Showing papers by "Guo-Wei Wei published in 2009"

Geometric and potential driving formation and evolution of biomolecular surfaces

Abstract: This paper presents new geometrical flow equations for the theoretical modeling of biomolecular surfaces in the context of multiscale implicit solvent models. To account for the local variations near the biomolecular surfaces due to interactions between solvent molecules, and between solvent and solute molecules, we propose potential driven geometric flows, which balance the intrinsic geometric forces that would occur for a surface separating two homogeneous materials with the potential forces induced by the atomic interactions. Stochastic geometric flows are introduced to account for the random fluctuation and dissipation in density and pressure near the solvent–solute interface. Physical properties, such as free energy minimization (area decreasing) and incompressibility (volume preserving), are realized by some of our geometric flow equations. The proposed approach for geometric and potential forces driving the formation and evolution of biological surfaces is illustrated by extensive numerical experiments and compared with established minimal molecular surfaces and molecular surfaces. Local modification of biomolecular surfaces is demonstrated with potential driven geometric flows. High order geometric flows are also considered and tested in the present work for surface generation. Biomolecular surfaces generated by these approaches are typically free of geometric singularities. As the speed of surface generation is crucial to implicit solvent model based molecular dynamics, four numerical algorithms, a semi-implicit scheme, a Crank–Nicolson scheme, and two alternating direction implicit (ADI) schemes, are constructed and tested. Being either stable or conditionally stable but admitting a large critical time step size, these schemes overcome the stability constraint of the earlier forward Euler scheme. Aided with the Thomas algorithm, one of the ADI schemes is found to be very efficient as it balances the speed and accuracy.

Matched interface and boundary (MIB) for the implementation of boundary conditions in high‐order central finite differences

Abstract: High-order central finite difference schemes encounter great difficulties in implementing complex boundary conditions. This paper introduces the matched interface and boundary (MIB) method as a novel boundary scheme to treat various general boundary conditions in arbitrarily high-order central finite difference schemes. To attain arbitrarily high order, the MIB method accurately extends the solution beyond the boundary by repeatedly enforcing only the original set of boundary conditions. The proposed approach is extensively validated via boundary value problems, initial-boundary value problems, eigenvalue problems, and high-order differential equations. Successful implementations are given to not only Dirichlet, Neumann, and Robin boundary conditions, but also more general ones, such as multiple boundary conditions in high-order differential equations and time-dependent boundary conditions in evolution equations. Detailed stability analysis of the MIB method is carried out. The MIB method is shown to be able to deliver high-order accuracy, while maintaining the same or similar stability conditions of the standard high-order central difference approximations. The application of the proposed MIB method to the boundary treatment of other non-standard high-order methods is also considered.

Matched interface and boundary (MIB) method for the vibration analysis of plates

Abstract: This paper proposes a novel approach, the matched interface and boundary (MIB) method, for the vibration analysis of rectangular plates with simply supported, clamped and free edges, and their arbitrary combinations. In previous work, the MIB method was developed for three-dimensional elliptic equations with arbitrarily complex material interfaces and geometric shapes. The present work generalizes the MIB method for eigenvalue problems in structural analysis with complex boundary conditions. The MIB method utilizes both uniform and non-uniform Cartesian grids. Fictitious values are utilized to facilitate the central finite difference schemes throughout the entire computational domain. Boundary conditions are enforced with fictitious values—a common practice used in the previous discrete singular convolution algorithm. An essential idea of the MIB method is to repeatedly use the boundary conditions to achieve arbitrarily high-order accuracy. A new feature in the proposed approach is the implementation of the cross derivatives in the free boundary conditions. The proposed method has a banded matrix. Nine different plates, particularly those with free edges and free corners, are employed to validate the proposed method. The performance of the proposed method is compared with that of other established methods. Convergence and comparison studies indicate that the proposed MIB method works very well for the vibration analysis of plates. In particular, modal bending moments and shear forces predicted by the proposed method vanish at boundaries for free edges. Copyright © 2008 John Wiley & Sons, Ltd.

On the accuracy and stability of a variety of differential quadrature formulations for the vibration analysis of beams

Abstract: The occurrence of spurious complex eigenvalues is a serious stability problem in many differential quadrature methods (DQMs). This paper studies the accuracy and stability of a variety of different differential quadrature formulations. Special emphasis is given to two local DQMs. One utilizes both fictitious grids and banded matrices, called local adaptive differential quadrature method (LaDQM). The other has banded matrices without using fictitious grids to facilitate boundary conditions, called finite difference differential quadrature methods (FDDQMs). These local DQMs include the classic DQMs as special cases given by extending their banded matrices to full matrices. LaDQMs and FDDQMs are implemented on a variety of treatments of boundary conditions, distributions of grids (i.e., uniform grids and Chebyshev grids), and lengths of stencils. A comprehensive comparison among these methods over beams of six different combinations of supporting edges sheds light on the stability and accuracy of DQMs.

Computational methods for optical molecular imaging.

Abstract: A new computational technique, the matched interface and boundary (MIB) method, is presented to model the photon propagation in biological tissue for the optical molecular imaging. Optical properties have significant differences in different organs of small animals, resulting in discontinuous coefficients in the diffusion equation model. Complex organ shape of small animal induces singularities of the geometric model as well. The MIB method is designed as a dimension splitting approach to decompose a multidimensional interface problem into one-dimensional ones. The methodology simplifies the topological relation near an interface and is able to handle discontinuous coefficients and complex interfaces with geometric singularities. In the present MIB method, both the interface jump condition and the photon flux jump conditions are rigorously enforced at the interface location by using only the lowest-order jump conditions. This solution near the interface is smoothly extended across the interface so that central finite difference schemes can be employed without the loss of accuracy. A wide range of numerical experiments are carried out to validate the proposed MIB method. The second-order convergence is maintained in all benchmark problems. The fourth-order convergence is also demonstrated for some three-dimensional problems. The robustness of the proposed method over the variable strength of the linear term of the diffusion equation is also examined. The performance of the present approach is compared with that of the standard finite element method. The numerical study indicates that the proposed method is a potentially efficient and robust approach for the optical molecular imaging.

Special issue on recent advances in computational techniques for biomedical imaging

Abstract: SUMMARY A total of 12 papers in the area of mathematical methods and computational techniques for biomedical imaging and image analysis are presented in this special issue. Copyright q 2009 John Wiley & Sons, Ltd.