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arXiv 2024年

作者： Yadav, Ravindra Kumar Satapathy, Sitakanta Deshmukh, Prathmesh Datta, Biswajit Sharma, Addhyaya Olsson, Andrew Chen, Junsheng Laursen, Bo W. Flood, Amar H. Sfeir, Matthew Y. Menon, Vinod M. Department of Physics The City College of New York 85 St. Nicholas Terrace 85 St. Nicholas Terrace New York10031 United States Department of Chemistry Indiana University IN47405 United States Nano-Science Center Department of Chemistry University of Copenhagen Denmark Photonics Initiative Advanced Science Research Center City University of New York New York 85 St. Nicholas Terrace New York10031 United States The PhD Program in Physics Graduate Center of the City University of New York 365 5th Ave New York10016 United States

Realizing lattices of exciton polariton condensates has been of much interest owing to the potential of such systems to realize analog Hamiltonian simulators and physical computing architectures. Prior work on polariton condensate lattices has primarily been on GaAs-based systems, with the recent advent of organic molecules and perovskite systems allowing room-temperature operation. However, in most of these room temperature systems, the lattices are defined using a bottom-up approach by patterning the bottom mirrors, significantly limiting the types of lattices and refractive index contrast that can be realized. Here, we report a direct write approach that uses a Focused Ion Beam (FIB) to etch 2D lattice into a planar microcavity. Such etching of the cavity allows for realizing high refractive index contrast lattices. We realize the polariton condensate lattice using the highly photostable host-guest Frenkel excitons of an organic dye small molecular ionic lattice (SMILES).1,2 The lattice structures are defined on a planar microcavity embedded with SMILES using FIB, allowing the realization of lattices with different geometries, including defect sites on demand. The band structure of the lattice and the emergence of condensation are imaged using momentum-resolved spectroscopy. The present approach allows us to study periodic, quasi-periodic, and disordered polariton condensate lattices at room temperature using a top-down approach without compromising on the quantum yield of the organic excitonic material embedded in the cavity. © 2024, CC BY.

关键词： Room temperature

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Thermalization of fluorescent protein exciton-polaritons at room temperature

arXiv

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arXiv 2022年

作者： Satapathy, Sitakanta Liu, Bin Deshmukh, Prathmesh Molinaro, Paul M. Dirnberger, Florian Khatoniar, Mandeep Koder, Ronald L. Menon, Vinod M. Department of Physics Center for Discovery and Innovation The City College of New York 85 St. Nicholas Terrace New YorkNY10031 United States The PhD Program in Physics The Graduate Center of the City University of New York 365 5th Ave New YorkNY10016 United States Department of Electrical Engineering and Computer Science University of Michigan Ann ArborMI48109 United States

Fluorescent proteins (FPs) have recently emerged as a serious contender for realizing ultra-low threshold room temperature exciton-polariton condensation and lasing. Our contribution investigates the thermalization of FP microcavity exciton-polaritons upon optical pumping under ambient conditions. We realize polariton cooling using a new FP molecule, called mScarlet, coupled strongly to the optical modes in a Fabry-Pérot cavity. Interestingly, at the threshold excitation energy (fluence) of ~9 nJ/pulse (15.6 mJ/cm2), we observe an effective temperature, Teff ~350 ± 35 K close to the lattice temperature indicative of strongly thermalized exciton-polaritons at equilibrium. This efficient thermalization results from the interplay of radiative pumping facilitated by the energetics of the lower polariton branch and the cavity Qfactor. Direct evidence for dramatic switching from an equilibrium state into a metastable state is observed for the organic cavity polariton device at room temperature via deviation from the Maxwell-Boltzmann statistics at k1 = 0 above the threshold. Thermalized polariton gases in organic systems at equilibrium hold substantial promise for designing room temperature polaritonic circuits, switches, and lattices for analog simulation. © 2022, CC BY-NC-SA.

关键词： Polariton

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Mutually beneficial confluence of structure-based modeling of protein dynamics and machine learning methods

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Current Opinion in Structural Biology 2023年 78卷 102517页

作者： Banerjee, Anupam Saha, Satyaki Tvedt, Nathan C. Yang, Lee-Wei Bahar, Ivet Computational and Systems Biology University of Pittsburgh School of Medicine Pittsburgh 15261 PA United States Computational and Applied Mathematics and Statistics The College of William and Mary Williamsburg 23185 VA United States Institute of Bioinformatics and Structural Biology and PhD Program in Biomedical Artificial Intelligence National Tsing Hua University Hsinchu 300044 Taiwan Physics Division National Center for Theoretical Sciences Taipei 106319 Taiwan

Proteins sample an ensemble of conformers under physiological conditions, having access to a spectrum of modes of motions, also called intrinsic dynamics. These motions ensure the adaptation to various interactions in the cell, and largely assist in, if not determine, viable mechanisms of biological function. In recent years, machine learning frameworks have proven uniquely useful in structural biology, and recent studies further provide evidence to the utility and/or necessity of considering intrinsic dynamics for increasing their predictive ability. Efficient quantification of dynamics-based attributes by recently developed physics-based theories and models such as elastic network models provides a unique opportunity to generate data on dynamics for training ML models towards inferring mechanisms of protein function, assessing pathogenicity, or estimating binding affinities. © 2022 The Authors

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Modifying BiVO4 as a photocatalyst for water oxidation using constant-duration alkaline-etched post treatments

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New Journal of Chemistry 2023年第2期48卷 569-577页

作者： Hsu, Chuan-Chih Chuang, Kai-Jie Huang, Hsiao-Wen Pan, Bo-Jin Chen, Hung-Ming Husain, Sadang Yougbaré, Sibidou Hsiao, Yu-Cheng Wu, Yung-Fu Lin, Lu-Yin Division of Cardiovascular Surgery Department of Surgery School of Medicine College of Medicine Taipei Medical University Taiwan Division of Cardiovascular Surgery Department of Surgery Taipei Medical University Hospital Taiwan Department of Chemical Engineering and Biotechnology National Taipei University of Technology Taipei Taiwan Department of Chemical Engineering Ming Chi University of Technology New Taipei City24301 Taiwan Gingen Technology Co. Ltd. Rm. 7 10F. No. 189 Sec. 2 Keelung Rd. Xinyi Dist. Taipei11054 Taiwan Department of Physics Faculty of Mathematics and Natural Science Lambung Mangkurat University Banjarmasin70124 Indonesia /Nanoro Ouagadougou03 Burkina Faso International PhD Program in Biomedical Engineering College of Biomedical Engineering Taipei Medical University Taipei11031 Taiwan Stanford Byers Center for Biodesign Stanford University CA94305-5428 United States Graduate Institute of Biomedical Optomechatronics College of Biomedical Engineering Taipei Medical University Taipei11031 Taiwan Cell Physiology and Molecular Image Research Center Wan Fang Hospital Taipei Medical University Taipei11696 Taiwan

BiVO4 with suitable band edges and a small band gap is considered an efficient photocatalyst for the oxygen evolution reaction (OER), but short charge-transfer lengths limit its photocatalytic ability. Increasing active sites can essentially enhance oxidation reactions and photocatalytic ability. The alkaline etching technique can refine the surface properties of BiVO4 by introducing oxygen vacancies and possibly establishing a heterojunction, but suitable alkaline etching methods are rarely discussed. In this study, three alkaline etching methods, including hydrothermal, soaking, and electrodeposition processes, are first applied for a constant duration to tailor the surface properties of BiVO4 as a photocatalyst for the OER. Alkaline-etched BiVO4 prepared using hydrothermal and soaking processes shows better photocatalytic abilities due to the generation of additional oxygen vacancies, while poor photocatalytic ability is found for that fabricated using electrodeposition due to the formation of less photocatalytic VO2. The highest photocurrent density of 2.38 mA cm−2 is obtained at 1.23 V versus a reversible hydrogen electrode in an electrolyte without a hole scavenger for the BiVO4 etched in the hydrothermal process, while the untreated BiVO4 presents a photocurrent density of 0.58 mA cm−2. A photocurrent retention of 92.3% is achieved after 5000 seconds of continuous illumination. The study supplies blueprints for establishing effective alkaline etching methods for enhancing the photocatalytic ability of BiVO4, with the exception of time costs. © 2024 The Royal Society of Chemistry.

关键词： Charge transfer

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Biological Networks Regulating Cell Fate Choice Are Minimally Frustrated

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Physical Review Letters 2020年第8期125卷 088101-088101页

作者： Shubham Tripathi David A. Kessler Herbert Levine PhD Program in Systems Synthetic and Physical Biology Rice University Houston Texas 77005 USA Center for Theoretical Biological Physics Rice University Houston Texas 77005 USA Department of Physics Northeastern University Boston Massachusetts 02115 USA Department of Physics Bar-Ilan University Ramat-Gan 52900 Israel

Characterization of the differences between biological and random networks can reveal the design principles that enable the robust realization of crucial biological functions including the establishment of different cell types. Previous studies, focusing on identifying topological features that are present in biological networks but not in random networks, have, however, provided few functional insights. We use a Boolean modeling framework and ideas from the spin glass literature to identify functional differences between five real biological networks and random networks with similar topological features. We show that minimal frustration is a fundamental property that allows biological networks to robustly establish cell types and regulate cell fate choice, and that this property can emerge in complex networks via Darwinian evolution. The study also provides clues regarding how the regulation of cell fate choice can go awry in a disease like cancer and lead to the emergence of aberrant cell types.

关键词： Network structure Biological networks Gene regulatory networks Metropolis algorithm

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Fixational eye movements enhance the precision of visual information transmitted by the primate retina

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Nature Communications 2024年第1期15卷 7964页

作者： Wu, Eric G. Brackbill, Nora Rhoades, Colleen Kling, Alexandra Gogliettino, Alex R. Shah, Nishal P. Sher, Alexander Litke, Alan M. Simoncelli, Eero P. Chichilnisky, E.J. Department of Electrical Engineering Stanford University Stanford CA United States Department of Physics Stanford University Stanford CA United States Department of Bioengineering Stanford University Stanford CA United States Department of Neurosurgery Stanford University Stanford CA United States Department of Ophthalmology Stanford University Stanford CA United States Hansen Experimental Physics Laboratory Stanford University 452 Lomita Mall Stanford 94305 CA United States Neurosciences PhD Program Stanford University Stanford CA United States Santa Cruz Institute for Particle Physics University of California Santa Cruz Santa Cruz CA United States Flatiron Institute Simons Foundation New York NY United States Center for Neural Science New York University New York NY United States Courant Institute of Mathematical Sciences New York University New York NY United States

Fixational eye movements alter the number and timing of spikes transmitted from the retina to the brain, but whether these changes enhance or degrade the retinal signal is unclear. To quantify this, we developed a Bayesian method for reconstructing natural images from the recorded spikes of hundreds of retinal ganglion cells (RGCs) in the macaque retina (male), combining a likelihood model for RGC light responses with the natural image prior implicitly embedded in an artificial neural network optimized for denoising. The method matched or surpassed the performance of previous reconstruction algorithms, and provides an interpretable framework for characterizing the retinal signal. Reconstructions were improved with artificial stimulus jitter that emulated fixational eye movements, even when the eye movement trajectory was assumed to be unknown and had to be inferred from retinal spikes. Reconstructions were degraded by small artificial perturbations of spike times, revealing more precise temporal encoding than suggested by previous studies. Finally, reconstructions were substantially degraded when derived from a model that ignored cell-to-cell interactions, indicating the importance of stimulus-evoked correlations. Thus, fixational eye movements enhance the precision of the retinal representation. © The Author(s) 2024.

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Symmetries and synchronization from whole-neural activity in C. elegans connectome: Integration of functional and structural networks

arXiv

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arXiv 2024年

作者： Avila, Bryant Augusto, Pedro Phillips, David Gili, Tommaso Zimmer, Manuel Makse, Hernán A. Levich Institute and Physics Department City College of New York New YorkNY10031 United States Vienna Austria Vienna Biocenter PhD Program Doctoral School the University of Vienna Medical University of Vienna Vienna Austria Mechanical Engineering Department University of New Mexico AlbuquerqueNM87131 United States Networks Unit IMT Scuola Alti Studi Lucca Piazza San Francesco 15 Lucca55100 Italy Department of Radiology Neuroradiology Service Memorial Sloan Kettering Cancer Center New YorkNY10065 United States CUNY Neuroscience Graduate Center City University of New York New YorkNY10031 United States

Understanding the dynamical behavior of complex systems from their underlying network architectures is a long-standing question in complexity theory. Therefore, many metrics have been devised to extract network features like motifs, centrality, and modularity measures. It has previously been proposed that network symmetries are of particular importance since they are expected to underly the synchronization of a system’s units, which is ubiquitously observed in nervous system activity patterns. However, perfectly symmetrical structures are difficult to assess in noisy measurements of biological systems, like neuronal connectomes. Here, we devise a principled method to infer network symmetries from combined connectome and neuronal activity data. Using nervous system-wide population activity recordings of the *** backward locomotor system, we infer structures in the connectome called fibration symmetries, which can explain which group of neurons synchronize their activity. Our analysis suggests functional building blocks in the animal’s motor periphery, providing new testable hypotheses on how descending interneuron circuits communicate with the motor periphery to control behavior. Our approach opens a new door to exploring the structure-function relations in other complex systems, like the nervous systems of larger animals. © 2024, CC BY.

关键词： Synchronization

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A plug-and-play molecular approach for room temperature polariton condensation

arXiv

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arXiv 2023年

作者： Deshmukh, Prathmesh Satapathy, Sitakanta Michail, Evripidis Olsson, Andrew H. Bushati, Rezlind Yadav, Ravindra Kumar Khatoniar, Mandeep Chen, Junsheng John, George Laursen, Bo W. Flood, Amar H. Sfeir, Matthew Y. Menon, Vinod M. Department of Physics Center for Discovery and Innovation The City College of New York 85 St. Nicholas Terrace New YorkNY10031 United States The PhD Program in Physics The Graduate Center of the City University of New York 365 5th Ave New YorkNY10016 United States Photonics Initiative Advanced Science Research Center City University of New York New YorkNY10031 United States Department of Chemistry Indiana University BloomingtonIN47405 United States Nano-Science Center Department of Chemistry University of Copenhagen Denmark Department of Chemistry Center for Discovery and Innovation The City College of New York 85 St. Nicholas Terrace New YorkNY10031 United States

Exciton-polaritons (EP), half-light half-matter quasiparticles that form in optical cavities, are attractive platforms for creating macroscopic coherent states like BECs. EPs based on organic molecules are of particular interest for realizing such states at room temperature while offering the promise of synthetic tunability. However, the demonstrations of such condensates have been limited to a few specific molecular systems1. Here we report a universal platform for realizing molecular polariton condensates using commercial dyes that solves long standing material challenges. This solution is made possible using a new and programable molecular material called small-molecule, ionic isolation lattices (SMILES) with the potential to incorporate a wide array of molecular fluorophores2. We show EP condensation in rhodamine by incorporating it into SMILES lattice placed in a planar microcavity. The SMILES approach overcomes the major drawbacks of organic molecular photophysical systems such as self-quenching, which sets the foundation for realizing practical polaritonic devices operating at ambient temperatures covering wide spectral range. © 2023, CC BY-NC-ND.

关键词： Condensation

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Establishment and risk factor assessment of the abnormal body temperature probability prediction model (ABTP) for dairy cattle

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Scientific Reports 2024年第1期14卷 1-12页

作者： Lee, Tsair-Fwu Chiu, Chien-Liang Liu, Yen-Hsien Chang, Chu-Ho Shao, Jen-Chung Guo, Shih-Sian Liao, Yi-Lun Chen, Chia-Hui Tseng, Chin-Dar Chao, Pei-Ju Lee, Shen-Hao Department of Electronic Engineering National Kaohsiung University of Science and Technology Kaohsiung 80778 Taiwan Medical Physics and Informatics Laboratory of Electronic Engineering National Kaohsiung University of Science and Technology Kaohsiung 80778 Taiwan Department of Medical Imaging and Radiological Sciences Kaohsiung Medical University Kaohsiung 80708 Taiwan PhD Program in Biomedical Engineering Kaohsiung Medical University Kaohsiung 80708 Taiwan School of Dentistry College of Dental Medicine Kaohsiung Medical University Kaohsiung 80708 Taiwan Department of Radiation Oncology Linkou Chang Gung Memorial Hospital and Chang Gung University College of Medicine Linkou Taiwan

The study aims to develop an abnormal body temperature probability (ABTP) model for dairy cattle, utilizing environmental and physiological data. This model is designed to enhance the management of heat stress impacts, providing an early warning system for farm managers to improve dairy cattle welfare and farm productivity in response to climate change. The study employs the Least Absolute Shrinkage and Selection Operator (LASSO) algorithm to analyze environmental and physiological data from 320 dairy cattle, identifying key factors influencing body temperature anomalies. This method supports the development of various models, including the Lyman Kutcher-Burman (LKB), Logistic, Schultheiss, and Poisson models, which are evaluated for their ability to predict abnormal body temperatures in dairy cattle effectively. The study successfully validated multiple models to predict abnormal body temperatures in dairy cattle, with a focus on the temperature-humidity index (THI) as a critical determinant. These models, including LKB, Logistic, Schultheiss, and Poisson, demonstrated high accuracy, as measured by the AUC and other performance metrics such as the Brier score and Hosmer–Lemeshow (HL) test. The results highlight the robustness of the models in capturing the nuances of heat stress impacts on dairy cattle. The research develops innovative models for managing heat stress in dairy cattle, effectively enhancing detection and intervention strategies. By integrating advanced technologies and novel predictive models, the study offers effective measures for early detection and management of abnormal body temperatures, improving cattle welfare and farm productivity in changing climatic conditions. This approach highlights the importance of using multiple models to accurately predict and address heat stress in livestock, making significant contributions to enhancing farm management practices. © The Author(s) 2024.

关键词： Abnormal body temperature probability (ABTP) Dairy cattle Least absolute shrinkage and selection operator (LASSO) Temperature-humidity index (THI)

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Eclipse timing variations in the WD+dM eclipsing binary RR Cae

arXiv

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arXiv 2021年

作者： Rattanamala, R. Awiphan, S. Komonjinda, S. Phriksee, A. Sappankum, P. A-Thano, N. Chitchak, S. Rittipruk, P. Sawangwit, U. Poshyachinda, S. Reichart, D.E. Haislip, J.B. PhD Program in Astronomy Department of Physics and Materials Science Faculty of Science Chiang Mai University Chiang Mai50200 Thailand Physics and General Science Program Faculty of Science and Technology Nakhon Ratchasima Rajabhat University Nakhon Ratchasima30000 Thailand 260 Moo 4 Donkaew Mae Rim Chiang Mai50180 Thailand Department of Physics and Materials Science Faculty of Science Chiang Mai University Chiang Mai50200 Thailand Institute of Astronomy National Tsing Hua University Hsinchu30013 Taiwan Department of Physics Faculty of Science Udon Thani Rajabhat University Udon Thani41000 Thailand Department of Physics and Astronomy University of North Carolina at Chapel Hill Chapel HillNC27599 United States

We present the binary model and the eclipse timing variations of the eclipsing binary RR Cae, which consists of a white dwarf eclipsed by an M-type dwarf companion. The multi-wavelength optical photometry from the Transiting Exoplanet Survey Satellite (TESS), the 0.6-m PROMPT-8 telescope, and the 0.7-m Thai Robotic Telescope at Spring Brook Observatory, combined with archive H-alpha radial velocities from the Very Large Telescope (VLT) are analysed. From the data, the physical parameters of the system are obtained along with 430 new times of minima. The TESS light curves in 2018 and 2020 show out-of-eclipse variations, which might be caused by a large spot on the secondary component. The light travel time effect models due to the gravitational interaction of one or two circumbinary objects are adopted to fit the cyclic variations in the RR Cae’s O-C curve. The fitting solution of the O-C curve with one circumbinary object model shows a periodic variation with a period of 16.6 ± 0.2 yr and an amplitude of 14 ± 1 s, which can be caused by a planet with a minimum mass of 3.4 ± 0.2 MJup. When we consider the model with two circumbinary objects, the O-C curve shows cyclic variations with periods of 15.0 ± 0.5 yr and 39 ± 5 yr and amplitudes of 12 ± 1 s and 20 ± 5 s, respectively, corresponding to minimum masses of 3.0 ± 0.3 MJup and 2.7 ± 0.7 MJup Copyright © 2021, The Authors. All rights reserved.

关键词： Travel time

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