arXiv subjects

Erwin Frey

Publications and source records attributed to Erwin Frey.

At least 19 recordsLinked to original sources

arXiv2026

Classification of Intracellular Protein Patterns from Reactive Equilibria

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.

physics.bio-ph↗

arXiv2026

Stochastic Yield Catastrophe in Delay-Facilitated Self-Assembly

Self-assembly of supramolecular structures in cells and synthetic applications often proceeds under unfavorable biochemical conditions and at low copy numbers of final target structures, ranging from tens of bacterial microcompartments to a single bacterial flagellum per cell. Spatial organization through coupled reaction compartments of different reactivity (delay-facilitated assembly) can recover high yield in such environments at the mean-field level, but its robustness to stochastic fluctuations at low target numbers is unclear. Using stochastic simulations of a minimal two-compartment model, we show that delay-facilitated assembly is susceptible to a stochastic yield catastrophe at low target numbers: even when each compartment in isolation allows for high-yield assembly, slow exchange between them induces a substantial drop in the final yield. We trace the mechanism to a specific assembly stage, where the random order of rate-limiting exchange events of subunits and partially completed structures determines the ratio of productive growth to excess nucleation. Restricting the exchange of larger structures -- either by suppressing it entirely or letting exchange rates decrease with size -- restores most of the yield without altering the mean-field behavior. The same phenomenology appears for two-dimensional hexagonal subunits and in a cytosol-membrane geometry, where diffusion-limited exchange naturally implements the required size dependence. Our results show that equal success of assembly strategies at high target numbers does not imply their equal success at low target numbers, and that competing slow events occurring in random order are a common signature of stochastic yield catastrophes.

physics.bio-ph↗

arXiv2026

Active Model B$^-$ from Mass-Conserving Reaction-Diffusion Systems

We show that the late-time dynamics of a minimal three-component mass-conserving reaction--diffusion system reduce to a scalar active field theory, Active Model B$^-$ (AMB$^-$), in which a density-dependent interfacial coefficient $\kappa(\phi)$ turns negative at high density. This drives a finite-wavelength instability and stabilises microphase-separated patterns, in contrast to the unbounded coarsening of two-component mass-conserving systems. Unlike Active Model B$^+$, AMB$^-$ retains a chemical potential that remains a state function, inherited from the underlying conservation law, but admits no equation of state for the pressure.

cond-mat.soft↗

arXiv2026

Duality Between Chemical Potential Dynamics and Reaction-Diffusion Systems

Pattern formation in soft, active, and biological matter is described by two ostensibly distinct continuum frameworks: phase-field theories driven by chemical-potential gradients, and mass-conserving reaction-diffusion (McRD) dynamics governed by local interconversion kinetics. Here we establish a constructive, equation-level duality valid in the nonlinear, far-from-equilibrium regime. McRD is the broader class: every chemical-potential theory with conserved order parameters embeds as the slow dynamics on an attracting manifold of an McRD system; conversely, every McRD with attractive nullcline admits an exact chemical-potential representation in the fast-interconversion limit, with the constitutive relation set by the nullcline. The construction resolves the generic non-invertibility of the chemical-potential as a function of density in phase-separating regimes by embedding it as an attracting manifold in an extended two-field description with conserved total density. Gradient stiffness maps faithfully onto an intrinsic reaction-diffusion length set by the auxiliary field, yielding a diagonal-diffusion normal form whose interface profile matches the original Cahn-Hilliard model by construction. The duality yields an explicit dictionary for phase coexistence: the Maxwell equal-area construction is exactly equivalent to the reactive turnover-balance condition. It extends to weakly nonconservative dynamics, unifying reaction-arrested coarsening and mesa splitting, and to multicomponent theories with broken Maxwell symmetry. As a concrete payoff, the dual sharp-interface picture yields a closed-form velocity law for traveling waves in nonreciprocal Cahn-Hilliard dynamics, in quantitative agreement with simulations.

cond-mat.soft↗

arXiv2026

Local composition controls pattern formation in conserved active emulsions

Phase separation in passive systems leads to uncontrolled droplet growth, limiting structural control in soft materials and cells. We identify a generic mechanism to arrest coarsening based on chemical interconversion between molecular species with different diffusivities. Sharp-interface theory and simulations show that when the faster-diffusing species becomes enriched inside droplets, composition gradients emerge that oppose mass influx. This transport asymmetry stabilizes droplet sizes even without interaction asymmetries, offering a minimal route to regulate structure formation in active emulsions.

cond-mat.soft↗

arXiv2026

Non-equilibrium phase coexistence in conserved chemically active mixtures

Chemical activity is known to affect phase coexistence and coarsening in liquid mixtures, most commonly through reaction-induced changes of intermolecular interactions. Here, we analyze a scenario in which chemical reactions regulate particle transport while leaving thermodynamic interactions unchanged. We study an incompressible mixture of thermodynamically identical solutes with unequal diffusivities that interconvert through driven chemical reactions. Using linear stability analysis and finite-element simulations, we show that the system can phase-separate into solute-rich and solute-poor domains via two qualitatively different pathways. When interactions are too weak to induce phase separation, patterns arise through a generalized mass-redistribution instability and coarsen uninterruptedly. When interactions favor phase separation, coarsening can be arrested if chemical activity locally enriches faster-diffusing solutes within dense domains. In the limit of fast chemical turnover, the system always coarsens, and phase coexistence is governed by an effective free energy that explicitly depends on kinetic parameters. Beyond this limit, we develop a sharp-interface theory that predicts the onset of arrested coarsening, stationary droplet sizes, and nucleation conditions under chemical driving. Taken together, our results establish kinetic regulation as a minimal and robust mechanism to control phase coexistence and coarsening in chemically active mixtures.

cond-mat.soft↗

arXiv2026

Active fluctuations induce buckling of living surfaces

Active tissues exhibit tension fluctuations that are correlated in space and time. We study a minimal overdamped surface model in which such fluctuations enter as a zero-mean, multiplicative modulation of the local surface tension. Although the deterministic elastic dynamics (tension plus bending) stabilizes the flat state for all nonzero wave numbers, we find that sufficiently persistent active fluctuations generate positive ensemble growth rates for a finite band of Fourier modes, leading to stochastic buckling with wavelength selection. A non-Markovian theory based on the Novikov--Furutsu theorem captures the instability threshold and unstable band observed in simulations.

cond-mat.soft↗

arXiv2025

Pattern Formation Beyond Turing: Physical Principles of Mass-Conserving Reaction--Diffusion Systems

Intracellular protein patterns govern essential cellular functions by dynamically redistributing proteins between membrane-bound and cytosolic states, conserving their total numbers. This review presents a theoretical framework for understanding such patterns based on mass-conserving reaction--diffusion systems. The emergence, selection, and evolution of patterns are analyzed in terms of mass redistribution and interface motion, resulting in mesoscale laws of coarsening and wavelength selection. A geometric phase-space perspective provides a conceptual tool to link local reactive equilibria with global pattern dynamics through conserved mass fluxes. The Min protein system of \emph{Escherichia coli} provides a paradigmatic example, enabling direct comparison between theory and experiment. Successive model refinements capture both the robustness of pattern formation and the diversity of dynamic regimes observed \emph{in vivo} and \emph{in vitro}. The Min system thus illustrates how to extract predictive, multiscale theory from biochemical detail, providing a foundation for understanding pattern formation in more complex and synthetic systems.

physics.bio-ph↗

arXiv2025

Delay-facilitated self-assembly in compartmentalized systems

Self-assembly processes in biological and synthetic biomolecular systems are often governed by the spatial separation of biochemical processes. While previous work has focused on optimizing self-assembly through fine-tuned reaction parameters or using phase-separated liquid compartments with fast particle exchange, the role of slow inter-compartmental exchange remains poorly understood. Here, we demonstrate that slow particle exchange between reaction domains can enhance self-assembly efficiency through a cooperative mechanism: delay-facilitated assembly. Using a minimal model of irreversible self-assembly in two compartments with distinct reaction and exchange dynamics, we identify scenarios that maximize yield and minimize assembly time, even under conditions where isolated compartments would fail to facilitate any self-assembly. The mechanism relies on a separation of timescales between intra-compartmental reactions and inter-compartmental exchange and is robust across a wide range of geometries, including spatially extended domains with diffusive transport. We demonstrate that this effect enables geometric control of self-assembly processes through compartment volumes and exchange rates, eliminating the need for fine-tuning local reaction rates. These results offer a conceptual framework for leveraging spatial separation in synthetic self-assembly design and suggest that biological systems may use slow particle exchange to improve assembly efficiency. A video summary of this paper can be found at https://doi.org/10.5446/72056

physics.bio-ph↗

arXiv2025

Capillary wave formation in conserved active emulsions

The dynamics of phase-separated interfaces shape the behavior of both passive and active condensates. While surface tension in equilibrium systems minimizes interface length, non-equilibrium fluxes can destabilize flat or constantly curved interfaces, giving rise to complex interface morphologies. Starting from a minimal model that couples a conserved, phase-separating species to a self-generated chemical field, we identify the conditions under which interfacial instabilities may emerge. Specifically, we show that non-reciprocal chemotactic interactions induce two distinct types of instabilities: a stationary (non-oscillatory) instability that promotes interface deformations, and an oscillatory instability that can give rise to persistent capillary waves propagating along the boundaries of phase-separated domains. To characterize these phenomena, we develop a perturbative framework that predicts the onset, wavelength, and velocity of capillary waves, and quantitatively validate these predictions through numerical simulations. Beyond the linear regime, our simulations reveal that capillary waves undergo a secondary instability, leading to either stationary or dynamically evolving superpositions of different wave modes. Finally, we investigate whether capillary waves can facilitate directed mass transport, either along phase boundaries (conveyor belts) or through self-sustained liquid gears crawling along a solid wall. Taken together, our results establish a general framework for interfacial dynamics in active phase-separating systems and suggest new strategies for controlling mass transport in soft matter and biological condensates.

cond-mat.soft↗

arXiv2025

Stochastic bubble dynamics in phase-separated scalar active matter

In ABP systems, phase separation is accompanied by the emergence of vapor bubbles within liquid domains. Using large-scale particle-based simulations, we study the stochastic dynamics of these bubbles and find that most nucleate, grow, and dissolve within liquid domains. We show that their area dynamics can be described by a Langevin equation with a constant negative drift and noise proportional to the perimeter, fully characterizing bubble area and lifetime statistics. Additionally, we develop a lattice gas model that captures the morphological properties, including the decrease in bubble asphericity with increasing area. These findings provide new insights into phase separation in active matter and highlight limitations in current continuum theories.

cond-mat.soft↗

arXiv2024

Acoustic signaling enables collective perception and control in active matter systems

Emergent cooperative functionality in active matter systems plays a crucial role in various applications of active swarms, ranging from pollutant foraging and collective threat detection to tissue embolization. In nature, animals like bats and whales use acoustic signals to communicate and enhance their evolutionary competitiveness. Here, we show that information exchange by acoustic waves between active agents creates a large variety of multifunctional structures. In our realization of collective swarms, each unit is equipped with an acoustic emitter and a detector. The swarmers respond to the resulting acoustic field by adjusting their emission frequency and migrating toward the strongest signal. We find self-organized structures with different morphology, including snake-like self-propelled entities, localized aggregates, and spinning rings. These collective swarms exhibit emergent functionalities, such as phenotype robustness, collective decision-making, and environmental sensing. For instance, the collectives show self-regeneration after strong distortion, allowing them to penetrate through narrow constrictions. Additionally, they exhibit a population-scale perception of reflecting objects and a collective response to acoustic control inputs. Our results provide insights into fundamental organization mechanisms in information-exchanging swarms. They may inspire design principles for technical implementations in the form of acoustically or electromagnetically communicating microrobotic swarms capable of performing complex tasks and concerting collective responses to external cues.

cond-mat.soft↗

arXiv2024

Deciphering the Interface Laws of Turing Mixtures and Foams

For cellular functions like division and polarization, protein pattern formation driven by NTPase cycles is a central spatial control strategy. Operating far from equilibrium, no general theory links microscopic reaction networks and parameters to the pattern type and dynamics. We discover a generic mechanism giving rise to an effective interfacial tension organizing the macroscopic structure of non-equilibrium steady-state patterns. Namely, maintaining protein-density interfaces by cyclic protein attachment and detachment produces curvature-dependent protein redistribution which straightens the interface. We develop a non-equilibrium Neumann angle law and Plateau vertex conditions for interface junctions and mesh patterns, thus introducing the concepts of ``Turing mixtures'' and ``Turing foams''. In contrast to liquid foams and mixtures, these non-equilibrium patterns can select an intrinsic wavelength by interrupting an equilibrium-like coarsening process. Data from in vitro experiments with the E. coli Min protein system verifies the vertex conditions and supports the wavelength dynamics. Our study uncovers interface laws with correspondence to thermodynamic relations that arise from distinct physical processes in active systems. It allows the design of specific pattern morphologies with potential applications as spatial control strategies in synthetic cells.

physics.bio-ph↗

arXiv2024

Chemotaxis-induced phase separation

Chemotaxis allows single cells to self-organize at the population level, as classically described by Keller-Segel models. We show that chemotactic aggregation can be understood using a generalized Maxwell construction based on the balance of density fluxes and reactive turnover. This formulation implies that aggregates generically undergo coarsening, which is interrupted and reversed by cell growth and death. Together, both stable and spatiotemporally dynamic aggregates emerge. Our theory mechanistically links chemotactic self-organization to phase separation and reaction-diffusion patterns.

cond-mat.soft↗

arXiv2024

Coarsening dynamics of chemotactic aggregates

Auto-chemotaxis, the directed movement of cells along gradients in chemicals they secrete, is central to the formation of complex spatiotemporal patterns in biological systems. Since the introduction of the Keller--Segel model, numerous variants have been analyzed, revealing phenomena such as coarsening of aggregates, stable aggregate sizes, and spatiotemporally chaotic dynamics. Here, we consider general mass-conserving Keller--Segel models, that is, models without cell growth and death, and analyze the generic long-time dynamics of the chemotactic aggregates. Building on and extending our previous work, which demonstrated that chemotactic aggregation can be understood through a generalized Maxwell construction balancing density fluxes and reactive turnover, we use singular perturbation theory to derive the rates of mass competition between well-separated aggregates. We analyze how this mass-competition process drives coarsening in both diffusion- and reaction-limited regimes, with the diffusion-limited rate aligning with our previous quasi-steady-state analyses. Our results generalize earlier mathematical findings, demonstrating that coarsening is driven by self-amplifying mass transport and aggregate coalescence. Additionally, we provide a linear stability analysis of the lateral instability, predicting it through a nullcline-slope criterion that parallels the curvature criterion in spinodal decomposition. Overall, our findings suggest that chemotactic aggregates behave similarly to phase-separating droplets, providing a robust framework for understanding the coarse-grained dynamics of auto-chemotactic cell populations and a quantitative basis for comparing chemotactic coarsening to canonical non-equilibrium phase separation.

cond-mat.soft↗

arXiv2024

Phase Separation on Deformable Membranes: interplay of mechanical coupling and dynamic surface geometry

The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments. When phase-separating proteins are membrane-bound and locally disturb it, the mechanical response of the membrane mediates interactions between these proteins. How these membrane-mediated interactions influence the steady state of the protein density distribution is thus an important question to investigate in order to understand the rich diversity of protein and membrane-shape patterns present at the cellular level. This work starts with a widely used model for membrane-bound phase-separating proteins. We numerically solve our system to map out its phase space and perform a careful, systematic expansion of the model equations to characterize the phase transitions through linear stability analysis and free energy arguments. We observe that the membrane-mediated interactions, due to their long-range nature, are capable of qualitatively altering the equilibrium state of the proteins. This leads to arrested coarsening and length-scale selection instead of simple demixing and complete coarsening. In this study, we unambiguously show that long-range membrane-mediated interactions lead to pattern formation in a system that otherwise would not do so. This work provides a basis for further systematic study of membrane-bound pattern-forming systems.

cond-mat.soft↗

arXiv2024

Light-induced cortical excitability reveals programmable shape dynamics in starfish oocytes

Chemo-mechanical waves on active deformable surfaces are a key component for many vital cellular functions. In particular, these waves play a major role in force generation and long-range signal transmission in cells that dynamically change shape, as encountered during cell division or morphogenesis. Reconstituting and controlling such chemically controlled cell deformations is a crucial but unsolved challenge for the development of synthetic cells. Here, we develop an optogenetic method to elucidate the mechanism responsible for coordinating surface contraction waves that occur in oocytes of the starfish Patiria miniata during meiotic cell division. Using spatiotemporally-patterned light stimuli as a control input, we create chemo-mechanical cortical excitations that are decoupled from meiotic cues and drive diverse shape deformations ranging from local pinching to surface contraction waves and cell lysis. We develop a quantitative model that entails the hierarchy of chemical and mechanical dynamics, which allows to relate the variety of mechanical responses to optogenetic stimuli. Our framework systematically predicts and explains transitions of programmed shape dynamics. Finally, we qualitatively map the observed shape dynamics to elucidate how the versatility of intracellular protein dynamics can give rise to a broad range of mechanical phenomenologies. More broadly, our results pave the way toward real-time control over dynamical deformations in living organisms and can advance the design of synthetic cells and life-like cellular functions.

physics.bio-ph↗

arXiv2024

Availability versus carrying capacity: Phases of asymmetric exclusion processes competing for finite pools of resources

We address how the interplay between the finite availability and carrying capacity of particles at different parts of a spatially extended system can control the steady state currents and density profiles in the one-dimensional current-carrying lanes connecting the different parts of the system. To study this, we set up a minimal model consisting of two particle reservoirs of the same finite carrying capacity connected by two equally sized anti-parallel asymmetric exclusion processes (TASEP). We focus on the steady-state currents and particle density profiles in the two TASEP lanes. The ensuing phases and the phase diagrams, which can be remarkably complex, are parametrized by the model parameters defining particle exchange between the TASEP lanes and the reservoirs and the filling fraction of the particles that determine the total resources available. These parameters may be tuned to make the densities of the two TASEP lanes globally uniform or piece-wise continuous in the form of a combination of a single localized domain wall and a spatially constant density or a pair of delocalized domain walls. Our model reveals that the two reservoirs can be preferentially populated or depopulated in the steady states.

cond-mat.stat-mech↗