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CPP: Fachverband Chemische Physik und Polymerphysik
CPP 25: Biomaterials and Biopolymers II (joint session BP/CPP)
CPP 25.10: Talk
Wednesday, March 13, 2013, 12:15–12:30, H43
Biomolecular translocation through nanopores: from statistics to real DNA conformations — •Maria Fyta1, Simone Melchionna2, Sauro Succi3, and Efthimios Kaxiras4 — 1Institut für Computerphysik, Universität Stuttgart, Germany — 2IPCF-CNR, Università La Sapienza, P.le A. Moro 2, 00185 Rome, Italy — 3IAC-CNR, Via dei Taurini 19, 00185 Rome Italy — 4Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge MA 02138, U.S.A
We apply a multiscale computational scheme to model a biomolecule translocating through a narrow pore, an intensively studied subject due to its variety of applications such as ultra-fast DNA sequencing. The model uses a mesoscopic lattice Boltzmann method to treat the solvent and a Molecular Dynamics scheme to deal with the biomolecule. Our first results involve an anonymous polymer translocating in pure water. We have obtained important insight into the statistics and dynamics of the process. The translocation time exponent compares well with the experimental values, while we were able to monitor multiconformational translocation. As a next step, we include electrokinetic effects, i.e. ions, as well as a realistic quantum-mechanically derived potential for double stranded DNA. We are now able to reveal in more detail the structural conformations of the DNA molecule as well as the ion distribution within the pore. The results also provide a qualitative and quantitative understanding of the ionic conductance and DNA blockade as compared to the experiments. Our conclusions also involve the effect of the pore geometry in the DNA translocation process.