Imperial College London

ProfessorJaspervan Thor

Faculty of Natural SciencesDepartment of Life Sciences

Professor of Molecular Biophysics



+44 (0)20 7594 5071j.vanthor Website




703Sir Ernst Chain BuildingSouth Kensington Campus




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

van Thor group 2016

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

Ultrafast lab van ThorThe 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

Ultrafast XFEL X-ray 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

Nonlinear optical crystallography

Recent news selection

Femtosecond infrared crystallography of Photosystem II

Revealing photosynthetic exciton dynamics in space and time

Current members of the Laboratory

show research

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



show research
  • 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. ‘New science for European ps time-resolved Laue X-ray diffraction'
  • 2008 - 2009 Royal Society Research grant ‘Time-resolved absorption measurements of light sensitive proteins'
  • 2004 - 2007 Interdisciplinary Research Centre (IRC), University of Oxford ‘Single-Molecule Studies of DNA / Photoreceptor Protein Nanomachines.'
  • 2004 - 2005 Royal Society Research grant ‘Light-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

show research

user-friendly data analysis for multi-pulse spectroscopy

    Global Fit Toolbox
  • 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 Tool Box
  • 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


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

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