Accessibility to nucleosomal dna is an important factor in transcription and gene expression. During transcription, rna polymerase exerts a force on the nucleosome under which the nucleosome...Show moreAccessibility to nucleosomal dna is an important factor in transcription and gene expression. During transcription, rna polymerase exerts a force on the nucleosome under which the nucleosome unwraps, and, as recently shown experimentally, this can happen asymmetrically. In this thesis, we show, using computer simulations of sequence-dependent coarse-grained dna, what causes this asymmetry. We will also show a proof of concept that we can design dna sequences that unwrap in a predetermined way.Show less
Increasing effort into parallel single molecule force experiments has led to the development of acoustic force spectroscopy (AFS). Acoustic standing waves of MHz frequencies are able to exert...Show moreIncreasing effort into parallel single molecule force experiments has led to the development of acoustic force spectroscopy (AFS). Acoustic standing waves of MHz frequencies are able to exert forces on microspheres, which can be used for the manipulation of single bio-molecules. The performance of acoustic tweezers is greatly dependent on setup design and the proper driving frequency. The need for AFS flow cell design modeling software is apparent. In this thesis we present a physical model for calculating the acoustic frequency response of a flow cell. We have found that an oil immersion objective lowers AFS performance drastically as opposed to an air objective and that the optimal driving frequency lies around 10.3 MHz for our prototype flow cell. Limited by the 10 MHz cap of our AC driver and problems with flow cell assembly yields, we were not able to demonstrate an acoustic pulling force. We need to switch to an air objective and, in order to make AFS work in our laboratory, either a new AC generator needs to be implemented or a piezoelectric transducer with a thickness mode within 8-10 MHz needs to be included.Show less
