Publication Date: 2023/07/11
Abstract: The traditional computational modeling of biomolecular structure, dynamics, and interactions remains difficult for many biomolecular systems. One possible way for overcoming the size problem of biologically important macromolecules is through coarse-graining, in which, instead of describing the molecules in their atomic details, groups of atoms in the molecules are merged into a “super-atomic units” and then compute the structure and dynamics of the molecules in terms of the motion and interactions of units. In the present report, we present results from our coarse-grained molecular dynamics simulation studies on some microbiologically important supercoiled DNA molecules, namely pBR322 plasmid and phix174 RF I (replicative form I) DNA along with a few smaller DNA mini-circles with random sequences. The coarse- grained description of the structure and the force field were obtained from oxDNA. We show that the structures, energies, and base-pairing propensities of the molecules in the coarse-grained representation follow experimentally observed trends.
Keywords: No Keywords Available
DOI: https://doi.org/10.5281/zenodo.8133498
PDF: https://ijirst.demo4.arinfotech.co/assets/upload/files/IJISRT23JUN2411.pdf
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