Molecular dynamics simulations of DNA strands under GHz oscillatory flow

The interaction between elastic liposome-structures immersed in the oscillatory shear flow will be studied in scales where thermal fluctuations are significant, by using a novel computational tool (FLUAM) based on the Immersed Boundary Method.20 FLUAM runs in Graphics Processor Units (GPU) cards, in an extremely efficient way (about 100 faster than standard CPU nodes) using Fast Fourier Transforms to solve incompressible fluctuating Navier-Stokes. The soft matter structures immersed in the fluid can be constructed with standard coarse-grained models, on which P6 has extensive experience. Aside from the flow drag on the immersed structures, we expect that part of the dissipation arises from the vibrational modes of the structures and chains, excited by the interaction with flow oscillations. This is indeed a highly non-trivial problem which requires the state-of-the-art simulation techniques. Results will be used by P2 for the rational design of liposome structures of high dissipative capability.