Spinach (software) explained

Spinach software
Latest Release Version:	2.8
Programming Language:	Matlab
Operating System:	Windows, Linux, macOS
Language:	English
Genre:	Magnetic resonance
Developer:	Ilya Kuprov (lead developer)
License:	MIT License

Spinach is an open-source magnetic resonance simulation package initially released in 2011 and continuously updated since. The package is written in Matlab and makes use of the built-in parallel computing and GPU interfaces of Matlab.

The name of the package whimsically refers to the physical concept of spin and to Popeye the Sailor who, in the eponymous comic books, becomes stronger after consuming spinach.

Overview

\rho \left( t \right) in the time domain:\begin{matrix} (\partial)/(\partial t) \rho \left( t \right) =- i L \left( t \right) \rho \left( t \right) \ \Downarrow \ \rho \left( t + dt \right) = \exp \left[ - i L \left( t \right)dt \right] \rho \left( t \right) \ \end{matrix} L \left( t \right) is a sum of the Hamiltonian commutation superoperator H \left( t \right) , relaxation superoperator R , kinetics superoperator K , and potentially other terms that govern spatial dynamics and coupling to other degrees of freedom:L \left( t \right) = H \left( t \right) + i R + i K + ...

Computational efficiency is achieved through the use of reduced state spaces, sparse matrix arithmetic, on-the-fly trajectory analysis, and dynamic parallelization.

Standard functionality

As of 2023, Spinach is cited in over 300 academic publications. According to the documentation and academic papers citing its features, the most recent version 2.8 of the package performs:

• Time-domain nuclear magnetic resonance (NMR) simulations of:
  • Standard NMR experiments (DEPT, COSY, NOESY, HSQC, TOCSY, etc.).
  • Protein and nucleic acid NMR experiments (HNCA, HNCOCA, HNCO, etc.).
  • Magic angle spinning NMR experiments (CP-MAS, MQMAS, WISE, etc.).
  • Experiments involving residual dipolar coupling and other residual order effects.
  • Zero- and ultra-low field experiments, including Earth's field NMR.
  • Nuclear quadrupole resonance, including overtone NMR.
• Time-domain magnetic resonance imaging (MRI) simulations, including:
  • Standard and user-specified imaging sequences.
  • Diffusion coefficient and diffusion tensor imaging.
  • Three-dimensional point-resolved NMR spectroscopy.
  • Ultrafast spatially encoded NMR spectroscopy.
• Time-domain electron spin resonance (ESR) simulations of:
  • Standard pulsed ESR experiments (HYSCORE, ENDOR, ESEEM, etc.).
  • Pulsed dipolar spectroscopy (DEER, RIDME, etc.).
  • Dynamic nuclear polarization for static and spinning samples.

Common models of spin relaxation (Redfield theory, stochastic Liouville equation, Lindblad theory) and chemical kinetics are supported, and a library of powder averaging grids is included with the package.

Optimal control module

Spinach contains an implementation the gradient ascent pulse engineering (GRAPE) algorithm for quantum optimal control. The documentation and the book describing the optimal control module of the package list the following features:

• L-BFGS quasi-Newton and Newton-Raphson GRAPE optimizers.
• Spin system trajectory analysis by coherence and correlation order.
• Spectrogram analysis of the pulse waveform.
• Prefixes, suffixes, keyholes, and freeze masks.
• Optimization of cooperative pulses and phase cycles.
• Waveform penalty functionals and instrument response.

Dissipative background evolution generators and control operators are supported, as well as ensemble control over distributions in common instrument calibration parameters, such as control channel power and offset.

References

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Notes and References

1. Hogben . H.J. . Krzystyniak . M. . Charnock . G.T.P. . Hore . P.J. . Kuprov . I. . Spinach – a software library for simulation of spin dynamics in large spin systems . Journal of Magnetic Resonance . 208 . 2 . 2011 . 1090-7807 . 10.1016/j.jmr.2010.11.008 . 179–194.
2. Web site: Spinach Documentation Wiki . SpinDynamics.org – Spin Dynamics Group . 28 July 2023 . 4 November 2023.
3. Concilio . M.G. . Large‐scale magnetic resonance simulations: a tutorial . Magnetic Resonance in Chemistry . 58 . 8 . 2020 . 0749-1581 . 10.1002/mrc.5018 . 691–717. free .
4. Krushelnitsky . A. . Hempel . G. . Jurack . H. . Ferreira . T.M. . Rocking motion in solid proteins studied by the ¹⁵N proton-decoupled R_1ρ relaxometry . Physical Chemistry Chemical Physics . 25 . 23 . 2023 . 1463-9076 . 10.1039/d3cp00444a . 15885–15896. free .
5. Book: Gutmann, T. . Groszewicz . P.B. . Buntkowsky . G. . Annual Reports on NMR Spectroscopy . Solid-state NMR of nanocrystals . 2019 . 0066-4103 . 10.1016/bs.arnmr.2018.12.001 . 1–82.
6. Williams . R.V. . Yang . J.-Y. . Moremen . K.W. . Amster . I.J. . Prestegard . J.H. . Measurement of residual dipolar couplings in methyl groups via carbon detection . Journal of Biomolecular NMR . 73 . 3-4 . 2019 . 0925-2738 . 10.1007/s10858-019-00245-5 . 191–198. 7020099 .
7. Kaseman . D.C. . Malone . M.W. . Tondreau . A. . Espy . M.A. . Williams . R.F. . Quantitation of nuclear magnetic resonance spectra at Earth’s magnetic field . Analytical Chemistry . 93 . 46 . 2021 . 0003-2700 . 10.1021/acs.analchem.1c02910 . 15349–15357.
8. Haies . I.M. . Jarvis . J.A. . Bentley . H. . Heinmaa . I. . Kuprov . I. . Williamson . P.T.F. . Carravetta . M. . ¹⁴N overtone NMR under MAS: signal enhancement using symmetry-based sequences and novel simulation strategies . Physical Chemistry Chemical Physics . 17 . 9 . 2015 . 1463-9076 . 10.1039/c4cp03994g . 6577–6587. free . 4673505 .
9. Web site: Spinach - a fast and general spin dynamics simulation library . 2023-11-27.
10. Book: Kuprov, I. . Spin: from basic symmetries to quantum optimal control . Notes on software engineering . Springer . 2023 . 978-3-031-05606-2 . 10.1007/978-3-031-05607-9_9 . 351–373.
11. Book: Kuprov, I. . Spin: from basic symmetries to quantum optimal control . Optimal control of spin systems . Springer . 2023 . 978-3-031-05606-2 . 10.1007/978-3-031-05607-9_8 . 313–349.
12. Khaneja . N. . Reiss . T. . Kehlet . C. . Schulte-Herbrüggen . T. . Glaser . S.J. . Optimal control of coupled spin dynamics: design of NMR pulse sequences by gradient ascent algorithms . Journal of Magnetic Resonance . 172 . 2 . 2005 . 1090-7807 . 10.1016/j.jmr.2004.11.004 . 296–305.
13. Dumez . J.-N. . Frequency-swept pulses for ultrafast spatially encoded NMR . Journal of Magnetic Resonance . 323 . 2021 . 1090-7807 . 10.1016/j.jmr.2020.106817 . 106817.
14. Allami . A.J. . Concilio . M.G. . Lally . P. . Kuprov . I. . Quantum mechanical MRI simulations: solving the matrix dimension problem . Science Advances . 5 . 7 . 2019-07-05 . 2375-2548 . 10.1126/sciadv.aaw8962 . free . 6641938 .
15. Guduff . L. . Kuprov . I. . van Heijenoort . C. . Dumez . J.-N. . Spatially encoded 2D and 3D diffusion-ordered NMR spectroscopy . Chemical Communications . 53 . 4 . 2017 . 1359-7345 . 10.1039/c6cc09028a . 701–704.
16. Book: Kuprov, I. . Spin: from basic symmetries to quantum optimal control . Incomplete basis sets . Springer . 2023 . 978-3-031-05606-2 . 10.1007/978-3-031-05607-9_7 . 291–312.
17. Redrouthu . V.S. . Mathies . G. . Efficient pulsed dynamic nuclear polarization with the X-inverse-X sequence . Journal of the American Chemical Society . 144 . 4 . 2022 . 0002-7863 . 10.1021/jacs.1c09900 . 1513–1516.