The European Physical Journal E最新文献

{"title":"Random organization criticality with long-range hydrodynamic interactions","authors":"Tristan Jocteur,&nbsp;Cesare Nardini,&nbsp;Eric Bertin,&nbsp;Romain Mari","doi":"10.1140/epje/s10189-025-00519-x","DOIUrl":"10.1140/epje/s10189-025-00519-x","url":null,"abstract":"<p>Driven soft athermal systems may display a reversible-irreversible transition between an absorbing, arrested state and an active phase where a steady-state dynamics sets in. A paradigmatic example consists in cyclically sheared suspensions under stroboscopic observation, for which in absence of contacts during a shear cycle particle trajectories are reversible and the stroboscopic dynamics is frozen, while contacts lead to diffusive stroboscopic motion. The random organization model (ROM), which is a minimal model of the transition, shows a transition which falls into the conserved directed percolation universality class. However, the ROM ignores hydrodynamic interactions between suspended particles, which make contacts a source of long-range mechanical noise that in turn can create new contacts. Here, we generalize the ROM to include long-range interactions decaying like inverse power laws of the distance. Critical properties continuously depend on the decay exponent when it is smaller than the space dimension. Upon increasing the interaction range, the transition turns convex (that is, with an order parameter exponent <span>(beta &gt;1)</span>), fluctuations turn from diverging to vanishing, and hyperuniformity at the transition disappears. We rationalize this critical behavior using a local mean-field model describing how particle contacts are created via mechanical noise, showing that diffusive motion induced by long-range interactions becomes dominant for slowly decaying interactions.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"48 10-12","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145237708","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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":"A critical assessment of reinforcement learning methods for microswimmer navigation in complex flows","authors":"Selim Mecanna,&nbsp;Aurore Loisy,&nbsp;Christophe Eloy","doi":"10.1140/epje/s10189-025-00522-2","DOIUrl":"10.1140/epje/s10189-025-00522-2","url":null,"abstract":"<p>Navigating in a fluid flow while being carried by it, using only information accessible from on-board sensors, is a problem commonly faced by small planktonic organisms. It is also directly relevant to autonomous robots deployed in the oceans. In the last ten years, the fluid mechanics community has widely adopted reinforcement learning, often in the form of its simplest implementations, to address this challenge. But it is unclear how good are the strategies learned by these algorithms. In this paper, we perform a quantitative assessment of reinforcement learning methods applied to navigation in partially observable flows. We first introduce a well-posed problem of directional navigation for which a quasi-optimal policy is known analytically. We then report on the poor performance and robustness of commonly used algorithms (Q-Learning, Advantage Actor Critic) in flows regularly encountered in the literature: Taylor-Green vortices, Arnold–Beltrami–Childress flow, and two-dimensional turbulence. We show that they are vastly surpassed by PPO (Proximal Policy Optimization), a more advanced algorithm that has established dominance across a wide range of benchmarks in the reinforcement learning community. In particular, our custom implementation of PPO matches the theoretical quasi-optimal performance in turbulent flow and does so in a robust manner. Reaching this result required the use of several additional techniques, such as vectorized environments and generalized advantage estimation, as well as hyperparameter optimization. This study demonstrates the importance of algorithm selection, implementation details, and fine-tuning for discovering truly smart autonomous navigation strategies in complex flows.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"48 10-12","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145210446","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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":"Thermal signatures of biomolecules: an effective tool for screening biological defects","authors":"Sourav Kundu","doi":"10.1140/epje/s10189-025-00520-4","DOIUrl":"10.1140/epje/s10189-025-00520-4","url":null,"abstract":"<p>We investigate the impact of environmental factors and biological defects on the thermal properties of single-helical proteins by analyzing their electronic specific heat (ESH) at constant volume (<span>(C_v)</span>). To accurately model these biomolecules, we consider their helical structure and long-range electron hopping within a tight-binding framework. Our findings demonstrate that the ESH spectra can differentiate between defective and pure helical protein molecules, even a sample with a very low contamination (single site defect) level. By comparing the ESH spectra of perfect and defective proteins, we can identify the relative location of the defect and distinguish them based on the level of contamination. This approach could be valuable for medical diagnosis of biological defects and serve as a preliminary screening method before resorting to whole genome sequencing, thereby saving time and resources.</p><p>Schematic view of a single helical protein molecule. The solid black dots along the helix (green curve) represent the amino acid residues. The dotted black lines between adjacent residues indicate the respective hopping amplitudes (t1 - t6)</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"48 10-12","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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":"Concentration-dependent responses of C. reinhardtii to silver ions: hormetic response in growth and reduction of motility","authors":"Hemanta Pradhan,&nbsp;Arpan Poudel,&nbsp;Diksha Shrestha,&nbsp;Ariel Rogers,&nbsp;Michael Stewart,&nbsp;Amani Jereb,&nbsp;Jack Harper,&nbsp;Ming Li,&nbsp;Wen Zhang,&nbsp;Jingyi Chen,&nbsp;Yong Wang","doi":"10.1140/epje/s10189-025-00521-3","DOIUrl":"10.1140/epje/s10189-025-00521-3","url":null,"abstract":"<p>Elevated levels of silver in aquatic environments arising from widespread use of silver nitrate and silver nanoparticles in different sectors of industry and medicine pose significant biophysical challenges to aquatic microorganisms. Despite extensive toxicity studies of silver on bacteria and microbial communities, its influence on other aquatic microorganisms, such as microalgae, remains poorly understood. In this study, we investigated the biophysical response of <i>C. reinhardtii</i> microalgae to silver ion exposure in terms of their population growth dynamics, chlorophyll content, and swimming motility. We found that silver ions at different concentrations (from 0.29 to 1.18 <span>(upmu )</span>M) elongated the lag phase of the microalgal growth. However, the growth of the microalgae was boosted by silver ions at low concentrations (e.g., 0.29 <span>(upmu )</span>M), showing higher OD₇₅₀ values at the stationary phase and higher maximum growth rates. This hormetic response exhibited by microalgae upon exposure to silver ions indicates a nonlinear coupling between ionic stress and cellular growth. Additionally, we quantified the chlorophyll content in the microalgae with different concentrations of silver ions using spectrophotometric analysis, which revealed that the microalgae cells contained twice as high concentrations of chlorophyll when exposed to silver ions at lower concentrations. More importantly, we monitored the motion of microalgae in the presence of silver ions, detected and tracked their motion using a deep learning algorithm, and determined the effects of silver ions on the swimming motility of individual <i>C. reinhardtii</i> microalgae. Our results showed reduced average swimming speed and increased directional change of microalgae upon silver ion exposure.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"48 8-9","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1140/epje/s10189-025-00521-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145062263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Subdiffusion from competition between multi-exponential friction memory and energy barriers","authors":"Anton Klimek,&nbsp;Benjamin A. Dalton,&nbsp;Roland R. Netz","doi":"10.1140/epje/s10189-025-00518-y","DOIUrl":"10.1140/epje/s10189-025-00518-y","url":null,"abstract":"<p>Subdiffusion is a hallmark of complex systems, ranging from protein folding to transport in viscoelastic media. However, despite its pervasiveness, the mechanistic origins of subdiffusion remain contested. Here, we analyze both Markovian and non-Markovian dynamics, in the presence and absence of energy barriers, in order to disentangle the distinct contributions of memory-dependent friction and energy barriers to the emergence of subdiffusive behavior. Focusing on the mean squared displacement (MSD), we develop an analytical framework that connects subdiffusion to multi-scale memory effects in the generalized Langevin equation (GLE), and derive the subdiffusive scaling behavior of the MSD for systems governed by multi-exponential memory kernels. We identify persistence and relaxation timescales that delineate dynamical regimes in which subdiffusion arises from either memory or energy barrier effects. By comparing analytical predictions with simulations, we confirm that memory dominates the overdamped dynamics for barrier heights up to approximately <span>(2,k_BT)</span>, a regime recently shown to be relevant for fast-folding proteins. Overall, our results advance the theoretical understanding of anomalous diffusion and provide practical tools that are broadly applicable to fields as diverse as molecular biophysics, polymer physics, and active matter systems.</p><p>Subdiffusion in the context of the generalized Langevin equation can arise due to energy barriers, from friction memory or from a combination of both. We derive the power-law scaling for multi-exponential memory functions that directly translates to the subdiffusive scaling in the MSD. This allows us to disentangle contributions from energy barriers and from memory. It turns out that memory governs the subdiffusion for small energy barriers in the order of a few <span>(k_BT)</span>. For higher energy barriers, the short time dynamics are still dominated by memory and long-time dynamics are governed by a combination of memory effects and energy barrier contributions.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"48 8-9","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1140/epje/s10189-025-00518-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145037353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fluctuations of local plastic strain in granular media","authors":"I. Awada,&nbsp;M. Bornert,&nbsp;V. Langlois,&nbsp;J. Léopoldès","doi":"10.1140/epje/s10189-025-00515-1","DOIUrl":"10.1140/epje/s10189-025-00515-1","url":null,"abstract":"<div><p>We experimentally study the heterogeneity of strain in a granular medium subjected to oscillatory shear in a rotating drum. Two complementary methods are used. The first method relies on optical imaging and grain tracking, allowing us to compute some components of the strain tensor and their variance. The second method, diffuse acoustic wave spectroscopy (DAWS), provides the quadratic strain within the bulk. Our results show that strain is spatially heterogeneous, with fluctuations about ten times larger than the mean, primarily dominated by variability at the grain scale. We then analyze in detail the strain fluctuations occurring during the forward and backward branches of the shear stress cycles, along with the intracycle plastic strain resulting from each cycle. Both methods reveal that each shear cycle consists of two consecutive diffusive-like branches, and that the resulting plastic strain fluctuations scale with the mean plastic shear strain. We propose that plastic strain fluctuations result from irreversible strain heterogeneity that increases with applied shear—reflected in forward–backward strain anticorrelations—but is constrained by load-controlled induced memory.</p></div>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"48 8-9","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144998546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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":"In vivo mimicking multiphase model towards impact of host on avascular tumour growth","authors":"Abdush Salam Pramanik,&nbsp;Bibaswan Dey,&nbsp;G. P. Raja Sekhar","doi":"10.1140/epje/s10189-025-00517-z","DOIUrl":"10.1140/epje/s10189-025-00517-z","url":null,"abstract":"<p>Tumour growth involves dynamic interactions among tumour cells, extracellular materials, and host tissue. The tumour exerts mechanical stresses on the host tissue and simultaneously experiences compression across the tumour–host interface. This article presents a mathematical model that mimics an in vivo set-up, where an avascular tumour is surrounded by healthy/normal tissue, utilizing conservation principles for the constituents in each region. Tumour and host tissues are separately treated as biphasic mixtures comprising cells and extracellular materials. This study incorporates the diffusion-dominated transport and metabolism of cell-nourishing agents (<i>CNA</i>), such as oxygen, nutrients, and growth factors. The mechanical impact of normal host tissue on tumour growth dynamics while maintaining stress continuity at the tumour–host interface is analysed through numerical simulations. The key findings are that when <i>CNA</i> levels decline below a specific threshold, the tumour cell volume fraction decreases from the periphery to the centre, resulting in necrotic cell death alongside apoptosis. This study indicates that host tissue reduces <i>CNA</i> tension, accelerating tumour necrosis. The increased viscosity of normal host cells indicates stronger intercellular bonds, causing the cells to adhere more tightly and stiffen the host. With increasing viscosity-induced resistance, the host tissue more effectively impedes tumour expansion, thereby slowing tumour growth due to rising compressive stress. Analytical results for a solvable scenario are also provided to explore the comparative behaviour with numerical simulations of the complete model. Furthermore, analytical results indicate that an increased viscosity of normal host tissue may delay the initiation of necrotic cell death.</p><p>Higher host cell viscosity lowers the growth rate of an in vivo tumour</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"48 8-9","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145005534","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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":"Proportional modulation of proliferation and motility under 2D compressive stress depends on mesenchymal phenotype","authors":"Zacchari Ben Meriem,&nbsp;Moetassem Billah Meksassi,&nbsp;Céline Denais,&nbsp;Julie Guillermet-Guibert,&nbsp;Morgan Delarue","doi":"10.1140/epje/s10189-025-00516-0","DOIUrl":"10.1140/epje/s10189-025-00516-0","url":null,"abstract":"<p>Tumor development is accompanied by strong physico-chemical modifications. Among them, compressive stress can emerge in both the epithelial and stromal compartments. Using a simple two-dimensional compression assay which consisted in placing an agarose weight on top of adherent cells, we studied the impact of compressive stress on cell proliferation and motility in different pancreatic cancer cell lines. We observed a proportional reduction of both proliferation and motility in all tested cell types, with genotypes displaying a more “mesenchymal” phenotype (high velocity-to-proliferation ratio) and others related to a more “epithelial” phenotype (low velocity-to-proliferation ratio). Moreover, “mesenchymal” cells seemed more sensitive to compression, a result that was further suggested by a TGF<span>(mathrm {beta })</span>1 induction of epithelial-to-mesenchymal transition. Finally, we measured that the change in cell proliferation was associated with a change in intracellular macromolecular crowding, which could modulate a plethora of biochemical reactions. Our results together suggest a mechanism in which all biochemical reactions related to proliferation and motility can be modulated by a change in macromolecular crowding, itself depending on the phenotype, leading to differential sensitivity to pressure.</p><p>Stability map on the plane Rayleigh number–solutal Rayleigh Number</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"48 8-9","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144929242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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":"Double-diffusive convection in a plane layer with low thermal conductivity boundaries","authors":"Sergei Prokopev,&nbsp;Tatyana Lyubimova","doi":"10.1140/epje/s10189-025-00514-2","DOIUrl":"10.1140/epje/s10189-025-00514-2","url":null,"abstract":"<p>This study examines double-diffusive convection in a horizontal fluid layer with low thermal conductivity boundaries, where the heat flux is fixed. Using linear stability analysis and nonlinear modeling, the behavior of the system is explored under different thermal and concentration gradients. Two instability modes are identified: monotonous and oscillatory. The monotonous mode, exhibiting longwave patterns, dominates when both gradients contribute to instability. The oscillatory mode occurs when the gradients oppose each other, with stability thresholds dependent on system parameters. Nonlinear modeling confirms the linear theory, showing longwave patterns near the instability threshold and oscillatory behavior when gradients are opposed. These findings offer insights into double-diffusive convection in systems with low thermal conductivity boundaries.</p><p>Stability map on the plane Rayleigh number–solutal Rayleigh Number</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"48 8-9","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144853560","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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":"Probing protein–protein interactions with drag flow: a case study of F-actin and tropomyosin","authors":"Camille Bagès,&nbsp;Morgan Chabanon,&nbsp;Wouter Kools,&nbsp;Thomas Dos Santos,&nbsp;Rebecca Pagès,&nbsp;Maria Elena Sirkia,&nbsp;Cécile Leduc,&nbsp;Anne Houdusse,&nbsp;Antoine Jégou,&nbsp;Guillaume Romet-Lemonne,&nbsp;Hugo Wioland","doi":"10.1140/epje/s10189-025-00509-z","DOIUrl":"10.1140/epje/s10189-025-00509-z","url":null,"abstract":"<p>Tropomyosins are central regulators of the actin cytoskeleton, controlling the binding and activity of the other actin binding proteins. The interaction between tropomyosin and actin is quite unique: single tropomyosin dimers bind weakly to actin filaments but get stabilised by end-to-end attachment with neighbouring tropomyosin dimers, forming clusters which wrap around the filament. Force spectroscopy is a powerful approach for studying protein–protein interactions, but classical methods which usually pull with pN forces on a single protein pair, are not well adapted to tropomyosins. Here, we propose a method in which a hydrodynamic drag force is applied directly to the proteins of interest, by imposing a controlled fluid flow inside a microfluidic chamber. The breaking of the protein bonds is directly visualised with fluorescence microscopy. Using this approach, we reveal that very low forces from 0.01 to 0.1 pN per tropomyosin dimer trigger the detachment of entire tropomyosin clusters from actin filaments. We show that the tropomyosin cluster detachment rate depends on the cytoplasmic tropomyosin isoform (Tpm1.6, 1.7, 1.8) and increases exponentially with the applied force. These observations lead us to propose a cluster detachment model which suggests that tropomyosins dynamically explore different positions over the actin filament. Our experimental setup can be used with many other cytoskeletal proteins, and we show, as a proof-of-concept, that the velocity of myosin-X motors is reduced by an opposing fluid flow. Overall, this method expands the range of protein–protein interactions that can be studied by force spectroscopy.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"48 8-9","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144832147","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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}