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This paper investigates the error analysis of a mixed finite element method with Crank-Nicolson time-stepping for simulating the molecular beam epitaxy (MBE) model. The fourth-order differential equation of the MBE model is replaced by a system of equations consisting of one nonlinear parabolic equation and an elliptic equation. Then a mixed finite element method requiring only continuous elements is proposed to approximate the resulting system. It is proved that the semidiscrete and fully discrete versions of the numerical schemes satisfy the nonlinearity energy stability property, which is important in the numerical implementation. Moreover, detailed analysis is provided to obtain the convergence rate. Numerical experiments are carried out to validate the theoretical results. © 2015 Society for Industrial and Applied Mathematics.