Solvating, manipulating, damaging, and repairing DNA in a computer
This work highlights four different topics in modeling of DNA: (i) the importance of water and ions together with the structure and function of DNA; the hydration structure around the ions appears to be the determining factor in the ion coordination to DNA, as demonstrated in the results of our MD simulations; (ii) how MD simulations can be used to simulate single molecule manipulation experiments as a complement to reveal the structural dynamics of the studied biomolecules; (iii) how damaged DNA can be studied in computer simulations; and (iv) how repair of damaged DNA can be studied theoretically. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Internal Structure and Dynamics of the Decamer D(ATGCAGTCAG) 2 In Li + -H 2 O Solution: A molecular Dynamics Simulation Study
Molecular dynamics simulation of the decamer d(ATGCAGTCAG) 2 in aqueous solution, electroneutralized by Li + ions has been carried out. Emphasis is on the verification of the equilibrium conditions and the related structural and dynamical properties. Applicability of the kinetic part of Boltzmann's H function as a measure of thermodynamic equilibrium is tested. Overall structural stability has been confirmed by different RMSDs. Conformational and helicoidal parameters have been analyzed statistically and dynamically. Dynamical analysis reveals the existence of dynamical sub-states, which typically appear as abrupt changes from a mean level to another in the value of parameter. In statistica…