Authors :
ASHIQ MAHAMMAD; DR. ANSUMAN LAHIRI
Volume/Issue :
Volume 8 - 2023, Issue 6 - June
Google Scholar :
https://bit.ly/3TmGbDi
Scribd :
https://tinyurl.com/yp7adwrb
DOI :
https://doi.org/10.5281/zenodo.8133498
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.
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.
