Approximate and efficient calculation of dominant Lyapunov exponents of high-dimensional nonlinear dynamic systems

This short communication presents an efficient method for calculating dominant Lyapunov exponents (LEs) of high-dimensional nonlinear dynamic systems based on their reduced-order models obtained from the linear model reduction theory. Mathematical derivation shows that the LEs of the reduced-order models correspond to the dominant LEs of the original systems. Two numerical examples are provided to demonstrate the effectiveness of the method.     

C_(2~6)烯烃在H-ZSM-5分子筛周期性模型上吸附的理论研究

采用密度泛函理论中的PBE-D方法研究了C2~6直链烯烃以及丁烯异构体在H-ZSM-5分子筛周期性模型上的吸附行为。结果表明,对于C2~6直链烯烃,随着碳数的增加,烯烃的吸附能以-12 kJ/mol的常数线性增大,体系中色散校正能ED以-13 kJ/mol的常数线性增大,而不考虑范德华力的能量E*随碳数增加变化不大,只在C5和C6时由于空间阻力凸显而减小。ED显著大于E*,说明烯烃在分子筛孔道中吸附时范德华力起主要作用,且碳数增加其影响增大。丁烯异构体吸附能大小顺序为:反式-2-丁烯顺式-2-丁烯正丁烯异丁烯。正丁烯的3种异构体ED相近且都比正丁烯的大,3种异构体的吸附能差异由E*不同引起。差分电荷密度分析表明,烯烃双键与酸性中心之间有电子聚集,且聚集程度与π配位作用相一致,而且酸性中心H原子有质子化趋向,O原子及其周围电子增加。     

Conditionally Specified Space-Time Models for Multivariate Processes

This article proposes a class of conditionally specified models for the analysis of multivariate space-time processes. Such models are useful in situations where there is sparse spatial coverage of one of the processes and much more dense coverage of the other process(es). The dependence structure across processes and over space, and time is completely specified through a neighborhood structure. These models are applicable to both point and block sources; for example, multiple pollutant monitors (point sources) or several county-level exposures (block sources). We introduce several computational tricks that are integral for model fitting, give some simple sufficient and necessary conditions for the space-time covariance matrix to be positive definite, and implement a Gibbs sampler, using Hybrid MC steps, to sample from the posterior distribution of the parameters. Model fit is assessed via the DIC. Predictive accuracy, over both time and space, is assessed both relatively and absolutely via mean squared prediction error and coverage probabilities. As an illustration of these models, we fit them to particulate matter and ozone data collected in the Los Angeles, CA, area in 1995 over a three-month period. In these data, the spatial coverage of particulate matter was sparse relative to that of ozone.     

Estimating Precision in Functional Images

Abstract

Functional imaging of biologic parameters like in vivo tissue metabolism is made possible by Positron Emission Tomography (PET). Many techniques have been suggested for extracting such images from dynamic time-course sequences of reconstructed PET scans. Quantitating the precision of these estimates is important for drawing inferences on the biologic parameters. Analytic variance formulas are not immediate owing to the nonlinear methods used in extraction. The usual resampling approach is infeasible because each image reconstruction in PET is a computationally demanding solution to a high-dimensional linear inverse problem. We suggest an alternative simulation approach that approximates the distribution of reconstructed PET scans and performs a parametric bootstrap in the imaging domain. Results on a simplified model chosen to match the characteristics of PET reconstruction are very encouraging. Mixture analysis is used to estimate functional images; however, the suggested approach is general enough to extend to other techniques or imaging methods.     

Differential equation dynamical system based assessment model in GNSS interoperability

With the development of Global Navigation Satellite System (GNSS),the idea of GNSS interoperability is born and has become the focus of study in the field of satellite navigation.The popularity for GNSS to augment the interoperability with the existing ones necessitates the study of the assessment algorithm of this idea.In this paper,an assessment algorithm for interoperability comprehensive benefits based on the differential equation dynamical system is discussed.There are two important aspects in GNSS tha...     

A three‐dimensional Cartesian cut cell method for incompressible viscous flow with irregular domains

A three‐dimensional Cartesion cut cell method is presented for the simulations of incompressible viscous flows with irregular domains. A new model (referred to as ‘6+N’ model) is proposed to describe arbitrarily shaped cut cells and treat all the cells as polyhedrons with 6+N faces. The finite volume discretization of the Navier–Stokes equation is then implemented by using the ‘6+N’ model to separate the surface flux integrals into two parts, that is, the fluxes through the basic face of the hexahedron and those through the cutting surfaces. The previously proposed Kitta Cube algorithm and volume computer‐aided design platform (J. Comput. Aided. Des. 2005; 37(4): 1509–1520. Doi:10.1016/j.cad.2005.03.006) are adopted to generate cut cells and provide shape data and physical attributes for the numerical analysis. A modified SIMPLE‐based smoothing pressure correction scheme is applied to suppress checkerboard pressure oscillations caused by the collocated arrangement of velocities and pressure. The calculation accuracy of the numerical method expressed by L₁ and L _∞ norm errors is first demonstrated by the simulation of a pipe flow. Then its feasibility, efficiency, and potential in engineering applications are verified by applying it to solve natural convections between concentric spheres and between eccentric spheres. The heat transfer patterns in eccentric spheres are also obtained by using the numerical method. Copyright © 2011 John Wiley & Sons, Ltd.     

Exact Eigenfunctions of N-body System with Quadratic Pair Potential

We obtain the energy spectrum and all the corresponding eigenfunctions of N-body Bose and Fermi systems with Quadratic Pair Potentials in one dimension. The original first excited state or energy level is disappeared in one dimension, which results from the operation of symmetry or antisymmetry of identical particles. In two and higher dimensions, we give the energy spectrum and the analytical ground state wave functions and the degree of degeneracy. By comparison, we refine Avinash Khare's results by making some items in his article precisely.     

GPU‐accelerated direct numerical simulations of decaying compressible turbulence employing a GKM‐based solver

Gas Kinetic Method‐based flow solvers have become popular in recent years owing to their robustness in simulating high Mach number compressible flows. We evaluate the performance of the newly developed analytical gas kinetic method (AGKM) by Xuan et al. in performing direct numerical simulation of canonical compressible turbulent flow on graphical processing unit (GPU)s. We find that for a range of turbulent Mach numbers, AGKM results shows excellent agreement with high order accurate results obtained with traditional Navier–Stokes solvers in terms of key turbulence statistics. Further, AGKM is found to be more efficient as compared with the traditional gas kinetic method for GPU implementation. We present a brief overview of the optimizations performed on NVIDIA K20 GPU and show that GPU optimizations boost the speedup up‐to 40x as compared with single core CPU computations. Hence, AGKM can be used as an efficient method for performing fast and accurate direct numerical simulations of compressible turbulent flows on simple GPU‐based workstations. Copyright © 2016 John Wiley & Sons, Ltd.     

Using polarizable POSSIM force field and fuzzy‐border continuum solvent model to calculate pKa shifts of protein residues

Our Fuzzy‐Border (FB) continuum solvent model has been extended and modified to produce hydration parameters for small molecules using POlarizable Simulations Second‐order Interaction Model (POSSIM) framework with an average error of 0.136 kcal/mol. It was then used to compute pK _a shifts for carboxylic and basic residues of the turkey ovomucoid third domain (OMTKY3) protein. The average unsigned errors in the acid and base pK _a values were 0.37 and 0.4 pH units, respectively, versus 0.58 and 0.7 pH units as calculated with a previous version of polarizable protein force field and Poisson Boltzmann continuum solvent. This POSSIM/FB result is produced with explicit refitting of the hydration parameters to the pK _a values of the carboxylic and basic residues of the OMTKY3 protein; thus, the values of the acidity constants can be viewed as additional fitting target data. In addition to calculating pK _a shifts for the OMTKY3 residues, we have studied aspartic acid residues of Rnase Sa. This was done without any further refitting of the parameters and agreement with the experimental pK _a values is within an average unsigned error of 0.65 pH units. This result included the Asp79 residue that is buried and thus has a high experimental pK _a value of 7.37 units. Thus, the presented model is capable or reproducing pK _a results for residues in an environment that is significantly different from the solvated protein surface used in the fitting. Therefore, the POSSIM force field and the FB continuum solvent parameters have been demonstrated to be sufficiently robust and transferable. © 2016 Wiley Periodicals, Inc.     

A comparison of different approaches to integrate flamelet tables with presumed-shape PDF in flamelet models for turbulent flames

Flamelet models for turbulent combustion modelling make use of presumed-shape probability density functions (PDFs) for integrating laminar flamelet solutions to obtain an integrated flamelet table that can readily be used for turbulent flame calculations. The existence of non-unique approaches for such an integration has rarely been investigated before. For the first time, this work studies systematically the non-uniqueness of the flamelet table integration approaches. A flamelet model called the flamelet/progress variable model is used in the study, although the issue exists generally in many other flamelet models. Two classes of table integration approaches are investigated, one preserving the laminar flamelet structures during integration and the other not. Three different table integration approaches are examined and compared in detail to provide a thorough understanding of the different approaches. A partially stirred reactor is used as a test case for examining the different approaches. A method based on the transported PDF method is also employed to provide a reference for the assessment of the different flamelet table integration approaches. It is found in general that the flamelet preserving integration approach yields a more reasonable joint PDF of the mixture fraction and the progress variable, and the prediction results are closer to the referenced transported PDF results.