Laboratory of Biophysics
- We study the primary processes of bacterial photosynthesis spectroscopically and by computer modeling
- The samples under study are pigment-protein complexes separated from natural or genetically modified photosynthetic bacteria. Several biochemisrty labs around the world provide us the samples.
- We measure absorption, emission and polarization spectra from ultraviolet (protein bands) to near infrared (pigment bands).
- Continuous wave lasers are used for high-resolution spectroscopy and ultrafast pulsed lasers for the measurement of emission decay kinetics.
- A diamond anvil cell enables to apply to the samples hydrostatic pressure up to 50 kbar and a helium cryostat to cool them down to 10 K temperature.
- Spectral and time-dependent data measured at different pressures and temperatures for various different complexes combined with the results of molecular dynamics and quantum chemical calculations and the structure data give new information about the energy transfer processes in photosynthesis.
- Additional info on biophysics lab is available from: utbiophys.eu
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| Arvi Freiberg head of lab professor in biophysics, dr. sci., academician, TÜMRI chair of biophysics and plant physiology E-mail: arvi.freiberg@ut.ee Phone: 5645 3175, 737 4612 Office: D101 CV, references: ETIS, ORCID, Eesti TA Publications: Google Scholar, Publons, Mendeley, Scopus, Researchgate Teaching: UT Study Info System ( + Search )Supervision: UT DSpace |
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| Margus Rätsep † associate professor in optics and spectroscopy, PhD CV, references: ETIS, ORCID Publications: Mendeley, Scopus, Researchgate Teaching: UT Study Info System ( + Search )Supervision: UT DSpace |
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| Kõu Timpmann associate professor in biophysics, cand. sci. E-mail: kou.timpmann@ut.ee Phone: 5345 6149, 737 4738, 737 4739 Office: D103, Lab: D113 CV, viited: ETIS, ORCID Publikatsioonid: Mendeley, Scopus, Researchgate Teaching: UT Study Info System ( + Search )Supervision: UT DSpace |
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| Erko Jalviste research fellow in optics and spectroscopy, PhD E-mail: erko.jalviste@ut.ee Phone: 505 2383, 737 4738 Office: D103 CV, references: ETIS, ORCID, LinkedIn Publications: Google Scholar, Publons, Mendeley, Scopus, Researchgate Teaching: UT Study Info System ( + Search ) |
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| Liina Kangur research fellow in biochemistry, PhD E-mail: liina.kangur@ut.ee Phone: 507 1061 Lab: D116 CV, references: ETIS Publications: Mendeley, Scopus, Researchgate Teaching: UT Study Info System ( + Search )Supervision: UT DSpace |
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| Kristjan Leiger research fellow in biophysics, PhD E-mail: kristjan.leiger@ut.ee Phone: 737 4747 Office: D111, Lab: D115 CV, references: ETIS, ORCID Publications: Mendeley, Scopus, Researchgate Teaching: UT Study Info System ( + Search )Supervision: UT DSpace |
| Ali Jafarov MSc student | |
| Alexandra Lehtmets MSc student | |
| Laura Hitrova student | |
| Joanna Liisa Orav student | |
| Helis Paas student | |
| Lee Vaalma student |
- Team grant "New Insights into Photosynthetic Excitations Enabled by High-pressure Perturbation Spectroscopy" (2020-2024) PRG664 Arvi Freiberg
- Start-up grant "Energy transfer in the photosynthetic unit of green sulphur bacterium" (2019−2022) PSG264 Juha Matti Linnanto
- COST action CA21146 "Fundamentals and applications of purple bacteria biotechnology for resource recovery from waste (PURPLEGAIN)" (2022-2025) Arvi Freiberg
- Estonian-Hungarian joint research project supported by their academies of sciences “Structural dynamics of Photosystem II as studied by steady-state and time-resolved spectroscopy at high pressures” (2022–2024) Arvi Freiberg
- M. Rätsep; L. Kangur; K. Leiger; Z.Y. Wang-Otomo; A. Freiberg (2025). "Comparative thermo- and piezostability study of photosynthetic core complexes containing bacteriochlorophyll a or b." Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1866 (1), 149527.
- K. Timpmann; M. Rätsep; E. Jalviste; A. Freiberg (2024). "Tuning by Hydrogen Bonding in Photosynthesis." The Journal of Physical Chemistry B, 128 (38), 9120−9131.
- M. Rätsep; A. Lehtmets; L. Kangur; K. Timpmann; K. Leiger; Z.Y. Wang-Otomo; A. Freiberg (2023). "Evaluation of the relationship between color-tuning of photosynthetic excitons and thermodynamic stability of light-harvesting chromoproteins." Photosynthetica, 61 (3), 308−317.
- K. Timpmann; M. Rätsep; A. Freiberg (2023). "Dominant role of excitons in photosynthetic color-tuning and light-harvesting." Frontiers in Chemistry, 11, ARTN 1231431.
- J.R. Reimers; M. Rätsep; J.M. Linnanto; A. Freiberg (2022). "Chlorophyll spectroscopy: conceptual basis, modern high-resolution approaches, and current challenges." Proceedings of the Estonian Academy of Sciences, 71 (2), 127-164.
- K. Timpmann; J.M. Linnanto; D. Yadav; L. Kangur; A.Freiberg (2021). "Hydrostatic High-Pressure-Induced Denaturation of LH2 Membrane Proteins." The Journal of Physical Chemistry B, 125 (35), 9979–9989.
- K. Timpmann; L. Kangur; A Lehtmets; Z.Y. Wang-Otomo, A. Freiberg (2021). "Exciton Origin of Color-Tuning in Ca2+-Binding Photosynthetic Bacteria." International Journal of Molecular Sciences, 22 (14), 7338.
- K. Leiger; J.M. Linnanto; A. Freiberg (2020). "Establishment of the Qy Absorption Spectrum of Chlorophyll a Extending to Near-Infrared." Molecules, 25 (17), 3796.
J.R. Reimers; M. Rätsep; A. Freiberg (2020). "Asymmetry in the Qy Fluorescence and Absorption Spectra of Chlorophyll a Pertaining to Exciton Dynamics." Frontiers in Chemistry, 588289. - E. Jalviste; K. Timpmann; M. Chenchiliyan; L. Kangur; M. R. Jones; A. Freiberg (2020). "High-Pressure Modulation of Primary Photosynthetic Reactions." The Journal of Physical Chemistry B, 124 (5), 718−726.
- K. Timpmann; E. Jalviste; M. Chenchiliyan; L. Kangur; M.R. Jones; A. Freiberg (2020). "High-pressure tuning of primary photochemistry in bacterial photosynthesis: membrane-bound versus detergent-isolated reaction centers." Photosynthesis Research, 144, 209–220
- L. Kangur; M. Rätsep; K. Timpmann; Z.-Y. Wang-Otomo; A. Freiberg (2020). "The two light-harvesting membrane chromoproteins of Thermochromatium tepidum expose distinct robustness against temperature and pressure." Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1861 (8), 148205.
- A. Kölsch; C. Radon; M. Golub; A. Baumert; J. Bürger; T. Mielke; F. Lisdat; A. Feoktystov; J. Pieper; A. Zouni; P. Wendler (2020). "Current limits of structural biology: the transient interaction between cytochrome c and photosystem I." Current Research in Structural Biology, 2, 171−179.
- M. Golub; R. Hussein; M. Ibrahim; M. Hecht; D.C.F. Wieland; A. Martel; B. Machado; A. Zouni; J. Pieper (2020). "Solution Structure of the Detergent-Photosystem II Core Complex Investigated by Small Angle Scattering Techniques." The Journal of Physical Chemistry B, 124 (39), 8583−8592.
- J. Pieper; K.D. Irrgang (2020). "Nature of low-energy exciton levels in light-harvesting complex II of green plants as revealed by satellite hole structure." Photosynthesis Research, 146 (1-3), 279−285.
- L. Kangur; K. Timpmann; D. Zeller; P. Masson; J. Peters; A. Freiberg (2019). "Structural stability of human butyrylcholinesterase under high hydrostatic pressure." Biochimica et Biophysica Acta - Proteins and Proteomics, 1867 (2), 107−113.
- M. Rätsep; J.M. Linnanto; A. Freiberg (2019). "Higher Order Vibronic Sidebands of Chlorophyll a and Bacteriochlorophyll a for Enhanced Excitation Energy Transfer and Light Harvesting." The Journal of Physical Chemistry B, 123 (33), 7149−7156.
- M. Pajusalu; M. Rätsep; L. Kangur; A. Freiberg (2019). "High-pressure control of photosynthetic excitons." Chemical Physics, 525, 110404
- K. Leiger; J.M. Linnanto; M. Rätsep; K. Timpmann; A.A. Ashikhmin; A.A. Moskalenko; T.Y. Fufina; A.G. Gabdulkhakov; A. Freiberg (2019). "Controlling Photosynthetic Excitons by Selective Pigment Photooxidation." The Journal of Physical Chemistry B, 123 (1), 29−38.
- M. Rätsep; J.M. Linnanto; R. Muru; M. Biczysko; J.R. Reimers; A. Freiberg (2019). "Absorption-emission symmetry breaking and the different origins of vibrational structures of the 1Qy and 1Qx electronic transitions of pheophytin a." Journal of Chemical Physics, 151 (16), 165102.
- M. Golub; J. Pieper; J. Peters; L. Kangur; E.C. Martin; C.N. Hunter; A. Freiberg (2019). "Picosecond Dynamical Response to a Pressure-Induced Break of the Tertiary Structure Hydrogen Bonds in a Membrane Chromoprotein." The Journal of Physical Chemistry B, 123, 2087−2093.
- M. Golub; M. Moldenhauer; F.-J. Schmitt; W. Lohstroh; E. Maksimov; T. Friedrich; J. Pieper (2019). "Solution Structure and Conformational Flexibility in the Active State of the Orange Carotenoid Protein. Part II: Quasielastic Neutron Scattering." The Journal of Physical Chemistry B, 123 (45), 9536–9545.
- M. Golub; M. Moldenhauer; F.-J. Schmitt; A. Feoktystov; H. Mändar; E. Maksimov; T. Friedrich; J. Pieper (2019). "Solution Structure and Conformational Flexibility in the Active State of the Orange Carotenoid Protein. Part I: Small-Angle Scattering." The Journal of Physical Chemistry B, 123 (45), 9525−9535.
Picosecond fluorescence spectrochronograph (room D113)
- Spectra Physics solid-state cw laser Millennia: 6 W output, wavelength 532 nm
- Coherent femtosecond oscillator Mira-900: output power 1 W at 800 nm, tuning range 690 - 1000 nm, pulse width 120 fs, repetition rate 76 MHz
- Pulse selector (APE): repetition rate of output pulses 15 kHz - 4 MHz, diffraction efficiency 60 %, contrast ratio > 100:1
- Harmonic generator (APE): SHG: output wavelength range 350 - 500 nm, THG: output wavelength range 230 - 330 nm
- Synchroscan streak camera: temporal resolution 5 ps, spectral response 400-1100 nm, repetition rate 76 MHz, signal amplification 1000
- Time-correlated single-photon counting system SPC-150 (Becker & Hickl GmbH): IRF with id 100-20 detector (Quantique) is 60 ps, IRF with HPM 100-40 detector (B&H GmbH) is 160 ps
- Double subtractive dispersion monochromator DTMc300 (Bentham instruments Ltd): focal length 0.6 m, scanning range 300-1200 nm, spectral resolution 0.05 nm
- CCD cameras DV420A-OE and DU416A-LDC-DD (Andor Technology)
- Liquid helium cryostat 4.2 - 300 K (Utreks)
Selective spectroscopy setup (room D114)
- Cary 60 UV-Vis Spectrophotometer (Agilent): 190-1100 nm
- Solid-state cw laser Millennia(Spectra Physics): 10 W output, wavelength 532 nm
- Model 375 dye laser (Spectra Physics): 565-700 nm
- Model 3900S Ti:sapphire laser (Spectra Physics): 675-1060 nm, adjustable 2.1 - 15 GHz spectral bandwidth
- Shamrock 303i spectrograph (Andor Technology)
- Fibre-coupled monochromator THR1500 (Jobin Yvon)
- CCD cameras DV420-OE and DV420A-OE (Andor Technology)
- Liquid helium cryostat 1.8 - 300 K (Utreks)
- Optistat DN liquid nitrogen cryostat 77 - 320 K (Oxford Instruments)
Microspectroscopy setup (room D115)
- Inverted microscope IX-71 (Olympus)
- Spectrograph Shamrock 303i (Andor Technology)
- CCD camera DU-420A-BR-DD and EMCCD camera iXon 897 (Andor Technology)
- He-Ne laser 25-LYR-173-230 (Melles-Griot): 594 nm, 2 mW
- Nd-YAG laser (Viasho): 1064 nm, 1W
Circular dichroism (CD) spectrometry (room D116)
- Chirascan-plus CD-spectrometer (Applied Photophysics): CD and absorption 180 – 1100 nm, fluorescence 200 - 850 nm
- Spectrograph Kymera 193i (Andor Technology): 200 - 1100 nm
High-pressure instrumentation based on conventional and diamond anvil cells for optical measurements at variable pressures up to 50 kbar and temperatures down to 10 K
Tõnu Pullerits (1991)
Veera Krasnenko (2008)
Liina Kangur (2013)
Mihkel Pajusalu (2014)
Manoop Chenchiliyan (2016)
