Terahertz dielectric study of bio-molecules using time-domain spectrometry and molecular dynamics simulations

.............................................................................................5 Acknowledgements................................................................................7 List of figures .....................................................................................11 List of tables.......................................................................................15 List of abbreviations.............................................................................16 1. Terahertz radiation............................................................................18 1.1 THz range of electromagnetic spectrum............................................18 1.2 Application of THz technologies in biochemistry...............................21 1.3 Interactions between THz Wave and Bio-molecules ...........................23 2. THz Time Domain Spectroscopy...........................................................27 2.1 Principles of operation .................................................................27 2.2 Application of THz-TDS ............................................................31 2.3 Measurement facilities in the QML laboratory .................................34 3. Signal processing in relation to THz-TDS ...............................................38 3.1 Simple material parameters extraction procedure...............................38 3.2 A procedure for more accurate determination of ̃ ............................40 3.3 Dependence of estimates of and on initial guesses.........................40 3.4 Fabry-Perot Effect ..................................................................45 3.5 Error analysis for the extraction procedure.......................................48 3.6 Potential issues that influence optical constants extraction ....................54 3.6.1 Sample preparation.......................................................54 3.6.2 Alignment..................................................................55 3.6.3 DR limitations and resolution of the system..........................56 3.6.4 Humidity...................................................................57 3.7 Numerical thickness determination algorithm....................................58 3.8 Precise material parameter extraction in multilayered structure.................61 3.9 Brief summary of the chapter ......................................................64 4. Investigation of solvation dynamics of TRP-cage, BPTI and lysozyme, proteins by means of VDOS using Gromacs...........................................................65 4.1 Overview..............................................................................65 4.2 Gromacs simulation details.........................................................68 10 4.3 The structure of selected proteins..................................................70 4.4 Hydration shell: buried vs surface water molecules.............................71 4.5 Determination of hydration shell size from MD simulations..................74 4.6 Concluding remarks..................................................................77 5. Investigation of hydration shell thickness and electromagnetic field absorbance of solvated protein molecules in the sub-THz frequency domain......................78 5.