| 1. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)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. |
- Banerjee, Ambar, 1985-, et al.
(author)
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Simulating fluorine K -edge resonant inelastic x-ray scattering of sulfur hexafluoride and the effect of dissociative dynamics
- 2023
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In: Physical Review A: covering atomic, molecular, and optical physics and quantum information. - : American Physical Society (APS). - 2469-9926 .- 2469-9934. ; 108:2
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Journal article (peer-reviewed)abstract
- We report on a computational study of resonant inelastic x-ray scattering (RIXS), at different fluorine K-edge resonances of the SF6 molecule, and corresponding nonresonant x-ray emission. Previously measured polarization dependence in RIXS is reproduced and traced back to the local σ and π symmetry of the molecular orbitals and corresponding states involved in the RIXS process. Also electron-hole coupling energies are calculated and related to experimentally observed spectator shifts. The role of dissociative S-F bond dynamics is explored to model detuning of RIXS spectra at the |F1s-16a1g1) resonance, which shows challenges to accurately reproduce the required steepness for core-excited potential energy surface. We show that the RIXS spectra can only be properly described by considering breaking of the global inversion symmetry of the electronic wave function and core-hole localization, induced by vibronic coupling. Due to the core-hole localization we have symmetry forbidden transitions, which lead to additional resonances and changing width of the RIXS profile.
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| 3. |
- C. Couto, Rafael, 1987-, et al.
(author)
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Selective gating to vibrational modes through resonant X-ray scattering
- 2017
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In: Nature Communications. - : Macmillan Publishers Ltd.. - 2041-1723. ; 8, s. 14165-1-14165-7
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Journal article (peer-reviewed)abstract
- The dynamics of fragmentation and vibration of molecular systems with a large number of coupled degrees of freedom are key aspects for understanding chemical reactivity and properties. Here we present a resonant inelastic X-ray scattering (RIXS) study to show how it is possible to break down such a complex multidimensional problem into elementary components. Local multimode nuclear wave packets created by X-ray excitation to different core-excited potential energy surfaces (PESs) will act as spatial gates to selectively probe the particular ground-state vibrational modes and, hence, the PES along these modes. We demonstrate this principle by combining ultra-high resolution RIXS measurements for gas-phase water with state-of-the-art simulations.
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| 4. |
- Céolin, Denis, et al.
(author)
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Recoil-induced ultrafast molecular rotation probed by dynamical rotational Doppler effect
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Other publication (other academic/artistic)abstract
- Observing and controlling molecular motion, and in particular rotation,is a fundamental topic in physics and chemistry. In order toinitiate ultrafast rotation, one needs a way to transfer a large angularmomentum to the molecule. As a showcase, this was performedby hard x-ray C1s ionization of carbon monoxide, accompanied byspinning-up the molecule via the recoil “kick” of the emitted fast photoelectron.To visualize this molecular motion, we use the dynamicalrotational Doppler effect and an X-ray “pump-probe” device offeredby nature itself: the recoil-induced ultrafast rotation is probed by subsequentAuger electron emission. The time information in our experimentorigins from the natural delay between the C1s photoionizationinitiating the rotation and the ejection of the Auger electron. From amore general point of view, time-resolved measurements can be performedin two ways: either to vary the "delay" time as in conventionaltime-resolved pump-probe spectroscopy and to use the dynamicsgiven by the system, or to keep constant "delay" time and to manipulatethe dynamics. Since in our experiment we cannot change the delaytime given by the core-hole lifetime $\tau$, we use the second optionand control the rotational speed by changing the kinetic energy of thephotoelectron. The recoil-induced rotational dynamics controlled insuch a way is observed as a photon-energy dependent asymmetryof the Auger lineshape, in full agreement with theory. This asymmetryis explained by a significant change of the molecular orientationduring the core-hole lifetime, which is comparable with the rotationalperiod.
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| 5. |
- Ceolin, Denis, et al.
(author)
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Recoil-induced ultrafast molecular rotation probed by dynamical rotational Doppler effect
- 2019
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In: Proceedings of the National Academy of Sciences of the United States of America. - : NATL ACAD SCIENCES. - 0027-8424 .- 1091-6490. ; 116:11, s. 4877-4882
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Journal article (peer-reviewed)abstract
- Observing and controlling molecular motion and in particular rotation are fundamental topics in physics and chemistry. To initiate ultrafast rotation, one needs a way to transfer a large angular momentum to the molecule. As a showcase, this was performed by hard X-ray C1s ionization of carbon monoxide accompanied by spinning up the molecule via the recoil "kick" of the emitted fast photoelectron. To visualize this molecular motion, we use the dynamical rotational Doppler effect and an X-ray "pump-probe" device offered by nature itself: the recoil-induced ultrafast rotation is probed by subsequent Auger electron emission. The time information in our experiment originates from the natural delay between the C1s photoionization initiating the rotation and the ejection of the Auger electron. From a more general point of view, time-resolved measurements can be performed in two ways: either to vary the "delay" time as in conventional time-resolved pump-probe spectroscopy and use the dynamics given by the system, or to keep constant delay time and manipulate the dynamics. Since in our experiment we cannot change the delay time given by the core-hole lifetime tau, we use the second option and control the rotational speed by changing the kinetic energy of the photoelectron. The recoil-induced rotational dynamics controlled in such a way is observed as a photon energy-dependent asymmetry of the Auger line shape, in full agreement with theory. This asymmetry is explained by a significant change of the molecular orientation during the core-hole lifetime, which is comparable with the rotational period.
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| 6. |
- da Cruz, Vinicius Vaz, et al.
(author)
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Anomalous polarization dependence in vibrationally resolved resonant inelastic x-ray scattering of H2O
- 2018
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In: Physical Review A: covering atomic, molecular, and optical physics and quantum information. - : American Physical Society. - 2469-9926 .- 2469-9934. ; 98:1
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Journal article (peer-reviewed)abstract
- It is well established that different electronic channels, in resonant inelastic x-ray scattering (RIXS), display different polarization dependences due to different orientations of their corresponding transition dipole moments in the molecular frame. However, this effect does not influence the vibrational progression in the Franck-Condon approximation. We have found that the transition dipole moments of core excitation and deexcitation experience ultrafast rotation during dissociation in the intermediate core-excited state. This rotation makes the vibrational progression in RIXS sensitive to the polarization of the x-ray photons. We study the water molecule, in which the effect is expressed in RIXS through the dissociative core-excited state where the vibrational scattering anisotropy is accompanied also by violation of parity selection rules for the vibrations.
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| 7. |
- da Cruz, Vinicius Vaz, et al.
(author)
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Nuclear dynamics in resonant inelastic X-ray scattering and X-ray absorption of methanol
- 2019
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In: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 150:23
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Journal article (peer-reviewed)abstract
- We report on a combined theoretical and experimental study of core-excitation spectra of gas and liquid phase methanol as obtained with the use of X-ray absorption spectroscopy (XAS) and resonant inelastic X-ray scattering (RIXS). The electronic transitions are studied with computational methods that include strict and extended second-order algebraic diagrammatic construction [ADC(2) and ADC(2)-x], restricted active space second-order perturbation theory, and time-dependent density functional theory-providing a complete assignment of the near oxygen K-edge XAS. We show that multimode nuclear dynamics is of crucial importance for explaining the available experimental XAS and RIXS spectra. The multimode nuclear motion was considered in a recently developed "mixed representation" where dissociative states and highly excited vibrational modes are accurately treated with a time-dependent wave packet technique, while the remaining active vibrational modes are described using Franck-Condon amplitudes. Particular attention is paid to the polarization dependence of RIXS and the effects of the isotopic substitution on the RIXS profile in the case of dissociative core-excited states. Our approach predicts the splitting of the 2a RIXS peak to be due to an interplay between molecular and pseudo-atomic features arising in the course of transitions between dissociative core- and valence-excited states. The dynamical nature of the splitting of the 2a peak in RIXS of liquid methanol near pre-edge core excitation is shown. The theoretical results are in good agreement with our liquid phase measurements and gas phase experimental data available from the literature. (C) 2019 Author(s).
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| 8. |
- da Cruz, Vinicius Vaz, et al.
(author)
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Probing hydrogen bond strength in liquid water by resonant inelastic X-ray scattering
- 2019
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10
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Journal article (peer-reviewed)abstract
- Local probes of the electronic ground state are essential for understanding hydrogen bonding in aqueous environments. When tuned to the dissociative core-excited state at the O1s pre-edge of water, resonant inelastic X-ray scattering back to the electronic ground state exhibits a long vibrational progression due to ultrafast nuclear dynamics. We show how the coherent evolution of the OH bonds around the core-excited oxygen provides access to high vibrational levels in liquid water. The OH bonds stretch into the long-range part of the potential energy curve, which makes the X-ray probe more sensitive than infra-red spectroscopy to the local environment. We exploit this property to effectively probe hydrogen bond strength via the distribution of intramolecular OH potentials derived from measurements. In contrast, the dynamical splitting in the spectral feature of the lowest valence-excited state arises from the short-range part of the OH potential curve and is rather insensitive to hydrogen bonding.
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| 9. |
- Eckert, Sebastian, et al.
(author)
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From the Free Ligand to the Transition Metal Complex : FeEDTA- Formation Seen at Ligand K-Edges
- 2022
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In: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 61:27, s. 10321-10328
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Journal article (peer-reviewed)abstract
- Chelating agents are an integral part of transition metal complex chemistry with broad biological and industrial relevance. The hexadentate chelating agent ethylenediaminetetraacetic acid (EDTA) has the capability to bind to metal ions at its two nitrogen and four of its carboxylate oxygen sites. We use resonant inelastic X-ray scattering at the 1s absorption edge of the aforementioned elements in EDTA and the iron(III)-EDTA complex to investigate the impact of the metal-ligand bond formation on the electronic structure of EDTA. Frontier orbital distortions, occupation changes, and energy shifts through metal- ligand bond formation are probed through distinct spectroscopic signatures.
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| 10. |
- Eckert, Sebastian, et al.
(author)
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One-dimensional cuts through multidimensional potential-energy surfaces by tunable x rays
- 2018
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In: Physical Review A: covering atomic, molecular, and optical physics and quantum information. - : AMER PHYSICAL SOC. - 2469-9926 .- 2469-9934. ; 97:5
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Journal article (peer-reviewed)abstract
- The concept of the potential-energy surface (PES) and directional reaction coordinates is the backbone of our description of chemical reaction mechanisms. Although the eigenenergies of the nuclear Hamiltonian uniquely link a PES to its spectrum, this information is in general experimentally inaccessible in large polyatomic systems. This is due to (near) degenerate rovibrational levels across the parameter space of all degrees of freedom, which effectively forms a pseudospectrum given by the centers of gravity of groups of close-lying vibrational levels. We show here that resonant inelastic x-ray scattering (RIXS) constitutes an ideal probe for revealing one-dimensional cuts through the ground-state PES of molecular systems, even far away from the equilibrium geometry, where the independent-mode picture is broken. We strictly link the center of gravity of close-lying vibrational peaks in RIXS to a pseudospectrum which is shown to coincide with the eigenvalues of an effective one-dimensional Hamiltonian along the propagation coordinate of the core-excited wave packet. This concept, combined with directional and site selectivity of the core-excited states, allows us to experimentally extract cuts through the ground-state PES along three complementary directions for the showcase H2O molecule.
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