The Larsen laboratory focuses mainly on studying man-made and nature-made complexes that exhibit photo-activated functions that modulate either the transmission of energy (i.e. photosynthesis), the transfer of information (i.e. photoreceptors) or the transfer of redox capacity (i.e. photocatalysis).

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Delmar Larsen Lab is new laboratory located in the chemistry department at UC Davis. Lab research extends across many scientific disciplines including biophysics, physical chemistry, molecular biology and computational modeling, where the common thread among these different scientific areas of study is the investigation and characterization of rapid condensed phase dynamics.

Below is a short description of Delmar Larsen research. For recent updates go to Delmar Larsen group webpage.

Photosynthesis

Photoreceptors

Photocatalysis

Shaping pulse structures in coherent control experiments on light-harvesting proteins with incoherent mechanisms

Excited State Dynamics of Carotenoids in Light Harvesting Complexes: 2. Dissecting Pulse Structures obtained from Optimal Control Experiments, Emmanouil Papagiannakis, Mikas Vengris, Leonas Valkunas, Rienk van Grondelle, Delmar S. Larsen, Journal of Physical Chemistry B 110, 5737-5746 (2006). pdf

The primary objective in the Larsen laboratory is to understand the different ways that Nature converts photon energy into useful biological function. This entails identifying and characterizing, on a molecular level, the protein-cofactor interactions that result in biological function with particular emphasis on the role of dynamical processes. The ultimate goal is not only to describe how proteins function, but to understand the underlying mechanisms to a degree that new proteins can be constructed to possess or perform desired functions.

Evolution has fine-tuned the properties of protein environments to optimize specific aspects of embedded reactions (e.g. the use of energy "funnels" to harvest sunlight in photosynthetic light harvesting complexes and the specific use of unique electron transfer pathways in bacterial reaction centers). Proteins use these evolutionary adaptations to alter intra-protein reactions through both structural and dynamical processes. Even though the influence of the structural properties to these reactions have been extensively investigated with X-ray scattering and NMR studies, the function of protein dynamical effects in controlling these reactions is still poorly understood. Using non-linear, time-resolved spectroscopic techniques in conjunction with molecular dynamics simulations, we characterize the specific protein motions responsible for influencing the photo-induced activity. The interplay of simulations and experiment provides for a novel, detailed study of the factors responsible for affecting biological reactions and hence biological functions.

Systems studied:

Phytochromes

Photoactive Yellow Protein

Green Fluorescence Proteins

Retinal Binding Proteins

Delmar Larsen publications

Excited State Dynamics of Carotenoids in Light Harvesting Complexes: 1. Exploring the Relationship between the S₁ and S* States, Emmanouil Papagiannakis, Ivo H.M. van Stokkum, Mikas Vengris, Rienk van Grondelle, Delmar S. Larsen, Journal of Physical Chemistry B 110, 5727-5736 (2006). pdf

32. Characterizing Excitation Dynamics in Multi-Chromophoric Aggregates One Pulse at a Time, Leonas Valkunas, Rienk van Grondelle, Delmar S. Larsen, in preparation.

31. Excitation Mobility in Native DNA Helices, Delmar S. Larsen, Askat Jailaubekov, Christina A. To, Peter Qin, Stephen E. Bradforth, in preparation.

30. Excited State Dynamics of Carotenoids in Light Harvesting Complexes: 2. Dissecting Pulse Structures obtained from Optimal Control Experiments, Emmanouil Papagiannakis, Mikas Vengris, Leonas Valkunas, Rienk van Grondelle, Delmar S. Larsen, Journal of Physical Chemistry B 2006 110, 5737-5746 (2006). pdf

29. Excited State Dynamics of Carotenoids in Light Harvesting Complexes: 1. Exploring the Relationship between the S1 and S* States, Emmanouil Papagiannakis, Ivo H.M. van Stokkum, Mikas Vengris, Rienk van Grondelle, Delmar S. Larsen, Journal of Physical Chemistry B 2006 110, 5727-5736 (2006). pdf

28. Using Ultrafast Dispersed Pump-Dump-Probe and Pump-Repump Probe Spectroscopies to Explore the Light Induced Dynamics of Peridinin in Solution, Emmanouil Papagiannakis, Mikas Vengris, Delmar S. Larsen , Ivo H.M. van Stokkum, Roger G. Hiller, Rienk van Grondelle, Journal of Physical Chemistry B 110, 512-521 (2006). pdf

27. Mediation of Light Harvesting by a central dimer in Phycoerythrin 545 studied with Ultrafast Transient Absorption, Alexander B. Doust, Ivo H.M. van Stokkum, Delmar S. Larsen, Krystyna E. Wilk, Paul M.G. Curmi, Rienk van Grondelle, Gregory D. Scholes. Journal of Physical Chemistry B 109, 14219-14226 (2005). pdf

26. Ultrafast Dynamics of Isolated Model Photoactive Yellow Protein Chromophores: "Chemical Perturbation Theory" in the Laboratory, Mikas Vengris, Delmar S. Larsen, Michael A. van der Horst, Olaf F.A. Larsen, Klass Hellingwerf, Rienk van Grondelle, Journal of Physical Chemistry A, 109, 4197-4208 (2005). pdf

25. Initial Photo-induced Dynamics of the Photoactive Yellow Protein, Delmar S. Larsen and Rienk van Grondelle, ChemPhysChem 6, 828-837 (2005). pdf

24. Stimulated Emission-Three Pulse Photo Echo Peakshift: A Mixed Pump-Probe and Photon-Echo Technique to Study Excited-State Dynamics, Delmar S. Larsen, Journal of Chemical Physics 121 (11), 5039-5042, (2004). pdf

23. Uncovering the hidden ground state of the green fluorescent protein, John Kennis, Delmar S. Larsen, Ivo H.M. van Stokkum, Mikas Vengris, Jasper van Thor, Rienk van Grondelle, Proceedings of the National Academy of Science 52, 17988-17993 (2004). pdf

22. Disentangling the Excited States of Peridinin with Multi-Pulse Ultrafast Transient Absorption Spectroscopy, Emmanouil Papagiannakis, Delmar S. Larsen, Ivo H.M. van Stokkum, Mikas Vengris, Roger G. Hiller, Rienk van Grondelle, Biochemistry 43 (49), 15303-15309 (2004). pdf

21. Primary Photochemistry in the Photoactive Yellow Protein: The Prototype Xanthopsin, Delmar S. Larsen, Rienk van Grondelle, Klaas J. Hellingwerf, ChemPhysChem, 6, 828-837 (2005). pdf

20. Contrasting the Excited-State Dynamics of the Photoactive Yellow Protein Chromophore: Protein vs. Solvent Effects, Mikas Vengris, Michael A. van der Horst, Goran Zgrablic, Ivo H.M. van Stokkum, Stefan Haacke, Majed Chergui, Klaas J. Hellingwerf, Rienk van Grondelle, Delmar S. Larsen, Biophysical Journal 87 (3), 1848-1857 (2004). pdf

19. Global and Target Analysis of Time-Resolved Spectra, Ivo H.M. van Stokkum, Delmar S. Larsen, Rienk van Grondelle, Biochimica et Biophysica Acta: Bioenergetics 1657, 82-104 (2004). pdf

18. Incoherent Manipulation of the Photoactive Yellow Protein Photocyle with Dispersed Pump-Dump-Probe Spectroscopy, Delmar S. Larsen, Mikas Vengris, Ivo H.M. van Stokkum, Michael A. van der Horst, Frank L. de Weerd, Klaas J. Hellingwerf, Rienk van Grondelle, Biophysical Journal 87 (3), 1858-1872 (2004). pdf

17. Ultrafast excited and ground-state dynamics of the Green Fluorescent Protein chromophore in Aqueous Solutions, Mikas Vengris, Ivo H.M. van Stokkum, Xiang He, Alasdair F. Bell, Peter J. Tonge, Rienk van Grondelle, Delmar S. Larsen, Journal of Physical Chemistry A, 108, 4587-4598 (2004). pdf

16. Influence of Intramolecular Vibrations in Time-Domain Spectroscopies, Delmar S. Larsen, Kaoru Ohta, Mino Yang, Qinh-hua Xu, Graham R. Fleming, in: Recent Advances in Ultrafast Spectroscopy, Proceedings for the 12th Conference on Ultrafast Processes in Spectroscopy Conference, edited by S. Califano, P. Foggi, and R. Righini.297-302 (Leo S. Olschki, Rome, 2003).

15. Photoisomerization and Photoionization of the Photoactive Yellow Protein Chromophore in Solution, Delmar S. Larsen, Mikas Vengris, Ivo H.M. van Stokkum, Michael A. van der Horst, Frank L. de Weerd, Klaas J. Hellingwerf, Rienk van Grondelle Biophysical Journal, 86, 2538-2550 (2004). pdf

14. Excited State Dynamics of B-Carotene Explored with Dispersed Multi-Pulse Experiments, Delmar S. Larsen, Emmanouil Papagiannakis, Ivo H.M. van Stokkum, Mikas Vengris, John T.M. Kennis, Rienk van Grondelle Chemical Physics Letters 381 (5-6), 733-742 (2003). pdf

13. Initial Steps of Signal Generation in Photoactive Yellow Protein Revealed with Femtosecond Mid-Infrared Spectroscopy, Marie-Louise Groot, Luuk van Wilderen, Delmar S. Larsen, Michael A. van der Horst, Ivo H.M. van Stokkum, Klaas J. Hellingwerf, Rienk van Grondelle, Biochemistry 42, 10054-10059 (2003). pdf

12. Initial Photo-induced Dynamics of the Photoactive Yellow Protein Chromophore in Solution, Delmar S. Larsen, Mikas Vengris, Ivo H.M. van Stokkum, Michael A. van der Horst, Robert A. Cordfunke, Klaas J. Hellingwerf, Rienk van Grondelle, Chemical Physics Letters 369 (5-6), 563 - 569 (2003). pdf

11. Ultrafast protein Dynamics of Bacteriorhodopsin probed by Photon Echo and Transient Absorption Spectroscopy, John Kennis, Delmar S. Larsen, Kaoru Ohta, Marc T. Facciotti, Robert M. Glaeser, Graham R. Fleming, Journal of Physical Chemistry B 106(23), 6067-6080 (2002). pdf

10. A Small Volume, Rapid Translation Cryostat Insert Constructed from Commercial Components for the Detection of Ultrafast Optical Signals, Delmar S. Larsen, Review of Scientific Instruments, 73, 1325-1328 (2002). pdf

9. Investigation of non-dipolar Solvation Dynamics, Delmar S. Larsen, Ph. D. Thesis, Department of Chemistry, University of Chicago, 2001. pdf

8. Influence of Intramolecular Vibrations in Third-Order, Time Domain Resonant Spectroscopies: 2. Theoretical Calculations, Kaoru Ohta, Delmar S. Larsen, Mino Yang, and Graham R. Fleming, Journal of Chemical Physics, 114, 8020-8039 (2001). pdf

7. Influence of Intramolecular Vibrations in Third-Order, Time Domain Resonant Spectroscopies: 1. Experiments, Delmar S. Larsen, Kaoru Ohta, Qing-hua Xu, Michelle Cyrier, and Graham R. Fleming, Journal of Chemical Physics, 114, 8008-8019 (2001). pdf

6. Origin of Line Broadening in the Electronic Absorption Spectra of Conjugated Polymers: Three-Pulse-Echo studies of MEH-PPV in Toluene, Gregory D. Scholes, Delmar S. Larsen, Graham R. Fleming, Garry Rumbles, and Paul L. Burn, Physical Review B, 61, 13670-13678 (2000). pdf

5. Measurement of Pick-up Cross-Sections of ⁴He Clusters: Polar versus Non-polar Molecules, Henry Hess, Delmar S. Larsen, and Adi A. Scheidemann, Philosophical Magazine B: Physics of Condensed Matter, Statistical Mechanics, Electronic Optical and Magnetic Properties 79, 1437-1444 (1999). pdf

4. Three Pulse photon echo studies of Nondipolar Solvation: Comparison with a Viscoelastic model, Delmar S. Larsen, Kaoru Ohta, and Graham R. Fleming, Journal of Chemical Physics 111, 8970-8979 (1999). pdf

3. Studies of Molecular Interactions and Collective Liquid Motion with Two-Dimensional Raman Spectroscopy, A. Tokmakoff, M. J. Lang, Delmar S. Larsen, Xanthippe J. Jordanides, and Graham R. Fleming, in: Ultrafast Phenomena XI, edited by T. Elsaesser, J.G. Fujimoto, D.A. Wiersma, and W. Zinth, 538-540 (Springer, New York 1998).

2. Intrinsic Optical Heterodyne Detection of a Two-Dimensional Fifth Order Raman Response, Andrei Tokmakoff, Mathew J. Lang, Delmar S. Larsen, and Graham R. Fleming, Chemical Physics Letters 272, 48-54 (1997). pdf

1. Two-Dimensional Raman Spectroscopy of Vibrational Interactions in Liquids, A. Tokmakoff, M. J. Lang, D. S. Larsen, G. R. Fleming, V. Chernyak, and S. Mukamel, Physical Review Letters 79, 2702-2705 (1997). pdf

Conference Presentations

18. Delmar S. Larsen, et al. "Incoherent Control of the Photoactive Yellow Protein Photocycle with Dispersed Pump-Dump-Probe Spectroscopy," The Human Frontiers Science Program 15th Anniversary-Fourth Annual Awardees Meeting, Hakone, Japan, May, 15th-18th, 2004. (Poster)

17. Delmar S. Larsen, et al. "Incoherent Control of the Photoactive Yellow Protein Photocycle with Dispersed Pump-Dump-Probe Spectroscopy," Minerva-Gentner Symposium on Optical Spectroscopy of Biomolecular Dynamics, Benedictine-Cloister Banz, Germany, March 21st-25th, 2004. (Poster)

16. Delmar S. Larsen, et al. "Incoherent Control of the Photoactive Yellow Protein Photocycle (& others) with Multi-Pulse Spectroscopy," Frontiers in Biophysical Methods symposium at the 226th AMERICAN CHEMICAL SOCIETY National Meeting, New York, USA, Sept. 7th-11th, 2003. (Oral)

15. Delmar S. Larsen, et al. "Incoherent Control of the Photoactive Yellow Protein Photocycle with Multi-Pulse Spectroscopy," and "When incoherent contributions contaminate coherent control experiments: Saturation effects and multi-pulse structured laser pulses," Excited State Processes of Carotenoids in Photosynthesis, Physikzentrum Bad Honnef, Germany, October 20th-22nd, 2003. (Poster)

14. Delmar S. Larsen, Mikas Vengris, Ivo H.M. van Stokkum, Michael van der Horst, Frank de Weerd, Rienk van Grondelle, "Incoherent Control of the Photoactive Yellow Protein Photocycle with Multi-Pulse Spectroscopy", XXIst International Conference on Photochemistry, The Student Symposium on Future Photochemistry, Nara, Japan, July 26-31, 2003. (Oral and co-organizer) Main Conference Info

13. Delmar S. Larsen, Mikas Vengris, Ivo H.M. van Stokkum, Michael van der Horst, Frank de Weerd, Rienk van Grondelle, "Incoherent Control of the Photoactive Yellow Protein Photocycle with Multi-Pulse Spectroscopy", The International Nanophotonics Symposium Handai: "Nanophotonics: Integrating Photochemistry, Optics, and Nano/Bio Materials Studies", Osaka, Japan, July 24-26, 2003. (Poster)

12. Delmar S. Larsen, Mikas Vengris, Ivo H.M. van Stokkum, Michael van der Horst, Frank de Weerd, Rienk van Grondelle, "Incoherent Control of the Photoactive Yellow Protein Photocycle with Multi-Pulse Spectroscopy", Femtochemistry VI Conference, Paris (Maison de la Chimie), France, July 6-10, 2003. (Poster) Info

11. Delmar S. Larsen, Mikas Vengris, Ivo H.M. van Stokkum, Michael van der Horst, Frank de Weerd, Rienk van Grondelle, "Incoherent Control of the Photoactive Yellow Protein Photocycle with Multi-Pulse Spectroscopy", ESF SUMMER SCHOOL: MOLECULAR BASIS OF FAST AND ULTRAFAST PROCESSES, Algarve, Portugal, June 12th-15th, 2003. (Oral) Info

10. Delmar S. Larsen, Mikas Vengris, Ivo H.M. van Stokkum, Michael van der Horst, Frank de Weerd, Rienk van Grondelle, "Incoherent Control of the Photoactive Yellow Protein Photocycle with Multi-Pulse Spectroscopy", "Photoceptors: Spectroscopy, Structure and Function" Minisymposium, Amsterdam, The Netherlands, April 2nd, 2003. (Oral)

9. Delmar S. Larsen, John Kennis, Mikas Vengris, Ivo H.M. van Stokkum, Jasper van Thor, Rienk van Grondelle, "Identification and Characterization of the Ground State Dynamics of the Green Fluorescent Protein with Pump-Dump-Probe Spectroscopy", NWO/Chemical Sciences Symposium on Theory and Spectroscopy, Lunteren, The Netherlands, January 27-28, 2003. (Poster)

8. Delmar S. Larsen et al., "Transient Absorption Measurements of Photoactive Yellow Protein Systems: Dynamics within Model Chromophores, Denatured and Folded Proteins", 13th International Conference on Ultrafast Phenomena, Vancouver, BC, Canada, May 12-17, 2002. (Oral) Info

7. John Kennis, Delmar S. Larsen, Kaoru Ohta, Marc T. Facciotti, Robert M. Glaeser, Graham R. Fleming "Protein Dynamics of Bacteriorhodopsin probed by Photon Echo and Transient Absorption Spectroscopy", 13th International Conference on Ultrafast Phenomena, Vancouver, BC, Canada, May 12-17, 2002. (Poster) Info

6. Delmar S. Larsen et al., "Transient Absorption Measurements of Photoactive Yellow Protein Systems: Dynamics within Model Chromophores, Denatured and Folded Proteins", ESF-Ultra program workshop on 'Fundamental events in photobiology', Saariselk�, Lapland, Finland, April 25 - 29, 2002. (Oral) Info

5. Delmar S. Larsen, Kaoru Ohta, Mino Yang, Qinh-hua Xu, Graham R. Fleming, "Influence of Intramolecular Vibrations in Time-Domain Spectroscopies", 12th Conference on Ultrafast Processes in Spectroscopy, Florence, Italy, October 28-November 1, 2001. (Oral & Poster)

4. Delmar S. Larsen, K. Ohta, M. Yang, Q. Xu, Graham R. Fleming, "Influence of Intramolecular Vibrations in Time-Domain Spectroscopies", Femtochemistry V conference, Toledo (Facultad de Ciencias del Medio Ambiente,Universidad de Castilla-La Mancha), Toledo, Spain, September 2-6, 2001. (Poster) Info

3. Delmar S. Larsen, Kaoru Ohta, Mino Yang, Qing-hua Xu, Graham R. Fleming, "Influence of Intramolecular Vibrations in Time-Domain Spectroscopies", Gordon Research Conference on the Physics and Chemistry of Liquids, Holderness School, New Hampshire, The USA, August 5-10, 2001. (Poster) Info

2. Delmar S. Larsen, Kaoru Ohta, Mino Yang, Qing-hua Xu, Graham R. Fleming, "Influence of Intramolecular Vibrations in Time-Domain Spectroscopies", AMERICAN PHYSICS SOCIETY ANNUAL MEETING: Condensed Phase Dynamics: Multidimensional Spectroscopies., Seattle, Washington, The USA, March 12-16, 2001. (Oral) Info

1. Delmar S. Larsen, Kaoru Ohta, Mino Yang, Qing-hua Xu, Graham R. Fleming, "Investigation of the Wavelength Dependent Properties of Resonant Third-order Time Domain Spectroscopies", Sixth Symposium on Molecular Reaction Dynamics in Condensed Matter, Laguna Beach, California, The USA, February 28-March 3, 2001. (Oral)

Invited Presentations

18. "Investigations of Ultrafast Dynamics of the Green Fluorescent Protein and its isolated chromophore in solution," TAHRA GROUP MEETING: RIKEN RESEARCH INSTITUE, Tokyo, Japan, May 24th, 2004.

17. "Disentangling the Excited States of Carotenoids with Multi-Pulse Ultrafast Transient Absorption Spectroscopy," PHYSICS SEMINAR: OSAKA CITY UNIVERSITY, Osaka, Japan, May 21st, 2004.

16. "Investigations of Ultrafast Dynamics of the Photoactive Yellow Protein with Dispersed Pump-Dump-Probe Spectroscopy," PHYSICS SEMINAR: OSAKA UNIVERSITY (SUITE CAMPUS), Osaka, Japan, May 20th, 2004.

15. "Disentangling the Excited States of Carotenoids with Multi-Pulse Ultrafast Transient Absorption Spectroscopy," TOMINAGA GROUP MEETING: KOBE UNIVERSITY, Kobe, Japan, May 20th, 2004.

14. "Investigations of Ultrafast Dynamics of the Photoactive Yellow Protein with Dispersed Pump-Dump-Probe Spectroscopy," SANDIA NATIONAL LAB, Livermore, California, USA, May 6th, 2004.

13. "Ultrafast Dynamics of the Green Fluorescent Protein and its isolated Chromophore in Solution," RIED GROUP MEETING: NIVERSITY OF WASHINGTON, Seattle, Washington, USA, May 4th, 2004.

12. "Explorations of Ultrafast Dynamics with Dispersed Multi-pulse Spectroscopies," SUNDSTR�M LAB GROUP MEETING: LUND UNIVERSITY, Lund, Sweden, March 11th, 2004.

11. "Incoherent Control of the Photoactive Yellow Protein Photocycle with Multi-Pulse Spectroscopy", State University of New Yrok (SUNY) at Stony Brook, Tonge Group, Stony Brook, Sept. 12, 2003.

10. "Incoherent Control of the Photoactive Yellow Protein Photocycle with Multi-Pulse Spectroscopy", Kobe University, Kobe, Japan, July 23, 2003.

9. "New Insights into the Initial Photophysics of the Photoactive Yellow Protein", Royal Netherlands Academy of Arts and Sciences (KNAW): Biophysics Workdiscussion, The Trippenhuis, Amsterdam, The Netherlands, December 17th, 2002. Info

8. "The Physics of Isomerization in Biomolecules", Caput on "Biophysics Master Course", Free University Amsterdam, Amsterdam, The Netherlands, November 25th, 2002. Info

7. "Initial Photodynamics of the Photoactive Yellow Protein studied with dispersed Multi-(de)excitation Spectroscopy," Chergui Laser Group, Universite De Lausanne, Lausanne, Switzerland, Nov. 22th, 2002.

6. "The role of dephasing in Ultrafast spectroscopies: 2. Non-Linear signals from a Microscopic Perspective", Caput on "Ultrafast Phenomena in Biology: New Developments," Free University Amsterdam, Amsterdam, The Netherlands, March 28th, 2002.

5. "The role of dephasing in Ultrafast spectroscopies: 1. Lineshapes and Broadening Mechanisms," Caput on "Ultrafast Phenomena in Biology: New Developments," Free University Amsterdam, Amsterdam, The Netherlands, March 21st, 2002.

4. "Polarized transient absorption studies of the initial isomerization dynamics of the photoactive yellow protein and model chromophore compounds." Masuhara Laboratories, Osaka University, Osaka, Japan, March 13th, 2002.

3. "Recent Advances in Time-Resolved Coherent Spectroscopies," Research Center for Superconductive Photonics, Osaka University, Osaka, Japan, February 25th, 2002. Info

2. "Ultrafast Studies of the Initial Photoinduced Reaction Dynamics of Several Biological Photoreceptors: Bacteriorhodopsin & Photoactive Yellow Protein," Photonics Seminar Series (Photonics Research Ontario), Toronto, Canada, February 6th, 2002. Info

1. "Several Complicating Effects in Echo Peakshift Data Collection and Analysis," Material Science Center seminar, University of Groningen, Groningen, The Netherlands, November 12th, 2001.