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In this article, we discuss the stability of soft quasicrystalline phases in a coupled-mode Swift-Hohenberg model for three-component systems, where the characteristic length scales are governed by the positive-definite gradient terms. Classic two-mode approximation method and direct numerical minimization are applied to the model. In the latter approach, we apply the projection method to deal with the potentially quasiperiodic ground states. A variable cell method of optimizing the shape and size of higher-dimensional periodic cell is developed to minimize the free energy with respect to the order parameters. Based on the developed numerical methods, we rediscover decagonal and dodecagonal quasicrystalline phases, and find diverse periodic phases and complex modulated phases. Furthermore, phase diagrams are obtained in various phase spaces by comparing the free energies of different candidate structures. It does show not only the important roles of system parameters, but also the effect of optimizing computational domain. In particular, the optimization of computational cell allows us to capture the ground states and phase behavior with higher fidelity. We also make some discussions on our results and show the potential of applying our numerical methods to a larger class of mean-field free energy functionals.
Mesh generation is a bottleneck for finite element simulations of biomolecules. A robust and efficient approach, based on the immersed boundary method proposed in , has been developed and implemented to generate large-scale mesh body-fitted to molecular shape for general parallel finite element simulations. The molecular Gaussian surface is adopted to represent the molecular surface, and is finally approximated by piecewise planes via the tool phgSurfaceCut in PHG , which is improved and can reliably handle complicated molecular surfaces, through mesh refinement steps. A coarse background mesh is imported first and then is distributed into each process using a mesh partitioning algorithm such as space filling curve  or METIS . A bisection method is used for the mesh refinements according to the molecular PDB or PQR file which describes the biomolecular region. After mesh refinements, the mesh is optionally repartitioned and redistributed for load balancing. For finite element simulations, the modification of region mark and boundary types is done in parallel. Our parallel mesh generation method has been successfully applied to a sphere cavity model, a DNA fragment, a gramicidin A channel and a huge Dengue virus system. The results of numerical experiments show good parallel efficiency. Computations of electrostatic potential and solvation energy also validate the method. Moreover, the meshing process and adaptive finite element computation can be integrated as one PHG project to avoid the mesh importing and exporting costs, and improve the convenience of application as well.
In this paper a three-step scheme is applied to solve the Camassa-Holm (CH) shallow water equation. The differential order of the CH equation has been reduced in order to facilitate development of numerical scheme in a comparatively smaller grid stencil. Here a three-point seventh-order spatially accurate upwinding combined compact difference (CCD) scheme is proposed to approximate the firstorder derivative term. We conduct modified equation analysis on the CCD scheme and eliminate the leading discretization error terms for accurately predicting unidirectional wave propagation. The Fourier analysis is carried out as well on the proposed numerical scheme to minimize the dispersive error. For preserving Hamiltonians in Camassa- Holm equation, a symplecticity conserving time integrator has been employed. The other main emphasis of the present study is the use of u–P–α formulation to get nondissipative CH solution for peakon-antipeakon and soliton-anticuspon head-on wave collision problems.
In order to solve the partial differential equations that arise in the Hartree- Fock theory for diatomicmolecules and inmolecular theories that include electron correlation, one needs efficient methods for solving partial differential equations. In this article, we present numerical results for a two-variablemodel problem of the kind that arises when one solves the Hartree-Fock equations for a diatomic molecule. We compare results obtained using the spline collocation and domain decomposition methods with third-order Hermite splines to results obtained using the more-established finite difference approximation and the successive over-relaxation method. The theory of domain decomposition presented earlier is extended to treat regions that are divided into an arbitrary number of subregions by families of lines parallel to the two coordinate axes. While the domain decomposition method and the finite difference approach both yield results at the micro-Hartree level, the finite difference approach with a 9- point difference formula produces the same level of accuracy with fewer points. The domain decompositionmethod has the strength that it can be applied to problemswith a large number of grid points. The time required to solve a partial differential equation for a fine grid with a large number of points goes down as the number of partitions increases. The reason for this is that the length of time necessary for solving a set of linear equations in each subregion is very much dependent upon the number of equations. Even though a finer partition of the region has more subregions, the time for solving the set of linear equations in each subregion is very much smaller. This feature of the theory may well prove to be a decisive factor for solving the two-electron pair equation, which – for a diatomic molecule – involves solving partial differential equations with five independent variables. The domain decomposition theory also makes it possible to study complex molecules by dividing them into smaller fragments that are calculated independently. Since the domain decomposition approachmakes it possible to decompose the variable space into separate regions in which the equations are solved independently, this approach is well-suited to parallel computing.
A multigrid method is proposed to compute the ground state solution of Bose-Einstein condensations by the finite element method based on the multilevel correction for eigenvalue problems and the multigrid method for linear boundary value problems. In this scheme, obtaining the optimal approximation for the ground state solution of Bose-Einstein condensates includes a sequence of solutions of the linear boundary value problems by the multigrid method on the multilevel meshes and some solutions of nonlinear eigenvalue problems some very low dimensional finite element space. The total computational work of this scheme can reach almost the same optimal order as solving the corresponding linear boundary value problem. Therefore, this type of multigrid scheme can improve the overall efficiency for the simulation of Bose-Einstein condensations. Some numerical experiments are provided to validate the efficiency of the proposed method.
In the late stage of the mitotic cycle of eukaryotic cells, cytokinesis ensues during which a parent cell replicates its nucleus with the necessary genetical substances (i.e., DNAs and chromosomes) and splits into two similar offspring cells. This mitotic process involves complex chemical, biophysical andmechanical processes whose details are just beginning to be unfolded experimentally. In this paper, we propose a full 3-D hydrodynamical model using a phase field approach to study the cellular morphological change during cytokinesis. In this model, the force along the contracting ring induced by remodeling of actin-myosin filament on cell cortex layer at the division plane of the parent cell during cytokinesis, is approximated using a proxy force anchored on the newly formed nuclei. The symmetric or asymmetric cell division is simulated numerically with the model. Our numerical results show that the location of the division plane and the contracting force along the cytokinetic ring on the division plane are essential for the cell division. In addition, our numerical study also shows that, during cytokinesis, surface tension of the cell membrane also contributes to this process by retaining the morphological integrity of the offspring cells. This model and the accompanying numerical simulation tool provide a solid framework to build upon with more sophisticated whole cell models to probe the cell mitotic process.
We apply the immersed boundary (or IB) method to simulate deformation and detachment of a periodic array of wall-bounded biofilm colonies in response to a linear shear flow. The biofilm material is represented as a network of Hookean springs that are placed along the edges of a triangulation of the biofilm region. The interfacial shear stress, lift and drag forces acting on the biofilm colony are computed by using fluid stress jump method developed by Williams, Fauci and Gaver [Disc. Con-tin. Dyn. Sys. B 11(2):519–540, 2009], with a modified version of their exclusion filter. Our detachment criterion is based on the novel concept of an averaged equivalent continuum stress tensor defined at each IB point in the biofilm which is then used to determine a corresponding von Mises yield stress; wherever this yield stress exceeds a given critical threshold the connections to that node are severed, thereby signalling the onset of a detachment event. In order to capture the deformation and detachment behaviour of a biofilm colony at different stages of growth, we consider a family of four biofilm shapes with varying aspect ratio. For each aspect ratio, we varied the spacing between colonies to investigate role of spatial clustering in offering protection against detachment. Our numerical simulations focus on the behaviour of weak biofilms (with relatively low yield stress threshold) and investigate features of the fluid-structure interaction such as locations of maximum shear and increased drag. The most important conclusions of this work are: (a) reducing the spacing between colonies reduces drag by from 50 to 100% and alters the interfacial shear stress profile, suggesting that even weak biofilms may be able to grow into tall structures because of the protection they gain from spatial proximity with other colonies; (b) the commonly employed detachment strategy in biofilm models based only on interfacial shear stress can lead to incorrect or inaccurate results when applied to the study of shear induced detachment of weak biofilms. Our detachment strategy based on equivalent continuum stresses provides a unified and consistent IB framework that handles both sloughing and erosion modes of biofilm detachment, and is consistent with strategies employed in many other continuum based biofilm models.
A finite difference method which is second-order accurate in time and in space is proposed for two-dimensional fractional percolation equations. Using the Fourier transform, a general approximation for the mixed fractional derivatives is analyzed. An approach based on the classical Crank-Nicolson scheme combined with the Richardson extrapolation is used to obtain temporally and spatially second-order accurate numerical estimates. Consistency, stability and convergence of the method are established. Numerical experiments illustrating the effectiveness of the theoretical analysis are provided.
The Von Mises quasi-linear second order wave equation, which completely describes an irrotational, compressible and barotropic classical perfect fluid, can be derived from a nontrivial least action principle for the velocity scalar potential only, in contrast to existing analog formulations which are expressed in terms of coupled density and velocity fields. In this article, the classicalHamiltonian field theory specifically associated to such an equation is developed in the polytropic case and numerically verified in a simplified situation. The existence of such a mathematical structure suggests new theoretical schemes possibly useful for performing numerical integrations of fluid dynamical equations. Moreover it justifies possible new functional forms for Lagrangian densities and associated Hamiltonian functions in other theoretical classical physics contexts.
Neighbour search (NS) is the core of any implementations of smoothed particle hydrodynamics (SPH). In this paper,we present an efficient neighbour search method based on the plane sweep (PW) algorithm with N being the number of SPH particles. The resulting method, dubbed the PWNS method, is totally independent of grids (i.e., purely meshfree) and capable of treating variable smoothing length, arbitrary particle distribution and heterogenous kernels. Several state-of-the-art data structures and algorithms, e.g., the segment tree and the Morton code, are optimized and implemented. By simply allowingmultiple lines to sweep the SPH particles simultaneously from different initial positions, a parallelization of the PWNS method with satisfactory speedup and load-balancing can be easily achieved. That is, the PWNS SPH solver has a great potential for large scale fluid dynamics simulations.
We develop numerical methods for the simulation of laden-flows where particles interact with the carrier fluid through drag forces. Semi-Lagrangian techniques are presented to handle the Vlasov-type equation which governs the evolution of the particles. We discuss several options to treat the coupling with the hydrodynamic system describing the fluid phase, paying attention to strategies based on staggered discretizations of the fluid velocity.