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arXiv 2024年

作者： Liu, Zhuoyi Grigas, Alex T. Sumner, Jacob Knab, Edward Davis, Caitlin M. O’Hern, Corey S. Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Integrated Graduate Program in Physical and Engineering Biology Yale University New HavenCT06520 United States Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Department of Chemistry Yale University New HavenCT06520 United States Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States

Proteins naturally occur in crowded cellular environments and interact with other proteins, nucleic acids, and organelles. Since most previous experimental protein structure determination techniques require that proteins occur in idealized, non-physiological environments, the effects of realistic cellular environments on protein structure are largely unexplored. Recently, Förster resonance energy transfer (FRET) has been shown to be an effective experimental method for investigating protein structure in vivo. Inter-residue distances measured in vivo can be incorporated as restraints in molecular dynamics (MD) simulations to model protein structural dynamics in vivo. Since most FRET studies only obtain inter-residue separations for a small number of amino acid pairs, it is important to determine the minimum number of restraints in the MD simulations that are required to achieve a given root-mean-square deviation (RMSD) from the experimental structural ensemble. Further, what is the optimal method for selecting these inter-residue restraints? Here, we implement several methods for selecting the most important FRET pairs and determine the number of pairs Nr that are needed to induce conformational changes in proteins between two experimentally determined structures. We find that enforcing only a small fraction of restraints, Nr/N 0.08, where N is the number of amino acids, can induce the conformational changes. These results establish the efficacy of FRET-assisted MD simulations for atomic scale structural modeling of proteins in vivo. © 2024, CC BY.

关键词： Conformations

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When climate variables improve the dengue forecasting: a machine learning approach

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The European Physical Journal Special Topics 2024年 1-15页

作者： da Silva, Sidney T. Gabrick, Enrique C. Protachevicz, Paulo R. Iarosz, Kelly C. Caldas, Iberê L. Batista, Antonio M. Kurths, Jürgen Federal University of Paraná Curitiba Brazil Potsdam Institute for Climate Impact Research Potsdam Germany Department of Physics Humboldt University Berlin Berlin Germany Graduate Program in Science State University of Ponta Grossa Ponta Grossa Brazil Institute of Physics University of São Paulo São Paulo Brazil University Center UNIFATEB Telêmaco Borba Brazil Department of Mathematics and Statistics State University of Ponta Grossa Ponta Grossa Brazil

Dengue is a viral vector-borne infectious disease that affects many countries worldwide, infecting around 390 million people per year. The main outbreaks occur in subtropical and tropical countries. We, therefore, study here the influence of climate on dengue. In particular, we consider dengue and meteorological data from Natal (2016–2019), Brazil, Iquitos (2001–2012), Peru, and Barranquilla (2011–2016), Colombia. For the analysis and simulations, we apply machine learning (ML) techniques, especially the random forest (RF) algorithm. We utilize dengue disease cases and climate data delayed by up to one week to forecast the cases of dengue. In addition, regarding as feature in the ML technique, we analyze three possibilities: only dengue cases (D); climate and dengue cases (CD); humidity and dengue cases (HD). Depending on the city, our results show that the climate data can improve or not the forecast. For instance, for Natal, the case D induces a better forecast. For Iquitos, it is better to use all the climate variables. Nonetheless, for Barranquilla, the forecast is better, when we include cases and humidity data. Another important result is that each city has an optimal region based on the training length. For Natal, when we use more than 64% and less than 80% of the time series for training, we obtain results with correlation coefficients (r) among 0.917 and 0.949 and mean absolute errors (MAE) among 57.783 and 71.768 for the D case in forecasting. The optimal range for Iquitos is obtained when 79% up to 88% of the time series is considered for training. For this case, the best case is CD, having a minimum r equal to 0.850 and maximum 0.887, while values of MAE oscillate among 2.780 and 4.156. For Barranquilla, the optimal range occurs between 72% until 82% of length training. In this case, the better approach is HD, where the measures exhibit a minimum r equal to 0.942 and maximum 0.953, while the minimum and maximum MAE vary among 6.085 and 6.669. We sho

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To Sharpen or not to Sharpen? On the Effect of Sharpening Filters Applied to Magnified Images 14

To Sharpen or not to Sharpen? On the Effect of Sharpening Fi...

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14th International Conference on Digital Image Processing, ICDIP 2022

作者： Emmendorfer, Leonardo R. de Olviveira, Vinicius Menezes Schein, Tatiana T. de Jesus, Junior C. Rodriguez, Bárbara D.A. Electrical Energy Processing Department Federal University of Santa Maria 97105-340 Brazil Center for Computational Science Federal University of Rio Grande 96201-900 Brazil Computational Modeling PhD Program Federal University of Rio Grande 96201-900 Brazil Computer Engineering Graduate Program Federal University of Rio Grande 96201-900 Brazil Institute of Mathematics Statistics and Physics Federal University of Rio Grande 96201-900 Brazil

ISBN: (纸本)9781510657564

Super-resolution algorithms aim to produce magnified high-resolution versions from low-resolution images. Some methods, however, are prone to generate blur during the process. Simple sharpening filters are adopted to alleviate this type of artifact. However, the actual effectiveness of this approach is not clear-cut in the literature. This work evaluates the effect of three simple sharpening filters on the quality of images obtained from super-resolution methods. Two metrics were considered in the evaluation: the Peak signal-to-noise ratio (PSNR) metric, and the Learned Perceptual Image Patch Similarity (LPIPS). One of the filters could consistently improve the LPIPS metric of magnified images from diverse benchmark sets on top of seven super-resolution methods. The increments obtained for the perceptual metric seem to occur due to the sharpening effect. Improvements on PSNR values were not as consistent. © 2022 SPIE.

关键词： Quality control

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Reducing Effective System Dimensionality with Long-Range Collective Dipole-Dipole Interactions

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Physical Review Letters 2024年第17期132卷 173803-173803页

作者： Ashwin K. Boddeti Yi Wang Xitlali G. Juarez Alexandra Boltasseva Teri W. Odom Vladimir Shalaev Hadiseh Alaeian Zubin Jacob Elmore Family School of Electrical and Computer Engineering Purdue University West Lafayette Indiana 47907 USA Birck Nanotechnology Center Purdue University West Lafayette Indiana 47907 USA Graduate Program in Applied Physics Northwestern University Evanston Illinois 60208 USA Department of Materials Science and Engineering Northwestern University Evanston Illinois 60208 USA Department of Chemistry Northwestern University Evanston Illinois 60208 USA School of Physics and Astronomy Purdue University West Lafayette Indiana 47907 USA

Dimensionality plays a crucial role in long-range dipole-dipole interactions (DDIs). We demonstrate that a resonant nanophotonic structure modifies the apparent dimensionality in an interacting ensemble of emitters, as revealed by population decay dynamics. Our measurements on a dense ensemble of interacting quantum emitters in a resonant nanophotonic structure with long-range DDIs reveal an effective dimensionality reduction to d¯=2.20(12), despite the emitters being distributed in 3D. This contrasts with the homogeneous environment, where the apparent dimension is d¯=3.00. Our work presents a promising avenue to manipulate dimensionality in an ensemble of interacting emitters.

关键词： Light-matter interaction Long-range interactions Metamaterials Optics & lasers Photonics Plasmonics Quantum optics

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Evanescent wave spectral singularities in non-Hermitian photonics

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Physical Review B 2024年第4期109卷 L041405-L041405页

作者： Huan He Zhaoxian Chen Huanan Li Cheng-Hou Tu Jingjun Xu Andrea Alù MOE Key Laboratory of Weak-Light Nonlinear Photonics School of Physics Nankai University Tianjin 300071 China College of Engineering and Applied Sciences Collaborative Innovation Center of Advanced Microstructures and National Laboratory of Solid State Microstructures Nanjing University Nanjing 210023 China Photonics Initiative Advanced Science Research Center City University of New York New York New York 10031 USA Physics Program Graduate Center City University of New York New York New York 10016 USA

Spectral singularities (SSs) emerge at isolated real frequencies when the scattering coefficients of a system diverge, producing scattering anomalies in non-Hermitian systems. Here, based on parity-time symmetry, we introduce SSs for evanescent waves, and explore their exotic features. We show that evanescent wave SSs can realize highly reconfigurable unidirectional lasers and absorbers, and offer the opportunity to observe extreme scattering anomalies associated with SSs in fully passive platforms, decoupling their extreme scattering responses from energy considerations. More broadly, our study opens avenues for non-Hermitian wave engineering, showcasing a link between non-Hermitian physics and structured waves, with implications in nano-optics for extreme wave-matter interactions and functional devices.

关键词： Evanescent waves Wave scattering Non-Hermitian systems

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Twist, splay, and uniform domains in ferroelectric nematic liquid crystals

arXiv

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arXiv 2025年

作者： Lavrentovich, Maxim O. Kumari, Priyanka Lavrentovich, Oleg D. Department of Earth Environment and Physics Worcester State University WorcesterMA01602 United States Department of Physics & Astronomy University of Tennessee KnoxvilleTN37996 United States Advanced Materials and Liquid Crystal Institute Kent State University KentOH44240 United States Materials Science Graduate Program Kent State University KentOH44240 United States Department of Physics Kent State University KentOH44240 United States

The recently-discovered ferroelectric nematic (NF) liquid crystal presents a host of defect phenomena due to its unique polar nature and long-ranged electrostatic interactions. Like the solid state ferroelectrics, the depolarization field in the material favors a spontaneous spatial variation of the polarization P, manifesting in myriad ways including a twist in the bulk and different arrangements of alternating polarization domains. Unlike the solid-state ferroelectrics with a bulk crystalline structure, the configuration of the NF fluids is determined not only by the reduction of depolarization fields but also by the alignment of molecules at interfaces. In this work, we consider an NF confined to a thin cell, pre-patterned with various types of apolar surface anchoring produced by photoalignment. For uniform planar alignment, we find that the sample forms a series of striped domains. For a cell pre-patterned with a radial +1 defect pattern, the NF breaks up into "pie-slice" polarization domains. We calculate the elastic and electrostatic energy balance which determines the observed configurations and demonstrate that the electrostatic interactions tend to decrease the characteristic domain size λ while the elastic and surface anchoring interactions facilitate a larger λ. We also demonstrate that ionic screening mitigates electrostatic interactions, increasing λ and, above some critical concentration, eliminating the domains altogether. Copyright © 2025, The Authors. All rights reserved.

关键词： Depolarization

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Robustness of contextuality under different types of noise as quantifiers for parity-oblivious multiplexing tasks

arXiv

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arXiv 2024年

作者： Fonseca, Amanda M. Rossi, Vinicius P. Baldijão, Roberto D. Selby, John H. Sainz, Ana Belén Institute of Physics University of São Paulo São Paulo05508-090 Brazil International Centre for Theory of Quantum Technologies University of Gdańsk Gdansk80-309 Poland Theoretical Sciences Visiting Program Okinawa Institute of Science and Technology Graduate University Onna904-0495 Japan Basic Research Community for Physics e.V. Germany

Generalized contextuality is the notion of nonclassicality powering up a myriad of quantum tasks, among which is the celebrated case of a two-party information processing task where classical information is compressed in a quantum channel, the parity-oblivious multiplexing (POM) task. The success rate is the standard quantifier of resourcefulness for this task, while robustness-based quantifiers are as operationally motivated and have known general properties. In this work, we leverage analytical and numerical tools to estimate robustness of contextuality in POM scenarios under different types of noise. We conclude that for the 3-to-1 case robustness of contextuality to depolarisation, as well as a minimisation of robustness of contextuality to dephasing over all bases, are good quantifiers for the nonclassical advantage of this scenario. Moreover, we obtain a general relation between robustness of contextuality to depolarisation and the success rate in any n-to-1 POM scenario and show how it can be used to bound the number of bits encoded in this task. © 2024, CC BY.

关键词： Depolarization

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Chiral ground states of ferroelectric liquid crystals

arXiv

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arXiv 2024年

作者： Kumari, Priyanka Basnet, Bijaya Lavrentovich, Maxim O. Lavrentovich, Oleg D. Advanced Materials and Liquid Crystal Institute Kent State University KentOH44242 United States Materials Science Graduate Program Kent State University KentOH44242 United States Department of Earth Environment and Physics Worcester State University WorcesterMA01602 United States Department of Physics Kent State University KentOH44242 United States

Ferroelectric nematic liquid crystals are formed by achiral molecules with large dipole moments. Its three-dimensional orientational order is universally described as unidirectionally polar. We demonstrate that the ground state of ferroelectric nematic unconstrained by externally imposed alignment directions is chiral, with left- and right-hand twists of polarization. Although the helicoidal deformations and defect walls separating domains of opposite handedness increase the elastic energy, the twists reduce the electrostatic energy and become weaker when the material is doped with ions. The study shows that the polar orientational order of molecules could trigger chirality in the soft matter with no chemically induced chiral centers. © 2024, CC BY.

关键词： Ground state

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Controllable Transmission Switch Based on Asymmetric Coupled Nonlinear Resonances

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Physical Review Applied 2023年第6期19卷 064002-064002页

作者： Hady Moussa Michele Cotrufo Andrea Alù Photonics Initiative Advanced Science Research Center City University of New York New York New York 10031 USA Department of Electrical Engineering City College of City University of New York New York 10031 USA Physics Program Graduate Center City University of New York New York New York 10016 USA

We explore the design and implementation of a passive reconfigurable switch based on nonlinear Fano resonators asymmetrically coupled to two ports. It was recently shown that asymmetric nonlinear resonators could provide passive bias-free nonreciprocal transmission when they were excited only from one port at a time. Here, we show that, by suitably exploiting time-reversal symmetry, this class of devices can also lead to controllable transmission routing, whereby a low-power pulse injected from one port controls the transmission of a larger power signal injected from the opposite port. This effect can be used to realize a power- and/or phase-controlled transmission switch with minimal power consumption. We first analyze the device with a circuit model to gain physical insights into its operation and to establish optimal operation conditions. We then provide a proof-of-principle experimental demonstration, reporting a device whereby the transmission of a 20-dBm signal can be switched from about 10% to 40% by controlling either the power or phase of a signal about 10 times weaker. This work demonstrates an alternative way to develop low-energy power-controlled reconfigurable switches for applications ranging from radar technology to wireless communications.

关键词： Metamaterials Nonlinear waveguides Optoelectronics Radio frequency techniques Devices

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Nernst-Ettingshausen effect in thin Pt and W films at low temperatures

arXiv

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arXiv 2023年

作者： Luo, Renjie Legvold, Tanner J. Chen, Liyang Natelson, Douglas Department of Physics and Astronomy Rice University HoustonTX77005 United States Applied Physics Graduate Program Smalley-Curl Institute Rice University HoustonTX77005 United States Department of Electrical and Computer Engineering Department of Materials Science and NanoEngineering Rice University HoustonTX77005 United States

As spin caloritronic measurements become increasingly common techniques for characterizing material properties, it is important to quantify potentially confounding effects. We report measurements of the Nernst-Ettingshausen response from room temperature to 5 K in thin film wires of Pt and W, metals commonly used as inverse spin Hall detectors in spin Seebeck characterization. Johnson-Nyquist noise thermometry is used to assess the temperature change of the metals with heater power at low temperatures, and the thermal path is analyzed via finite-element modeling. The Nernst-Ettingshausen response of W is found to be approximately temperature-independent, while the response of Pt increases at low temperatures. These results are discussed in the context of theoretical expectations and the possible role of magnetic impurities in Pt. Copyright © 2023, The Authors. All rights reserved.

关键词： Inverse problems

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