Iterative operator-splitting methods with higher-order time integration methods and applications for parabolic partial differential equations

In this paper we design higher-order time integrators for systems of stiff ordinary differential equations. We combine implicit Runge–Kutta and BDF methods with iterative operator-splitting methods to obtain higher-order methods. The idea of decoupling each complicated operator in simpler operators with an adapted time scale allows to solve the problems more efficiently. We compare our new methods with the higher-order fractional-stepping Runge–Kutta methods, developed for stiff ordinary differential equations. The benefit is the individual handling of each operator with adapted standard higher-order time integrators. The methods are applied to equations for convection–diffusion reactions and we obtain higher-order results. Finally we discuss the applications of the iterative operator-splitting methods to multi-dimensional and multi-physical problems.     

Achieving Brouwer’s law with implicit Runge–Kutta methods

In high accuracy long-time integration of differential equations, round-off errors may dominate truncation errors. This article studies the influence of round-off on the conservation of first integrals such as the total energy in Hamiltonian systems. For implicit Runge–Kutta methods, a standard implementation shows an unexpected propagation. We propose a modification that reduces the effect of round-off and shows a qualitative and quantitative improvement for an accurate integration over long times. AMS subject classification (2000)  65L06, 65G50, 65P10     

Characterizing PSPACE with pointers

This paper gives an implicit characterization of the class of functions computable in polynomial space by deterministic Turing machines – PSPACE. It gives an inductive characterization of PSPACE with no ad‐hoc initial functions and with only one recursion scheme. The main novelty of this characterization is the use of pointers (also called path information) to reach PSPACE. The presence of the pointers in the recursion on notation scheme is the main difference between this characterization of PSPACE and the well‐known Bellantoni‐Cook characterization of the polytime functions – PTIME. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

用摄动配置方法求解含时薛定谔方程

将摄动配置方法应用到含时薛定谔方程,在计算实现的基础上结合摄动配置的特征提出了一类新的数值积分方法,并给出了一个2级2阶和一个3级4阶的辛摄动配置方法对含时薛定谔方程的数值算例.为了检验新的数值积分方法,我们还给出了与两个辛摄动配置格式在理论上等价的辛龙格-库塔方法以及同阶的非辛方法的数值模拟.展示了一些数值结果,并给出了一些分析.     

Accelerating molecular dynamic simulation on graphics processing units

We describe a complete implementation of all‐atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Lattice-Boltzmann type relaxation systems and high order relaxation schemes for the incompressible Navier-Stokes equations

A relaxation system based on a Lattice-Boltzmann type discrete velocity model is considered in the low Mach number limit. A third order relaxation scheme is developed working uniformly for all ranges of the mean free path and Mach number. In the incompressible Navier-Stokes limit the scheme reduces to an explicit high order finite difference scheme for the incompressible Navier-Stokes equations based on nonoscillatory upwind discretization. Numerical results and comparisons with other approaches are presented for several test cases in one and two space dimensions.

     

渐近φ伪压缩映象有限族的迭代程序的强收敛(英文)

Strong convergence theorems for approximation of common fixed points of asymptoticallyφ-quasi-pseudocontractive mappings and asymptoticallyφ-strictly- pseudocontractive mappings are proved in real Banach spaces by using a new compos- ite implicit iteration scheme with errors.The results presented in this paper extend and improve the main results of Sun,Gu and Osilike published on J.Math.Anal. Appl.     

平面叶栅跨音流场气动特性的数值研究

通过对模型方程的分析，给出了一种新的隐格式构造思想。将它运用到关通量分裂格式中，可得到无近似因子分解、无矩阵运算的高效二阶精度隐式矢通量分裂差分格式，并用来直接求解时间平均Ｎａｖｉｅｒ－Ｓｔｏｋｅｓ方程组。数值计算标明：该方法具有精度高、稳定性好、计算量少、收敛快等优点，在平面叶栅跨音流场的计算中，较好地捕获了激波，与实验比较，结果令人满意。     

An N log N approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions

Presented here is a method, the hierarchical charge partitioning (HCP) approximation, for speeding up computation of pairwise electrostatic interactions in biomolecular systems. The approximation is based on multiple levels of natural partitioning of biomolecular structures into a hierarchical set of its constituent structural components. The charge distribution in each component is systematically approximated by a small number of point charges, which, for the highest level component, are much fewer than the number of atoms in the component. For short distances from the point of interest, the HCP uses the full set of atomic charges available. For long‐distance interactions, the approximate charge distributions with smaller sets of charges are used instead. For a structure consisting of N charges, the computational cost of computing the pairwise interactions via the HCP scales as O(N log N), under assumptions about the structural organization of biomolecular structures generally consistent with reality. A proof‐of‐concept implementation of the HCP shows that for large structures it can lead to speed‐up factors of up to several orders of magnitude relative to the exact pairwise O(N²) all‐atom computation used as a reference. For structures with more than 2000–3000 atoms the relative accuracy of the HCP (relative root‐mean‐square force error per atom), approaches the accuracy of the particle mesh Ewald (PME) method with parameter settings typical for biomolecular simulations. When averaged over a set of 600 representative biomolecular structures, the relative accuracies of the two methods are roughly equal. The HCP is also significantly more accurate than the spherical cutoff method. The HCP has been implemented in the freely available nucleic acids builder (NAB) molecular dynamics (MD) package in Amber tools. A 10 ns simulation of a small protein indicates that the HCP based MD simulation is stable, and that it can be faster than the spherical cutoff method. A critical benefit of the HCP approximation is that it is algorithmically very simple, and unlike the PME, the HCP is straightforward to use with implicit solvent models. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010