Eulerian spatial and temporal autocorrelations: assessment of Taylor's hypothesis and a model

We present measurements of Eulerian longitudinal velocity autocorrelations in homogeneous, isotropic, high-intensity (～9%) free-stream turbulence behind an active grid. Spatial correlations are measured using particle image velocimetry as well as with two-point hot-wire anemometry (HWA), while temporal correlations are measured using HWA. The temporal correlations are transformed into spatial correlations by using Taylor's ‘frozen’ hypothesis with both the mean as well as instantaneous velocities. A model relating Eulerian spatial and temporal autocorrelations is also used for this purpose. The differences from the measured spatial correlation resulting from the use of Taylor's hypothesis on the temporal correlation is quantified; even at this moderately high level of turbulent intensity, the result from the use of the instantaneous velocity as convection velocity is practically indistinguishable from that obtained using the mean velocity. Use of the model produces a good agreement between the estimates of the spatial correlation function. A relation between Eulerian spatial and temporal integral scales is also derived.     

A continuum description for cholesteric and nematic twist-bend phases based on symmetry considerations

ABSTRACT

The recently discovered twist-bend nematic phase, N_tb, is a non-uniform equilibrium nematic phase that presents a spontaneous bend with a precession of the nematic director, n, on a conical helix with a tilt angle θ and helical pitch P. The stability of the N_tb phase has been recently demonstrated from the elastic point of view by extending the Frank elastic energy density of the nematic phase to include the symmetry element of the helical axis, t. In the present article, we investigate the influence of an external bulk field (magnetic or electric) on the N_tb phase. Using symmetry arguments we derive the expression for the flexoelectric polarisation in twist-bend nematic phases. We show that, besides the standard contribution related to the spatial variation of the nematic director, two new contributions connected with the existence of the helical axis appear. In the ground state, where the nematic deformation is a pure heliconical deformation, the new contribution vanishes identically, and the total flexoelectric polarisation is perpendicular to the nematic director. Furthermore, as an example, we study the role of an external magnetic field applied parallel to the helical axis for a material with positive magnetic susceptibility anisotropy. We show that the field modifies the range of values of the coupling parameter between the director and the helical axis, thus shifting the interval of values for which this coupling results in the N_tb phase.     

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.     

Modeling of Solute-Solvent Interactions Using an External Electric Field—From Tautomeric Equilibrium in Nonpolar Solvents to the Dissociation of Alkali Metal Halides

An implicit account of the solvent effect can be carried out using traditional static quantum chemistry calculations by applying an external electric field to the studied molecular system. This approach allows one to distinguish between the effects of the macroscopic reaction field of the solvent and specific solute–solvent interactions. In this study, we report on the dependence of the simulation results on the use of the polarizable continuum approximation and on the importance of the solvent effect in nonpolar solvents. The latter was demonstrated using experimental data on tautomeric equilibria between the pyridone and hydroxypyridine forms of 2,6-di-tert-butyl-4-hydroxy-pyridine in cyclohexane and chloroform.     

1,3,5-Triaza-7-Phosphaadamantane (PTA) as a 31P NMR Probe for Organometallic Transition Metal Complexes in Solution

Due to the rigid structure of 1,3,5-triaza-7-phosphaadamantane (PTA), its ³¹P chemical shift solely depends on non-covalent interactions in which the molecule is involved. The maximum range of change caused by the most common of these, hydrogen bonding, is only 6 ppm, because the active site is one of the PTA nitrogen atoms. In contrast, when the PTA phosphorus atom is coordinated to a metal, the range of change exceeds 100 ppm. This feature can be used to support or reject specific structural models of organometallic transition metal complexes in solution by comparing the experimental and Density Functional Theory (DFT) calculated values of this ³¹P chemical shift. This approach has been tested on a variety of the metals of groups 8–12 and molecular structures. General recommendations for appropriate basis sets are reported.     

A generalised model of hydrogen diffusion in metals with multiple trap types

Continuum modelling of hydrogen diffusion in metals, which accounts for both trapping and an imposed force field, is revisited. A generalised model of hydrogen diffusion and trapping is developed as a continuous interpretation of the discrete random-walk theory. A system of nonlinear equations describing the phenomenon of diffusion with multiple types of traps is derived without the assumption of a local equilibrium among hydrogen populations in dissimilar positions. Lattice-trap interchange kinetics can degenerate into local equilibrium as a limit case. Moreover, certain terms in general equations may be negligible in specific situations. By removing these terms, known particularised models of hydrogen diffusion and trapping are recovered. Determining the terms, which are disregarded in reduced models, enables a straightforward assessment of the applicability of these models. The advantages and limitations of particularised models applied to hydrogen embrittlement analyses are discussed.     

线性响应和两种态特定方法模拟AF350电子跃迁的溶剂效应

在极化连续模型框架下比较了线性响应与两种不同态特定方法计算的溶液中Alexa Fluor 350(AF350)分子激发能和光谱移动值的差异. AF350的第一激发态S0→S1电子跃迁属于π→π^*跃迁, 主要对应于最高占据分子轨道(HOMO)到最低空轨道(LUMO)的跃迁. 该分子激发态偶极矩大于基态偶极矩, 激发态时溶质溶剂相互作用比基态时更强, 随着溶剂极性增大, 会发生光谱红移的现象. 与实验值相比, 线性响应和两种态特定方法均高估了激发能, 其中以IBSF(Improta-Barone-Scalmani-Frisch)方法得到的激发能最小, 矫正的基态反应场方法(cGSRF)得到的激发能最大. 对于光谱移动值, 3种方法与实验值相比都偏小, 线性响应方法(LR)计算出的误差最大, 而IBSF方法得到的结果与实验值最吻合, 是预测溶液中AF350分子激发能和光谱移动值最准确的方法. 对比了Marcus传统理论和基于约束平衡的非平衡溶剂化理论的结果, 发现后者得到的激发能和光谱移动值更接近于实验值.     

基于连续模型的人员疏散仿真分析

行人流连续模型直观地反映人群疏散过程中的疏散特征,本文基于行人流连续模型。研究行人在典型疏散场景下的疏散特征．在COMSOL中建立行人流连续模型及其方程,通过编写MATLAB代码,实现了连续模型及其循环求解框架．利用快速扫描法求解Eikonal方程得到背景场值,在每一步迭代循环中将背景场值作为模型的初始变量导入,调用COMSOL计算模块求解模型的瞬态控制方程．通过两个标准算例,重现了典型的行人流自组织现象,验证了连续模型的合理性．结果表明,本文的疏散仿真分析模型和计算程序是可靠的,疏散仿真分析可以为实际工程中的人员疏散方案的制定以及平面设计与安全布置等方面提供技术支撑．     

A new set of atomic radii for accurate estimation of solvation free energy by Poisson–Boltzmann solvent model

The Poisson–Boltzmann implicit solvent (PB) is widely used to estimate the solvation free energies of biomolecules in molecular simulations. An optimized set of atomic radii (PB radii) is an important parameter for PB calculations, which determines the distribution of dielectric constants around the solute. We here present new PB radii for the AMBER protein force field to accurately reproduce the solvation free energies obtained from explicit solvent simulations. The presented PB radii were optimized using results from explicit solvent simulations of the large systems. In addition, we discriminated PB radii for N‐ and C‐terminal residues from those for nonterminal residues. The performances using our PB radii showed high accuracy for the estimation of solvation free energies at the level of the molecular fragment. The obtained PB radii are effective for the detailed analysis of the solvation effects of biomolecules. © 2014 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.