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Luo, Siwei

University of British Columbia

Coarse-grained (CG) models reduce the number of degrees of freedom in a system, allowing the dynamics of large systems to be studied for longer times. Many biological simulations today are performed using CG potentials. However, the use of Newtonian equations of motion (EOM) for mesoscopic variables only yields correct equilibrium properties but with the wrong dynamics. Conventional CG mapping schemes such as the center-of-mass mapping are also not suitable for coarse-graining nonbonded fluid systems. The conservative terms in the CG EOM derived using Mori-Zwanzig theory are studied. The fluid systems are divided into cubic subcells with equal volumes. Atomistic particles associated with a subcell are mapped to a set of position-dependent CG variables using either a Heaviside function or a fuzzy function. A diffusion blob model is developed to qualitatively understand the correlation between two subcells. The distribution of CG mass is found to change from symmetric and discrete to skewed and continuous. The form of the CG potential can be approximated as a multivariate Gaussian. Distribution function theory is used to derive the parameters of the CG potential analytically. The behaviour of the potential parameters as a function of different geometric relationships, the size of the subcell or the fuzziness of the subcell boundary, is discussed. A density-based expansion method is developed to quantitatively understand the behaviour of the one-dimensional distribution of CG variables. The origin of the skewed mass distribution comes from the asymmetry in the variance of CG mass distribution conditioned on a fixed number of atoms. The projected fluxes are studied with distribution function theory and Gaussian process regression. This work provides a basis for correctly simulating complex fluid systems at a mesoscopic scale without any ad-hoc assumptions. The Gaussian-like CG potential is general for single-component, atomic fluids. Parameters of a CG potential are, for the first time, computed from analytical theories. Understanding the source of the skewed mass gives a complete solution to finding the correct fluctuation for densities. This solves a long-standing problem in fluctuating hydrodynamics. The density-based expansion formula gives a complete solution to the back-mapping problem in performing multiscale simulations.

Text

2022-12-23

Attribution-NonCommercial-NoDerivatives 4.0 International

http://hdl.handle.net/2429/83509

Chemistry

University of British Columbia

UBCV

http://creativecommons.org/licenses/by-nc-nd/4.0/