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arXiv 2025年

作者： Ebata, H. Nishizawa, K. van Esterik, F.A.S. Tao, Y. Inokuchi, S. Ise, H. Mizuno, D. Department of Physics Kyushu University Fukuoka819-0395 Japan Department of Applied Physics Graduate School of Engineering Tohoku University Sendai980-8579 Japan Institute for Materials Chemistry and Engineering Kyushu University Fukuoka819-0395 Japan

Cytoplasmic viscoelasticity is crucial for various intracellular processes. However, the dynamic shear modulus, G(ω), has been reported to vary considerably, often without consistent patterns or rules, even within the same cell. Thus, uncovering the physical basis of cytoplasmic rheology, and whether any universal feature exists, remains a major challenge. Here, we employed microrheology with a 3D feedback technique to minimize artifacts such as laser phototoxicity and examined cytoplasmic viscoelasticity across varied mechanical environments, cell types, and cytoskeletal disruptions. Unlike previous studies, a single power-law rheology G(ω) ∝ (−ιω)0.5 was observed over a broad frequency range for all conditions except ATP depletion. While the vimentin cytoskeleton significantly contributed to steady shear viscosity measured by pulling a particle over large distances, cytoskeletal disruptions had only a minor effect on locally measured viscoelasticity. These findings demonstrate that molecular crowding governs the observed universality, providing a framework to systematically investigate cytoplasmic mechanics across diverse cellular contexts. © 2025, CC BY-NC-SA.

关键词： Shear flow

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Viscosity in water from first-principles and deep-neural-network simulations

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npj Computational Materials 2022年第1期8卷 1318-1327页

作者： Cesare Malosso Linfeng Zhang Roberto Car Stefano Baroni Davide Tisi SISSA—Scuola Internazionale Superiore di Studi Avanzati 34136TriesteItaly Program in Applied and Computational Mathematics Princeton UniversityPrincetonNJ08544USA DP Technology Beijing100080PR China Department of Chemistry Department of Physicsand Princeton Institute for the Science and Technology of MaterialsPrinceton UniversityPrincetonNJUSA CNR Istituto Officina dei Materiali SISSA Unit34136TriesteItaly

We report on an extensive study of the viscosity of liquid water at near-ambient conditions,performed within the Green-Kubo theory of linear response and equilibrium ab initio molecular dynamics(AIMD),based on density-functional theory(DFT).In order to cope with the long simulation times necessary to achieve an acceptable statistical accuracy,our ab initio approach is enhanced with deep-neural-network potentials(NNP).This approach is first validated against AIMD results,obtained by using the Perdew–Burke–Ernzerhof(PBE)exchange-correlation functional and paying careful attention to crucial,yet often overlooked,aspects of the statistical data ***,we train a second NNP to a dataset generated from the Strongly Constrained and Appropriately Normed(SCAN)*** the error resulting from the imperfect prediction of the melting line is offset by referring the simulated temperature to the theoretical melting one,our SCAN predictions of the shear viscosity of water are in very good agreement with experiments.

关键词： viscosity Strongly ambient

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Fundamentals of crystalline Hopf insulators

arXiv

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arXiv 2023年

作者： Wang, Yuxin Tyner, Alexander C. Goswami, Pallab Department of Physics and Astronomy Northwestern University EvanstonIL60208 United States Graduate Program in Applied Physics Northwestern University EvanstonIL60208 United States

Three-dimensional, crystalline Hopf insulators are generic members of unitary Wigner-Dyson class, which can break all global discrete symmetries and point group symmetries. In the absence of first Chern number for any two-dimensional plane of Brillouin zone, the Hopf invariant NH ∈ Z. But in the presence of Chern number NH ∈ Z2q, where q is the greatest common divisor of Chern numbers for xy, yz, and xz planes of Brillouin zone. How does NH affect topological quantization of isotropic, magneto-electric coefficient? We answer this question with calculations of Witten effect for a test, magnetic monopole. Furthermore, we construct N-band tight-binding models of Hopf insulators and demonstrate their topological stability against spectral flattening. Copyright © 2023, The Authors. All rights reserved.

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Hole Statistics of Equilibrium 2D and 3D Hard-Sphere Crystals

arXiv

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arXiv 2024年

作者： Wang, Haina Huse, David A. Torquato, Salvatore Department of Chemistry Princeton University PrincetonNJ08544 United States Department of Physics Princeton University PrincetonNJ08544 United States Department of Chemistry Department of Physics Princeton Institute of Materials and Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

The probability of finding a spherical "hole" of a given radius r contains crucial structural information about many-body systems. Such hole statistics, including the void conditional nearest-neighbor probability functions GV (r), have been well studied for hard-sphere fluids in d-dimensional Euclidean space Rd. However, little is known about these functions for hard-sphere crystals for values of r beyond the hard-sphere diameter, as large holes are extremely rare in crystal phases. To overcome these computational challenges, we introduce a biased-sampling scheme that accurately determines hole statistics for equilibrium hard spheres on ranges of r that far extend those that could be previously explored. We discover that GV (r) in crystal and hexatic states exhibits oscillations whose amplitudes increase rapidly with the packing fraction, which stands in contrast to GV (r) for fluid states that is monotonic in r. The oscillations in GV (r) for 2D crystals are strongly correlated with the local orientational order metric in the vicinity of the holes, and variations in GV (r) for 3D states indicate a transition between tetrahedral and octahedral holes, demonstrating the power of GV (r) as a probe of local coordination geometry. To further study the statistics of interparticle spacing in hard-sphere systems, we compute the local packing fraction distribution f(l) of Delaunay cells, and find that for d ≤ 3, the excess kurtosis of f(l) switches sign at a certain transitional global packing fraction. Our investigation facilitates the study of structural and bulk properties of materials that involve the creation of rare large holes, such as the solubility of alloys. © 2024, CC BY.

关键词： Spheres

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Connecting polymer collapse and the onset of jamming

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Physical Review E 2024年第3期109卷 034406-034406页

作者： Alex T. Grigas Aliza Fisher Mark D. Shattuck Corey S. O'Hern Graduate Program in Computational Biology and Bioinformatics Yale University New Haven Connecticut 06520 USA Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven Connecticut 06520 USA Department of Mechanical Engineering and Materials Science Yale University New Haven Connecticut 06520 USA Benjamin Levich Institute and Physics Department The City College of New York New York New York 10031 USA Department of Physics Yale University New Haven Connecticut 06520 USA Department of Applied Physics Yale University New Haven Connecticut 06520 USA

Previous studies have shown that the interiors of proteins are densely packed, reaching packing fractions that are as large as those found for static packings of individual amino-acid-shaped particles. How can the interiors of proteins take on such high packing fractions given that amino acids are connected by peptide bonds and many amino acids are hydrophobic with attractive interactions? We investigate this question by comparing the structural and mechanical properties of collapsed attractive disk-shaped bead-spring polymers to those of three reference systems: static packings of repulsive disks, of attractive disks, and of repulsive disk-shaped bead-spring polymers. We show that the attractive systems quenched to temperatures below the glass transition T≪Tg and static packings of both repulsive disks and bead-spring polymers possess similar interior packing fractions. Previous studies have shown that static packings of repulsive disks are isostatic at jamming onset, i.e., the number of interparticle contacts Nc matches the number of degrees of freedom, which strongly influences their mechanical properties. We find that repulsive polymer packings are hypostatic at jamming onset (i.e., with fewer contacts than degrees of freedom) but are effectively isostatic when including stabilizing quartic modes, which give rise to quartic scaling of the potential energy with displacements along these modes. While attractive disk and polymer packings are often considered hyperstatic with excess contacts over the isostatic number, we identify a definition for interparticle contacts for which they can also be considered as effectively isostatic. As a result, we show that the mechanical properties (e.g., scaling of the potential energy with excess contact number and low-frequency contribution to the density of vibrational modes) of weakly attractive disk and polymer packings are similar to those of isostatic repulsive disk and polymer packings. Our results demonstrate that static

关键词： Jamming Polymer folding Protein folding Single polymer chains

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Solitons and real-space screening of bulk topology of quantum materials

arXiv

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arXiv 2023年

作者： Tyner, Alexander C. Goswami, Pallab Graduate Program in Applied Physics Northwestern University EvanstonIL60208 United States Department of Physics and Astronomy Northwestern University EvanstonIL60208 United States

Recent years have seen multiple high-throughput studies reveal an immense number of topological materials through use of symmetry indicators. Despite this success, three-dimensional topological insulators (TIs) admitting a band-gap larger than Bi2Se3 and two-dimensional TIs admitting a band gap larger than β-bismuthene, two of the originally proposed TIs, remain extremely rare. Simultaneously, a significant effort has been made to understand and identify topological phases "invisible" to symmetry indicators. Such phases offer a unique opportunity to expand the search for a large band-gap TI, however their identification requires sophisticated probes of bulk topology. Magnetic flux tubes or vortices have emerged as one such probe in two-dimensions when inserted into the bulk. In this work, we develop an automated workflow to perform vortex insertion and apply it to a current database of high-quality, experimentally realized, two-dimensional insulators. The results reveal multiple novel two-dimensional topological insulators supporting large bands gaps, including the 1H-MX2 (M=Mo,W) and (X=S,Se,Te) family of transition metal dichalcogenides. Our work has broad implications for current theoretical and experimental efforts to employ these materials in superconducting and Moire systems. Copyright © 2023, The Authors. All rights reserved.

关键词： Energy gap

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Sensing Beyond the Exceptional Point for High Detectivity

Sensing Beyond the Exceptional Point for High Detectivity

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Conference on Lasers and Electro-Optics (CLEO)

作者： Zhichao Li Ciril S. Prasad Xielin Wang Ding Zhang Gururaj V. Naik Applied Physics Graduate Program Smalley-Curl Institute Rice University Houston TX USA Department of Electrical and Computer Engineering Rice University Houston TX USA Department of Physics and Astronomy Rice University Houston TX USA

Exceptional point (EP)-based optical sensors exhibit exceptional sensitivity but poor detectivity. Slightly off EP operation boosts detectivity without much loss in sensitivity. We experimentally demonstrate a high-de... 详细信息

ISBN: (纸本)9798350369311

关键词： Proteins Optical losses Sensitivity Optical device fabrication Measurement by laser beam Lasers and electrooptics Optical sensors Laser applications Electro-optical waveguides

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Alkyne-tag Raman imaging and sensing of bioactive compounds

NATURE REVIEWS METHODS PRIMERS

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NATURE REVIEWS METHODS PRIMERS 2025年第1期5卷 1页

作者： [Anonymous] RIKEN Center for Sustainable Resource Science Wako Japan Department of Pure and Applied Chemistry Technology and Innovation Centre University of Strathclyde Glasgow UK Graduate School of Pharmaceutical Sciences Tohoku University Sendai Japan Department of Applied Physics Graduate School of Engineering Osaka University Suita Japan Department of Dermatology Graduate School of Medicine Osaka University Suita Japan Institute for Open and Transdisciplinary Research Initiatives Osaka University Suita Japan

An alkyne is an unsaturated hydrocarbon characterized by the presence of at least one C≡C bond. Alkyne groups generate a strong Raman peak in the cellular-silent region, a region between 1,800 and 2,800 cm−1where endogenous molecules do not produce a Raman signal. As a result, alkynes are regularly used as tags to label and visualize small molecules in live cells using Raman microscopy, a method referred to as alkyne-tag Raman imaging (ATRI). ATRI has been applied to various compounds to enable their cellular localization and, recently, alkyne-tagged compounds have been used as Raman sensors to detect intracellular biomolecules, such as metal ions or reactive oxygen species. ATRI has unique advantages over existing methods for localizing small molecules intracellularly, such as enabling super-multiplex detection and incurring a smaller impact on labelled compounds. In this Primer, we describe the principles and key techniques involved in ATRI, including the design of alkyne-tagged molecules, sample preparation and the set-up of Raman microscopes. We showcase the demonstration and application of ATRI, encompassing the development of responsive alkyne-tagged compounds for sensing biomolecules. Finally, we discuss the limitations and potential applications of ATRI, shedding light on the future possibilities of this method.

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Vitrification of hazardous wastes from ship recycling: circular economy solutions for asbestos and synthetic vitreous fibers

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Environmental Science and Pollution Research 2025年第13期32卷 8183-8200页

作者： Pereira, Newton Narciso de Castro Bertagnolli, Denise da Silva, Ladário Faria, Eliel Eleutério Junior, José Mauro Moraes de Araujo de Monteiro Barros, Munique Eva Paiva Miranda, Tainara Alves de Oliveira Lima, Eduardo da Silva Almeida, Vitor Duarte Department of Production Engineering School of Industrial Engineering and Metallurgy at Volta Redonda - EEIMVR – Federal Fluminense University UFF Av. dos Trabalhadores 420 – Sala C77 Vila Sta. Cecília RJ Volta Redonda27255-125 Brazil Department of Chemistry Exact Sciences Institute Federal Fluminense University UFF Rua Desembargador Ellis Hermydio Figueira 783 RJ AterradoVolta Redonda27213-145 Brazil Department of Physics Exact Sciences Institute Federal Fluminense University UFF Rua Desembargador Ellis Hermydio Figueira 783 RJ AterradoVolta Redonda27213-145 Brazil Department of Physics Universidade Federal de Roraima Av. Cap. Ene Garcez N. 2413 Paricarana Roraima Boa Vista69310-000 Brazil Departament of Metallurgical Engineering Federal Fluminense University UFF Av. dos Trabalhadores 420 Vila Sta. Cecília RJ Volta Redonda27255-125 Brazil Physics Post-Graduate Program Brazilian Center for Physics Research Rua Doutor Xavier Sigaud 150 Urca RJ Rio de Janeiro22290-180 Brazil Physics Post-Graduate Program Physics Institute Federal Fluminense University UFF Av. Gal. Milton Tavares de Souza S/nº Praia Vermelha Campus RJ Niterói24210-346 Brazil

Ship recycling at the end of its useful life presents significant environmental and health challenges due to the presence of hazardous materials, such as asbestos and synthetic vitreous fibers (SVFs). This study aimed to convert SVFs and asbestos into safe, reusable co-products by incorporating them into a glassy matrix. The materials were melted at 1200 °C for 1 h with utilization of niobium pentoxide (Nb2O5) to lower fusion temperatures. Samples collected from an offshore vessel and platform being recycled in Rio de Janeiro, Brazil, were analyzed using energy-dispersive x-ray spectroscopy (EDS) and scanning electron microscopy (SEM), revealing the presence of SVFs but not asbestos. Seven types of glass were produced, with their non-crystalline, glassy nature confirmed by the presence of an amorphous halo in X-ray diffraction (XRD) and a glass transition observed in differential scanning calorimetry (DSC). These findings demonstrate the potential to transform hazardous waste into value-added products, advancing a circular economy in ship recycling operations. © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2025.

关键词： Asbestos

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A Facile NMR Method for Pre-MRI Evaluation of Trigger-Responsive T1 Contrast Enhancement

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Small Methods 2024年第10期8卷 e2301603页

作者： Jian, Cheng-Bang Wu, Ying-Yann Lin, Ming-Huang Gao, Hua-De Chen, Chong-Yan Leong, Shwee Khuan Tzou, Der-Lii M. Hwang, Dennis W. Lee, Hsien-Ming Institute of Chemistry Academia Sinica Taipei11529 Taiwan Nano Science and Technology Program Taiwan International Graduate Program Academia Sinica and National Taiwan University Taipei11529 Taiwan Department of Chemistry National Taiwan University Taipei10617 Taiwan Institute of Biomedical Sciences Academia Sinica Taipei11529 Taiwan Sustainable Chemical Science and Technology Program Taiwan International Graduate Program Academia Sinica and National Yang Ming Chiao Tung University Taipei11529 Taiwan Department of Applied Chemistry National Yang Ming Chiao Tung University Hsinchu30093 Taiwan

There is a growing interest in developing paramagnetic nanoparticles as responsive magnetic resonance imaging (MRI) contrast agents, which feature switchable T1 image contrast of water protons upon biochemical cues for better discerning diseases. However, performing an MRI is pragmatically limited by its cost and availability. Hence, a facile, routine method for measuring the T1 contrast is highly desired in early-stage development. This work presents a single-point inversion recovery (IR) nuclear magnetic resonance (NMR) method that can rapidly evaluate T1 contrast change by employing a single, optimized IR pulse sequence that minimizes water signal for "off-state" nanoparticles and allows for sensitively measuring the signal change with "switch-on" T1 contrast. Using peptide-induced liposomal gadopentetic acid (Gd3+-DTPA) release and redox-sensitive manganese oxide (MnO2) nanoparticles as a demonstration of generality, this method successfully evaluates the T1 shortening of water protons caused by liposomal Gd3+-DTPA release and Mn2+ formation from MnO2 reduction. Furthermore, the NMR measurement is highly correlated to T1-weighted MRI scans, suggesting its feasibility to predict the MRI results at the same field strength. This NMR method can be a low-cost, time-saving alternative for pre-MRI evaluation for a diversity of responsive T1 contrast systems. © 2024 Wiley-VCH GmbH.

关键词： Nuclear magnetic resonance spectroscopy

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