Appendix C: literature citations

The following papers describe the major features found in Spinach. Please cite whatever is appropriate depending on the functionality that you use.

Primary citation

1. H.J. Hogben, M. Krzystyniak, G.T.P. Charnock, P.J. Hore, I. Kuprov, "Spinach - a software library for simulation of spin dynamics in large spin systems", Journal of Magnetic Resonance, 208 (2011) 179-194.

Kernel functionality

1. D.L. Goodwin, I.Kuprov, "Auxiliary matrix formalism for interaction representation transformations, optimal control, and spin relaxation theories", Journal of Chemical Physics, 143 (2015) 084113.
2. L.J. Edwards, I Kuprov, "Parallel density matrix propagation in spin dynamics simulations", Journal of Chemical Physics, 136 (2012) 044108.
3. A. Karabanov, I. Kuprov, G.T.P. Charnock, A. van der Drift, L.J. Edwards, W. Köckenberger, "On the accuracy of the state space restriction approximation for spin dynamics simulations", Journal of Chemical Physics, 135 (2011) 084106.
4. M. Krzystyniak, L.J. Edwards, I. Kuprov, "Destination state screening of active spaces in spin dynamics simulations", Journal of Magnetic Resonance, 210 (2011) 228-232.
5. H.J. Hogben, P.J. Hore, I. Kuprov, "Strategies for state space restriction in densely coupled spin systems with applications to spin chemistry", Journal of Chemical Physics, 132 (2010), 174101.
6. I. Kuprov, "Polynomially scaling spin dynamics II: further state space compression using Krylov subspace techniques and zero track elimination", Journal of Magnetic Resonance 195 (2008) 45-51.
7. I. Kuprov, N. Wagner-Rundell, P.J. Hore, "Polynomially scaling spin dynamics simulation algorithm based on adaptive state space restriction", Journal of Magnetic Resonance 189 (2007) 241-250.

Relaxation theory module

1. D.L. Goodwin, I.Kuprov, "Auxiliary matrix formalism for interaction representation transformations, optimal control, and spin relaxation theories", Journal of Chemical Physics, 143 (2015) 084113.
2. H.J. Hogben, P.J. Hore, I. Kuprov, "Multiple decoherence-free states in multi-spin systems", Journal of Magnetic Resonance, 211 (2011) 217-220.
3. I. Kuprov, "Diagonalization-free implementation of spin relaxation theory for large spin systems", Journal of Magnetic Resonance, 209 (2011) 31-38.
4. I. Kuprov, N. Wagner-Rundell, P.J. Hore, "Bloch-Redfield-Wangsness theory engine implementation using symbolic processing software", Journal of Magnetic Resonance 184 (2007) 196-206.

Optimal control module

1. D.L. Goodwin, I.Kuprov, "Modified Newton-Raphson GRAPE methods for optimal control of spin systems", Journal of Chemical Physics, 144 (2016) 204107.
2. D.L. Goodwin, I.Kuprov, "Auxiliary matrix formalism for interaction representation transformations, optimal control, and spin relaxation theories", Journal of Chemical Physics, 143 (2015) 084113.
3. I. Kuprov, "Spin system trajectory analysis under optimal control pulses", Journal of Magnetic Resonance, 233 (2013) 107-112.
4. P. de Fouquieres, S.G. Schirmer, S.J. Glaser, I. Kuprov, "Second order gradient ascent pulse engineering", Journal of Magnetic Resonance, 212 (2011) 412-417.
5. I. Kuprov, C.T. Rodgers, "Derivatives of spin dynamics simulations", Journal of Chemical Physics, 131 (2009) 234108.

DNP module

1. A. Karabanov, A. van der Drift, L.J. Edwards, I Kuprov, W. Köckenberger, "Quantum mechanical simulation of solid effect dynamic nuclear polarization using Krylov-Bogolyubov time averaging and a restricted state space", Physical Chemistry Chemical Physics, 14 (2012) 2658-2668.

Fokker-Planck module

1. I.M. Haies, J.A. Jarvis, L.J. Brown, I. Kuprov, P.T.F. Williamson, M. Carravetta, "14N overtone transition in double rotation solid-state NMR", Physical Chemistry Chemical Physics, 17 (2015) 23748-23753.
2. I.M. Haies, J.A. Jarvis, H. Bentley, I. Heinmaa, I. Kuprov, P.T.F. Williamson, M. Carravetta, "14N overtone NMR under MAS: signal enhancement using symmetry-based sequences and novel simulation strategies", Physical Chemistry Chemical Physics, 17 (2015) 6577-6587.
3. L.J. Edwards, D.V. Savostyanov, A.A. Nevzorov, M. Concistrè, G. Pileio, I. Kuprov, "Grid-free powder averages: On the applications of the Fokker–Planck equation to solid state NMR", Journal of Magnetic Resonance, 235 (2013) 121-129.

Tensor train module

1. D.V. Savostyanov, S.V. Dolgov, J.M. Werner, I. Kuprov, "Exact NMR simulation of protein-size spin systems using tensor train formalism", Physical Review B, 90 (2014) 085139.

Protein NMR module

1. D.V. Savostyanov, S.V. Dolgov, J.M. Werner, I. Kuprov, "Exact NMR simulation of protein-size spin systems using tensor train formalism", Physical Review B, 90 (2014) 085139.
2. L.J. Edwards, D.V. Savostyanov, Z.T. Welderufael, D. Lee, I. Kuprov, "Quantum mechanical NMR simulation algorithm for protein-size spin systems", Journal of Magnetic Resonance, 243 (2014) 107-113.

Built-in pulse sequences

1. R. Raj, I. Kuprov, K. Pervushin, "Benchmarking NMR experiments: a relational database of protein pulse sequences", Journal of Magnetic Resonance, 203 (2010), 129-137.

Graphical user interface

1. A. Biternas, G.T.P. Charnock, I. Kuprov, "A standard format and a graphical user interface for spin system specification", Journal of Magnetic Resonance, 240 (2014) 124-131.

Overtone spectroscopy

1. I.M. Haies, J.A. Jarvis, L.J. Brown, I. Kuprov, P.T.F. Williamson, M. Carravetta, "14N overtone transition in double rotation solid-state NMR", Physical Chemistry Chemical Physics, 17 (2015) 23748-23753.
2. I.M. Haies, J.A. Jarvis, H. Bentley, I. Heinmaa, I. Kuprov, P.T.F. Williamson, M. Carravetta, "14N overtone NMR under MAS: signal enhancement using symmetry-based sequences and novel simulation strategies", Physical Chemistry Chemical Physics, 17 (2015) 6577-6587.

PCS module

1. G.T.P. Charnock, I. Kuprov, "A partial differential equation for pseudocontact shift", Physical Chemistry Chemical Physics, 16 (2014) 20184-20189.