VIRTUAL DYNAMICS · Application of virtual dynamics" approach to study dynamics of molecular systems"
6РП — Действия „Мария Кюри“
- Период
- 2004-01-01 → 2004-12-31
- Финансиране от ЕС
- 23 711 €
- Участници
- 1
- Схема
- ERG
Линиите свързват координатора с партньорите. За проекти отпреди 2014 г. CORDIS не винаги дава точни координати. Тези точки са на ниво град или държава.
Накратко на български
Молекулярните симулации на течности и полимери се ускоряват чрез замяна на сложни изчисления с линейни приближения. Това помага за по-бързо и точно описание на движението на отделните частици в разтворите.
Кратко обяснение, генерирано от езиков модел по текста на CORDIS. Оригиналът е по-долу.
Резултати накратко
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.
Текст от CORDIS, на английски · Данни: CORDIS, © Европейски съюз
Цел на проекта
The project is based on the results of the initial Marie Curie Individual Fellowship during which we have developed the simulation scheme consisting in intertwining the short interval of standard molecular dynamics simulation with the longer interval of li nearly predicted dynamics with the overall speed-up close to 6 in comparison to standard molecular dynamics simulations of a system consisting of a few hundred flexible oxygen molecules. During the reintegration phase we would like to understand better the open methodological questions of the approach. The first methodological question which will be studied is the (linear) predictability of the systems simulated with and without the cut-off, as we have empirically found that the mean square 1-step predictio n error of the system simulated without the cut-off is by two orders of magnitude lower. The other methodological question is the comparison of the linearly predicted molecular dynamics trajectory against its extrapolation based on a Taylor series. As we h ave found that the linear prediction approach provides the trajectory which is much closer to real" trajectory, we will investigate the relation between the two. As the second part of the project we will implement the method into the gen eric simulation package and will test the efficiency of the method in simulations of the molecules of applied importance. The application of the method to more complex molecules and molecular fragments (towards the ultimate goal - proteins and DNA) will be tried and the limits of the approach will be outlined. During the second part of the project we will study the possibility to accelerate molecular dynamics simulations by using other non-traditional simulation techniques (playing the role of "vir tual dynamics"), such as autoregressive modelling and, cellular automata. We will apply the autoregressive modelling to simulate stochastic force in the simulation of polymer liquids."
Оригинален текст от CORDIS (на английски).
Участници
- UNIVERSITY OF PAVOL JOZEF SAFARIK · KOSICEКоординаторНиво градСловакия
Връзки
Данни: CORDIS, © Европейски съюз