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The European Physical Journal Plus

Springer Science and Business Media LLC

Preprints posted in the last 30 days, ranked by how well they match The European Physical Journal Plus's content profile, based on 13 papers previously published here. The average preprint has a 0.01% match score for this journal, so anything above that is already an above-average fit.

1
Emergence of travelling wave patterns in resource-mediated tissue competition

Brinas-Pascual, N.; Alarcon, T.; Calvo, J.; Guerrero, P.; Oliver-Bonafoux, R.

2026-08-19 biophysics 10.64898/2026.08.11.744236 medRxiv
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The study of tissue dynamics has been stimulated during the last decades thanks to the use of quantitative descriptions, with the development of several theoretical and computational frameworks, many of them revolving around the notion of reaction-diffusion systems, eventually with additional structure variables beyond time and space. The use of structure variables can accommodate phenotypic traits. In this work, we study a family of competition models, where a given population depends on a resource (e.g. oxygen) and several populations are competing for it. Our quantitative description incorporates phenotypic traits and heterogeneity at the level of cell cycle variations, which influence replication rates via oxygen consumption. This enables us to replicate the fitness of specific subpopulations to environmental conditions (e.g. oxygen shortage or external influences). Using numerical simulations, we show that such models display dynamical pattern formation in the form of coupled travelling wave profiles that expand or retreat at the same wave speed. The full theoretical analysis of such dynamics is quite involved; to circumvent this difficulty, we introduce a quasi-stationary approximation for the resource dynamics. We find that this approximation can reproduce the overall behaviour very accurately, with the additional benefit of allowing theoretical treatment of the reduced model. In this way, we provide estimates on the wave speed which are numerically shown to be robust across a wide range of macroscopic parameters of the full model. The wave speeds are thus found to depend strongly on the proliferation rate of the fittest population, resembling a winner-takes-all dynamics.

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Distributions of threshold crossing times of messenger RNA

Verma, A. K.; Barman, H. K.; Rijal, K.; Das, D.

2026-08-23 biophysics 10.64898/2026.08.20.745891 medRxiv
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Within the studies of stochastic gene expression, apart from the variability of copy number of gene products, the problems of threshold crossing of those products are biologically important as they often lead to terminal cellular events. Here, we study the threshold crossing problem of the messenger ribonucleic acid (mRNA) and present an exact probability distribution of first passage times in Laplace space. The function furnishes moments of any order and also predicts the characteristic time of the exponential tail of the distribution, which we match against Gillespie simulations. We find that all the measures of relative fluctuations of the threshold crossing times show U-shapes within this simple model of mRNA, as was found earlier in more mathematically involved models of threshold crossing time statistics of proteins. Furthermore, we extend the exact formula to include the phenomenon of DNA duplication and the corresponding doubling of transcription rate. As expected, the distribution varies considerably depending on the onset of the duplication stage within the cell cycle.

3
Quantitative Model of Transcriptional Noise Regulation by mRNA Condensates

Lanitis, A.; Kolomeisky, A. B.

2026-08-20 biophysics 10.64898/2026.08.16.745099 medRxiv
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A fundamental biological process of transcription occurs in the cell nucleus, which is a complex medium that also contains multiple heterogeneous structures known as biomolecular condensates. Interestingly, some of these condensates contain mRNA molecules in addition to proteins, suggesting an important cellular role in transcription that is not yet well understood. In this work, we develop a minimal theoretical framework for quantitative investigation of the role of reversible mRNA condensation in transcription. Our discrete-state stochastic approach accounts for the most relevant processes, allowing us to explicitly evaluate the properties of the system and clarify the effects of condensation. Analytical calculations supported by computer simulations suggest that reversible mRNA condensation influences the transcription processes by maintaining a constant level of free mRNA in the nucleoplasm while lowering the degree of stochastic noise and increasing the robustness against external perturbations. Physicochemical arguments are presented to explain these observations. The proposed theoretical framework elucidates important microscopic aspects of transcription, providing a convenient quantitative tool for investigating complex biological phenomena.

4
A Reduced Mechanobiological Framework for Platelet Priming: From Hemodynamic Shear to Mechanosensitive Calcium Entry

Chen, Y.; Liu, X.; Vigolo, D.; Zhuang-Hall, M. S.; Yong, K.-T.

2026-08-09 biophysics 10.64898/2026.08.03.742655 medRxiv
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BackgroundPlatelet activation in flowing blood is a multiscale process in which vessel-scale hemodynamics, red blood cell (RBC) mechanics, adhesive receptor interactions, and intracellular signalling jointly determine thrombotic risk. Individual components are well studied, but a single reduced description that carries each explicitly from vessel-scale flow to mechanosensitive calcium entry, with dimensionally consistent couplings, remains uncommon. ObjectivesWe develop and analyse a reduced, six-module mechanobiological framework for platelet priming spanning the cascade from hemodynamic shear to mechanosensitive calcium entry, and we delineate which elements are supported by existing evidence and which are new, testable hypotheses. MethodsThe framework comprises six coupled modules: (I) hemodynamic forcing from the incompressible Navier-Stokes equations, with an objective principal-strain-rate measure for extensional flow; (II) RBC-mediated platelet margination and near-wall delivery, closed by a near-wall arrival flux; (III) von Willebrand factor (VWF) activation with a bounded kernel and glycoprotein Ib (GPIb) catch-slip capture, resolved through an explicit contact area and a bond-dependent mobility that progressively immobilises wall-interacting platelets; (IV) a single-load membrane-stimulus formulation; (V) mechanosensitive gating and a dimensionally consistent cytosol-store calcium model with extracellular influx; and (VI) a phenomenological mechanical-memory state. We formally derive that the single-platelet stochastic dynamics and the continuum population balance form a Fokker-Planck pair, with the spatially varying diffusivity handled by an explicit drift correction. ResultsThe framework yields a family of mechanochemical dimensionless groups delineating priming regimes. Its central prediction is reformulated as a falsifiable, history-sensitive signature: in a conditioning-test protocol, a low-tension conditioning block charges the memory state, and a fixed sub-threshold test pulse then reports a delay-dependent calcium facilitation that decays on the memory time{tau} m and is distinguishable from no-memory gating, channel adaptation, and residual-calcium priming. We show explicitly that the previously proposed pulsatile-versus-monotone contrast is a nonlinear convexity/thresholding effect of the gating nonlinearity--its difference-in-differences is approximately zero-- and is therefore not a valid test of memory; the conditioning-test signature is. A second prediction links RBC stiffening to reduced near-wall delivery and captured-platelet calcium response, upstream of intrinsic platelet signalling. ConclusionsThe framework provides a dimensionally consistent, mechanistically grounded and hypothesis-generating description linking hemodynamic forcing to mechanosensitive calcium entry. It demonstrates how history-dependent platelet priming may arise from a phenomenological sensitisation state and proposes a conditioning-test protocol for comparison against adhesive, channel and intracellular-store persistence. The framework is calibratable rather than validated, and the quantitative outputs shown use representative uncalibrated parameters.

5
Shear effects in active models of normal and cancer cells

Sadhukhan, S.; Das, R.; Zhao, L.; Losert, W.; Thirumalai, D.

2026-08-20 biophysics 10.64898/2026.08.15.744982 medRxiv
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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 (Np) of cells was chosen to have enhanced activity and decreased stiffness. As Np 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 Rs embedded in normal tissue, show that as Rs increases, the yield stress increases. Interestingly, the cells migrate collectively as Rs 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.

6
Nanoscale numerical simulations explain apparently opposing experimental findings on ephaptic coupling

Jaeger, K. H.; Tveito, A.

2026-08-19 biophysics 10.64898/2026.08.11.744093 medRxiv
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A classical study found no excitation transfer when isolated cardiomyocytes were placed side by side, whereas a recent paper reported action potential transfer in carrdiomyocytes placed end to end. We use nanoscale numerical simulations based on the full Poisson-Nernst-Planck equations to investigate whether these apparently opposing observations can be explained by the different geometrical configurations. The computations show that in the end-to-end configuration, ephaptic coupling occurs when the intercellular cleft is sufficiently narrow and a sufficiently large fraction of the sodium channels is localized at the intercalated disc. Coupling is strengthened when the sodium channels are concentrated in fewer clusters and when ionic diffusion within the cleft is reduced. Under these conditions, excitation transfer occurs on a timescale consistent with rapid cell-to-cell activation. Conduction depends biphasically on cleft width and terminates abruptly beyond a critical width. Localization of potassium channels at the intercalated disc has only a moderate effect, whereas gap junctions substantially improve conduction and reduce the relative contribution of ephaptic coupling. In the side-by-side configuration, excitation transfer does not occur under physiological conditions and requires highly flattened cells, minimal separation, and unrealistically strong sodium-channel clustering. The different outcomes of the side-by-side and end-to-end experiments can therefore be explained by the fundamentally different geometrical conditions for ephaptic coupling.

7
Why is the purse string not enough?

Vicente Munuera, P.; Munoz, J. J.; Mao, Y.

2026-08-11 biophysics 10.64898/2026.08.05.743165 medRxiv
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Wound repair is an important mechanism to preserve tissue integrity in organisms after injury. However, why different tissues exhibit different mechanisms to repair wounds is a long-standing question that remains unanswered. In this work, we theoretically explore the role of the purse string, an actomyosin contractile cable used by tissues to close small wounds. Does the tissue 3D geometry influence the efficiency of the purse string in driving wound closure? Using a 3D biophysical model, we study in silico tissues with the same cell volumes but different aspect ratios, ranging from squamous to thick and tall tissues. The model predicts that taller cells are easily deformed by the purse string. In contrast, very squamous cells require a very strong purse string that might demand additional cellular mechanisms to close the gap. These findings establish a theoretical framework to predict the optimal biophysical mechanisms of wound healing in different tissues. Graphical abstractCells of different aspect ratios can be observed in a range of organisms with different function and mechanics. The wound healing efficiency of the purse string increases with the cell aspect ratio in our theoretical exploration. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/743165v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@d44ab0org.highwire.dtl.DTLVardef@1737cbaorg.highwire.dtl.DTLVardef@101b5d4org.highwire.dtl.DTLVardef@1487f26_HPS_FORMAT_FIGEXP M_FIG C_FIG

8
Markovian Dynamics and Spectral Relaxation of Metastatic Networks

Margarit, D.

2026-08-18 biophysics 10.64898/2026.08.13.743956 medRxiv
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Structural network representations of metastatic dissemination typically focus on static topology without resolving transport dynamics, relaxation timescales, or steady-state behaviour. Here, we formulate a discrete Markovian transport model on a directed higher-order network with transition rates derived from qualitative clinical affinity classes. By constructing a non-Hermitian row-stochastic transfer operator, we characterise the relaxation dynamics through its spectral decomposition. The system exhibits a fast-mixing regime characterised by a spectral gap of {gamma} {approx} 0.67, corresponding to a characteristic relaxation timescale of {tau} {approx} 1.49 discrete steps, with the influence of the primary tumour origin progressively attenuated during dissemination. Convergence towards a non-equilibrium steady state (NESS) is accompanied by a reduction in Shannon entropy, concentrating probability mass within specific topological sinks. This spectral relaxation delineates two distinct dynamical regimes: early transient dissemination (n < {tau}), dominated by local organ-specific transition probabilities (organotropism), and the asymptotic regime (n > {tau}), determined increasingly by the global transport architecture of the network. Comparison with independent clinical and autopsy observations across 21 primary tumours and 23 target organs indicates that the predicted stationary distribution is consistent with the observed hierarchy of metastatic organ involvement.

9
Propagation electrodynamics and differential conduction of action potentials in geometrically branched squid giant axons

Liu, X.; Fang, W.; Perlin, K.

2026-08-07 biophysics 10.64898/2026.08.03.742547 medRxiv
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Classical neuronal cable theory relies on quasi-static electric field approximations and neglects magnetic induction, Lorentz force coupling, and transient electromagnetic currents, limiting its ability to fully characterize action potential propagation within geometrically branched axons and dendrites. This work develops a coupled Maxwell-electromagnetic cable framework by integrating finite-difference time-domain (FDTD) solutions of Maxwells equations with extended Hodgkin-Huxley and Fitzhugh-Nagumo membrane dynamics, incorporating magnetic gating perturbations, electromagnetic trans-membrane currents IEM, and nanoscale quantum corrections for thin neural segments. Controlled propagation experiments are designed to quantify deviations from standard cable predictions across asymmetric and symmetric axonal bifurcation geometries. Numerical results demonstrate that inductive magnetic effects lower the critical branch radius for junction conduction failure and break symmetric action potential invasion in geometrically identical child branches under external transverse magnetic fields. An electromagnetic corrected geometric ratio GREM is proposed to revise impedance-matching conditions at branch points, accounting for size-dependent axial current imbalance induced by magnetic and displacement currents. Parent axon conduction velocity deviates substantially from the canonical [Formula] scaling law when electromagnetic feedback and quantum charge distributions are included, triggering early signal blockage at large cable diameters. Collectively, this study establishes that quasi-static cable models underestimate electromagnetic corrections to propagation speed, waveform shape, and bifurcation transmission fidelity; the coupled Maxwell-cable framework provides a comprehensive multi-physics tool for modeling electrodynamic signal behavior in complex neuronal architectures.

10
The Role Of Liquid Crystal Ordering In The Structural Organization Of DNA In Bacteria.

Krupyanskii, Y. F.; Kovalenko, V.; Loiko, N.; Generalova, A.; Tereshkin, E.; Tereshkina, K.; Sokolova, O.; Peters, G.

2026-09-01 biophysics 10.64898/2026.08.31.748243 medRxiv
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This paper presents and critically reviews the results of original and some literature based experimental studies conducted by the authors last years on the structural organization of DNA in dormant (starvation stress), anabiotic dormant (4 HR treatment) E. coli cells, as well as the K12 {Delta}dps strain, which lacks the Dps protein (Dps null E. coli). The experimental data includes small-angle synchrotron radiation diffraction (SAXS) and transmission electron microscopy (TEM) data. Synchrotron radiation diffraction experiments on K12{Delta}dps cells allowed us to conclude that peaks at 44.3, 22.1, and 14.8 angstrom resolutions are associated exclusively with ordered DNA organization. Peaks at 44.3, 22.1, and 14.8 angstrom resolutions are also observed for samples of dormant (starvation stress) cells and anabiotically dormant cells. Therefore, this ordered DNA organization also applies to samples of dormant and anabiotically dormant cells. A model is proposed that considers the ordered DNA organization in the cell as a cholesteric liquid crystal. The powder diffraction pattern calculated based on this model is compared with experimental small angle X ray scattering (SAXS) data obtained on Dps-null cell samples. The model completely reproduces the key features of the experimental diffraction pattern from Dps-null cell samples. Accordingly, the cholesteric liquid crystal model corresponds to DNA packaging in dormant and anabiotically dormant cells. Cholesteric liquid crystal ordering should be further considered in all models of cellular DNA packaging. To address the question of which structural organization of DNA predominates in the cell: the cholesteric liquid crystal or nanocrystalline or whether they coexist and fully manifest themselves under different external conditions, it is necessary to utilize the latest methodological advances in structural analysis.

11
Analysis and Design of Frequency-Based Biological Signaling Cascades

Naeini, A. E.; Nejad, S.; O'Donnell, D.; Kuhlman, T. E.

2026-08-24 biophysics 10.64898/2026.08.19.745833 medRxiv
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Based on our experimental observation of activation state oscillations of different frequencies used to communicate information by the master human stress response regulator protein p38 MAPK 1, we develop a simple graphical approach for understanding and predicting the behavior of complex biological networks acting upon signals carrying information as different frequency waves of chemicals. This approach uses the same techniques used for analyzing and understanding information transmission using waves of electrical currents and fields used in electrical alternating current (AC) circuits. We show how biological components can be organized to behave as standard components found in electronic telecommunications circuits. Finally, we demonstrate how such components can be organized into complex biological signaling cascades whose behavior can be qualitatively and quantitatively understood, and whose output resembles that experimentally observed in p38.

12
Transmembrane coupling of protein condensates via membrane-mediated interactions: A simulation study

Argun, B. R.; Stachowiak, J.; Ren, P.

2026-08-21 biophysics 10.64898/2026.08.14.744969 medRxiv
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Recent experiments show that protein condensates sitting on opposite surfaces of a flat lipid membrane move together and prefer to overlap, even though they cannot touch each other. This points to an indirect, membrane-mediated interaction. Two mechanisms could be responsible: a curvature-induced interaction, which is energetic in origin, and a fluctuation-induced interaction, which is entropic. Here we study both with coarse-grained molecular dynamics simulations, using Cookes implicit-solvent lipid model together with a generic bead-spring polymer model for the condensate. We compute the potential of mean force between two condensates across the membrane. For condensates of the same size, full overlap is unfavorable, and the pair instead settles into a partially overlapping state that bends the membrane into an S-like shape. When the two condensates differ strongly in size, full overlap becomes favorable. We explain this with a simple geometric picture. The condensate wets the membrane as a thin film and imposes curvature only along its rim, while membrane tension flattens the membrane under its interior. The resulting ring of curvature can trap a smaller condensate on the opposite side. We also compare the bending undulations and the effective bending modulus of a bare membrane, a membrane with one condensate, and a membrane with condensates on both sides. A wetting condensate suppresses the undulation modes and stiffens the membrane, but whether this makes overlap entropically favorable remains inconclusive. Our results indicate that the coupling is driven mainly by curvature, and that it depends on the wetting mechanism and on the membrane tension.

13
Assessing the fractional contributions of static, slow and fast dynamic scatterer components to the flow index derived by continuous wave diffuse correlation spectroscopy

Mogharari, N.; Kacprzak, M.; Borycki, D.

2026-08-18 bioengineering 10.64898/2026.08.14.744820 medRxiv
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Continuous wave diffuse correlation spectroscopy (cw-DCS) is a noninvasive optical technique to monitor the tissues blood flow changes. This technique measures the tissue blood flow index (BFI) by evaluating the decay rate of the autocorrelation function. The derived BFI is proportional to mean squared displacements of the red blood cells considered as the fast-dynamic scatterer component of tissue in time. However, biological tissue contains static scatterer component and slow-dynamic scatterer component which affect the decay rate of autocorrelation function and as a result the derived BFI. In this study, we assessed the fractional contribution of static, slow-dynamic and fast-dynamic scatterer components of a medium in the flow index derived by cw-DCS. The measurements performed on Agar-based phantom with tube showed that presence of static scatterer component and slow-dynamic scatterer component led to substantial underestimation ({approx} 123%) of the flow index derived by Siegert relation, compared to effective diffusion coefficient of fast-dynamic scatterers components derived by modified Siegert relation and bi-exponential model. The less underestimation was observed for the corresponding parameters obtained from the liquid phantom measurements ({approx} 25%) as well as during the forearm occlusion test and respiratory challenges ({approx} 16% - 26%).

14
Contributions of single-cell mechanics and cell-cell adhesion to multicellular spheroid mechanics

Dolgitzer, D.; Parajon, E.; Robinson, D. N.; Iglesias, P. A.

2026-08-09 biophysics 10.64898/2026.08.04.742605 medRxiv
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Tumor spheroid mechanics arise from both the mechanical properties of individual cells and the adhesive interactions that organize them into tissues. The relative contribution of these two factors to the bulk mechanical behavior, however, remains difficult to disentangle experimentally. Here, we develop a computational model of micropipette aspiration to compare the mechanical response of isolated cells and multicellular spheroids within a common computational framework. By independently varying single-cell stiffness and cell-cell adhesion, we quantify their effects on aspiration dynamics, effective elastic modulus, and viscoelastic relaxation. Our results show that increasing single-cell stiffness substantially alters the mechanics of isolated cells but has limited influence on the effective elastic modulus of multicellular spheroids. In contrast, changes in cell-cell adhesion produce pronounced effects on spheroid effective elastic modulus. Nevertheless, both parameters increase the retardation time governing the transition from the initial elastic response to long-time viscous deformation. These findings suggest that multicellular elasticity is governed primarily by intercellular mechanical coupling, whereas the dynamical response to applied stress depends jointly on cell-scale mechanics and cell-cell adhesion.

15
On the determinants of residence times and dissociation mechanisms of complexes of interleukin-13 with its low and high affinity receptors

Herb, N.; Brajkovic, M.; DArrigo, G.; Kokh, D. B.; Wade, R. C.

2026-08-21 biophysics 10.64898/2026.08.13.743369 medRxiv
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Interleukin-13 (IL-13) is an immunomodulatory cell signaling cytokine that has been implicated in neurodegenerative disease and chronic inflammation. IL-13 binds to its low and high affinity receptors, IL-13 receptor 1 (IL-13R1) and IL-13 receptor 2 (IL-13R2), respectively, with residence times that vary accordingly. As the binding kinetics of the cytokine-receptor complexes influence cellular responses, we employed the molecular dynamics (MD) simulation-based{tau} -random acceleration molecular dynamics method ({tau}RAMD) to compute relative residence times for wild-type (WT) IL-13 and 19 IL-13 mutants to the two receptors. Comparison with experimental kinetic data shows that the{tau} RAMD computations capture the trends in residence times. Analysis of simulated dissociation trajectories of the cytokine-receptor complexes reveals two distinct dissociation pathways of IL-13 from each of the receptors. This study thus pinpoints key determinants of the interaction of IL-13 with its receptors which could be targeted for therapeutic design. Statement of SignificanceCytokines are regulatory proteins that bind to cell surface receptors and thereby send signals to the cellular interior. Interleukin-13 (IL-13) is a cytokine that has a low and a high affinity receptor. It has important physiological roles, and its deregulation is involved in diseases such as atopic dermatitis and asthma. We employed a molecular dynamics simulation-based method to compute the effects of changes in the sequence of IL-13 on the lifetimes of complexes of IL-13 and its receptors. Comparison with experiments supports the validity of the computational approach and analysis of the simulations reveals two distinct ways in which IL-13 dissociates from each receptor. These results thus provide a map for targeting IL-13 - receptor interactions for the design of therapeutics.

16
Modeling Dynamics of Contact Inhibition of Proliferation and Structural Order in a Confluent Epithelium

Ghosh, J.; Bhattacharjee, T.; Dutta, S.

2026-08-29 biophysics 10.64898/2026.08.26.747344 medRxiv
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Contact inhibition of proliferation (CIP) enables epithelial tissues to self-regulate growth and maintain tissue homeostasis. However, how cell-level mechanical contact, tissue-scale structural order, and proliferation kinetics interplay remains a fundamental open question in living matter physics. Here, we present a particle-based model of a confluent epithelial monolayer governed by overdamped dynamics, where individual cells interact via a two-dimensional hard core- soft shoulder potential. By comparing structural evolution during quasistatic densification with previously reported experimental division kinetics, we find that the dynamics of proliferation arrest mimics the onset of direct steric contacts between the hard cores of the shell. Identifying hard core contacts as the physical driver of CIP, we couple our mechanical model with a stochastic Monte Carlo division scheme in which the instantaneous division rate decreases to zero from an intrinsic value as the number of hard core contact increases to six from zero. We demonstrate that for high intrinsic division rates, the cellular densification outpaces mechanical relaxation. This kinetic mismatch drives premature hard-core contact formation, shifts the onset of jamming and contact inhibition to lower packing fractions, and induces increasingly disordered transient configurations before the tissue universally converges to a hexagonal close-packed limit. Our model's predicted division kinetics and structural order evolution are consistent with epithelial monolayer experiments, both reported and our own. This minimal physical framework links single-cell steric contact mechanics directly to tissue-scale growth regulation and structural evolution.

17
Polarized neutrons for the study of individual and collective fast dynamics in proteins

Nidriche, A.; Ollivier, J.; Stewart, R.; Peters, J.

2026-09-01 biophysics 10.64898/2026.08.30.748099 medRxiv
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Neutron scattering is a powerful technique to investigate atomic structures and molecular dynamics of proteins at the nano-scale. When it comes to dynamics, incoherent and coherent scattering respectively provide information on the single and collective dynamics of nuclei. In proteins, hydrogen has the highest incoherent cross-section, and it is common practice to overlook the contribution of coherent terms stemming from all nuclei. However, the fast collective dynamics of heavier nuclei could also be studied if coherent scattering and incoherent scattering were experimentally separated. The recent advent of polarized neutron spectroscopy with sufficient flux and energy resolution has made it possible, and opens new perspectives to investigate the relative importance of coherent scattering and the information it provides on biological samples. The present study reports on the use of polarized quasi-elastic neutron scattering (QENS) and the application of a minimalistic model adapted to both individual and collective dynamics. Using a perdeuterated green fluorescent protein as a model globular protein, the study provides an interpretation of the dynamical parameters obtained with QENS, and a comparative study of the Elastic Coherent and Incoherent Scattering Factor. Based on both experiments and calculations, we discuss the relative importance of distinct and self components of coherent scattering, which is often wrongly assumed to be representative of collective dynamics only. The results highlight the current impediments rendering complicated a straightforward analysis of fast collective dynamics in hydrated protein samples.

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Entanglement dilution and high fractal dimension mediated by loop extrusion revealed in simulations of active polymer melts

Chan, B.; Rubinstein, M.

2026-08-14 biophysics 10.64898/2026.08.08.743709 medRxiv
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In the active loop extrusion model, the cohesin protein complex creates chromatin loops in eukaryotic cells. Extrusion maintains topologically associated domains (TADs), which are contiguous segments of chromatin that preferentially colocalize in space and are typically bounded by CTCF proteins that pause cohesin translocation. Here, we model active loop extrusion with hybrid molecular dynamics - Monte Carlo simulations in entangled flexible linear polymer melts. Intra-chain contact probabilities of polymers with active loop extrusion are enhanced compared to their equilibrium, passive counterparts. Extrusion causes the size of chain segments to be much smaller than in passive melts. While the overlap parameter in passive melts without extrusion monotonically increases with segment length, it is nonmonotonic in active melts and on the order of unity within the parameters of this study. Active loop extrusion suppresses contacts between TADs in favor of intra-TAD contacts. Reduction of overlaps between chain segments dilutes entanglements in active melts. Depending on parameters, active extrusion without TADs may induce more compact conformations than with TADs, due in part to fractal loopy globule-like dynamics. This work suggests that active loop extrusion reduces overlaps between TADs, contributing to effective gene regulation by cis-regulatory elements.

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Percolation-inspired criticality in complement activation: universal scaling and transport-limited complement surface amplification

Monson, S.; Kulkarni, S.; Myerson, J.; Brenner, J.; Radhakrishnan, R.

2026-08-19 biophysics 10.64898/2026.08.14.744667 medRxiv
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The collective spatial phenomenon of complement protein opsonization on nanoparticle surfaces is a key component of the immune response to viruses, engineered nanoparticles, and diseased cells. Recent work showed this opsonization follows a sharp, percolation-like transition versus the spacing d between surface-bound attachment sites, leaving two open questions: 1) whether the transition exhibits hallmarks of true criticality, such as diverging susceptibility, and 2) whether it can be distinguished from an alternative first-order cooperative (Hill-type) process producing an equally sharp threshold without true criticality. Here, we resolve both questions using a hierarchical statistical-mechanics treatment spanning stochastic, mean-field, and spatial reaction-diffusion models. The variance of two order parameters, peak complement activity and activation lifetime, diverges near threshold and sharpens systematically with system size, the defining signature of a critical point rather than a smooth cooperative response. Extending the analysis across site spacing and intrinsic kinetic rate constants traces a two-dimensional locus of critical points with consistent critical exponents throughout, establishing a single, robust universality class. The mean-field dynamic exponent for activation lifetime agrees quantitatively with the exact value predicted for the general epidemic process. Finally, a reaction-diffusion model of the nanoparticle surface shows the critical locus is set by a diffusion-limited length scale, establishing complement percolation as a fundamentally transport-limited surface reaction. These results place complement activation within the percolation universality class and identify the physical parameters, diffusion, catalysis, and decay, that govern its critical threshold, with direct implications for rational design of complement-evading nanomaterials, immunology, and evolutionary biology.

20
A generalizable deep learning model for automated 3D segmentation of orthopteran head anatomy in micro-CT

Cheron, A.; Morita, S.; Morimoto, N.; Ohde, T.

2026-08-13 developmental biology 10.64898/2026.08.12.744546 medRxiv
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Deep learning tools are increasingly used today, particularly in medical segmentation. A gap nonetheless remains in automating segmentation for insects. This work addresses the following question: can a generalist segmentation model, trained on several phylogenetically related orthopteran species, reliably automate head tissue segmentation from micro-CT images? To answer this, we used nnU-Net, a self-configuring 3D deep learning segmentation framework originally developed for medical imaging, whose core function, learning to recognize tissues of interest, applies directly to this context. Six anatomical classes were automated, comparing two training strategies: sequential fine-tuning, which adds species one at a time under the assumption that progressive learning would strengthen predictive power, and from-scratch training, in which the model learns the entire dataset simultaneously. The fine-tuning model (ModelB) reached a Dice coefficient (a measure of overlap between automated segmentation and manual ground truth, ranging from 0 to 1) of 0.7715, compared to 0.7664 for the from-scratch model (ModelC). Although both models produced accurate automated segmentations, no significant difference was found between the two training strategies (paired Wilcoxon test, n = 24, p = 0.243). Despite a dataset limited to 20 individuals and the absence of one method clearly outperforming the other, the models remain usable across the three species studied (Gryllus bimaculatus, Loxoblemmus equestris, L. doenitzi), including in the presence of pronounced sexual dimorphism. It reduces a 20 hour segmentation task to under a minute.