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Physics Physics Biological Physics

physics.bio-ph Watch Biological Physics

Tuesday 25 August

Biological Physics · Cross-listed from physics.optics

Metalens stereoscopic optical palpation for imaging cancer mechanics

Haoyi Yu, Rhys Jones, Chi Li et al. (+13 more)

Accurate intraoperative margin assessment is critical for complete resection of solid tumours. However, surgeons routinely rely on manual palpation, which is highly subjective and fundamentally limited by poor spatial resolution, and pre-operative imaging lacks real-time feedback. While emerging optical elastography techniques offer quantitative mechanical contrast, their reliance on bulky optical components necessitates cumbersome alignment and hinders integration into miniaturised surgical instruments. Here, we report metalens stereoscopic optical palpation (MSOP), a nanophotonic imaging platform leveraging a binocular metalens integrated with a single CMOS sensor to achieve high-fidelity, self-aligned elastography. By replacing complex bulk optics with a compact stereoscopic architecture, MSOP enables robust, high-contrast mapping of tissue surface stress. Following validation in heterogeneous silicone phantoms, we demonstrate MSOP's translational potential by characterising the mechanical signatures of malignancies in fresh mouse pancreatic cancer models, as well as excised human breast and liver specimens. By providing reliable, label-free mechanical contrast across diverse oncological landscapes, MSOP offers a compact tool for precise intraoperative margin delineation to reduce re-excision rates and improve surgical outcomes.
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All authors Haoyi Yu, Rhys Jones, Chi Li, Bo He, Renate Zilkens, Louise N. Winteringham, Laura Gale, Mireille Hardie, Fiona Bellamy, Saud Hamza, Christobel M. Saunders, Liver Cancer Collaborative, Stefan A. Maier, Brendan F. Kennedy, Haoran Ren, Qi Fang

Biological Physics

Quantifying the Biophysical Properties of Red Blood Cells in Gaucher Disease

Zhaojie Chai, Marine de Person, Pierre A. Buffet et al. (+2 more)

Gaucher disease (GD), the most common lysosomal storage disorder, alters red blood cell (RBC) mechanics and circulation, contributing to vascular occlusions, bone infarcts, and splenomegaly. However, the individual roles of GD-RBC biophysical properties in these processes remain unclear. Here, we present a combined computational-experimental investigation to quantitatively characterize GD-RBC biophysical properties and determine how specific mechanical parameters drive abnormal RBC behavior. Informed by experimental data, we independently quantify key RBC properties, including shear modulus (mu), surface-to-volume ratio (S/V), and bending modulus (k_c). Based on these parameters, we construct three GD-RBC subtypes (GD-RBC1-3) to systematically isolate their individual contributions. At the single-cell level, optical tweezers simulations show up to ~27% reduction in axial diameter and ~42% reduction in transverse compression. Tank-treading dynamics exhibit non-monotonic behavior, with rotation frequencies increasing by up to ~70% or decreasing under elevated bending rigidity. In confined flow, traversal times through microchannel constrictions increase by more than a factor of two, while splenic slit passage times rise from ~250 ms (control) to >1200 ms for the severe GD-RBC subtype, approaching a functional no-passage threshold. At the population level, viscosity simulations demonstrate that these alterations collectively elevate blood viscosity, with small fractions (~4.0%) of highly rigid cells disproportionately increasing flow resistance. Overall, this study provides a quantitative and mechanistic framework that disentangles the contributions of key RBC parameters to abnormal behavior in GD, linking cellular-scale biophysics to hematologic dysfunction and microvascular occlusion.
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All authors Zhaojie Chai, Marine de Person, Pierre A. Buffet, Melanie Franco, George Em Karniadakis

Monday 24 August

Biological Physics · Cross-listed from cond-mat.stat-mech

Entropy Production Bounds the Accuracy of Computation in Markov Networks

Songela W. Chen and David T. Limmer

Biological and artificial networks compute by transforming time-dependent inputs into functional outputs. Because the internal state of a stochastic network relaxes on finite timescales, its output generally lags behind a changing environment, producing computational errors. We show that for reversible continuous-time Markov networks the error admits a universal thermodynamic bound. Decomposing the total error into representation and lag contributions, we derive an inequality relating the lag error to the entropy production rate and a memory time equal to the integrated equilibrium autocorrelation of the output observable. The bound implies that accurate dynamical computation requires either substantial dissipation or long-lived memory encoded in slowly relaxing modes. We demonstrate these principles in artificial Markov networks and in models of biochemical information processing. Our results establish a thermodynamic limit on information processing in stochastic networks and provide a quantitative framework for understanding the energetic costs of biological computation.
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Biological Physics · Cross-listed from eess.SP

Physics-Constrained Deep Learning Model for Contactless Blood Pressure Monitoring from Triaxial Bodyseismography

Yuanyuan Zhang, Yida Zhang, Jiahui Li et al. (+6 more)

Ballistocardiography (BCG) is promising for unobtrusive long-term blood pressure (BP) monitoring in laboratory settings, but traditional BCG signals are vulnerable to the variations in body-bed interaction with shifted fiducial points in temporal or amplitude axis, and BP varies with personal hemodynamic changes, causing misaligned representations that affect model generalizability and robustness. In this work, we propose Phy-BP, a physics-constrained BP estimation framework based on triaxial bodyseismography (BSG) acquired using bed-mounted sensors as an extension of single-axis BCG. Firstly, we design an adaptive quality-control algorithm combining neighboring beat patterns and universal cardiogenic templates to retain reliable cardiac components. Secondly, we propose a physical model of wave propagation through the body-bed system to constrain latent feature evolution, aligning triaxial representations generated by a shared cardiogenic excitation. These mechanical constraints connect multi-axis feature learning to body-bed dynamics and complement data-driven regression from vibration signals. Evaluation on a 162-hour hospital dataset from 21 subjects against invasive arterial BP yields a mean absolute error of 5.07 mmHg, a prediction-error standard deviation of 7.24 mmHg, and a Pearson correlation coefficient of 0.86 for mean arterial pressure. This framework is intended for unobtrusive monitoring during rest and sleep, with potential applications in overnight hospital and home monitoring.
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All authors Yuanyuan Zhang, Yida Zhang, Jiahui Li, Yuyan Wu, Fei Dou, Xiao Yin, Zhenlin An, Hae Young Noh, Wenzhan Song

Biological Physics

Roles of vortices and turbulent eddies in particle preferential concentration and deposition in the human respiratory tract

Mengtao Li, Yawei Wang, Wentao Feng et al. (+1 more)

Precise targeting of pharmaceutical aerosols is critical to the efficacy and safety of inhaled therapies. This study focused on the influences of vortices and turbulent eddies on preferential concentration and deposition of pharmaceutical aerosols within the human respiratory tract. By reconstructing a high-fidelity respiratory tract geometry spanning the nasal cavity down to sequential bronchi from computed tomography (CT) images and assigning physiologically realistic transient breathing profiles, an unsteady Reynolds-averaged Navier-Stokes (URANS) framework using the shear stress transport (SST) k-w turbulence model and a stress-blended eddy simulation (SBES) framework of human respiratory tract were built. Beyond flow field analyses, Vorono diagrams and a set of newly-defined spatial accuracy metrics were adopted to quantitatively characterize particle distributions and localized prediction discrepancies. Spectral analysis revealed that the SBES simulations adequately recovered the prominent Kolmogorov -5/3 inertial scaling law. Such turbulent motion induces pronounced radial turbulent dispersion, forming particle clusters with higher cluster fractal dimensions D> 1.2 on the mid-plane of the laryngopharynx. Spatial accuracy metrics uncovered a critical dual deficiency of the URANS model: globally over-smears near-wall deposition by roughly 20%, simultaneously fails to resolve most high-concentration `hotspots' (the top 5% local extrema). These findings highlighted that the numerical resolution of transient vortices and turbulent eddies constitutes an indispensable prerequisite for accurately predicting of particle transport and deposition in the human respiratory tract.
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All authors Mengtao Li, Yawei Wang, Wentao Feng, Yubo Fan

Biological Physics · Cross-listed from cond-mat.mtrl-sci

The Achilles tendon enthesis rebuilds its mineralization front on reloading but retains a nanoscale imprint of unloading

M.L. Stammer, C. Camy, M. Frewein et al. (+16 more)

The enthesis is a graded fibrocartilaginous interface that transfers load between tendon and bone, yet the nanoscale mechanisms stabilizing its mineralization front remain unclear. Here, we combine multimodal 2D/3D X-ray imaging with nonlinear optical microscopy to map structural, crystalline and extracellular matrix organization across the murine Achilles tendon enthesis under unloading and reloading. Unloading reduces the tidemark-associated two-photon fluorescence (2PF) peak and is accompanied by diffuse mineralization into previously unmineralized fibrocartilage. This unloading-associated mineral exhibits increased apparent crystallite size, an enlarged c-axis lattice parameter, reduced crystalline texture and a diminished collagen order gradient, consistent with an altered mineralization environment. Upon reloading, the 2PF peak recovers, but a new tidemark forms ~20 um from the original boundary, creating a zone with a persistent nanoscale imprint in the mineral tessellation. These findings establish the enthesis as a mechanically governed graded interface in which matrix-mediated boundary control constrains mineral formation and in which a record of mechanical history is imprinted into the nanostructure.
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All authors M.L. Stammer, C. Camy, M. Frewein, I. Silva Barreto, C. Genovesio, M. Eckermann, A. Karimbana, K. Iliopoulos, R. Ranjan, N. Wittig, T. Fovet, T. Brioche, A. Chopard, M. Burghammer, S. Brasselet, H. Birkedal, M. Pithioux, S. Roffino, T.A. Grünewald

Biological Physics

From Maxwell Fluid to Kelvin Voigt Solid: A Transient Network Model of Condensate Aging and Morphology Transition in Phase Separation

Bhanjan Debnath

Biomolecular condensates can undergo striking changes, such as transitioning from a liquid-like to a gel- or a solid-like aggregate due to changes in molecular interactions in response to changes in the biochemical environment. The question of how modified molecular interactions lead to such a transition in the material properties and spatial organization of condensates has not yet been elucidated. To address this question, we represent the biochemical environment as a triphasic mixture comprising a liquid-like protein-rich phase, a network-like protein-rich phase, and solvent. Owing to a change in the biochemical environment, protein molecules can reversibly switch between two conformational states. In a switched conformational state, the cross-linking domains of molecules are exposed which promote transient network formation in phase separated states. We develop a transient-network model and a continuum framework that couples phase separation, molecular switching, and dynamic cross-linking to predict condensate morphology and mechanics. The transient-network model predicts that a non-aging network behaves like a Maxwell fluid. When a network slowly ages via stabilization of cross-links, it shows Maxwell-like behavior and waiting time-dependent relaxation. However, a strongly aged network shows elastic recoil like characteristic of a Kelvin-Voigt solid. Our coupled continuum model demonstrates that the interplay of molecular switching and dynamic cross-linking in network formation shapes the spatial organization of condensate phases. In summary, this work demonstrates a mechanistic route explaining how conformational switching and molecular cross-linking regulate material properties and morphology of condensates.
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Sunday 23 August

Biological Physics · Cross-listed from physics.chem-ph

From Steady-State to Ultrafast: Resonance Raman Approaches for Biological Samples

Juan J. Romero, Bruno Robert and Manuel J. Llansola-Portoles

Vibrational spectroscopy reports on molecular structure with chemical-bond specificity, but in biological systems the vibrational signals of a target chromophore are typically buried under contributions from the surrounding matrix. Resonance Raman (RR) spectroscopy addresses this problem by matching the excitation wavelength to an electronic transition of the chromophore of interest, which increases Raman cross sections by up to six orders of magnitude and restricts the enhanced modes to those coupled to the resonant electronic state. This chapter introduces the physical basis of resonance enhancement and shows how RR isolates chromophore-specific vibrational markers in complex biological systems. We then extend the same principle into the time domain with femtosecond stimulated resonance Raman spectroscopy (FSRRS). In FSRRS, the Raman pump is tuned across the visible range and can be placed in resonance with the transient absorption of a chosen excited-state species, which makes the Raman pump wavelength an additional experimental variable. Sampling this variable across the excited-state absorption manifold provides a selection criterion that separates coexisting transient species sharing a common vibrational window.
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Saturday 22 August

Biological Physics · Cross-listed from cond-mat.soft

Voltage dynamics of spherical membranes from single ion channel currents

Sirui Ning, Joshua B. Fernandes, Karthik Shekhar et al. (+1 more)

Ion channels and pumps drive ion-selective currents through cell membranes at localized sites, yet a cell's electrical state is routinely summarized by a single transmembrane voltage. Combining theory and numerical simulations, we resolve the spatiotemporal dynamics of charge reorganization driven by a localized current on a spherical membrane vesicle. At early times, the response is insensitive to membrane geometry: as in the case of a flat membrane (arXiv:2407.11947; arXiv:2508.14001), the transmembrane voltage decays in a monopolar fashion, varying inversely with distance from the source, and crosses over to a dipolar tail that scales as the inverse cube of distance. Under sustained current, this monopolar response spreads outward from the source. Because the vesicle is closed, this response cannot persist indefinitely; once the monopolar front traverses the entire vesicle, the subsequent charging dynamics is dominated by a spatially uniform mode corresponding to capacitive charging of the membrane. We further decompose the bulk potentials into an electrostatic image-charge component that generates the bulk electric fields and a spatially uniform capacitive mode that can be represented as an equivalent circuit. We also derive a nonlocal cable equation governing the transmembrane voltage dynamics and show that the uniform mode is its long-time solution. This work provides a first-principles basis for the electrophysiological simplification of an electrotonically compact cell.
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All authors Sirui Ning, Joshua B. Fernandes, Karthik Shekhar, Kranthi K. Mandadapu

Biological Physics · Cross-listed from cond-mat.soft

Non-uniform swelling of polyelectrolyte hydrogels: effects of charge regulation

Du Chen, Rudolph Podgornik, David Andelman et al. (+4 more)

We investigate the impact of charge regulation (CR) on the non-uniform swelling behavior of polyelectrolyte hydrogels. The Poisson-Boltzmann theory with electro-elastic coupling between the local polymer density and elastic deformation is considered. We investigate the spatial distributions of the elastic displacement and polymer density under different salt concentrations and compare charge-regulated gels with fixed-charge (non-CR) gels of the same net charge. Our results show that the CR induces spatially varying charge fractions, which strengthen the electro-elastic response and lead to stronger non-uniform swelling compared with non-CR gels. These findings provide a theoretical basis for understanding and controlling non-uniform swelling in responsive polyelectrolyte hydrogels.
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All authors Du Chen, Rudolph Podgornik, David Andelman, Xianghong Wang, Linli He, Shigeyuki Komura, Bin Zheng

Friday 21 August

Biological Physics · Cross-listed from physics.soc-ph

Earth as a Closed Life-Support System: Finite Buffers, Dynamical Thresholds, and Planetary Sustainability

Jean-Pierre Gazeau

We formulate planetary sustainability as a minimal nonequilibrium problem for coupled finite stocks and fluxes, using the operational language of closed life-support systems: inventories, flux balances, recycling efficiencies, processing capacities, reserve times and failure thresholds. Rather than asserting that waste is universally more limiting than resources, we propose a reserve-time principle: the binding constraint is whichever buffer becomes critical first. A nonlinear model coupling a regenerative resource stock, an accumulated waste stock and an activity variable exhibits a soft threshold, where waste suppresses growth while processing remains formally capable, and a hard threshold, where waste production exceeds maximal processing capacity. With immediate waste feedback, activity settles globally at the soft threshold; the hard threshold is crossed only transiently or under exogenous forcing. A resource-side threshold completes the picture. We extend the model to recycling and to multiple resource and waste classes, give a numerical example, situate the four-function description of life against the origin of life, viruses and aging, contrast the biosphere's two long-term failure modes, and relate the approach to Spaceship Earth, planetary boundaries, Limits to Growth, System Dynamics and stock-pollution economics.
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Biological Physics

Amphibian water to land transition reveals physical limits of olfaction

Martin James, Loranzie S. Rogers, Moreira Salsman et al. (+3 more)

The evolutionary transition from water to land required animals to sense chemicals under fundamentally different physical constraints. Because chemicals diffuse orders of magnitude more slowly in water than in air, aquatic olfaction faces significant challenges in odor capture. Yet, aquatic organisms exhibit strikingly sensitive and rapid chemosensory behaviors. Amphibians represent a powerful model to address this discrepancy because they transition from aquatic to terrestrial environments within a single lifetime. Here, we combine metamorphosis of adult axolotls with asymptotic theory and numerical simulations to show that odorants are captured by diffusion in tens of seconds in water compared with milliseconds in air; yet aquatic axolotls respond to odorants on a much more rapid timescale. Despite inefficiency, we find that proximity to large patches of highly concentrated odor supports sensation in the presence of flow. While aquatic axolotls did not display any respiratory flow, they display behavioral adaptations that generate flow and may even draw in odor through ciliary pumping. Thus, aquatic olfaction is slower and more wasteful than terrestrial olfaction, but behavioral adaptations support olfaction as an effective proximal sense.
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All authors Martin James, Loranzie S. Rogers, Moreira Salsman, Francesco Viola, Nicholas W. Bellono, Agnese Seminara

Biological Physics

Thermal scaling laws for open-water swimming

Henry van den Bedem and Ellen Kuhl

Open-water swimming defines a thermal phase-boundary problem in which metabolic heat production competes with environmental heat loss. We derive a scaling law that predicts the critical water temperature and shows how body size, swim pace, and insulation shift this boundary. Longitudinal warm- and cold-water data reveal transient dynamics that exceed single-compartment predictions, but emerge naturally from core–peripheral physiology. Together, our results suggest that thermal safety depends on swimmer-specific characteristics and swimming conditions, not on water temperature alone.
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Thursday 20 August

Biological Physics · Cross-listed from cond-mat.stat-mech

The Memory Hidden in Response Fluctuations: Trajectory-Level Fluctuation-Response Theory and Inequalities for Non-Markovian Jump Dynamics

Jiming Zheng and Zhiyue Lu

Modern experiments often record nonequilibrium dynamics as sequences of discrete events whose rates depend on the realized past. We develop a fluctuation-response theory for such non-Markovian jump processes directly on the observed event record. Memory can destroy a closed master equation for the state probabilities. Each transition count nevertheless obeys an exact stochastic equation. After the history-dependent mean event tendency is subtracted, the remaining random increment is a martingale increment–the part of the event that cannot be predicted from the past. Martingale increments associated with different transitions and different times are orthogonal. These increments form a complete orthogonal basis for the random deviation of any observable measured from the record, such as a current, occupation time, or event count. The coefficient of a given increment is the event-consequence kernel. It measures how that event changes the predicted final observable, relative to continuing without the event, for the particular history already realized. Multiplying this kernel by the event intensity gives the history-conditioned response to perturbing the corresponding transition rate. Thus, the intensity-normalized response is exactly the expansion coefficient of that event in the observable fluctuation. This identification yields exact finite-time and finite-frequency fluctuation-response relations. Averaging over histories leaves a nonnegative response-heterogeneity gap. The gap measures how strongly the consequence of the same event varies across histories and tests whether a proposed memory coordinate is response-sufficient. Finite-history versions can be estimated from spontaneous trajectories. Bounding the logarithmic rate sensitivity further gives response-kinetic uncertainty relations controlled by dynamical activity.
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Biological Physics

Growth phases of an active tissue: determinate, indeterminate, and proportionate

Jigyasa Watwani, K. Vijay Kumar and Vishal Vasan

Growth may cease at a target size or continue throughout life: the determinate and indeterminate phenotypes. We develop an active viscoelastic continuum model of a tissue growing along one axis, in which cell division and death generate active stresses. We find two asymptotic states: one in which the tissue reaches a relative size fixed by its material parameters, and one in which it elongates linearly without bound. Which state is realised is set by the ratio of active stress to elastic modulus. The transition originates in a bound on the elastic stress the tissue can support: a sufficiently large activity can never be balanced. In a tissue made of parts with different material properties, the growing phase settles into fixed length proportions, set by the mechanical impedances of the parts rather than inherited; matching impedances to initial lengths preserves the proportions the tissue began with. Determinate, indeterminate and proportionate growth thus appear as regimes of one continuum mechanical framework.
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Biological Physics

SoilWaterNow: Soil water nowcasting for mapping plant available water (PAW) across paddocks for improved on-farm decision-making

Yi Yu, Mikaela J. Tilse, Patrick Filippi et al. (+1 more)

Timely, paddock-scale estimates of plant-available water (PAW) can support crop management in water-limited grain systems. We present the Sydney Soil Water-Energy Balance (SWEB) model, a scalable, physically consistent modelling framework that integrates satellite and climate data with soil properties to estimate crop evapotranspiration and root-zone soil moisture (RZSM) at daily, 30 m resolution. SWEB was validated nationally against different SM monitoring networks across Australia, which demonstrated robust performance across diverse grain-growing environments (correlation coefficients generally ranged from 0.70 to 0.85 for most regions). In future applications, mid-season PAW nowcasts could be combined with water-use-efficiency approaches to estimate water-limited yield potential and inform responsive management decisions, such as nitrogen fertiliser top-up recommendations.
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All authors Yi Yu, Mikaela J. Tilse, Patrick Filippi, Thomas F. A. Bishop

Wednesday 19 August

Biological Physics

Elongation suppresses rheotaxis and enables microfluidic enrichment of e̱ta}-lactam-resistant bacteria

Ran Tao, Nathaniel C. Esteves, Jay Zhu et al. (+1 more)

Antimicrobial resistance (AMR) complicates the treatment of diseases including lung and urinary tract infections (UTIs), which are among the most common bacterial infections worldwide. Motile pathogens can use rheotaxis to swim upstream against fluid flows, potentially promoting access to upper regions of anatomical tracts. However, it remains unclear how antibiotic exposure and resistance influence this transport process. Here, using single-cell tracking microscopy, we investigate how elongation induced by e̱ta}-lactam antibiotics affects the rheotactic migration of E. coli in confined microfluidic channels. Remarkably, we find that rheotaxis can be inhibited 100-fold by antibiotics, even if the susceptible elongated cells remain fully motile. However, resistant bacteria remain short and retain upstream migration under the same conditions. Using genetically engineered bacteria with tunable cell length, we show that the underlying mechanism that governs rheotaxis is the coupling between cell morphology and flow vorticity, where elongated cells are rapidly rotated downstream. Finally, we exploit this length-dependent transport difference to separate short and elongated cells under flow and enrich ampicillin-resistant cells from mixed populations. Together, these results establish bacterial elongation as a key control parameter for rheotactic transport, and provide a proof-of-concept strategy for enriching e̱ta}-lactam-resistant bacteria for potential use in rapid AMR detection.
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All authors Ran Tao, Nathaniel C. Esteves, Jay Zhu, Arnold J. T. M. Mathijssen

Tuesday 18 August

Biological Physics

A higher-derivative model predicts a smoothness vs duration relationship in head-pointing movements

N. Boulanger, F. Buisseret, J. Burny et al. (+4 more)

Head movements require integration of visual, proprioceptive, vestibular, and cervical motor signals. The dynamical principles governing their temporal organization remain unclear. We tested whether a Pais-Uhlenbeck oscillator – a higher-derivative model with one internal frequency parameter $\omega$ – can model head kinematics during virtual-reality-based head pointing. Our model predicts a parabolic relationship between movement duration ($T$) and smoothness (log-dimensionless jerk, $LDLJ$) that we have experimentally checked. Sixty-two healthy young adults performed horizontal and vertical head movements with an amplitude of 30{\deg}. Movement duration, endpoint accuracy, peak angular velocity, overshoot, and $LDLJ$ were extracted from headset kinematics. A mixed-effects parabolic regression confirmed the predicted $LDLJ$ vs $T$ parabolic relation ($R^2 = 0.851$). The quadratic coefficient was not significantly modified by direction or participant, but the intercept and linear coefficient differed between horizontal and vertical movements. As an internal consistency check of the model, we find that the parameter $\omega$, as estimated from the regressions, gives time durations that closely match the measured ones. These findings outline a nonlinear temporal organization of head pointing modulated by direction-specific biomechanical constraints, and suggest that higher-derivative mechanics may provide a principled, non-invasive framework for quantifying cervical motor planning, warranting further validation in clinical populations.
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All authors N. Boulanger, F. Buisseret, J. Burny, F. Dierick, W. Estievenart, A. Teregulov, O. White

Biological Physics

An information-theoretic perspective on feed-forward loop abundances in transcriptional networks

Mintu Nandi, Sudip Chattopadhyay and Suman K Banik

In the transcriptional networks of Escherichia coli and Saccharomyces cerevisiae, the eight feed-forward loop (FFL) motifs occur at markedly different frequencies. Although previous studies have linked the abundant C1- and I1-FFLs to specific dynamical functions, a common account of the broader pattern is lacking. To address this gap, we adopt an information-theoretic approach. An FFL transmits information through two paths that share an input and converge on an output, suggesting that their interaction may contribute to differences among motifs. To investigate this, we decompose input-output mutual information (MI) into pathway MI and interference MI (IMI). Here, the pathway MI collects the contributions of individual pathways, whereas IMI identifies the contribution that arises from their interference. We find that within a representative parameter regime, IMI values of FFLs produce a hierarchy that closely resembles the abundance ordering in E. coli, whereas total and pathway MIs do not. Motivated by this observation, we perform constrained optimization that identifies parameter regimes compatible with abundance-like targets for both S. cerevisiae and E. coli. We relate the optimized IMI hierarchy to pathway interference strength and local pathway sensitivities to understand the underlying biophysical origin. Our framework thus probes the correspondence between pathway interference, information transmission, and motif-abundance hierarchies.
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Biological Physics

MolDStruct: benchmarking a hybrid Monte Carlo/Molecular Dynamics model for X-ray free-electron laser ionisation and fragmentation dynamics

Friederike Krüger, Simon Liljeblad, Sebastian Cardoch et al. (+6 more)

Single Particle Imaging with intense X-ray free-electron laser pulses requires modelling of the resulting ionisation and Coulomb explosion dynamics of biomolecules to optimise experimental parameters and enable correct structural reconstruction, yet simulating the complete dynamics at protein scale is beyond the reach of quantum-mechanical methods. To address this, we developed \moldstruct, a hybrid Monte Carlo/Molecular Dynamics code built on GROMACS that couples high intense X-ray ionisation dynamics modelled through a Monte Carlo module with classical Molecular Dynamics for atomic propagation. Benchmarked against quantum mechanical calculations for di-alanine, MolDStruct agrees in fragmentation patterns above a mean charge per atom of $\bar{z} \approx 1.35$. Compared with Coulomb explosion imaging experimental data for 2-iodopyridine, simulated momentum distributions reproduce the experimental Newton plots in fragment direction and fall within the range of experimental absolute momenta, with a moderate overestimation. We further apply MolDStruct to Protein Explosion Imaging, a method that classifies molecular structures from explosion ion maps recorded on a detector, demonstrating via dimensionality reduction that conformers of the 16-residue peptide $\mathrm{Ala}_16$ and five chromophore-labelled ubiquitin mutants are distinguishable. These results establish MolDStruct as a practical tool for simulating radiation damage and Coulomb explosion dynamics of biomolecules at protein scale, where quantum-mechanical methods are computationally infeasible.
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All authors Friederike Krüger, Simon Liljeblad, Sebastian Cardoch, Måns Rosenbaum, Lasse Eisenach, Ibrahim Dawod, Nicuşor Tîmneanu, Carl Caleman, Tomas André

Monday 17 August

Biological Physics · Cross-listed from quant-ph

Scientific applications of quantum computing: challenges and opportunities

Bruno Camino, C. Richard A. Catlow, John Buckeridge et al. (+13 more)

The predictive simulation of molecules and materials has had a broad and significant impact. It nevertheless remains constrained by the cost of accurately treating electronic correlation, excited states, and complex energy landscapes. Quantum computing offers a fundamentally different computational paradigm in which quantum states are encoded and manipulated directly rather than approximated on classical hardware. Here we discuss where this approach may provide a genuine scientific advantage in chemistry, materials science, and biochemistry. Promising directions include the high-accuracy treatment of correlated active spaces, improved excited-state simulations, and accelerated exploration of combinatorial structure spaces. The central challenge is therefore not qubit scaling alone, but demonstrably chemically meaningful gains in predictive reliability. We argue that near-term value is most likely to come from disciplined workflow integration rather than wholesale replacement of classical methods. Noisy physical devices, error-mitigated utility experiments, early fault-tolerant devices, and fully fault-tolerant quantum computers offer different scientific prospects, and claims of usefulness must be tied to the specific regime being discussed. Quantum computing will become scientifically valuable when it demonstrably reduces uncertainty in computed energies, rates, spectra, or materials stability after the full costs of state preparation, measurement, error handling, and coupling to classical simulation are included.
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All authors Bruno Camino, C. Richard A. Catlow, John Buckeridge, Alin M. Elena, Vladimir V. Gusev, Sarah Harris, Thomas W. Keal, Glenn Jones, Vivien Kendon, Syma Khalid, Phalgun Lolur, Jamal A. Nasir, Matthew J. Rosseinsky, Chris-Kriton Skylaris, Paul A. Warburton, Scott M. Woodley

Saturday 15 August

Biological Physics · Cross-listed from q-bio.NC

The effect of the excitatory feedback in anticipated synchronization and phase bistability regimes in neuronal populations

Julio N. Machado, Joana M. G. L. Silva, Katiele V. Brito et al. (+2 more)

Anticipated synchronization (AS), in which the receiver leads the sender and the phase lag is negative, can emerge in unidirectionally coupled dynamical systems when the receiver has faster internal dynamics than the sender. In cortical-like population models, AS and bistability between AS and delayed synchronization (DS) have been reported mainly in unidirectional motifs and have been proposed as possible explanations for phase relations observed in electrophysiological recordings. Because cortical areas are often connected bidirectionally, it is important to understand how excitatory feedback from the receiver to the sender affects the emergence and persistence of anticipatory synchronization and phase-bistable regimes. Here, we investigate the effect of the excitatory feedback on the phase relations between two cortical-like neuronal populations. We show that AS and phase bistability are not restricted to strictly unidirectional architectures, but remain robust in the presence of reciprocal coupling. In addition, we find that the transition from AS to DS can occur through different routes within the same motif, either via a bistable regime or via zero-lag synchronization, depending on the inhibitory coupling. More generally, the model exhibits a rich repertoire of phase relations, including: positive, negative, and zero-lag phase-lockings, as well as phase bistability, and phase-drift regimes. These results are consistent with the diversity of phase relations reported in electrophysiological experiments and suggest that fixed structural connectivity may support rapid reconfiguration of functional dynamics without requiring structural rewiring.
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All authors Julio N. Machado, Joana M. G. L. Silva, Katiele V. Brito, Rodrigo Pena, Fernanda Selingardi Matias

Biological Physics · Cross-listed from cs.LG

Earth Observation Foundation Models for Terrestrial Ecohydrology: From Representation Learning to Process Inference

Yi Yu, Jian Peng, Yucheng Lin et al. (+2 more)

Earth observation foundation models (EOFMs) are emerging as reusable representation frameworks for data-driven retrieval, prediction and process modelling within ecohydrology, which integrate EO, meteorological forcing and process models to characterise coupled water, energy and carbon dynamics in vegetation and soil across scales. However, there is yet to be an ecohydrology-specific synthesis assessing the EOFM relevance, application evidence or evaluation requirements under uncertain reference data, scale mismatch and temporal dependence. Here, we develop a framework for determining when EOFMs support interpretable inference and identify a mismatch between EOFMs and ecohydrological requirements. Firstly, an observation-to-inference hierarchy shows that relevance depends on target-specific sensing pathways, spatial-temporal support and traceable uncertainty. Secondly, a meta-analysis shows that pretraining is dominated by reflected optical and active-microwave data, with sparse thermal coverage and no passive-microwave-emission sources. Thirdly, our synthesis of ecohydrological applications finds strongest support for spatial context, label-efficient adaptation and hybrid workflows. Evidence declines with inference depth; independent validation of fluxes, coupled dynamics, event trajectories, calibrated uncertainty and decision benefits remains sparse. Fourthly, our benchmark audit finds stronger coverage of fair adaptation and reproducibility in general EOFM suites, and of process targets, direct reference evidence and distribution shifts in ecohydrological evaluations; physical consistency and uncertainty remain weakly assessed. These findings motivate a process-aware framework aligning EOFM design and evaluation with the target variable, observation pathway and process timescale, supporting trustworthy monitoring and interpretation of coupled water, energy and carbon dynamics.
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All authors Yi Yu, Jian Peng, Yucheng Lin, Trevor F. Keenan, Thomas F. A. Bishop

Biological Physics · Cross-listed from cond-mat.soft

Shear effects in active models of normal and cancer cells

Souvik Sadhukhan, Rajsekhar Das, Lin Zhao et al. (+2 more)

Mechanical properties of biological tissues, driven by passive and active forces, play a vital role in several processes ranging from development to cancer metastasis. However, the dynamical responses of cells in tissues, subject to mechanical deformations such as shear and the associated rheological properties, are not well characterized. Here, we use three-dimensional agent-based models for normal and cancer tissues to investigate their responses to simple shear as a function of cell stiffness and stochastic active forces. In the normal epithelium, with uniform strength of active force, the yield stress as a function of shear rate follows the Herschel-Bulkley form over a range of cell volume fraction. Strikingly, the shear rate dependence and the elasticity-dependent changes in the yield stress fall on master curves upon suitable scaling. To model cancer-like behavior, a certain fraction ($N_p$) of cells was chosen to have enhanced activity and decreased stiffness. As $N_p$ increases, the extent of collective cell movement decreases, transitioning from affine (collective) to non-affine (individualistic) movement, a finding that is in accord with imaging experiments. Simulations of a model of a stiff solid tumor, with radius $R_s$ embedded in normal tissue, show that as $R_s$ increases, the yield stress increases. Interestingly, the cells migrate collectively as $R_s$ increases. A Gaussian Mixture Model (GMM) and a mean field theory quantitatively account for the simulation as well as experimental results on cancerous, non-cancerous, and a mixture of these two types. The combined theoretical and experimental study establishes that heterogeneity in stiffness and activity determines non-affine movements in normal and cancer tissues.
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All authors Souvik Sadhukhan, Rajsekhar Das, Lin Zhao, Wolfgang Losert, D. Thirumalai

Biological Physics · Cross-listed from nlin.CD

An Idealized Delay-Differential Model of Scuba Diver Porpoising and Runaway Ascent

Sandy Hardian Susanto Herho, Faizal Ade Rahmahuddin Abdullah, Iwan Pramesti Anwar et al. (+5 more)

A scuba diver holding constant depth balances on an unstable equilibrium: the gas carried in the suit and buoyancy compensator compresses with depth, so the buoyant force falls as the diver sinks and rises as the diver ascends. We represent the diver as a proportional-derivative controller that regulates this compressible-buoyancy saddle after a finite reaction delay, and we derive the governing delay differential equation from the vertical force balance and the isothermal gas law, reducing it to a damping ratio, two control gains, and a dimensionless delay. The characteristic spectrum, obtained by pseudospectral collocation of the semigroup generator and checked against a direct Newton solution of the characteristic equation, locates the Hopf boundary that separates stable hovering from sustained porpoising; for the baseline diver the critical reaction delay is 3.36 s and the onset period is 28.8 s. The bifurcation is supercritical, and because the saturating force is the quadratic hydrodynamic drag, the limit-cycle amplitude grows in proportion to the delay excess rather than as its square root. The safe-operating envelope shows that runaway ascent is triggered by saturation of the compensator, not by loss of linear stability, so a stable and an unstable diver can share the same escape threshold. As onset is approached, the lag-one autocorrelation and variance rise while the fitted recovery rate falls and matches the spectral abscissa, giving an eigenvalue-exact early warning of the transition.
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All authors Sandy Hardian Susanto Herho, Faizal Ade Rahmahuddin Abdullah, Iwan Pramesti Anwar, Faruq Khadami, Alfita Puspa Handayani, Karina Aprilia Sujatmiko, Rusmawan Suwarman, Dasapta Erwin Irawan

Biological Physics · Cross-listed from q-bio.PE

Social Discounting Enables Fast and Reliable Collective Escape

Zachary P Kilpatrick

Solitary animals face a tradeoff when detecting threats: faster detection means accepting more false alarms. We show that groups can manage this tradeoff better by treating an undisturbed neighbor as evidence against a threat, becoming both faster and more accurate than lone individuals. Modeling each animal as a noisy evidence-accumulator that flees when its belief crosses a threshold, we find that a neighbor's flight signals danger while its stillness signals safety. A naive responder reacts only to flights and inflates false alarms as the group grows; a Bayesian responder weighs both, approximated by a single social discounting rate that interpolates between these limits. This yields closed-form expressions for group performance, including cascade branching ratios that stay strongly subcritical in safety and turn supercritical under threat, so the rate at which an animal discounts a threat while its neighbors stay still can be inferred from behavior alone, and it sets a ceiling on how many neighbors an animal can attend before discounting alone can no longer hold its false-alarm rate. Wild sulphur molly shoals under bird attack are best described by discounting rates well above what individually Bayesian updating supplies over any neighborhood they could plausibly attend, and the same model, at the inferred value, predicts a false-alarm rate that stays constant as shoals grow.
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Friday 14 August

Biological Physics

Length scale of cellular activity determines signatures of epithelial remodeling

Sahil Islam, Anupam Gupta and Mohd. Suhail Rizvi

Cellular activity drives epithelial fluidization — a widespread phenomenon observed during tissue development, remodeling, and repair both in vivo and in vitro. Yet the physical origins and spatial organization of active forces vary widely across biological systems and are often represented by a single generic mechanism in theoretical models. Here, using an active vertex model, we systematically compare four modes of epithelial activity spanning subcellular to tissue scales: apolar motility, polar motility, fluctuating contractility, and mechanochemical regulation. Although all four mechanisms drive the same global transition from a solid-like rectangular tissue to a fluid-like circular morphology, they reach this state through distinct pathways — differing in the rates and topology of junctional rearrangements, cell elimination, and collective motion and leave distinguishable signatures in tissue architecture, cell dynamics, and mechanical relaxation. Among these observables, spatial velocity correlations directly capture the spatial organization of activity: their correlation length and functional form together resolve all four mechanisms. The robustness of these signatures across activity strengths suggests that spatial velocity correlations offer an experimentally accessible means of identifying the physical origin of epithelial activity from live-cell imaging alone.
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Thursday 13 August

Biological Physics

Classification of Intracellular Protein Patterns from Reactive Equilibria

Henrik Weyer, Ching Yee Leung and Erwin Frey

Self-organized spatial patterns are central to nonequilibrium physics and cell biology, yet locating instabilities in multi-component, reaction-diffusion networks remains challenging because standard eigenvalue analyses scale with the number of biochemical states and rely on reaction kinetics often poorly constrained by experiments. Exploiting the common mass-conserving structure of protein reaction kinetics and the fact that nonlinear feedback is typically confined to membrane reactions while lateral membrane diffusion is negligible, we develop a geometric classification that predicts stationary, and approximately also oscillatory, pattern-forming instabilities from reactive equilibria. The developed criteria reduce the stability analysis from the full component space to the space of conserved species. On this reduced space, slope matrices—describing the change of equilibrium cytosolic densities with respect to total species densities—govern onset. Based on densities in chemical equilibrium, this approach eliminates the requirement of comprehensive kinetic knowledge frequently lacking in experimental systems. Thus, a broad range of instabilities can be understood as mass-redistribution instabilities—self-amplifying mass redistribution caused by shifting local equilibria. We apply these criteria to models for the Escherichia coli Min system and the Caenorhabditis elegans polarity system and show that the reduction extends to the mixed-dimensional dynamics in systems coupling bulk cytosolic dynamics with membrane dynamics on the boundary. Together, these results provide an interpretable, broadly applicable, and experimentally accessible framework for diagnosing and designing pattern formation in multicomponent nonequilibrium systems on the basis of conservation laws.
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Biological Physics · Cross-listed from physics.ins-det

Scan-Coil Delay Causes Anisotropic Signal Loss in Fast 4D-STEM

Vishal Kumar, Andreas Jehle, Tizian Lorenzen et al. (+4 more)

Fast pixelated detectors are driving 4D-STEM toward microsecond dwell times, a regime in which the finite response of the scan deflection coils becomes comparable to the dwell time itself. Using direct probe imaging and sub-frame diffraction analysis, we document a significant intra-dwell scan-coil delay that systematically smears the recorded signal anisotropically along the fast scan direction, with a settling timescale of several tens of microseconds. We present a phase-correlation-based sub-frame alignment procedure that measures and corrects this smearing, and we assess its impact on focused and defocused 4D-STEM reconstructions over a range of scan step sizes. The correction restores signal across a broad range of spatial frequencies, with the largest gains at the large step sizes required for low-dose biological imaging. Because it operates on existing data with no modification to the microscope, the method offers a practical route to recovering signal that would otherwise be lost to scan-coil delay.
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All authors Vishal Kumar, Andreas Jehle, Tizian Lorenzen, Julika Radecke, Knut Müller-Caspary, Massimo Kube, Henning Stahlberg

Biological Physics · Cross-listed from cond-mat.soft

Blinking membrane patterns induced by protein binding/unbinding

Hiroshi Noguchi

Nonequilibrium membrane pattern formation is studied using meshless membrane simulation. Bound proteins are considered to have two states that generate different membrane spontaneous curvatures. Protein binding and unbinding occur cyclically owing to chemical potential differences, as an off-lattice active Potts model. It is found that this cyclic binding/unbinding can induce blinking domains, with oscillating size: convex domains of the proteins with a higher spontaneous curvature grow, and subsequently, the proteins change to the other state with a lower spontaneous curvature, resulting in domain shrinkage. These processes repeat. In thermal equilibrium, hexagonal convex domains are formed by the competition between bending and surface tension energies, so that they are stably formed only under positive surface tension. However, blinking domains can form even in tensionless membranes.
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