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.     

谈图书馆的数字资源整合

论述了数字资源整合的概念、意义,分析了数字资源整合中存在的问题,提出了若干有关数字资源整合的建议.     

对“机电一体化”发展的研究

随着科技的高速发展,机电一体化的发展是必然的结果。下面,对国内外机电一体化的现状和发展作一下分析。     

浅析PSC海事安全标准的发展及执行(英文)

通过介绍港口国控制、全球主要港口国控制组织的基本情况和PSC法律基础的国际海事安全标准的发展,对比分析东京备忘录和巴黎备忘录在港口国监督年度报告中关于海事安全标准执行情况的数据,得到国际海事安全标准的发展趋势,提出对船东和有关当局的挑战.     

Well/Ill Posedness for the Euler-Korteweg-Poisson System and Related Problems

We consider a general Euler-Korteweg-Poisson system in R ³, supplemented with the space periodic boundary conditions, where the quantum hydrodynamics equations and the classical fluid dynamics equations with capillarity are recovered as particular examples. We show that the system admits infinitely many global-in-time weak solutions for any sufficiently smooth initial data including the case of a vanishing initial density - the vacuum zones. Moreover, there is a vast family of initial data, for which the Cauchy problem possesses infinitely many dissipative weak solutions, i.e. the weak solutions satisfying the energy inequality. Finally, we establish the weak-strong uniqueness property in a class of solutions without vacuum. In this paper we show that, even in presence of a dispersive tensor, we have the same phenomena found by De Lellis and Székelyhidi.     

FEW: A workflow tool for free energy calculations of ligand binding

In the later stages of drug design projects, accurately predicting relative binding affinities of chemically similar compounds to a biomolecular target is of utmost importance for making decisions based on the ranking of such compounds. So far, the extensive application of binding free energy approaches has been hampered by the complex and time‐consuming setup of such calculations. We introduce the free energy workflow (FEW) tool that facilitates setup and execution of binding free energy calculations with the AMBER suite for multiple ligands. FEW allows performing free energy calculations according to the implicit solvent molecular mechanics (MM‐PB(GB)SA), the linear interaction energy, and the thermodynamic integration approaches. We describe the tool's architecture and functionality and demonstrate in a show case study on Factor Xa inhibitors that the time needed for the preparation and analysis of free energy calculations is considerably reduced with FEW compared to a fully manual procedure. © 2013 Wiley Periodicals, Inc.     

Comparative assessment of computational methods for the determination of solvation free energies in alcohol‐based molecules

The determination of differences in solvation free energies between related drug molecules remains an important challenge in computational drug optimization, when fast and accurate calculation of differences in binding free energy are required. In this study, we have evaluated the performance of five commonly used polarized continuum model (PCM) methodologies in the determination of solvation free energies for 53 typical alcohol and alkane small molecules. In addition, the performance of these PCM methods, of a thermodynamic integration (TI) protocol and of the Poisson–Boltzmann (PB) and generalized Born (GB) methods, were tested in the determination of solvation free energies changes for 28 common alkane‐alcohol transformations, by the substitution of an hydrogen atom for a hydroxyl substituent. The results show that the solvation model D (SMD) performs better among the PCM‐based approaches in estimating solvation free energies for alcohol molecules, and solvation free energy changes for alkane‐alcohol transformations, with an average error below 1 kcal/mol for both quantities. However, for the determination of solvation free energy changes on alkane‐alcohol transformation, PB and TI yielded better results. TI was particularly accurate in the treatment of hydroxyl groups additions to aromatic rings (0.53 kcal/mol), a common transformation when optimizing drug‐binding in computer‐aided drug design. © 2013 Wiley Periodicals, Inc.     

Integrating open‐source software applications to build molecular dynamics systems

Three open‐source applications, NanoEngineer‐1, packmol, and mis2lmp are integrated using an open‐source file format to quickly create molecular dynamics (MD) cells for simulation. The three software applications collectively make up the open‐source software (OSS) suite known as MD Studio (MDS). The software is validated through software engineering practices and is verified through simulation of the diglycidyl ether of bisphenol‐a and isophorone diamine (DGEBA/IPD) system. Multiple simulations are run using the MDS software to create MD cells, and the data generated are used to calculate density, bulk modulus, and glass transition temperature of the DGEBA/IPD system. Simulation results compare well with published experimental and numerical results. The MDS software prototype confirms that OSS applications can be analyzed against real‐world research requirements and integrated to create a new capability. © 2014 Wiley Periodicals, Inc.