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Application of "virtual dynamics" approach to study dynamics of molecular systems

Final Activity Report Summary - VIRTUAL DYNAMICS (Application of "virtual dynamics" approach to study dynamics of molecular systems)

The main objectives of the project were based on the work by B. Brutovsky et al., Journal of Chemical Physics 118, 6179 (2003), where we introduced the simulation scheme enabling multiple speedup of atomistic molecular dynamics simulation of liquid oxygen by periodic replacement of significant parts of exactly calculated Lennard-Jones forces by their linear estimates.

During the current project we concentrated on the further methodological development. As a result, we proposed a much simpler scheme for determination of the linear predictor coefficients, as described in a manuscript by B. Brutovsky and G. R. Kneller., which, by the time of the project completion, was in press by Computer Physics Communications, and opened the way to the broader application of the technique. Another important result we published therein was that Taylor extrapolation corresponded to the limit case of linear prediction for the sampling time approaching to zero. We clearly demonstrated that the linear predictor was superior to Taylor extrapolation for typically applied sampling times equal to 0.5 to 2 fs.

The second part of the project was devoted to the study of flexible polymers’ dynamics in dilute solution. We proposed the joint Rouse-Zimm (RZ) theory that contained well-established Rouse and Zimm models as the respective limiting cases. The type of the bead motion changed within time from the Rouse to the Zimm behaviour. We demonstrated better agreement of the approach by interpreting the first recent observation of the kinetics of individual polymer monomers, using the fluorescence correlation technique that was proposed by R. Shusterman et al., in Physical Review Letters 92, 048303, 2004. The optimisation of the generalised RZ theory to the data on double-stranded and single-stranded deoxyribonucleic acid DNA coils, namely dsDNA and ssDNA, led to the determination of the parameters for the statistical and mechanical description of these polymers’ behaviour.