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Knust, Sebastian: Optical tweezers for DNA translocation and cell elasticity experiments. 2020
Inhalt
Contents
General Introduction and Theory
Introduction and Motivation
Microfluidics
Hydrodynamics
Navier-Stokes equation
Hagen-Poiseuille flow
Reynolds number
Stokes friction
Surface potential and the electrical double layer
Electrokinetics
Electrophoresis and electroosmosis
Dielectrophoresis
Brownian motion and diffusion
Optical Tweezers
History
Gaussian and laser optics
Free space Gaussian optics
Focused Gaussian optics
Real Gaussian beams
Laser
Fibre laser
Polarisation
Theory of optical trapping
2D optical traps
3D optical traps
Non-Gaussian beam profiles
Hooke's Law
Langevin equation
Force analysis
Scattered light analysis
Video-based analysis
Interference effects in the vicinity of surfaces
Force calibration
Stokes' Law
Power Spectral Density (PSD) analysis
Theory of Nanopore translocation
DNA
Structure and role
Entropic behaviour
Electrical resistance of nanopores
Theory of Cell Elasticity
Setup of a cell
Viscoelasticity
Stress and Strain
Viscoelastic models
Purely elastic behaviour (spring)
Purely viscous behaviour (dashpot)
Series and parallel behaviour
Multi-element models
Experimental determination of viscoelastic parameters
Creep recovery test
Stress relaxation test
Oscillatory analysis
General method
DNA translocation through nanopores in boron nitride and molybdenum disulfide
Experimental setup
Optical setup
Microfluidic setup
Software
Monolayer membrane and nanopore preparation
Boron nitride
Material properties
Exfoliation
Transfer to substrate
Monolayer identification
Transfer to membrane
Molybdenum disulphide
Material properties
Exfoliation
Transfer to substrate
Monolayer identification
Transfer to membrane
Nanopore milling
Results
High-speed force detection
Boron nitride
Silicon wafer substrate
PDMS substrate
PMMA substrate
Molybdenum disulphide
Identification of monolayer flakes on PDMS
Wedging transfer
Transfer by viscoelastic stamping
Nanopore milling
DNA translocation with optical tweezers
Free DNA translocation
Conclusions and Outlook
Cell elasticity investigation with Elasto-Tweezers
Experimental setup
Optical tweezers setup
Microfluidics setup
General setup
Microfluidic chip
Temperature control
Software
Experimental protocols
Cell culture
Manufacture of microfluidic chips
PDMS chips
COC chips
Bead surface modifications
Declogging of microfluidic switches
Preparation of solutions
Installation and preparation of microfluidic chip
Cell viability verification
Results
Temperature control
Polarisation
Bead surface modifications
Carboxylated beads
Amino coated beads
Uncoated beads
Microfluidic design performance
Design 1: Corridors with adjacent trapping chambers
Design 2: Linear design
Design 3: Cross design with integrated experimental areas
Cell elasticity measurements
Cluster of HEK-293 cells and PDMS residue
Single HEK-293 cell with one static bead
Single HEK-293 cell with two optically trapped beads
Very stiff single HEK-293 cell
Cell viability verification
Conclusions and Outlook
Conclusions, Outlook and Appendix
Summary and Outlook
User manual for the nanopore setup
Safety information
System overview
Hardware overview
Software overview
Performing experiments
Turning the system on
Controlling andor.vi
Controlling tweezer2.vi
Packing data
Analysing data
Measurement selection
Frame Selection & Edge Detection Settings
Autofocus calibration
Force Analysis
Results
User manual for the Elasto-Tweezers setup
Safety information
System overview
Hardware overview
Software overview
Performing experiments
Turning the system on
Controlling ET.vi
Controlling overview.vi
Resolving common issues
Packing data
Force analysis
Measurement selection
Frame Selection & Edge Detection Settings
Force Analysis
Results
Stress / strain analysis
Fitting numerical solutions of first-order differential equations with Gnuplot
List of figures
List of publications and conference contributions
Bibliography
Danksagung