Molecular Dynamics Simulation of High Density DNA Arrays
Abstract
:1. Introduction
2. Simulating DNA Arrays
2.1. Modeling the Solvent Grand Canonical (Osmotic Isobaric) Ensemble
2.2. Bathing Solution
2.3. Model Interaction Potential Parametrization in DNA Arrays
2.4. Structural Characterization of the High Density DNA Subphase
3. Adaptive Resolution Simulations of a DNA Molecule Solvated in Salt Solution
3.1. AdResS—Single DNA
3.2. Dielectric Properties
4. Simulating Osmotic Isobaric Ensemble: Densely Packed DNA Arrays
4.1. Computation of Osmotic Pressure
4.2. Hexagonal Columnar (H) → Orthorhombic (OR) Phase Transition
4.3. Orientational Order Parameters
5. Conclusions and Perspectives
Acknowledgments
Conflicts of Interest
References
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Podgornik, R.; Zavadlav, J.; Praprotnik, M. Molecular Dynamics Simulation of High Density DNA Arrays. Computation 2018, 6, 3. https://doi.org/10.3390/computation6010003
Podgornik R, Zavadlav J, Praprotnik M. Molecular Dynamics Simulation of High Density DNA Arrays. Computation. 2018; 6(1):3. https://doi.org/10.3390/computation6010003
Chicago/Turabian StylePodgornik, Rudolf, Julija Zavadlav, and Matej Praprotnik. 2018. "Molecular Dynamics Simulation of High Density DNA Arrays" Computation 6, no. 1: 3. https://doi.org/10.3390/computation6010003