The differentiation operator in the space of uniformly convergent Dirichlet series

Continuity, compactness, the spectrum and ergodic properties of the differentiation operator are investigated, when it acts in the Fréchet space of all Dirichlet series that are uniformly convergent in all half-planes for each . The properties of the formal inverse of the differentiation are also investigated.     

More efficient time integration for Fourier pseudospectral DNS of incompressible turbulence

Time integration of Fourier pseudospectral DNS is usually performed using the classical fourth-order accurate Runge-Kutta method or other second- or third-order methods, with a fixed step size. We investigate the use of higher-order Runge-Kutta pairs and automatic step size control based on local error estimation. We find that the fifth-order accurate Runge-Kutta pair of Bogacki and Shampine gives much greater accuracy at a significantly reduced computational cost. Specifically, we demonstrate speedups of 2× to 10× for the same accuracy. Numerical tests (including the Taylor-Green vortex, Rayleigh-Taylor instability, and homogeneous isotropic turbulence) confirm the reliability and efficiency of the method. We also show that adaptive time stepping provides a significant computational advantage for some problems (like the development of a Rayleigh-Taylor instability) without compromising accuracy.     

Accurate integration over atomic regions bounded by zero‐flux surfaces

The approach for the integration over a region covered by zero‐flux surface is described. This approach based on the surface triangulation technique is efficiently realized in a newly developed program TWOE . The elaborated method is tested on several atomic properties including the source function. TWOE results are compared with those produced by using well‐known existing programs. Absolute errors in computed atomic properties are shown to range usually from 10^?6 to 10^?5 au. The demonstrative examples prove that present realization has perfect convergence of atomic properties with increasing size of angular grid and allows to obtain highly accurate data even in the most difficult cases. It is believed that the developed program can be bridgehead that allows to implement atomic partitioning of any desired molecular property with high accuracy. © 2012 Wiley Periodicals, Inc.     

Higher-order time integration with a local Lax–Wendroff procedure for a central scheme on an overlapping grid

We have implemented a high-order Lax–Wendroff type time integration for a central scheme on an overlapping grid for conservation law problems. Using a local iterative approach presented by Dumbser et al. (JCP, 2008) [12], we extend a local high-order spatial reconstruction on each cell to a local higher-order space–time polynomial on the cell. We rewrite the central scheme in a fully discrete form to avoid volume integration in the space–time domain. The fluxes at cell interfaces are calculated directly via integrating a higher-order space–time reconstruction of the flux. We compare this approach with the corresponding multi-stage Runge–Kutta time integration (RK). Numerical results show that the new time integration is more cost-effective.     

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.     

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.