A Computational Model of Protein Induced Membrane Morphology with Geodesic Curvature Driven Protein-Membrane Interface

Continuum or hybrid modeling of bilayer membrane morphological dynamics induced by embedded proteins necessitates the identification of protein-membrane interfaces and coupling of deformations of two surfaces. In this article we developed (i) a minimal total geodesic curvature model to describe these interfaces, and (ii) a numerical one-one mapping between two surface through a conformal mapping of each surface to the common middle annulus. Our work provides the first computational tractable approach for determining the interfaces between bilayer and embedded proteins. The one-one mapping allows a convenient coupling of the morphology of two surfaces. We integrated these two new developments into the energetic model of protein-membrane interactions, and developed the full set of numerical methods for the coupled system. Numerical examples are presented to demonstrate (1) the efficiency and robustness of our methods in locating the curves with minimal total geodesic curvature on highly complicated protein surfaces, (2) the usefulness of these interfaces as interior boundaries for membrane deformation, and (3) the rich morphology of bilayer surfaces for different protein-membrane interfaces

Unconditionally Energy Stable Linear Schemes for a Two-Phase Diffuse Interface Model with Peng-Robinson Equation of State

Many problems in the fields of science and engineering, particularly in materials science and fluid dynamic, involve flows with multiple phases and components. From mathematical modeling point of view, it is a challenge to perform numerical simulations of multiphase flows and study interfaces between phases, due to the topological changes, inherent nonlinearities and complexities of dealing with moving interfaces. In this work, we investigate numerical solutions of a diffuse interface model with Peng-Robinson equation of state. Based on the invariant energy quadratization approach, we develop first and second order time stepping schemes to solve the liquid-gas diffuse interface problems for both pure substances and their mixtures. The resulting temporal semi-discretizations from both schemes lead to linear systems that are symmetric and positive definite at each time step, therefore they can be numerically solved by many efficient linear solvers. The unconditional energy stabilities in the discrete sense are rigorously proven, and various numerical simulations in two and three dimensional spaces are presented to validate the accuracies and stabilities of the proposed linear schemes

Decoupled, Linear, and Energy Stable Finite Element Method for the Cahn-Hilliard-Navier-Stokes-Darcy Phase Field Model

In this paper, we consider the numerical approximation for a phase field model of the coupled two-phase free flow and two-phase porous media flow. This model consists of Cahn—Hilliard—Navier—Stokes equations in the free flow region and Cahn—Hilliard—Darcy equations in the porous media region that are coupled by seven interface conditions. The coupled system is decoupled based on the interface conditions and the solution values on the interface from the previous time step. A fully discretized scheme with finite elements for the spatial discretization is developed to solve the decoupled system. In order to deal with the difficulties arising from the interface conditions, the decoupled scheme needs to be constructed appropriately for the interface terms, and a modified discrete energy is introduced with an interface component. Furthermore, the scheme is linearized and energy stable. Hence, at each time step one need only solve a linear elliptic system for each of the two decoupled equations. Stability of the model and the proposed method is rigorously proved. Numerical experiments are presented to illustrate the features of the proposed numerical method and verify the theoretical conclusions. © 2018 Society for Industrial and Applied Mathematics