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1. Auxin Response Factors promote organogenesis by chromatin-mediated repression of the pluripotency gene SHOOTMERISTEMLESS

   https://doi.org/10.1038/s41467-019-08861-3  

   Chung, Yuhee; Zhu, Yang; Wu, Miin-Feng; Simonini, Sara; Kuhn, Andre; Armenta-Medina, Alma; Jin, Run; Østergaard, Lars; Gillmor, C. Stewart; Wagner, Doris (December 2019, Nature Communications)

   Abstract Specification of new organs from transit amplifying cells is critical for higher eukaryote development. In plants, a central stem cell pool maintained by the pluripotency factor SHOOTMERISTEMLESS (STM), is surrounded by transit amplifying cells competent to respond to auxin hormone maxima by giving rise to new organs. Auxin triggers flower initiation through Auxin Response Factor (ARF) MONOPTEROS (MP) and recruitment of chromatin remodelers to activate genes promoting floral fate. The contribution of gene repression to reproductive primordium initiation is poorly understood. Here we show that downregulation of the STM pluripotency gene promotes initiation of flowers and uncover the mechanism for STM silencing. The ARFs ETTIN (ETT) and ARF4 promote organogenesis at the reproductive shoot apex in parallel with MP via histone-deacetylation mediated transcriptional silencing of STM . ETT and ARF4 directly repress STM , while MP acts indirectly, through its target FILAMENTOUS FLOWER ( FIL ). Our data suggest that – as in animals- downregulation of the pluripotency program is important for organogenesis in plants. 

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2. Short-Term Long-Term Compute-In-Memory Architecture: A Hybrid Spin/CMOS Approach Supporting Intrinsic Consolidation

   https://doi.org/10.1109/JXCDC.2020.2983450  

   Sheikhfaal, Shadi; DeMara, Ronald F. (March 2020, IEEE Journal on Exploratory Solid-State Computational Devices and Circuits)

   Biological memory structures impart enormous retention capacity while automatically providing vital functions for chronological information management and update resolution of domain and episodic knowledge. A crucial requirement for hardware realization of such cortical operations found in biology is to first design both Short-Term Memory (STM) and Long-Term Memory (LTM). Herein, these memory features are realized via a beyond-CMOS based learning approach derived from the repeated input information and retrieval of the encoded data. We first propose a new binary STM-LTM architecture with composite synapse of Spin Hall Effect-driven Magnetic Tunnel Junction (SHE-MTJ) and capacitive memory bit-cell to mimic the behavior of biological synapses. This STM-LTM platform realizes the memory potentiation through a continual update process using STM-to-LTM transfer, which is applied to Neural Networks based on the established capacitive crossbar. We then propose a hardware-enabled and customized STM-LTM transition algorithm for the platform considering the real hardware parameters. We validate the functionality of the design using SPICE simulations that show the proposed synapse has the potential of reaching ~30.2pJ energy consumption for STM-to-LTM transfer and 65pJ during STM programming. We further analyze the correlation between energy, array size, and STM-to-LTM threshold utilizing the MNIST dataset. 

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3. Atomic-scale identification of nitrogen dopants in graphene on Ir(111) and Ru(0001)

   https://doi.org/10.1088/1361-648X/ace229  

   Yang, Huan; Abilio, Ivan; Bernal Romero, Juan; Rodriguez, Carlos; Escobar Godoy, Miguel; Little, Mitchell; Mckee, Patrick; Carbajal, Vanessa; Li, Joey; Chen, Xing; et al (July 2023, Journal of Physics: Condensed Matter)

   Abstract Nitrogen (N) doped graphene materials have been synthesized using the sole precursor adenine on the Ir(111) and Ru(0001) surfaces. X-ray photoelectron spectroscopy and scanning tunneling microscopy (STM) have been used to characterize the obtained N-doped graphene materials. Several graphitic and pyridinic N dopants have been identified on the atomic scale by combining STM measurements and STM simulations based on density functional theory calculations. 

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4. Sub-molecular resolution imaging of self-assembled metallocene dimer under aqueous environment

   https://doi.org/10.1016/j.optcom.2025.132119  

   Chen, Yen-Chen; Li, Cynthia; Tareq, Abu Montakim; Madison, Lindsey R; Chiang, Naihao (October 2025, Optics Communications)

   Scanning tunneling microscopy (STM) offers unparalleled sub-molecular resolution for visualizing surface-bound molecular assemblies. We developed a custom 3D-printed liquid cell that enabled stable, long-duration liquid-phase STM imaging of a metallocene dimer assembled on a highly oriented pyrolytic graphite (HOPG) substrate. High-resolution images revealed two distinct molecular packing structures. However, STM alone is difficult to pinpoint the detailed molecular arrangements, resonance Raman spectroscopy (RRS) was used to provide complementary information. Aided with density functional theory (DFT) calculated RRS, a cis conformer of the metallocene dimer was identified as the more probable form in both crystal and surface-bound states. These findings led to assemblies with cyclopentadienyl rings pointing towards the HOPG, and the carbonyl groups towards the water. This work demonstrates the synergistic power of integrating STM, RRS, and DFT in elucidating molecular assembling structures at the solid–liquid interface. 

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5. Detecting and distinguishing Majorana zero modes with the scanning tunnelling microscope

   https://doi.org/10.1038/s42254-021-00328-z  

   Jäck, Berthold; Xie, Yonglong; Yazdani, Ali (January 2021, Nature Reviews Physics)

   null (Ed.)

   One of the most exciting areas of research in quantum condensed matter physics is the push to create topologically protected qubits using non-Abelian anyons. The focus of these efforts has been Majorana zero modes (MZMs), which are predicted to emerge as localized zero-energy states at the ends of 1D topological superconductors. A key role in the search for experimental signatures of these quasiparticles has been played by the scanning tunnelling microscope (STM). The power of high-resolution STM techniques is perhaps best illustrated by their application in identifying MZMs in 1D chains of magnetic atoms on the surface of a superconductor. In this platform, STM spectroscopic mapping has demonstrated the localized nature of MZM zero-energy excitations at the ends of such chains, and experiments with superconducting and magnetic STM tips have been used to uniquely distinguish them from trivial edge modes. Beyond the atomic chains, STM has also uncovered signatures of MZMs in 2D materials and topological surface and boundary states, when they are subjected to the superconducting proximity effect. Looking ahead, future STM experiments may be able to demonstrate the non-Abelian statistics of MZMs. 

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