软凝聚态物理
查看 最近的 文章
显示 2025年10月03日， 星期五 新的列表
- [1] arXiv:2510.01420 [中文pdf, pdf, html, 其他]
-
标题： 经典成核理论对晶体成核基底化学异质性的鲁棒性标题： Robustness of classical nucleation theory to chemical heterogeneity of crystal nucleating substrates评论： 12页，13图，6表主题： 软凝聚态物理 (cond-mat.soft) ; 材料科学 (cond-mat.mtrl-sci) ; 统计力学 (cond-mat.stat-mech)
异质成核是一个过程，其中外来杂质通过降低成核能垒促进冻结，并在大多数系统中构成结晶的主要机制。经典成核理论（\textsc{计数}）在预测异质成核的动力学方面取得了显著的成功，即使在化学和拓扑结构不均匀的表面上也是如此，尽管它依赖于几个限制性假设，例如晶体核的理想球冠几何形状。在这里，我们采用分子动力学模拟和跳跃正向通量采样来研究模型原子液体中异质晶体成核的动力学和机制。我们考察了化学均匀、弱吸引力的液相亲和表面以及由交替的液相亲和和液相疏离区域组成的棋盘状表面。我们发现，在两种系统中，成核速率都保持了由\textsc{计数}预测的典型温度依赖性。此外，晶体核的接触角对核的大小和温度表现出可忽略的依赖性。在棋盘状表面上，核通过在区域边界钉扎并垂直生长到体相中，保持固定的接触角。这些发现为\textsc{计数}在实验场景中的鲁棒性提供了见解，其中成核表面通常包含被惰性或液相疏离区域包围的活性热点。
Heterogeneous nucleation is a process wherein extrinsic impurities facilitate freezing by lowering nucleation barriers and constitutes the dominant mechanism for crystallization in most systems. Classical nucleation theory (\textsc{Cnt}) has been remarkably successful in predicting the kinetics of heterogeneous nucleation, even on chemically and topographically non-uniform surfaces, despite its reliance on several restrictive assumptions, such as the idealized spherical-cap geometry of the crystalline nuclei. Here, we employ molecular dynamics simulations and jumpy forward flux sampling to investigate the kinetics and mechanism of heterogeneous crystal nucleation in a model atomic liquid. We examine both a chemically uniform, weakly attractive liquiphilic surface and a checkerboard surface comprised of alternating liquiphilic and liquiphobic patches. We find the nucleation rate to retain its canonical temperature dependence predicted by \textsc{Cnt} in both systems. Moreover, the contact angles of crystalline nuclei exhibit negligible dependence on nucleus size and temperature. On the checkerboard surface, nuclei maintain a fixed contact angle through pinning at patch boundaries and vertical growth into the bulk. These findings offer insights into the robustness of \textsc{Cnt} in experimental scenarios, where nucleating surfaces often feature active hotspots surrounded by inert or liquiphobic domains.
- [2] arXiv:2510.01506 [中文pdf, pdf, html, 其他]
-
标题： 折痕作为弹性毛细管门用于自主液滴控制标题： Creases as elastocapillary gates for autonomous droplet control评论： 11页，6图主题： 软凝聚态物理 (cond-mat.soft) ; 流体动力学 (physics.flu-dyn)
液滴是微流控技术中的核心功能单元，这些技术旨在在一个平台上集成计算和反应。 实现这些液滴的定向传输和控制通常需要复杂的基底图案化、外部场的调制以及实时反馈。 在这里，我们揭示了在软界面设计的褶皱图案可以自主地门控和引导液滴，通过远距离弹性毛细排斥作用，允许信息的可编程流动。 作为能量障碍，褶皱阻挡了小于临界尺寸的液滴，而无需接触。 我们揭示了描述液滴与单个褶皱之间相互作用的多尺度排斥力-距离定律。 利用这一机制，我们展示了基于液滴尺寸和表面张力的被动和主动过滤，并实现了路径引导、可调滞后器、脉冲调制器以及加法器等基本逻辑操作等功能。 因此，这种基于褶皱的门控方法展示了复杂的单元内处理能力——通常只能通过复杂的表面和流体修饰才能实现——为界面组装和生物化学检测中的液滴控制提供了一种多模式、潜在可重写的策略。
Droplets are the core functional units in microfluidic technologies that aim to integrate computation and reaction on a single platform. Achieving directed transport and control of these droplets typically demands elaborate substrate patterning, modulation of external fields, and real-time feedback. Here we reveal that an engineered pattern of creases on a soft interface autonomously gate and steer droplets through a long-range elastocapillary repulsion, allowing programmable flow of information. Acting as an energy barrier, the crease bars incoming droplets below a critical size, without making contact. We uncover the multi-scale, repulsive force-distance law describing interactions between a drop and a singular crease. Leveraging this mechanism, we demonstrate passive and active filtration based on droplet size and surface tension, and implement functionalities such as path guidance, tunable hysterons, pulse modulators, and elementary logic operations like adders. This crease-based gating approach thus demonstrates complex in-unit processing capabilities - typically accessible only through sophisticated surface and fluidic modifications - offering a multimodal, potentially rewritable strategy for droplet control in interfacial assembly and biochemical assays.
- [3] arXiv:2510.01713 [中文pdf, pdf, html, 其他]
-
标题： 边界程序变形在孤立主动网络中标题： Boundaries Program Deformation in Isolated Active NetworksZixiang Lin, Shichen Liu, Shahriar Shadkhoo, Jialong Jiang, Heun Jin Lee, David Larios, Chunhe Li, Hongyi Bian, Anqi Li, Rob Phillips, Matt Thomson, Zijie Qu评论： arXiv管理员注释：与arXiv:2101.08464有大量文本重叠主题： 软凝聚态物理 (cond-mat.soft)
细胞结构必须在严格的物理约束内自我组织，使用有限的资源和明确的边界运作。 经典系统对边界的响应仅是被动的，从肥皂膜中的表面能最小化到弹性网络中的应变分布。 活性物质从根本上改变了这一范式——内部产生的应力在边界几何形状和质量守恒之间建立了双向耦合，从而实现了对网络组织的动态控制。 在这里，我们展示了边界几何形状在重建的微管-驱动蛋白系统中主动引导网络变形，通过受控的边界操作揭示了一种可编程的形状变换区域。 一个粗粒度的理论框架揭示了边界几何如何通过质量守恒与内部应力场耦合，产生不同的动力学模式，从而实现工程变形。 理论预测并经实验验证的形状保持和形状变化区域的出现，确立了边界几何作为活性材料的基本控制参数。 基于边界的控制原理不仅加深了对生物组织的理解，还实现了具有可编程变形的合成活性物质器件的设计。
Cellular structures must organize themselves within strict physical constraints, operating with finite resources and well-defined boundaries. Classical systems demonstrate only passive responses to boundaries, from surface energy minimization in soap films to strain distributions in elastic networks. Active matter fundamentally alters this paradigm - internally generated stresses create a bidirectional coupling between boundary geometry and mass conservation that enables dynamic control over network organization. Here we demonstrate boundary geometry actively directs network deformation in reconstituted microtubule-kinesin systems, revealing a programmable regime of shape transformation through controlled boundary manipulation. A coarse-grained theoretical framework reveals how boundary geometry couples to internal stress fields via mass conservation, producing distinct dynamical modes that enable engineered deformations. The emergence of shape-preserving and shape-changing regimes, predicted by theory and confirmed through experiments, establishes boundary geometry as a fundamental control parameter for active materials. The control principle based on boundaries advances both the understanding of biological organization and enables design of synthetic active matter devices with programmable deformation.
- [4] arXiv:2510.01847 [中文pdf, pdf, html, 其他]
-
标题： 非高斯旋转扩散和双球探针在二维胶体中的摆动运动标题： Non-Gaussian Rotational Diffusion and Swing Motion of Dumbbell Probes in Two Dimensional Colloids评论： 12页，8图主题： 软凝聚态物理 (cond-mat.soft) ; 化学物理 (physics.chem-ph)
二维（2D）胶体表现出与三维不同的有趣相行为，以及类似于玻璃形成液体的动力学异质性。 在这里，我们使用不连续分子动力学模拟，研究了双胶体哑铃探针在液态-六方晶相转变中的报告动力学，其中六边形键取向序（HBOO）扩展到准长程。 哑铃探针的旋转动力学忠实捕捉了宿主的结构和动力学特征：在各向同性液体中为布朗运动，在六方晶相和固相中为非高斯行为，反映了介质的HBOO和动力学异质性。 在二维六方晶相和固相中，探针旋转反映了异质性，因为哑铃探针采样了宿主系统的多个动力学域：在移动域中，它们根据HBOO发生$\pi/3$旋转跳跃，而在不动域中，它们在周围圆盘形成的笼子内摆动。 当由尺寸多分散性驱动的宿主介质重新熔化时，这种非高斯性消失，突显了HBOO与探针动力学之间的紧密联系。 此外，探针动力学揭示了单个粒子层面的耦合和系综平均层面的解耦：摆动运动成为其主要扩散模式，而无论如何定义旋转扩散系数，德拜-斯托克斯-爱因斯坦关系都会失效。
Two dimensional (2D) colloids exhibit intriguing phase behaviors distinct from those in three dimensions, as well as dynamic heterogeneity reminiscent of glass-forming liquids. Here, using discontinuous molecular dynamics simulations, we investigate the reporting dynamics of dicolloidal dumbbell probes in 2D colloids across the liquid-hexatic phase transition, where hexagonal bond-orientational order (HBOO) extends to quasi-long-ranged one. The rotational dynamics of dumbbell probes faithfully capture the structural and dynamical features of the host: Brownian in the isotropic liquid, and non-Gaussian in the hexatic and solid phases, reflecting both HBOO and dynamic heterogeneity of the medium. In the 2D hexatic and solid phases, probe rotation reflects heterogeneity as the dumbbells sample multiple dynamical domains of the host system: in mobile domains, they undergo rotational jumps of $\pi/3$ in accordance with HBOO, whereas in immobile domains they librate within cages formed by surrounding discs. Such non-Gaussianity disappears upon reentrant melting of the host medium driven by size polydispersity, highlighting a close connection between HBOO and probe dynamics. Furthermore, probe dynamics reveal both coupling (at a single particle level) and decoupling (at an ensemble-averaged level) between translation and rotation: swing motion emerges as their primary diffusion mode, while the Debye-Stokes-Einstein relation breaks down regardless of how the rotational diffusion coefficient is defined.
- [5] arXiv:2510.02135 [中文pdf, pdf, html, 其他]
-
标题： libMobility：用于Smoluchowski水平流体力学的Python库标题： libMobility: A Python library for hydrodynamics at the Smoluchowski levelRyker Fish, Adam Carter, Pablo Diez-Silva, Rafael Delgado-Buscalioni, Raul P. Pelaez, Brennan Sprinkle评论： 42页，7图主题： 软凝聚态物理 (cond-mat.soft)
有效水动力模型对于准确预测生物物理学和材料科学等不同领域中的流体-粒子相互作用至关重要。 由于流体力学的复杂性，开发和实现水动力算法具有挑战性，需要对大规模计算和复杂的边界条件进行高效管理。 此外，将这些算法适应于GPU等大规模并行架构上会增加额外的复杂性。 本文介绍了libMobility软件库，该库提供了一套CUDA支持的求解器，用于在Rotne-Prager-Yamakawa（RPY）水平上模拟颗粒系统的水动力相互作用。 该库能够精确模拟受外力和力矩影响的粒子位移，包括确定性和随机成分。 libMobility的显著功能包括其处理线性和角位移、热波动以及各种域几何形状的能力。 通过Python接口，libMobility为计算流体力学及相关领域的研究人员提供了全面的工具，以高效地模拟粒子迁移。 本文详细介绍了libMobility的技术架构、功能和广泛应用。 libMobility可在https://github.com/stochasticHydroTools/libMobility获取。
Effective hydrodynamic modeling is crucial for accurately predicting fluid-particle interactions in diverse fields such as biophysics and materials science. Developing and implementing hydrodynamic algorithms is challenging due to the complexity of fluid dynamics, necessitating efficient management of large-scale computations and sophisticated boundary conditions. Furthermore, adapting these algorithms for use on massively parallel architectures like GPUs adds an additional layer of complexity. This paper presents the libMobility software library, which offers a suite of CUDA-enabled solvers for simulating hydrodynamic interactions in particulate systems at the Rotne-Prager-Yamakawa (RPY) level. The library facilitates precise simulations of particle displacements influenced by external forces and torques, including both the deterministic and stochastic components. Notable features of libMobility include its ability to handle linear and angular displacements, thermal fluctuations, and various domain geometries effectively. With an interface in Python, libMobility provides comprehensive tools for researchers in computational fluid dynamics and related fields to simulate particle mobility efficiently. This article details the technical architecture, functionality, and wide-ranging applications of libMobility. libMobility is available at https://github.com/stochasticHydroTools/libMobility.
- [6] arXiv:2510.02160 [中文pdf, pdf, html, 其他]
-
标题： p-atic对称性和缺陷在融合上皮中的光谱标题： A spectrum of p-atic symmetries and defects in confluent epitheliaLea Happel, Griseldis Oberschelp, Anneli Richter, Gwenda Roselene Rode, Valeriia Grudtsyna, Amin Doostmohammadi, Axel Voigt主题： 软凝聚态物理 (cond-mat.soft)
拓扑缺陷提供了一种统一的语言，用于描述活性和生命物质中取向序如何崩溃。 将细胞视为伸长粒子，连续的上皮组织可以被解释为向列场，其缺陷已被与挤出、迁移和形态发生转变相关联。 然而，上皮细胞并不局限于向列序：它们不规则的形状可以表现出更高的旋转对称性，从而产生p-向列序。 在这里，我们引入了一个框架，可以直接从实验图像中提取p-向列场及其缺陷。 将这种方法应用于MDCK细胞，我们发现所有对称性都会产生缺陷。没有发现向列缺陷和六重缺陷之间的强位置或取向相关性，表明不同的对称性在很大程度上独立共存。 这些结果表明，上皮组织不应仅用向列序来描述，而是包含一系列p-向列对称性。 我们的工作提供了这种有序多价性的第一个直接实验证据，并提供了一条测试和改进生命物质新兴p-向列液晶理论的途径。
Topological defects provide a unifying language to describe how orientational order breaks down in active and living matter. Considering cells as elongated particles confluent, epithelial tissues can be interpreted as nematic fields and its defects have been linked to extrusion, migration, and morphogenetic transformations. Yet, epithelial cells are not restricted to nematic order: their irregular shapes can express higher rotational symmetries, giving rise to p-atic order. Here we introduce a framework to extract p-atic fields and their defects directly from experimental images. Applying this method to MDCK cells, we find that all symmetries generate defects.No strong positional or orientational correlations are found between nematic and hexatic defects, suggesting that different symmetries coexist largely independently. These results demonstrate that epithelial tissues should not be described by nematic order alone, but instead host a spectrum of p-atic symmetries. Our work provides the first direct experimental evidence for this multivalency of order and offers a route to test and refine emerging p-atic liquid crystal theories of living matter.
新提交 (展示 6 之 6 条目 )
- [7] arXiv:2510.01503 (交叉列表自 cond-mat.mes-hall) [中文pdf, pdf, html, 其他]
-
标题： 耦合自由表面几何与局部离子剂量的连续介质模型辐射诱导纳米图案化标题： Coupling free-surface geometry and localized ion dose for continuum models of radiation-induced nanopatterning主题： 中尺度与纳米尺度物理 (cond-mat.mes-hall) ; 软凝聚态物理 (cond-mat.soft)
对辐射半导体表面之上高度规则的纳米尺度结构的自组织现象的第一性原理理解已经寻求了几十年。 虽然存在许多可以解释这一现象某些方面的模型，但能够解释模式形成所有细节的统一物理模型仍然难以捉摸。 然而，越来越明显的是，这样的模型将需要理解由离子注入引发的碰撞级联的双重影响：首先，作为材料传输的来源，通过短时间尺度上的溅射和原子位移；其次，作为缺陷的来源，允许在长时间尺度上持续辐射形成的薄非晶层内发生粘性流动。 为了更好地理解后者，我们开发了几个渐近近似方法，用于将局部离子剂量与演化的自由界面耦合。 然后，我们展示了通常用于与实验观察进行比较的理论预测量——如波纹波长、图案化开始的临界辐射角度以及表面粗糙化——对这种耦合的细节表现出令人惊讶的敏感性。
A first-principles understanding of the self-organization of highly regular, nanometer-scale structures atop irradiated semiconductor surfaces has been sought for decades. While numerous models exist which explain certain aspects of this phenomenon, a unified, physical model capable of explaining all details of pattern formation has remained elusive. However, it is increasingly apparent that such a model will require understanding the dual influence of the collision cascade initiated by ion implantation: first, as a source of material transport by sputtering and atomic displacements occurring over short time scales, and, second, as a source of defects permitting viscous flow within the thin, amorphous layer that results from sustained irradiation over longer time scales. To better understand the latter, we develop several asymptotic approximations for coupling the localized ion dose with an evolving free interface. We then show how theoretical predictions of quantities commonly used for comparison with experimental observations -- such as ripple wavelengths, critical irradiation angle for patterning onset, and surface roughening -- exhibit surprising sensitivity to the details of this coupling.
- [8] arXiv:2510.01866 (交叉列表自 physics.bio-ph) [中文pdf, pdf, html, 其他]
-
标题： 原位观察布拉格峰中质子诱导的DNA断裂：水的保护作用证据标题： In Situ Observation of Proton-Induced DNA Fragmentation in the Bragg Peak: Evidence for a Protective Role of Water期刊参考： 《物理评论研究》7，043004（2025）主题： 生物物理 (physics.bio-ph) ; 软凝聚态物理 (cond-mat.soft) ; 仪器与探测器 (physics.ins-det) ; 医学物理 (physics.med-ph)
我们报告了在水中浸没的DNA中质子诱导的双链断裂（DSBs）的原位单分子测量结果，使用实时荧光追踪沿着整个质子路径，包括布拉格峰区域。 通过化学抑制自由基介导的过程，我们隔离了直接的DNA损伤机制，并确定了DSBs截面作为深度的函数。 在布拉格峰附近，我们观察到水中的DNA相比干燥DNA的DSB截面减少了十倍，为水的保护作用提供了定量证据。 这些发现强调了分子间能量耗散在减轻凝聚生物物质中的辐射损伤的重要性，对放射生物学和质子治疗建模有重要意义。
We report in situ single-molecule measurements of proton-induced double-strand breaks (DSBs) in DNA immersed in water, using real-time fluorescence tracking along the entire proton path, including the Bragg peak region. By chemically suppressing radical-mediated processes, we isolate direct DNA damage mechanisms and determine DSB cross sections as a function of depth. Near the Bragg peak, we observe a tenfold reduction in DSB cross sections in aqueous DNA compared to dry DNA, providing quantitative evidence for the protective role of water. These findings highlight the importance of intermolecular energy dissipation in mitigating radiation-induced damage in condensed biological matter, with implications for radiobiology and proton therapy modeling.
- [9] arXiv:2510.01890 (交叉列表自 quant-ph) [中文pdf, pdf, html, 其他]
-
标题： 在最小网格上使用量子启发编码折叠晶格蛋白质标题： Folding lattice proteins confined on minimal grids using a quantum-inspired encoding评论： 22页，5图期刊参考： 物理评论E 112, 045302 (2025)主题： 量子物理 (quant-ph) ; 软凝聚态物理 (cond-mat.soft) ; 生物物理 (physics.bio-ph) ; 生物大分子 (q-bio.BM)
立体冲突在使用传统显式链方法探索密集蛋白质系统时是一个挑战。 一个最小的例子是一个单晶格蛋白被限制在一个最小的网格上，没有自由位点。 找到它的最低能量是一个困难的优化问题，与调度问题有相似之处。 它可以重新表述为一个适用于经典和量子方法的无约束二次二进制优化（QUBO）问题。 我们表明，通过使用经典模拟退火或在D-Wave系统上的混合量子-经典退火，可以快速且一致地解决长度为48的链的该问题。 事实上，后者的计算大约需要10秒。 我们还测试了线性和二次规划方法，这些方法在晶格气体中表现良好，但在处理链约束时遇到困难。 所有方法都与从全面结构枚举中获得的精确结果进行了基准测试，但计算成本较高。
Steric clashes pose a challenge when exploring dense protein systems using conventional explicit-chain methods. A minimal example is a single lattice protein confined on a minimal grid, with no free sites. Finding its minimum energy is a hard optimization problem, withsimilarities to scheduling problems. It can be recast as a quadratic unconstrained binary optimization (QUBO) problem amenable to classical and quantum approaches. We show that this problem in its QUBO form can be swiftly and consistently solved for chain length 48, using either classical simulated annealing or hybrid quantum-classical annealing on a D-Wave system. In fact, the latter computations required about 10 seconds. We also test linear and quadratic programming methods, which work well for a lattice gas but struggle with chain constraints. All methods are benchmarked against exact results obtained from exhaustive structure enumeration, at a high computational cost.
- [10] arXiv:2510.02090 (交叉列表自 cond-mat.stat-mech) [中文pdf, pdf, html, 其他]
-
标题： 弹性系统中相关无序的有效介质理论标题： Effective-medium theory for elastic systems with correlated disorder评论： 9页，5图主题： 统计力学 (cond-mat.stat-mech) ; 无序系统与神经网络 (cond-mat.dis-nn) ; 软凝聚态物理 (cond-mat.soft)
相关结构与各种无序系统表现出的有趣现象密切相关，例如软胶体凝胶、生物聚合物网络以及接近剪切致密化转变的胶体悬浮液。 这些系统在刚性开始出现时的普遍临界行为通常被传统方法描述为相干势近似——这是一种有效的介质理论的多功能版本，但迄今为止缺乏关键要素来描述无序的空间相关性。 在这里，我们提出了一种多用途的相干势近似推广方法，以描述具有空间相关无序的弹性网络的力学行为。 我们将我们的理论应用于一个简单的刚性渗透模型用于胶体凝胶，并研究了相关性对临界点和整体标度行为的影响。 我们发现，尽管存在空间相关性（模拟凝胶的吸引相互作用）将临界填充分数向较低值移动，表明亚等价行为，但相关网络的临界配位数仍保持等价。 更重要的是，我们讨论了如何利用我们的理论来描述具有空间相关无序的多种系统。
Correlated structures are intimately connected to intriguing phenomena exhibited by a variety of disordered systems such as soft colloidal gels, bio-polymer networks and colloidal suspensions near a shear jamming transition. The universal critical behavior of these systems near the onset of rigidity is often described by traditional approaches as the coherent potential approximation - a versatile version of effective-medium theory that nevertheless have hitherto lacked key ingredients to describe disorder spatial correlations. Here we propose a multi-purpose generalization of the coherent potential approximation to describe the mechanical behavior of elastic networks with spatially-correlated disorder. We apply our theory to a simple rigidity-percolation model for colloidal gels and study the effects of correlations in both the critical point and the overall scaling behavior. We find that although the presence of spatial correlations (mimicking attractive interactions of gels) shifts the critical packing fraction to lower values, suggesting sub-isostatic behavior, the critical coordination number of the associated network remains isostatic. More importantly, we discuss how our theory can be employed to describe a large variety of systems with spatially-correlated disorder.
交叉提交 (展示 4 之 4 条目 )
- [11] arXiv:2406.19202 (替换) [中文pdf, pdf, html, 其他]
-
标题： 毫米尺寸颗粒的高浓度悬浮液中的早期阶段冲击动力学标题： Early-stage impact dynamics in dense suspensions of millimeter-sized particles评论： 11页，12张图。以下文章已提交至《流体物理》。发表后，可在以下链接找到：https://pubs.aip.org/aip/pof主题： 软凝聚态物理 (cond-mat.soft)
本研究探讨了密集悬浮液中由冲击引起的硬化早期阶段动力学现象，其中材料在冲击下发生固化。 虽然斯托克斯流理论传统上适用于具有微米级颗粒的悬浮液，因为它们的雷诺数较低，但含有较大颗粒的悬浮液则违背了这种理想化。 我们的工作通过动态冲击实验，聚焦于含有毫米级颗粒的悬浮液的早期阶段冲击硬化。 我们特别关注最大阻力力$F_\mathrm{max}$作为冲击速度$u_0$的函数。 我们成功地使用这些悬浮液进行了实验，并确认了之前研究中观察到的相对较大的$u_0$的关系$F_\mathrm{max}\sim u_0^{3/2}$。 我们的研究结果表明，毫米级颗粒悬浮液的早期行为与浮力模型的预测相符，该模型通常适用于斯托克斯流条件。 这项研究揭示了密集悬浮液中由冲击引起的硬化的复杂动力学，特别是对于较大颗粒，推动了我们对常规微米级系统的理解。
This study investigates the phenomenon of the early-stage dynamics of impact-induced hardening in dense suspensions, where materials undergo solidification upon impact. While Stokes flow theory traditionally applies to suspensions with micrometer-sized particles due to their low Reynolds numbers, suspensions containing larger particles defy such idealizations. Our work focuses on the early-stage impact-induced hardening of suspensions containing millimeter-sized particles through dynamic impact experiments. We are particularly interested in the maximum drag force $F_\mathrm{max}$ acting on the projectile as a function of the impact speed $u_0$. We successfully conducted experiments using these suspensions and confirmed the relation $F_\mathrm{max}\sim u_0^{3/2}$ for relatively large $u_0$ as observed in the previous studies suspensions of micrometer-sized particles. Our findings reveal that the early-stage behaviors of millimeter-sized particle suspensions align well with predictions from the floating model, typically applicable under Stokes flow conditions. This research sheds light on the complex dynamics of impact-induced hardening in dense suspensions, particularly with larger particles, advancing our understanding beyond conventional micrometer-sized systems.
- [12] arXiv:2503.01446 (替换) [中文pdf, pdf, html, 其他]
-
标题： 双折叠随机分支环状聚合物的涌现动力学标题： The emergent dynamics of double-folded randomly branching ring polymers主题： 软凝聚态物理 (cond-mat.soft) ; 计算物理 (physics.comp-ph)
随机分支双折叠环状聚合物的统计特性与RNA的二级结构、螺旋DNA的大规模分支（因此是细菌染色体）、单环状聚合物通过障碍物阵列时的构象，以及真核染色体和皱缩的非连接环状聚合物熔体的构象统计有关。 双折叠环状聚合物根据双折叠所依赖的随机树状图是淬火的还是退火的，以及这些树在空间嵌入中是否可以自由进行布朗运动，而属于不同的动态普适类。 从局部来看，可以区分（i）围绕固定树的类似repton的质量传输，（ii）侧枝的自发产生和删除，以及（iii）树节点的位移，在这种情况下互补的环段在空间中一起扩散。 在此，我们采用适合的弹性晶格聚合物模型的动态蒙特卡洛模拟，研究不同组合的上述局部模式在三种不同系统中的介观动力学：理想不相互作用的环、自避环以及熔融状态下的环。 我们观察到环状链的预期标度区域，即在障碍物阵列中双折叠环的动力学，以及Rouse-like树动力学作为极限情况。 特别值得注意的是，对于具有$\nu=1/3$的皱缩环，$g_1\sim t^{0.4}$的单体均方位移类似于细菌染色体中观察到的亚扩散区域。 在我们的分析中，我们关注不同局部动力学模式对出现的动力学的贡献在多大程度上是简单的叠加。 值得注意的是，当所有三种类型的局部运动都存在时，我们揭示了相互作用环的动力学出现了非平凡的加速。
The statistics of randomly branching double-folded ring polymers are relevant to the secondary structure of RNA, the large-scale branching of plectonemic DNA (and thus bacterial chromosomes), the conformations of single-ring polymers migrating through an array of obstacles, as well as to the conformational statistics of eukaryotic chromosomes and melts of crumpled, non-concatenated ring polymers. Double-folded rings fall into different dynamical universality classes depending on whether the random tree-like graphs underlying the double-folding are quenched or annealed, and whether the trees can undergo unhindered Brownian motion in their spatial embedding. Locally, one can distinguish (i) repton-like mass transport around a fixed tree, (ii) the spontaneous creation and deletion of side branches, and (iii) displacements of tree node, where complementary ring segments diffuse together in space. Here we employ dynamic Monte Carlo simulations of a suitable elastic lattice polymer model of double-folded, randomly branching ring polymers to explore the mesoscopic dynamics that emerge from different combinations of the above local modes in three different systems: ideal non-interacting rings, self-avoiding rings, and rings in the melt state. We observe the expected scaling regimes for ring reptation, the dynamics of double-folded rings in an array of obstacles, and Rouse-like tree dynamics as limiting cases. Of particular interest, the monomer mean-square displacements of $g_1\sim t^{0.4}$ observed for crumpled rings with $\nu=1/3$ are similar to the subdiffusive regime observed in bacterial chromosomes. In our analysis, we focus on the question to which extent contributions of different local dynamical modes to the emergent dynamics are simply additive. Notably, we reveal a non-trivial acceleration of the dynamics of interacting rings, when all three types of local motion are present.
- [13] arXiv:2503.24120 (替换) [中文pdf, pdf, html, 其他]
-
标题： 再生化力学和生长囊泡的随机热力学标题： Renormalized mechanics and stochastic thermodynamics of growing vesicles主题： 软凝聚态物理 (cond-mat.soft) ; 生物物理 (physics.bio-ph)
揭示定义生物细胞的膜的非平衡动力学规则对于理解生命系统的物理机制具有重要意义。 我们通过理论和计算方法研究了能够交换膜组分、内部体积和热量的柔性准球形囊泡的行为。 储层施加的过量化学势和渗透压差作为广义的热力学驱动力，调节囊泡的形态。 我们表明，非平衡驱动对膜机械性能的重整化导致了一种形态转变，即在弱驱动区域，生长的囊泡保持准球形，而在强驱动区域，囊泡通过发展表面皱褶来适应快速的膜吸收。 此外，我们提出了一种最小的囊泡生长-形状定律，该定律基于随机热力学的见解，即使在强驱动、远离平衡的区域也能稳健地描述囊泡的生长动力学。
Uncovering the rules governing the nonequilibrium dynamics of the membranes that define biological cells is of central importance to understanding the physics of living systems. We theoretically and computationally investigate the behavior of flexible quasispherical vesicles that exchange membrane constituents, internal volume, and heat with an external reservoir. The excess chemical potential and osmotic pressure difference imposed by the reservoir act as generalized thermodynamic driving forces that modulate vesicle morphology. We show that the renormalization of membrane mechanical properties by nonequilibrium driving gives rise to a morphological transition between a weakly driven regime, in which growing vesicles remain quasispherical, and a strongly driven regime, in which vesicles accommodate rapid membrane uptake by developing surface wrinkles. Additionally, we propose a minimal vesicle growth-shape law, derived using insights from stochastic thermodynamics, that robustly describes vesicle growth dynamics even in strongly driven, far-from-equilibrium regimes.
- [14] arXiv:2505.00357 (替换) [中文pdf, pdf, html, 其他]
-
标题： 非互易反对齐活性混合物：推导精确的玻尔兹曼碰撞算子标题： Non-reciprocal anti-aligning active mixtures: deriving the exact Boltzmann collision operator评论： 35页，5图主题： 统计力学 (cond-mat.stat-mech) ; 软凝聚态物理 (cond-mat.soft)
我们考虑在具有反对齐相互作用的自推进粒子二元混合物中非互易性的影响，其中类型A的粒子对类型B的粒子的反应与反之不同。 从一个已知的微观Langevin模型出发，建立相应的精确N粒子Fokker-Planck方程，并做出低密度和单侧分子混沌的假设，推导出带有精确碰撞算子的非线性活性Boltzmann方程。 在此推导中，显式地考虑了相空间压缩以及二元相互作用期间对相关性的建立，从而得到超越平均场的理论描述。 这扩展了之前关于互易相互作用的结果，其中发现纯反对齐相互作用的系统中可以出现取向序。 尽管运动方程比互易系统更复杂，但该理论仍然导致解析表达式和预测。 与基于代理的模拟比较显示，在低密度和/或小耦合极限下动态和静态行为有很好的定量一致性。
We consider the effect of non-reciprocity in a binary mixture of self-propelled particles with anti-aligning interactions, where a particle of type A reacts differently to a particle of type B than vice versa. Starting from a well-known microscopic Langevin-model for the particles, setting up the corresponding exact N-particle Fokker-Planck equation and making Boltzmann's assumptions of low density and one-sided molecular chaos, the non-linear active Boltzmann equation with the exact collision operator is derived. In this derivation, the effect of phase-space compression and the build-up of pair-correlations during binary interactions is explicitly taken into account, leading to a theoretical description beyond mean-field. This extends previous results for reciprocal interactions, where it was found that orientational order can emerge in a system with purely anti-aligning interactions. Although the equations of motion are more complex than in the reciprocal system, the theory still leads to analytical expressions and predictions. Comparisons with agent-based simulations show excellent quantitative agreement of the dynamic and static behavior in the low density and/or small coupling limit.
- [15] arXiv:2509.24905 (替换) [中文pdf, pdf, html, 其他]
-
标题： 拓扑SPAM：形态发生和生物活性物质的拓扑基础仿真平台标题： TopoSPAM: Topology grounded Simulation Platform for morphogenesis and biological Active MatterAbhinav Singh (1,2), Abhijeet Krishna (1,2), Aboutaleb Amiri (3), Anne Materne (1,2,3), Pietro Incardona (1,2), Charlie Duclut (3,4), Carlos M. Duque (1,2), Alicja Szałapak (1,2), Mohammadreza Bahadorian (1,2), Sachin Krishnan Thekke Veettil (1,2), Philipp H. Suhrcke (1,2,5), Frank Jülicher (2,3,6), Ivo F. Sbalzarini (1,2,5,6), Carl D. Modes (1,2,6) ((1) Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany, (2) Center for Systems Biology Dresden, Dresden, Germany, (3) Max Planck Institute for the Physics of Complex Systems, Dresden, Germany, (4) Laboratoire Physique des Cellules et Cancer, CNRS UMR 168, Institut Curie, Université Paris Sciences et Lettres, Sorbonne Université, Paris, France, (5) Dresden University of Technology, Faculty of Computer Science, Dresden, Germany, (6) Physics of Life Cluster of Excellence, TU Dresden, Dresden, Germany)评论： 10页，4图主题： 生物物理 (physics.bio-ph) ; 软凝聚态物理 (cond-mat.soft)
我们提出一个基于拓扑的多尺度模拟平台，用于形态发生和生物活性物质。 形态发生和生物活性物质是生物学中的核心问题，并在生物医学科学中具有更广泛的含义。 解决这些问题将需要灵活的跨尺度组织形状、发育和功能障碍模型，这些模型可以调整以理解和预测相关个例。 目前模拟解剖或细胞子系统的做法往往依赖于静态的假设形状。 同时，拓扑学在提供自然的维度降低和形状及动态结果的组织方面的潜力尚未被充分利用。 TopoSPAM结合了易用性与强大的模拟算法和方法进展，包括活性向列凝胶、由拓扑缺陷驱动的形状动力学以及组织的活性三维顶点模型。 它能够确定不同尺度上的涌现流和形状。
We present a topology grounded, multiscale simulation platform for morphogenesis and biological active matter. Morphogenesis and biological active matter represent keystone problems in biology with additional, far-reaching implications across the biomedical sciences. Addressing these problems will require flexible, cross-scale models of tissue shape, development, and dysfunction that can be tuned to understand, model, and predict relevant individual cases. Current approaches to simulating anatomical or cellular subsystems tend to rely on static, assumed shapes. Meanwhile, the potential for topology to provide natural dimensionality reduction and organization of shape and dynamical outcomes is not fully exploited. TopoSPAM combines ease of use with powerful simulation algorithms and methodological advances, including active nematic gels, topological-defect-driven shape dynamics, and an active 3D vertex model of tissues. It is capable of determining emergent flows and shapes across scales.