Joint numerical-experimental investigation of the dynamics of single- and doubly-tethered DNA molecules in shear flow

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The main objective of the project is to investigate the micromechanical behaviour of DNA immersed in a hydrodynamic flow by joint numerical and experimental investigations. This topic is highly relevant for the development of novel single-molecule manipulation techniques in biophysics and bionanotechnology where complex DNA-liquid interactions occur. The current project focuses on the following tasks. (i) Based on our previous work, we will develop a validated numerical simulation tool which is able to predict the behavior of tethered DNA molecules immersed in a liquid flow and is suitable for efficient three-dimensional computations of DNA stretching. (ii) We will investigate the micromechanical behavior of individual DNA molecules, tethered at both ends, exposed to a shear flow. The mechanical interaction between DNA and flow along with the corresponding DNA morphology will be predicted quantitatively. (iii) Finally, a more complex system will be considered by introducing DNA-protein interaction. We will investigate if the mechanical response of DNA to hydrodynamic flow can be used for local sensing, leading to the concept of using an immobilized DNA molecule as a mechano-fluidic sensor for single association events. The development of single-molecule concepts is of large importance for future applications in proteomics, genomics and biomedical diagnostics.