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1. Tempo and mode of gene expression evolution in the brain across primates

   https://doi.org/10.7554/eLife.70276  

   Rickelton, Katherine; Zintel, Trisha M; Pizzollo, Jason; Miller, Emily; Ely, John J; Raghanti, Mary Ann; Hopkins, William D; Hof, Patrick R; Sherwood, Chet C; Bauernfeind, Amy L; et al (January 2024, eLife)

   Primate evolution has led to a remarkable diversity of behavioral specializations and pronounced brain size variation among species (Barton, 2012; DeCasien and Higham, 2019; Powell et al., 2017). Gene expression provides a promising opportunity for studying the molecular basis of brain evolution, but it has been explored in very few primate species to date (e.g. Khaitovich et al., 2005; Khrameeva et al., 2020; Ma et al., 2022; Somel et al., 2009). To understand the landscape of gene expression evolution across the primate lineage, we generated and analyzed RNA-seq data from four brain regions in an unprecedented eighteen species. Here, we show a remarkable level of variation in gene expression among hominid species, including humans and chimpanzees, despite their relatively recent divergence time from other primates. We found that individual genes display a wide range of expression dynamics across evolutionary time reflective of the diverse selection pressures acting on genes within primate brain tissue. Using our samples that represent a 190-fold difference in primate brain size, we identified genes with variation in expression most correlated with brain size. Our study extensively broadens the phylogenetic context of what is known about the molecular evolution of the brain across primates and identifies novel candidate genes for the study of genetic regulation of brain evolution. 

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2. Cryo-Electron Tomography in Plant Biology

   https://doi.org/10.1146/annurev-arplant-070225-042126  

   Martínez-Martínez, Coral; Zhan, Hong; Moser, Trevor H; Otegui, Marisa S (May 2026, Annual Review of Plant Biology)

   Cryo-electron tomography (cryo-ET) is a transformative technique in cell biology that enables three-dimensional visualization of cellular structures in near-native states and at nanometer and even subnanometer resolution. Unlike traditional imaging methods, cryo-ET preserves the ultrastructure of cells without chemical fixation or staining, allowing researchers to observe macromolecular complexes in situ. Cryo-focused ion beam milling has overcome sample thickness limitations, enabling high-resolution imaging of complex and large specimens. When combined with correlative light microscopy and subtomogram averaging, cryo-ET can localize and resolve macromolecular assemblies within the cell. We discuss how cryo-ET has provided unprecedented insights into cellular architecture by bridging the gap between molecular and cellular scales and highlight examples in photosynthetic organisms. We also discuss new efforts to increase automation, throughput, and validation that make cryo-ET accessible to a larger community of scientists, including plant biologists. 

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3. Conveyor-belt magneto-optical trapping of molecules

   https://doi.org/10.1088/1367-2630/adc032  

   Li, Grace K; Hallas, Christian; Doyle, John M (April 2025, New Journal of Physics)

   Abstract Laser cooling is used to produce ultracold atoms and molecules for quantum science and precision measurement applications. Molecules are more challenging to cool than atoms due to their vibrational and rotational internal degrees of freedom. Molecular rotations lead to the use of type-II transitions ( $F\text{⩾}{F}^{\prime }$) for magneto-optical trapping (MOT). When typical red detuned light frequencies are applied to these transitions, sub-Doppler heating is induced, resulting in higher temperatures and larger molecular cloud sizes than realized with the type-I MOTs most often used with atoms. To improve type-II MOTs, Jarviset al(2018Phys. Rev. Lett.120083201) proposed a blue-detuned MOT to be applied after initial cooling and capture with a red-detuned MOT. This was successfully implemented (Burauet al2023Phys. Rev. Lett.130193401; Jorapuret al2024Phys. Rev. Lett.132163403; Liet al2024Phys. Rev. Lett.132233402), realizing colder and denser molecular samples. Very recently, Hallaset al(2024 arXiv:2404.03636) demonstrated a blue-detuned MOT with a ‘1+2’ configuration that resulted in even stronger compression of the molecular cloud. Here, we describe and characterize theoretically the conveyor-belt mechanism that underlies this observed enhanced compression. We perform numerical simulations of the conveyor-belt mechanism using both stochastic Schrödinger equation and optical Bloch equation approaches. We investigate the conveyor-belt MOT characteristics in relation to laser parameters,g-factors and the structure of the molecule, and find that conveyor-belt trapping should be applicable to a wide range of laser-coolable molecules. 

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4. Spin state of a single-molecule magnet (SMM) creating long-range ordering on ferromagnetic layers of a magnetic tunnel junction – a Monte Carlo study

   https://doi.org/10.1039/d1ra05473b  

   Grizzle, Andrew; D'Angelo, Christopher; Martínez-Lillo, José; Tyagi, Pawan (September 2021, RSC Advances)

   Paramagnetic single-molecule magnets (SMMs) interacting with the ferromagnetic electrodes of a magnetic tunnel junction (MTJ) produce a new system. The properties and future scope of new systems differ dramatically from the properties of isolated molecules and ferromagnets. However, it is unknown how far deep in the ferromagnetic electrode the impact of the paramagnetic molecule and ferromagnet interactions can travel for various levels of molecular spin states. Our prior experimental studies showed two types of paramagnetic SMMs, the hexanuclear Mn 6 and octanuclear Fe–Ni molecular complexes, covalently bonded to ferromagnets produced unprecedented strong antiferromagnetic coupling between two ferromagnets at room temperature leading to a number of intriguing observations (P. Tyagi, et al. , Org. Electron. , 2019, 64 , 188–194. P. Tyagi, et al. , RSC Adv. , 2020, 10 , (22), 13006–13015). This paper reports a Monte Carlo Simulations (MCS) study focusing on the impact of the molecular spin state on a cross junction shaped MTJ based molecular spintronics device (MTJMSD). Our MCS study focused on the Heisenberg model of MTJMSD and investigated the impact of various molecular coupling strengths, thermal energy, and molecular spin states. To gauge the impact of the molecular spin state on the region of ferromagnetic electrodes, we examined the spatial distribution of molecule-ferromagnet correlated phases. Our MCS study shows that under a strong coupling regime, the molecular spin state should be ∼30% of the ferromagnetic electrode's atomic spins to create long-range correlated phases. 

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5. Modeling entanglement dynamics of molecules interacting with entangled photons through Lindblad master equation approach

   https://doi.org/10.1063/5.0254272  

   Giri, Sajal Kumar; Schatz, George C (March 2025, The Journal of Chemical Physics)

   This work presents a new approach for simulating the interaction between molecular aggregate systems and multi-modal energy–time entangled light by solving the Lindblad master equation. The density matrix that describes both molecular and photonic states is propagated on a time grid, with excited-state dephasing included via the Lindblad superoperator. Molecular exciton entanglement, induced by entangled photons, is analyzed from the time-evolved density matrix. The calculations are based on a model of a molecular dimer introduced by Bittner et al. [J. Chem. Phys. 152, 071101 (2020)], along with entangled light that is approximated by a finite number of modes. Our results demonstrate that photonic entanglement plays a significant role in influencing molecular exciton entanglement, highlighting the interplay between the photonic and excitonic subsystems in such interactions. 

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