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.     

Point-of-care testing (POCT): Current techniques and future perspectives

Point-of-care testing (POCT) is a laboratory-medicine discipline that is evolving rapidly in analytical scope and clinical application. In this review, we first describe the state of the art of medical-laboratory tests that can be performed near the patient. At present, POCT ranges from basic blood-glucose measurement to complex viscoelastic coagulation assays. POCT shortens the time to clinical decision-making about additional testing or therapy, as delays are no longer caused by transport and preparation of clinical samples, and biochemical-test results are rapidly available at the point of care. Improved medical outcome and lower costs may ensue.Recent, evolving technological advances enable the development of novel POCT instruments. We review the underlying analytical techniques. If new instruments are not yet in practical use, it is often hard to decide whether the underlying analytical principle has real advantage over former methods. However, future utilization of POCT also depends on health-care trends and new areas of application. But, even today, it can be assumed that, for certain applications, near-patient testing is a useful complement to conventional laboratory analyses.     

NorTRACK product tracking system—development and implementation

This paper presents the experience gained by developers and users with implementation and operation of NorTRACK^TM, a real-time computerized product tracking system. A Programmable Logic Controller (PLC) collects and transfers data in real time to NorTRACK’s Oracle^TM database on a Windows NT^TM server network. After extensive development and Beta testing at MDS Nordion’s Canadian Irradiation Centre in Montreal, Canada, NorTRACK was installed in January 1997 with a new irradiation facility in Ethicon Endo-Surgery Inc.’s Albuquerque plant in the United States. NorTRACK communicates with the irradiator control and safety system, the plant's central manufacturing database, an innovative pallet staging and tote loading robot, and an automated dosimetry reading system. This integrated system allows the sterilization facility to monitor the irradiator operation and the flow of many products, through varied processing modes, continuously and reliably. As a result of operating with NorTRACK, both MDS Nordion’s CIC facility and the Endo-Surgery manufacturing site, are beginning to realize unique benefits in their respective operations. MDS Nordion is also initiating several future product enhancements and additional productivity modules. This paper describes the NorTRACK system, the various stages of the development project and Beta tests, and the experience of the users to date in their operations.     

Localized orbitals for optimal decomposition of molecular properties

We present the procedure for transforming delocalized molecular orbitals into the localized property-optimized orbitals (LPOs) designed for building the most accurate, in the Frobenius norm sense, approximation to the first-order reduced density matrix in form of the sum of localized monoatomic and diatomic terms. In this way, a decomposition of molecular properties into contributions associated with individual atoms and the pairs of atoms is obtained with the a priori known upper bound for the decomposition accuracy. Additional algorithm is proposed for obtaining the set of “the Chemist's LPOs” (CLPOs) containing a single localized orbital, with nearly double occupancy, per a pair of electrons. CLPOs form an idealized Lewis structure optimized for the closest possible reproduction of one-electron properties derived from the original many-electron wavefunction. The computational algorithms for constructing LPOs and CLPOs from a general wavefunction are presented and their implementation within the open-source freeware program JANPA ( http://janpa.sourceforge.net /) is discussed. The performance of the proposed procedures is assessed using the test set of density matrices of 33 432 small molecules obtained at both Hartree-Fock and second-order Moller-Plesset theory levels and excellent agreement with the chemist's Lewis-structure picture is found.     

Automatic spike correction using UNIFIT 2020

The improvement of the software UNIFIT 2020 from an analysis processing software for photoelectron spectroscopy (XPS) only to a powerful tool for XPS, Auger electron spectroscopy (AES), X-ray absorption spectroscopy (XAS), and Raman spectroscopy requires new additional programme routines. Particularly, the implementation of the analysis of Raman spectra needs a well-working automatic spike correction. The application of the modified discrete Laplace operator method allows for a perfect localization and correction of the spikes and finally a successful peak fit of the spectra. The theoretical basis is described. Test spectra allow for the evaluation of the presented method. A comparison of the original and spike-corrected real measurements demonstrates the high quality of the method used.     

Open source capillary electrophoresis

Open source paradigm is becoming widely accepted in scientific communities and open source hardware is finding its steady place in chemistry research. In this review article, we provide the reader with the most up‐to‐date information on open source hardware and software resources enabling the construction and utilization of an “open source capillary electrophoresis instrument”. While CE is still underused as a separation technique, it offers unique flexibility, low‐cost, and high efficiency and is particularly suitable for open source instrumental development. We overview the major parts of CE instruments, such as high voltage power supplies, detectors, data acquisition systems, and CE software resources with emphasis on availability of the open source information on the web and in the scientific literature. This review is the first of its kind, revealing accessible blueprints of most parts from which a fully functional open source CE system can be built. By collecting the extensive information on open source capillary electrophoresis in this review article, the authors aim at facilitating the dissemination of knowledge on CE within and outside the scientific community, fosters innovation and inspire other researchers to improve the shared CE blueprints.     

Influence of salt and acetonitrile on the capillary zone electrophoresis analysis of imatinib in plasma samples

A simple, sensitive, specific, and cost‐effective analytical methodology was developed for the analysis of human plasma samples spiked with imatinib by CZE with on‐line UV detection in the context of Therapeutic Drug Monitoring. Several analytical conditions such as the ionic strength (I) and the pH of the BGE composed of citric acid and ε‐amino caproic acid were studied in regards of the presence of sodium chloride (NaCl) in plasma samples (1% m/v). Computer simulations (Simul software) were used to confirm the experimental results and to understand imatinib electrophoretic behavior in the presence of NaCl. Furthermore, the advantages of adding ACN to the sample containing NaCl to combine efficient protein precipitation and on‐line CZE stacking of imatinib were demonstrated. LOD and LOQ values of 48 and 191 ng/mL were obtained from plasma sample supernatant after protein precipitation with ACN, which is much lower than mean imatinib plasma level observed for patients treated by imatinib mesylate (about 1000 ng/mL). Good linearity was obtained in the concentration range 191–5000 ng/mL (R² > 0.997). RSD of less than 1.68% and 2.60% (n = 6) for migration times and corrected peak areas, respectively, were observed at the LOQ.     

autoDIAS: a python tool for an automated distortion/interaction activation strain analysis

The distortion/interaction activation strain (DIAS) analysis is a powerful tool for the investigation of energy barriers. However, setup and data analysis of such a calculation can be cumbersome and requires lengthy intervention of the user. We present autoDIAS, a python tool for the automated setup, performance, and data extraction of the DIAS analysis, including automated detection of fragments and relevant geometric parameters. © 2019 Wiley Periodicals, Inc.     

在GPU上求解大规模优化问题的反向策略的PSO算法

本文通过对传统粒子群算法(PSO)的分析,在GPU(Graphic Process Unit)上设计了基于一般反向学习策略的粒子群算法,并用于求解大规模优化问题.主要思想是通过一般反向学习策略转化当前解空间,提高算法找到最优解的几率,同时使用GPU大量线程并行来加速收敛速度.对比数值实验表明,对于求解大规模高维的优化问题,本文算法比其他智能算法具有更好的精度和更快的收敛速度.