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Article ; Online: The Carbonyl Group in β2 of the Carotenoid Tunes the Photocycle Kinetics in Orange Carotenoid Protein.

Chukhutsina, Volha U / Hutchison, Christopher D M / van Thor, Jasper J

2024 Volume 436, Issue 5, Page(s) 168463

Abstract: Adaptation to rapid environmental changes is crucial for maintaining optimal photosynthetic efficiency and is ultimately key to the survival of all photosynthetic organisms. Like most of them, cyanobacteria protect their photosynthetic apparatus against ... ...

Abstract	Adaptation to rapid environmental changes is crucial for maintaining optimal photosynthetic efficiency and is ultimately key to the survival of all photosynthetic organisms. Like most of them, cyanobacteria protect their photosynthetic apparatus against rapidly increasing light intensities by nonphotochemical quenching (NPQ). In cyanobacteria, NPQ is controlled by Orange Carotenoid Protein (OCP) photocycle. OCP is the only known photoreceptor that uses carotenoid for its light activation. How carotenoid drives and controls this unique photoactivation process is still unknown. However, understanding and potentially controlling the OCP photocycle may open up new possibilities for improving photosynthetic biomass. Here we investigate the effect of the carbonyl group in the β2 ring of the carotenoid on the OCP photocycle. We report microsecond to minute OCP light activation kinetics and Arrhenius plots of the two OCP forms: Canthaxanthin-bound OCP (OCP
MeSH term(s)	Bacterial Proteins/chemistry ; Bacterial Proteins/radiation effects ; Light ; Photoreceptors, Microbial/chemistry ; Photoreceptors, Microbial/radiation effects ; Photosynthesis ; Spectrum Analysis ; Kinetics
Chemical Substances	Bacterial Proteins ; orange carotenoid protein, Synechocystis ; Photoreceptors, Microbial
Language	English
Publishing date	2024-02-01
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2024.168463
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Article ; Online: Application of density matrix Wigner transforms for ultrafast macromolecular and chemical x-ray crystallography.

Perrett, Samuel / Chatrchyan, Viktoria / Buckup, Tiago / van Thor, Jasper J

The Journal of chemical physics

2024 Volume 160, Issue 10

Abstract: Time-Resolved Serial Femtosecond Crystallography (TR-SFX) conducted at X-ray Free Electron Lasers (XFELs) has become a powerful tool for capturing macromolecular structural movies of light-initiated processes. As the capabilities of XFELs advance, we ... ...

Abstract	Time-Resolved Serial Femtosecond Crystallography (TR-SFX) conducted at X-ray Free Electron Lasers (XFELs) has become a powerful tool for capturing macromolecular structural movies of light-initiated processes. As the capabilities of XFELs advance, we anticipate that a new range of coherent control and structural Raman measurements will become achievable. Shorter optical and x-ray pulse durations and increasingly more exotic pulse regimes are becoming available at free electron lasers. Moreover, with high repetition enabled by the superconducting technology of European XFEL (EuXFEL) and Linac Coherent Light Source (LCLS-II) , it will be possible to improve the signal-to-noise ratio of the light-induced differences, allowing for the observation of vibronic motion on the sub-Angstrom level. To predict and assign this coherent motion, which is measurable with a structural technique, new theoretical approaches must be developed. In this paper, we present a theoretical density matrix approach to model the various population and coherent dynamics of a system, which considers molecular system parameters and excitation conditions. We emphasize the use of the Wigner transform of the time-dependent density matrix, which provides a phase space representation that can be directly compared to the experimental positional displacements measured in a TR-SFX experiment. Here, we extend the results from simple models to include more realistic schemes that include large relaxation terms. We explore a variety of pulse schemes using multiple model systems using realistic parameters. An open-source software package is provided to perform the density matrix simulation and Wigner transformations. The open-source software allows us to define any arbitrary level schemes as well as any arbitrary electric field in the interaction Hamiltonian.
Language	English
Publishing date	2024-03-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0188888
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Article ; Online: Photoacid Dynamics in the Green Fluorescent Protein.

van Thor, Jasper J / Champion, Paul M

Annual review of physical chemistry

2023 Volume 74, Page(s) 123–144

Abstract: The photoacid dynamics of fluorescent proteins include both electronic excited- and ground-state mechanisms of proton transfer. The associated characteristic timescales of these reactions range over many orders of magnitude, and the tunneling, barrier ... ...

Abstract	The photoacid dynamics of fluorescent proteins include both electronic excited- and ground-state mechanisms of proton transfer. The associated characteristic timescales of these reactions range over many orders of magnitude, and the tunneling, barrier crossing, and relevant thermodynamics have in certain cases been linked to coherent nuclear motion. We review the literature and summarize the experiments and theory that demonstrate proton tunneling in the electronic ground state of the green fluorescent protein (GFP). We also discuss the excited-state proton-transfer reaction of GFP that takes place on the picosecond timescale. Although this reaction has been investigated using several vibrational spectroscopic methods, the interpretation remains unsettled. We discuss recent advances as well as remaining questions, in particular those related to the vibrational mode couplings that involve low-frequency modulations of chromophore vibrations on the timescale of proton transfer.
MeSH term(s)	Green Fluorescent Proteins/chemistry ; Green Fluorescent Proteins/metabolism ; Protons
Chemical Substances	Green Fluorescent Proteins (147336-22-9) ; Protons
Language	English
Publishing date	2023-01-25
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	1470474-2
ISSN	1545-1593 ; 0066-426X
ISSN (online)	1545-1593
ISSN	0066-426X
DOI	10.1146/annurev-physchem-091422-102619
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Article ; Online: Coherent two-dimensional electronic and infrared crystallography.

van Thor, Jasper J

The Journal of chemical physics

2019 Volume 150, Issue 12, Page(s) 124113

Abstract: 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 ... ...

Abstract	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.
Language	English
Publishing date	2019-03-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/1.5079319
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Article: Advances and opportunities in ultrafast X-ray crystallography and ultrafast structural optical crystallography of nuclear and electronic protein dynamics.

van Thor, Jasper J

Structural dynamics (Melville, N.Y.)

2019 Volume 6, Issue 5, Page(s) 50901

Abstract: Both nuclear and electronic dynamics contribute to protein function and need multiple and complementary techniques to reveal their ultrafast structural dynamics response. Real-space information obtained from the measurement of electron density dynamics ... ...

Abstract	Both nuclear and electronic dynamics contribute to protein function and need multiple and complementary techniques to reveal their ultrafast structural dynamics response. Real-space information obtained from the measurement of electron density dynamics by X-ray crystallography provides aspects of both, while the molecular physics of coherence parameters and frequency-frequency correlation needs spectroscopy methods. Ultrafast pump-probe applications of protein dynamics in crystals provide real-space information through direct X-ray crystallographic structure analysis or through structural optical crystallographic analysis. A discussion of methods of analysis using ultrafast macromolecular X-ray crystallography and ultrafast nonlinear structural optical crystallography is presented. The current and future high repetition rate capabilities provided by X-ray free electron lasers for ultrafast diffraction studies provide opportunities for optical control and optical selection of nuclear coherence which may develop to access higher frequency dynamics through improvements of sensitivity and time resolution to reveal coherence directly. Specific selection of electronic coherence requires optical probes, which can provide real-space structural information through photoselection of oriented samples and specifically in birefringent crystals. Ultrafast structural optical crystallography of photosynthetic energy transfer has been demonstrated, and the theory of two-dimensional structural optical crystallography has shown a method for accessing the structural selection of electronic coherence.
Language	English
Publishing date	2019-09-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	2758684-4
ISSN	2329-7778
ISSN	2329-7778
DOI	10.1063/1.5110685
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Article ; Online: Theory of two-dimensional spectroscopy with intense laser fields.

Bressan, Giovanni / van Thor, Jasper J

The Journal of chemical physics

2021 Volume 154, Issue 24, Page(s) 244111

Abstract: Two-dimensional vibrational and electronic spectroscopic observables of isotropically oriented molecular samples in solution are sensitive to laser field intensities and polarization. The third-order response function formalism predicts a signal that ... ...

Abstract	Two-dimensional vibrational and electronic spectroscopic observables of isotropically oriented molecular samples in solution are sensitive to laser field intensities and polarization. The third-order response function formalism predicts a signal that grows linearly with the field strength of each laser pulse, thus lacking a way of accounting for non-trivial intensity-dependent effects, such as saturation and finite bleaching. An analytical expression to describe the orientational part of the molecular response, which, in the weak-field limit, becomes equivalent to a four-point correlation function, is presented. Such an expression is evaluated for Liouville-space pathways accounting for diagonal and cross peaks for all-parallel and cross-polarized pulse sequences, in both the weak- and strong-field conditions, via truncation of a Taylor series expansion at different orders. The results obtained in the strong-field conditions suggest how a careful analysis of two-dimensional spectroscopic experimental data should include laser pulse intensity considerations when determining molecular internal coordinates.
Language	English
Publishing date	2021-07-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0051435
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Article ; Online: Linear and Non-Linear Population Retrieval with Femtosecond Optical Pumping of Molecular Crystals for the Generalised Uniaxial and Biaxial Systems

Christopher D. M. Hutchison / Alisia Fadini / Jasper J. van Thor

Applied Sciences, Vol 12, Iss 4309, p

2022 Volume 4309

Abstract: Femtosecond optical measurements of photoexcitable molecular crystals carry ultrafast dynamics information with structural sensitivity. The creation and detection of transient dynamics depend on the optical parameters, as well as the explicit molecular ... ...

Abstract	Femtosecond optical measurements of photoexcitable molecular crystals carry ultrafast dynamics information with structural sensitivity. The creation and detection of transient dynamics depend on the optical parameters, as well as the explicit molecular structure, crystal symmetry, crystal orientation, polarisation of the photoexciting beam, and interaction geometry. In order to retrieve the linear and non-linear population transfer in photoexcited crystals, excitation theory is combined here with the calculation of birefringence decomposition and is shown for both the generalised uniaxial and biaxial systems. A computational tool was constructed based on this treatment to allow modelling of electric field decomposition, dipole projections, and non-linear excitation population levels. This is available open source and with a GUI for ease of use. Such work has applications in two areas of ultrafast science: multidimensional optical crystallography and femtosecond time-resolved X-ray crystallography.
Keywords	SFX ; TR-SFX ; crystallography ; XFEL ; 2DES ; birefringence ; Technology ; T ; Engineering (General). Civil engineering (General) ; TA1-2040 ; Biology (General) ; QH301-705.5 ; Physics ; QC1-999 ; Chemistry ; QD1-999
Subject code	535
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Excited State Frequencies of Chlorophyll f and Chlorophyll a and Evaluation of Displacement through Franck-Condon Progression Calculations.

Zamzam, Noura / van Thor, Jasper J

Molecules (Basel, Switzerland)

2019 Volume 24, Issue 7

Abstract: We present ground and excited state frequency calculations of the recently discovered extremely red-shifted chlorophyll f. We discuss the experimentally available vibrational mode assignments of chlorophyll f and chlorophyll a which are characterised by ... ...

Abstract	We present ground and excited state frequency calculations of the recently discovered extremely red-shifted chlorophyll f. We discuss the experimentally available vibrational mode assignments of chlorophyll f and chlorophyll a which are characterised by particularly large downshifts of 13¹-keto mode in the excited state. The accuracy of excited state frequencies and their displacements are evaluated by the construction of Franck-Condon (FC) and Herzberg-Teller (HT) progressions at the CAM-B3LYP/6-31G(d) level. Results show that while CAM-B3LYP results are improved relative to B3LYP calculations, the displacements and downshifts of high-frequency modes are underestimated still, and that the progressions calculated for low temperature are dominated by low-frequency modes rather than fingerprint modes that are Resonant Raman active.
MeSH term(s)	Algorithms ; Chlorophyll/analogs & derivatives ; Chlorophyll/chemistry ; Chlorophyll A/chemistry ; Models, Chemical ; Models, Molecular ; Spectrum Analysis
Chemical Substances	chlorophyll f ; Chlorophyll (1406-65-1) ; Chlorophyll A (YF5Q9EJC8Y)
Language	English
Publishing date	2019-04-04
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules24071326
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Article ; Online: Optical control, selection and analysis of population dynamics in ultrafast protein X-ray crystallography.

Hutchison, Christopher D M / van Thor, Jasper J

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences

2019 Volume 377, Issue 2145, Page(s) 20170474

Abstract: Ultrafast pump-probe X-ray crystallography has now been established at X-ray free electron lasers that operate at hard X-ray energies. We discuss the performance and development of current applications in terms of the available data quality and ... ...

Abstract	Ultrafast pump-probe X-ray crystallography has now been established at X-ray free electron lasers that operate at hard X-ray energies. We discuss the performance and development of current applications in terms of the available data quality and sensitivity to detect and analyse structural dynamics. A discussion of technical capabilities expected at future high repetition rate applications as well as future non-collinear multi-pulse schemes focuses on the possibility to advance the technique to the practical application of the X-ray crystallographic equivalent of an impulse time-domain Raman measurement of vibrational coherence. Furthermore, we present calculations of the magnitude of population differences and distributions prepared with ultrafast optical pumping of single crystals in the typical serial femtosecond crystallography geometry, which are developed for the general uniaxial and biaxial cases. The results present opportunities for polarization resolved anisotropic X-ray diffraction analysis of photochemical populations for the ultrafast time domain. This article is part of the theme issue 'Measurement of ultrafast electronic and structural dynamics with X-rays'.
Language	English
Publishing date	2019-04-03
Publishing country	England
Document type	Journal Article
ZDB-ID	208381-4
ISSN	1471-2962 ; 0080-4614 ; 0264-3820 ; 0264-3952 ; 1364-503X
ISSN (online)	1471-2962
ISSN	0080-4614 ; 0264-3820 ; 0264-3952 ; 1364-503X
DOI	10.1098/rsta.2017.0474
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Article ; Online: The Design of Relativistic Ultrafast Electron Diffraction and Imaging (RUEDI) Facility for Materials in Extremes.

Murooka, Yoshie / Bryan, William / Clarke, James / Ellis, Michael / Kirkland, Angus I / Maskell, Simon / McKenzie, Julian / Layla Mehdi, B / Dwayne Miller, R J / Noakes, Timothy C Q / Robinson, Ian / Schroeder, Sven L M / van Thor, Jasper / Welsch, Carsten / Browning, Nigel D

Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada

2023 Volume 29, Issue Supplement_1, Page(s) 1487–1488

Language	English
Publishing date	2023-08-23
Publishing country	England
Document type	Journal Article
ZDB-ID	1385710-1
ISSN	1435-8115 ; 1431-9276
ISSN (online)	1435-8115
ISSN	1431-9276
DOI	10.1093/micmic/ozad067.764
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