Physical Review X物理评论X
Physical Review X(英文缩写 PHYS REV X),ISSN 2160-3308,eISSN 2160-3308,中文译名:物理评论X 是一本学术期刊。本页汇总该期刊的最新影响因子、分区信息以及最新收录于 PubMed 的文献,帮助您快速了解期刊全貌。
发文量统计区间：2025-11-01 至 2026-10-31，按本站收录文献的发表日期统计。
期刊介绍
历年影响因子趋势
| JCR 数据年份 | 影响因子 | JCR 分区 |
|---|---|---|
| 2021 | 14.417 | Q1 |
| 2022 | 12.500 | Q1 |
| 2023 | 11.600 | Q1 |
| 2024 | 15.700 | Q1 |
| 2025 | 16.800 | Q1 |
Physical Review X 最新收录文献
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1. Connectivity Structure and Dynamics of Nonlinear Recurrent Neural Networks.
1. 非线性循环神经网络的连接结构与动力学PMID:日期:2025-11-03Studies of the dynamics of nonlinear recurrent neural networks often assume independent and identically distributed couplings, but large-scale connectomics data indicate that biological neural circuits exhibit markedly different connectivity properties. These include rapidly decaying singular-value spectra and structured singular-vector overlaps. Here, we develop a theory to analyze how these forms of structure shape high-dimensional collective activity in nonlinear recurrent neural networks. We first introduce the random-mode model, a random-matrix ensemble related to the singular-value decomposition that enables control over the spectrum and right-left mode overlaps. Then, using a novel path-integral calculation, we derive analytical expressions that reveal how connectivity structure affects features of collective dynamics: the dimension of activity, which quantifies the number of high-variance collective-activity fluctuations, and the temporal correlations that characterize the timescales of these fluctuations. We show that connectivity structure can be invisible in single-neuron activities while dramatically shaping collective activity. Furthermore, despite the nonlinear, high-dimensional nature of these networks, the dimension of activity depends on just two connectivity parameters-the variance of the couplings and the effective rank of the coupling matrix, which quantifies the number of dominant rank-one connectivity components. We contrast the effects of single-neuron heterogeneity and low dimensional connectivity, making predictions about how z-scoring data affects the dimension of activity. Finally, we demonstrate the presence of structured overlaps between left and right modes in the connectome, incorporate them into the theory, and show how they further shape collective dynamics.
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2. Topology and Nuclear Size Determine Cell Packing on Growing Lung Spheroids.
PMID:日期:2025-03-21Within multicellular living systems, cells coordinate their positions with spatiotemporal accuracy to form various tissue structures and control development. These arrangements can be regulated by tissue geometry, biochemical cues, as well as mechanical perturbations. However, how cells pack during dynamic three-dimensional multicellular architectures formation remains unclear. Here, examining a growing spherical multicellular system, human lung alveolospheres, we observe an emergence of hexagonal packing order and a structural transition of cells that comprise the spherical epithelium. Surprisingly, the cell packing behavior on the spherical surface of lung alveolospheres resembles hard-disks packing on spheres, where the less deformable cell nuclei act as effective "hard disks" and prevent cells from getting too close. Nucleus-to-cell size ratio increases during lung spheroids growth; as a result, we find more hexagon-concentrated cellular packing with increasing bond orientational order. Furthermore, by osmotically changing the compactness of cells on alveolospheres, we observe a more ordered packing when nucleus-to-cell size ratio increases, and vice versa. These more ordered cell packing characteristics are consistent with reduced cell dynamics, together suggesting that better cellular packing stabilizes local cell neighborhoods and may regulate more complex biological functions such as cellular maturation and tissue morphogenesis.
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3. Spontaneous Brain Activity Emerges from Pairwise Interactions in the Larval Zebrafish Brain.
PMID:日期:2024-09-23Brain activity is characterized by brainwide spatiotemporal patterns that emerge from synapse-mediated interactions between individual neurons. Calcium imaging provides access to recordings of whole-brain activity at single-neuron resolution and, therefore, allows the study of how large-scale brain dynamics emerge from local activity. In this study, we use a statistical mechanics approach-the pairwise maximum entropy model-to infer microscopic network features from collective patterns of activity in the larval zebrafish brain and relate these features to the emergence of observed whole-brain dynamics. Our findings indicate that the pairwise interactions between neural populations and their intrinsic activity states are sufficient to explain observed whole-brain dynamics. In fact, the pairwise relationships between neuronal populations estimated with the maximum entropy model strongly correspond to observed structural connectivity patterns. Model simulations also demonstrated how tuning pairwise neuronal interactions drives transitions between observed physiological regimes and pathologically hyperexcitable whole-brain regimes. Finally, we use virtual resection to identify the brain structures that are important for maintaining the brain in a physiological dynamic regime. Together, our results indicate that whole-brain activity emerges from a complex dynamical system that transitions between basins of attraction whose strength and topology depend on the connectivity between brain areas.
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4. Electric Field of DNA in Solution: Who Is in Charge?
4. 溶液中DNA的电场：谁在掌控？PMID:日期:2024-09-05In solution, DNA, the "most important molecule of life," is a highly charged macromolecule that bears a unit of negative charge on each phosphate of its sugar-phosphate backbone. Although partially compensated by counterions (cations of the solution) adsorbed at or condensed near it, DNA still produces a substantial electric field in its vicinity, which is screened by buffer electrolytes at longer distances from the DNA. This electric field is experienced by any charged or dipolar species approaching and interacting with the DNA. So far, such a field has been explored predominantly within the scope of a primitive model of the electrolytic solution, not considering more complicated structural effects of the water solvent. In this paper, we investigate the distribution of electric field around DNA using linear response nonlocal electrostatic theory, applied here for helix-specific charge distributions, and compare the predictions of such a theory with specially performed, fully atomistic, large-scale, molecular dynamics simulations. Both approaches are applied to unravel the role of the structure of water at close distances to and within the grooves of a DNA molecule in the formation of the electric field. As predicted by the theory and reported by the simulations, the main finding of this study is that oscillations in the electrostatic potential distribution are present around DNA, caused by the overscreening effect of structured water. Surprisingly, electrolyte ions at physiological concentrations do not strongly disrupt these oscillations and are rather distributed according to these oscillating patterns, indicating that water structural effects dominate the short-range electrostatics. We also show that (i) structured water adsorbed in the grooves of DNA leads to a positive electrostatic potential core relative to the bulk, (ii) the Debye length some 10 Å away from the DNA surface is reduced, effectively renormalized by the helical pitch of the DNA molecule, and (iii) Lorentzian contributions to the nonlocal dielectric function of water, effectively reducing the dielectric constant close to the DNA surface, enhance the overall electric field. The impressive agreement between the atomistic simulations and the developed theory substantiates the use of nonlocal electrostatics when considering solvent effects in molecular processes in biology.
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5. Discontinuous Shear Thickening in Biological Tissue Rheology.
5. 生物组织流变学中的不连续剪切增稠PMID:日期:2024-02-22During embryonic morphogenesis, tissues undergo dramatic deformations in order to form functional organs. Similarly, in adult animals, living cells and tissues are continually subjected to forces and deformations. Therefore, the success of embryonic development and the proper maintenance of physiological functions rely on the ability of cells to withstand mechanical stresses as well as their ability to flow in a collective manner. During these events, mechanical perturbations can originate from active processes at the single-cell level, competing with external stresses exerted by surrounding tissues and organs. However, the study of tissue mechanics has been somewhat limited to either the response to external forces or to intrinsic ones. In this work, we use an active vertex model of a 2D confluent tissue to study the interplay of external deformations that are applied globally to a tissue with internal active stresses that arise locally at the cellular level due to cell motility. We elucidate, in particular, the way in which this interplay between globally external and locally internal active driving determines the emergent mechanical properties of the tissue as a whole. For a tissue in the vicinity of a solid-fluid jamming or unjamming transition, we uncover a host of fascinating rheological phenomena, including yielding, shear thinning, continuous shear thickening, and discontinuous shear thickening. These model predictions provide a framework for understanding the recently observed nonlinear rheological behaviors .
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6. Exact Analysis of the Subthreshold Variability for Conductance-Based Neuronal Models with Synchronous Synaptic Inputs.
6. 具有同步突触输入的基于电导的神经元模型亚阈值变异性的精确分析PMID:日期:2024-02-16The spiking activity of neocortical neurons exhibits a striking level of variability, even when these networks are driven by identical stimuli. The approximately Poisson firing of neurons has led to the hypothesis that these neural networks operate in the asynchronous state. In the asynchronous state, neurons fire independently from one another, so that the probability that a neuron experience synchronous synaptic inputs is exceedingly low. While the models of asynchronous neurons lead to observed spiking variability, it is not clear whether the asynchronous state can also account for the level of subthreshold membrane potential variability. We propose a new analytical framework to rigorously quantify the subthreshold variability of a single conductance-based neuron in response to synaptic inputs with prescribed degrees of synchrony. Technically, we leverage the theory of exchangeability to model input synchrony via jump-process-based synaptic drives; we then perform a moment analysis of the stationary response of a neuronal model with all-or-none conductances that neglects postspiking reset. As a result, we produce exact, interpretable closed forms for the first two stationary moments of the membrane voltage, with explicit dependence on the input synaptic numbers, strengths, and synchrony. For biophysically relevant parameters, we find that the asynchronous regime yields realistic subthreshold variability (voltage variance ≃4-9 mV) only when driven by a restricted number of large synapses, compatible with strong thalamic drive. By contrast, we find that achieving realistic subthreshold variability with dense cortico-cortical inputs requires including weak but nonzero input synchrony, consistent with measured pairwise spiking correlations. We also show that, without synchrony, the neural variability averages out to zero for all scaling limits with vanishing synaptic weights, independent of any balanced state hypothesis. This result challenges the theoretical basis for mean-field theories of the asynchronous state.
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7. Morphological Entanglement in Living Systems.
7. 生命系统中的形态纠缠PMID:日期:2024-01-25Many organisms exhibit branching morphologies that twist around each other and become entangled. Entanglement occurs when different objects interlock with each other, creating complex and often irreversible configurations. This physical phenomenon is well studied in nonliving materials, such as granular matter, polymers, and wires, where it has been shown that entanglement is highly sensitive to the geometry of the component parts. However, entanglement is not yet well understood in living systems, despite its presence in many organisms. In fact, recent work has shown that entanglement can evolve rapidly and play a crucial role in the evolution of tough, macroscopic multicellular groups. Here, through a combination of experiments, simulations, and numerical analyses, we show that growth generically facilitates entanglement for a broad range of geometries. We find that experimentally grown entangled branches can be difficult or even impossible to disassemble through translation and rotation of rigid components, suggesting that there are many configurations of branches that growth can access that agitation cannot. We use simulations to show that branching trees readily grow into entangled configurations. In contrast to nongrowing entangled materials, these trees entangle for a broad range of branch geometries. We, thus, propose that entanglement via growth is largely insensitive to the geometry of branched trees but, instead, depends sensitively on timescales, ultimately achieving an entangled state once sufficient growth has occurred. We test this hypothesis in experiments with snowflake yeast, a model system of undifferentiated, branched multicellularity, showing that lengthening the time of growth leads to entanglement and that entanglement via growth can occur for a wide range of geometries. Taken together, our work demonstrates that entanglement is more readily achieved in living systems than in their nonliving counterparts, providing a widely accessible and powerful mechanism for the evolution of novel biological material properties.
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8. Crumpled polymer with loops recapitulates key features of chromosome organization.
8. 带有环的皱褶聚合物重现了染色体组织的关键特征PMID:日期:2023-11-13Chromosomes are exceedingly long topologically-constrained polymers compacted in a cell nucleus. We recently suggested that chromosomes are organized into loops by an active process of loop extrusion. Yet loops remain elusive to direct observations in living cells; detection and characterization of myriads of such loops is a major challenge. The lack of a tractable physical model of a polymer folded into loops limits our ability to interpret experimental data and detect loops. Here, we introduce a new physical model - a polymer folded into a sequence of loops, and solve it analytically. Our model and a simple geometrical argument show how loops affect statistics of contacts in a polymer across different scales, explaining universally observed shapes of the contact probability. Moreover, we reveal that folding into loops reduces the density of topological entanglements, a novel phenomenon we refer as "the dilution of entanglements". Supported by simulations this finding suggests that up to ~ 1 - 2Mb chromosomes with loops are not topologically constrained, yet become crumpled at larger scales. Our theoretical framework allows inference of loop characteristics, draws a new picture of chromosome organization, and shows how folding into loops affects topological properties of crumpled polymers.
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9. Quantitatively Visualizing Bipartite Datasets.
9. 定量可视化二分数据集PMID:日期:2023-04-04As experiments continue to increase in size and scope, a fundamental challenge of subsequent analyses is to recast the wealth of information into an intuitive and readily interpretable form. Often, each measurement conveys only the relationship between a pair of entries, and it is difficult to integrate these local interactions across a dataset to form a cohesive global picture. The classic localization problem tackles this question, transforming local measurements into a global map that reveals the underlying structure of a system. Here, we examine the more challenging bipartite localization problem, where pairwise distances are available only for bipartite data comprising two classes of entries (such as antibody-virus interactions, drug-cell potency, or user-rating profiles). We modify previous algorithms to solve bipartite localization and examine how each method behaves in the presence of noise, outliers, and partially observed data. As a proof of concept, we apply these algorithms to antibody-virus neutralization measurements to create a basis set of antibody behaviors, formalize how potently inhibiting some viruses necessitates weakly inhibiting other viruses, and quantify how often combinations of antibodies exhibit degenerate behavior.
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10. Tie-Line Analysis Reveals Interactions Driving Heteromolecular Condensate Formation.
10. 系链线分析揭示驱动异分子凝聚体形成的相互作用PMID:日期:2022-12-30Phase separation of biomolecules gives rise to membraneless organelles that contribute to the spatiotemporal organization of the cell. In most cases, such biomolecular condensates contain multiple components, but the manner in which interactions between components control the stability of condensates have remained challenging to elucidate. Here, we develop an approach to determine tie-line gradients in ternary biomolecular phase-separation systems based on measurements of the dilute phase concentration of only one component. We show that the sign of the tie-line gradient is related to the cross-interaction energy between the polymers in the system and discriminates between associative and segregative phase separation. Using this approach, we study the interaction between protein fused in sarcoma (FUS) and polyethylene glycol (PEG) polymer chains and measure positive tie-line gradients. Our results show that PEG drives phase separation through an associative interaction with FUS, other than through acting as an inert crowder. We further study the interaction between poly(A) ribonucleic acid (RNA) (3.0 ± 0.5 kDa [kilodalton]) and the protein G3BP1, and using the tie-line gradient as a reporter for the stoichiometry of polymers in the condensate, we determine a G3BP1-to-poly(A) RNA molar ratio of 1 : 4 in the dense phase. Our framework for measuring tie-line gradients opens up a route for the characterization of interaction types and compositions in ternary phase-separation systems.