHC...

Sensitive layers for optical biosensors and protein chips The goal of this thesis was the development of sensitive surfaces for optical affinity biosensors detecting in complex biological media. The practical application of these surface-based technologies has been hampered by protein fouling from biological media, in particular blood plasma, where the vast majority of relevant analytes are present. The work of the thesis was centred in three main foci:  Design and preparation of antifouling and non-fouling surfaces  Evaluation and conceptualisation of their resistance to fouling from blood plasma and serum as well as other biological fluids  Preparation of sensitive layers for detection in complex biological media Three approaches were used to prepare protein resistance surfaces, i) ω-functional self-assembled monolayers (SAM), ii) end-tethered polymers and iii) polymer brushes prepared by surface initiated controlled radical polymerisation. Investigation of proteins in the blood plasma deposits on PEG- based surfaces revealed that some fouling is unavoidable in PEG-based surface modifications. A novel type of non-fouling polymer brushes based on poly[N-(2-hydroxypropyl) methacrylamide] challenged the accepted ideas for the design of protein resistant surfaces. For the first time a...