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1. Proximal Molecular Probe Transfer (PROMPT), a new approach for identifying sites of protein/nucleic acid interaction in cells by correlated light and electron microscopy

   https://doi.org/10.1038/s41598-023-45413-8  

   Castillon, Guillaume A; Phan, Sebastien; Hu, Junru; Boassa, Daniela; Adams, Stephen R; Ellisman, Mark H (December 2023, Scientific Reports)

   Abstract The binding and interaction of proteins with nucleic acids such as DNA and RNA constitutes a fundamental biochemical and biophysical process in all living organisms. Identifying and visualizing such temporal interactions in cells is key to understanding their function. To image sites of these events in cells across scales, we developed a method, named PROMPT for PROximal Molecular Probe Transfer, which is applicable to both light and correlative electron microscopy. This method relies on the transfer of a bound photosensitizer from a protein known to associate with specific nucleic acid sequence, allowing the marking of the binding site on DNA or RNA in fixed cells. The method produces a fluorescent mark at the site of their interaction, that can be made electron dense and reimaged at high resolution in the electron microscope. As proof of principle, we labeled in situ the interaction sites between the histone H2B and nuclear DNA. As an example of application for specific RNA localizations we labeled different nuclear and nucleolar fractions of the protein Fibrillarin to mark and locate where it associates with RNAs, also using electron tomography. While the current PROMPT method is designed for microscopy, with minimal variations, it can be potentially expanded to analytical techniques. 

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2. Large-Angle Rocking Beam Electron Diffraction of Large Unit Cell Crystals Using Direct Electron Detector

   https://doi.org/10.1093/mam/ozae088  

   Busch, Robert; Ni, Hsu-Chih; Shao, Yu-Tsun; Zuo, Jian-Min (October 2024, Microscopy and Microanalysis)

   Abstract We report a large-angle rocking beam electron diffraction (LARBED) technique for electron diffraction analysis. Diffraction patterns are recorded in a scanning transmission electron microscope (STEM) using a direct electron detector with large dynamical range and fast readout. We use a nanobeam for diffraction and perform the beam double rocking by synchronizing the detector with the STEM scan coils for the recording. Using this approach, large-angle convergent beam electron diffraction (LACBED) patterns of different reflections are obtained simultaneously. By using a nanobeam, instead of a focused beam, the LARBED technique can be applied to beam-sensitive crystals as well as crystals with large unit cells. This paper describes the implementation of LARBED and evaluates the performance using silicon and gadolinium gallium garnet crystals as test samples. We demonstrate that our method provides an effective and robust way for recording LARBED patterns and paves the way for quantitative electron diffraction of large unit cell and beam-sensitive crystals. 

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3. A novel state-resolved actinometry method to determine the nitrogen atom number density in the ground state and intra-shell excited states in low-pressure electron cyclotron resonance plasmas

   https://doi.org/10.1088/1361-6595/ad4238  

   Zhu, Xi-Ming; Wang, Lu; Wang, Yan-Fei; Wang, Yang; Yu, Da-Ren; Bartschat, Klaus (May 2024, Plasma Sources Science and Technology)

   Abstract The active-particle number density is a key parameter for plasma material processing, space propulsion, and plasma-assisted combustion. The traditional actinometry method focuses on measuring the density of the atoms in the ground state, but there is a lack of an effective optical emission spectroscopy method to measure intra-shell excited-state densities. The latter atoms have chemical selectivity and higher energy, and they can easily change the material morphology as well as the ionization and combustion paths. In this work, we present a novel state-resolved actinometry (SRA) method, supported by a krypton line-ratio method for the electron temperature and density, to measure the number densities of nitrogen atoms in the ground and intra-shell excited states. The SRA method is based on a collisional-radiative model, considering the kinetics of atomic nitrogen and krypton including their excited states. The densities measured by our method are compared with those obtained from a dissociative model in a miniature electron cyclotron resonance (ECR) plasma source. Furthermore, the saturation effect, in which the electron density remains constant due to the microwave propagation in an ECR plasma once the power reaches a certain value, is used to verify the electron density measured by the line-ratio method. An ionization balance model is also presented to examine the measured electron temperature. All the values obtained with the different methods are in good agreement with each other, and hence a set of verified rate coefficient data used in our method can be provided. A novel concept, the ‘excited-state system’, is presented to quickly build an optical diagnostic method based on the analysis of quantum number propensity and selection rules. 

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4. A hybrid quantum-classical method for electron-phonon systems

   https://doi.org/10.1038/s42005-023-01353-3  

   Denner, M. Michael; Miessen, Alexander; Yan, Haoran; Tavernelli, Ivano; Neupert, Titus; Demler, Eugene; Wang, Yao (August 2023, Communications Physics)

   Abstract Interactions between electrons and phonons play a crucial role in quantum materials. Yet, there is no universal method that would simultaneously accurately account for strong electron-phonon interactions and electronic correlations. By combining methods of the variational quantum eigensolver and the variational non-Gaussian solver, we develop a hybrid quantum-classical algorithm suitable for this type of correlated systems. This hybrid method tackles systems with arbitrarily strong electron-phonon coupling without increasing the number of required qubits and quantum gates, as compared to purely electronic models. We benchmark our method by applying it to the paradigmatic Hubbard-Holstein model at half filling, and show that it correctly captures the competition between charge density wave and antiferromagnetic phases, quantitatively consistent with exact diagonalization. 

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5. Triple electron–electron–proton excitations and second-order approximations in nuclear–electronic orbital coupled cluster methods

   https://doi.org/10.1063/5.0106173  

   Pavošević, Fabijan; Hammes-Schiffer, Sharon (August 2022, The Journal of Chemical Physics)

   The accurate description of nuclear quantum effects, such as zero-point energy, is important for modeling a wide range of chemical and biological processes. Within the nuclear–electronic orbital (NEO) approach, such effects are incorporated in a computationally efficient way by treating electrons and select nuclei, typically protons, quantum mechanically with molecular orbital techniques. Herein, we implement and test a NEO coupled cluster method that explicitly includes the triple electron–electron–proton excitations, where two electrons and one proton are excited simultaneously, using automatic differentiation. Our calculations show that this NEO-CCSDT eep method provides highly accurate proton densities and proton affinities, outperforming any previously studied NEO method. These examples highlight the importance of the triple electron–electron–proton excitations for an accurate description of nuclear quantum effects. Additionally, we also implement and test the second-order approximate coupled cluster with singles and doubles (NEO-CC2) method as well as its scaled-opposite-spin (SOS) versions. The NEO-SOS′-CC2 method, which scales the electron–proton correlation energy as well as the opposite-spin and same-spin components of the electron–electron correlation energy, achieves nearly the same accuracy as the NEO-CCSDT eep method for the properties studied. Because of its low computational cost, this method will enable a wide range of chemical and photochemical applications for large molecular systems. This work sets the stage for a variety of developments and applications within the NEO framework. 

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