Regensburg 2019 – wissenschaftliches Programm

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CPP: Fachverband Chemische Physik und Polymerphysik

CPP 17: Poster Session I

CPP 17.40: Poster

Montag, 1. April 2019, 17:30–19:30, Poster B1

Free energy of interaction between polymers and Guanine-Quadruplexes using Molecular Dynamics Simulations — •Sanwardhini Pantawane and Stephan Gekle — Biofluid Simulation and Modeling Group, Theoretische Physik VI, Universität Bayreuth, 95440 Bayreuth Germany

In this investigation, free energy calculations on a system consisting of Poly(3-hexylthiopene-2,5diyl) (P3HT) chains and Guanine-Quadruplex DNA molecule, immersed in water are carried out. Such a polymer-DNA assembled system can be used to construct DNA biosensors, but has yet not been accomplised due to the lack of understanding of their conformational and thermodynamical stability. We construct a system with a four repeat G-Quadruplex molecule sitting over a planar surface of five collaterally arranged P3HT chains with 20 repeats each and apply umbrella sampling to pull the DNA molecule away from the P3HT polymer surface. We carry out the free energy calculations derived from a series of umbrella sampling simulations using a Weighted Histogram Analysis Method (WHAM), which would give an insight on determining the probability of the DNA molecule to attach to the conjugated polymers. An additional study on the effect of oxidation on such a G-quadruplex structures is also presented here.