Using internal and collective variables in Monte Carlo simulations of nucleic acid structures: Chain breakage/closure algorithm

: This article describes a method for solving the geometric closure problem for simplified models of nucleic acid structures by using the constant bond lengths approximation. The resulting chain breakage/closure equations, formulated in the space of variable torsion and bond angles, are easy to solve, and have only two solutions. The analytical simplicity is in contrast with the high complexity of the closure problem in the torsion angle space with at most 16 solutions, which has been dealt with by several authors and was solved analytically by Wu and Deem (J. Chem. Phys. 1999, 111, 6625). The discussion on the choice of variables and associated Jacobians is focussed on the question of how conformational equilibration is affected in Monte Carlo simulations of molecular systems. In addition to the closure of the phosphate backbone, it is necessary to also solve the closure problem for the five-membered flexible furanose sugar ring. Explicit closure equations and the resulting Jacobians ...

• Type: Journal
• Year: 2006
• Where: JCC
• Authors: Heinz Sklenar, Daniel Wüstner, Remo Rohs
• Keywords: Closure Problem, JCC 2006, Monte Carlo Simulations, Nucleic Acids