Atomistic simulations time scale

Molecular dynamics simulations ([McCammon and Harvey 1987]) propagate an atomistic system by iteratively solving Newton s equation of motion for each atomic particle. Due to computational constraints, simulations can only be extended to a typical time scale of 1 ns currently, and conformational transitions such as protein domains movements are unlikely to be observed. 

Many practically important polymers have a chemical structure that is considerably more complicated than PE, and this fact further complicates the simulation of macromolecular materials. As a consequence of all these arguments, it is clear that a simulation of fully atomistic models of a sufficiently large system over time scales for which thermal equilibration could be reached at practically relevant temperatures, is absolutely impossible thus a different approach must be taken ... 

What is clear is that the overall strategy, in which the computationally intensive equilibration is performed with a model that does not have atomistic detail, but which can nevertheless be unambiguously identified with a specific real system with atomistic detail, markedly increases the utility of simulations for polymer science. It provides access to much larger systems, and to phenomena that occur on much longer time scales than could be investigated with simulations in which full atomistic detail is retained throughout. 

Finally, recently depolarized light scattering spectra [191] display an additional process that shows a much faster characteristic time and a much weaker temperature dependence than the dielectric j0-relaxation (more than three orders of magnitude faster time at -200 K and an activation energy of 0.16 eV, about half of the dielectric value). Also atomistic simulations on PB have indicated hopping processes of the frans-double bond [192,193] with an associated activation energy of -0.15 eV. Whether these observations may be related with the discrepancy in the apparent time scale of the NSE and dielectric experiments remains to be seen. 

Shim, Y., Amar, J.G., Uberuaga, B.P., Voter, A.F. Reaching extended length scales and time scales in atomistic simulations via spatially parallel temperature-accelerated dynamics. Phys. Rev. B 2007, 76, 205439-1-11. 

Although a first principle or ab initio atomistic simulation of a one-million atom system is being attempted with one of the most powerful computers, ab initio atomistic modeling of a macroscopic (1024 atoms) in a long time scale (103 s) is seemly not possible in a foreseeable future. The hierarchical multiscale simulation methods are implementable options for the time being. 

S Atomistic simulation assisted synthesis and investigations The classical atomistic simulation techniques based on the pair potentials are suitable for the simulations of ceria nanoparticles even with a real sized model. Molecular d)mamics studies with several thousands of ions and up to hundreds of nanoseconds in a time scale have been carried out to interpret the diffusion, and crystal growth behaviors for pure and doped-ceria nanoparticles. Traditionally, the technique has been used to explore the oxygen ionic conductivity in ionic conductors such as ceria and zirconia (Maicaneanu et al., 2001 Sayle et al., 2006). 

Unlike simulations of proteins and protein complexes, modeling and simulations of lipid systems is relatively easy in the sense that lipid molecules and (smallest) lipid aggregates are reasonably small, and the time scales related to many processes that take place in lipid systems are of the order of nanoseconds. Consequently, even atomistic modeling of lipid aggregates is feasible for reasonably complex systems. Here, we discuss briefly the three main levels of modeling associated with lipids. 

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