arXiv subjects

Benjamin Sorkin

Publications and source records attributed to Benjamin Sorkin.

13 recordsLinked to original sources

arXiv2026

Propelling catalytic structures using active phase separation

Living systems routinely consume energy to achieve motility, often using intricate biomolecular machinery. In this work, we show that active droplets can sustain indefinite self-propulsion of a spherical colloid in an otherwise homogeneous, isotropic, and autonomous environment. Our proposed minimal mechanism consists of phase-separating proteins, enzymes passivating them, and complementary enzymes anchored to the colloid surface that reactivate the proteins. This passivation-activation cycle gives rise to a symmetry breaking - nucleation and stabilization of a condensate near the colloid surface, which in turn exerts a repulsive force on the colloid. We numerically demonstrate that this mechanism can propel micron-sized colloids at speeds of up to a hundred microns per second. This propulsion mode is strongly resistant to Brownian fluctuations and external forces, suggesting that propulsion mechanisms based on biomolecular condensates may offer a complementary, motor-free route to biological transport.

cond-mat.soft↗

arXiv2026

Polymer-Residue Accessibility Shapes Sequence Dependence of Critical Temperatures for Phase Separation

Biological polymers, such as intrinsically disordered proteins, play a central role in cellular biology, including mediating phase separation and controlling activity of biological condensates. The physical properties and functions of biopolymers are determined by their residue sequence. Recently, significant computational and theoretical efforts have been devoted to characterizing the combinatorially complex sequence dependence of biopolymer phase diagrams. Here, we quantitatively show that monomer accessibility is central to determining the strength of pair interactions. We formulate an analytical perturbative approach, phenomenologically precluding two polymers' centers of mass from overlapping within a correlation hole. This theory yields the correction to the strength of mean-field interactions in terms of a residue-accessibility parameter (RAP), which accounts for the limited availability of inner monomers to interactions. Despite the simplicity of the approach, RAP rationalizes the variations in critical temperatures found in extensive Monte-Carlo simulations for thousands of two-letter polymer solutions of varying length and sequence. RAP may thus be effective for deciphering the polymer-sequence dependence of phase diagrams given any polymer length, set of monomer types, and polymer mixtures.

cond-mat.soft↗

arXiv2026

Consistent thermodynamics reconstructed from transitions between nonequilibrium steady-states

Constructing a thermodynamic framework for nonequilibrium systems remains a major challenge, as quantities such as temperature and free energy often become ambiguous when inferred solely from steady-state properties. Here we take a transformation-based approach and experimentally examine transitions between nonequilibrium steady states (NESS). Using an optically trapped microparticle driven by a tunable correlated stochastic force, we generate active-like steady states with controllable noise statistics. By abruptly changing the trap stiffness, we measure the stochastic work, heat, and entropy produced during NESS-to-NESS transformations. We identify a state-dependent effective temperature that restores the second law for these transitions, enabling the definition of a generalized work that incorporates the consequence of the nonequilibrium fluctuations. With this quantity, we derive and experimentally verify a Crooks-like fluctuation relation linking work distributions to a nonequilibrium free-energy difference defined through the effective temperature. Finally, we establish a fluctuation-response relation for the positional variance following stiffness changes. We demonstrate that this relation is key to distinguishing systems that can be described by a unique effective temperature (i.e., those under equilibrium or white-noise conditions) from those under colored-noise, where an equilibrium-like response cannot be restored. These results delineate the applicability and limits of effective-temperature thermodynamics in driven systems.

cond-mat.stat-mech↗

arXiv2025

Accelerated Ostwald ripening by chemical activity

Phase separation of biomolecular condensates promotes membrane-free compartmentalization in cells. The dynamics of these biocondensates is routinely regulated by energy-consuming processes. Here, we devise a theory pinpointing how active chemical reactions, interconverting molecules between phase-separating and inert forms, can drive faster condensate coarsening. We find that mass conservation limits droplet volume growth to being linear in time regardless of activity, resembling the passive Lifshitz-Slyozov law. However, if reactions are restricted to occur only outside droplets, the rate of Ostwald ripening can be increased by an arbitrarily large factor. Our theory is quantitatively supported by recent experiments on ripening in the presence of fueled interconversion reactions, under precisely the predicted conditions. We posit that the ability to induce rapid biocondensate coarsening can be advantageous in synthetic-biological contexts, e.g., as a regulator of metabolic channeling.

physics.bio-ph↗

arXiv2025

Effective synchronization amid noise-induced chaos

Two remote agents with synchronized clocks may use them to act in concert and communicate. This necessitates some means of creating and maintaining synchrony. One method, not requiring any direct interaction between the agents, is to expose them to a common, environmental, stochastic forcing. This "noise-induced synchronization" only occurs under sufficiently mild forcing; stronger forcing disrupts synchronization. We investigate the regime of strong noise, where the clocks' relative phases evolve chaotically. Using a simple realization of disruptive noise, we demonstrate effective synchronization. First, although the relative phases of the two clocks varied erratically, we confirm that they became statistically independent of initial conditions and hence equivalent after a well-defined timescale. Second, we show that an agent can estimate an effective phase that closely agrees with the other's phase. Thus, synchronization is practically attainable beyond the regime of conventional noise-induced synchronization. We finally discuss how it might be used in living systems.

cond-mat.stat-mech↗

arXiv2024

Second Law of Thermodynamics without Einstein Relation

Materials that are constantly driven out of thermodynamic equilibrium, such as active and living systems, typically violate the Einstein relation. This may arise from active contributions to particle fluctuations which are unrelated to the dissipative resistance of the surrounding medium. We show that in these cases the widely used relation between informatic entropy production and heat dissipation does not hold. Consequently, fluctuation relations for the mechanical work, such as the Jarzynski and Crooks theorems, are invalid. We relate the breaking of the correspondence between entropy production and heat dissipation to departure from the fluctuation-dissipation theorem. We propose a temperaturelike variable that restores this correspondence and gives rise to a generalized second law of thermodynamics, whereby the dissipated heat is necessarily non-negative and vanishes at equilibrium. The Clausius inequality, Carnot maximum efficiency theorem, and relation between the extractable work and the change of free energy are recovered as well.

cond-mat.stat-mech↗

arXiv2024

Consistent expansion of the Langevin propagator with application to entropy production

Stochastic thermodynamics is a developing theory for systems out of thermal equilibrium. It allows to formulate a wealth of nontrivial relations among thermodynamic quantities such as heat dissipation, excess work, and entropy production in generic nonequilibrium stochastic processes. A key quantity for the derivation of these relations is the propagator - the probability to observe a transition from one point in phase space to another after a given time. Here, applying stochastic Taylor expansions, we devise a formal expansion procedure for the propagator of overdamped Langevin dynamics. The three leading orders are obtained explicitly. The technique resolves the shortcomings of the current mathematical machinery for the calculation of the propagator. For the evaluation of the first two displacement cumulants, the leading order Gaussian propagator is sufficient. However, some functionals of the propagator, such as the entropy production, which we refer to as "first derivatives of the trajectory", need to be evaluated to a previously-unrecognized higher order. The method presented here can be extended to arbitrarily higher orders in order to accurately compute any other functional of the propagator.

cond-mat.stat-mech↗

arXiv2024

Uphill drift in the absence of current in single-file diffusion

Single-file diffusion is a paradigmatic model for the transport of Brownian colloidal particles in narrow one-dimensional channels, such as those found in certain porous media, where the particles cannot cross each other. We consider a system where a different external uniform potential is present to the right and left of an origin. For example, this is the case when two channels meeting at the origin have different radii. In equilibrium, the chemical potential of the particles are equal, the density is thus lower in the region with the higher potential, and by definition there is no net current in the system. Remarkably, a single-file tracer particle initially located at the origin, with position denoted by $Y(t)$, exhibits an average up-hill drift toward the region of highest potential. This drift has the late time behavior $\langle Y(t)\rangle= C t^{1/4}$, where the prefactor $C$ depends on the initial particle arrangement. This surprising result is shown analytically by computing the first two moments of $Y(t)$ through a simple and physically-illuminating method, and also via extensive numerical simulations.

cond-mat.stat-mech↗

arXiv2023

Single-file diffusion in spatially inhomogeneous systems

We study the effect of spatially-varying potential and diffusivity on the dispersion of a tracer particle in single-file diffusion. Non-interacting particles in such a system exhibit normal diffusion at late times, which is characterised by an effective diffusion constant $D_\mathrm{eff}$. Here we demonstrate the physically appealing result that the dispersion of single-file tracers in this system has the same long-time behavior as that for Brownian particles in a spatially-homogeneous system with constant diffusivity $D_\mathrm{eff}$. Our results are based on a late-time analysis of the Fokker-Planck equation, motivated by the mathematical theory of homogenization. The findings are confirmed by numerical simulations for both annealed and quenched initial conditions.

cond-mat.stat-mech↗

arXiv2023

Detecting and characterizing phase transitions in active matter using entropy

A major challenge in the study of active matter lies in quantitative characterization of phases and transitions between them. We show how the entropy of a collection of active objects can be used to classify regimes and spatial patterns in their collective behavior. Specifically, we estimate the contributions to the total entropy from correlations between the degrees of freedom of position and orientation. This analysis pin-points the flocking transition in the Vicsek model while clarifying the physical mechanism behind the transition. When applied to experiments on swarming Bacillus subtilis with different cell aspect ratios and overall bacterial area fractions, the entropy analysis reveals a rich phase diagram with transitions between qualitatively different swarm statistics. We discuss physical and biological implications of these findings.

cond-mat.soft↗

arXiv2023

Resolving entropy contributions in nonequilibrium transitions

We derive a functional for the entropy contributed by any microscopic degrees of freedom as arising from their measurable pair correlations. Applicable both in and out of equilibrium, this functional yields the maximum entropy which a system can have given a certain correlation function. When applied to different correlations, the method allows us to identify the degrees of freedom governing a certain physical regime, thus capturing and characterizing dynamic transitions. The formalism applies also to systems whose translational invariance is broken by external forces and whose number of particles may vary. We apply it to experimental results for jammed bidisperse emulsions, capturing the crossover of this nonequilibrium system from crystalline to disordered hyperuniform structures as a function of mixture composition. We discover that the cross-correlations between the positions and sizes of droplets in the emulsion play the central role in the formation of the disordered hyperuniform states. We discuss implications of the approach for entropy estimation out of equilibrium and for characterizing transitions in disordered systems.

cond-mat.stat-mech↗

arXiv2022

Universal Relation between Entropy and Kinetics

Relating thermodynamic and kinetic properties is a conceptual challenge with many practical benefits. Here, based on first principles, we derive a rigorous inequality relating the entropy and the dynamic propagator of particle configurations. It is universal and applicable to steady states arbitrarily far from thermal equilibrium. Applying the general relation to diffusive dynamics yields a relation between the entropy and the (normal or anomalous) diffusion coefficient. The relation can be used to obtain useful bounds for the late-time diffusion coefficient from the calculated steady-state entropy or, conversely, to estimate the entropy based on measured diffusion coefficients. We demonstrate the validity and usefulness of the relation through several examples and discuss its broad range of applications, in particular, for systems far from equilibrium.

cond-mat.stat-mech↗

arXiv2021

Persistent Collective Motion of a Dispersing Membrane Domain

We study the Brownian motion of an assembly of mobile inclusions embedded in a fluid membrane. The motion includes the dispersal of the assembly, accompanied by the diffusion of its center of mass. Usually, the former process is much faster than the latter, since the diffusion coefficient of the center of mass is inversely proportional to the number of particles. However, in the case of membrane inclusions, we find that the two processes occur on the same time scale, thus prolonging significantly the lifetime of the assembly as a collectively moving object. This effect is caused by the quasi-two-dimensional membrane flows, which couple the motions even of the most remote inclusions in the assembly. The same correlations also cause the diffusion coefficient of the center of mass to decay slowly with time, resulting in weak sub-diffusion. We confirm our analytical results by Brownian dynamics simulations with flow-mediated correlations. The effect reported here should have implications for the stability of nano-scale membrane heterogeneities.

physics.bio-ph↗