Berlin 2024 – wissenschaftliches Programm
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BP: Fachverband Biologische Physik
BP 15: Poster IIb
BP 15.26: Poster
Dienstag, 19. März 2024, 18:00–20:30, Poster F
Simulating synthetic, DNA-based systems across different scales — •Aaron Gadzekpo1, Xenia Tschurikow1, Mai Tran2, Rakesh Chatterjee3,4, Vasily Zaburdaev3,4, Kerstin Göpfrich2, and Lennart Hilbert1 — 1Karlsruhe Institute of Technology — 2Max Planck Institute for Medical Research — 3Max Planck Zentrum für Physik und Medizin — 4Friedrich-Alexander Universität Erlangen-Nürnberg
Molecular dynamics (MD) simulations at different scales can aid in the design and characterisation of synthetic biological systems. Combining coarse-grained MD-simulations with experiments allowed us to explain how the shape of droplets formed by self-interacting DNA-nanomotifs responds to adding increasing concentrations of amphiphilic nanomotifs. Currently, we are investigating how DNA-strands can serve as condensation surfaces for droplet formation at subsaturated nanomotif concentrations. To accurately simulate microscopic aspects of our DNA-based systems, such as transient hybridisation that underlies nanomotif interactions, we employ simulations at resolutions of one to a few nucleotides. Capturing macroscopic behaviour, such as phase separation, requires simulating larger systems sizes and time scales, for which we develop models averaging many nucleotides. We present ongoing research aimed at integrating simulations at different scales for model-guided design of synthetic, DNA-based systems.