Imperial College London

ProfessorJaspervan Thor

Faculty of Natural SciencesDepartment of Life Sciences

Professor of Molecular Biophysics
 
 
 
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Contact

 

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

 
 
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Location

 

703Sir Ernst Chain BuildingSouth Kensington Campus

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Summary

 

Publications

Publication Type
Year
to

71 results found

Hutchison CDM, van Thor JJ, 2019, Optical control, selection and analysis of population dynamics in ultrafast protein X-ray crystallography, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol: 377, Pages: 20170474-20170474, ISSN: 1364-503X

JOURNAL ARTICLE

van Thor JJ, 2019, Coherent two-dimensional electronic and infrared crystallography, The Journal of Chemical Physics, Vol: 150, ISSN: 0021-9606

The two-dimensional electronic and infrared spectroscopy of oriented single crystals is sensitive to structure and point group symmetry. The third order response of crystals is generally different from measurements of isotropic solutions because each coherence path that contributes to the measured field scales to the ensemble average of the four-point correlation functions of the four field-dipole interactions involved in the respective Feynman paths. An analytical evaluation of 2D optical crystallography which depends on the crystal symmetry, laboratory orientation, and the orientation in the crystallographic frame is presented. Applying a symmetry operator in the basis of the allowed polarised radiation modes provides a method for evaluation of non-zero fourth rank tensor elements alternative to direct inspection methods. Uniaxial and biaxial systems are distinguished and the contributions to the rephasing and non-rephasing directions are evaluated for isolated and coupled oscillators. By exploiting coordinate analysis, the extension of non-linear electronic and infrared crystallography for coupled oscillators demonstrates the structural, directional, and symmetry dependent selection of coherences to the four-wave mixing signal.

JOURNAL ARTICLE

Zamzam N, Kaucikas M, Nurnberg DJ, Rutherford AW, van Thor JJet al., 2019, Femtosecond infrared spectroscopy of chlorophyll f-containing photosystem I, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, Vol: 21, Pages: 1224-1234, ISSN: 1463-9076

JOURNAL ARTICLE

Sanchez-Gonzalez A, Johnson AS, Fitzpatrick A, Hutchison CDM, Fare C, Cordon-Preciado V, Dorlhiac G, Ferreira JL, Morgan RM, Marangos JP, Owada S, Nakane T, Tanaka R, Tono K, Iwata S, van Thor JJet al., 2017, Coincidence timing of femtosecond optical pulses in an X-ray free electron laser, JOURNAL OF APPLIED PHYSICS, Vol: 122, ISSN: 0021-8979

JOURNAL ARTICLE

Hutchison CDM, Cordon-Preciado V, Morgan RML, Nakane T, Ferreira J, Dorlhiac G, Sanchez-Gonzalez A, Johnson AS, Fitzpatrick A, Fare C, Marangos JP, Yoon CH, Hunter MS, DePonte DP, Boutet S, Owada S, Tanaka R, Tono K, Iwata S, van Thor JJet al., 2017, X-ray Free Electron Laser Determination of Crystal Structures of Dark and Light States of a Reversibly Photoswitching Fluorescent Protein at Room Temperature, INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, Vol: 18, ISSN: 1422-0067

JOURNAL ARTICLE

Dorlhiac GF, Fare C, van Thor JJ, 2017, PyLDM - An open source package for lifetime density analysis of time-resolved spectroscopic data, PLOS COMPUTATIONAL BIOLOGY, Vol: 13, ISSN: 1553-734X

JOURNAL ARTICLE

Kaucikas M, Nurnberg D, Dorlhiac G, Rutherford AW, van Thor JJet al., 2017, Femtosecond Visible Transient Absorption Spectroscopy of Chlorophyll f-Containing Photosystem I, BIOPHYSICAL JOURNAL, Vol: 112, Pages: 234-249, ISSN: 0006-3495

JOURNAL ARTICLE

Kaucikas M, Barber J, Renger T, Van Thor JJet al., 2017, Femtosecond infrared crystallography of photosystem II core complexes: Watching exciton dynamics and charge separation in real space and time, Photosynthesis and Bioenergetics, Pages: 81-116, ISBN: 9789813230293

© 2018 by World Scientific Publishing Co. Pte. Ltd. All rights reserved. We have shown structurally sensitive femtosecond time resolved infrared crystallography of oriented orthorhombic single crystals of photosystem II core complexes of Synechococcus elongatus, which allows a real-space analysis of exciton dynamics and charge separation. Directional selection of both the visible excitation and the infrared probes prepares and measures populations selectively which are analysed on the basis of X-ray crystallographic coordinates. Excited state chlorophyll a infrared absorption allows a real space probe of exciton dynamics in the local, single pigment, basis. Two contrasting models, known as the trap-limited and as transfer-to-the-trap limited model are critically tested. The dichroic amplitudes that result from photoselection are maintained on the ~60 ps time-scale that corresponds to the dominant energy transfer process which directly supports the transfer-to-the-trap limitation of the overall light-harvesting process. A detailed comparison with structure-based theory of exciton dynamics in photosystem II extends existing theory to the crystallographic case. On nanosecond time-scale non-crystallographic symmetry is developed for a structural measurement of the P680+/Pheo- charge separated state that supports the mode assignments for Pheo/Pheo- and P680/P680+.

BOOK CHAPTER

Hutchison CDM, van Thor JJ, 2017, Populations and coherence in femtosecond time resolved X-ray crystallography of the photoactive yellow protein, INTERNATIONAL REVIEWS IN PHYSICAL CHEMISTRY, Vol: 36, Pages: 117-143, ISSN: 0144-235X

JOURNAL ARTICLE

Kaucikas M, Maghlaoui K, Barber J, Renger T, van Thor JJet al., 2016, Ultrafast infrared observation of exciton equilibration from oriented single crystals of photosystem II, NATURE COMMUNICATIONS, Vol: 7, ISSN: 2041-1723

JOURNAL ARTICLE

Salna B, Benabbas A, Sage JT, van Thor J, Champion PMet al., 2016, Wide-dynamic-range kinetic investigations of deep proton tunnelling in proteins, NATURE CHEMISTRY, Vol: 8, Pages: 874-880, ISSN: 1755-4330

JOURNAL ARTICLE

Hutchison CDM, Kaucikas M, Tenboer J, Kupitz C, Moffat K, Schmidt M, van Thor JJet al., 2016, Photocycle populations with femtosecond excitation of crystalline photoactive yellow protein, CHEMICAL PHYSICS LETTERS, Vol: 654, Pages: 63-71, ISSN: 0009-2614

JOURNAL ARTICLE

Pande K, Hutchison CDM, Groenhof G, Aquila A, Robinson JS, Tenboer J, Basu S, Boutet S, DePonte DP, Liang M, White TA, Zatsepin NA, Yefanov O, Morozov D, Oberthuer D, Gati C, Subramanian G, James D, Zhao Y, Koralek J, Brayshaw J, Kupitz C, Conrad C, Roy-Chowdhury S, Coe JD, Metz M, Xavier PL, Grant TD, Koglin JE, Ketawala G, Fromme R, Srajer V, Henning R, Spence JCH, Ourmazd A, Schwander P, Weierstall U, Frank M, Fromme P, Barty A, Chapman HN, Moffat K, van Thor JJ, Schmidt Met al., 2016, Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein, SCIENCE, Vol: 352, Pages: 725-729, ISSN: 0036-8075

JOURNAL ARTICLE

Kim TW, Yang C, Kim Y, Kim JG, Kim J, Jung YO, Jun S, Lee SJ, Park S, Kosheleva I, Henning R, van Thore JJ, Ihee Het al., 2016, Combined probes of X-ray scattering and optical spectroscopy reveal how global conformational change is temporally and spatially linked to local structural perturbation in photoactive yellow protein, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, Vol: 18, Pages: 8911-8919, ISSN: 1463-9076

JOURNAL ARTICLE

Kaucikas M, Fitzpatrick A, Bryan E, Struve A, Henning R, Kosheleva I, Srajer V, Groenhof G, Van Thor JJet al., 2015, Room temperature crystal structure of the fast switching M159T mutant of the fluorescent protein dronpa, PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, Vol: 83, Pages: 397-402, ISSN: 0887-3585

JOURNAL ARTICLE

Kaucikas M, Tros M, van Thor JJ, 2015, Photoisomerization and Proton Transfer in the Forward and Reverse Photoswitching of the Fast-Switching M159T Mutant of the Dronpa Fluorescent Protein, JOURNAL OF PHYSICAL CHEMISTRY B, Vol: 119, Pages: 2350-2362, ISSN: 1520-6106

JOURNAL ARTICLE

van Thor JJ, Madsen A, 2015, A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography, STRUCTURAL DYNAMICS, Vol: 2, ISSN: 2329-7778

JOURNAL ARTICLE

van Wilderen LJGW, Silkstone G, Mason M, van Thor JJ, Wilson MTet al., 2015, Kinetic studies on the oxidation of semiquinone and hydroquinone forms of Arabidopsis cryptochrome by molecular oxygen, FEBS OPEN BIO, Vol: 5, Pages: 885-892, ISSN: 2211-5463

JOURNAL ARTICLE

Tenboer J, Basu S, Zatsepin N, Pande K, Milathianaki D, Frank M, Hunter M, Boutet S, Williams GJ, Koglin JE, Oberthuer D, Heymann M, Kupitz C, Conrad C, Coe J, Roy-Chowdhury S, Weierstall U, James D, Wang D, Grant T, Barty A, Yefanov O, Scales J, Gati C, Seuring C, Srajer V, Henning R, Schwander P, Fromme R, Ourmazd A, Moffat K, Van Thor JJ, Spence JCH, Fromme P, Chapman HN, Schmidt Met al., 2014, Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein, SCIENCE, Vol: 346, Pages: 1242-1246, ISSN: 0036-8075

JOURNAL ARTICLE

Thompson LM, Champion PM, Sage JT, Frisch MJ, van Thor JJ, Bearpark MJet al., 2014, Analytical harmonic vibrational frequencies for the green fluorescent protein computed with ONIOM: Chromophore mode character and its response to environment, 247th National Spring Meeting of the American-Chemical-Society (ACS), Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727

CONFERENCE PAPER

Thompson LM, Lasoroski A, Champion PM, Sage JT, Frisch MJ, van Thor JJ, Bearpark MJet al., 2014, Analytical Harmonic Vibrational Frequencies for the Green Fluorescent Protein Computed with ONIOM: Chromophore Mode Character and Its Response to Environment, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, Vol: 10, Pages: 751-766, ISSN: 1549-9618

JOURNAL ARTICLE

van Thor JJ, Warren MM, Lincoln CN, Chollet M, Lemke HT, Fritz DM, Schmidt M, Tenboer J, Ren Z, Srajer V, Moffat K, Graber Tet al., 2014, Signal to noise considerations for single crystal femtosecond time resolved crystallography of the Photoactive Yellow Protein, FARADAY DISCUSSIONS, Vol: 171, Pages: 439-455, ISSN: 1359-6640

JOURNAL ARTICLE

Juozapavicius M, Kaucikas M, Dimitrov SD, Barnes PRF, van Thor JJ, O'Regan BCet al., 2013, Evidence for "Slow" Electron Injection in Commercially Relevant Dye-Sensitized Solar Cells by vis-NIR and IR Pump-Probe Spectroscopy, JOURNAL OF PHYSICAL CHEMISTRY C, Vol: 117, Pages: 25317-25324, ISSN: 1932-7447

JOURNAL ARTICLE

Kaucikas M, Barber J, Van Thor JJ, 2013, Polarization sensitive ultrafast mid-IR pump probe micro-spectrometer with diffraction limited spatial resolution, OPTICS EXPRESS, Vol: 21, Pages: 8357-8370, ISSN: 1094-4087

JOURNAL ARTICLE

Kaucikas M, Warren M, Michailovas A, Antanavicius R, van Thor JJet al., 2013, Beam patterns in an optical parametric oscillator set-up employing walk-off compensating beta barium borate crystals, LASER PHYSICS, Vol: 23, ISSN: 1054-660X

JOURNAL ARTICLE

Warren MM, Kaucikas M, Fitzpatrick A, Champion P, Sage JT, van Thor JJet al., 2013, Ground-state proton transfer in the photoswitching reactions of the fluorescent protein Dronpa, NATURE COMMUNICATIONS, Vol: 4, ISSN: 2041-1723

JOURNAL ARTICLE

Juozapavicius M, Kaucikas M, van Thor JJ, O'Regan BCet al., 2013, Observation of Multiexponential Pico- to Subnanosecond Electron Injection in Optimized Dye-Sensitized Solar Cells with Visible-Pump Mid-Infrared-Probe Transient Absorption Spectroscopy, JOURNAL OF PHYSICAL CHEMISTRY C, Vol: 117, Pages: 116-123, ISSN: 1932-7447

JOURNAL ARTICLE

Kim TW, Lee JH, Choi J, Kim KH, van Wilderen LGW, Guerin L, Kim Y, Yung YO, Yang C, Kim J, Wulff M, van Thor JJ, Ihee Het al., 2013, Unravelling the protein structural dynamics of photoactive yellow protein in solution using pump-probe X-ray solution scattering

BOOK CHAPTER

van Thor JJ, Lincoln CN, Kellner B, Bourdakos KN, Thompson LM, Bearpark MJ, Champion PM, Sage JTet al., 2012, Ultrafast vibrational dynamics of parallel excited state proton transfer reactions in the Green Fluorescent Protein, VIBRATIONAL SPECTROSCOPY, Vol: 62, Pages: 1-6, ISSN: 0924-2031

JOURNAL ARTICLE

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