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Viscoelastic approach to cell migration in epiboly. 表观生物学中细胞迁移的粘弹性方法。
IF 2.2 3区 物理与天体物理
Physical Review E Pub Date : 2025-05-01 DOI: 10.1103/PhysRevE.111.054404
N O Rojas, P C Encina
{"title":"Viscoelastic approach to cell migration in epiboly.","authors":"N O Rojas, P C Encina","doi":"10.1103/PhysRevE.111.054404","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.054404","url":null,"abstract":"<p><p>In this work a viscoelastic model that couples enveloping cell layer velocities and tensions is built including the geometric corrections on the sphere surface, showing that stress anisotropy increases in the layer as a function of the polar coordinate. This trend is enforced as the enveloping cell front advances, which rules the mitotic spindle and contributes to tissue propagation. The theory is general and applicable to gastrulation phases in different vertebrates. Cell speeds and stresses obtained from the leading order of this theory are in good agreement with previous formulations, and an exact approach containing these results generalizes the theoretical model and includes inertial and advective terms, allowing to perform simulations of the enveloping cell layer during epiboly and at following stages such as disperse and reaggregation phases.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 5-1","pages":"054404"},"PeriodicalIF":2.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Collective motion of self-trapping chiral active particles induced by a noisy geometric environment. 噪声几何环境诱导的自捕获手性活性粒子的集体运动。
IF 2.2 3区 物理与天体物理
Physical Review E Pub Date : 2025-05-01 DOI: 10.1103/PhysRevE.111.055403
Jun Huang, Zhi-Gang Shao
{"title":"Collective motion of self-trapping chiral active particles induced by a noisy geometric environment.","authors":"Jun Huang, Zhi-Gang Shao","doi":"10.1103/PhysRevE.111.055403","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.055403","url":null,"abstract":"<p><p>Strategies for trapping and manipulating chiral active matter are crucial in fields ranging from nonequilibrium physics to chemical engineering and biology. While various methods for controlling active matter have been developed, achieving spontaneous trapping and collective manipulation in complex, variable, noisy environments remains an open challenge. In this paper, we investigate the self-trapping effect and collective motion patterns of chiral active particles induced by a noisy geometric environment in the chiral Vicsek-like model (CVLM). The heterogeneous environment relies on designing the topography by varying the spatial noise intensity, featuring a finite noiseless circular region with radius R_{0}. We identify two key conditions for self-trapping behavior: (i) sufficient interaction radius (r) to break symmetry and enable collective motion, and (ii) chirality (ω) that satisfies the geometric constraints, where stable and effective trapping occurs only if ω>ω_{c}, with ω_{c}≃v/R_{0}. We also analyze how different system parameters influence the fraction of trapped particles (FTP). Furthermore, our system reveals a variety of phase transitions driven by the interplay between ω and r. Interestingly, varying ω uncovers additional phases, such as self-reverting vortices, orbital polarization, and vibrational polarization. Additionally, changes in particle interaction r result in three regimes of particle motion: homogeneous disorder, multiple flocks, and single flocks. These findings may inspire innovative strategies for achieving spontaneous trapping and regulating chiral particles in complex environments.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 5-2","pages":"055403"},"PeriodicalIF":2.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327407","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Deep-learning interatomic potentials of the ɛ-ZrX_{2} series (X=H, D, and T). l -ZrX_{2}系列(X=H, D, T)的深度学习原子间势。
IF 2.2 3区 物理与天体物理
Physical Review E Pub Date : 2025-05-01 DOI: 10.1103/PhysRevE.111.055303
Kunyang Cheng, Xiujuan Cheng, Mingyang Shi, Xuying Zhou, Jiahao Deng, Gang Jiang, Jiguang Du
{"title":"Deep-learning interatomic potentials of the ɛ-ZrX_{2} series (X=H, D, and T).","authors":"Kunyang Cheng, Xiujuan Cheng, Mingyang Shi, Xuying Zhou, Jiahao Deng, Gang Jiang, Jiguang Du","doi":"10.1103/PhysRevE.111.055303","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.055303","url":null,"abstract":"<p><p>The ɛ-ZrH_{2} species act as an important component in zirconium-based composite hydrides, which have various applications in nuclear energy, hydrogen storage, and catalysis. In this work, deep-learning interatomic potentials for ɛ-ZrH_{2} have been developed by training density functional theory (DFT) data. The results indicate that the developed deep-learning interatomic potentials (DP) can accurately predict the structural, mechanical, and thermodynamic properties of ɛ-ZrH_{2} with DFT level accuracy. These deep-learning interatomic potentials are shown to be superior to the conventional modified embedded atom method potential. The H-isotope effect was also taken into account in constructing the deep-learning interatomic potentials, which facilitates molecular dynamic (MD) simulations under irradiation conditions. The development of these deep-learning interatomic potentials offers improved options for MD simulations of ɛ-ZrX_{2} (X=H, D, and T).</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 5-2","pages":"055303"},"PeriodicalIF":2.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Defect-free and defective adaptations of crystalline sheets to stretching deformation. 无缺陷和缺陷的晶体片适应拉伸变形。
IF 2.2 3区 物理与天体物理
Physical Review E Pub Date : 2025-05-01 DOI: 10.1103/PhysRevE.111.055504
Ranzhi Sun, Zhenwei Yao
{"title":"Defect-free and defective adaptations of crystalline sheets to stretching deformation.","authors":"Ranzhi Sun, Zhenwei Yao","doi":"10.1103/PhysRevE.111.055504","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.055504","url":null,"abstract":"<p><p>The elastic response of the crystalline sheet to the stretching deformation in the form of wrinkles has been extensively investigated. In this work, we extend this fundamental scientific question to the plastic regime by exploring the adaptations of crystalline sheets to the large uniaxial mechanical stretching. We reveal the intermittent plastic shear deformations leading to the complete fracture of the sheets wrapping the cylinder. Specifically, systematic investigations of crystalline sheets of varying geometry show that the fracture processes can be classified into defect-free and defective categories depending on the emergence of topological defects. We highlight the characteristic mechanical and geometric patterns in response to the large stretching deformation, including the shear-driven intermittent lattice tilting, the vortex structure in the displacement field, and the emergence of mobile and anchored dislocations as plastic excitations. The effects of noise and initial lattice orientation on the plastic deformation of the stretched crystalline sheet are also discussed. These results advance our understanding of the atomic level on the irreversible plastic instabilities of two-dimensional crystals under large uniaxial stretching and may have potential practical implications in the precise engineering of structural instabilities in packings of covalently bonded particulate systems.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 5-2","pages":"055504"},"PeriodicalIF":2.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Dynamic stabilization and parametric excitation of instabilities in an ablation front by a temporally modulated laser pulse. 时间调制激光脉冲消融锋面不稳定性的动态稳定和参数激励。
IF 2.2 3区 物理与天体物理
Physical Review E Pub Date : 2025-05-01 DOI: 10.1103/PhysRevE.111.055204
K G Zhao, J W Li, L F Wang, Z Y Li, Z H Di, C Xue, J Q Dong, H Zhang, J F Wu, H B Zhuo, W H Ye, C T Zhou, Y K Ding, W Y Zhang, X T He
{"title":"Dynamic stabilization and parametric excitation of instabilities in an ablation front by a temporally modulated laser pulse.","authors":"K G Zhao, J W Li, L F Wang, Z Y Li, Z H Di, C Xue, J Q Dong, H Zhang, J F Wu, H B Zhuo, W H Ye, C T Zhou, Y K Ding, W Y Zhang, X T He","doi":"10.1103/PhysRevE.111.055204","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.055204","url":null,"abstract":"<p><p>We conducted a numerical study of the effects of the modulation amplitude and period of a temporally modulated laser pulse on instabilities at an ablation front. The physical features of the oscillatory acceleration and ablation velocity in unperturbed ablative flows display periodic oscillations. As the modulation amplitude or period is increased, the asymmetry of the oscillatory acceleration and ablation velocity becomes more evident, and the peak values of these quantities increase. The numerical solution of the Mathieu equation [R. Betti et al., Phys. Rev. Lett. 71, 3131 (1993)10.1103/PhysRevLett.71.3131] with a fitted acceleration was used to evaluate the behaviors of the oscillatory acceleration. The spatial structure and interfacial evolution of a single-mode ablative Rayleigh-Taylor instability (ARTI) were analyzed for the modulated laser pulses with different modulation amplitudes and periods. It was also observed in a previous work [K. G. Zhao et al., Phys. Rev. E 109, 025213 (2024)10.1103/PhysRevE.109.025213] that the modulated laser exerts a stabilizing influence on the growth of the ARTI in the intermediate- and long-wavelength regions. We found that increasing either the modulation amplitude or period enhances the dynamic stabilization of the ARTI while simultaneously inducing a characteristic destabilization of the parametric instability, which may excite the short-wavelength perturbations through the parametric resonance [G. H. Wolf, Phys. Rev. Lett. 24, 444 (1970)10.1103/PhysRevLett.24.444].</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 5-2","pages":"055204"},"PeriodicalIF":2.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Exploring the gravity-driven failure of a cohesive granular column. 粘性颗粒柱重力驱动破坏研究。
IF 2.2 3区 物理与天体物理
Physical Review E Pub Date : 2025-05-01 DOI: 10.1103/PhysRevE.111.055401
Fanshuo Ma, Pierre-Yves Lagrée, Lydie Staron
{"title":"Exploring the gravity-driven failure of a cohesive granular column.","authors":"Fanshuo Ma, Pierre-Yves Lagrée, Lydie Staron","doi":"10.1103/PhysRevE.111.055401","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.055401","url":null,"abstract":"<p><p>Discrete two-dimensional simulations of cohesive granular collapse are carried out with a focus on the failure process. The existence of a reliable criterion to characterize the failure orientation is discussed. A criterion based on the distribution of the grains' cumulative displacement over the duration of the failure is selected. Questioning its reliability, it appears that a criterion based on grain displacement is fragile in the face of variations of system geometry and stability. Nevertheless, the measure of failure plane orientation appears fairly robust against moderate variations of the displacement criterion and against fluctuations of cohesive states close to the stability limit. This suggests that the measure of the failure orientation at the stability limit is reliable information. However, this work stresses the elusive nature of cohesive granular failure and the important role of fluctuations in granular matter in general.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 5-2","pages":"055401"},"PeriodicalIF":2.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
In-flow measurement of molecular diffusion coefficients using differential dynamic microscopy. 用差动显微镜测量分子扩散系数。
IF 2.2 3区 物理与天体物理
Physical Review E Pub Date : 2025-05-01 DOI: 10.1103/PhysRevE.111.055416
U Eberhard, M Usuelli, E Secchi, H J Seybold, M Holzner
{"title":"In-flow measurement of molecular diffusion coefficients using differential dynamic microscopy.","authors":"U Eberhard, M Usuelli, E Secchi, H J Seybold, M Holzner","doi":"10.1103/PhysRevE.111.055416","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.055416","url":null,"abstract":"<p><p>Understanding diffusive mass transport in fluid flows is fundamental in several fields, ranging from virus particles in chromatographic test kits to nutrients in ocean currents. However, experimentally resolving diffusion processes in flowing fluids is challenging due to local sample deformation caused by advective displacements under varying shear rates. Here we demonstrate that differential dynamic microscopy, combined with image velocimetry, provides a robust method to quantitatively measure molecular diffusion coefficients across a laminar flow profile within a rectangular microfluidic channel. By using subresolution tracer particles homogeneously distributed along the flow profile, we capture the effects of differing shear rates across the flow profile and measure the local diffusion coefficient by scanning through different focal planes with a microscope. While demonstrated with water, this approach can be easily adapted to more complex fluids with shear-dependent viscosity, offering broad applicability for studying diffusion in dynamic environments.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 5-2","pages":"055416"},"PeriodicalIF":2.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Layered patterns of active scalar fields in a two-dimensional magnetohydrodynamic system. 二维磁流体动力系统中活动标量场的分层模式。
IF 2.2 3区 物理与天体物理
Physical Review E Pub Date : 2025-05-01 DOI: 10.1103/PhysRevE.111.055107
F R Ramirez, P H Diamond
{"title":"Layered patterns of active scalar fields in a two-dimensional magnetohydrodynamic system.","authors":"F R Ramirez, P H Diamond","doi":"10.1103/PhysRevE.111.055107","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.055107","url":null,"abstract":"<p><p>We observe the formation of staircase patterns in the magnetic potential (A) in a weakly magnetized two-dimensional magnetohydrodynamic system driven by a forced, fluctuating vortex array. Layering occurs due to inhomogeneous mixing of A by vortex cells. Magnetic Reynolds number (R_{m})-dependent quenching of the turbulent diffusion of A by weak magnetic fields increases the disparity between the (short) cell circulation time and the (long) time for intercell transport of magnetic potential. Thus, magnetic fields strengthen transport barriers between cells and reinforce the staircase, relative to its passive scalar counterpart. The analysis reveals a feedback mechanism, which promotes staircase formation. Magnetic staircases persist in both the flux expulsion (R_{m}v_{A}^{2}/U_{0}^{2}<1) and vortex disruption (R_{m}v_{A}^{2}/U_{0}^{2}≥1) limits. In the latter case, residual vortex cells homogenize A. Global layering morphology is shown to be well characterized by staircase curvature. Stochastic forcing of magnetic potential can support magnetic staircases against resistive decay.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 5-2","pages":"055107"},"PeriodicalIF":2.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Nonmonotonic emergence of order from chaos in turbulent thermoacoustic fluid systems. 湍流热声流体系统中混沌有序的非单调出现。
IF 2.2 3区 物理与天体物理
Physical Review E Pub Date : 2025-05-01 DOI: 10.1103/PhysRevE.111.055105
Aswin Balaji, Shruti Tandon, Norbert Marwan, Jürgen Kurths, R I Sujith
{"title":"Nonmonotonic emergence of order from chaos in turbulent thermoacoustic fluid systems.","authors":"Aswin Balaji, Shruti Tandon, Norbert Marwan, Jürgen Kurths, R I Sujith","doi":"10.1103/PhysRevE.111.055105","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.055105","url":null,"abstract":"<p><p>Self-sustained order can emerge in complex systems due to internal feedback between coupled subsystems. Here, we present our discovery of a nonmonotonic emergence of order amidst chaos in a turbulent thermoacoustic fluid system. Fluctuations play a vital role in determining the dynamical state and transitions in a system. In this work, we use complex networks to encode jumps in amplitude scales owing to fluctuations as links between nodes representing amplitude bins. The number of possible amplitude transitions at a fixed timescale reflects the complexity of dynamics at that timescale. The network entropy quantifies the number of and uncertainty associated with such transitions. Using network entropy, we show that the uncertainty in fluctuations first increases and then decreases as the system transitions from chaos via intermittency to order. The competition between turbulence and nonlinear interactions leads to such nonmonotonic emergence of order amidst chaos in turbulent thermoacoustic fluid systems.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 5-2","pages":"055105"},"PeriodicalIF":2.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Numerical investigation of a recent radiation reaction model and comparison to the Landau-Lifschitz model. 最新辐射反应模型的数值研究及与Landau-Lifschitz模型的比较。
IF 2.2 3区 物理与天体物理
Physical Review E Pub Date : 2025-05-01 DOI: 10.1103/PhysRevE.111.055309
C Bild, H Ruhl, D-A Deckert
{"title":"Numerical investigation of a recent radiation reaction model and comparison to the Landau-Lifschitz model.","authors":"C Bild, H Ruhl, D-A Deckert","doi":"10.1103/PhysRevE.111.055309","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.055309","url":null,"abstract":"<p><p>In Bild, Deckert, and Ruhl [Phys. Rev. D 99, 096001 (2019)2470-001010.1103/PhysRevD.99.096001] we presented an explicit and nonperturbative derivation of the classical radiation reaction force for a cutoff modeled by a special choice of tube of finite radius around the charge trajectories. In this paper, we provide a further, simpler, and so-called reduced radiation reaction model together with a systematic numerical comparison between both the respective radiation reaction forces and the one of Landau-Lifschitz as a reference. We explicitly construct the numerical flow for the new forces and present the numerical integrator used in the simulations, a Gauss-Legendre method adapted for delay equations. As comparison, we consider the cases of a constant electric field, a constant magnetic field, and a plane wave. In all these cases, the deviations between the three force laws are shown to be small. This excellent agreement is an argument for plausibility of both new equations but also means that an experimental differentiation remains hard. Furthermore, we discuss the effect of the tube radius on the trajectories, which turns out to be small in the regarded regimes. We conclude with a comparison of the numerical cost of the three corresponding integrators and argue that, numerically, the integrator of the reduced radiation reaction seems most efficient and the integrator of Landau-Lifschitz least efficient.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 5-2","pages":"055309"},"PeriodicalIF":2.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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