Tag: Science

  • Better data sets won’t solve the problem — we need AI for Africa to be developed in Africa

    Better data sets won’t solve the problem — we need AI for Africa to be developed in Africa

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    In May 2023 Sam Altman, chief executive of OpenAI in San Francisco, California, embarked on a 17-city world tour to promote artificial intelligence (AI) tools. One of the stops in the first week of the tour was Lagos, Nigeria. Yet, research assessing the performance of OpenAI’s chatbot ChatGPT on a data set of 670 languages shows that African languages have the least support1. The large language model GPT-4, which underlies ChatGPT, recognizes sentences written in Hausa, Nigeria’s most widely spoken language, only 10–20% of the time.

    As a computer scientist and former machine-learning engineer at Google AI in Accra, I have long known about the limitations of importing AI tools devoid of local context into Africa. And we need to give African computer scientists the opportunity to develop home-grown solutions.

    For instance, in 2018, when my colleagues and I set out to track changes in the built environment of South Africa’s historically Black townships, we quickly discovered the limitations of AI models commonly used to detect features such as houses and street patterns in aerial images. Because the post-Apartheid constitution prioritizes uplifting disenfranchised communities, our project aimed to assess whether improvements in well-being were visible in satellite imagery. Unfortunately, available AI models — trained on Western cities, which often have grid-like layouts — struggled to adapt to the nation’s unique urban landscapes.

    It took us four years to develop an AI model tailored to the local context. Meanwhile, Western researchers who had access to similar satellite and census data focused on using night-time light levels to estimate poverty rates in several African countries2 — an approach that is doomed to fail in South African townships. There, well-lit streets, a legacy of Apartheid-era discriminatory policing, could easily be misread as signalling economically prosperous urban zones.

    Our challenging experience with ‘state-of-the-art’ AI models highlights the importance of local context and lived experience. That’s why African-built small language models, such as Lesan AI — a language translation and transcription tool — can match and even outperform Western counterparts on tasks such as speech-to-text transcription. To build the model, Lesan’s co-founder, Asmelash Hadgu in Berlin, hired fluent speakers of Tigrinya and Amharic to create unique data sets and then used those to train the AI. As a technologist who speaks both languages, Hadgu was able to build a rich data set by focusing on the most descriptive parts of his language.

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  • Personalized ranges for blood-test results enable precision diagnostics

    Personalized ranges for blood-test results enable precision diagnostics

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    Blood tests are fundamental to modern medicine, and are typically interpreted against broad reference ranges, based on population averages. Yet this standard approach overlooks a crucial point — many blood measurements (biomarkers) are highly individualized and regulated around unique stable values called setpoints, which differ between people. For many people, their ‘normal’ blood values fall within a narrow range — one that is much smaller than the population-based reference range1. Writing in Nature, Foy et al.2 present evidence that underscores the importance of these personalized setpoints, analysing decades of blood-test data across nine key parameters. The authors’ findings suggest that integrating personalized reference intervals into clinical diagnostics could bring about a new level of precision medicine.

    Competing Interests

    S.J.R.M. received research grants, research support, consultancy fees and lecture fees from diagnostic companies, including Roche Diagnostics, Abbott Laboratories and Werfen, all paid to his employer (Maastricht University Medical Center), and unrelated to the topic discussed in this manuscript. K.M.A. has served on advisory boards for Roche Diagnostics, Radiometer, Siemens Healthineers and SpinChip, and received consultant honoraria from CardiNor, lecturing honorarium from Siemens Healthineers, Roche Diagnostics, Mindray and Snibe Diagnostics and research grants from Siemens Healthineers and Roche Diagnostics. K.M.A. is also Associate Editor of Clinical Biochemistry and Chair of the IFCC Committee of Clinical Application of Cardiac Bio-markers.

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  • How the latest materials are taking biosensors to the next level

    How the latest materials are taking biosensors to the next level

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    A CG illustration showing soft blue bottlebrush shapes interspersed with long grey mesh tubes

    A rendering of a bottlebrush elastomer and carbon-nanotube composite that researchers believe has potential use as a brain electrode.Credit: Xu, P. et al. Nature Commun. 14, 623 (2023)/CC BY 4.0

    When Shuai Xu set out to create a wearable biosensor to monitor the vital signs of premature infants and newborns, he faced a major challenge: the skin of these children is so delicate that the adhesive used to attach a sensor could damage it, potentially leading to infection. The stiff device pulling against the skin as the baby moved, and the wires that might pull it in a different direction, added to the problem. The solution was to build a sensor that was soft and stretchable, with flexible circuit boards and thin, 50-millimetre wires, a huge change from the rigid devices that had long been a mainstay of this type of engineering. It was encased in a bendable silicone, transmitted its readings via Bluetooth, and was stuck to the body using a hydrogel, a polymer-based substance made mostly of water. Xu, a dermatologist, helped develop the device as a postdoctoral researcher in the laboratory of John Rogers, an engineer and materials scientist at Northwestern University in Evanston, Illinois, a pioneer in soft materials.

    Xu went on to become a founder and chief executive of Sibel Health in Chicago, Illinois, a medical device company that won Nature’s Spinoff Prize in 2020 and sells wearable sensors for monitoring patients. Xu’s challenges are common among researchers trying to develop biosensors and the materials that go into creating them. The devices must be small and lightweight, and must attach to the body with minimum irritation. In some cases, they require long-lasting batteries and circuitry that can handle a growing suite of artificial-intelligence algorithms that make sense of the data they collect.

    According to one estimate, the global market for health sensors was worth an estimated US$42.6 billion in 2023 and expected to grow to US$142.2 billion by 2030. The wrist-worn or finger-worn devices that were designed to count steps can now measure heartbeat and blood-oxygen levels, and they’ve been joined by patches that allow diabetics to perform continuous monitoring of their glucose levels.

    “That’s nothing to sneeze at,” Xu says. “But there are so many other things that are out there, biochemical and biophysical, that we still can’t do in a practical, continuous way.” Figuring out how to measure a variety of physical and chemical signals cheaply and non-invasively could provide diagnostic information that could reshape medicine. And this might go beyond sensors that take mechanical measurements, such as heart rate. Researchers are also working on chemical sensors that can detect biomarkers in blood, sweat and tears, as well as in fluids that surround cells.

    Aida Ebrahimi, a biosensor engineer at Pennsylvania State University in State College, is working on materials that can detect neurotransmitters in saliva or urine such as dopamine, serotonin, adrenaline and noradrenaline, which change in people with diseases such as Parkinson’s or Alzheimer’s. She’s focused on 2D materials, which are only one atomic layer thick, such as molybdenum disulfide. With a material in which, effectively, the “whole thing is surface, you are going to get high sensitivity in the ability to detect a very low concentration of biomolecules”, says Ebrahimi. The material properties of such atomically thin films are also sensitive to surface modification. For example, attaching molecules of manganese gives the material an affinity for dopamine, creating an ultrasensitive detector1.

    The upper torso of a small baby in a NICU cot shown with caring hands in shot and traditional wire monitors; a plaster-like clear wireless biosensor is visible on its' chest

    A soft and stretchable sensor was developed for a newborn’s sensitive skin.Credit: Northwestern University

    Similar materials with different molecules attached could be used as sensors for other chemicals that can provide information about health, says Ebrahimi. Her team built a prototype of the sensor in 2020 that they showed could measure dopamine1, but building it and validating it for use could be several years off.

    One measuring challenge is that a lot of signalling, particularly in the brain, is performed by the movement of ions, whereas most monitoring equipment is designed to detect electrical currents carried by the flow of electrons. Sahika Inal, a bioengineer at KAUST in Thuwal, Saudi Arabia, is using organic electrochemical transistors (OECTs)2, devices that can detect signals from biomolecules, cells and lipid layers and turn them into readings that can be measured by electronic equipment. OECTs can be built using organic mixed ionic–electronic conductors (OMIECs), which have been the focus of much interest in the past few years. OMIECs are polymers that both ions and electrons can flow across easily. When part of the transistor experiences a small change in a property it is measuring, the OMIEC amplifies that signal. Because it’s an organic polymer, the material is much more compatible with the wet environment of the body than a standard electronic transistor, which has to be encapsulated to protect it from fluids. As a result, electronics can be developed “that can be integrated directly with the biological system,” Inal says.

    OECT’s could be printed directly on the skin’s surface to detect biological signals, for instance, or built on top of threads of fabric to create biosensing garments and wraps that could survive washing. They also have the potential to replace the stiff electrodes used in brain implants to control prosthetic devices and monitor electrical activity in seizure patients. Their flexibility and biocompatibility might cause less irritation to brain tissue, which can render the electrodes less sensitive.

    At the University of Toronto, mechanical engineer, Xinyu Liu, and chemical engineer, Helen Tran, have developed another material with the softness and flexibility to be used as a brain electrode3. Dubbed the bottlebrush elastomer, their rubber-like substance is made from a molecule that has a long, stiff spine, which maintains its structure, surrounded by short, flexible bristles, for softness. To give the material electrical conductivity, Liu and Tran add a filler — either carbon nanotubes or a mixture of silver flakes and eutectic gallium indium, a semiconductor in liquid form. They worry, though, that the filler could leech out and have toxic effects, so they’d like to eliminate it. “Ultimately, we would like to design a polymer that is soft and electron-conducting,” Tran says. “These demands are often at odds.”

    Liu’s lab is also working on wearable sensors. One, based on a hydrogel, is designed to conform to the skin and measure strain when a body part, a knee, for example — is bent4. Such a device could be useful in monitoring an athlete’s performance or assessing arthritis.

    Another sensor they are developing places nanowires of zinc oxide on a cotton thread to create electronic textiles that can measure substances such as lactate and sodium in sweat. The material could be woven into a shirt or a sweatband to monitor an athlete’s health5.

    Xu sees a lot of opportunities for new biosensors. “AI is generating new algorithms,” he says, that can then be integrated into sensors to learn from, and react, to measurements they’re recording. That would require developing processors that can work with the limited power available in a sensor. Better batteries might help, as would alternatives such as harvesting power from movement or body heat, he says. Devices that can combine readings — glucose levels with heart rate, for instance — could be transformative, he says. He would also like to be able to detect stress hormones that could be used to monitor fatigue, or drug metabolites to check patients have taken medications.

    Biosensors have the potential to collect a lot of useful information, and to do it in everyday settings that might give a more realistic picture of health than a one-time doctor’s test. “Whether you’re ill or not”, says Xu, people do not spend most of their time in a clinic or hospital. The ability to track health “and use the technology yourself, I think is really important”.

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  • Lipid-delivery system could treat life-threatening pregnancy complication

    Lipid-delivery system could treat life-threatening pregnancy complication

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    Nature, Published online: 11 December 2024; doi:10.1038/d41586-024-03853-w

    Pre-eclampsia is a common and dangerous pregnancy-related illness. Using tiny lipid particles to deliver messenger RNA directly to the placenta to boost blood-vessel function might prove to be an effective treatment.

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  • Formation of a low-mass galaxy from star clusters in a 600-million-year-old Universe

    Formation of a low-mass galaxy from star clusters in a 600-million-year-old Universe

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    Image preparation

    The cluster field MACS J1423.8 + 2404 was observed with JWST/NIRCam imaging using filters F090W, F115W, F150W, F200W, F277W, F356W, F410M and F444W with exposure times of 6.4 ks each, reaching a signal-to-noise ratio between 5 and 10 for an mAB = 29 point source. It was also observed with JWST/NIRISS imaging using filters F115W, F150W and F200W.

    To reduce the imaging data, we use the photometric pipeline that is presented in more detail in ref. 44. Briefly, the raw data has been reduced using the public grism redshift and line analysis software Grizli43, which masks imaging artefacts, provides astrometric calibrations based on the Gaia Data Release 3 catalogue13 and shifts images using Astrodrizzle. The photometric zero-points are applied as described in ref. 34. RGB image created using six filters of NIRCam observation of the Firefly Sparkle is shown in Fig. 1. We used images from which bright cluster galaxies and intracluster light have been removed, as described in ref. 25. The methodology for modelling and removing diffuse light from cluster galaxies and intracluster light (ICL) is presented in ref. 25. The NIRCam depths (0.3′ diameter aperture) for F090W, F115W, F150W, F200W, F277W, F356W, F410M and F444W are 7.2, 6.6, 5.2, 4.4, 3.0, 2.9, 5.5 and 4.3 nJy, respectively, and the NIRISS depths for F115WN, F150WN and F200WN are 3.6, 4.3 and 4.0 nJy, respectively41.

    Photometry of Firefly Sparkle

    We perform photometry in 10 JWST bands (NIRISS: F115WN, F150WN and F200WN; NIRCam: F115W, F150W, F200W, F277W, F356W, F410M and F444W) in which the Firefly Sparkle is detected from their morphological fit with GALFIT. In other JWST and HST filters, the Firefly Sparkle is not or barely detected; hence, we place upper limits for the entire source. As the object is resolved into at least 10 distinct clusters and a diffuse galaxy component, we perform a morphological fit using Galfit10 to extract the photometric information.

    Point spread functions are extracted empirically by median stacking bright, isolated, non-saturated stars following the methodology described in ref. 28. Convolution kernels for homogenizing all data to the F444W resolution are created with photutils.psf.matching using a SplitCosineBellWindow() windowing function to remove high-frequency noise, which results from floating-point imprecision when taking the ratio of Fourier transforms. We optimize the shape of each window function to minimize the median residual between convolved stars from each source filter that is convolved and stars from the target F444W filter.

    For the morphological fit, we create 10″ × 10″ postage stamps in all 10 filters from the BCG-subtracted images. We determine the priors for the centres of the 10 clusters by visual inspection. Although nine out of the ten appear as point sources, FF-4 has an elongated shape and appears unresolved. We first determine the central coordinates of the 10 clusters and the arc by fitting (1) an elliptical Gaussian for FF-4; (2) nine point sources for the other nine clusters; and (3) another elliptical Gaussian with the bending mode turned on for the diffuse arc to the F115W image, which has the highest resolution (smallest PSF). The free parameters are the centres and total fluxes of all the components, the radius and axis ratio of FF-4, and the radius, axis ratio and bending mode (B2) of the arc. The initial guesses for the coordinates were determined by visual inspection of the F115W image. Once we obtain the fitted central coordinates of all the components from F115W, we again fit all 11 components in F444W, which has the highest signal-to-noise ratio for the arc and FF-4, to determine the radius, axis ratio, position angles of the ellipses, and the bending mode B2 of the arc.

    We use the best-fit centre coordinates from F115W as the central coordinates in all the filters. However, instead of fixing the central coordinates, we allow GALFIT to fit for them in every filter within a very narrow range of ±0.5 pixels (0.02″) to account for the uncertainty in the PSF centre. We also fix the bending mode B2 (2.14), ellipse radius (3.9″), axis ratio (0.08) and position angle (−51.8°) of the arc from the F444W fit. We fix the morphology of FF4 also with radius = 0.59″, axis ratio = 0.1 and position angle = −53°.

    We now fit all 11 components in all 10 filters to determine their fluxes. The resulting models and residuals are shown in Extended Data Fig. 1. Residuals from the fits are negligible, as shown by χ2/ν ~ 1 in the GALFIT fits in all filters. This confirms the original visual impression that nine of the ten clusters are unresolved and an additional smooth component is present.

    To derive the uncertainty in our flux estimation, we inject the full Firefly Sparkle model in 100 random locations in our 10″ × 10″ postage stamps (avoiding the edge) and refit with the exact same setting of GALFIT. We find no significant systematic offset between the fitted flux and the injected flux for any of the 11 components, in any of the filters, showing that our photometric technique is robust to background variations across all filters. The uncertainty in the photometry is calculated from the bi-weight scale of the 100 refitted fluxes. The resulting photometry and the RGB image of the model and the residual are shown in Extended Data Fig. 1. The agreement between NIRISS and NIRCam fluxes in the three overlapping filters is another confirmation of the robustness of photometry. We have used updated zero-points34 and corrected for Milky Way extinction using the colour excess E(B − V) = 0.0272 from ref. 6 and assuming the extinction law in ref. 35 using the factor between the extinction coefficient and colour excess RV = 3.1.

    Spectroscopy extraction and spectral fitting

    NIRSpec spectroscopy has been acquired for MACS J1423.8 + 2404 and spectra were obtained for the Firefly Sparkle, FF-BF and FF-NBF. The spectra for the FF-BF were part of the sample in ref. 23, with zspec = 8.2953 ± 0.0005. The spectra were observed using the PRISM/CLEAR disperser and filter, through three Micro-Shutter Assembly (MSA) masks per cluster with a total exposure time of 2.9 ks per MSA configuration.

    The NIRSpec data were processed using the STScI JWST pipeline (software v.1.8.4 and jwst_1030.pmap) and the msaexp package31. We used the standard JWST pipeline for the level 1 processing, in which we obtained the rate fits files from the raw data. We enabled the jump step option expand_large_events to mitigate contamination by snowball residuals and used a custom persistence correction that masked out pixels that approach saturation within the following 1,200 s for any readout groups. We then used msaexp for level 2 processing, for which we performed the standard wavelength calibration, flat-fielding, path-loss correction and photometric calibration and obtained the 2D spectrum before background subtraction. As the central and upper shutters contain different clusters (see Fig. 2a to find the shutter positions), we need custom background subtraction to avoid self-subtraction. We did this by building the background 2D spectrum by stacking and smoothing the sky spectrum in the empty pixels and obtained the background subtracted 2D spectrum of Firefly Sparkle. We confirmed that this custom background subtraction method works as well as a standard drizzle background subtraction method used in the literature33, using a well-isolated galaxy spectrum from the CANUCS observation (Asada et al., in prep.). We finally extract the 1D spectrum separately in slit 1 and slit 2, by collapsing the 2D spectrum using an inverse-variance weighted kernel following the prescription in ref. 24. We verified that the uncertainty array of the 1D spectrum has the appropriate normalization by testing the distribution of spectral fluctuations in an empty sky region and finding the fractions of pixels at >1 and >2σ as expected.

    Spectral fitting in Firefly Sparkle slit 1

    The resulting 1D spectrum of Firefly Sparkle in slit 1, dominated by the cluster FF-6, is shown in Fig. 2.

    The spectrum exhibits a Balmer jump at λobs ~ 3.5 μm and a turnover at λobs 1.4 μm, probably because of two-photon emission. These features suggest that the nebular continuum should dominate over the stellar continuum in the rest frame UV to optical spectrum within slit 1 (as found for a z = 5.9 galaxy in ref. 12). We thus model the continuum of the spectrum with nebular continuum using the photoionization code CLOUDY v.23 (ref. 5). To determine the dust attenuation value in the continuum model fitting, we first measure the Hγ/Hβ ratio by fitting the Gaussian profiles. The ratio agrees well with the case B recombination, and no significant dust attenuation is indicated. Therefore, in the continuum spectral modelling, we use pure hydrogen gas irradiated by an ionizing source having black-body SED without dust attenuation. We vary the effective temperature of the black body (Teff) and the electron temperature of the (ionized) hydrogen gas (\({T}_{{\rm{e}},{{\rm{H}}}^{+}}\)), and search for the best-fitting model continuum by χ2 minimization. In the continuum fitting, we mask out emission line regions and all wavelengths λobs < 1.2 μm at which the Lyman break is seen in the slit 2 spectrum, because this region may be affected by a neutral hydrogen damping wing. The best-fit model has log(Teff/K) = 5.10 and \(\log ({T}_{{\rm{e}},{{\rm{H}}}^{+}}/K)=4.34\), which is fully consistent with the results in ref. 12. The result of continuum fitting does not change if we consider a slight dust attenuation (AV = 0.1 mag) in the fitting. As discussed in ref. 12, the effective temperature of log(Teff/K) = 5.10 is much hotter than typical massive type O stars and is suggestive of this star-forming cluster having a top-heavy IMF. The IMF of this cluster is further discussed in section ‘SED fitting analysis’.

    Note that the UV continuum turnover feature could be because of the absorption from dense neutral hydrogen either in the intergalactic medium (IGM) or in the circumgalactic medium (CGM). However, in the case of slit 1 spectrum, we expect the effect of IGM and CGM damping absorption to be negligible or limited at λobs < 1.2 μm based on the blue continuum and sharp drop-out in the slit 2 spectrum (see section ‘Spectral fitting in Firefly Sparkle slit 2’ for details of slit 2 spectrum). Considering the spatial proximity of the slit 1 and slit 2 regions (Fig. 2), we can assume the absorption feature from line-of-sight neutral hydrogen to be the same in the slit 1 and slit 2 spectra. The slit 2 spectrum is rather blue and has a sharp Lyman break starting at λobs = 1.2 μm, whereas the slit 1 spectrum shows the turnover starting at λobs ~ 1.4 μm. Thus, the turnover feature should not be because of the neutral hydrogen absorption, but rather because of the intrinsic continuum shape of the source. Nevertheless, to avoid the possible effect of the neutral hydrogen absorption, we mask out λobs < 1.2 μm in the nebular continuum fitting above (corresponding to 1,290 Å in the rest frame).

    Having the model continuum, we subtract the underlying model continuum from the observed spectrum and measure the spectroscopic redshift and emission line fluxes by fitting Gaussian profiles. The best-fitting model spectrum with nebular continuum and Gaussian profiles is shown in Fig. 2b (red solid curve). We securely detect emission lines of [O iii]λλ4959, 5007, Hβ, [Oiii]λ4363, Hγ, Hδ and [Neiii]λλ3869, 3889. We do not find significant detection of [Oii]λ3727 and obtain an upper limit for the flux of this line. There is a tentative detection of the blended line of [Oiii]λλ1661 + 1666, although the spectral resolution of the prism is low at this wavelength making this doublet difficult to securely detect and separate from Heiiλ1640. We use these emission line fluxes to estimate the physical parameters in slit 1. We first estimate the dust attenuation based on Balmer decrements. Both the Hγ/Hβ and Hδ/Hβ ratios are consistent with theoretical predictions in case B recombination21 within the uncertainties, suggesting there is no significant dust attenuation (Extended Data Fig. 3, red squares in the left). This result is consistent with the initial measurement before the continuum fitting above and supports the validity of the dust-free assumption in the nebular continuum fitting process. Therefore, we do not correct for dust attenuation in the following measurements of emission line ratios and physical parameters in this section.

    We next measure the electron temperature using temperature-sensitive emission line ratios: [Oiii]4959+5007/[Oiii]4363 and [Oiii]5007/[Oiii]1661+1666. We assume the electron density to be ne = 103 cm−3, which is consistent with recent JWST observations of similarly high-z galaxies7 and obtain consistent independent temperature measurements within the uncertainties (\({T}_{{\rm{e}},{{\rm{O}}}^{++}}={4.0}_{-0.9}^{+2.6}\,{\rm{K}}\) and \({2.9}_{-0.4}^{+0.7}\times 1{0}^{4}\,{\rm{K}}\), respectively; Extended Data Fig. 3 (right)). Note that because the [Oiii]λλ1661 + 1666 detection is tentative and potentially blended with Heiiλ1640, we consider [Oiii]λ4363 to be more reliable.

    We note that in ref. 16, the authors measured a similar ratio of [Oiii]4959+5007/[Oiii]4363 in the z = 6 galaxy RXCJ2248-ID to that of slit 1. In ref. 16, medium resolution spectroscopy was used to determine the electron density directly. They found that when using lines with higher ionization potential than O+, the electron density was higher (ne ~ 105 cm−3) than is typically found from [Oii]λ3727 (ref. 7). This high electron density leads to a lower electron temperature for their galaxy of \({T}_{{\rm{e}},{{\rm{O}}}^{++}}=2.5\times 1{0}^{4}\,{\rm{K}}\). Similarly, if we assume the electron density of ne = 105 cm−3 instead for our slit 1 spectrum, the electron temperature from [Oiii]λ4363 becomes \({T}_{{\rm{e}},{{\rm{O}}}^{++}}={3.2}_{-0.96}^{+1.6}\), which is in between the two measurements based on [Oiii]λλ1661 + 1666 and [Oiii]λ4363 when assuming ne ~ 103 cm−3 above. To consider the possibility of a somewhat higher electron density in the highly ionized region, we adopt the mean value of our two electron temperature measurements (\({T}_{{\rm{e}},{{\rm{O}}}^{++}}=3.5\times 1{0}^{4}\,{\rm{K}}\)) as our fiducial value and propagate the full range of the two measurement uncertainties into the following metallicity measurement.

    Based on the electron temperature measurement, we obtained the oxygen abundance from [Oiii]4959+5007/Hβ and [Oii]3727/Hβ ratios, following the prescription in ref. 8. We assume the electron density to be ne = 103 cm−3. The total oxygen abundance is calculated from O++/H+ and O+/H+, and the higher ionizing state oxygen is ignored30. As the [Oii]λ3727 emission line is undetected, we can obtain only an upper limit for O+/H+, but the upper limit for the abundance of the singly ionized oxygen is negligibly small as compared with the doubly ionized oxygen. We thus derived the total oxygen abundance from O++/H+, yielding \(12+\log ({\rm{O/H}})=7.0{5}_{-0.37}^{+0.22}\) (\({Z}_{{\rm{gas}}}/{Z}_{\odot }=0.0{2}_{-0.01}^{+0.04}\) assuming the solar abundance to be 8.69; ref. 38).

    We also derive the ionization parameters using the ionization-sensitive emission line ratios: [Oiii]5007/[Oii]3727 and [Neiii]3869/[Oii]3727. Following the prescription in refs. 45,46, we obtain the lower limit for the ionization parameters (log  U) from these two ratios. Both ratios provide a similar limit of log U > −2.0.

    All the emission line flux measurements and the derived physical parameters in Firefly Sparkle slit 1 are presented in Extended Data Table 1. We also compare the diagnostic emission line ratios in Firefly Sparkle with those in other galaxy population in Fig. 2d. We use the ionization-sensitive line ratio O32 ([Oiii]5007/[Oii]3727) and the temperature-sensitive line ratio RO3 ([Oiii]4959+5007/[Oiii]4363) and compare these line ratios with other [Oiii]λ4363-detected galaxies at z = 2–9 from previous JWST observations2 and those in the local universe from SDSS observations14. Extended Data Fig. 3 (middle) presents a similar comparison but uses another ionization-sensitive line ratio Ne3O2 ([Neiii]3869/[Oii]3727) instead of O32.

    Spectral fitting in Firefly Sparkle slit 2

    In contrast to slit 1, the extracted 1D spectrum in Firefly Sparkle slit 2 does not show nebular continuum features, and the blue continuum is rather smooth with a sharp drop-out because of the Lyman break at λobs ~ 1.2 μm. We thus derive the emission line fluxes from the slit 2 spectrum by fitting Gaussian profiles with the continuum being modelled by a constant offset around each emission line. We detect [Oiii]λλ4959,5007, Hβ, Hγ, Hδ, [Neiii]λ3869 and [Oii]λ3727 emission lines in the slit 2 spectrum but do not detect [Oiii]λ4363.

    We then derive the physical properties in the same way as done for Firefly Sparkle slit 1 spectrum. We measure the dust attenuation from Balmer decrement, Hγ/Hβ and Hδ/Hβ, and find both line ratios agree well with the predicted ratios under case B recombination (blue squares in Extended Data Fig. 3 (left)). This suggests that the dust attenuation is negligible in the slit 2 spectrum as well, and we do not make a dust attenuation correction.

    As we do not detect the temperature-sensitive emission lines of [Oiii]λ1666 or [Oiii]λ4363 in the slit 2 spectrum, we cannot measure the electron temperature and the metallicity from the direct-temperature method. We thus obtain only the upper limit for the electron temperature (\({T}_{{\rm{e}},{{\rm{O}}}^{++}}\)) from the non-detection of [Oiii]λ4363. The electron temperature in Firefly Sparkle slit 2 is shown to be \({T}_{{\rm{e}},{{\rm{O}}}^{++}} < 1.8\times 1{0}^{4}\,{\rm{K}}\) (1σ) or <4.5 × 104 K (3σ). To visualize the difference in physical properties in slit 1 and slit 2, we show the diagnostic emission line ratios of Firefly Sparkle slit 2 in Fig. 2d and Extended Data Fig. 3 (middle) as well.

    SED fitting analysis

    SEDs derived from our photometry were analysed using a slightly modified version of the Dense Basis method18,47 to determine non-parametric SFHs, masses and ages for our sources in Firefly Sparkle. We adopt the Calzetti attenuation law48 and a Kroupa IMF32 with a flat prior for the high-mass slope α [1., 4.]. We run fits using both the MILES stellar libraries29 and MESA Isochrones and Stellar Tracks (MIST; ref.  17), as well as the Binary Population and Spectral Synthesis (BPASS; refs. 26,36) models to consider for the presence of binary populations. As the latest BPASS version in FSPS (-bin-imf135all 100) assumes a Salpeter IMF with an upper mass cutoff of 100M and does not allow for a varying IMF, we only vary the top-heavy slope of the Kroupa IMF in the MILES + MIST runs with an upper mass cutoff of 120M. This should be considered while comparing the physical properties from the two runs, as allowing for a varying IMF based on the MILES + MIST configuration results in lower stellar masses for those runs because they are preferentially fit with top-heavy SSPs with a greater fraction of light coming from more massive stars. We fix the redshift to that found from the NIRSpec Prism spectroscopy by the [Oiii] λ4959 line at zspec = 8.296 ± 0.001. All other parameters are left free. We run the SED fits in two configurations to account for different possibilities of the nature of the individual clusters:

    1. 1.

      SSP fits: to account for the possibility that the individual clumps are star clusters, which is likely given the physical scales of the clusters and the extreme emission lines in the spectra, we modify the code to fit for instantaneous bursts of star formation, described by SSPs. In this case, we assume a flat prior in the log age of the SSP from 105 years to the age of the universe at zspec = 8.296 ± 0.001 instead of the non-parametric defaults for the SFH in Dense Basis.

    2. 2.

      Non-parametric SFH fits (Dense Basis): to fit the diffuse body of the galaxy and to account for the possibility that the clusters are nuclear star clusters or remnants of previous mergers, we also run fits with non-parametric SFHs with a Dirichlet prior. The main advantage of using Dense Basis with non-parametric SFHs is that they allow us to account for flexible stellar populations, which is important at these redshifts49 because star formation is expected to be stochastic and may be underestimated if fit using traditional parametric assumptions39,50.

    We perform our fitting in two stages—we initially perform a joint spectrophotometric fit to the NIRSpec Prism spectrum along with the HST + NIRISS + NIRCam photometry in the slits in which both exist (Extended Data Fig. 4). We correct for slit loss considering two factors—the amount of light lost due to the changing PSF as a function of wavelength and an overall multiplicative correction to match the spectrum against the photometric measurements. We modify the default Dense Basis method in this stage to additionally fit for the slope at the massive end of the IMF, the gas-phase metallicity and the ionization parameter, using the relevant parameters from FSPS (imf3, gas_logz and gas_logu). Doing so allows us to substantially constrain priors on star formation rate, IMF, dust, ionization parameter and metallicity that we then use to fit the photometry. We find that the fits are consistent with negligible dust attenuation, consistent with our estimates from measuring the Balmer decrement. We also find that our fits rule out the part of parameter space consistent with the canonical Chabrier-like or Kroupa-like IMF (with the high-mass slope ≈ 2.3) in favour of more top-heavy slopes of about \({1.5}_{-0.6}^{+0.7}\) for slit 1, which contains portions of clusters 3, 4, 5 and 6. We find weaker constraints from the spectrum for slit 2, which still skews towards top-heaviness but with large uncertainties of about \({1.7}_{-0.7}^{+0.9}\). Finally, we find estimates of both stellar and gas-phase metallicities to be sub-solar, consistent with estimates from the line ratios.

    Using our photometry (Extended Data Table 4), we now determine the stellar properties of each individual component by running a second set of fits using the same set of parameters that are used to fit the spectrophotometry. Although parameters such as the metallicity and ionization parameter are only loosely constrained by these fits, we obtain parameter estimates for the stellar masses, star formation rates and ages of the individual star clusters with uncertainties that marginalize over the variations in the other parameters.

    Both photometry and corresponding fits to the SED fit are shown in Extended Data Fig. 5, with variations in the stellar mass, age and reduced χ2 of the fits for each of the four scenarios (SSPs fits with MILES + MIST and BPASS, and Dense Basis fits with MILES + MIST and BPASS) shown in Extended Data Table 2. All 10 components have intrinsic (corrected for magnification) stellar masses of about 105–106M and sSFR of 10−7 yr−1. Although the error bars are large, the distinct colours of the clusters hint at different formation times. Although the smooth component contains a large fraction of the stellar mass, the bulk (about 57%) lies in the clusters. Extended Data Table 3 lists the physical properties of the individual components as well as the full Firefly Sparkle, BF and NBF galaxies.

    We find that the SSP fits are generally less massive compared with the Dense Basis fits, because the light from the SED is modelled by a single epoch of star formation instead of an extended episode. As light from the massive stars responsible for young star formation are much brighter than older stellar populations, they can describe the observed SED with a lower mass. However, the SSP fits often cannot capture both the UV slopes and the nebular emission in the rest-optical, as seen for clusters 1, 3, 7 and 8 in Extended Data Fig. 5 and often approximate it using a Balmer break, leading to posteriors consistent with much older ages than the median values.

    Although the tage from SSP and t50 from Dense Basis fits (Extended Data Table 2) may seem inconsistent, it is important to note that the Dense Basis fits for most star clusters indicate a sharp burst of star formation within the past 10 million years (Extended Data Fig. 6). By design, an SSP is biased towards this recent burst, whereas a non-parametric SFH can accommodate extended episodes of star formation. However, with our current data, we cannot distinguish between extended SFH in the star clusters and the contribution of light from the diffused arc.

    The masses of the clusters also scale with the top-heaviness of the high-mass end of the IMF in the MILES + MIST fits, with lower masses for more top-heavy IMF values as that scale the amount of light from massive stars. In comparison, the BPASS fits in the current setup are done at the canonical Kroupa IMF, leading to higher masses for those fits. At the same IMF slope, the masses are comparable within uncertainties for the different SPS models, and the sSFR and age/t50 values are consistent even marginalizing over the IMF posteriors. Given the observational constraints and the χ2 from the fits in Extended Data Table 2, it is not currently possible to definitively rule out any of the current fitting approaches.

    Lens modelling

    We use Lenstool9 to build a strong lensing model of the MACS 1423 cluster, to be fully presented in Desprez et al. (manuscript in preparation). This model is constrained with the three multiple image systems that were leveraged in ref. 3, for which we provide additional information obtained from the CANUCS data. The first two systems are those presented in ref. 27, one at z = 2.84 for which we account for the two clusters visible in the four images of the objects, and the second one with three images at z = 1.779 for which we identify another cluster in the two northernmost images for improved constraints. The last system is composed of five images11 for which we provide a new spectroscopic redshift measurement of z = 1.781 that is in agreement with photometric and geometric redshifts previously measured.

    The different mass components are parameterised as double Pseudo-Isothermal Elliptical (dPIE) profiles4. The model is composed of a large cluster scale mass halo, an independent galaxy scale centred on the brightest cluster galaxy and small galaxy scale mass components to account for the contribution of all cluster members that follow a mass–luminosity scaling relation22. For all galaxies, their positions, ellipticities and orientations have been fixed to these measured from the images. The final best model manages to reproduce the position of the input multiple images with a distance rms of 0.46″.

    Magnifications are obtained by generating convergence and shear maps around the Firefly Sparkle with a size of 20″ and a resolution of 10 milli-arcsec per pixel. Uncertainties in the magnifications are computed from 100 randomly selected models from the optimization of Lenstool after its convergence around the minimum χ2. The numbers provided in Extended Data Table 3 are the median and ±1σ limits on the distribution of the 100 values obtained at the position of each cluster. We measured the average magnification of the FF-arc by using the GALFIT model of the arc (in F200W) and selecting all pixels with flux >10% of maximum flux. We then computed the best magnification value for all selected pixels and computed the mean and standard deviation values for these to find the magnification of the arc (μ = 24.4 ± 6.0).

    The source plane reconstruction is made using the best GALFIT model to compute the source plane positions and magnification for the 10 star clusters. We use Lenstool to generate a source plane image reconstruction of the diffuse light of the galaxy with a smooth PSF-deconvolved model of its light profile. We use GALFIT to add 10 point sources convolved with the appropriate PSFs to the diffused source plane model at the source plane positions of the star clusters with the demagnified fluxes. This process is repeated to generate source plane models in all filters. We also generate a mass map using the same prescription, replacing the demagnified fluxes with the demagnified masses. The resulting source plane RGB image and mass map are shown in Fig. 4c,d.

    Size and surface density of star clusters

    We now investigate the spatial properties of the star clusters. Nine out of the ten star clusters are unresolved even in our highest resolution F115W NIRCam image. FF-4 has a slightly elongated shape visually but has a best-fit major axis size (0.01) smaller than the smallest PSF, making the size estimate unreliable. Hence, we use the half-width half-max of the NIRCam F115W PSF (0.02) to set an upper limit on the size of all 10 star clusters. To determine the upper limits of the sizes of unresolved sources, we use the tangential eigenvalue of magnification 1/λt, which ranges between 14 and 24. This results in a size upper limit between 4 pc and 7 pc. The central star clusters have the highest magnification and the smallest upper limits, whereas the ones near the two ends of the arc have the lowest. We use the upper limit on sizes and the demagnified stellar masses to calculate the lower limit on stellar surface densities as shown in Fig. 3b.

    Abundance matching for MW and M31 progenitors

    To estimate the range of stellar masses of progenitors of both MW-mass and M31-mass galaxies at higher redshift, we adopt a semi-empirical approach combining both simulations and observations. We assume an evolving co-moving number density with redshift, as determined by the abundance matching code from ref. 20, with z = 0 number densities of \(\log (n/{{\rm{Mpc}}}^{3})=-\,2.95\) and \(\log (n/{{\rm{Mpc}}}^{3})=-\,3.4\), respectively, for MW and M31 mass analogues. The code calculates a past median galaxy number density at z2, given an initial number density at z1, using peak halo mass functions. As the merger rate per unit halo per unit Δz is roughly constant, the evolution of the cumulative number density of progenitors of any given galaxy is a power law, with the change described by (0.16Δz) dex.

    In ref. 20, peak halo mass functions are used because the resultant median number densities are less affected by the scatter in stellar mass and luminosity. However, this scatter does affect the 1σ errors in cumulative number density. The 1σ or 68 percentile range grows with increasing redshift, but this growth is also higher for more massive galaxies.

    As the code from ref. 20 does not calculate stellar masses, we obtain the stellar mass ranges of the progenitor populations of MW and M31 analogues using stellar mass functions (SMFs) from various surveys15,19,40. We take the median cumulative number densities at each Δz to find the stellar mass associated with that number density from the corresponding SMF. Moreover, the 1σ errors on the given number density for each redshift are then used to determine the 1σ errors on the stellar mass of the progenitors. At z = 8.3, the median stellar mass of MW progenitors is \(\log ({M}_{\star }/{M}_{\odot })=6.4\pm 0.7\) and the median stellar mass of M31 progenitors is \(\log ({M}_{\star }/{M}_{\odot })=6.9\pm 0.8\). The Firefly Sparkle with a stellar mass of \(\log ({M}_{\star }/{M}_{\odot })={7.0}_{-0.3}^{+1.0}\) is definitely within 1σ stellar mass range of both Milky Way and M31 progenitors. More details on the progenitor matching technique can be found in ref. 37.

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  • Recyclable CuZn electrodes could reshape CO₂ reduction technologies

    Recyclable CuZn electrodes could reshape CO₂ reduction technologies

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    Chungnam National University researchers uncover breakthrough in copper-zinc electrodes for electrochemical CO₂ reduction
    Electrochemical performance of CuZn electrodes during multiple recycling cycles in CO₂ reduction. The study highlights the impact of surface oxidation states on catalytic efficiency and product selectivity. Credit: Chungnam National University

    A researcher’s team at Chungnam National University has unlocked new potential for copper-zinc (CuZn) electrodes in electrochemical CO₂ reduction (EC CO₂R). This research, led by Professor Youngku Sohn, explores the performance and recyclability of CuZn electrodes, comparing them with single-metal alternatives like copper and zinc, and highlighting their superior catalytic properties.

    This research is published in the journal Applied Surface Science.

    “Electrochemical methods present a promising solution for repurposing CO₂, but electrode stability has always been challenging,” says Prof. Sohn. “Our study shows that CuZn electrodes can stabilize over time through recycling, preserving their catalytic effectiveness and selectivity for valuable hydrocarbons.”

    A key highlight of the study was the use of laser techniques to control the oxidation states of the electrodes, allowing researchers to fine-tune their catalytic properties. By analyzing the performance of these electrodes through multiple recycling cycles, the team found that CuZn alloys outperformed single-metal electrodes, providing insights into the importance of surface oxidation states for catalytic efficiency and product selectivity.

    The team utilized advanced techniques such as depth-profiling X-ray photoelectron spectroscopy (XPS) to track the changes in oxidation states and compositions of the electrodes. This method revealed that the CuZn electrodes not only stabilize over time but also exhibited a superior ability to maintain selectivity for complex hydrocarbons compared to the single-metal electrodes.

    “We also explored the influence of oxidation states on product selectivity,” adds Ms. Seon Young Hwang, a co-author and master’s student in the Department of Chemistry at Chungnam National University. “By controlling the oxidation states, we were able to significantly enhance the electrodes’ performance in reducing CO₂ to valuable products.”

    This study is particularly relevant for real-world applications, as it enhances the understanding of electrode recyclability and the design of more selective catalysts. The findings could help create high-efficiency CO₂ reduction systems for the conversion of CO₂ into sustainable fuels or valuable chemicals, potentially transforming industries such as energy, manufacturing, and environmental conservation.

    “The long-term implications of this work are profound,” says Prof. Sohn. “This research could play a crucial role in developing carbon-neutral industrial processes, contributing to a circular carbon economy by efficiently recycling CO₂ into useful products.”

    While the study marks a significant milestone, further research is needed to optimize the scalability of these electrodes for industrial applications. The team’s next step is to examine these electrodes under real-world conditions to understand their capabilities better.

    More information:
    Seon Young Hwang et al, Dynamic recycling behavior of Cu/Zn-based electrodes in electrochemical CO2 reduction, Applied Surface Science (2024). DOI: 10.1016/j.apsusc.2024.160628

    Provided by
    Chungnam National University Evaluation Team

    Citation:
    Recyclable CuZn electrodes could reshape CO₂ reduction technologies (2024, December 10)
    retrieved 10 December 2024
    from https://phys.org/news/2024-12-recyclable-cuzn-electrodes-reshape-reduction.html

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  • Ultrafast electron imaging captures never-before-seen nuclear motions in hydrocarbon molecules excited by light

    Ultrafast electron imaging captures never-before-seen nuclear motions in hydrocarbon molecules excited by light

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    Speedy nuclei do the twist
    Researchers retrieved the time-varying molecular structure of photoexcited o-nitrophenol from ultrafast electron diffraction data using a genetic algorithm. Credit: J. P. F. Nunes (generated using Microsoft Copilot)

    The interactions between light and nitroaromatic hydrocarbon molecules have important implications for chemical processes in our atmosphere that can lead to smog and pollution. However, changes in molecular geometry due to interactions with light can be very difficult to measure because they occur at sub-Angstrom length scales and femtosecond time scales.

    In a study, published in the journal Physical Chemistry Chemical Physics, researchers used an ultrafast electron camera to image the motions of hydrocarbon molecules on scales 10,000 times smaller than the width of a human hair.

    This ultra-precise and ultrafast imaging technique, supported by advanced computations, reveals a proton transfer step followed by an out-of-plane twisting motion as key components of energy relaxation. (Relaxation is the process by which the molecule moves from an excited, high-energy state to a lower energy ground state after absorbing light.)

    Previous studies have proposed various ways that hydrocarbon molecules may relax after interacting with light. However, scientists lacked experimental data to verify which process occurs.

    In this research, scientists used the relativistic ultrafast electron diffraction (UED) instrument to observe the relaxation of photoexcited o-nitrophenol. Then, they used a genetic structure fitting algorithm to extract new information about small changes in the molecular shape from the UED data that were imperceptible in previous studies.

    Specifically, the experiment resolved the key processes in the relaxation of o-nitrophenol: proton transfer and deplanarization (i.e., a rotation of part of the molecule out of the molecular plane). Ab-initio multiple spawning simulations confirmed the experimental findings.

    The researchers were able to identify a key relaxation pathway involving proton transfer and molecular “twisting.” This result lays the groundwork for studies of more complex molecules that scientists believe undergo similar interactions. It will also help researchers better understand how pollution forms.

    More information:
    J. P. F. Nunes et al, Photo-induced structural dynamics of o-nitrophenol by ultrafast electron diffraction, Physical Chemistry Chemical Physics (2024). DOI: 10.1039/D3CP06253H

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    Citation:
    Ultrafast electron imaging captures never-before-seen nuclear motions in hydrocarbon molecules excited by light (2024, December 10)
    retrieved 10 December 2024
    from https://phys.org/news/2024-12-ultrafast-electron-imaging-captures-nuclear.html

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  • Predicting atomic structures proves useful in energy and sustainability

    Predicting atomic structures proves useful in energy and sustainability

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    Predicting atomic structures proves useful in energy and sustainability
    Unphyiscal CN1 (coordination number of 1) carbons can be effectively reduced by K cycles of restart sampling. Credit: Machine Learning: Science and Technology (2024). DOI: 10.1088/2632-2153/ad8c10

    Researchers at Lawrence Livermore National Laboratory (LLNL) have developed a new approach that combines generative artificial intelligence (AI) and first-principles simulations to predict three-dimensional atomic structures of highly complex materials.

    This research highlights LLNL’s efforts in advancing machine learning for materials science research and supporting the Lab’s mission to develop innovative technological solutions for energy and sustainability.

    The study, recently published in Machine Learning: Science and Technology, represents a potential leap forward in the application of AI for materials characterization and inverse design.

    The approach uses X-ray absorption near edge structure (XANES) spectroscopy. Accurately determining atomic structures from spectroscopic data has long posed a challenge, particularly for complex systems, such as shapeless materials.

    In response, LLNL scientists have introduced a generative framework based on diffusion models, which are an emerging machine learning technique. The authors demonstrate how this framework enables the prediction of 3D atomic arrangements from XANES spectra.

    “Our method bridges a crucial gap between spectroscopic analysis and precise structure determination,” said Hyuna Kwon, a materials scientist in LLNL’s Quantum Simulations Group, Materials Science Division. “By conditioning the generative model on XANES data, we can reconstruct atomic structures that align closely with the target spectra, offering a powerful tool for material analysis and custom design.”

    The project was a collaborative effort, with Kwon and Tim Hsu from LLNL’s Center for Applied Scientific Computing contributing equally. The team demonstrated that their AI model also scales effectively from small datasets for generating realistic, large-scale structures. This scale-agnostic property demonstrates the model’s ability to bridge scales from nanoscale to microscale, enabling detailed atomic structure generation even at complex features like grain boundaries and phase interfaces.

    “This approach can be leveraged beyond just structural analysis,” said Anh Pham, the principal investigator of the project. “It can be extended to inverse design—where we start from a desired material property and engineer the corresponding atomic structure—accelerating the discovery of materials with tailored functionalities.”

    More information:
    Hyuna Kwon et al, Spectroscopy-guided discovery of three-dimensional structures of disordered materials with diffusion models, Machine Learning: Science and Technology (2024). DOI: 10.1088/2632-2153/ad8c10

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    Citation:
    Predicting atomic structures proves useful in energy and sustainability (2024, December 10)
    retrieved 10 December 2024
    from https://phys.org/news/2024-12-atomic-energy-sustainability.html

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  • Experts share why commonly used measuring method for fluorescence is not always appropriate

    Experts share why commonly used measuring method for fluorescence is not always appropriate

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    Reshaping tradition: good old ways are not always good
    Scientists from the IPC PAS adding a variable to the known theories on fluorescence in the form of diffusion have come to quite new conclusions. The picture, which refers in a symbolic way to the laser analysis of particle motion, was realized at the hospitable thresholds of the Warsaw University of Technology. Credit: IPC PAS, Grzegorz Krzyzewski

    Fluorescence is a well-known phenomenon with many practical applications that has been studied for decades. Despite this, a commonly used mathematical formalism to describe how it evolves over time does not make physical sense under certain conditions, as researchers from the Institute of Physical Chemistry, Polish Academy of Sciences have recently discovered.

    Namely, they showed that a mathematical tool that can be safely used in solids, where molecules are practically immobile, cannot always be used in liquids, where they can move freely. If applied incorrectly, this widely used approach can lead to erroneous interpretations of experimental data and wrong conclusions. This is what their paper in the The Journal of Chemical Physics warns us about.

    Everything glows, but not in the same way. It has been known for more than a century that anybody at a given temperature above the inaccessible absolute zero emits photons. Some substances also emit light after undergoing a chemical or biochemical reaction, an electrochemical reaction, or after being excited by another light source. These phenomena are known as chemi-, bio-, electrochemi- and photo-luminescence, respectively.

    You may have seen photos of Australian coastlines full of bright blue algae at night, or glowing fireflies in the forest. You may have noticed the green and blue flakes in banknotes under an ultraviolet lamp. In all these examples, the observed light is a luminescence process in which molecules in excited states of their electrons relax back to the comfortable relaxed state, giving off the excess energy in the form of photons, and not just heating up their environment.

    This phenomenon of luminescence was first described in Europe in the 16th century by Nicolas de Monardes: lucky enough to be at the center of the world at the time, he received some wood samples from Mexico that, when soaked in alkaline water, glowed blue. The Americans had known for a long time that this was a sign of a well-prepared medicine against kidney diseases from a certain plant known to Monardes as Lignum nephriticum.

    Today, luminescence, in particular fluorescence, is used intensively for the same purpose: to report on the structure and properties of biological samples. Fluorescence microscopy techniques have evolved to the point where single molecules can be observed.

    An interesting characteristic of fluorescent samples is that the duration of light emission depends on many external factors. Therefore, not only the color of the emission is used in the above applications, but also its temporal decay. In the simplest case, this fluorescence decay is well described by an exponential function. This is analogous to the exponential decay of the intensity of ionizing radiation (alpha, beta, or gamma) emitted by a sample containing a single type of radioactive isotope.

    It is often observed that when the sample is structurally complex, non-homogeneous or very viscous, a simple mathematical function such as the exponential is not sufficient to describe the temporal evolution of fluorescence. Sometimes a sum of several such functions is sufficient.

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    If the complexity is high enough, the number of these functions can be very large, so it makes more sense to use continuous distributions of decays. This is a very elegant formalism that can provide a lot of insight into the structure of the environment in which the fluorescent species is embedded. For example, in a living cell, a fluorophore (our little reporter) might be located in places in the membrane, or in the citoplasm, or in the mitochondria, or attached to some proteins.

    All these different environments will affect the properties of the fluorophore in such a way that its luminescent relaxation will vary, leading to slightly different colors of luminescence with distinct decay times.

    One important phenomenon that occurs to excited molecules is called quenching. This is usually a chemical reaction that impedes the molecules from emitting light, reducing, quenching, the total amount of light observed from the sample. This also shortens the observed duration of the fluorescent glow: it is then said that the decay kinetics are affected by quenching.

    Merging both scenarios, complex environments and quenching by chemical reactions with other substances, is not an easy thing to study, but it happens all the time. One might be tempted to use the same sums of exponential functions or continuous distributions of lifetimes to explain the observations. Until now, we did not know that this was wrong:

    “We have shown that this mathematical approach has a clear physical interpretation only when the fluorophore and quencher molecules are stationary, as in the solid state. However, if we consider the mobility of the fluorophore with respect to the quencher, such an interpretation becomes impossible. Therefore, for systems in which the relative motion of fluorophores and quenchers cannot be ignored, it is not appropriate to use the time-independent rate or decay time distributions to explain, fit, or rationalize experimental results on fluorescence decay,” says Prof. Gonzalo Angulo of ICP PAS.

    In addition, ICP PAS scientists have provided a new insight into the description of molecular systems where the relative motion of fluorophore and quencher is taken into account. They have shown that it is possible to use a theoretical approach to predict the time-dependent decay rate distribution, provided that the initial microscopic properties of the system, such as the distribution of quenchers around the fluorophore and the microscopic transfer rates, are known. Such a time-dependent distribution can correctly describe fluorescence decay even in the presence of molecular motion.

    As is usually the case in theoretical studies, a few simplifying assumptions were made, “First, we assumed that the quenchers interact with a fluorophore but do not “feel” each other: their interactions are neglected. Furthermore, although we considered the fluorophore-quencher excluded volume—through the presence of the pair distribution function—we neglected the quencher-quencher excluded volume effect. Therefore, we can assume that the quencher positions are independent,” says Dr. Jakub Jędrak.

    However, he emphasizes that the main result is very general and does not depend on the presence and exact form of interactions between molecules in solution.

    Their results show how important it is to re-examine existing theories and models and to look at well-studied assumptions. So there is still a lot of work to be done, even if we think that everything is well studied and well known.

    More information:
    Jakub Jędrak et al, Limitations of the rate-distribution formalism in describing luminescence quenching in the presence of diffusion, The Journal of Chemical Physics (2024). DOI: 10.1063/5.0223438

    Provided by
    Polish Academy of Sciences


    Citation:
    Reshaping tradition: Experts share why commonly used measuring method for fluorescence is not always appropriate (2024, December 10)
    retrieved 10 December 2024
    from https://phys.org/news/2024-12-reshaping-tradition-experts-commonly-method.html

    This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no
    part may be reproduced without the written permission. The content is provided for information purposes only.



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