Simulations multiscale

UNRAVELING THE MECHANISMS OF RIBOZYME CATALYSIS WITH MULTISCALE SIMULATIONS... 

Abstract Description of a multiscale simulation strategy we have developed to attack problems... 

Keywords Ribozyme catalysis, multiscale simulation, linear-scaling method, QM/MM, DFT... 

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. 

Li, J., Ouyang, J., Gao, S., Ge, W., Yang, N. and Song, W., "Multiscale Simulation of Particle-Fluid Complex Systems (in Chinese)". Science Press, Beijing (2005). 

Goldenfeld, N., B.P. Athreya, and J.A. Dantzig. 2005. Renormalization group approach to multiscale simulation of polycrystalline materials using the phase field crystal model. Phys. Rev. E 72 1-4. 

In molecular models, a surface site is modeled using an analogous molecular reaction. This is the simplest approach, which requires the least amount of computational resources. The selection of a molecule that can more or less adequately reproduce the properties of the surface site under study determines the success or failure of the approach. This approach was used in Ref. [20] in the multiscale simulation of zirconium and hafnium oxide film growth. 

The development of multiscale simulation techniques that involve the atomistic modeling of various structures and processes still remains at its early stage. There are many problems to be solved associated with more accurate and detailed description of these structures and processes. These problems include the development of efficient and fast methods for quantum calculations at the atomistic level, the development of transferable interatomic potentials (especially, reactive potentials) for molecular dynamic simulations, and the development of strategies for the application of multiscale simulation methods to other important processes and materials (optical, magnetic, sensing, etc.). 

N. Choly et al Multiscale simulations in simple metals A density-functional-based methodology. Phys. Rev. B 71, 094101 (2005)... 

Heyden A, Lin H et al (2007) Adaptive partitioning in combined quantum mechanical and molecular mechanical calculations of potential energy functions for multiscale simulations. J Phys Chem B 111 2231... 

A. Onion-type Hybrid Multiscale Simulations and Algorithms 15... 

B. Application of Onion-type Hybrid Multiscale Simulation to Growth of Materials 17... 

Science in 2004 that have been dedicated to Complex Systems and Multi-scale Methodology, the forth issue of the 29th volume in Computers in Chemical Engineering on Multiscale Simulation published in 2005, the Springer-Verlag IMA edited book on Dispersive Transport Equations and Multiscale Models resulting from a related workshop, numerous workshops, and a topical conference on Multiscale Analysis in the 2005 AIChE meeting, just to mention a few. 

A hierarchy of models can often be derived from a more detailed model under certain assumptions. This approach was discussed above in the case of deterministic, continuum models (see Fig. 3a). Such hierarchical models can be valuable in multiscale modeling. Let us just mention two cases. First, one could use different models from a hierarchy of models for different situations or length scales. This approach plays a key role in hybrid multiscale simulation discussed extensively below. Second, one could easily apply systems tasks to a simpler model to obtain an approximate solution that is then refined by employing a more sophisticated, accurate, and expensive model from the hierarchy. 

Fig. 5. Schematic of onion-type hybrid multiscale simulation. At each scale a different model is used. Consecutive scale models are simultaneously solved in the overlap region where exchange of information occurs.

Below, the various types of multiscale simulation are elaborated and various examples are provided. The presentation on coarse graining is mainly focused on stochastic (KMC) simulations to provide the underlying foundations and ideas in some depth. Coarse graining of other atomistic, e.g., MD, and mesoscopic tools will be covered in a forthcoming communication. Some excellent reviews on coarse graining in soft-matter physics problems are available (e.g., Kremer and Muller-Plathe, 2001 Muller-Plathe, 2002, 2003 Nielsen et al., 2004). 

Hybrid multiscale simulation is the most developed branch of multiscale simulation and will be covered in this section. The onion-type hybrid simulation... 

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