Optical Manipulation and Biological Applications of Quantum Dots

This thesis is concerned with optical manipulation of small particles. This includes dielectric spheres in a standing wave evanescent field and, in particular, quantum dots in the optical trap. The forces acting on the small particles in the optical fields are characterized and quantized. Ultimately to use the particles as force transducers on the pN scale. This is desirable for many biophysical applications. Calculations of optical forces in a plane wave evanescent field are presented. The forces acting on a sphere in the field is decomposed and the gradient force and the scattering force are calculated individually. The trapping potential and trapping strength is considered and a possible comparison to the observed diffusive behavior of a bead in the field is sketched. Optical trapping of colloidal quantum dots is reported. The properties of quantum dots as force transducers are characterized. We measure the trapping strength of different sizes of quantum dots and estimate the polarizabilities. Furthermore, we report two-photon excitation in the optical trap. This thesis is also concerned with the traffic of RNA polymerases on the DNA and how this regulates the gene in living cell. The lac operon is a well-known system of genes where one transcription factor regulates two feedback loops. In addition to this, the transcription factor binds to a site on its own gene and hinders the RNA polymerase to produce a transcript. A model to explore the consequences of auto-regulation is presented and the cells response to different environments is investigated. Finally, another application of quantum dots is considered. The use of quantum dots for tracking individual polymerases on the DNA. This includes the attachment of a quantum dot to an RNA polymerase and the activity of this complex is measured. Furthermore, different appropriate geometries to follow this complex is discussed. In relation to this, we present the use of quantum dots as tracker particles in a geometry where DNA is anchored to the surface.