A standard format and a graphical user interface for spin system specification

Biternas, A.G.; Charnock, G. T. P.; Kuprov, Ilya

doi:10.1016/j.jmr.2014.01.004

Cited by 11 publications

(5 citation statements)

References 27 publications

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“…for use in follow-up parameterized spin-physics simulations in the Spinach code [22]. FHI-aims can produce output files in the SpinXML data format that facilitate this task [107].…”

Section: Larger Scale Calculationsmentioning

confidence: 99%

Molecular NMR shieldings, J-couplings, and magnetizabilities from numeric atom-centered orbital based density-functional calculations

Laasner,

Mandzhieva,

Huhn

et al. 2024

Electron. Struct.

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This paper reports and benchmarks a new implementation of nuclear magnetic resonance shieldings, magnetizabilities, and J-couplings for molecules within semilocal density functional theory, based on numeric atom-centered orbital (NAO) basis sets. NAO basis sets are attractive for the calculation of these nuclear magnetic resonance (NMR) parameters because NAOs provide accurate atomic orbital representations especially near the nucleus, enabling high-quality results at modest computational cost. Moreover, NAOs are readily adaptable for linear scaling methods, enabling efficient calculations of large systems. The paper has five main parts: (1) It reviews the formalism of density functional calculations of NMR parameters in one comprehensive text to make the mathematical background available in a self-contained way. (2) The paper quantifies the attainable precision of NAO basis sets for shieldings in comparison to specialized Gaussian basis sets, showing similar performance for similar basis set size. (3) The paper quantifies the precision of calculated magnetizabilities, where the NAO basis sets appear to outperform several established Gaussian basis sets of similar size. (4) The paper quantifies the precision of computed J-couplings, for which a group of customized NAO basis sets achieves precision of ∼ Hz for smaller basis set sizes than some established Gaussian basis sets. (5) The paper demonstrates that the implementation is applicable to systems beyond 1,000 atoms in size.

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“…for use in follow-up parameterized spin-physics simulations in the Spinach code [22]. FHI-aims can produce output files in the SpinXML data format that facilitate this task [107].…”

Section: Larger Scale Calculationsmentioning

confidence: 99%

Molecular NMR shieldings, J-couplings, and magnetizabilities from numeric atom-centered orbital based density-functional calculations

Laasner,

Mandzhieva,

Huhn

et al. 2024

Electron. Struct.

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show abstract

“…must be specified in a certain formal way that the program expects. Standard formats are starting to emerge, but at the moment, every simulation package has its own way of specifying the spin system. Spinach uses Matlab data structures that are described in this section.…”

Section: Specifying the Systemmentioning

confidence: 99%

Large‐scaleNMRsimulations in liquid state: A tutorial

Kuprov

2017

Magnetic Reson in Chemistry

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Liquid state nuclear magnetic resonance is the only class of magnetic resonance experiments for which the simulation problem is solved comprehensively for spin systems of any size. This paper contains a practical walkthrough for one of the many available simulation packages — Spinach. Its unique feature is polynomial complexity scaling: the ability to simulate large spin systems quantum mechanically and with accurate account of relaxation, diffusion, chemical processes, and hydrodynamics. This paper is a gentle introduction written with a PhD student in mind.

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“…For instance, Bond et al [49] studied the encoding of Electrocardiogram (ECG) data using XML format, while Biternas et al [61] introduced in their work a simple and general XML format for spin system description in magnetic resonance imaging. The aim is to unify under one unique format the principle spin interaction specification conventions.…”

Section: Exchange Of Informationmentioning

confidence: 99%

On the Use of XML in Medical Imaging Web-Based Applications

Mata

Oliver

Lalande

et al. 2017

IRBM

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The rapid growth of digital technology in medical fields over recent years has increased the need for applications able to manage patient medical records, imaging data, and chart information. Web-based applications are implemented with the purpose to link digital databases, storage and transmission protocols, management of large volumes of data and security concepts, allowing the possibility to read, analyze, and even diagnose remotely from the medical center where the information was acquired. The objective of this paper is to analyze the use of the XML protocol in web-based medical imaging applications, analyzing how this protocol allows indexing and exchanging the huge amount of information associated with each medical case. The purpose of this paper is to point out the main advantages and drawbacks of the XML technology in order to provide key ideas for future web-based applications. As already explained by the email of Dr. Alain Lalande, in this paper we review the advances that the XML exchanging information protocol has provided to web-based applications applied to the medical imaging field.As suggested, we've checked the associated editors list and we think that either Alfredo Hernandez or Frederique Frouin could manage the current submission.All authors have checked the manuscript and have agreed to the submission. We have no conflict of interest. We think the research topic the paper is dealing with perfectly fits the scope of the journal. Acknowledgements:This work was partially funded by the Spanish R+D+I grant n. TIN2012-37171-C02-01. C. Mata holds a Mediterranean Office for Youth mobility grant. Finally, the Regional Council of Burgundy under the PARI 1 scheme sponsored this work. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 On the use of XML in medical imaging web-based applications Title/Authors/Affiliations AbstractThe rapid growth of digital technology in medical fields over recent years has increased the need for applications able to manage patient medical records, imaging data, and chart information. Web-based applications are implemented with the purpose to link digital databases, storage and transmission protocols, management of large volumes of data and security concepts, allowing the possibility to read, analyze, and even diagnose remotely from the medical center where the information was acquired. The objective of this paper is to analyze the use of the XML protocol in webbased medical imaging applications, analyzing how this protocol allows indexing and exchanging the huge amount of information associated with each medical case. The purpose of this paper is to point out the main advantages and drawbacks of the XML technology in order to provide key ideas for future web-based applications.

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A standard format and a graphical user interface for spin system specification

Cited by 11 publications

References 27 publications

Molecular NMR shieldings, J-couplings, and magnetizabilities from numeric atom-centered orbital based density-functional calculations

Molecular NMR shieldings, J-couplings, and magnetizabilities from numeric atom-centered orbital based density-functional calculations

Large‐scaleNMRsimulations in liquid state: A tutorial

On the Use of XML in Medical Imaging Web-Based Applications

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