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February 28, 2014

Speaker: Hendrick de Haan, Assistant Professor, Faculty of Science, Ontario Tech University

Title: Computational nanobiophysics: Exploring the intersection of biophysics and nanotechnology via simulations

Abstract: With the current state of nanofabrication, it is now possible to design and build nanoscale devices and particles. Since the smallest scale for biological molecules is typically on the order of nanometers, such devices allow for the isolation, study, manipulation and even alteration of single biopolymers such as DNA and proteins. Similarly, nanoparticles can be engineered and synthesized to interact with specific molecules, cells, and tissue. This technology opens the door to an enormous range of new medical, biotechnology and nanotechnology applications. In this talk, Dr. de Haan will give an overview of some of his projects in this research area, including:

  • DNA in a nanopit system
  • magnetic nanoparticles as contrast agents in MRI
  • twitcher cells moving across surfaces
  • DNA translocation through a nanopore

For each system, he will outline how the system is modelled, as well as the simulation approach employed to reproduce the dynamics. At the end of the talk, he will focus on DNA translocation through a nanopore by presenting results concerning translocation in a crowded environment. He will show that for DNA starting halfway through a nanopore, a bias favouring translocation to one side is obtained not only when there is a gradient in the obstacle concentration across the membrane, but also when the concentration is the same but the arrangement of the obstacles differs. These results imply that for translocation in a heterogeneous environment, a purely entropic driving force can arise in the system.