Poster abstracts
Poster number 39 submitted by Mithila Agnihotri
Electrokinetic effects of biomolecules: Methods and Application to DNA oligomer
Mithila V. Agnihotri (Biophysics Program, The Ohio State University), Si-Han Chen (Chemistry Department, The Ohio State University), Corey Beck (Chemistry Department, The Ohio State University), Sherwin J. Singer (Chemistry Department and Biophysics Program, The Ohio State University)
Abstract:
The goal of our work is to theoretically examine the dynamics of a DNA oligomer and its counter-ion atmosphere in response to a time varying electric field. These effects, termed electrokinetic effects, are of interest for technological reasons since electric fields can be harnessed to manipulate and transport biomolecules in a controlled fashion in micro- and nano-scale biomedical devices1. Another motivation for this work stems from the need to interpret the results of dielectric spectroscopy, which is a commonly used probe of the properties of biomolecules and their surrounding electrical double layer. Our study of a DNA oligomer is motivated by recent experiments on short oligomers, the first time that data is available for oligomers small enough to be accessible to molecular dynamics simulations. One of the difficulties faced in these calculations is due to the large time scale associated with biomolecule motions. Hence one needs to accumulate very long trajectories, which requires large storage capabilities. We have re-formulated the theory in a way that enables calculation of transport properties from both equilibrium and non-equilibrium simulations using sparse sampling of data without compromising accuracy2. We have shown proof-of-principle by calculating the flow velocity profile for electro-osmotic flow (a type of electrokinetic phenomenon) for a simple electrolyte system using both equilibrium and non-equilibrium simulations. We have also calculated the ionic contribution to frequency dependent electric susceptibility for the same system. Calculation of the electrokinetic properties of a double stranded DNA dodecamer are ongoing. Preliminary data are presented.
References:
[1] Yaling Liu, Qingjiang Guo, Shunqiang Wang, and Walter Hu. Electrokinetic effects on detection time of nanowire biosensor. Applied Physics Letters, 100(15):153502, April 2012.
[2] Mithila V. Agnihotri, Si-Han Chen, Corey Beck, and Sherwin J. Singer. Displacements, Mean-Squared Displacements, and Codisplacements for the Calculation of Nonequilibrium Properties. The Journal of Physical Chemistry B, 118(28):8170–8178, July 2014.
Keywords: DNA dynamics, Dielectric spectroscopy, molecular dynamics