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arXiv 2022年

作者： Gabrick, Enrique C. Sayari, Elaheh Protachevicz, Paulo R. Szezech, José D. Iarosz, Kelly C. de Souza, Silvio L.T. Almeida, Alexandre C.L. Viana, Ricardo L. Caldas, Iberê L. Batista, Antonio M. Graduate Program in Science State University of Ponta Grossa PR Ponta Grossa84030-900 Brazil Institute of Physics University of São Paulo SP São Paulo Brazil Institute for Complex Systems and Mathematical Biology University of Aberdeen Aberdeen United Kingdom Department of Mathematics and Statistics State University of Ponta Grossa PR Ponta Grossa84030-900 Brazil University Center UNIFATEB Telêmaco Borba PR 84266-010 Brazil Graduate Program in Chemical Engineering Federal Technological University of Paraná PR Ponta Grossa Brazil Federal University of São João del-Rei Campus Centro-Oeste Divinópolis MG 35501-296 Brazil Physics and Mathematics Department Federal University of São João del-Rei MG Ouro Branco36415-000 Brazil Department of Physics Federal University of Paraná PR Curitiba Brazil

In this work, we study the unpredictability of seasonal infectious diseases considering a SEIRS model with seasonal forcing. To investigate the dynamical behaviour, we compute bifurcation diagrams type hysteresis and their respective Lyapunov exponents. Our results from bifurcations and the largest Lyapunov exponent show bistable dynamics for all the parameters of the model. Choosing the inverse of latent period as control parameter, over 70% of the interval comprises the coexistence of periodic and chaotic attractors, bistable dynamics. Despite the competition between these attractors, the chaotic ones are preferred. The bistability occurs in two wide regions. One of these regions is limited by periodic attractors, while periodic and chaotic attractors bound the other. As the boundary of the second bistable region is composed of periodic and chaotic attractors, it is possible to interpret these critical points as tipping points. In other words, depending on the latent period, a periodic attractor (predictability) can evolve to a chaotic attractor (unpredictability). Therefore, we show that unpredictability is associated with bistable dynamics preferably chaotic, and, furthermore, there is a tipping point associated with unpredictable dynamics. © 2022, CC BY.

关键词： Dynamics

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Critical pore radius and transport properties of disordered hard- And overlapping-sphere models

arXiv

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arXiv 2021年

作者： Klatt, Michael A. Ziff, Robert M. Torquato, Salvatore Department of Physics Princeton University PrincetonNJ08544 United States Institut für Theoretische Physik FAU Erlangen-Nürnberg Staudtstr. 7 Erlangen91058 Germany Center for the Study of Complex Systems Department of Chemical Engineering University of Michigan Ann ArborMI48109 United States Department of Physics Princeton University PrincetonNJ08544 United States Department of Chemistry Princeton Institute for the Science and Technology of Materials Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

Transport properties of porous media are intimately linked to their pore-space microstructures. We quantify geometrical and topological descriptors of the pore space of certain disordered and ordered distributions of spheres, including pore-size functions and the critical pore radius δc. We focus on models of porous media derived from maximally random jammed sphere packings, overlapping spheres, equilibrium hard spheres, "quantizer" sphere packings, and crystalline sphere packings. For precise estimates of the percolation thresholds, we use a strict relation of the void percolation around sphere configurations to weighted bond percolation on the corresponding Voronoi networks. We use the Newman-Ziff algorithm to determine the percolation threshold using universal properties of the cluster size distribution. The critical pore radius δc is often used as the key characteristic length scale that determines the fluid permeability k. A recent study [Torquato. Adv. Wat. Resour. 140,103565 (2020)] suggested for porous media with a well-connected pore space an alternative estimate of k based on the second moment of the pore size hδ2i, which is easier to determine than δc. Here, we compare δc to the second moment of the pore size hδ2i, and indeed confirm that, for all porosities and all models considered, δc2 is to a good approximation proportional to hδ2i. However, unlike hδ2i, the permeability estimate based on δc2 does not predict the correct ranking of k for our models. Thus, we confirm hδ2i to be a promising candidate for convenient and reliable estimates of the fluid permeability for porous media with a well-connected pore space. Moreover, we compare the fluid permeability of our models with varying degrees of order, as measured by the τ order metric. We find that (effectively) hyperuniform models tend to have lower values of k than their nonhyperuniform counterparts. Our findings could facilitate the design of porous media with desirable transport properties via target

关键词： Porous materials

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Mutational signatures and transmissibility of SARS-CoV-2 Gamma and Lambda variants

arXiv

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arXiv 2021年

作者： Oróstica, Karen Y. Contreras, Sebastian Mohr, Sebastian B. Dehning, Jonas Bauer, Simon Medina-Ortiz, David Iftekhar, Emil N. Mujica, Karen Covarrubias, Paulo C. Ulloa, Soledad Castillo, Andrés E. Verdugo, Ricardo A. Fernández, Jorge Olivera-Nappa, Álvaro Priesemann, Viola Santiago Chile Max Planck Institute for Dynamics and Self-Organization Am Faßberg 17 Göttingen37077 Germany Department of Chemical Engineering Biotechnology and Materials Universidad de Chile Beauchef 851 Santiago8370448 Chile Centre for Biotechnology and Bioengineering Universidad de Chile Beauchef 851 Santiago8370456 Chile Human Genetics Program Institute of Biomedical Sciences Faculty of Medicine University of Chile Santiago Chile Institute for the Dynamics of Complex Systems University of Göttingen Friedrich-Hund-Platz 1 Göttingen37077 Germany

The emergence of SARS-CoV-2 variants of concern endangers the long-term control of COVID-19, especially in countries with limited genomic surveillance. In this work, we explored genomic drivers of contagion in Chile. We sequenced 3443 SARS-CoV-2 genomes collected between January and July 2021, where the Gamma (P.1), Lambda (C.37), Alpha (B.1.1.7), B.1.1.348, and B.1.1 lineages were predominant. Using a Bayesian model tailored for limited genomic surveillance, we found that Lambda and Gamma variants’ reproduction numbers were about 5% and 16% larger than Alpha’s, respectively. We observed an overabundance of mutations in the Spike gene, strongly correlated with the variant’s transmissibility. Furthermore, the variants’ mutational signatures featured a breakpoint concurrent with the beginning of vaccination (mostly CoronaVac, an inactivated virus vaccine), indicating an additional putative selective pressure. Thus, our work provides a reliable method for quantifying novel variants’ transmissibility under subsampling (as newly-reported Delta, B.1.617.2) and highlights the importance of continuous genomic surveillance. Copyright © 2021, The Authors. All rights reserved.

关键词： SARS

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Time-Varying ℓ₀ Optimization for Spike Inference from Multi-Trial Calcium Recordings

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Data Science in Science 2024年第1期3卷

作者： Shen, Tong Du, Mingyu Johnston, Kevin Grieco, Steven F. Crary, Rachel Guzowski, John F. Lur, Gyorgy Xu, Xiangmin Ombao, Hernando Guindani, Michele Yu, Zhaoxia Department of Statistics University of California Irvine 92697 CA United States Center for Complex Biological Systems University of California Irvine 92697 CA United States Department of Mathematics and The NSF-Simons Center for Multiscale Cell Fate Research University of California Irvine 92697 CA United States Department of Anatomy and Neurobiology School of Medicine University of California Irvine 92697 CA United States Department of Neurobiology and Behavior University of California Irvine 92697 CA United States The Center for the Neurobiology of Learning and Memory University of California Irvine 92697 CA United States Department of Biomedical Engineering University of California Irvine 92697 CA United States Department of Computer Science University of California Irvine 92697 CA United States The Center for Neural Circuit Mapping University of California Irvine 92697 CA United States Statistics Program KAUST Thuwal Saudi Arabia Department of Biostatistics University of California Los Angeles CA United States

Optical imaging of genetically encoded calcium indicators is a powerful tool to record the activity of a large number of neurons simultaneously over a long period of time from freely behaving animals. However, determining the exact time at which a neuron spikes and estimating the underlying firing rate from calcium fluorescence data remains challenging, especially for calcium imaging data obtained from a longitudinal study. We propose a multi-trial time-varying ℓ₀ penalized method to jointly detect spikes and estimate firing rates by robustly integrating evolving neural dynamics across trials. Our simulation study shows that the proposed method performs well in both spike detection and firing rate estimation. We demonstrate the usefulness of our method on calcium fluorescence trace data from two studies, with the first study showing differential firing rate functions between two behaviors and the second study showing evolving firing rate functions across trials due to learning. © 2024 The Author(s). Published with license by Taylor & Francis Group, LLC.

关键词： calcium imaging firing rate spike detection Time-varying penalty ℓ0 regularization

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Surface bio-engineering of melt electrowritten tubular scaffolds via plasma immersion ion implantation (PIII)

Materials Today Bio

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Materials Today Bio 2025年 33卷

作者： Anyu Zhang Anne Metje van Genderen Bingyan Liu Junyi Qian Jirawat Iamsamang Ziyu Wang Miguel Castilho Behnam Akhavan School of Biomedical Engineering University of Sydney Sydney Australia School of Physics University of Sydney Sydney Australia Sydney Nano Institute University of Sydney 2006 NSW Australia School of Engineering University of Newcastle Callaghan 2308 NSW Australia Div. Pharmacology Utrecht Institute for Pharmaceutical Sciences Utrecht University the Netherlands Department of Biomedical Engineering Eindhoven University of Technology Eindhoven the Netherlands Charles Perkins Centre University of Sydney 2006 NSW Australia School of Life and Environmental Sciences University of Sydney 2006 NSW Australia Institute for Complex Molecular Systems Eindhoven University of Technology Eindhoven the Netherlands Hunter Medical Research Institute (HMRI) Precision Medicine Program New Lambton Heights 2305 NSW Australia

Melt electrowriting (MEW) enables the fabrication of highly controlled, open-pore tubular constructs for replicating the complex architectures of vascular, renal, and other tissues. However, a key challenge is to functionalize their surfaces so that they not only support but also instruct key biological interactions, particularly in promoting vascularization. Here, we propose plasma immersion ion implantation (PIII) as a biofunctionalization strategy for open-pore tubular constructs fabricated by MEW. Surface chemistry analysis confirmed homogeneous treatment across PIII-treated MEW 3D structures, while uniaxial tensile tests demonstrated no significant changes in mechanical properties following the treatment. Electron paramagnetic resonance (EPR) data provided evidence of the formation of a stable, radical-rich surface, which was further validated by fluorescence imaging with a model molecule, confirming the radicals’ role in enabling uniform covalent biomolecule attachment. The PIII-treated MEW constructs were covalently functionalized with vascular endothelial growth factor (VEGF), thereby modulating the behavior of seeded cells. Endothelialization studies using conditionally immortalized glomerular endothelial cells (ciGEnC) demonstrated that VEGF-immobilized MEW tubes effectively support monolayer formation, achieving outcomes comparable to those observed with VEGF supplementation in culture media. Remarkably, the immobilized VEGF sustained endothelialization with a similar effectiveness to traditional VEGF suspension methods over prolonged culture conditions (21 days), but without the need for continuous VEGF supplementation. These findings establish a novel biofunctionalization strategy for vascularized tissue engineering scaffolds and pave the way for plasma-modified MEW tubes as platforms for preclinical models and regenerative medicine applications.

关键词： Vascular tube Biofunctionalization Plasma surface engineering Covalent immobilization

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Emergent Dimer-Model Topological Order and Quasiparticle Excitations in Liquid Crystals: Combinatorial Vortex Lattices

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Physical Review X 2025年第2期15卷 021084-021084页

作者： Cuiling Meng Jin-Sheng Wu Žiga Kos Jörn Dunkel Cristiano Nisoli Ivan I. Smalyukh Department of Physics and Chemical Physics Program University of Colorado Boulder Colorado 80309 USA International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM) Hiroshima University Higashihiroshima Hiroshima Japan Department of Mathematics Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA Faculty of Mathematics and Physics University of Ljubljana Ljubljana Slovenia Department of Condensed Matter Physics Jožef Stefan Institute Ljubljana Slovenia Theoretical Division Physics of Condensed Matter and Complex Systems and Center For Nonlinear Studies Los Alamos National Laboratory Los Alamos New Mexico 87545 USA Department of Electrical Computer and Energy Engineering Materials Science and Engineering Program University of Colorado Boulder Colorado 80309 USA Renewable and Sustainable Energy Institute National Renewable Energy Laboratory University of Colorado Boulder Colorado 80309 USA

Liquid crystals have proven to provide a versatile experimental and theoretical platform for studying topological objects such as vortices, skyrmions, and hopfions. In parallel, in hard condensed matter physics, the concept of topological phases and topological order has been introduced in the context of spin liquids to investigate emergent phenomena like quantum Hall effects and high-temperature superconductivity. Here, we bridge these two seemingly disparate perspectives on topology in physics. Combining experiments and simulations, we show how topological defects in liquid crystals can be used as versatile building blocks to create complex, highly degenerate topological phases, which we refer to as “combinatorial vortex lattices” (CVLs). CVLs exhibit extensive residual entropy and support locally stable quasiparticle excitations in the form of charge-conserving topological monopoles, which can act as mobile information carriers and be linked via Dirac strings. CVLs can be rewritten and reconfigured on demand, endowed with various symmetries, and modified through laser-induced topological surgery—an essential capability for information storage and retrieval. We demonstrate experimentally the realization, stability, and precise optical manipulation of CVLs, thus opening new avenues for understanding and technologically exploiting higher-hierarchy topology in liquid crystals and other ordered media.

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Adaptive Coordination Offsets for Signalized Arterial Intersections using Deep Reinforcement Learning

arXiv

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arXiv 2020年

作者： Diaz, Keith Anshilo Dailisan, Damian Sharaf, Umang Santos, Carissa Gan, Qijian Uy, Francis Aldrine Lim, May T. Bayen, Alexandre M. The School of Civil Environmental and Geological Engineering Mapua University Manila Philippines The National Institute of Physics University of the Philippines Diliman Philippines The Analytics Computing and Complex Systems Laboratory Asian Institute of Management Philippines The Electrical Engineering and Computer Sciences department at University of California Berkeley United States The PATH program in the Institute of Transportation Studies University of California Berkeley United States The Electrical Engineering and Computer Sciences Department The Department of Civil and Environmental Engineering The Institute of Transportation Studies University of California Berkeley United States

Coordinating intersections in arterial networks is critical to the performance of urban transportation systems. Deep reinforcement learning (RL) has gained traction in traffic control research along with data-driven approaches for traffic control systems. To date, proposed deep RL-based traffic schemes control phase activation or duration. Yet, such approaches may bypass low-volume links for several cycles to optimize the network-level traffic flow. Here we propose a deep RL framework that dynamically adjusts offsets based on traffic states and preserves the planned phase timings and order derived from model-based methods. This framework improves arterial coordination while maintaining phase order and timing predictability. Using a validated and calibrated traffic model, we trained the policy of a deep RL agent that aims to reduce travel delays in the network. To evaluate the resulting policy, we compared its performance against the phase offsets deployed along a segment of Huntington Drive in the city of Arcadia. The resulting policy dynamically readjusts phase offsets in response to changes in traffic demand. Simulation results show that the proposed deep RL agent outperformed the baseline on average, effectively reducing delay time by 13.21% in the AM Scenario, 2.42% in the Noon scenario, and 6.2% in the PM scenario when offsets are adjusted in 15-minute intervals. Finally, we also show the robustness of our agent to extreme traffic conditions, such as demand surges in off-peak hours and localized traffic incidents. Copyright © 2020, The Authors. All rights reserved.

关键词： Reinforcement learning

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Nontrivial coupling of light into a defect:the interplay of nonlinearity and topology

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Light(Science & Applications) 2020年第1期9卷 646-655页

作者： Shiqi Xia Dario Jukic Nan Wang Daria Smirnova Lev Smirnov Liqin Tang Daohong Song Alexander Szameit Daniel Leykam Jingjun Xu Zhigang Chen Hrvoje Buljan The MOE Key Laboratory of Weak-Light Nonlinear Photonics TEDA Applied Physics Institute and School of PhysicsNankai UniversityTianjin 300457China Faculty of Civil Engineering University of ZagrebA.Kacica Miosica 2610000 ZagrebCroatia Nonlinear Physics Centre Research School of PhysicsAustralian National UniversityCanberraACT 2601Australia Institute of Applied Physics Russian Academy of ScienceNizhny Novgorod 603950Russia Collaborative Innovation Center of Extreme Optics Shanxi UniversityTaiyuan 030006 ShanxiPR China Institut für Physik Universitat RostockAlbert-Einstein-Strasse 2318059 RostockGermany Center for Theoretical Physics of Complex Systems Institute for Basic Science(IBS)Daejeon 34126Republic of Korea Basic Science Program Korea University of Science and TechnologyDaejeon 34113Republic of Korea Department of Physics and Astronomy San Francisco State UniversitySan FranciscoCA 94132USA Department of Physics Faculty of ScienceUniversity of ZagrebBijenička c.3210000 ZagrebCroatia

The flourishing of topological photonics in the last decade was achieved mainly due to developments in linear topological photonic ***,when nonlinearity is introduced,many intriguing questions *** example,are there universal fingerprints of the underlying topology when modes are coupled by nonlinearity,and what can happen to topological invariants during nonlinear propagation?To explore these questions,we experimentally demonstrate nonlinearity-induced coupling of light into topologically protected edge states using a photonic platform and develop a general theoretical framework for interpreting the mode-coupling dynamics in nonlinear topological *** on laser-written photonic Su-Schrieffer-Heeger lattices,our experiments show the nonlinear coupling of light into a nontrivial edge or interface defect channel that is otherwise not permissible due to topological *** theory explains all the observations ***,we introduce the concepts of inherited and emergent nonlinear topological phenomena as well as a protocol capable of revealing the interplay of nonlinearity and *** concepts are applicable to other nonlinear topological systems,both in higher dimensions and beyond our photonic platform.

关键词： nonlinearity topological coupling

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Critical mass effect in evolutionary games triggered by zealots

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Physical Review Research 2020年第2期2卷 023305-023305页

作者： Alessio Cardillo Naoki Masuda Department of Engineering Mathematics University of Bristol Bristol BS8 1UB United Kingdom Department of Computer Science and Mathematics University Rovira i Virgili E-43007 Tarragona Spain GOTHAM Lab – Institute for Biocomputation and Physics of Complex Systems (BIFI) University of Zaragoza E-50018 Zaragoza Spain Department of Mathematics State University of New York at Buffalo Buffalo New York 14260-2900 USA Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo Buffalo New York 14260-5030 USA

Tiny perturbations may trigger large responses in systems near criticality, shifting them across equilibria. Committed minorities are suggested to be responsible for the emergence of collective behaviors in many physical, social, and biological systems. Using evolutionary game theory, we address the question whether a finite fraction of zealots can drive the system to large-scale coordination. We find that a tipping point exists in coordination games, whereas the same phenomenon depends on the selection pressure, update rule, and network structure in other types of games. Our study paves the way to understand social systems driven by the individuals' benefit in the presence of zealots, such as human vaccination behavior or cooperative transports in animal groups.

关键词： Patterns in complex systems Social systems

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Configurable antiferromagnetic domains and lateral exchange bias in atomically thin CrPS4

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Nature Materials 2025年 1-10页

作者： Yu-Xuan Wang Thomas K. M. Graham Xin-Yue Zhang Brian B. Zhou Ricardo Rama-Eiroa Elton J. G. Santos Mohammad H. Badarneh Md Ariful Islam Rafael Nunes Gontijo Ganesh Prasad Tiwari Tibendra Adhikari Zhong Lin Kenji Watanabe Takashi Taniguchi Claire Besson Department of Physics Boston College Chestnut Hill MA USA Donostia International Physics Center (DIPC) Donostia-San Sebastián Spain Institute for Condensed Matter and Complex Systems School of Physics and Astronomy University of Edinburgh Edinburgh UK Higgs Centre for Theoretical Physics University of Edinburgh Edinburgh UK Department of Physics Applied Physics and Astronomy Binghamton University Binghamton NY USA Materials Science and Engineering Program Binghamton University Binghamton NY USA Research Center for Electronic and Optical Materials National Institute for Materials Science Tsukuba Japan Research Center for Materials Nanoarchitectonics National Institute for Materials Science Tsukuba Japan Department of Chemistry Binghamton University Binghamton NY USA

Interfacial exchange coupling between antiferromagnets (AFMs) and ferromagnets (FMs) crucially makes it possible to shift the FM hysteresis, known as exchange bias, and to switch AFM states. Two-dimensional magnets unlock opportunities to combine AFM and FM materials; however, the buried AFM–FM interfaces obtained by stacking remains challenging to understand. Here we demonstrate interfacial control via intralayer exchange coupling in the layered AFM CrPS4, where connected even and odd layers realize pristine lateral interfaces between AFM-like and FM-like regions. We distinguish antiphase even-layer states by scanning nitrogen-vacancy centre magnetometry due to a weak surface magnetization. This surface magnetization enables control over the even-layer state, with different regions switching at distinct fields due to their own lateral couplings. We toggle three AFM domains adjacent to a FM-like region and demonstrate a tunable multilevel exchange bias. Our nanoscale visualization unveils the microscopic origins of exchange bias and advances single two-dimensional crystals for hybrid AFM–FM technologies.

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