Relevant bibliographies by topics / Crystallization – Experiments – Software

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Academic literature on the topic 'Crystallization – Experiments – Software'

Author: Grafiati
Published: 4 June 2021
Last updated: 10 February 2022

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Journal articles on the topic "Crystallization – Experiments – Software"

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Watts, David, Jochen Müller-Dieckmann, Gohar Tsakanova, Victor S. Lamzin, and Matthew R. Groves. "Quantitive evaluation of macromolecular crystallization experiments using 1,8-ANS fluorescence." Acta Crystallographica Section D Biological Crystallography 66, no. 8 (July 10, 2010): 901–8. http://dx.doi.org/10.1107/s0907444910020664.

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Modern X-ray structure analysis and advances in high-throughput robotics have allowed a significant increase in the number of conditions screened for a given sample volume. An efficient evaluation of the increased amount of crystallization trials in order to identify successful experiments is now urgently required. A novel approach is presented for the visualization of crystallization experiments using fluorescence from trace amounts of a nonspecific dye. The fluorescence images obtained strongly contrast protein crystals against other phenomena, such as precipitation and phase separation. Novel software has been developed to quantitatively evaluate the crystallization outcome based on a biophysical metric correlated with voxel protein concentration. In >1500 trials, 85.6% of the successful crystallization experiments were correctly identified, yielding a 50% reduction in the number of `missed hits' compared with current automated approaches. The use of the method in the crystallization of three previously uncharacterized proteins from the malarial parasitePlasmodium falciparumis further demonstrated.
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Mele, Katarina, Rongxin Li, Vincent J. Fazio, and Janet Newman. "Quantifying the quality of the experiments used to grow protein crystals: theiQCsuite." Journal of Applied Crystallography 47, no. 3 (May 29, 2014): 1097–106. http://dx.doi.org/10.1107/s1600576714009728.

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Millions of crystallization trials are set up each year, with no clear metrics for determining if the experiments were correctly dispensed. This article reports the development of a software tool (iQC–image Quality Control) that recognizes factors associated with suboptimal experimental control during the setting up of protein crystallization trials. In its simplest form,iQCreturns a report that gives an overall rating to the quality of an experimental setup. TheiQCsoftware is able to identify many common problems observed in setting up crystallization trials – droplets that have associated splatter; droplets with air bubbles; the positional accuracy of droplet placement; elongated or otherwise `non-circular' drops – as well as detecting small and large droplets. An obvious use of this application is to track the status of the instrumentation used to set up crystallization trials in a multi-user laboratory.
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Wilson, Julie, and Ian Berry. "The use of gradient direction in pre-processing images from crystallization experiments." Journal of Applied Crystallography 38, no. 3 (May 13, 2005): 493–500. http://dx.doi.org/10.1107/s0021889805007442.

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Robots are now used routinely to perform crystallization experiments and many laboratories now have imaging systems to record the results. These images must be evaluated rapidly and the results fed back into optimization procedures. Software to analyse the images is being developed; described here are methods to restrict the area of the image to be analysed in order to speed up processing. Properties of the gradient of greyscale images are used to identify first the well and then the crystallization drop for various crystallization trays and different imaging systems. Methods are discussed to identify artefacts in the images that are not related to the experimental outcome, but can cause problems for the machine-learning algorithms used in classification and waste time during analysis. Gradient angles are exploited to eliminate faults in the crystallization trays, bubbles and splatter droplets prior to analysis.
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Audic, Stéphane, Fabrice Lopez, Jean-Michel Claverie, Olivier Poirot, and Chantal Abergel. "SAmBA: An interactive software for optimizing the design of biological macromolecules crystallization experiments." Proteins: Structure, Function, and Genetics 29, no. 2 (October 1997): 252–57. http://dx.doi.org/10.1002/(sici)1097-0134(199710)29:2<252::aid-prot12>3.0.co;2-n.

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Yamada, Yusuke, Naohiro Matsugaki, Masahiko Hiraki, Ryuichi Kato, and Toshiya Senda. "In-situ diffraction experiments at the Photon Factory MX beamlines." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C500. http://dx.doi.org/10.1107/s2053273314094996.

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Crystallization trial is one of the most important but time-consuming steps in macromolecular crystallography. Once a crystal appears in a certain crystallization condition, the crystal is typically harvested from the crystallization drop, soaked into a cryoprotection buffer, flash-cooled with a liquid nitrogen or cold gas flow and finally evaluated its diffraction quality by an X-ray beam. During these long process, crystal may be damaged and the result from the diffraction experiment does not necessarily reflect a nature of the crystal. On in-situ diffraction experiment, where a crystal in a crystallization drop is directly irradiated to an X-ray beam, a diffraction image from a crystal without any external factors such as harvesting and cryoprotection and, as a result, a nature of crystal can be evaluated quickly. In the Photon Factory, a new table-top diffractometer for in-situ diffraction experiments has been developed. It consists of XYZ translation stages with a plate handler, on-axis viewing system with a large numeric aperture and a plate rack where ten crystallization plates can be placed. These components sit on a common plate and it is placed on the existing diffractometer table in the beamline endstation. The CCD detector with a large active area and a pixel array detector with a small active area are used for acquiring diffraction images from crystals. Dedicated control software and user interface were also developed. Since 2014, user operation of the new diffractometer was started and in-situ diffraction experiments were mainly performed for evaluations of crystallization plates from a large crystallization screening project in our facility. BL-17A [1], one of micro-focus beamlines at the Photon Factory, is planned to be upgraded in March 2015. With this upgrade, a new diffractometer, which has a capability to handle a crystallization plate, will be installed so that diffraction data sets from crystals in crystallization drop can be collected.
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Kang, Yue, Chao Liu, Yuzhu Zhang, and Hongwei Xing. "Influence of Crystallization Behavior of Gas Quenching Blast Furnace Slag on the Preparation of Amorphous Slag Beads." Crystals 10, no. 1 (January 10, 2020): 30. http://dx.doi.org/10.3390/cryst10010030.

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Slag beads with different crystal content could be obtained through the gas quenching blast furnace slag (BFS) process. In order to increase the additional value of the slag beads as much as possible, it was necessary to restrain the crystallization of the slag beads as much as possible. In this paper, the mineral types and crystallization temperatures of BFS with different basicities and cooling rates were studied by using Factsage thermodynamic software, XRD, and differential scanning calorimeter (DSC) experiments, which obtained the gas quenching temperature and the cooling rate needed to restrain crystallization behavior in the gas quenching process; The crystallization mechanism was studied by calculating crystallization activation energy (Ec) using the DSC experiment, at the same time, the thermodynamic results were verified. The proper basicity and cooling rate of BFS were found to be conducive to the preparation of amorphous slag beads. The results showed that the initial crystallization temperature decreased with decreasing the basicity and increasing the cooling rate, which could increase the amorphous content of slag beads in the gas quenching process. The crystallization activation energy (Ec) increased with decreasing basicity, which increased the crystallization barrier.
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7

Junius, Niels, Esko Oksanen, Maxime Terrien, Christophe Berzin, Jean-Luc Ferrer, and Monika Budayova-Spano. "A crystallization apparatus for temperature-controlled flow-cell dialysis with real-time visualization." Journal of Applied Crystallography 49, no. 3 (April 22, 2016): 806–13. http://dx.doi.org/10.1107/s1600576716004635.

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Many instrumentation developments in crystallization have concentrated on massive parallelization assays and reduction of sample volume per experiment to find initial crystallization conditions. Yet improving the size and diffraction quality of the crystals for diffraction studies often requires decoupling of crystal nucleation and growth. This in turn requires the control of variables such as precipitant and protein concentration, equilibration rate, and temperature, which are all difficult parameters to control in the existing setups. The success of the temperature-controlled batch method, originally developed to grow very large crystals for neutron crystallography, demonstrated that the rational optimization of crystal growth has potential in structural biology. A temperature-controlled dialysis button has been developed for our previous device, and a prototype of an integrated apparatus for the rational optimization of crystal growth by mapping and manipulating temperature–precipitant concentration phase diagrams has been constructed. The presented approach differs from the current paradigm, since it involves serial instead of parallel experiments, exploring multiple crystallization conditions with the same protein sample. The sample is not consumed in the experiment and the conditions can be changed in a reversible fashion, using dialysis with a flowing precipitant reservoir as well as precise temperature control. The control software allows visualization of the crystals, as well as control of the temperature and composition of the crystallization solution. The rational crystallization optimization strategies presented here allow tailoring of crystal size, morphology and diffraction quality, significantly reducing the time, effort and amount of expensive protein material required for structure determination.
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Frølich, Simon, and Henrik Birkedal. "MultiRef: software platform for Rietveld refinement of multiple powder diffractograms fromin situ, scanning or diffraction tomography experiments." Journal of Applied Crystallography 48, no. 6 (November 19, 2015): 2019–25. http://dx.doi.org/10.1107/s1600576715020099.

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Modern advanced diffraction experiments such asin situdiffraction, position-resolved diffraction or diffraction tomography generate extremely large data sets with hundreds to many thousands of diffractograms. Analyzing such data sets by Rietveld refinement is hampered by the logistics of running the Rietveld refinement program, extracting and analyzing the results, and possibly re-refining the data set based on an analysis of the preceding cycle of refinements. The complexity of the analysis may prevent some researchers either from performing the experiments or from conducting an exhaustive analysis of collected data. To this end, a MATLAB framework,MultiRef, which facilitates automated refinements, data extraction and intelligent choice of refinement model based on user choices, has been developed The use ofMultiRefis illustrated on data sets from diffraction tomography, position-resolved diffraction andin situpowder diffraction investigations of crystallization.
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Murthy, Tal, Yongcheng Wang, Colin Reynolds, and Titus J. Boggon. "Automated Protein Crystallization Trials Using the Thermo Scientific Matrix Hydra II eDrop." JALA: Journal of the Association for Laboratory Automation 12, no. 4 (August 2007): 213–18. http://dx.doi.org/10.1016/j.jala.2007.04.001.

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Obtaining suitable crystals for X-ray diffraction experiments is one of the rate-limiting steps in macromolecular crystallography. Robotic platforms that can increase throughput are highly desirable for crystal screening operations. The Thermo Scientific Matrix Hydra II eDrop is a liquid handling robot capable of dispensing sub-microliter and microliter volumes of solutions. Equipped with single-channel noncontact microdispenser, 96-channel syringe-based contact microdispenser and user-friendly ControlMate software, the Thermo Scientific Matrix Hydra II eDrop is appropriately designed for crystal screening experiments. The microdispensers are used in a single operational process to rapidly dispense sub-microliter volumes of liquids for automated crystallization plate setup. In this report, we discuss the design of the Thermo Scientific Matrix Hydra II eDrop. We also discuss an automated protocol for macromolecular crystallization trials that has successfully been used to produce crystals of a membrane protein, the rhomboid family intramembrane protease, GlpG. (JALA 2007;12:213–8)
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Tian, Runze, Yu Zhang, Anhua Xu, Xuemei Li, Yunlong Hou, and Bowen Tai. "Impact of Cooling on Water and Salt Migration of High-Chlorine Saline Soils." Geofluids 2021 (August 30, 2021): 1–12. http://dx.doi.org/10.1155/2021/8612762.

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Secondary salinization is a common problem in saline soil projects. In order to grasp the mechanism of water and salt migration of high-chlorine saline soil during the cooling process, the saline soils along the Qarhan-Golmud Highway in the Qinghai-Tibet Plateau were selected as test samples. Firstly, the basic physical parameter test and the soluble salt chemical experiment were carried out and obtained liquid and plastic limits, dry density, etc. Secondly, freezing temperature experiments and water-salt migration experiments under one-way cooling conditions were conducted according to the actual environmental conditions, and after the temperature gradient line of the soil sample was stable, water content and labile salt chemistry experiments were conducted to obtain the distribution of water and salt contents of soil samples. Finally, the effect of crystallization-water phase transition on water and salt migration and the effect of chloride salt on the temperature of crystallization-water phase transition were considered, and a mathematical model applicable to the water and salt migration of highly chlorinated saline soils under the effect of unidirectional cooling was established and solved with COMSOL Multiphysics software, and the correctness of the model was verified by comparing the simulation results with the experimental results. The study found that (1) during the one-way cooling process, both water and salt showed a tendency to migrate to the cold end. The MC (saline soil with medium chlorine content) with an initial water content of 16.9% and Cl− content of 3.373% was measured to reach a 17.6% water content and 3.76% Cl− content at the cold (top) end after the experiment. The HC (saline soil with high chlorine content) with an initial water content of 6.6% and Cl− content of 17.928% was measured to reach a 6.83% water content and 18.8% Cl− content after the experiment and (2) after the one-way cooling experiment of the MC, the water content at a distance of 1–2 cm from the cold end has abrupt changes, which may be caused by a small amount of crystallization—water phase transition at this location. At the same time, according to the temperature change graph during the cooling process, the phase change temperature was set to −9°C in the numerical simulation process to match the experimental results.
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Dissertations / Theses on the topic "Crystallization – Experiments – Software"

1

Mooranian, Mahsa. "My Crystal Diary (MCD) : an integrated software application for recording the observations and results of crystallisation experiments." University of Western Australia. School of Electrical, Electronic and Computer Engineering, 2008. http://theses.library.uwa.edu.au/adt-WU2008.0121.

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Recent technological advances in computer science have contributed to immense data generation in many critical areas of biology. These data can be used in intelligent information systems to better understand biological processes from the atomic details of biological molecules to the interaction of species in an ecosystem. This thesis presents My Crystal Diary (MCD), an integrated software application designed for use in an intelligent decision-support system for planning novel crystallisation experiments. PostgreSQL database server is the information repository containing both the experimental data and general knowledge. Web-based interfaces developed in Plone provide remote access to the database by utilizing a Zope Web application server.
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Book chapters on the topic "Crystallization – Experiments – Software"

1

Yan, Yuhong, Yong Liang, Abhijeet Roy, and Xinge Du. "Web Service Enabled Online Laboratory." In Electronic Services, 1236–52. IGI Global, 2010. http://dx.doi.org/10.4018/978-1-61520-967-5.ch075.

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Online experimentation allows students from anywhere to operate remote instruments at any time. The current techniques constrain users to bind to products from one company and install client side software. We use Web services and Service Oriented Architecture to improve the interoperability and usability of the remote instruments. Under a service oriented architecture for online experiment system, a generic methodology to wrap commercial instruments using IVI and VISA standard as Web services is developed. We enhance the instrument Web services into stateful services so that they can manage user booking and persist experiment results. We also benchmark the performance of this system when SOAP is used as the wire format for communication and propose solutions to optimize performance. In order to avoid any installation at the client side, the authors develop Web 2.0 based techniques to display the virtual instrument panel and real time signals with just a standard Web browser. The technique developed in this article can be widely used for different real laboratories, such as microelectronics, chemical engineering, polymer crystallization, structural engineering, and signal processing.
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