Multiscale modelling dynamics

Weinan, E. Vanden-Eijnden, E., in Multiscale Modelling and Simulation, LNCSE 39, 2004 (chapter Metastability, conformation dynamics, and transition pathways in complex systems)... 

Figure 2. Multiscale modeling hierarchy. AIMD ab initio molecular dynamics, MD molecular dynamics, KMC kinetic Monte Carlo modeling, and FEA finite element analysis.

Buehler et al. presented a preliminary study on formation of water from molecular oxygen and hydrogen using a series of atomistic simulations based on ReaxFF MD method.111 They described the dynamics of water formation at a Pt catalyst. By performing this series of studies, we obtain statistically meaningful trajectories that permit to derive the reaction rate constants of water formation. However, the method requires calibrations with either ab initio simulation results in order to correctly evaluate the energetics of OER on Pt. Thus, this method is system specific and less reliable than the ab initio methods and will not replace ab initio methods. Nevertheless, this work demonstrates that atomistic simulation to continuum description can be linked with the ReaxFF MD in a hierarchical multiscale model. 

Hybrid multiscale models enable us to focus on the relevant part of a system. For example, Leenders et al. studied the proton transfer process in the photoactive yellow protein (Figure 6.3) [9], They used Car-Parrinello molecular dynamics [10], a QM method for dynamics simulations, to describe the chromophore and its hydrogen-bonded network in the protein pocket (middle and right-hand circles). This was combined with a traditional MD force field of 28 600 atoms, simulating the entire protein in water (left-hand circle). 

As the structure, dynamics and properties are determined by phenomena on many length and time scales physical modelling is subdivided into the quantum mechanical, atomistic, mesoscale, microscale and continuum levels, while research into the way in which these levels are linked is known as hierarchical or multiscale modelling. The typical structural levels arising in the polymer field are shown Figure 1. 

Multiscale Modelling in Molecular Dynamics Biomolecular Conformations as Metastable States ... 

E. Meerbach et al. Multiscale Modelling in Molecular Dynamics Biomolecular Conformations as Metastable States, Lect. Notes Phys. 703, 495-517 (2006)... 

Xue, M K.K. Droegemeier, and Wong, V. (2000) The Advanced Regional Prediction System (ARPS) - A multiscale nonhydrostatic atmospheric simulation and prediction tool. Part I Model dynamics and verification, Meteor. Atmos. Physics. 75, 161-193. 

---