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- ItemAzapeptide activity-based probes for the SARS-CoV-2 main protease enable visualization of inhibition in infected cells(Cambridge : RSC, 2023) Vanhoutte, Roeland; Barniol-Xicota, Marta; Chiu, Winston; Vangeel, Laura; Jochmans, Dirk; De Jonghe, Steven; Zidane, Hadeer; Barr, Haim M.; London, Nir; Neyts, Johan; Verhelst, Steven H. L.The COVID-19 pandemic has revealed the vulnerability of the modern, global society. With expected waves of future infections by SARS-CoV-2, treatment options for infected individuals will be crucial in order to decrease mortality and hospitalizations. The SARS-CoV-2 main protease is a validated drug target, for which the first inhibitor has been approved for use in patients. To facilitate future work on this drug target, we designed a solid-phase synthesis route towards azapeptide activity-based probes that are capped with a cysteine-reactive electrophile for covalent modification of the active site of Mpro. This design led to the most potent ABP for Mpro and one of the most potent inhibitors reported thus far. We demonstrate that this ABP can be used to visualize Mpro activity and target engagement by drugs in infected cells.
- ItemTime-resolved luminescence detection of peroxynitrite using a reactivity-based lanthanide probe(Cambridge : RSC, 2020) Breen, Colum; Pal, Robert; Elsegood, Mark R.J.; Teat, Simon J.; Iza, Felipe; Wende, Kristian; Buckley, Benjamin R.; Butler, StephenPeroxynitrite (ONOO-) is a powerful and short-lived oxidant formed in vivo, which can react with most biomolecules directly. To fully understand the roles of ONOO- in cell biology, improved methods for the selective detection and real-time analysis of ONOO- are needed. We present a water-soluble, luminescent europium(iii) probe for the rapid and sensitive detection of peroxynitrite in human serum, living cells and biological matrices. We have utilised the long luminescence lifetime of the probe to measure ONOO- in a time-resolved manner, effectively avoiding the influence of autofluorescence in biological samples. To demonstrate the utility of the Eu(iii) probe, we monitored the production of ONOO- in different cell lines, following treatment with a cold atmospheric plasma device commonly used in the clinic for skin wound treatment. This journal is © The Royal Society of Chemistry.
- ItemExperimental strategies for optical pump - Soft x-ray probe experiments at the LCLS(Bristol : Institute of Physics Publishing, 2014) McFarland, B.K.; Berrah, N.; Bostedt, C.; Bozek, J.; Bucksbaum, P.H.; Castagna, J.C.; Coffee, R.N.; Cryan, J.P.; Fang, L.; Farrell, J.P.; Feifel, R.; Gaffney, K.J.; Glownia, J.M.; Martinez, T.J.; Miyabe, S.; Mucke, M.; Murphy, B.; Natan, A.; Osipov, T.; Petrovic, V.S.; Schorb, S.; Schultz, T.; Spector, L.S.; Swiggers, M.; Tarantelli, F.; Tenney, I.; Wang, S.; White, J.L.; White, W.; Gühr, M.Free electron laser (FEL) based x-ray sources show great promise for use in ultrafast molecular studies due to the short pulse durations and site/element sensitivity in this spectral range. However, the self amplified spontaneous emission (SASE) process mostly used in FELs is intrinsically noisy resulting in highly fluctuating beam parameters. Additionally timing synchronization of optical and FEL sources adds delay jitter in pump-probe experiments. We show how we mitigate the effects of source noise for the case of ultrafast molecular spectroscopy of the nucleobase thymine. Using binning and resorting techniques allows us to increase time and spectral resolution. In addition, choosing observables independent of noisy beam parameters enhances the signal fidelity.
- ItemPhotoemission of Bi2Se3 with circularly polarized light: Probe of spin polarization or means for spin manipulation?(College Park : American Institute of Physics Inc., 2014) Sánchez-Barriga, J.; Varykhalov, A.; Braun, J.; Xu, S.-Y.; Alidoust, N.; Kornilov, O.; Minár, J.; Hummer, K.; Springholz, G.; Bauer, G.; Schumann, R.; Yashina, L.V.; Ebert, H.; Hasan, M.Z.; Rader, O.Topological insulators are characterized by Dirac-cone surface states with electron spins locked perpendicular to their linear momenta. Recent theoretical and experimental work implied that this specific spin texture should enable control of photoelectron spins by circularly polarized light. However, these reports questioned the so far accepted interpretation of spin-resolved photoelectron spectroscopy.We solve this puzzle and show that vacuum ultraviolet photons (50-70 eV) with linear or circular polarization indeed probe the initial-state spin texture of Bi2Se3 while circularly polarized 6-eV low-energy photons flip the electron spins out of plane and reverse their spin polarization, with its sign determined by the light helicity. Our photoemission calculations, taking into account the interplay between the varying probing depth, dipole-selection rules, and spin-dependent scattering effects involving initial and final states, explain these findings and reveal proper conditions for light-induced spin manipulation. Our results pave the way for future applications of topological insulators in optospintronic devices.
- ItemSide-view holographic endomicroscopy via a custom-terminated multimode fibre(Washington, DC : Soc., 2021) Silveira, Beatriz M.; Pikálek, Tomáš; Stibůrek, Miroslav; Ondráčková, Petra; Jákl, Petr; Leite, Ivo T.; Čižmár, TomášMicroendoscopes based on optical fibres have recently come to the fore as promising candidates allowing in-vivo observations of otherwise inaccessible biological structures in animal models. Despite being still in its infancy, imaging can now be performed at the tip of a single multimode fibre, by relying on powerful holographic methods for light control. Fibre based endoscopy is commonly performed en face, resulting in possible damage of the specimen owing to the direct contact between the distal end of the probe and target. On this ground, we designed an all-fibre probe with an engineered termination that reduces compression and damage to the tissue under investigation upon probe insertion. The geometry of the termination brings the field of view to a plane parallel to the fibre’s longitudinal direction, conveying the probe with off-axis imaging capabilities. We show that its focusing ability also benefits from a higher numerical aperture, resulting in imaging with increased spatial resolution. The effect of probe insertion was investigated inside a tissue phantom comprising fluorescent particles suspended in agarose gel, and a comparison was established between the novel side-view probe and the standard en face fibre probe. This new concept paves the way to significantly less invasive deep-tissue imaging.
- ItemSub-15-fs X-ray pump and X-ray probe experiment for the study of ultrafast magnetization dynamics in ferromagnetic alloys(Washington, DC : Soc., 2021) Liu, Xuan; Merhe, Alaaeldine; Jal, Emmanuelle; Delaunay, Renaud; Jarrier, Romain; Chardonnet, Valentin; Hennes, Marcel; Chiuzbaian, Sorin G.; Légaré, Katherine; Hennecke, Martin; Radu, Ilie; Von Korff Schmising, Clemens; Grunewald, Særen; Kuhlmann, Marion; Lüning, Jan; Vodungbo, BorisIn this paper, we present a new setup for the measurement of element-specific ultrafast magnetization dynamics in ferromagnetic thin films with a sub-15-fs time resolution. Our experiment relies on a split and delay approach which allows us to fully exploit the shortest X-rays pulses delivered by X-ray Free Electrons Lasers (close to the attosecond range), in an X-ray pump – X-ray probe geometry. The setup performance is demonstrated by measuring the ultrafast elemental response of Ni and Fe during demagnetization of ferromagnetic Ni and Ni80Fe20 (Permalloy) samples upon resonant excitation at the corresponding absorption edges. The transient demagnetization process is measured in both reflection and transmission geometry using, respectively, the transverse magneto-optical Kerr effect (T-MOKE) and the Faraday effect as probing mechanisms.
- ItemInvestigation of the electrical properties of standard and low-gas-flow ICPs using novel probes for the direct measurements of RF voltage and current in the load coil and the corresponding calculation of the ICP power(Cambridge : Royal Society of Chemistry, 2015) Voronov, M.; Hoffmann, V.; Birus, D.; Engelhard, C.; Buscher, W.New probes for the direct measurement of high radio-frequency (RF) voltage and current in the load coil of an inductively coupled plasma (ICP) are presented. Based on these measurements, a method for the calculation of power in the ICP is developed. Electrical parameters of the ICP are measured for a wide range of operational conditions in a standard ICP torch with wet aerosol introduction. Further, changes of the electrical parameters are monitored when operating the ICP with a very low argon flow rate of only 0.6 L min−1 using a so-called “Static High-Sensitivity ICP” (SHIP) torch. Direct measurements with the new RF probes allow following the evolution of plasma properties as a function of time. Noteworthy, it is found that there is a strong correlation between the plasma power and temperature changes in the RF generator itself. Depending on the plasma parameters, the measured plasma power was shown to differ significantly from the applied power (in the vendor software settings).
- ItemParticles as probes for complex plasmas in front of biased surfaces(College Park, MD : Institute of Physics Publishing, 2009) Basner, R.; Sigeneger, F.; Loffhagen, D.; Schubert, G.; Fehske, H.; Kersten, H.An interesting aspect in the research of complex (dusty) plasmas is the experimental study of the interaction of micro-particles with the surrounding plasma for diagnostic purposes. Local electric fields can be determined from the behaviour of particles in the plasma, e.g. particles may serve as electrostatic probes. Since in many cases of applications in plasma technology it is of great interest to describe the electric field conditions in front of floating or biased surfaces, the confinement and behaviour of test particles is studied in front of floating walls inserted into a plasma as well as in front of additionally biased surfaces. For the latter case, the behaviour of particles in front of an adaptive electrode, which allows for an efficient confinement and manipulation of the grains, has been experimentally studied in terms of the dependence on the discharge parameters and on different bias conditions of the electrode. The effect of the partially biased surface (dc and rf) on the charged micro-particles has been investigated by particle falling experiments. In addition to the experiments, we also investigate the particle behaviour numerically by molecular dynamics, in combination with a fluid and particle-in-cell description of the plasma. © IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.
- ItemCompressively sampling the optical transmission matrix of a multimode fibre(London : Nature Publishing Group, 2021) Li, Shuhui; Saunders, Charles; Lum, Daniel J.; Murray-Bruce, John; Goyal, Vivek K.; Čižmár, Tomáš; Phillips, David B.The measurement of the optical transmission matrix (TM) of an opaque material is an advanced form of space-variant aberration correction. Beyond imaging, TM-based methods are emerging in a range of fields, including optical communications, micro-manipulation, and computing. In many cases, the TM is very sensitive to perturbations in the configuration of the scattering medium it represents. Therefore, applications often require an up-to-the-minute characterisation of the fragile TM, typically entailing hundreds to thousands of probe measurements. Here, we explore how these measurement requirements can be relaxed using the framework of compressive sensing, in which the incorporation of prior information enables accurate estimation from fewer measurements than the dimensionality of the TM we aim to reconstruct. Examples of such priors include knowledge of a memory effect linking the input and output fields, an approximate model of the optical system, or a recent but degraded TM measurement. We demonstrate this concept by reconstructing the full-size TM of a multimode fibre supporting 754 modes at compression ratios down to ∼5% with good fidelity. We show that in this case, imaging is still possible using TMs reconstructed at compression ratios down to ∼1% (eight probe measurements). This compressive TM sampling strategy is quite general and may be applied to a variety of other scattering samples, including diffusers, thin layers of tissue, fibre optics of any refractive profile, and reflections from opaque walls. These approaches offer a route towards the measurement of high-dimensional TMs either quickly or with access to limited numbers of measurements.
- ItemNonlocal dielectric function and nested dark excitons in MoS2(London : Nature Publishing Group, 2019) Koitzsch, A.; Pawlik, A.-S.; Habenicht, C.; Klaproth, T.; Schuster, R.; Büchner, B.; Knupfer, M.Their exceptional optical properties are a driving force for the persistent interest in atomically thin transition metal dichalcogenides such as MoS2. The optical response is dominated by excitons. Apart from the bright excitons, which directly couple to light, it has been realized that dark excitons, where photon absorption or emission is inhibited by the spin state or momentum mismatch, are decisive for many optical properties. However, in particular the momentum dependence is difficult to assess experimentally and often remains elusive or is investigated by indirect means. Here we study the momentum dependent electronic structure experimentally and theoretically. We use angle-resolved photoemission as a one-particle probe of the occupied valence band structure and electron energy loss spectroscopy as a two-particle probe of electronic transitions across the gap to benchmark a single-particle model of the dielectric function ϵ(q, ω) against momentum dependent experimental measurements. This ansatz captures key aspects of the data surprisingly well. In particular, the energy region where substantial nesting occurs, which is at the origin of the strong light–matter interaction of thin transition metal dichalcogenides and crucial for the prominent C-exciton, is described well and spans a more complex exciton landscape than previously anticipated. Its local maxima in (q≠0,ω) space can be considered as dark excitons and might be relevant for higher order optical processes. Our study may lead to a more complete understanding of the optical properties of atomically thin transition metal dichalcogenides.