| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 3. |
- Bruneau, Anne, et al.
(författare)
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Advances in Legume Systematics 14. Classification of Caesalpinioideae. Part 2: Higher-level classification
- 2024
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Ingår i: PhytoKeys. - Sofia : Pensoft Publishers. - 1314-2011 .- 1314-2003. ; 240, s. 1-552
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Tidskriftsartikel (refereegranskat)abstract
- Caesalpinioideae is the second largest subfamily of legumes (Leguminosae) with ca. 4680 species and 163 genera. It is an ecologically and economically important group formed of mostly woody perennials that range from large canopy emergent trees to functionally herbaceous geoxyles, lianas and shrubs, and which has a global distribution, occurring on every continent except Antarctica. Following the recent re-circumscription of 15 Caesalpinioideae genera as presented in Advances in Legume Systematics 14, Part 1, and using as a basis a phylogenomic analysis of 997 nuclear gene sequences for 420 species and all but five of the genera currently recognised in the subfamily, we present a new higher-level classification for the subfamily. The new classification of Caesalpinioideae comprises eleven tribes, all of which are either new, reinstated or re-circumscribed at this rank: Caesalpinieae Rchb. (27 genera / ca. 223 species), Campsiandreae LPWG (2 / 5-22), Cassieae Bronn (7 / 695), Cera-tonieae Rchb. (4 / 6), Dimorphandreae Benth. (4 / 35), Erythrophleeae LPWG (2 /13), Gleditsieae Nakai (3 / 20), Mimoseae Bronn (100 / ca. 3510), Pterogyneae LPWG (1 / 1), Schizolobieae Nakai (8 / 42-43), Sclerolobieae Benth. & Hook. f. (5 / ca. 113). Although many of these lineages have been recognised and named in the past, either as tribes or informal generic groups, their circumscriptions have varied widely and changed over the past decades, such that all the tribes described here differ in generic membership from those previously recognised. Importantly, the approximately 3500 species and 100 genera of the former subfamily Mimosoideae are now placed in the reinstated, but newly circumscribed, tribe Mimoseae. Because of the large size and ecological importance of the tribe, we also provide a clade-based classification system for Mimoseae that includes 17 named lower-level clades. Fourteen of the 100 Mimoseae genera remain unplaced in these lower-level clades: eight are resolved in two grades and six are phylogenetically isolated monogeneric lineages. In addition to the new classification, we provide a key to genera, morphological descriptions and notes for all 163 genera, all tribes, and all named clades. The diversity of growth forms, foliage, flowers and fruits are illustrated for all genera, and for each genus we also provide a distribution map, based on quality-controlled herbarium specimen localities. A glossary for specialised terms used in legume morphology is provided. This new phylogenetically based classification of Caesalpinioideae provides a solid system for communication and a framework for downstream analyses of biogeography, trait evolution and diversification, as well as for taxonomic revision of still understudied genera.
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| 4. |
- Schuettpelz, Eric, et al.
(författare)
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A community-derived classification for extant lycophytes and ferns
- 2016
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Ingår i: Journal of Systematics and Evolution. - : Wiley. - 1674-4918 .- 1759-6831. ; 54:6, s. 563-603
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Tidskriftsartikel (refereegranskat)abstract
- Phylogeny has long informed pteridophyte classification. As our ability to infer evolutionary trees has improved, classifications aimed at recognizing natural groups have become increasingly predictive and stable. Here, we provide a modern, comprehensive classification for lycophytes and ferns, down to the genus level, utilizing a community-based approach. We use monophyly as the primary criterion for the recognition of taxa, but also aim to preserve existing taxa and circumscriptions that are both widely accepted and consistent with our understanding of pteridophyte phylogeny. In total, this classification treats an estimated 11 916 species in 337 genera, 51 families, 14 orders, and two classes. This classification is not intended as the final word on lycophyte and fern taxonomy, but rather a summary statement of current hypotheses, derived from the best available data and shaped by those most familiar with the plants in question. We hope that it will serve as a resource for those wanting references to the recent literature on pteridophyte phylogeny and classification, a framework for guiding future investigations, and a stimulus to further discourse.
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| 5. |
- Tiegs, Scott D., et al.
(författare)
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Global patterns and drivers of ecosystem functioning in rivers and riparian zones
- 2019
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Ingår i: Science Advances. - Washington : American Association of Advancement in Science. - 2375-2548. ; 5:1
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Tidskriftsartikel (refereegranskat)abstract
- River ecosystems receive and process vast quantities of terrestrial organic carbon, the fate of which depends strongly on microbial activity. Variation in and controls of processing rates, however, are poorly characterized at the global scale. In response, we used a peer-sourced research network and a highly standardized carbon processing assay to conduct a global-scale field experiment in greater than 1000 river and riparian sites. We found that Earth's biomes have distinct carbon processing signatures. Slow processing is evident across latitudes, whereas rapid rates are restricted to lower latitudes. Both the mean rate and variability decline with latitude, suggesting temperature constraints toward the poles and greater roles for other environmental drivers (e.g., nutrient loading) toward the equator. These results and data set the stage for unprecedented "next-generation biomonitoring" by establishing baselines to help quantify environmental impacts to the functioning of ecosystems at a global scale.
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| 6. |
- de Oliveira, Vinicius Silva, et al.
(författare)
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Intensity noise optimization of a mid-infrared frequency comb difference-frequency generation source
- 2020
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Ingår i: Optics Letters. - 0146-9592 .- 1539-4794. ; 45:7, s. 1914-1917
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Tidskriftsartikel (refereegranskat)abstract
- We experimentally demonstrate in a difference-frequency generation mid-infrared frequency comb source the effect of temporal overlap between pump and signal pulses on the relative intensity noise (RIN) of the idler pulse. When scanning the temporal delay between our 130 fs long signal and pump pulses, we observe a RIN minimum with a 3 dB width of 20 fs delay and a RIN increase of 20 dB in 40 fs delay at the edges of this minimum. We also demonstrate active long-term stabilization of the mid-infrared frequency comb source to the temporal overlap setting corresponding to the lowest RIN operation point by an online RIN detector and active feedback control of the pump-signal pulse delay. This active stabilization setup allows us to dramatically increase the signal-to-noise ratio of mid-infrared absorption spectra. (C) 2020 Optical Society of America
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| 7. |
- Foltynowicz, Aleksandra, 1981-, et al.
(författare)
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Measurement and assignment of double-resonance transitions to the 8900-9100- cm-1 levels of methane
- 2021
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Ingår i: Physical Review A: covering atomic, molecular, and optical physics and quantum information. - : American Physical Society. - 2469-9926 .- 2469-9934. ; 103:2
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Tidskriftsartikel (refereegranskat)abstract
- Optical-optical double-resonance spectroscopy with a continuous wave pump and frequency comb probe allows measurement of sub-Doppler transitions to highly excited molecular states over a wide spectral range with high frequency accuracy. We report on assessment and characterization of sub-Doppler double-resonance transitions in methane measured using a 3.3-μm continuous wave optical parametric oscillator as a pump and a 1.67-μm frequency comb as a probe. The comb spectra were recorded using a Fourier transform spectrometer with comb-mode-limited resolution. With the pump tuned to nine different transitions in the ν3 fundamental band, we detected 36 ladder-type transitions to the 3ν3 overtone band region, and 18 V-type transitions to the 2ν3 overtone band. We describe in detail the experimental approach and the pump stabilization scheme, which currently limits the frequency accuracy of the measurement. We present the data analysis procedure used to extract the frequencies and intensities of the probe transitions for parallel and perpendicular relative pump-probe polarization. We compare the center frequencies and relative intensities of the ladder-type transitions to theoretical predictions from the TheoReTS and ExoMol line lists, demonstrating good agreement with TheoReTS.
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| 8. |
- Foltynowicz, Aleksandra, 1981-, et al.
(författare)
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Sub-Doppler Double-Resonance Spectroscopy of Methane Using a Frequency Comb Probe
- 2021
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 126:6
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Tidskriftsartikel (refereegranskat)abstract
- We report the first measurement of sub-Doppler molecular response using a frequency comb by employing the comb as a probe in optical-optical double-resonance spectroscopy. We use a 3.3 μm continuous wave pump and a 1.67 μm comb probe to detect sub-Doppler transitions to the 2ν3 and 3ν3 bands of methane with ∼1.7 MHz center frequency accuracy. These measurements provide the first verification of the accuracy of theoretical predictions from highly vibrationally excited states, needed to model the high-temperature spectra of exoplanets. Transition frequencies to the 3ν3 band show good agreement with the TheoReTS line list.
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| 9. |
- Foltynowicz, Aleksandra, 1981-, et al.
(författare)
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Sub-doppler double-resonance spectroscopy of methane using a frequency comb probe
- 2020
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Ingår i: Conference on Lasers and Electro-Optics. - : Optica Publishing Group (formerly OSA). - 9781943580767 - 9781728144184
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Konferensbidrag (refereegranskat)abstract
- We use a 3.3 µm continuous wave optical parametric oscillator as a pump and a 1.67 µm frequency comb as a probe to record 36 sub-Doppler double-resonance transitions in the 3v3 band of methane (including 26 previously unreported) with ~1.5 MHz center frequency accuracy.
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| 10. |
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| 11. |
- Hjältén, Adrian, 1988-, et al.
(författare)
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Accurate measurement and assignment of high rotational energy levels of the 3v3 ← v3 band of methane
- 2023
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Ingår i: 2023 conference on lasers and electro-optics, CLEO 2023. - : IEEE. - 9781957171258 - 9781665455688
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Konferensbidrag (refereegranskat)abstract
- We use optical-optical double-resonance spectroscopy with a high-power continuous wave pump and a cavity-enhanced comb probe to expand sub-Doppler measurements of the 3v3 ← v3 band of CH4 to higher rotational levels. We assign the final states using combination differences, i.e., by reaching the same state using different pump/probe combinations.
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| 12. |
- Nostrani, Marcos Paulo, et al.
(författare)
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AN ANALYSIS OF A DIGITAL ELECTRO HYDROSTATIC ACTUATOR FOR APPLICATION IN AIRCRAFT FLIGHT CONTROL SYSTEMS
- 2023
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Ingår i: PROCEEDINGS OF ASME/BATH 2023 SYMPOSIUM ON FLUID POWER AND MOTION CONTROL, FPMC2023. - : AMER SOC MECHANICAL ENGINEERS. - 9780791887431
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Konferensbidrag (refereegranskat)abstract
- With the global awareness of reducing greenhouse gas emissions, research into developing more energy efficient hydraulic systems has become important. The aeronautical industry has been looking for more efficient solutions for aircraft application, where the search for more efficient systems has increased considerably, bringing the concept called More Electric Aircraft. However, hydraulic actuators are unbeatable against other technologies, due to their high power/weight ratio and reliability, being the predominant technology in flight control surfaces. Nevertheless, the hydraulic systems have low energy efficiency. With the aim of improving the energy efficiency of hydraulic systems, digital hydraulics has become one of the main technologies under study. However, the use in aircraft is still new. Therefore, this paper presents a digital hydraulic actuator for aircraft flight control surfaces called Digital Electro Hydrostatic Actuator - DEHA. A mathematical model was elaborated and was validated in a test bench rig. The actuator was applied to control an aircraft in the Aero-Data Model in a Research Environment - ADMIRE model. Furthermore, a Servo Hydraulic Actuator - SHA model was developed for comparison. The results show that DEHA can fly the ADMIRE aircraft in the proposed missions, with an energy efficiency of 41.63% while the SHA reached an efficiency of 0.46%, considering the LOE. This represents an efficiency increasing of 90.5 times, which demonstrates that DEHA can be a promising solution for aeronautical application.
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| 13. |
- Silander, Isak, 1980-, et al.
(författare)
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In situ determination of the penetration depth of mirrors in Fabry-Perot refractometers and its influence on assessment of refractivity and pressure
- 2022
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Ingår i: Optics Express. - : Optica Publishing Group (formerly OSA). - 1094-4087. ; 30:14, s. 25891-25906
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Tidskriftsartikel (refereegranskat)abstract
- A procedure is presented for in situ determination of the frequency penetration depth of coated mirrors in Fabry-Perot (FP) based refractometers and its influence on the assessment of refractivity and pressure. It is based on assessments of the absolute frequency of the laser and the free spectral range of the cavity. The procedure is demonstrated on an Invar-based FP cavity system with high-reflection mirrors working at 1.55 µm. The influence was assessed with such a low uncertainty that it does not significantly contribute to the uncertainties (k = 2) in the assessment of refractivity (<8 × 10−13) or pressure of nitrogen (<0.3 mPa).
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| 14. |
- Silva de Oliveira, Vinicius, et al.
(författare)
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Double-Resonance Spectroscopy of Methane Using a Comb Probe
- 2021
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Ingår i: 2021 Conference on Lasers and Electro-Optics Europe and European Quantum Electronics Conference, CLEO/Europe-EQEC 2021. - : IEEE Lasers and Electro-Optics Society. - 9781665418768
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Konferensbidrag (refereegranskat)abstract
- Optical-optical double resonance (OODR) spectroscopy is a powerful tool for the experimental assignment of highly-excited molecular states, which in turn is needed for verification of the accuracy of theoretical predictions of high-temperature spectra observed in exoplanets and in combustion environments. Previous implementations of OODR used either continuous wave (cw) lasers, which limit the number of transitions that can be detected, or pulsed lasers, which limit the spectral resolution. Recently, we demonstrated OODR with a cw pump and a frequency comb probe and applied it to the detection and assignment of methane transitions in the 3ν 3 ← ν 3 range with sub-Doppler resolution over 200 cm -1 of bandwidth [1]. The pump [see Fig. 1(a) ] was a 1 W 3.3m idler of a cw optical parametric oscillator (cw-OPO), stabilized to the Lamb dip in a selected CH 4 transition in the ν 3 band using a signal from a reference cell. The probe was an amplified fully-stabilized Er:fiber comb ( f rep = 250 MHz), whose center wavelength was shifted to 1.67m using a soliton self-frequency shift fiber (SSSF). The sample of pure CH 4 was contained in an 80-cm-long single-pass cell cooled by liquid nitrogen. The probe spectra were detected using a Fourier transform spectrometer (FTS) with comb-mode-limited resolution [2] , and the final interleaved spectra had 2 MHz sampling point spacing. Figure 1(b) shows the 3ν 3 ← ν 3 R(1) transition at 6046.36008(5) cm -1 , detected with the pump on the ν 3 R(0) line. We measured, fit and assigned 36 probe transitions with the pump tuned to 9 different transitions. Figure 1(d) shows a comparison of the probe transition wavenumbers to predictions from the TheoReTS database [3] , demonstrating agreement within 1 cm -1.
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| 15. |
- Silva de Oliveira, Vinicius, et al.
(författare)
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Measurement and Assignment of Hot-Band Methane Transitions with Sub-MHz Accuracy
- 2022
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Ingår i: CLEO: 2022. - : Optica Publishing Group. - 9781557528209
-
Konferensbidrag (refereegranskat)abstract
- We use double-resonance spectroscopy with cavity-enhanced comb probe to measure sub-Doppler transitions in the 3ν3←ν3 band of CH4. We assign the final states using different pump/probe combinations reaching the same state, and the dependence of line intensities on relative pump/probe polarization.
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| 16. |
- Silva de Oliveira, Vinicius, et al.
(författare)
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Optical-optical double-resonance spectroscopy of methane using a cavity-enhanced comb probe
- 2021
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Ingår i: OSA Technical Digest. - : Optical Society of America. - 9781557528209
-
Konferensbidrag (refereegranskat)abstract
- We implement a cavity to enhance the absorption of a frequency comb probe in a double-resonance measurement of sub-Doppler 3ν3 ← ν3 methane transitions. This yields two orders of magnitude better sensitivity in 15 times shorter acquisition time compared to previous work using a single-pass cell.
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| 17. |
- Silva de Oliveira, Vinicius, et al.
(författare)
-
Sub-doppler optical-optical double-resonance spectroscopy of methane using a frequency comb probe
- 2021
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Ingår i: OSA Optical Sensors and Sensing Congress 2021 (AIS, FTS, HISE, SENSORS, ES). - : Optical Society of America. - 9781557528209
-
Konferensbidrag (refereegranskat)abstract
- We use a 3.3 µm high-power continuous wave pump and a 1.67 µm comb probe to detect transitions in the 3ν3 ← ν3 range of methane with sub-Doppler resolution over 6 THz of bandwidth. We achieve high absorption sensitivity for the comb probe using an enhancement cavity and a Fourier transform spectrometer with auto-balanced detection.
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| 18. |
- Silva de Oliveira, Vinicius, et al.
(författare)
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Sub-Doppler optical-optical double-resonance spectroscopy using a cavity-enhanced frequency comb probe
- 2024
-
Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 15:1
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Tidskriftsartikel (refereegranskat)abstract
- Accurate parameters of molecular hot-band transitions, i.e., those starting from vibrationally excited levels, are needed to accurately model high-temperature spectra in astrophysics and combustion, yet laboratory spectra measured at high temperatures are often unresolved and difficult to assign. Optical-optical double-resonance (OODR) spectroscopy allows the measurement and assignment of individual hot-band transitions from selectively pumped energy levels without the need to heat the sample. However, previous demonstrations lacked either sufficient resolution, spectral coverage, absorption sensitivity, or frequency accuracy. Here we demonstrate OODR spectroscopy using a cavity-enhanced frequency comb probe that combines all these advantages. We detect and assign sub-Doppler transitions in the spectral range of the 3ν3 ← ν3 resonance of methane with frequency precision and sensitivity more than an order of magnitude better than before. This technique will provide high-accuracy data about excited states of a wide range of molecules that is urgently needed for theoretical modeling of high-temperature data and cannot be obtained using other methods.
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| 19. |
- Zakrisson, Johan, et al.
(författare)
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Procedure for automated low uncertainty assessment of empty cavity mode frequencies in Fabry-Pérot cavity based refractometry
- 2024
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Ingår i: Optics Express. - : Optica Publishing Group (formerly OSA). - 1094-4087. ; 32:3, s. 3959-3973
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Tidskriftsartikel (refereegranskat)abstract
- A procedure for automated low uncertainty assessment of empty cavity mode frequencies in Fabry-Pérot cavity based refractometry that does not require access to laser frequency measuring instrumentation is presented. It requires a previously well-characterized system regarding mirror phase shifts, Gouy phase, and mode number, and is based on the fact that the assessed refractivity should not change when mode jumps take place. It is demonstrated that the procedure is capable of assessing mode frequencies with an uncertainty of 30 MHz, which, when assessing pressure of nitrogen, corresponds to an uncertainty of 0.3 mPa.
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