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Pioneering Simulations of Nanoscale Biomolecular Systems

Aleksei Aksimentiev, University of Illinois at Urbana-Champaign

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Aleksei Aksimentiev, Jejoong Yoo, Christopher Maffeo, Maxim Belkin, Manish Shankla, Shu-Han Chao, Chen-Yu Li, Karl Decker, Derek VanDamme, James Wilson, Dmitrii Kochkov, Leila Sloman, Scott Michael Slone, Shalini Lovis, Alex Finnegan, Han-Yi Chou, David Winogradoff, Wei Si, Isaac Freund, John Zeiders, Lauren Johnson, Shidi Zhao, Himanshu IMANSHU Joshi, Kumar Sarthak, Kush Coshic, Lauren Quednau

Using Blue Waters, the Aksimentiev group will carry out pioneering simulations of nanoscale biomolecular systems. The first class of systems to be studied using Blue Waters are nanopore sensors of biological information. In this area, the simulations will guide experimental efforts to build ultra-sensitive nanoscale probes for direct readout of the nucleotide sequence of DNA and RNA molecules and the amino-acid sequence of proteins. The systems to be explored include plasmonic nanopore tweezers and multilayer graphene membranes. The results of this work will have the potential to revolutionize the life sciences and medicine by offering easy access to fundamental biological information that governs functions of every living organism.

The second area of interest includes living cells’ systems that store, replicate, and repair genetic information. Specifically, all-atom and coarse-grained molecular dynamics simulations will elucidate how DNA is organized inside a human cell’s nucleus; how DNA is copied during a cell’s replication cycle and how cellular machinery finds and repairs damaged DNA. The results of this work will contribute to the understanding of the most fundamental biological processes and can potentially lead to discovery of new approaches to disease treatment and prevention.

In the third area of interest, the simulations will unravel the potential of nanomaterials for applications in biomedical engineering. The initial focus in this area will be on DNA nanotechnology, which offers effortless nanoscale fabrication through self-assembly. The simulations will explore the use of such materials for drug delivery, nanoscale electronics, energy conversion and sensing. The overarching goal in this area is integration of biological and inorganic components into advanced functionality systems that can interact both with biological and inorganic matter.