The Effects of Flexibility on dsDNA–dsDNA Interactions
Abstract
:1. Introduction
2. Methods
2.1. MD Simulations
2.2. ABF Calculations
2.3. Differential Entropy from Density Fluctuations
2.4. Localization of Diffusion Coefficients of Na+ Ions
3. Results and Discussion
3.1. Potential of Mean Force
3.2. vdW Interactions
3.3. Ion Distributions and Electrostatic Energy of Ions around dsDNA Pairs
3.4. Differential Entropy from Density Fluctuations
3.5. Localization of Diffusive Dynamics of Na+ Ions
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Chen, C.; Pettitt, B.M. The Effects of Flexibility on dsDNA–dsDNA Interactions. Life 2022, 12, 699. https://doi.org/10.3390/life12050699
Chen C, Pettitt BM. The Effects of Flexibility on dsDNA–dsDNA Interactions. Life. 2022; 12(5):699. https://doi.org/10.3390/life12050699
Chicago/Turabian StyleChen, Chuanying, and B. Montgomery Pettitt. 2022. "The Effects of Flexibility on dsDNA–dsDNA Interactions" Life 12, no. 5: 699. https://doi.org/10.3390/life12050699