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1. qFit 3: Protein and ligand multiconformer modeling for X‐ray crystallographic and single‐particle cryo‐EM density maps

   https://doi.org/10.1002/pro.4001  

   Riley, Blake T; Wankowicz, Stephanie A; de_Oliveira, Saulo_H P; van_Zundert, Gydo_C P; Hogan, Daniel W; Fraser, James S; Keedy, Daniel A; van_den_Bedem, Henry (January 2021, Protein Science)

   Abstract New X‐ray crystallography and cryo‐electron microscopy (cryo‐EM) approaches yield vast amounts of structural data from dynamic proteins and their complexes. Modeling the full conformational ensemble can provide important biological insights, but identifying and modeling an internally consistent set of alternate conformations remains a formidable challenge. qFit efficiently automates this process by generating a parsimonious multiconformer model. We refactored qFit from a distributed application into software that runs efficiently on a small server, desktop, or laptop. We describe the new qFit 3 software and provide some examples. qFit 3 is open‐source under the MIT license, and is available athttps://github.com/ExcitedStates/qfit-3.0. 

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2. Quasilinear Analysis in the Source Region of Jovian Hectometric Emission Associated With Upward Electron Beams

   https://doi.org/10.1029/2024JA033241  

   Yoon, P H; Menietti, J D; Allegrini, F; Kurth, W S; Hospodarsky, G B; Averkamp, T F; Faden, J B; Connerney, J E; Bolton, S J (February 2025, Journal of Geophysical Research: Space Physics)

   Abstract Intense upward electron beams were measured by the Juno JADE instrument in the northern hemisphere, low‐latitude auroral zone source region. In this study we report on how these electron beams interact with plasma near and within the Jovian hectometric (HOM) emission (1 MHz 5 MHz) source region. Within the source region large upward loss cones are observed in the northern polar region at radial distances of 2Rj, magnetic latitude of . Intense, narrow electron beams ( 3 keV) are then observed, but within one second wave‐particle scattering is observed, filling the loss cone to energies 50 keV. These energies persist for several seconds before fading, leaving an empty loss cone again. The loss cone provides a free‐energy source for HOM emission resulting from the cyclotron maser instability. We use quasilinear analysis to examine the generation of HOM and the dynamics of wave‐particle interaction of the electron beams with HOM, and the generation via Landau interaction of whistler mode emission. The dynamic spectrum of the HOM emission generated by the loss‐cone electrons as well as that of the low‐frequency whistler‐mode waves generated by the up‐going electron beam can be constructed by quasilinear theory, which compare well with observation. The saturated state of the energetic electron velocity distribution function constructed via quasilinear theory also compare reasonably with observation. 

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3. Development of a Modular Cryo-Transfer Station for the Side-Entry Transmission Electron Microscope

   https://doi.org/10.1093/mam/ozae063  

   Reifsnyder, Alexander; Hachtel, Jordan A; Lupini, Andrew R; McComb, David W (August 2024, Microscopy and Microanalysis)

   Abstract Cryo-transfer stations are essential tools in the field of cryo-electron microscopy, enabling the safe transfer of frozen vitreous samples between different stages of the workflow. However, existing cryo-transfer stations are typically configured for only the two most popular sample holder geometries and are not commercially available for all electron microscopes. Additionally, they are expensive and difficult to customize, which limits their accessibility and adaptability for research laboratories. Here, we present a new modular cryo-transfer station that addresses these limitations. The station is composed entirely of 3D-printed and off the shelf parts, allowing it to be reconfigured to a fit variety of microscopes and experimental protocols. We describe the design and construction of the station and report on the results of testing the cryo-transfer station, including its ability to maintain cryogenic temperatures and transfer frozen vitreous samples as demonstrated by vibrational spectroscopy. Our findings demonstrate that the cryo-transfer station performs comparably to existing commercial models, while offering greater accessibility and customizability. The design for the station is open source to encourage other groups to replicate and build on this development. We hope that this project will increase access to cryo-transfer stations for researchers in a variety of disciplines with nonstandard equipment. 

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4. PyQMC : An all-Python real-space quantum Monte Carlo module in PySCF

   https://doi.org/10.1063/5.0139024  

   Wheeler, William A.; Pathak, Shivesh; Kleiner, Kevin G.; Yuan, Shunyue; Rodrigues, João N.; Lorsung, Cooper; Krongchon, Kittithat; Chang, Yueqing; Zhou, Yiqing; Busemeyer, Brian; et al (March 2023, The Journal of Chemical Physics)

   We describe a new open-source Python-based package for high accuracy correlated electron calculations using quantum Monte Carlo (QMC) in real space: PyQMC. PyQMC implements modern versions of QMC algorithms in an accessible format, enabling algorithmic development and easy implementation of complex workflows. Tight integration with the PySCF environment allows for a simple comparison between QMC calculations and other many-body wave function techniques, as well as access to high accuracy trial wave functions. 

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5. RF antenna helicity dependent particle heating in a helicon source

   https://doi.org/10.1088/1361-6595/ad3a9c  

   Stevenson, K J; Gilbert, T J; Good, T N; Paul, M; Shi, P; Nirwan, R; Srivastav, P; Steinberger, T E; Scime, E E (April 2024, Plasma Sources Science and Technology)

   Abstract Experiments have demonstrated that ion phenomena, such as the lower hybrid resonance, play an important role in helicon source operation. Damping of the slow branch of the bounded whistler wave at the edge of a helicon source (i.e. the Trivelpiece-Gould mode) has been correlated with the creation of energetic electrons, heating of ions at the plasma edge, and anisotropic ion heating. Here we present ion velocity distribution function measurements, electron density and temperature measurements, and magnetic fluctuation measurements on both sides of an $m=|1|$helical antenna in a helicon source as a function of the driving frequency, magnetic field strength, and magnetic field orientation relative to the antenna helicity. Significant electron and ion heating (up to two times larger) occurs on the side of the antenna consistent with the launch of the $m=+1$mode. The electron and ion heating occurs within one electron skin depth of the plasma edge, where slow wave damping is expected. The source parameters for enhanced particle heating are also consistent with lower hybrid resonance effects, which can only occur for Trivelpiece-Gould wave excitation. 

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