Langevin and Brownian dynamics are often used to model the motion of particles in the molecular mechanics/continuum mechanics (MM/CM) model, which is one of the most popular multi-scale model. Limitations of the Langevin/Brownian dynamics algorithms are obvious. One is that the solvent influence to the solute dyanmics is assumed to be independent of solute conformation, but the conformations of biomolecules are quite flexible. Another one is that all atoms of biomolecules are assumed to be 100% surrounded by the solvent, i.e. the solvent dragging force and the stochastic term are applied to all atoms, which is not a good approximation since buried atoms only interact with solute atoms. In addition all atoms are unrealistically assumed to be of the same size. These approximations often lead to incorrect dynamics or sampling of biomolecular conformations. Finally an important feature lacking in many Langevin and Brownian dynamics studies is the hydrodynamic effect, a must in the studies of many biochemical processes that are diffusion-dorminant. In this study we are exploring a more physical approach for the MM/CM model to address the above limitations. Specifically, the Navier-Stokes equation or the Stokes equation is used to simulate the continuum solvent as a fluid and is coupled to the Newtonian equation for the particle-based biomolecular solute. This poster summarizes our work to develop numerical methods for simulations of both fluid dynamics (FD) region and molecule dynamics (MD) region, formulate a rigorous theory for the force calculations on the FD/MD interface, and finally develop a particle-particle particle-mesh (P3M) algorithm for full electrostatic interactions within the full nonlinear Poisson-Boltzmann model.

Multi-resolution model for biomolecular application

251st National Meeting (2016)

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