DIOPTAS: a program for reduction of two-dimensional X-ray diffraction data and data exploration

The amount of data collected during synchrotron X-ray diffraction (XRD) experiments is constantly increasing. Most of the time, the data are collected with image detectors, which necessitates the use of image reduction/integration routines to extract structural information from measured XRD patterns. This step turns out to be a bottleneck in the data processing procedure due to a lack of suitable software packages. In particular, fast-running synchrotron experiments require online data reduction and analysis in real time so that experimental parameters can be adjusted interactively. Dioptas is a Python-based program for on-the-fly data processing and exploration of two-dimensional X-ray diffraction area detector data, specifically designed for the large amount of data collected at XRD beamlines at synchrotrons. Its fast data reduction algorithm and graphical data exploration capabilities make it ideal for online data processing during XRD experiments and batch post-processing of large numbers of images.     

EAST极紫外空间分辨光谱分析软件的开发

基于Matlab软件的图形用户界面开发环境(GUIDE)设计开发了一套交互式界面，可以自动读取、解析原始数据，开展波长标定，将谱强度与谱仪系统空间测量位置以及EAST实验放电时间等信息相关联，从而快速、便捷地计算杂质离子发出的线光谱强度的空间分布并绘图。该空间分辨光谱分析软件的开发和应用大大提高了谱仪数据处理和分析的便捷性和效率，保证了放电期间数据处理的准实时性。     

Some physico-chemical characteristics of amino-acid derivatives containing rest of 1,2,4-triazole-3,4-di-substituted with potential antitumoral activity

Abstract

Dipeptide derivatives from p-aminobenzoyl-phenylglycine and p-aminobenzoyl-phenylalanine were grafted on 1,2,4-triazole heterocycle in order to get new substances with potential biological activity. The compounds synthetized and characterized in this paper have a structure that fits in the antimetabolites category, products used to treat malignant tumors. The presence of several bioactive groups in the same molecule permits us to study the chemical structure - biological activity correlation based on computational analyses using SPARTAN’14 software. Some correlations between the molecular parameters established with Spartan’14 software are evidenced in this paper.     

Various solution methods,accompanied by dynamic investigation,for the same problem as a means for enriching the mathematical toolbox

A geometrical task is presented with multiple solutions using different methods, in order to show the connection between various branches of mathematics and to highlight the importance of providing the students with an extensive ‘mathematical toolbox’. Investigation of the property that appears in the task was carried out using a computerized tool.     

A micrometer head integrated microfluidic device for facile droplet size control and automatic measurement of a droplet size

A novel microfluidic droplet generator is proposed, which can control the droplet size through turning an integrated micrometer head with ease, and the size of the produced micro-droplet can be automatically and real-time monitored by an open-sourced software and off-the-shelf hardware.     

The development of an artificial organic networks toolkit for LabVIEW

Two of the most challenging problems that scientists and researchers face when they want to experiment with new cutting‐edge algorithms are the time‐consuming for encoding and the difficulties for linking them with other technologies and devices. In that sense, this article introduces the artificial organic networks toolkit for LabVIEW? (AON‐TL) from the implementation point of view. The toolkit is based on the framework provided by the artificial organic networks technique, giving it the potential to add new algorithms in the future based on this technique. Moreover, the toolkit inherits both the rapid prototyping and the easy‐to‐use characteristics of the LabVIEW? software (e.g., graphical programming, transparent usage of other softwares and devices, built‐in programming event‐driven for user interfaces), to make it simple for the end‐user. In fact, the article describes the global architecture of the toolkit, with particular emphasis in the software implementation of the so‐called artificial hydrocarbon networks algorithm. Lastly, the article includes two case studies for engineering purposes (i.e., sensor characterization) and chemistry applications (i.e., blood–brain barrier partitioning data model) to show the usage of the toolkit and the potential scalability of the artificial organic networks technique. © 2015 Wiley Periodicals, Inc.     

MOLSIM: A modular molecular simulation software

The modular software MOLSIM for all‐atom molecular and coarse‐grained simulations is presented with focus on the underlying concepts used. The software possesses four unique features: (1) it is an integrated software for molecular dynamic, Monte Carlo, and Brownian dynamics simulations; (2) simulated objects are constructed in a hierarchical fashion representing atoms, rigid molecules and colloids, flexible chains, hierarchical polymers, and cross‐linked networks; (3) long‐range interactions involving charges, dipoles and/or anisotropic dipole polarizabilities are handled either with the standard Ewald sum, the smooth particle mesh Ewald sum, or the reaction‐field technique; (4) statistical uncertainties are provided for all calculated observables. In addition, MOLSIM supports various statistical ensembles, and several types of simulation cells and boundary conditions are available. Intermolecular interactions comprise tabulated pairwise potentials for speed and uniformity and many‐body interactions involve anisotropic polarizabilities. Intramolecular interactions include bond, angle, and crosslink potentials. A very large set of analyses of static and dynamic properties is provided. The capability of MOLSIM can be extended by user‐providing routines controlling, for example, start conditions, intermolecular potentials, and analyses. An extensive set of case studies in the field of soft matter is presented covering colloids, polymers, and crosslinked networks. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

QuickFF: A program for a quick and easy derivation of force fields for metal‐organic frameworks from ab initio input

QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal‐organic frameworks in an automated fashion. The force field parameters for the covalent interaction are derived from ab initio data. The mathematical expression of the covalent energy is kept simple to ensure robustness and to avoid fitting deficiencies as much as possible. The user needs to produce an equilibrium structure and a Hessian matrix for one or more building units. Afterward, a force field is generated for the system using a three‐step method implemented in QuickFF. The first two steps of the methodology are designed to minimize correlations among the force field parameters. In the last step, the parameters are refined by imposing the force field parameters to reproduce the ab initio Hessian matrix in Cartesian coordinate space as accurate as possible. The method is applied on a set of 1000 organic molecules to show the easiness of the software protocol. To illustrate its application to metal‐organic frameworks (MOFs), QuickFF is used to determine force fields for MIL‐53(Al) and MOF‐5. For both materials, accurate force fields were already generated in literature but they requested a lot of manual interventions. QuickFF is a tool that can easily be used by anyone with a basic knowledge of performing ab initio calculations. As a result, accurate force fields are generated with minimal effort. © 2015 Wiley Periodicals, Inc.     

Software tools for green and sustainable chemistry

In this review, we consider green chemistry metrics, related software tools, and the opportunities and challenges for their use in research laboratories. We provide an overview of state-of-the-art software designed both to aid researchers in planning and conducting chemical experiments and to assess sustainability of individual reactions and synthetic routes. The increasing digitalisation of research means that there is great opportunity for more extensive use of computational tools by synthetic chemists and for closer integration of green chemistry principles into the routine work of chemical laboratories. We discuss the scope for using software tools in the laboratory and assisting synthetic chemists in the adoption of green and sustainable chemistry approaches that are suitable for their specific purposes.     

互联网B/S架构交互式软件在核心概念教学中的应用*——以国际IB课程中“电解质”内容为例

基于核心概念教学的思路,国际IB课程互联网B/S架构交互式软件能够使学生围绕“电解质”核心概念,通过自行操作软件获得多个从微观到宏观、定性与定量相结合、可视化的实验证据,有利于学生深度理解概念与概念之间的逻辑和发展关系,促进学科知识系统框架的形成。