MOIN spin library - overview

The Magnetic resonance Open source INitiative (MOIN) spin library was designed and written in the Section Biomedical Imaging, Molecular Imaging North Competence Center (MOIN CC), Department of Radiology and Neuroradiology, University Medical Center Schleswig-Holstein (UKSH), Kiel University, by Andrey N. Pravdivtsev and Jan-Bernd Hövener in 2018. Much of the quantum mechanical part and its application to SABRE hyperpolarization was described in the publication:

A. N. Pravdivtsev and J.-B. Hövener, “Simulating Nonlinear Chemical and Physical (CAP) Dynamics of Signal Amplification By Reversible Exchange (SABRE)” // ‎Chem. Eur. J, 2019, 25, p. 7659, DOI: 10.1002/chem.201806133.

The MOIN spin library was developed for computation of various aspects of magnetic resonance (MR): performance of pulse sequences, hyperpolarization experiments, acquisition and reconstruction of MR-imaging and chemical exchange analysis. The library consists of three main parts:

1. Classical spin: evolution of single spin in homogeneous or inhomogeneous magnetic fields. Computation is realised using Block equations.
2. MR-imaging: evolution and acquisition of MR-signals from digital phantom with variably defined characteristics (proton (or other nuclei) density, initial polarization value, T1, T2-relaxation times) in inhomogeneous magnetic field. Computation is realised using Block equations for individual spin voxels.
3. Quantum mechanical treatment: evolution of a density matrix under arbitrary conditions. The purpose is to simulate multi spin systems in the liquid state, including NMR-spectra, spontaneous transfer of polarization or induced by RF, chemical exchange. The computations are realised using Liouville-von Neumann equations.

The library is an open source and comes with various examples and a manual. The user can use/modify/check already written functions/objects or develop his own. If there is an interest in shared development, we can move the code to GIThub.

In case of any questions, suggestions or contributions please contact:
Andrey N. Pravdivtsev, email: This email address is being protected from spambots. You need JavaScript enabled to view it. (This email address is being protected from spambots. You need JavaScript enabled to view it.), or
Jan-Bernd Hövener, email: This email address is being protected from spambots. You need JavaScript enabled to view it..

If you use the library for publications, please provide us with the source code so that we can make it available on this website. You may want to consider citing the above mentioned article or one of those below.

Disclaimer: some parts of the library are in developing stage and not have been tested properly and may contain mistakes. We are working on that. If you find issues, please let us know so that we can fix it.


MOIN spin library - releases

2019/02/20
The current version of the MOIN spin library [ link (ZIP) ]
Documentation of the MOIN spin library [ link (PDF) ]

List of papers where the MOIN library was used and the corresponding source codes:

1. A. N. Pravdivtsev, I. V. Skovpin, A. I. Svyatova, N. V. Chukanov, L. M. Kovtunova, V. I. Bukhtiyarov, E. Y. Chekmenev, K. V. Kovtunov, I. V. Koptyug, J.-B. Hövener, “Chemical exchange reaction effect on polarization transfer efficiency in SLIC-SABRE” // J. Phys. Chem. A, 2018, 122(46), pp 9107-9114. DOI: 10.1021/acs.jpca.8b07163. [link to the code archive (ZIP) ]

2. K. Buckenmaier, K. Scheffler, M. Plaumann, P. Fehling, J. Bernarding, M. Rudolph, C. Back, D. Koelled, R. Kleinerd, J.-B. Hövener, A. N. Pravdivtsev, “Hyperpolarized multiple quantum coherences at ultra‐low fields” // ChemPhysChem, 2019, DOI: 10.1002/cphc.201900757. [ link to the code archive (ZIP) ]

3. A. N. Pravdivtsev and J.-B. Hövener, “Simulating Nonlinear Chemical and Physical (CAP) Dynamics of Signal Amplification By Reversible Exchange (SABRE)” // ‎Chem. Eur. J, 2019, 25, p. 7659, DOI: 10.1002/chem.201806133. [ link to the code archive (ZIP) ]

4. D. A. Barskiy, M. Tayler, I. Marco-Rius, J. Kurhanewicz, D. B. Vigneron, S. Cikrikci, A. Aydogdu, M. Reh, A. N. Pravdivtsev, J.-B. Hovener, J. Blanchard, T. Wu, D. Budker, and A. Pines, “Zero-Field Nuclear Magnetic Resonance of Chemically Exchanging Systems” // Nat. Comm., 2019, 10(1), p. 3002, DOI: 10.1038/s41467-019-10787-9. [ link to the code archive (ZIP) ]

5. A. B. Schmidt, J. Wörner, A. N. Pravdivtsev, S. Knecht, H. Scherer, S. Weber, J. Hennig, D. von Elverfeldt, J.-B. Hövener, “Lifetime of parahydrogen in aqueous solutions and human blood” // ChemPhysChem, 2019, DOI: 10.1002/cphc.201900670. [ link to the code archive (ZIP) ]

6. A. N. Pravdivtsev F. D. Sönnichsen and J.-B. Hövener, “Continuous Radio Amplification by Stimulated Emission using Parahydrogen Induced Polarization (PHIP-raser) at 14 Tesla” // 07.2019. submitted. [ link to the code archive (ZIP) ]

Seminar materials

1. A. N. Pravdivtsev “My first MRI simulation” // DS-ISMRM, 12-13 September 2019, Kiel, Germany. [ link to the code archive (ZIP) ]

 

Last update 19.09.2019