Ultrafast structural dynamics
We work on the structural dynamics of light sensitive proteins, using primarily ultrafast pump-probe techniques. The main experimental methods that are used are ultrafast X-ray crystallography, ultrafast optical crystallography and ultrafast vibrational and visible spectroscopy. The research focuses on developing and using new experimental and also theoretical tools to find real-space information on ultrafast structural processes. We investigate light sensitive systems, including Fluorescent Proteins, Photosynthesis, and photoreceptor proteins such as Phytochromes and the Photoactive Yellow Protein
The van Thor group 2016
We combine ultrafast spectroscopy and ultrafast structural biology using X-ray Free Electron Lasers to reveal molecular dynamics details of important biological reactions.
Ultrafast spectroscopy
The ultrafast spectroscopy laboratory is a newly established state-of-the-art femtosecond spectroscopy lab located South Kensington Campus. We are using three KHz femtosecond regenerative amplifier systems to pump together seven OPA's as well as white light generators to provide a very wide range of experimental capabilities, some of which are unique, for ultrafast vibrational and visible spectroscopy, including multi-pulse and multi-colour experiments, bandwidth control and femtosecond pulse shaping in the visible, near-IR and mid-IR
Ultrafast vibrational dynamics are key and a focus in the laboratory, using broadband femtosecond infrared spectroscopy and Femtosecond Raman Spectroscopy. Complementary to our ultrafast X-ray studies we are developing methodologies for femtosecond optical crystallography, e.g. the polarised optical studies on oriented single crystals for the measurement of the structural dynamics using infrared and visible detection. For optimisation of TRIR we are using different bandgap selected 128 element MCT detector sets for dispersive and referenced detection and we develop instrumentation and software for improving sensitivity. The ultrafast spectroscopy laboratory is supported by the Royal Society, BBSRC, ERC, EPSRC and Imperial College London.
Software release - Ultrafast Spectroscopy Modelling Toolbox
SOFTWARE RELEASE - PyLDM - Open Source Lifetime Density Analysis
Ultrafast crystallography using X-ray free electron lasers
Femtosecond time resolved X-ray crystallography is a novel capability that uses X-ray Free Electron Lasers for pump-probe studies of reaction dynamics. A major challenge concerns the control of populations and coherence in protein crystals on ultrafast time scales, which needs supporting ultrafast spectroscopy, theory and calculation in order to prepare and assign femtosecond processes that are revealed. We are focusing on the development of increased experimental bandwidth and methods for detection of small transient populations. The XFEL research is supported by EPSRC and BBSRC
Recent news selection
Populations and Coherence in Femtosecond Time Resolved X-ray Crystallography
TR-SFX of biological Photoisomerisation
FEMTOSECOND INFRARED-OPTICAL CRYSTALLOGRAPHY
Polarised linear and non-linear optical measurements on oriented single crystals provide powerful and new structurally sensitive probes of protein dynamics. Femtosecond applications of visible or infrared optical crystallography methods can be uniquely analysed in real space provided that the X-ray crystallographic index is known for the laboratory orientation. The optical response functions hence become structurally filtered and response and dispersion depends on crystal symmetry.
Working on the interesting problem of photosynthetic exciton dynamics, we have shown a first ultrafast infrared crystallographic dynamics analysis of Photosystem II core complexes in real space and time
Recent news selection
Current members of the Laboratory
Dr Marius Kaucikas
Dr Violeta Cordon-Preciado
Mrs. Noura Zamzam
Dr. Christopher Hutchison
Mr Clyde Fare
Previous members
Dr Luuk J.G.W. van Wilderen
Dr Ann Fitzpatrick
Dr Craig N. Lincoln
Dr Mark Warren
Dr Konstantinos Bourdakos
Dr Pradeep Ramachandran
Mr Brendon Kellner
Dr K. C. Toh
Funding
- 2017-2021 BBSRC responsive mode grant: Serial Femtosecond Crystallography of Optogenetic Function
- 1015-2019 EPSRC responsive mode grant: Ultrafast time resolved protein X-ray crystallography
- 2014-2018 Leverhulme Trust grant. A Novel structural probe for the light reactions of Photosystem II
- 2010-2013 NSF/EPSRC international collaboration in Chemistry on control of excited state proton transfer in GFP
- 2010-2013 BBSRC responsive mode grant BB/H004238/1: Infrared crystallography of the Oxygen Evolving Complex reactions of Photosystem II. Co-IP Prof. Jim Barber
- 2008 - 2011. European Research Council, Starting Independent Researcher Grant. âNew science for European ps time-resolved Laue X-ray diffraction'
- 2008 - 2009 Royal Society Research grant âTime-resolved absorption measurements of light sensitive proteins'
- 2004 - 2007 Interdisciplinary Research Centre (IRC), University of Oxford âSingle-Molecule Studies of DNA / Photoreceptor Protein Nanomachines.'
- 2004 - 2005 Royal Society Research grant âLight-induced FTIR difference spectroscopy of the phytochrome Cph1
- 2002 - 1st October 2010 Royal Society University Research Fellowship
- 2000 - 2002 HFSP long-term research fellowship
- 2000 - 2000 EMBO long-term research fellowship
Ultrafast Spectroscopy Modelling Toolbox
user-friendly data analysis for multi-pulse spectroscopy
- User friendly Graphical User Interface, Matlab based
- Global analysis of time dependent data
- Demos and manual supplied with the program
- Singular Value Decomposition (SVD) and fitting of Left Singular Vectors using any model
- Instrument Response Function (IRF) and chirp
- Standard library of reaction models supplied
- Graphically design any connectivity ('target') model
- Store and re-use fitting session parameters
Photoselection theory applied to multiple pulses in the presence of decay
- Photoselection theory for finite bleach applied to pump-probe and multi-pulse (pump-dump-probe and pump-repump-probe) spectroscopy
- Explicit population, laser field orientation and decay dependence
- Angle resolved and ensemble averaged photolysed fraction calculation
- Beam diameters included for pump1, pump2 and probe
- Choice of Gaussian and multi-mode beams
- Fractional photolysis calculation required for correcting pump-dump-probe signal amplitudes
- Provides power density dependent corrections to measured anisotropy in photoselection studies
THIS SOFTWARE IS FREE TO DOWNLOAD AND USE.
Download Ultrafast_toolbox_v1_00
Please cite:
Modelling Multi-Pulse Population Dynamics from Ultrafast Spectroscopy. van Wilderen, L.J.G., Lincoln, C.N. & van Thor, J.J. (2011) PLoS ONE 6(3): e17373. doi:10.1371/journal.pone.0017373
email: j.vanthor@imperial.ac.uk
Guest Lectures
UK Bio-XFEL single particle imaging workshop, Rutherford Appleton Labs, Harwell, 2016
Protein Dynamics TSRC Conference at Les Houches, TSRC, Les Houches, France, 2016
4th International Workshop on Solar Energy for Sustainability “ Photosynthesis and Bioenergetics”, NTU, Singapore, 2016
Applications of Ultrafast and High Brightness X-rays, Imperial College London,, Physics Department, 2016
Technical University Munich, Chemistry Department, Munich, Germany, 2015
Protein Dynamics TSRC Conference, TSRC, Telluride, CO, USA, 2015
SILS XXIII 2015. Italian Synchrotron society, Trento University, Trento, Italy, 2015
TRVS, Timeresolved Vibrational Spectroscopy XVII, Madison, USA, 2015
EPSRC Midrange facility workshop, Kings College London, London, 2015
European XFEL MID, Materials Imaging and Dynamics Workshop, XFEL, Hamburg, 2015
QUEBS: Quantum effects on Biological Systems, Singapore, 2014
SwissFEL-PSI Photon Science Seminar, PSI, Swtzerland, 2014
110th International Titisee Conference, Structure, forces and dynamics of macromolecular complexes, Boehringer Ingleheim Foundation, 2014
IC3EM 2014, Lisbon, 2014
Prospective Applications of Attosecond Science workshop, Physics Department Imperial College London, 2014
Faraday Discussions Emerging Photon Technologies for Chemical Dynamics Faraday Discussion 171, Sheffield University, 2014
Protein Dynamics TSRC Conference, Les Houches, France,, 2014
1st Ringberg Meeting on Structural Biology with FELs, Ringberg castle, 2014
Bunty plot Imperial College, Imperial College London, 2013
ECSBM, European Conference on the Spectroscopy of Biological Molecules, St Catherine's College, 2013
TSRC Protein Dynamics, Telluride Science Research Conference, Telluride, Colorado, USA, 2013
International Conference on Photochemistry (ICP 2013), Leuven University, Belgium, 2013
TRVS, Timeresolved Vibrational Spectroscopy XVI, Beppu, Japan, 2013
BioCARS, Advanced Photon Source, Chicago, 2013
Exciton dynamics in natural and man made systems, Ein-Gedi, Israel, 2013
Chemometrics in time-resolved and imaging spectroscopy, Lille, France, 2012
American Crystallography Association Annual meeting, Boston, 2012
Ultrafast Dynamic Imaging of Matter Conference, Banff, Alberta, 2012
International Conference on Ultrafast Structural Dynamics (ICUSD), Berlin, Germany, 2012
Photoreceptor meeting, Kreuth, Germany, 2011
XXV International Conference on Photochemistry (ICP2011), Beijing, China, 2011
14th European Conference on the Spectroscopy of Biological Molecules (ECSBM, Portugal, 2011
TSRC Protein Dynamics, Telluride, USA, 2011
TRVS, Timeresolved Vibrational Spectroscopy XV, Ascona, Switzerland, 2011
Sixth International Conference on Advanced Vibrational Spectroscopy, California, 2011
Gentner symposium, Israel, 2010
Chemistry Department, Frankfurt University, Germany, 2010
Physics department, Free University Amsterdam, The Netherlands, 2010
TSRC Workshop on Protein Dynamics, Telluride, USA, USA, 2009
Northeastern University Boston, Boston, USA, 2009
TRVS, Meredith, USA, 2009
BCA annual spring meeting, Warwick, UK, 2009
PSI-XFEL Workshop, Basel, Switzerland, 2009
Bunty plot, Imperial College London, UK, 2008
New Light Source, Diamond House, UK, 2008
Max Born Institute, Berlin, Germany, 2008
Gordon conference on Photosensory receptors, Ventura, USA, 2008
12th European Conference on the Spectroscopy of Biological Molecules (ECSBM), Paris, France, 2007
TSRC Workshop on Protein Dynamics, Telluride, USA, 2007
6th European Biophysics Congress, London, 2007
Physics department, Free University Amsterdam, Netherlands, 2007
Clarendon Laboratory, Oxford, UK, 2007
ESRF, Grenoble, France, 2007
University College London, UK, 2007
Physics Department, Oxford University, 2007
Durham University, UK, 2006
Central Laser Facility, Chilton, UK, 2006
Durham University, UK, 2006
Cavendish laboratory, Cambridge University, UK, 2006
Gordon conference on Photosensory receptors, Italy, 2006
Spie Photonics West, San Jose, USA, 2006
Imperial College, London, 2005
Physical and Theoretical Chemistry Laboratory, Oxford, UK, 2005
Physical and Theoretical Chemistry Laboratory, Oxford University, UK, 2004
Workshop on Time Resolved Studies, Diamond, Abingdon, 2004
Imperial College, London, 2002
12th symposium on Bioluminescence and Chemilumiescence, Cambridge, UK, 2002
Biochemistry departmental seminar, Oxford University, UK, 2002
Protein Crystallography Data Collection Workshop, Daresbury Laboratory, Warrington, 2001