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1. Spin coherent quantum transport of electrons between defects in diamond

   https://doi.org/10.1515/nanoph-2019-0144  

   Oberg, Lachlan M.; Huang, Eric; Reddy, Prithvi M.; Alkauskas, Audrius; Greentree, Andrew D.; Cole, Jared H.; Manson, Neil B.; Meriles, Carlos A.; Doherty, Marcus W. (August 2019, Nanophotonics)

   Abstract The nitrogen-vacancy (NV) color center in diamond has rapidly emerged as an important solid-state system for quantum information processing. Whereas individual spin registers have been used to implement small-scale diamond quantum computing, the realization of a large-scale device requires the development of an on-chip quantum bus for transporting information between distant qubits. Here, we propose a method for coherent quantum transport of an electron and its spin state between distant NV centers. Transport is achieved by the implementation of spatial stimulated adiabatic Raman passage through the optical control of the NV center charge states and the confined conduction states of a diamond nanostructure. Our models show that, for two NV centers in a diamond nanowire, high-fidelity transport can be achieved over distances of order hundreds of nanometers in timescales of order hundreds of nanoseconds. Spatial adiabatic passage is therefore a promising option for realizing an on-chip spin quantum bus. 

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2. An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering

   https://doi.org/10.7554/elife.36307  

   Keedy, Daniel A; Hill, Zachary B; Biel, Justin T; Kang, Emily; Rettenmaier, T Justin; Brandão-Neto, José; Pearce, Nicholas M; von_Delft, Frank; Wells, James A; Fraser, James S (June 2018, eLife)

   Allostery is an inherent feature of proteins, but it remains challenging to reveal the mechanisms by which allosteric signals propagate. A clearer understanding of this intrinsic circuitry would afford new opportunities to modulate protein function. Here, we have identified allosteric sites in protein tyrosine phosphatase 1B (PTP1B) by combining multiple-temperature X-ray crystallography experiments and structure determination from hundreds of individual small-molecule fragment soaks. New modeling approaches reveal 'hidden' low-occupancy conformational states for protein and ligands. Our results converge on allosteric sites that are conformationally coupled to the active-site WPD loop and are hotspots for fragment binding. Targeting one of these sites with covalently tethered molecules or mutations allosterically inhibits enzyme activity. Overall, this work demonstrates how the ensemble nature of macromolecular structure, revealed here by multitemperature crystallography, can elucidate allosteric mechanisms and open new doors for long-range control of protein function. 

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3. Beyond Increasing Sample Sizes: Optimizing Effect Sizes in Neuroimaging Research on Individual Differences

   https://doi.org/10.1162/jocn_a_02297  

   DeYoung, Colin G; Hilger, Kirsten; Hanson, Jamie L; Abend, Rany; Allen, Timothy A; Beaty, Roger E; Blain, Scott D; Chavez, Robert S; Engel, Stephen A; Feilong, Ma; et al (January 2025, Journal of Cognitive Neuroscience)

   Linking neurobiology to relatively stable individual differences in cognition, emotion, motivation, and behavior can require large sample sizes to yield replicable results. Given the nature of between-person research, sample sizes at least in the hundreds are likely to be necessary in most neuroimaging studies of individual differences, regardless of whether they are investigating the whole brain or more focal hypotheses. However, the appropriate sample size depends on the expected effect size. Therefore, we propose four strategies to increase effect sizes in neuroimaging research, which may help to enable the detection of replicable between-person effects in samples in the hundreds rather than the thousands: (1) theoretical matching between neuroimaging tasks and behavioral constructs of interest; (2) increasing the reliability of both neural and psychological measurement; (3) individualization of measures for each participant; and (4) using multivariate approaches with cross-validation instead of univariate approaches. We discuss challenges associated with these methods and highlight strategies for improvements that will help the field to move toward a more robust and accessible neuroscience of individual differences. 

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4. Quantifying Competitive Degradation Processes in Supported Nanocatalyst Systems

   https://doi.org/https://doi.org/10.1021/acs.nanolett.1c01516  

   Horwath, James P. (June 2021, Nano letters)

   null (Ed.)

   The stability of supported metal nanoparticles determines the activity and lifetime of heterogeneous catalysts. Catalysts can destabilize through several thermodynamic and kinetic pathways, and the competition between these mechanisms complicates efforts to quantify and predict the overall evolution of supported nanoparticles in reactive environments. Pairing in situ transmission electron microscopy with unsupervised machine learning, we quantify the destabilization of hundreds of supported Au nanoparticles in real-time to develop a model describing the observed particle evolution as a competition between evaporation and surface diffusion. Data mining of particle evolution statistics allows us to determine physically reasonable values for the model parameters, quantify the particle size at which the Gibbs–Thomson pressure accelerates the evaporation process, and explore how individual particle interactions deviate from the mean-field model. This approach can be applied to a wide range of supported nanoparticle systems, allowing quantitative insight into the mechanisms that control their evolution in reactive environments. 

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5. Intracellular connections between basal bodies promote the coordinated behavior of motile cilia

   https://doi.org/10.1091/mbc.E22-05-0150  

   Soh, Adam W.; Woodhams, Louis G.; Junker, Anthony D.; Enloe, Cassidy M.; Noren, Benjamin E.; Harned, Adam; Westlake, Christopher J.; Narayan, Kedar; Oakey, John S.; Bayly, Philip V.; et al (September 2022, Molecular Biology of the Cell)

   Discher, Dennis (Ed.)

   Hydrodynamic flow produced by multiciliated cells is critical for fluid circulation and cell motility. Hundreds of cilia beat with metachronal synchrony for fluid flow. Cilia-driven fluid flow produces extracellular hydrodynamic forces that cause neighboring cilia to beat in a synchronized manner. However, hydrodynamic coupling between neighboring cilia is not the sole mechanism that drives cilia synchrony. Cilia are nucleated by basal bodies (BBs) that link to each other and to the cell’s cortex via BB-associated appendages. The intracellular BB and cortical network is hypothesized to synchronize ciliary beating by transmitting cilia coordination cues. The extent of intracellular ciliary connections and the nature of these stimuli remain unclear. Moreover, how BB connections influence the dynamics of individual cilia has not been established. We show by focused ion beam scanning electron microscopy imaging that cilia are coupled both longitudinally and laterally in the ciliate Tetrahymena thermophila by the underlying BB and cortical cytoskeletal network. To visualize the behavior of individual cilia in live, immobilized Tetrahymena cells, we developed Delivered Iron Particle Ubiety Live Light (DIPULL) microscopy. Quantitative and computer analyses of ciliary dynamics reveal that BB connections control ciliary waveform and coordinate ciliary beating. Loss of BB connections reduces cilia-dependent fluid flow forces. 

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