Physical Review E最新文献

{"title":"Minimal framework for optimizing vaccination protocols targeting highly mutable pathogens.","authors":"Saeed Mahdisoltani, Pranav Murugan, Arup K Chakraborty, Mehran Kardar","doi":"10.1103/PhysRevE.110.064137","DOIUrl":"10.1103/PhysRevE.110.064137","url":null,"abstract":"<p><p>A persistent public health challenge is identifying immunization schemes that are effective against highly mutable pathogens such as HIV and influenza viruses. To address this, we analyze a simplified model of affinity maturation, the Darwinian evolutionary process B cells undergo during immunization. The vaccination protocol determines the selection forces that steer affinity maturation to generate antibodies. We focus on identifying the optimal selection forces exerted by a generic time-dependent vaccination protocol to maximize the production of broadly neutralizing antibodies (bnAbs) that can protect against a broad spectrum of pathogen strains. The model utilizes a path integral representation and operator approximations within a mean-field limit and provides guiding principles for optimizing time-dependent vaccine-induced selection forces to enhance bnAb generation. We compare our analytical mean-field results with the outcomes of stochastic simulations, and we discuss their similarities and differences.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"110 6-1","pages":"064137"},"PeriodicalIF":2.2,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143366362","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}

{"title":"Nonuniversality for crossword puzzle percolation.","authors":"Alexander K Hartmann","doi":"10.1103/PhysRevE.110.064138","DOIUrl":"https://doi.org/10.1103/PhysRevE.110.064138","url":null,"abstract":"<p><p>A percolation model inspired by crossword puzzle games is introduced. A game proceeds by solving words, which are segments of sites in a two-dimensional lattice. As a test case, the iid variant allows for independently occupying sites with letters, only the percolation criterion depends on the existence of solved words. For the game variant, inspired by real crossword puzzles, it becomes more likely to solve crossing words which share sites with the already solved words. In this way avalanches of solved words may occur. Both model variants exhibit a percolation transition as a function of the a priori site or word solving probability, respectively. The iid variant is in the universality class of standard two-dimensional percolation. The game variant exhibits a nonuniversal critical exponent ν of the correlation length. The actual value of ν depends on the function which controls how much solved words accelerate the solution of crossing words.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"110 6-1","pages":"064138"},"PeriodicalIF":2.2,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143366456","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}

{"title":"Contraction and synchronization in reservoir systems.","authors":"Adrian S Wong, Robert S Martin, Daniel Q Eckhardt","doi":"10.1103/PhysRevE.110.064219","DOIUrl":"https://doi.org/10.1103/PhysRevE.110.064219","url":null,"abstract":"<p><p>This paper explores the conditions under which global contraction manifests in the leaky continuous time reservoirs, thus guaranteeing generalized synchronization. Results on continuous time reservoirs make use of the logarithmic norm of the connectivity matrix. Further analysis yields some simple guidelines on how to better construct the connectivity matrix in these systems. Additionally, we outline how the universal approximation property of discrete time reservoirs is readily satisfied by virtue of the activation function being contracting, and how continuous time reservoirs may inherit a limited form of universal approximation by virtue of them overlapping with neural ordinary differential equations. The ability of the reservoir computing framework to universally approximate topological conjugates, along with their fast training, make them a compelling data-driven, black-box surrogate of dynamical systems and a potential candidate for a component of digital twins.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"110 6-1","pages":"064219"},"PeriodicalIF":2.2,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143366484","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}

{"title":"Random walks on bifractal networks.","authors":"Kousuke Yakubo, Gentaro Shimojo, Jun Yamamoto","doi":"10.1103/PhysRevE.110.064318","DOIUrl":"https://doi.org/10.1103/PhysRevE.110.064318","url":null,"abstract":"<p><p>It has recently been shown that networks possessing scale-free and fractal properties may exhibit a bifractal nature, in which local structures are described by two different fractal dimensions. In this study, we investigate random walks on such fractal scale-free networks (FSFNs) by examining the walk dimension d_{w} and the spectral dimension d_{s}, to understand how the bifractality affects their dynamical properties. The walk dimension is found to be unaffected by the difference in local fractality of an FSFN and remains constant regardless of the starting node of a random walk, whereas the spectral dimension takes two values, d_{s}^{min} and d_{s}^{max}(>d_{s}^{min}), depending on the starting node. The dimension d_{s}^{min} characterizes the return probability of a random walker starting from an infinite-degree hub node in the thermodynamic limit, while d_{s}^{max} describes that of a random walker starting from a finite-degree non-hub node infinitely distant from hub nodes and is equal to the global spectral dimension D_{s}. The existence of two local spectral dimensions is a direct consequence of the bifractality of the FSFN. Furthermore, analytical expressions of d_{w}, d_{s}^{min}, and d_{s}^{max} are presented for FSFNs formed by the generator model and the giant components of critical scale-free random graphs, and are numerically confirmed.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"110 6-1","pages":"064318"},"PeriodicalIF":2.2,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143366495","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}

{"title":"Reliability of correlation-length measurements: A comparative study.","authors":"Aleksandr V Kukharskii, Sergey G Abaimov","doi":"10.1103/PhysRevE.110.064143","DOIUrl":"https://doi.org/10.1103/PhysRevE.110.064143","url":null,"abstract":"<p><p>Reliability and accuracy of lateral correlation length measurements are studied and quantified from the analysis of synthetic correlated profiles. First, we review available methods to characterize self-affine profiles; we discuss the autocorrelation, Hurst, interface width, and maximum difference functions as widely applicable. We demonstrate that the functions are essentially related and give comparable predictions of the scaling behavior. Second, we consider definitions of correlation length employed in practice. Roughly, they might be cast into two groups, selecting by whether they do not require or require fitting. Approaches from the first group are straightforward and easy to implement; however, they may over- or underestimate the value of correlation length on a small data set due to a size effect. Approaches from the second group may smooth possible oscillations; nevertheless, their precision highly depends on the fit quality. We demonstrate that correlation length found with different approaches might be easily rescaled one onto another. In addition, we introduce a parameter which is further used to estimate accuracy of measurements. Third, we estimate accuracy of all functions and methods on synthetic correlated profiles. We demonstrate influence of the size effect on statistical functions. We show that different methods have different accuracy and different convergence rate to the true value. Fourth, we estimate a parameter saying how much profile length should be larger than the measured value of correlation length in order to get the desirable accuracy of measurements. Finally, we conclude our paper with the recommendation to define correlation length as an abscissa of the e^{-1} point of the autocorrelation function, and note that the accuracy of 10% is achieved if 100 studied profiles are at least 50 times larger than the measured value of correlation length.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"110 6-1","pages":"064143"},"PeriodicalIF":2.2,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143366517","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}

{"title":"Direct manipulation of diffusion in colloidal glasses via controlled generation of quasi-particle-like defects.","authors":"Yi-Di Wang, Chu Xiao, Anupam Kumar, Yun-Hong Shi, Chun-Shing Lee, King-Cheong Lam, Man-Kin Fung, Chor-Hoi Chan, Yuen-Hong Tsang, Bo Li, Chi-Hang Lam, Cho-Tung Yip","doi":"10.1103/PhysRevE.110.064603","DOIUrl":"https://doi.org/10.1103/PhysRevE.110.064603","url":null,"abstract":"<p><p>We experimentally manipulate the structural relaxation of colloidal glass at an atomistically controlled position. We focus a laser beam to eject a particle from the colloidal system. This creates a void that transforms rapidly into a mobile soft spot (quasivoid) composed of a few neighboring free-volume fragments. The transformation and subsequent motions of the quasivoid trigger a sequence of well-connected stringlike motions emanating precisely from the point of laser action with free volumes flowing along the string. Furthermore, the sequence can be terminated by the annihilation of the quasivoid. The observations are supported by molecular dynamics (MD) simulations.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"110 6-1","pages":"064603"},"PeriodicalIF":2.2,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143366521","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}

{"title":"Impact of electron trapping on stimulated Raman scattering under incoherent broadband laser light in homogeneous plasma.","authors":"David R Blackman, Vladimir Tikhonchuk, Ondrej Klimo, Stefan Weber","doi":"10.1103/PhysRevE.110.065207","DOIUrl":"https://doi.org/10.1103/PhysRevE.110.065207","url":null,"abstract":"<p><p>Backward stimulated Raman scattering is a three-wave coupling instability requiring the matching of an incoming pump light wave to a scattered light wave and an electron plasma wave. It can be harmful to laser-driven inertial confinement fusion because of the reflection of a part of the incident laser flux and the generation of suprathermal electrons that preheat the fuel. It is believed that by increasing the laser bandwidth, one can suppress the excitation of Raman scattering and mitigate its detrimental effects. It is demonstrated in this paper that using a broad bandwidth laser has little effect on stimulated Raman scattering in the kinetic inflation regime where Landau damping dominates, as the additional bandwidth allows the electron plasma wave to match a wider range of laser frequencies. As a result, plasma wave saturation and Raman backscattering levels remain high even when the laser bandwidth is much larger than the effective instability growth rate.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"110 6-2","pages":"065207"},"PeriodicalIF":2.2,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143366577","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}

{"title":"Mitigation of stimulated Brillouin scattering in inhomogeneous plasmas by broadband lasers.","authors":"Yao Zhao, Anle Lei, Ning Kang, Fujian Li, Xiaofeng Li, Huiya Liu, Zhuwen Lin, Hongwei Yin, Yilin Xu, Yaozhi Yi, Zhengxi Xu","doi":"10.1103/PhysRevE.110.065206","DOIUrl":"https://doi.org/10.1103/PhysRevE.110.065206","url":null,"abstract":"<p><p>A theoretical model of stimulated Brillouin scattering (SBS) developed by a broadband laser in inhomogeneous plasmas is proposed and further investigated through a series of numerical simulations using the low-coherence laser model of the Kunwu facility. Polychromatic beamlets are coupled to develop a scattering mode, when all the poles of the beamlets are on the integration path of SBS dispersion relations. The coupled beamlets can be regarded as a monochromatic beam with the same incident energy, owing to their nearly identical amplification coefficients. Therefore, a broadband laser behaves as several decoupled beams with a frequency difference around the coupling threshold of the beamlets. In the direct-drive scheme, the overall saturation level of scattering light can be reduced by the broadband laser, if the bandwidth is larger than c_{s}/c∼10^{-3}, where c_{s} and c are the velocities of ion acoustic wave and light, respectively. Two-dimensional simulations demonstrate the robust mitigation of SBS by the low-coherence laser with a moderate bandwidth ∼0.6%, even in the ignition regime. The laser plasma parameters have a minor impact on the mitigation of SBS with broadband lasers. The speckle structures vary rapidly over time at the focal plane due to the introduction of the broadband, which results in the further reduction of SBS and filamentation compared with the monochromatic laser.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"110 6-2","pages":"065206"},"PeriodicalIF":2.2,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143366586","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}

{"title":"Producing entangled photon pairs and quantum squeezed states in plasmas.","authors":"Kenan Qu, Nathaniel J Fisch","doi":"10.1103/PhysRevE.110.065211","DOIUrl":"https://doi.org/10.1103/PhysRevE.110.065211","url":null,"abstract":"<p><p>Plasma is capable of mediating the conversion of two pump photons into two different photons through a relativistic four-wave mixing nonlinearity. Spontaneously created photon pairs are emitted at symmetric angles with respect to the colinear pump direction, and the emission rate is largest if they have identical frequency. Thus, two orthogonally polarized pumps can produce polarization-entangled photon pairs through a millimeter-long homogeneous plasma. The noise from Raman scattering can be avoided if the pump detuning differs from twice the plasma frequency. However, pump detuning exactly equal to twice the plasma frequency can significantly enhance the interaction rate, which allows for the production of strong two-mode squeezed states. Remarkably, the amplified noise from Raman scattering are correlated and hence can be suppressed in one of the output quadratures, thereby maintaining the squeezing magnitude.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"110 6-2","pages":"065211"},"PeriodicalIF":2.2,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143366600","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}

{"title":"Rare, noise-induced, bypass transition in plane Couette flow can bypass instantons.","authors":"Joran Rolland","doi":"10.1103/PhysRevE.110.065106","DOIUrl":"https://doi.org/10.1103/PhysRevE.110.065106","url":null,"abstract":"<p><p>This paper presents a study of rare noise-induced transitions from stable laminar flow to transitional turbulence in plane Couette flow, which we will term buildup. We wish to study forced paths that go all the way from laminar to turbulent flow and to focus the investigation on whether these paths share the properties of noise-induced transitions in simpler systems. The forcing noise has a red spectrum without any component in the natural, large-scale, linear receptivity range of the flow. As we decreased the forcing energy injection rate, the transitions became rare. The rare paths from laminar to turbulent flow are computed using adaptive multilevel splitting, a rare event simulation method, and are validated against direct numerical simulations at moderately small energy injection rates. On the computed trajectories, the flow manages to nonlinearly redistribute energy from the small forced scales to the unforced large scales so that the reactive trajectories display forced streamwise velocity tubes at the natural scale of velocity streaks. As the trajectory proceeds, these tubes gradually grow in amplitude until they cross the separatrix between laminar and turbulent flow. Streamwise vortices manifest themselves only after velocity tubes have reached near-turbulent amplitude, displaying a two-stage process reminiscent of the \"backward\" path from turbulence to laminar flow. We checked that these were not time-reversed turbulence collapse paths. As the domain size is increased from a minimal flow unit (MFU) type flow at L_{x}×L_{z}=6×4 (in half gap units) to a large domain L_{x}×L_{z}=36×24, spatial localization and then extension of the generated coherent streaks and vortices in the spanwise direction is observed in the reactive paths. The paths systematically computed in MFU display many of the characteristics of instantons that often structure noise-induced transitions: such as concentration of trajectories, exponentially increasing waiting times before transition, and Gumbel distribution of trajectory durations. However, bisections started from successive states on the reactive trajectories indicate that for all sizes and energy injection rates investigated, the trajectory lacks two key ingredients of instantons. First, they do not visit the neighborhood of the nearest saddle point and do not display the natural relaxation path from that saddle to transitional wall turbulence. This discrepancy is observed for all system sizes. Second, the reactive paths do not concentrate more and more around the same trajectory as energy injection rate is decreased, but instead gradually move in phase space. They might reconnect with instantons at very small energy injection rate and exceedingly long waiting times. They would explain why classical instanton calculations have proved to be tremendously difficult in wall flows.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"110 6-2","pages":"065106"},"PeriodicalIF":2.2,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143366616","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}