Difference between revisions of "Appendix C: literature citations"
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| − | The following papers describe the major features found in Spinach. Please cite whatever is appropriate depending on the functionality that you use. | + | The following papers describe the major features found in Spinach. Please cite whatever is appropriate depending on the functionality that you use. A complete unsorted list of our published papers is [http://spindynamics.org/publications here]. |
==Primary citation== | ==Primary citation== | ||
# 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. | # 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. | ||
| + | |||
| + | ==Tutorials== | ||
| + | # I.Kuprov, "''Large-scale NMR simulations in liquid state: a tutorial''", Magnetic Resonance in Chemistry, 2017 (early view, DOI: 10.1002/mrc.4660) | ||
==Kernel functionality== | ==Kernel functionality== | ||
| Line 22: | Line 25: | ||
# D.L. Goodwin, I.Kuprov, "''Modified Newton-Raphson GRAPE methods for optimal control of spin systems''", Journal of Chemical Physics, 144 ('''2016''') 204107. | # D.L. Goodwin, I.Kuprov, "''Modified Newton-Raphson GRAPE methods for optimal control of spin systems''", Journal of Chemical Physics, 144 ('''2016''') 204107. | ||
# 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. | # 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. | ||
| − | # I. Kuprov, "''Spin system trajectory analysis under optimal control pulses''", Journal of Magnetic Resonance, 233 (2013) 107-112. | + | # I. Kuprov, "''Spin system trajectory analysis under optimal control pulses''", Journal of Magnetic Resonance, 233 ('''2013''') 107-112. |
| − | # 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. | + | # 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. |
| − | # I. Kuprov, C.T. Rodgers, "''Derivatives of spin dynamics simulations''", Journal of Chemical Physics, 131 (2009) 234108. | + | # I. Kuprov, C.T. Rodgers, "''Derivatives of spin dynamics simulations''", Journal of Chemical Physics, 131 ('''2009''') 234108. |
==DNP module== | ==DNP module== | ||
| − | # 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. | + | # 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== | ==Fokker-Planck module== | ||
| − | # 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. | + | # 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. |
| − | # 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. | + | # 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. |
| − | # 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. | + | # 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. |
| + | # L. Guduff, A.J. Allami, C, van Heijenoort, J.-N. Dumez, I. Kuprov, "''Efficient simulation of ultrafast magnetic resonance experiments''", 19 ('''2017''') 17577-17586. | ||
| + | # L. Guduff, I. Kuprov, C. van Heijenoort, J.-N. Dumez, "''Spatially encoded 2D and 3D diffusion-ordered NMR spectroscopy''", 53 ('''2017''') 701-704. | ||
| + | # I. Kuprov, "''Fokker-Planck formalism in magnetic resonance simulations''", Journal of Magnetic Resonance 270 (2016) 124-135. | ||
==Tensor train module== | ==Tensor train module== | ||
| − | # 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. | + | # 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== | ==Protein NMR module== | ||
| − | # 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. | + | # 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. |
| − | # 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. | + | # 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== | ==Built-in pulse sequences== | ||
| − | # R. Raj, I. Kuprov, K. Pervushin, "''Benchmarking NMR experiments: a relational database of protein pulse sequences''", Journal of Magnetic Resonance, 203 (2010), 129-137. | + | # R. Raj, I. Kuprov, K. Pervushin, "''Benchmarking NMR experiments: a relational database of protein pulse sequences''", Journal of Magnetic Resonance, 203 ('''2010'''), 129-137. |
| − | ==SpinXML | + | ==SpinXML== |
| − | # 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. | + | # 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== | ==Overtone spectroscopy== | ||
| − | # 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. | + | # 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. |
| − | # 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. | + | # 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. |
| + | |||
| + | ==Paramagnetic NMR module== | ||
| + | # G.T.P. Charnock, I. Kuprov, "''A partial differential equation for pseudocontact shift''", Physical Chemistry Chemical Physics, 16 ('''2014''') 20184-20189. | ||
| + | # E.A. Suturina, I. Kuprov, "''Pseudocontact shifts from mobile spin labels''", Physical Chemistry Chemical Physics, 18 ('''2016''') 26412-26422. | ||
| + | # E.A. Suturina, D. Häussinger, K. Zimmermann, L. Garbuio, M. Yulikov, G. Jeschke, I. Kuprov, "''Model-free extraction of spin label position distributions from pseudocontact shift data''", 8 ('''2017''') 2751-2757. | ||
| − | + | ''Version 2.1, authors: [[Ilya Kuprov]]'' | |
| − | |||
| − | |||
Latest revision as of 12:22, 25 April 2026
The following papers describe the major features found in Spinach. Please cite whatever is appropriate depending on the functionality that you use. A complete unsorted list of our published papers is here.
Contents
Primary citation
- 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.
Tutorials
- I.Kuprov, "Large-scale NMR simulations in liquid state: a tutorial", Magnetic Resonance in Chemistry, 2017 (early view, DOI: 10.1002/mrc.4660)
Kernel functionality
- 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.
- L.J. Edwards, I Kuprov, "Parallel density matrix propagation in spin dynamics simulations", Journal of Chemical Physics, 136 (2012) 044108.
- 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.
- 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.
- 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.
- 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.
- 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
- 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.
- H.J. Hogben, P.J. Hore, I. Kuprov, "Multiple decoherence-free states in multi-spin systems", Journal of Magnetic Resonance, 211 (2011) 217-220.
- I. Kuprov, "Diagonalization-free implementation of spin relaxation theory for large spin systems", Journal of Magnetic Resonance, 209 (2011) 31-38.
- 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
- D.L. Goodwin, I.Kuprov, "Modified Newton-Raphson GRAPE methods for optimal control of spin systems", Journal of Chemical Physics, 144 (2016) 204107.
- 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.
- I. Kuprov, "Spin system trajectory analysis under optimal control pulses", Journal of Magnetic Resonance, 233 (2013) 107-112.
- 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.
- I. Kuprov, C.T. Rodgers, "Derivatives of spin dynamics simulations", Journal of Chemical Physics, 131 (2009) 234108.
DNP module
- 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
- 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.
- 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.
- 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.
- L. Guduff, A.J. Allami, C, van Heijenoort, J.-N. Dumez, I. Kuprov, "Efficient simulation of ultrafast magnetic resonance experiments", 19 (2017) 17577-17586.
- L. Guduff, I. Kuprov, C. van Heijenoort, J.-N. Dumez, "Spatially encoded 2D and 3D diffusion-ordered NMR spectroscopy", 53 (2017) 701-704.
- I. Kuprov, "Fokker-Planck formalism in magnetic resonance simulations", Journal of Magnetic Resonance 270 (2016) 124-135.
Tensor train module
- 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
- 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.
- 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
- R. Raj, I. Kuprov, K. Pervushin, "Benchmarking NMR experiments: a relational database of protein pulse sequences", Journal of Magnetic Resonance, 203 (2010), 129-137.
SpinXML
- 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
- 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.
- 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.
Paramagnetic NMR module
- G.T.P. Charnock, I. Kuprov, "A partial differential equation for pseudocontact shift", Physical Chemistry Chemical Physics, 16 (2014) 20184-20189.
- E.A. Suturina, I. Kuprov, "Pseudocontact shifts from mobile spin labels", Physical Chemistry Chemical Physics, 18 (2016) 26412-26422.
- E.A. Suturina, D. Häussinger, K. Zimmermann, L. Garbuio, M. Yulikov, G. Jeschke, I. Kuprov, "Model-free extraction of spin label position distributions from pseudocontact shift data", 8 (2017) 2751-2757.
Version 2.1, authors: Ilya Kuprov
