6533b81ffe1ef96bd1278eab
RESEARCH PRODUCT
Internal Structure and Dynamics of the Decamer D(ATGCAGTCAG) 2 In Li + -H 2 O Solution: A molecular Dynamics Simulation Study
Aatto LaaksonenRaimo A. LohikoskiAlexander P. LyubartsevJussi Timonensubject
Aqueous solutionChemistryThermodynamic equilibriumGeneral Chemical EngineeringThermodynamicsGeneral ChemistryCondensed Matter PhysicsKinetic energyMeasure (mathematics)IonMolecular dynamicssymbols.namesakeStructural stabilityModeling and SimulationBoltzmann constantsymbolsGeneral Materials ScienceStatistical physicsInformation Systemsdescription
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 statistical analysis these sub-states cannot often be detected. Correlation analysis shows concerted motions among many nearby structural parameters.
| year | journal | country | edition | language |
|---|---|---|---|---|
| 2003-01-01 | Molecular Simulation |