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Romanishkin ID, Akhlyustina EV, Meerovich GA, Loschenov VB, Strakhovskaya MG. Оn the aggregation of polycationic photosensitizer upon binding to Gram-negative bacteria. Methods Appl Fluoresc 2024; 12:035001. [PMID: 38537290 DOI: 10.1088/2050-6120/ad3892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/27/2024] [Indexed: 04/09/2024]
Abstract
Polycationic photosensitizers (PS) are not susceptible to aggregation in solutions, but their high local concentrations in Gram-negative bacteria can be sufficient for aggregation and reduced effectiveness of antibacterial photodynamic treatment. By measuring fluorescence spectra and kinetics we were able to evaluate the degree of aggregation of polycationic PS ZnPcChol8in Gram-negative bacteria E.coliK12 TG1. Binding of ZnPcChol8toE.coliK12 TG1 leads to an appearance of groups of molecules with shorter PS fluorescence lifetime, a decrease in fluorescence intensity and a shift in the fluorescence spectral maximum. However, we evaluated that about 88% of the fluorescing PS molecules in the bacteria were in an unaggregated state, which indicates only a small reduction in the generation of reactive oxygen species.
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Affiliation(s)
- Igor D Romanishkin
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Moscow 119991, Russia
| | | | - Gennady A Meerovich
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Moscow 119991, Russia
- National Research Nuclear University 'MEPhI', Moscow 115409, Russia
| | - Victor B Loschenov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Moscow 119991, Russia
- National Research Nuclear University 'MEPhI', Moscow 115409, Russia
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2
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Feuk H, Nilsson S, Richter M. Temperature resolved decay time components of Mg 4FGeO 6:Mn using the maximum entropy method. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2023; 94:034901. [PMID: 37012790 DOI: 10.1063/5.0141346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/13/2023] [Indexed: 06/19/2023]
Abstract
A thermographic phosphor's decay time distribution over its temperature-sensitive range was retrieved with the Maximum Entropy Method (MEM). A decay time distribution consists of a range of decay times, each with an associated weighting for the decay time component's prevalence in the analyzed decay curve. With the MEM, significant decay time contributions of a decay curve have high weighting and are therefore found as peaks in the decay time distribution, where the width and peak value are correlated with the relative weight of the decay time components. These peaks in the decay time distribution give increased insight into a phosphor's lifetime behavior, which often cannot accurately be represented by a single or even two decay time components. The changes in the location of peaks in the decay time distribution with temperature can be used for thermometry, and this method has the benefit of being less sensitive to the multi-exponentiality of phosphor decay than mono-exponential decay time fitting. The method also resolves the underlying decay components with no assumptions of the number of significant decay time components. Initially, when the decay time distribution of Mg4FGeO6:Mn was captured, the collected decay included decaying luminescence from the alumina oxide tube in the tube furnace. Therefore, a second calibration was performed where the luminescence from the alumina oxide tube was minimized. These two calibration datasets were used to demonstrate that the MEM could characterize decays from two separate sources simultaneously.
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Affiliation(s)
- Henrik Feuk
- Combustion Physics, Department of Physics, Lund University, Box 118, 221 00 Lund, Sweden
| | - Sebastian Nilsson
- Combustion Physics, Department of Physics, Lund University, Box 118, 221 00 Lund, Sweden
| | - Mattias Richter
- Combustion Physics, Department of Physics, Lund University, Box 118, 221 00 Lund, Sweden
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3
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Usoltsev SD, Raitman OA, Shokurov AV, Marfin YS. Variety of steady and excited state interactions in BODIPY aggregates: photophysics in antisolvent systems and floating layers. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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4
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Pominova D, Romanishkin I, Proydakova V, Kuznetsov S, Grachev P, Ryabova A, Tabachkova NY, Fedorov P, Loschenov V. Study of synthesis temperature effect on β-NaGdF 4: Yb 3+, Er 3+upconversion luminescence efficiency and decay time using maximum entropy method. Methods Appl Fluoresc 2022; 10. [PMID: 35263723 DOI: 10.1088/2050-6120/ac5bdc] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/09/2022] [Indexed: 11/11/2022]
Abstract
Upconversion materials have several advantages for many applications due to their great potential in converting infrared light to visible. For practical use, it is necessary to achieve high intensity of UC luminescence, so the studies of the optimal synthesis parameters for upconversion nanoparticles are still going on. In the present work, we analyzed the synthesis temperature effect on the efficiency and luminescence decay of β-NaGd0.78Yb0.20Er0.02F4 (15-25 nm) upconversion nanoparticles with hexagonal crystal structure synthesized by anhydrous solvothermal technique. The synthesis temperature was varied in the 290-320°C range. The synthesis temperature was shown to have a significant influence on the upconversion luminescence efficiency and decay time. The coherent scattering domain linearly depended on the synthesis temperature and was in the range 13.1-22.3 nm, while the efficiency of the upconversion luminescence increases exponentially from 0.02 to 0.10% under 1 W/cm2 excitation. For a fundamental analysis of the reasons for the upconversion luminescence intensity dependence on the synthesis temperature, it was proposed to use the maximum entropy method for luminescence decay kinetics processing. This method does not require a preliminary setting of the number of exponents and, due to this, makes it possible to estimate additional components in the luminescence decay kinetics, which are attributed to different populations of rare-earth ions in different conditions. Two components in the green luminescence and one component in the red luminescence decay kinetics were revealed for nanoparticles prepared at 290-300°C. An intense short and a weak long component in green luminescence decay kinetics could be associated with two different populations of ions in the surface quenching layer and the crystal core volume. With an increase in the synthesis temperature, the second component disappears, and the decay time increases due to an increase in the number of ions in the crystal core volume and a more uniform distribution of dopants.
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Affiliation(s)
- Daria Pominova
- Prokhorov General Physics Institute RAS, Vavilova str., 38, Moskva, 119991, RUSSIAN FEDERATION
| | - Igor Romanishkin
- Prokhorov General Physics Institute RAS, Vavilova str 38, Moskva, 119991, RUSSIAN FEDERATION
| | - Vera Proydakova
- Prokhorov General Physics Institute RAS, Vavilova str 38, Moskva, 119991, RUSSIAN FEDERATION
| | - Sergei Kuznetsov
- Prokhorov General Physics Institute RAS, Vavilova str 38, Moskva, 119991, RUSSIAN FEDERATION
| | - Pavel Grachev
- Prokhorov General Physics Institute RAS, Vavilova str 38, Moskva, 119991, RUSSIAN FEDERATION
| | - Anastasia Ryabova
- Prokhorov General Physics Institute RAS, Vavilova str 38, Moskva, 119991, RUSSIAN FEDERATION
| | - Natalie Yu Tabachkova
- Prokhorov General Physics Institute RAS, Vavilova str. 38, Moskva, 119991, RUSSIAN FEDERATION
| | - Pavel Fedorov
- Prokhorov General Physics Institute RAS, Vavilova str 38, Moskva, 119991, RUSSIAN FEDERATION
| | - Victor Loschenov
- Prokhorov General Physics Institute RAS, Vavilova str 38, Moskva, 119991, RUSSIAN FEDERATION
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5
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Beckwith JS, Rumble CA, Vauthey E. Data analysis in transient electronic spectroscopy – an experimentalist's view. INT REV PHYS CHEM 2020. [DOI: 10.1080/0144235x.2020.1757942] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Joseph S. Beckwith
- Department of Physical Chemistry, University of Geneva, Geneva, Switzerland
| | | | - Eric Vauthey
- Department of Physical Chemistry, University of Geneva, Geneva, Switzerland
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6
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Esposito R, Delfino I, Portaccio M, Iannuzzi C, Lepore M. An insight into pH-induced changes in FAD conformational structure by means of time-resolved fluorescence and circular dichroism. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:395-403. [PMID: 31053922 DOI: 10.1007/s00249-019-01369-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 04/02/2019] [Accepted: 04/25/2019] [Indexed: 11/26/2022]
Abstract
Optical properties of flavin adenine dinucleotide (FAD) moiety are widely used nowadays for biotechnological applications. Given the fundamental role played by FAD, additional structural information about this enzymatic cofactor can be extremely useful in order to obtain a greater insight into its functional role in proteins. For this purpose, we have investigated FAD behaviour in aqueous solutions at different pH values by a novel approach based on the combined use of time-resolved fluorescence and circular dichroism spectroscopies. The results showed that pH strongly affects time-resolved fluorescence emission and the analysis allowed us to detect a three-component decay for FAD in aqueous solution with pH-depending lifetimes and relative amplitudes. Circular dichroism data were analyzed by a multi-Gaussian fitting procedure and the trends of properly chosen parameters confirmed pH-depending changes. The comparison between the results obtained by these two optical techniques allowed us to improve the significance of the outcome of circular dichroism. This combined approach may provide a useful tool for biotechnological investigation.
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Affiliation(s)
- Rosario Esposito
- Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione industriale, Università Federico II, P.le Tecchio 80, 80125, Naples, Italy
| | - Ines Delfino
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Largo dell'Università snc, 01100, Viterbo, Italy.
| | - Marianna Portaccio
- Dipartimento di Medicina Sperimentale, Università della Campania "Luigi Vanvitelli", Via S.M. Costantinopoli 16, 80134, Naples, Italy
| | - Clara Iannuzzi
- Dipartimento di Medicina di Precisione, Università della Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138, Naples, Italy
| | - Maria Lepore
- Dipartimento di Medicina Sperimentale, Università della Campania "Luigi Vanvitelli", Via S.M. Costantinopoli 16, 80134, Naples, Italy
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7
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Smith DA, McKenzie G, Jones AC, Smith TA. Analysis of time-correlated single photon counting data: a comparative evaluation of deterministic and probabilistic approaches. Methods Appl Fluoresc 2017; 5:042001. [PMID: 29063861 DOI: 10.1088/2050-6120/aa8055] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We review various methods for analysing time-resolved fluorescence data acquired using the time-correlated single photon counting method in an attempt to evaluate their benefits and limitations. We have applied these methods to both experimental and simulated data. The relative merits of using deterministic approaches, such as the commonly used iterative reconvolution method, and probabilistic approaches, such as the smoothed exponential series method, the maximum entropy method and recently proposed basis pursuit denoising (compressed sensing) method, are outlined. In particular, we show the value of using multiple methods to arrive at the most appropriate choice of model. We show that the use of probabilistic analysis methods can indicate whether a discrete component or distribution analysis provides the better representation of the data.
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Affiliation(s)
- Darren A Smith
- EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom. School of Chemistry, ARC Centre of Excellence in Exciton Science, University of Melbourne, Parkville, Victoria, 3010, Australia
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8
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Esposito R, Mensitieri G, de Nicola S. Improved maximum entropy method for the analysis of fluorescence spectroscopy data: evaluating zero-time shift and assessing its effect on the determination of fluorescence lifetimes. Analyst 2016; 140:8138-47. [PMID: 26541293 DOI: 10.1039/c5an01811k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new algorithm based on the Maximum Entropy Method (MEM) is proposed for recovering both the lifetime distribution and the zero-time shift from time-resolved fluorescence decay intensities. The developed algorithm allows the analysis of complex time decays through an iterative scheme based on entropy maximization and the Brent method to determine the minimum of the reduced chi-squared value as a function of the zero-time shift. The accuracy of this algorithm has been assessed through comparisons with simulated fluorescence decays both of multi-exponential and broad lifetime distributions for different values of the zero-time shift. The method is capable of recovering the zero-time shift with an accuracy greater than 0.2% over a time range of 2000 ps. The center and the width of the lifetime distributions are retrieved with relative discrepancies that are lower than 0.1% and 1% for the multi-exponential and continuous lifetime distributions, respectively. The MEM algorithm is experimentally validated by applying the method to fluorescence measurements of the time decays of the flavin adenine dinucleotide (FAD).
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Affiliation(s)
- Rosario Esposito
- Dept. of Chemical, Materials and Production Engineering, University of Naples Federico II, P.le Tecchio 80, 80125 Naples, Italy.
| | - Giuseppe Mensitieri
- Dept. of Chemical, Materials and Production Engineering, University of Naples Federico II, P.le Tecchio 80, 80125 Naples, Italy.
| | - Sergio de Nicola
- CNR-SPIN Napoli, Complesso Universitario di Monte Sant'Angelo, via Cinthia, 80126 Napoli, Italy
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9
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Voltz K, Léonard J, Touceda PT, Conyard J, Chaker Z, Dejaegere A, Godet J, Mély Y, Haacke S, Stote RH. Quantitative sampling of conformational heterogeneity of a DNA hairpin using molecular dynamics simulations and ultrafast fluorescence spectroscopy. Nucleic Acids Res 2016; 44:3408-19. [PMID: 26896800 PMCID: PMC4838372 DOI: 10.1093/nar/gkw077] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/29/2016] [Indexed: 01/22/2023] Open
Abstract
Molecular dynamics (MD) simulations and time resolved fluorescence (TRF) spectroscopy were combined to quantitatively describe the conformational landscape of the DNA primary binding sequence (PBS) of the HIV-1 genome, a short hairpin targeted by retroviral nucleocapsid proteins implicated in the viral reverse transcription. Three 2-aminopurine (2AP) labeled PBS constructs were studied. For each variant, the complete distribution of fluorescence lifetimes covering 5 orders of magnitude in timescale was measured and the populations of conformers experimentally observed to undergo static quenching were quantified. A binary quantification permitted the comparison of populations from experimental lifetime amplitudes to populations of aromatically stacked 2AP conformers obtained from simulation. Both populations agreed well, supporting the general assumption that quenching of 2AP fluorescence results from pi-stacking interactions with neighboring nucleobases and demonstrating the success of the proposed methodology for the combined analysis of TRF and MD data. Cluster analysis of the latter further identified predominant conformations that were consistent with the fluorescence decay times and amplitudes, providing a structure-based rationalization for the wide range of fluorescence lifetimes. Finally, the simulations provided evidence of local structural perturbations induced by 2AP. The approach presented is a general tool to investigate fine structural heterogeneity in nucleic acid and nucleoprotein assemblies.
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Affiliation(s)
- Karine Voltz
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964, Centre National de Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - Jérémie Léonard
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, CNRS UMR 7504, Université de Strasbourg, Strasbourg, France
| | - Patricia Tourón Touceda
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, CNRS UMR 7504, Université de Strasbourg, Strasbourg, France
| | - Jamie Conyard
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, CNRS UMR 7504, Université de Strasbourg, Strasbourg, France
| | - Ziyad Chaker
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, CNRS UMR 7504, Université de Strasbourg, Strasbourg, France
| | - Annick Dejaegere
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964, Centre National de Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - Julien Godet
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch Cedex, France
| | - Yves Mély
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch Cedex, France
| | - Stefan Haacke
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, CNRS UMR 7504, Université de Strasbourg, Strasbourg, France
| | - Roland H Stote
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964, Centre National de Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, 67404 Illkirch, France
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10
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Tran VL, Génot V, Audibert JF, Prokazov Y, Turbin E, Zuschratter W, Kim HJ, Jung J, Park SY, Pansu RB. Nucleation and growth during a fluorogenic precipitation in a micro-flow mapped by fluorescence lifetime microscopy. NEW J CHEM 2016. [DOI: 10.1039/c5nj03400k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The first observation, enumeration and mapping of the early states of crystallization during an anti-solvent precipitation.
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Affiliation(s)
- Vu Long Tran
- Laboratoire PPSM ENS Cachan
- CNRS
- UMR8531 & IFR d'Alembert IFR12161
- 94235 Cachan cedex
- France
| | - Valérie Génot
- Laboratoire PPSM ENS Cachan
- CNRS
- UMR8531 & IFR d'Alembert IFR12161
- 94235 Cachan cedex
- France
| | - Jean-Frédéric Audibert
- Laboratoire PPSM ENS Cachan
- CNRS
- UMR8531 & IFR d'Alembert IFR12161
- 94235 Cachan cedex
- France
| | | | | | | | - Hyeong-Ju Kim
- Center for Supramolecular Optoelectronic Material
- Seoul National University
- Gwanak-gu 155-744 Seoul
- South Korea
| | - Jaehun Jung
- Center for Supramolecular Optoelectronic Material
- Seoul National University
- Gwanak-gu 155-744 Seoul
- South Korea
| | - Soo Young Park
- Center for Supramolecular Optoelectronic Material
- Seoul National University
- Gwanak-gu 155-744 Seoul
- South Korea
| | - Robert B. Pansu
- Laboratoire PPSM ENS Cachan
- CNRS
- UMR8531 & IFR d'Alembert IFR12161
- 94235 Cachan cedex
- France
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11
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Slavov C, Hartmann H, Wachtveitl J. Implementation and evaluation of data analysis strategies for time-resolved optical spectroscopy. Anal Chem 2015; 87:2328-36. [PMID: 25590674 DOI: 10.1021/ac504348h] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Time-resolved optical spectroscopy plays a key role in illuminating the mechanisms of many fundamental processes in physics, chemistry, and biology. However, to extract the essential information from the highly complex time-resolved data, advanced data analysis techniques are required. Here we present the implementation strategies and the evaluation of the familiar global lifetime and target analysis as well as the not so widely adopted lifetime distribution analysis (LDA). Furthermore, we demonstrate the implementation of analysis strategies dealing with a number of artifacts inherently present in data from ultrafast optical experiments. The focus of the work is placed on LDA as it allows invaluable exploration depth of the kinetic information contained in the experimental data. We establish a clear regularization procedure for the use of LDA in ultrafast optical spectroscopy and evaluate the performance of a number of factors that play a role in the reliable reconstruction of lifetime distributions. Our results show that the optimal regularization factor can be determined well with the L-curve and the generalized cross-validation techniques. Moreover, the performance evaluations indicate that the most efficient regularization norm is the identity matrix. The analytical procedures described in this work can be readily implemented and used for the analysis of any time-resolved data.
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Affiliation(s)
- Chavdar Slavov
- Institute of Physical and Theoretical Chemistry, Goethe University , Frankfurt am Main, Germany
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12
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Mérola F, Fredj A, Betolngar DB, Ziegler C, Erard M, Pasquier H. Newly engineered cyan fluorescent proteins with enhanced performances for live cell FRET imaging. Biotechnol J 2013; 9:180-91. [DOI: 10.1002/biot.201300198] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 09/17/2013] [Accepted: 10/31/2013] [Indexed: 11/06/2022]
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