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.     

MOVIPAC: Vibrational spectroscopy with a robust meta‐program for massively parallel standard and inverse calculations

We present the software package MO VI PAC for calculations of vibrational spectra, namely infrared, Raman, and Raman Optical Activity (ROA) spectra, in a massively parallelized fashion. MO VI PAC unites the latest versions of the programs SNF and AKIRA alongside with a range of helpful add‐ons to analyze and interpret the data obtained in the calculations. With its efficient parallelization and meta‐program design, MO VI PAC focuses in particular on the calculation of vibrational spectra of very large molecules containing on the order of a hundred atoms. For this purpose, it also offers different subsystem approaches such as Mode‐ and Intensity‐Tracking to selectively calculate specific features of the full spectrum. Furthermore, an approximation to the entire spectrum can be obtained using the Cartesian Tensor Transfer Method. We illustrate these capabilities using the example of a large π‐helix consisting of 20 (S)‐alanine residues. In particular, we investigate the ROA spectrum of this structure and compare it to the spectra of α‐ and 3₁₀‐helical analogs. © 2012 Wiley Periodicals, Inc.     

Modern information technologies in construction of kinetic models for reactions of metal complex catalysis

For detailed study of complex chemical reactions mechanisms experiment is conducted for selected private reactions. This causes a problem of kinetic parameters getting—the same set of rate constants must describe both public and private reaction stages, and also a general mechanism. In this paper, solution of this problem for a reaction of olefins hydroalumination is proposed. To optimize the computational process a methodology of parallelization is elaborated. On the base of parallel computations, a kinetic model for the reaction assigned is constructed, and on its base, the physical and chemical conclusions about reaction mechanism are done.     

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.     

Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi

Due to the enormous importance of electrostatics in molecular biology, calculating the electrostatic potential and corresponding energies has become a standard computational approach for the study of biomolecules and nano‐objects immersed in water and salt phase or other media. However, the electrostatics of large macromolecules and macromolecular complexes, including nano‐objects, may not be obtainable via explicit methods and even the standard continuum electrostatics methods may not be applicable due to high computational time and memory requirements. Here, we report further development of the parallelization scheme reported in our previous work (Li, et al., J. Comput. Chem. 2012, 33, 1960) to include parallelization of the molecular surface and energy calculations components of the algorithm. The parallelization scheme utilizes different approaches such as space domain parallelization, algorithmic parallelization, multithreading, and task scheduling, depending on the quantity being calculated. This allows for efficient use of the computing resources of the corresponding computer cluster. The parallelization scheme is implemented in the popular software DelPhi and results in speedup of several folds. As a demonstration of the efficiency and capability of this methodology, the electrostatic potential, and electric field distributions are calculated for the bovine mitochondrial supercomplex illustrating their complex topology, which cannot be obtained by modeling the supercomplex components alone. © 2013 Wiley Periodicals, Inc.     

PHI: A powerful new program for the analysis of anisotropic monomeric and exchange‐coupled polynuclear d‐ and f‐block complexes

A new program, PHI, with the ability to calculate the magnetic properties of large spin systems and complex orbitally degenerate systems, such as clusters of d‐block and f‐block ions, is presented. The program can intuitively fit experimental data from multiple sources, such as magnetic and spectroscopic data, simultaneously. PHI is extensively parallelized and can operate under the symmetric multiprocessing, single process multiple data, or GPU paradigms using a threaded, MPI or GPU model, respectively. For a given problem PHI is been shown to be almost 12 times faster than the well‐known program MAGPACK, limited only by available hardware. © 2013 Wiley Periodicals, Inc.     

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.