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.     

Enantiomeric distribution of major chiral volatile organic compounds in juniper‐flavored distillates

The enantiomeric ratios of chiral volatile organic compounds in juniper‐flavored spirits produced by various processing technologies in different EU countries were determined by multidimensional GC using solid‐phase microextraction and liquid–liquid extraction as a sample pretreatment procedure. In total, more than 260 compounds were detected in studied spirits from which linalool, α‐terpineol, 4‐terpineol, linalool oxides, α‐pinene, and verbenone were selected for enantiomeric separation. The significant differences in enantiomeric ratio of linalool and cis‐linalool oxide allowed us to distinguish between samples produced in Slovakia and the United Kingdom from those produced in Germany, Czech Republic, and Belgium. The pure enantiomer of trans‐linalool oxide was found only in samples from Germany. It was shown that the enantiomeric ratio is independent of the sample treatment procedure, and only small differences up to 1% were observed.     

有机化学教学中的“三融合、二反思、四进阶”创新教学模式*

为培养出新时代创新人才,构建的“三融合、二反思、四进阶”教学模式有效提升了学生们科技创新能力。依据有机化学特点,创设科学发现情境,通过核心知识点网融合(挑战度)、理论实践交叉融合(高阶性)和化学思政融合(课程思政)“三融合”策略,不断激发学生们学习兴趣;通过教师反思、学生反思的“二反思”过程不断优化教学过程,改善教学效果;最终使具有不同知识层次的学生通过“四进阶”教学策略逐步提升科创能力(创新性)。     

融合STREAM理念的中学化学核心素养的培养及实践研究*——以“水的组成”为例

STREAM教育属于典型的跨学科教育形式,在学科融合的背景下,基于STREAM理念视角解决实际问题,注重在实践过程中培养和增强学生的批判思维与解决问题的能力,提升跨学科和创造性思维,使学生成为具有科学创新和革新精神的全面发展的人。融合STREAM理念开发初中化学教学案例,并将其应用于教学中,通过使用原创教学案例“水的组成”进行实践教学,研究其对教学效果及学生化学核心素养的提升作用;在实践过程中设有实验班与对照班,通过纸笔测试和问卷调查进行数据收集,结果显示不管在知识掌握度还是素养养成和促进方面,实验组都明显优于对照组,这说明融合STREAM理念对化学的教与学都具有积极作用。     

AN ADAPTIVE UNSTRUCTURED TRI-TREE ITERATIVE SOLVER FOR MIXED FINITE ELEMENT FORMULATION OF THE STOKES EQUATIONS

An iterative adaptive equation solver for solving the implicit Stokes equations simultaneously with tri-tree grid generation is developed. The tri-tree grid generator builds a hierarchical grid structure which is mapped to a finite element grid at each hierarchical level. For each hierarchical finite element grid the Stokes equations are solved. The approximate solution at each level is projected onto the next finer grid and used as a start vector for the iterative equation solver at the finer level. When the finest grid is reached, the equation solver is iterated until a tolerated solution is reached. In order to reduce the overall work, the element matrices are integrated analytically beforehand. The efficiency and behaviour of the present adaptive method are compared with those of the previously developed iterative equation solver which is preconditioned by incomplete LU factorization with coupled node fill-in. The efficiency of the incomplete coupled node fill-in preconditioner is shown to be largely dependent on the global node numbering. The preconditioner is therefore tested for the natural node ordering of the tri-tree grid generator and for different ways of sorting the nodes.     

Monthly Increase in Vitamin D Levels upon Supplementation with 2000 IU/Day in Healthy Volunteers: Result from “Integriamoci”, a Pilot Pharmacokinetic Study

Vitamin D (VD) is a calcium- and phosphate-controlling hormone used to treat bone disorders; yet, several other effects are progressively emerging. VD deficiency is highly prevalent worldwide, with suboptimal exposure to sunlight listed among the leading causes: oral supplementation with either cholecalciferol or calcitriol is used. However, there is a scarcity of clinical studies investigating how quickly VD concentrations can increase after supplementation. In this pilot study, the commercial supplement ImmuD3 (by Erboristeria Magentina^®) was chosen as the source of VD and 2000 IU/day was administered for one month to 21 healthy volunteers that had not taken any other VD supplements in the previous 30 days. Plasma VD levels were measured through liquid chromatography coupled to tandem mass spectrometry after 7, 14, and 28 days of supplementation. We found that 95% of the participants had insufficient VD levels at baseline (<30 ng/mL; median 23.72 ng/mL; IQR 18.10–26.15), but after 28 days of supplementation, this percentage dropped to 62% (median 28.35 ng/mL; IQR 25.78–35.20). The median increase in VD level was 3.09 ng/mL (IQR 1.60–5.68) after 7 days and 8.85 ng/mL (IQR 2.85–13.97F) after 28 days. This study suggests the need for continuing VD supplementation and for measuring target level attainment.     

高中物理“教-学-评一体化”课堂教学探索——以“示波器的原理——带电粒子在电场中的偏转”为例

"教-学-评一体化"的课堂是指围绕教学目标,教师的教学、学生的学习以及教师对学生的评价组成一个有机的、整体的有效课堂.教学"有效"的唯一证据在于目标的达成,在于学生学习结果的质量,在于何以证明学生学会了什么.因此,教学中要关注对学生的评价.本文以"示波器的原理——带电粒子在电场中的偏转"为例,论述在"教-学-评一体化"的课堂中如何用评价促进学生思维发展.     

非齐次动力学方程的一种精细积分单步方法

针对非齐次动力学方程■,结合精细积分法和微分求积法,利用同阶的显式龙格-库塔法对计算过程中待求的v_(k+i/s)(i=1,2,…,s)进行预估,提出了一种避免状态矩阵求逆的高效精细积分单步方法。该方法采用精细积分法计算e~(Ht),而Duhamel积分项采用s级s阶的时域微分求积法,计算格式统一且易于编程,可灵活实现变阶变步长。仿真结果表明,与其他单步法及预估校正-辛时间子域法进行数值比较,该方法具有高精度、高效率及良好的稳定性,在求解大规模动力系统时间响应问题中具有较大的优势。     

A discontinuous Galerkin immersed boundary solver for compressible flows: Adaptive local time stepping for artificial viscosity–based shock-capturing on cut cells

We present a higher-order cut cell immersed boundary method (IBM) for the simulation of high Mach number flows. As a novelty on a cut cell grid, we evaluate an adaptive local time stepping (LTS) scheme in combination with an artificial viscosity–based shock-capturing approach. The cut cell grid is optimized by a nonintrusive cell agglomeration strategy in order to avoid problems with small or ill-shaped cut cells. Our approach is based on a discontinuous Galerkin discretization of the compressible Euler equations, where the immersed boundary is implicitly defined by the zero isocontour of a level set function. In flow configurations with high Mach numbers, a numerical shock-capturing mechanism is crucial in order to prevent unphysical oscillations of the polynomial approximation in the vicinity of shocks. We achieve this by means of a viscous smoothing where the artificial viscosity follows from a modal decay sensor that has been adapted to the IBM. The problem of the severe time step restriction caused by the additional second-order diffusive term and small nonagglomerated cut cells is addressed by using an adaptive LTS algorithm. The robustness, stability, and accuracy of our approach are verified for several common test cases. Moreover, the results show that our approach lowers the computational costs drastically, especially for unsteady IBM problems with complex geometries.     

薄板弯曲分析的节点积分高阶无网格法

采用高阶无网格法求解薄板弯曲问题,在已发展的线性曲率光顺方案的基础上,通过引入泰勒展开技术,建立了能够精确再现纯弯曲和线性弯曲模式的节点积分方法。与之相比,目前无网格薄板分析主要采用的节点积分方法仅能精确再现纯弯曲模式。数值结果表明,本文方法可精确通过纯弯曲和线性弯曲试验,且能得到光滑、无振荡的弯矩场。与标准的高斯积分方法和目前已存在的节点积分方法相比,本文方法在计算精度、效率以及弯矩分布等方面均展现出显著优势。