TCBG Seminar

Open Boundary Molecular Dynamics of DNA

Matej Praprotnik
National Institute of Chemistry
Libljana, Slovenia

Monday, February 3, 2020
3:00 pm (CT)
3269 Beckman Institute


The electrolyte concentration of the aqueous bathing environment can profoundly affect the behavior of biomolecules. Nevertheless, due to computational limitations, molecular simulations of biophysical systems are usually performed either at nominally zero salt concentration or at excessive salt concentrations. In this talk, I will present an efficient molecular simulation approach for an atomistic DNA molecule at realistic physiological ionic conditions. The simulations are performed by employing the open boundary molecular dynamics method, which allows for simulations of open systems that can exchange mass, momentum, and energy with the environment. In our approach, the computational burden is drastically alleviated by embedding the DNA molecule in a mixed explicit/implicit salt-bathing solution. In the explicit domain, the water molecules and ions are both overtly present in the system, whereas in the implicit water domain, only the ions are explicitly present and the water is described as a continuous dielectric medium. Water molecules are inserted and deleted into/from the system in the intermediate buffer domain that acts as a water reservoir to the explicit domain, with both water molecules and ions free to enter or leave the explicit domain. The presented approach is general and allows for efficient molecular simulations of biomolecules solvated in bathing salt solutions at any ionic strength condition.

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