生物物理

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新提交 (展示 2 之 2 条目 )

[1] arXiv:2510.01397 [中文pdf, pdf, 其他]

标题： 集体有所不同：自组织模式中的信息交换与速度-准确性权衡 显示英文标题

标题： Collective is different: Information exchange and speed-accuracy trade-offs in self-organized patterning

Ashutosh Tripathi, Jörn Dunkel, Dominic J. Skinner

评论： 正文：18页，9图。附录材料：20页，8图

主题： 生物物理 (physics.bio-ph) ; 适应性与自组织系统 (nlin.AO)

在发育过程中，高度有序的结构出现，因为细胞之间协同合作。 尽管最近的进展已经阐明了单个细胞如何处理和响应外部信号，但理解集体细胞决策仍然是一个主要挑战。 在这里，我们引入了一个最小的、可解析的模型，通过局部细胞间通信进行细胞图案形成。 使用这个框架，我们确定了集体图案形成的速度和准确性之间的权衡，并通过适应随机化学动力学的技术，量化了在图案形成过程中细胞间的信息流动。 我们的分析揭示了集体图案形成的反直觉特征：全局优化的解决方案不一定最大化细胞间的信息传递，单独的细胞可能看起来是次优的。 此外，该模型预测，在图案形成过程中，细胞间即时共享的信息可能随时间呈非单调变化。 对果蝇蛹腹部侧向抑制的最新实验数据的分析发现了一种定性相似的效果。 显示英文摘要

During development, highly ordered structures emerge as cells collectively coordinate with each other. While recent advances have clarified how individual cells process and respond to external signals, understanding collective cellular decision making remains a major challenge. Here, we introduce a minimal, analytically tractable, model of cell patterning via local cell-cell communication. Using this framework, we identify a trade-off between the speed and accuracy of collective pattern formation and, by adapting techniques from stochastic chemical kinetics, quantify how information flows between cells during patterning. Our analysis reveals counterintuitive features of collective patterning: globally optimized solutions do not necessarily maximize intercellular information transfer and individual cells may appear suboptimal in isolation. Moreover, the model predicts that instantaneous information shared between cells can be non-monotonic in time as patterning occurs. An analysis of recent experimental data from lateral inhibition in Drosophila pupal abdomen finds a qualitatively similar effect.

[2] arXiv:2510.01866 [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 显示英文标题

标题： In Situ Observation of Proton-Induced DNA Fragmentation in the Bragg Peak: Evidence for a Protective Role of Water

R.Liénard, P.Barberet, K.Chatzipapas, G.Devès, T.Dhôte, T.Guérin, H.Seznec, F.Gobet

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。 显示英文摘要

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.

交叉提交 (展示 4 之 4 条目 )

[3] arXiv:2510.01808 (交叉列表自 q-bio.PE) [中文pdf, pdf, html, 其他]

标题： 通过侧向敏感性最大化抵抗细菌的消除的顺序治疗优化 显示英文标题

标题： Optimization of sequential therapies to maximize extinction of resistant bacteria through collateral sensitivity

Javier Molina-Hernández, José A. Cuesta, Beatriz Pascual-Escudero, Saúl Ares, Pablo Catalán

评论： 7页，5图，8份补充材料页，9份补充材料图，2份补充材料表

主题： 种群与进化 (q-bio.PE) ; 生物物理 (physics.bio-ph)

抗菌药物耐药性（AMR）威胁全球健康。 一种有前景但尚未充分研究的应对策略是利用侧向敏感性（CS）的顺序治疗，即对一种药物的耐药性会增加对另一种药物的敏感性。 在这里，我们开发了一个四基因型的随机出生-死亡模型，使用两种抑菌抗生素，以确定在亚抑制浓度下最大化细菌灭绝的切换周期。 我们表明，灭绝概率非线性依赖于切换周期，逐步增加与离散切换事件一致：快速的顺序治疗效果不佳，因为它们不允许耐药性的进化，而这是这些治疗的关键要素。 一个几何分布框架准确预测了累积灭绝概率，其中每次切换的灭绝概率随着切换周期的增加而上升。 我们进一步推导了一个基于单个耐药突变体固定时间的灭绝概率启发式近似。 敏感性分析显示，这种策略要有效需要强的相互侧向敏感性，并我们探讨了增加抗生素剂量和更高的突变率如何以非单调方式调节灭绝。 最后，我们讨论了最佳切换周期如何依赖于治疗持续时间。 我们的结果为体外和临床顺序抗生素治疗提供了定量设计原则，强调了基于侧向敏感性的方案在抑制耐药性进化和根除感染方面的潜力。 显示英文摘要

Antimicrobial resistance (AMR) threatens global health. A promising and underexplored strategy to tackle this problem are sequential therapies exploiting collateral sensitivity (CS), whereby resistance to one drug increases sensitivity to another. Here, we develop a four-genotype stochastic birth-death model with two bacteriostatic antibiotics to identify switching periods that maximize bacterial extinction under subinhibitory concentrations. We show that extinction probability depends nonlinearly on switching period, with stepwise increases aligned to discrete switch events: fast sequential therapies are suboptimal as they do not allow for the evolution of resistance, a key ingredient in these therapies. A geometric distribution framework accurately predicts cumulative extinction probabilities where the per-switch extinction probability rises with switching period. We further derive a heuristic approximation for the extinction probability based on times to fixation of single-resistant mutants. Sensitivity analyses reveal that strong reciprocal CS is required for this strategy to work, and we explore how increasing antibiotic doses and higher mutation rates modulate extinction in a nonmonotonic manner. Finally, we discuss how optimal switching periods depend on treatment duration. Our results provide quantitative design principles for in vitro and clinical sequential antibiotic therapies, underscoring the potential of CS-guided regimens to suppress resistance evolution and eradicate infections.

[4] 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 显示英文标题

标题： Folding lattice proteins confined on minimal grids using a quantum-inspired encoding

Anders Irbäck, Lucas Knuthson, Sandipan Mohanty

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。 显示英文摘要

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.

[5] arXiv:2510.02073 (交叉列表自 cs.LG) [中文pdf, pdf, html, 其他]

标题： 从光电容积描记术中推断光学组织特性使用混合摊销推理 显示英文标题

标题： Inferring Optical Tissue Properties from Photoplethysmography using Hybrid Amortized Inference

Jens Behrmann, Maria R. Cervera, Antoine Wehenkel, Andrew C. Miller, Albert Cerussi, Pranay Jain, Vivek Venugopal, Shijie Yan, Guillermo Sapiro, Luca Pegolotti, Jörn-Henrik Jacobsen

主题： 机器学习 (cs.LG) ; 生物物理 (physics.bio-ph) ; 机器学习 (stat.ML)

智能可穿戴设备通过光电容积描记法（PPG）实现对已确立生物标志物如心率、心率变异性以及血氧饱和度的连续追踪。 除了这些指标，PPG波形包含更丰富的生理信息，正如最近的深度学习（DL）研究所示。 然而，DL模型通常依赖于具有不明确生理意义的特征，这在预测能力、临床可解释性和传感器设计之间产生了矛盾。 我们通过引入PPGen来解决这一差距，PPGen是一个将PPG信号与可解释的生理和光学参数相关联的生物物理模型。 基于PPGen，我们提出了混合摊销推理（HAI），能够在纠正模型误指的情况下，从PPG信号中快速、稳健且可扩展地估计相关生理参数。 在广泛的仿真实验中，我们展示了HAI在各种噪声和传感器条件下的准确生理参数推断能力。 我们的结果展示了一条路径，使PPG模型在保留用于基于DL的特征所需的保真度的同时，支持临床解释和有根据的硬件设计。 显示英文摘要

Smart wearables enable continuous tracking of established biomarkers such as heart rate, heart rate variability, and blood oxygen saturation via photoplethysmography (PPG). Beyond these metrics, PPG waveforms contain richer physiological information, as recent deep learning (DL) studies demonstrate. However, DL models often rely on features with unclear physiological meaning, creating a tension between predictive power, clinical interpretability, and sensor design. We address this gap by introducing PPGen, a biophysical model that relates PPG signals to interpretable physiological and optical parameters. Building on PPGen, we propose hybrid amortized inference (HAI), enabling fast, robust, and scalable estimation of relevant physiological parameters from PPG signals while correcting for model misspecification. In extensive in-silico experiments, we show that HAI can accurately infer physiological parameters under diverse noise and sensor conditions. Our results illustrate a path toward PPG models that retain the fidelity needed for DL-based features while supporting clinical interpretation and informed hardware design.

[6] arXiv:2510.02105 (交叉列表自 physics.chem-ph) [中文pdf, pdf, 其他]

标题： 实时和空间上成像和控制生物系统的电子运动和化学结构动力学 显示英文标题

标题： Imaging and controlling electron motion and chemical structural dynamics of biological system in real time and space

Ligong Zhao, Mohamed Sennary, Dina Hussein, Anaisa Coelho, Tingting Yang, Mohamed Y. El-Naggar, Mohammed Th. Hassan

评论： 18页，5图

主题： 化学物理 (physics.chem-ph) ; 原子与分子簇 (physics.atm-clus) ; 生物物理 (physics.bio-ph)

超快电子显微镜（UEM）在物理学、化学和材料科学中得到了广泛的应用，使在超快时间尺度上实现实空间动态成像成为可能。 最近的进展将UEM的时间分辨率推进到了阿秒领域，使得阿秒显微技术能够直接观察电子运动。 在本研究中，我们扩展了这一强大成像工具的能力，通过成像和控制多细胞电缆细菌导电网络中的光诱导电子和化学变化，来研究生物系统中的超快电子动力学。 使用电子能量损失谱（EELS），我们首先观察到激光诱导的{\pi }-电子密度增加，伴随着光谱峰展宽和蓝移特征，表明导电性增强和结构改变。 我们还通过监测等离子体类似共振峰的变化，追踪了超快激光泵浦对体等离子体电子振荡的影响。 此外，我们在实空间中可视化了激光诱导的电缆细菌化学结构变化。 成像结果揭示了碳的富集以及氮和氧的耗竭，突显了化学动力学的可控性。 此外，时间分辨EELS测量进一步揭示了{\pi }-电子和等离子体特征在皮秒尺度上的衰减和恢复，这归因于电子声子耦合。 除了揭示电缆细菌中电子运动的机制外，这些发现展示了导电性的超快调制和切换，强调了它们作为在超快时间尺度上运行的生物光电子元件的潜力。 显示英文摘要

Ultrafast electron microscopy (UEM) has found widespread applications in physics, chemistry, and materials science, enabling real-space imaging of dynamics on ultrafast timescales. Recent advances have pushed the temporal resolution of UEM into the attosecond regime, enabling the attomicroscopy technique to directly visualize electron motion. In this work, we extend the capabilities of this powerful imaging tool to investigate ultrafast electron dynamics in a biological system by imaging and controlling light induced electronic and chemical changes in the conductive network of multicellular cable bacteria. Using electron energy loss spectroscopy (EELS), we first observed a laser induced increase in {\pi}-electron density, accompanied by spectral peak broadening and a blueshift features indicative of enhanced conductivity and structural modification. We also traced the effect of ultrafast laser pumping on bulk plasmon electron oscillations by monitoring changes in the plasmon like resonance peak. Additionally, we visualized laser induced chemical structural changes in cable bacteria in real space. The imaging results revealed carbon enrichment alongside a depletion of nitrogen and oxygen, highlighting the controllability of chemical dynamics. Moreover, time resolved EELS measurements further revealed a picosecond scale decay and recovery of both {\pi}-electron and plasmonic features, attributed to electron phonon coupling. In addition to shedding light on the mechanism of electron motion in cable bacteria, these findings demonstrate ultrafast modulation and switching of conductivity, underscoring their potential as bio-optoelectronic components operating on ultrafast timescales.

替换提交 (展示 3 之 3 条目 )

[7] arXiv:2506.08642 (替换) [中文pdf, pdf, html, 其他]

标题： 运动诱导相分离期间的接触时间网络 显示英文标题

标题： Contact temporal network during motility induced phase separation

Italo Salas, Francisca Guzmán-Lastra, Denisse Pastén, Ariel Norambuena

主题： 生物物理 (physics.bio-ph)

运动诱导相分离（MIPS）是活性物质中典型的非平衡转变，由佩克莱特数和填充分数决定。 我们使用复杂网络方法研究MIPS的单相和相分离区域，其中网络是通过有限时间窗口内的粒子相互作用构建的。 在单相（气体状）区域，度分布$P(k)$呈现高斯行为，并类似于随机图的分布。 绘制$P(k)$峰值的位置和高度揭示了在固定填充分数下不同佩克莱特数之间的通用曲线。 在相分离区域，我们分别分析致密相和稀疏相。 $P(k)$分布揭示了不同的集体动力学，包括致密相中的笼效应以及长时间后活性固态结构的出现。 两个相中的聚类系数和平均路径长度迅速稳定，表明短时间模拟足以捕捉关键的网络特征。 总体而言，我们的结果表明网络度量揭示了活性物质动力学的普遍性和相特异性方面。 值得注意的是，我们在MIPS区域内致密相和稀疏相中识别出之前未报告的不同拓扑结构。 显示英文摘要

Motility-induced phase separation (MIPS) is a paradigmatic non-equilibrium transition in active matter, determined by the P\'eclet number and packing fraction. We investigate the single-phase and phase-separated regimes of MIPS using a complex network approach, where networks are constructed from particle interactions over finite time windows. In the single-phase (gas-like) regime, the degree distributions $P(k)$ exhibit Gaussian behavior and resemble those of random graphs. Plotting the location and height of the $P(k)$ peak reveals a universal curve across different P\'eclet numbers at fixed packing fraction. In the phase-separated regime, we analyze the dense and dilute phases independently. The $P(k)$ distributions unveil distinct collective dynamics, including caging in the dense phase and the emergence of active solid-like structures at longer times. Clustering coefficients and average path lengths in both phases stabilize rapidly, indicating that short simulations are sufficient to capture essential network features. Overall, our results show that network metrics expose both universal and phase-specific aspects of active matter dynamics. Notably, we identify distinct and previously unreported topological structures arising in the dense and dilute phases within the MIPS regime.

[8] 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 显示英文标题

标题： TopoSPAM: Topology grounded Simulation Platform for morphogenesis and biological Active Matter

Abhinav 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。 显示英文摘要

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.

[9] 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 显示英文标题

标题： Renormalized mechanics and stochastic thermodynamics of growing vesicles

Jordan L. Shivers, Michael Nguyen, Aaron R. Dinner, Petia Vlahovska, Suriyanarayanan Vaikuntanathan

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。 显示英文摘要

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.