Spin Dynamics - from quantum theory to cancer diagnostics
Lead Research Organisation:
University of Oxford
Department Name: Oxford e-Research Centre
Abstract
This project addresses a long-standing problem in the physics and chemistry of magnetic phenomena -- the lack of efficient simulation algorithms for quantum spin dynamics.All magnetic processes can be traced back to a property of elementary particles called 'spin', but until recently the calculations of realistic systems could only be done for less than ten spins - a major limitation, particularly in chemical and biological magnetic spectroscopy, where the molecules often contain hundreds of spins.We recently solved this theoretical problem and will now proceed to implement and use the resulting high-efficiency algorithms to boost a number of research projects in magnetochemistry and biological magnetic resonance.Specifically, biological magnetoreceptors (some migratory birds feel the Earth's magnetic field and use it for navigation) can now be simulated and analysed, and so can paramagnetic cancer diagnostics agents, which are currently used in early cancer detection by MRI (magnetic resonance imaging). We have published a number of research papers in both areas and expect these research fields to benefit significantly from the expanded simulation capabilities.There are also a number of long-standing problems within chemistry itself, which can be solved now that large spin systems can be simulated -- protein structure determination can be streamlined and simplified, the analysis of magnetic spectroscopy experiments is no longer constrained by the available computer power, the questions about the possible chemical and biological effects of mobile phones and power transmission lines can be evaluated using quantum mechanical simulations of spin dynamics. Last, but not least, money can be saved and animal lives spared by theoretical pre-screening of molecules before running an experiment.On the practical level, the research programme will include:1. Theoretical segment: further investigation and optimization of high-efficiency spin dynamics simulation algorithms.2. Software segment: creation and testing of powerful user-friendly open-source software package for spin dynamics simulation of chemical and biological systems.3. Applications segment: application of the resulting theory and software to the investigation of magnetic phenomena in chemistry and biology.We believe this is an exciting and timely research project that will bring direct benefits to the society by creating powerful and efficient tools for fundamental and applied research as well as by addressing current questions and concerns relating to magnetism.
Organisations
People |
ORCID iD |
Ilya Kuprov (Principal Investigator) |
Publications
Auer R
(2011)
Mathematical treatment of adiabatic fast passage pulses for the computation of nuclear spin relaxation rates in proteins with conformational exchange.
in Journal of biomolecular NMR
Biternas AG
(2014)
A standard format and a graphical user interface for spin system specification.
in Journal of magnetic resonance (San Diego, Calif. : 1997)
Chalmers KH
(2010)
Design principles and theory of paramagnetic fluorine-labelled lanthanide complexes as probes for (19)F magnetic resonance: a proof-of-concept study.
in Chemistry (Weinheim an der Bergstrasse, Germany)
Charnock G
(2014)
A partial differential equation for pseudocontact shift
Charnock G
(2012)
Molecular structure refinement by direct fitting of atomic coordinates to experimental ESR spectra
in Journal of Magnetic Resonance
Charnock GT
(2014)
A partial differential equation for pseudocontact shift.
in Physical chemistry chemical physics : PCCP
De Fouquieres P
(2011)
Second order gradient ascent pulse engineering.
in Journal of magnetic resonance (San Diego, Calif. : 1997)
Dias DM
(2011)
Enantioselective binding of a lanthanide(III) complex to human serum albumin studied by 1H STD NMR techniques.
in Organic & biomolecular chemistry
Dmitry Savostyanov (Author)
(2013)
Quasioptimality of maximum-volume cross interpolation of tensors
in SIAM Journal on Matrix Analysis and Applications
Dolgov S
(2014)
Computation of extreme eigenvalues in higher dimensions using block tensor train format
in Computer Physics Communications
Edwards L
(2011)
Parallel density matrix propagation in spin dynamics simulations
Edwards L
(2014)
Quantum mechanical NMR simulation algorithm for protein-size spin systems
in Journal of Magnetic Resonance
Edwards LJ
(2012)
Parallel density matrix propagation in spin dynamics simulations.
in The Journal of chemical physics
Edwards LJ
(2014)
Simulation of coherence selection by pulsed field gradients in liquid-state NMR using an auxiliary matrix formalism.
in Journal of magnetic resonance (San Diego, Calif. : 1997)
Edwards LJ
(2013)
Grid-free powder averages: on the applications of the Fokker-Planck equation to solid state NMR.
in Journal of magnetic resonance (San Diego, Calif. : 1997)
Goodwin DL
(2016)
Modified Newton-Raphson GRAPE methods for optimal control of spin systems.
in The Journal of chemical physics
Goodwin DL
(2015)
Auxiliary matrix formalism for interaction representation transformations, optimal control, and spin relaxation theories.
in The Journal of chemical physics
Haies I
(2015)
14 N overtone NMR under MAS: signal enhancement using symmetry-based sequences and novel simulation strategies
in Physical Chemistry Chemical Physics
Haies IM
(2015)
(14)N overtone transition in double rotation solid-state NMR.
in Physical chemistry chemical physics : PCCP
Harvey P
(2011)
Lanthanide Complexes as Paramagnetic Probes for 19 F Magnetic Resonance
in European Journal of Inorganic Chemistry
Hogben H
(2011)
Multiple decoherence-free states in multi-spin systems
Hogben H
(2011)
Spinach - A software library for simulation of spin dynamics in large spin systems
in Journal of Magnetic Resonance
Hogben HJ
(2011)
Multiple decoherence-free states in multi-spin systems.
in Journal of magnetic resonance (San Diego, Calif. : 1997)
Hogben HJ
(2010)
Strategies for state space restriction in densely coupled spin systems with applications to spin chemistry.
in The Journal of chemical physics
Jarvis JA
(2019)
Quantitative analysis of 14N quadrupolar coupling using 1H detected 14N solid-state NMR.
in Physical chemistry chemical physics : PCCP
Jarvis JA
(2017)
Measurement of 14N quadrupole couplings in biomolecular solids using indirect-detection 14N solid-state NMR with DNP.
in Chemical communications (Cambridge, England)
Karabanov A
(2012)
Quantum mechanical simulation of solid effect dynamic nuclear polarisation using Krylov-Bogolyubov time averaging and a restricted state-space.
in Physical chemistry chemical physics : PCCP
Karabanov A
(2011)
On the accuracy of the state space restriction approximation for spin dynamics simulations.
in The Journal of chemical physics
Kolmer A
(2015)
Conformational analysis of small organic molecules using NOE and RDC data: A discussion of strychnine and a-methylene-?-butyrolactone.
in Journal of magnetic resonance (San Diego, Calif. : 1997)
Krzystyniak M
(2011)
Destination state screening of active spaces in spin dynamics simulations.
in Journal of magnetic resonance (San Diego, Calif. : 1997)
Kummerlöwe G
(2011)
Variable angle NMR spectroscopy and its application to the measurement of residual chemical shift anisotropy.
in Journal of magnetic resonance (San Diego, Calif. : 1997)
Kuprov I
(2011)
Diagonalization-free implementation of spin relaxation theory for large spin systems.
in Journal of magnetic resonance (San Diego, Calif. : 1997)
Kuprov I
(2009)
Derivatives of spin dynamics simulations.
in The Journal of chemical physics
Kuprov I
(2018)
Large-scale NMR simulations in liquid state: A tutorial.
in Magnetic resonance in chemistry : MRC
Kuprov I
(2015)
Anomalous Nuclear Overhauser Effects in Carbon-Substituted Aziridines: Scalar Cross-Relaxation of the First Kind
in Angewandte Chemie International Edition
Kuprov I
(2013)
Spin system trajectory analysis under optimal control pulses.
in Journal of magnetic resonance (San Diego, Calif. : 1997)
Kuprov I
(2015)
Anomalous Nuclear Overhauser Effects in Carbon-Substituted Aziridines: Scalar Cross-Relaxation of the First Kind
in Angewandte Chemie
Mamone S
(2013)
Nuclear magnetic resonance of hydrogen molecules trapped inside C70 fullerene cages.
in Chemphyschem : a European journal of chemical physics and physical chemistry
Natrajan LS
(2010)
Probing the structure, conformation, and stereochemical exchange in a family of lanthanide complexes derived from tetrapyridyl-appended cyclen.
in Inorganic chemistry
Pileio G
(2012)
Long-lived nuclear singlet order in near-equivalent 13C spin pairs.
in Journal of the American Chemical Society
Santabarbara S
(2010)
Directionality of electron-transfer reactions in photosystem I of prokaryotes: universality of the bidirectional electron-transfer model.
in The journal of physical chemistry. B
Savostyanov D
(2013)
Quasioptimality of maximum-volume cross interpolation of tensors
Savostyanov D
(2014)
Quasioptimality of maximum-volume cross interpolation of tensors
in Linear Algebra and its Applications
Savostyanov D
(2014)
Exact NMR simulation of protein-size spin systems using tensor train formalism
in Physical Review B
Title | Spin dynamics simulation package |
Description | The algorithms resulting from this project have been implemented into the open source simulation package, called Spinach, maintained by Kuprov group (http://spindynamics.org). |
Type Of Technology | Software |
Year Produced | 2012 |
Open Source License? | Yes |
Impact | See the published papers |
URL | http://spindynamics.org |