@article{19785,
  abstract     = {We consider a family of totally asymmetric simple exclusion processes (TASEPs), consisting of particles on a lattice that require binding by a “token” in various physical configurations to advance over the lattice. Using a combination of theory and simulations, we address the following questions: (i) How does token binding kinetics affect the current-density relation on the lattice? (ii) How does this current-density relation depend on the scarcity of tokens? (iii) How do tokens propagate the effects of the locally imposed disorder (such as a slow site) over the entire lattice? (iv) How does a shared pool of tokens couple concurrent TASEPs running on multiple lattices? and (v) How do our results translate to TASEPs with open boundaries that exchange particles with the reservoir? Since real particle motion (including in biological systems that inspired the standard TASEP model, e.g., protein synthesis or movement of molecular motors) is often catalyzed, regulated, actuated, or otherwise mediated, the token-driven TASEP dynamics analyzed in this paper should allow for a better understanding of real systems and enable a closer match between TASEP theory and experimental observations.},
  author       = {Kavcic, Bor and Tkačik, Gašper},
  issn         = {2470-0053},
  journal      = {Physical Review E},
  number       = {5},
  publisher    = {American Physical Society},
  title        = {{Token-driven totally asymmetric simple exclusion processes}},
  doi          = {10.1103/physreve.111.054122},
  volume       = {111},
  year         = {2025},
}

@article{20483,
  abstract     = {A parallel plate capacitor containing an electrolytic solution is the simplest model of a supercapacitor or electric double-layer capacitor. Using both analytical and numerical techniques, we solve the Poisson-Nernst-Planck equations for such a system, describing the mean-field charging dynamics of the capacitor, when a constant potential difference is abruptly applied to its plates. Working at constant total number of ions, we focus on the physical processes involved in the relaxation and, whenever possible, give its functional shape and exact time constants. We first review and study the case of a symmetric binary electrolyte, where we assume the two ionic species to have the same charges and diffusivities. We then relax these assumptions and present results for a generic strong (i.e fully dissociated) binary electrolyte. At low electrolyte concentration, the relaxation is simple to understand, as the dynamics of positive and negative ions appear decoupled. At higher electrolyte concentration, we distinguish several regimes. In the linear regime (low voltages), relaxation is multiexponential, it starts by the buildup of the equilibrium charge profile and continues with neutral mass diffusion, and the relevant timescales feature both the average and the Nernst-Hartley diffusion coefficients. In the purely nonlinear regime (intermediate voltages), the initial relaxation is slowed down exponentially due to increased capacitance, while bulk effects become more and more evident. In the fully nonlinear regime (high voltages), the dynamics of charge and mass are completely entangled and, asymptotically, the relaxation is linear in time. We finally discuss nonideal behavior in real capacitors and provide conditions for which mean-field is expected to hold.},
  author       = {Palaia, Ivan and Asta, Adelchi J. and Dutta, Megh and Warren, Patrick B. and Rotenberg, Benjamin and Trizac, Emmanuel},
  issn         = {2470-0053},
  journal      = {Physical Review E},
  number       = {3},
  publisher    = {American Physical Society},
  title        = {{Poisson-Nernst-Planck charging dynamics of an electric double-layer capacitor: Symmetric and asymmetric binary electrolytes}},
  doi          = {10.1103/p4dg-snqf},
  volume       = {112},
  year         = {2025},
}

@article{20847,
  abstract     = {We report on an experimental active matter system with motion restricted to four cardinal directions. Our particles are magnetite-doped colloidal spheres driven by the Quincke electrorotational instability. The absence of a magnetic field (|𝑩|=0) leads to circular trajectories interspersed with short spontaneous runs. Intermediate fields (|𝑩|≲20mT) linearize the motion along the axis perpendicular to 𝑩. At high magnetic fields, we observe the surprising emergence of a second, distinct linearization along the axis parallel to 𝑩. With numerical simulations, we show that this behavior can be explained by anisotropic magnetic susceptibility.},
  author       = {Fitzgerald, Eavan and Clavaud, Cécile and Das, Debasish and Lenton, Isaac C and Waitukaitis, Scott R},
  issn         = {2470-0053},
  journal      = {Physical Review E},
  number       = {6},
  publisher    = {American Physical Society},
  title        = {{Rolling at right angles: Magnetic anisotropy enables dual-anisotropic active matter}},
  doi          = {10.1103/1ss8-31rb},
  volume       = {112},
  year         = {2025},
}

@article{17892,
  abstract     = {Enzyme-substrate kinetics form the basis of many biomolecular processes. The interplay between substrate binding and substrate geometry can give rise to long-range interactions between enzyme binding events. Here we study a general model of enzyme-substrate kinetics with restricted long-range interactions described by an exponent −𝛾. We employ a coherent-state path integral and renormalization group approach to calculate the first moment and two-point correlation function of the enzyme-binding profile. We show that starting from an empty substrate the average occupancy follows a power law with an exponent 1/(1−𝛾) over time. The correlation function decays algebraically with two distinct spatial regimes characterized by exponents −𝛾 on short distances and −(2/3)⁢(2−𝛾) on long distances. The crossover between both regimes scales inversely with the average substrate occupancy. Our work allows associating experimental measurements of bound enzyme locations with their binding kinetics and the spatial conformation of the substrate.},
  author       = {Olmeda, Fabrizio and Rulands, Steffen},
  issn         = {2470-0053},
  journal      = {Physical Review E},
  number       = {2},
  publisher    = {American Physical Society},
  title        = {{Field theory of enzyme-substrate systems with restricted long-range interactions}},
  doi          = {10.1103/PhysRevE.110.024404},
  volume       = {110},
  year         = {2024},
}

@article{18704,
  abstract     = {Clathrin-mediated endocytosis is the main pathway used by eukaryotic cells to take up extracellular material, but the dominant physical mechanisms driving this process are still elusive. Recently, several high-resolution imaging techniques have been used on different cell lines to measure the geometrical properties of clathrin-coated pits over their whole lifetime. Here, we first show that the combination of all datasets with the recently introduced cooperative curvature model defines a consensus pathway, which is characterized by a flat-to-curved transition at finite area, followed by linear growth and subsequent saturation of curvature. We then apply an energetic model for the composite of the plasma membrane and clathrin coat to this consensus pathway to show that the dominant mechanism for invagination could be coat stiffening, which might originate from cooperative interactions between the different clathrin molecules and progressively drives the system toward its intrinsic curvature. Our theory predicts that two length scales determine the invagination pathway, namely the patch size at which the flat-to-curved transition occurs and the final pit radius.},
  author       = {Frey, Felix F and Schwarz, Ulrich S.},
  issn         = {2470-0053},
  journal      = {Physical Review E},
  number       = {6},
  publisher    = {American Physical Society},
  title        = {{Coat stiffening can explain invagination of clathrin-coated membranes}},
  doi          = {10.1103/PhysRevE.110.064403},
  volume       = {110},
  year         = {2024},
}

@article{15322,
  abstract     = {The tendency of materials to order in triboelectric series has prompted suggestions that contact electrification might have a single, unified underlying description. However, the possibility of “triboelectric cycles,” i.e., series that loop back onto themselves, is seemingly at odds with such a coherent description. In this work, we propose that if multiple charge carrying species are at play, both triboelectric series and cycles are possible. We show how series arise naturally if only a single charge carrier species is involved and if the driving mechanism is approach toward thermodynamic equilibrium, and simultaneously, that cycles are forbidden under such conditions. Suspecting multiple carriers might relax the situation, we affirm this is the case by explicit construction of a cycle involving two carriers, and then extend this to show how more complex cycles emerge. Our work highlights the importance of series and cycles towards determining the underlying mechanism(s) and carrier(s) in contact electrification.},
  author       = {Sobarzo Ponce, Juan Carlos A and Waitukaitis, Scott R},
  issn         = {2470-0053},
  journal      = {Physical Review E},
  number       = {3},
  publisher    = {American Physical Society},
  title        = {{Multiple charge carrier species as a possible cause for triboelectric cycles}},
  doi          = {10.1103/PhysRevE.109.L032108},
  volume       = {109},
  year         = {2024},
}

@article{12545,
  abstract     = {We study active surface wetting using a minimal model of bacteria that takes into account the intrinsic motility diversity of living matter. A mixture of “fast” and “slow” self-propelled Brownian particles is considered in the presence of a wall. The evolution of the wetting layer thickness shows an overshoot before stationarity and its composition evolves in two stages, equilibrating after a slow elimination of excess particles. Nonmonotonic evolutions are shown to arise from delayed avalanches towards the dilute phase combined with the emergence of a transient particle front.},
  author       = {Rojas Vega, Mauricio Nicolas and De Castro, Pablo and Soto, Rodrigo},
  issn         = {2470-0053},
  journal      = {Physical Review E},
  number       = {1},
  publisher    = {American Physical Society},
  title        = {{Wetting dynamics by mixtures of fast and slow self-propelled particles}},
  doi          = {10.1103/PhysRevE.107.014608},
  volume       = {107},
  year         = {2023},
}

@article{12789,
  abstract     = {Experiments have shown that charge distributions of granular materials are non-Gaussian, with broad tails that indicate many particles with high charge. This observation has consequences for the behavior of granular materials in many settings, and may bear relevance to the underlying charge transfer mechanism. However, there is the unaddressed possibility that broad tails arise due to experimental uncertainties, as determining the shapes of tails is nontrivial. Here we show that measurement uncertainties can indeed account for most of the tail broadening previously observed. The clue that reveals this is that distributions are sensitive to the electric field at which they are measured; ones measured at low (high) fields have larger (smaller) tails. Accounting for sources of uncertainty, we reproduce this broadening in silico. Finally, we use our results to back out the true charge distribution without broadening, which we find is still non-Guassian, though with substantially different behavior at the tails and indicating significantly fewer highly charged particles. These results have implications in many natural settings where electrostatic interactions, especially among highly charged particles, strongly affect granular behavior.},
  author       = {Mujica, Nicolás and Waitukaitis, Scott R},
  issn         = {2470-0053},
  journal      = {Physical Review E},
  number       = {3},
  publisher    = {American Physical Society},
  title        = {{Accurate determination of the shapes of granular charge distributions}},
  doi          = {10.1103/PhysRevE.107.034901},
  volume       = {107},
  year         = {2023},
}

@article{12890,
  abstract     = {We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately geometrically round cultures get a competitive advantage. We first analyze the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e., freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely, that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity, and the central European plain has less clear cultural borders.},
  author       = {Klausen, Frederik Ravn and Lauritsen, Asbjørn Bækgaard},
  issn         = {2470-0053},
  journal      = {Physical Review E},
  number       = {5},
  publisher    = {American Physical Society},
  title        = {{Stochastic cellular automaton model of culture formation}},
  doi          = {10.1103/PhysRevE.108.054307},
  volume       = {108},
  year         = {2023},
}

@article{13231,
  abstract     = {We study ab initio approaches for calculating x-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula that expresses the inelastic contribution in terms of the dielectric function. We study the electronic dynamic structure factor computed from the Mermin dielectric function using an ab initio electron-ion collision frequency in comparison to computations using a linear-response time-dependent density functional theory (LR-TDDFT) framework for hydrogen and beryllium and investigate the dispersion of free-free and bound-free contributions to the scattering signal. A separate treatment of these contributions, where only the free-free part follows the Mermin dispersion, shows good agreement with LR-TDDFT results for ambient-density beryllium, but breaks down for highly compressed matter where the bound states become pressure ionized. LR-TDDFT is used to reanalyze x-ray Thomson scattering experiments on beryllium demonstrating strong deviations from the plasma conditions inferred with traditional analytic models at small scattering angles.},
  author       = {Schörner, Maximilian and Bethkenhagen, Mandy and Döppner, Tilo and Kraus, Dominik and Fletcher, Luke B. and Glenzer, Siegfried H. and Redmer, Ronald},
  issn         = {2470-0053},
  journal      = {Physical Review E},
  number       = {6},
  publisher    = {American Physical Society},
  title        = {{X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula}},
  doi          = {10.1103/PhysRevE.107.065207},
  volume       = {107},
  year         = {2023},
}

@article{12257,
  abstract     = {Structural balance theory is an established framework for studying social relationships of friendship and enmity. These relationships are modeled by a signed network whose energy potential measures the level of imbalance, while stochastic dynamics drives the network toward a state of minimum energy that captures social balance. It is known that this energy landscape has local minima that can trap socially aware dynamics, preventing it from reaching balance. Here we first study the robustness and attractor properties of these local minima. We show that a stochastic process can reach them from an abundance of initial states and that some local minima cannot be escaped by mild perturbations of the network. Motivated by these anomalies, we introduce best-edge dynamics (BED), a new plausible stochastic process. We prove that BED always reaches balance and that it does so fast in various interesting settings.},
  author       = {Chatterjee, Krishnendu and Svoboda, Jakub and Zikelic, Dorde and Pavlogiannis, Andreas and Tkadlec, Josef},
  issn         = {2470-0053},
  journal      = {Physical Review E},
  number       = {3},
  publisher    = {American Physical Society},
  title        = {{Social balance on networks: Local minima and best-edge dynamics}},
  doi          = {10.1103/physreve.106.034321},
  volume       = {106},
  year         = {2022},
}

@article{10352,
  abstract     = {In the nuclear pore complex, intrinsically disordered nuclear pore proteins (FG Nups) form a selective barrier for transport into and out of the cell nucleus, in a way that remains poorly understood. The collective FG Nup behavior has long been conceptualized either as a polymer brush, dominated by entropic and excluded-volume (repulsive) interactions, or as a hydrogel, dominated by cohesive (attractive) interactions between FG Nups. Here we compare mesoscale computational simulations with a wide range of experimental data to demonstrate that FG Nups are at the crossover point between these two regimes. Specifically, we find that repulsive and attractive interactions are balanced, resulting in morphologies and dynamics that are close to those of ideal polymer chains. We demonstrate that this property of FG Nups yields sufficient cohesion to seal the transport barrier, and yet maintains fast dynamics at the molecular scale, permitting the rapid polymer rearrangements needed for transport events.},
  author       = {Davis, Luke K. and Ford, Ian J. and Šarić, Anđela and Hoogenboom, Bart W.},
  issn         = {2470-0053},
  journal      = {Physical Review E},
  number       = {2},
  publisher    = {American Physical Society},
  title        = {{Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics}},
  doi          = {10.1103/physreve.101.022420},
  volume       = {101},
  year         = {2020},
}

@article{6779,
  abstract     = {Recent studies suggest that unstable recurrent solutions of the Navier-Stokes equation provide new insights
into dynamics of turbulent flows. In this study, we compute an extensive network of dynamical connections
between such solutions in a weakly turbulent quasi-two-dimensional Kolmogorov flow that lies in the inversion symmetric subspace. In particular, we find numerous isolated heteroclinic connections between different
types of solutions—equilibria, periodic, and quasiperiodic orbits—as well as continua of connections forming
higher-dimensional connecting manifolds. We also compute a homoclinic connection of a periodic orbit and
provide strong evidence that the associated homoclinic tangle forms the chaotic repeller that underpins transient
turbulence in the symmetric subspace.},
  author       = {Suri, Balachandra and Pallantla, Ravi Kumar and Schatz, Michael F. and Grigoriev, Roman O.},
  issn         = {2470-0053},
  journal      = {Physical Review E},
  number       = {1},
  publisher    = {American Physical Society},
  title        = {{Heteroclinic and homoclinic connections in a Kolmogorov-like flow}},
  doi          = {10.1103/physreve.100.013112},
  volume       = {100},
  year         = {2019},
}