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Enhanced diffusion of colloidal tracers due to enzymatic activity
Authors:
Mauricio Gomez,
Erick Leyva,
Justine Miqueu-Petit,
Dakota Feldcamp,
Anthony Estrada,
W. Benjamin Rogers,
Jennifer L. Ross,
Wylie W. Ahmed
Abstract:
Enzymatic catalysis can generate nonequilibrium fluctuations, but how these couple to tracer motion at larger length scales depends on physical context. Here, we investigate colloidal tracers in two configurations: passive particles dispersed in an enzymatically active solution, and enzyme-decorated particles where catalysis occurs directly at the tracer surface. We combine differential dynamic mi…
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Enzymatic catalysis can generate nonequilibrium fluctuations, but how these couple to tracer motion at larger length scales depends on physical context. Here, we investigate colloidal tracers in two configurations: passive particles dispersed in an enzymatically active solution, and enzyme-decorated particles where catalysis occurs directly at the tracer surface. We combine differential dynamic microscopy (DDM), which probes ensemble-averaged long-time diffusion, with optical tweezer (OT) measurements of short-time force fluctuations, and compare several complementary metrics for quantifying activity-induced enhancement. For 1 $μ$m tracers, we observe activity-induced enhancements in both configurations, with the strongest effects for enzyme-decorated particles, which exhibit enhanced diffusion and increased non-thermal force fluctuations. For 200 nm tracers, enhancements are more subtle and method-dependent: DDM detects modest increases in diffusion for bare particles, while corresponding signatures are not resolved by the OT. These results demonstrate that enzymatic activity can be transduced from molecular to microscale motion and forces, but that the apparent magnitude and detectability of enhancement depend strongly on tracer size, localization of activity, the timescales probed by the measurement, and the metric used to quantify enhancement. More broadly, understanding how enzyme activity modifies transport and fluctuations across scales is important for interpreting nonequilibrium dynamics in active soft matter, intracellular transport, and chemically crowded biological environments.
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Submitted 12 July, 2026;
originally announced July 2026.
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Anisotropic magnetoresistance and magnetic field-tunable Weyl nodes in Weyl metal SrRuO$_{3}$ thin films
Authors:
Uddipta Kar,
Akhilesh Kr. Singh,
Elisha Cho-Hao Lu,
P. V. Sreenivasa Reddy,
Fu-En Cheng,
Wazid Ahmed,
Song Yang,
Chun-Yen Lin,
Chia-Hung Hsu,
Guang-Yu Guo,
Wei-Li Lee
Abstract:
Weyl semimetals are a unique class of topological materials, possessing Fermi-arc surface states and exhibiting the chiral anomaly effect. The chiral anomaly refers to non-equilibrium charge transfer within a Weyl-node pair of opposite chirality under the condition of aligned electric and magnetic fields ($\bf{E} \parallel \bf{B}$), leading to non-conserved chiral charges and thus enhanced electri…
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Weyl semimetals are a unique class of topological materials, possessing Fermi-arc surface states and exhibiting the chiral anomaly effect. The chiral anomaly refers to non-equilibrium charge transfer within a Weyl-node pair of opposite chirality under the condition of aligned electric and magnetic fields ($\bf{E} \parallel \bf{B}$), leading to non-conserved chiral charges and thus enhanced electrical conductivity. In experiments, such an enhanced conductivity due to the chiral anomaly manifests as a negative longitudinal magnetoresistance (MR) when the external field $\bf{H}$ is applied along the bias current direction $\bf{I}$. In this work, we present rigorous $φ$- and $α$-dependent magnetotransport measurements to investigate such a negative longitudinal MR due to the chiral anomaly in a sunbeam-shaped device fabricated from an untwinned Weyl metal SrRuO$_{3}$ (SRO) thin film. Here, $φ$($α$) represents the angle between $\bf{I}$ and the in-plane $\bf{H}$(SRO monoclinic [001]$_{\rm o}$). Unusual $φ$ dependences of in-plane MR and Hall effects were uncovered at low temperatures, accompanied by the emergence of the fourfold-symmetric component in the in-plane MR. These results indicate that the chiral anomaly and resistivity anisotropy in SRO play important roles. In particular, the dramatic variation of Weyl nodes near the Fermi level through magnetic field manipulation of the magnetization orientation, as revealed by band structure calculations, is consistent with the observed in-plane MR and Hall effect.
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Submitted 22 February, 2026;
originally announced February 2026.
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Macroscopic active matter under confinement: dynamical heterogeneity, bursts, and glassy behavior in a few-body system of self-propelling camphor surfers
Authors:
Marco Leoni,
Matteo Paoluzzi,
Christian Alistair Dumaup,
Farbod Movagharnemati,
Lauren Nguyen-Leon,
Tiffany Nguyen,
Sarah Eldeen,
Wylie W. Ahmed
Abstract:
We study a few-body system composed of self-propelling camphor surfers confined within a circular boundary. These millimeter-sized particles move in a regime where inertia and long-ranged interactions play a significant role, leading to surprisingly complex and subtle collective dynamics. These dynamics include self-organized bursts and glassy behavior at intermediate densities--phenomena not appa…
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We study a few-body system composed of self-propelling camphor surfers confined within a circular boundary. These millimeter-sized particles move in a regime where inertia and long-ranged interactions play a significant role, leading to surprisingly complex and subtle collective dynamics. These dynamics include self-organized bursts and glassy behavior at intermediate densities--phenomena not apparent from ensemble-averaged steady-state measures. By analyzing quantities like the overlap order parameter, we observe that the system exhibits dynamical slowing down as particle density increases. This slowdown is also reflected in the bursting activity, where both the amplitude and frequency of bursts decrease with increasing particle density. A minimal inertial active-particle model reproduces these dynamical steady states, revealing the importance of a new intermediate length scale--larger than the particle size. This intermediate scale is critical for the formation of structures resembling caging and plays a key role in the glass-like transition. Our results describe a macroscopic analog of an active glass with the additional phenomena of density-dependent bursting.
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Submitted 16 April, 2026; v1 submitted 4 November, 2025;
originally announced November 2025.
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Topological Hall Response from Canted Antiferromagnetic Order in $d$-Electron Kagome Systems
Authors:
Waquar Ahmed,
Steffen Schäfer,
Pierre Lombardo,
Roland Hayn,
Imam Makhfudz
Abstract:
In a two-dimensional kagome monolayer, a nontrivial intrinsic Berry curvature may arise in the $d$-electron system from the interaction with a non-collinear spin order induced by an underlying antiferromagnetic exchange. This opens the route for a quantum anomalous Hall effect in the multi-orbital system, even without an external magnetic field, explicit spin-orbit coupling or relativistic effects…
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In a two-dimensional kagome monolayer, a nontrivial intrinsic Berry curvature may arise in the $d$-electron system from the interaction with a non-collinear spin order induced by an underlying antiferromagnetic exchange. This opens the route for a quantum anomalous Hall effect in the multi-orbital system, even without an external magnetic field, explicit spin-orbit coupling or relativistic effects. For spin orders with an out-of-plane component, the scalar spin chirality is finite, and the integration of the Berry curvature over the Brillouin zone may yield integer Hall conductivities in units of $e^2/h$. For a Fermi level within a nontrivial gap, the canted configuration offers, at least in principle, the possibility of a maximal Chern number, $C=\pm 5$. Candidate materials are considered in this paper. In existing materials, the electron hopping is generally highly anisotropic, leading to a quantum anomalous Hall effect with smaller Chern numbers. A topological phase transition between Hall plateaus of opposite $C$ can be driven by flipping the out-of-plane component of the spin order, alluding to the potential of this system to applications in quantum information.
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Submitted 10 July, 2026; v1 submitted 13 September, 2025;
originally announced September 2025.
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Inertia suppresses signatures of activity of active Brownian particles in a harmonic potential
Authors:
Angelica Arredondo,
Catania Calavitta,
Mauricio Gomez,
Jose Mendez-Villanueva,
Wylie W. Ahmed,
Nicholas D. Brubaker
Abstract:
A harmonically trapped active Brownian particle exhibits two types of positional distributions -- one has a single peak, the other has a single well -- that signify steady-state dynamics with low and high activity, respectively. Adding inertia to the translational motion preserves this strict single peak/well classification of the densities but shifts the dividing boundary between the states in th…
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A harmonically trapped active Brownian particle exhibits two types of positional distributions -- one has a single peak, the other has a single well -- that signify steady-state dynamics with low and high activity, respectively. Adding inertia to the translational motion preserves this strict single peak/well classification of the densities but shifts the dividing boundary between the states in the parameter space. We characterize this shift for the dynamics in one spatial dimension using the static Fokker--Planck equation for the full joint distribution of the state space. We derive local results analytically with a perturbation method for a small rotational velocity and then extend them globally with a numerical approach
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Submitted 3 March, 2023;
originally announced March 2023.
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Non-equilibrium fluctuations and nonlinear response of an active bath
Authors:
Hunter Seyforth,
Mauricio Gomez,
W. Benjamin Rogers,
Jennifer L. Ross,
Wylie W. Ahmed
Abstract:
We analyze the dynamics of a passive colloidal probe immersed in an active bath using an optical trap to study three physical processes: (1) the non-equilibrium fluctuations transferred to the probe by the active bath, (2) the friction experienced by the probe as it is driven through the active bath, and (3) the force relaxation of the probe returning to its equilibrium position. We measure the lo…
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We analyze the dynamics of a passive colloidal probe immersed in an active bath using an optical trap to study three physical processes: (1) the non-equilibrium fluctuations transferred to the probe by the active bath, (2) the friction experienced by the probe as it is driven through the active bath, and (3) the force relaxation of the probe returning to its equilibrium position. We measure the local force dynamics where all of the following characteristics are of $\mathcal{O}(1)$: the size of the probe colloid relative to active bath particle; the size of the probe colloid relative to the characteristic run-length of an active particle; and the timescale of probe movement to the persistence time of an active particle. We find at Péclet (Pe) $\ll 1$ the active suspension exhibits shear thinning down to the solvent viscosity (but not below); at $0.85 <$ Pe $\leq 5.1$ the active bath shear thickens; and at Pe $\geq 8.5$ the effective viscosity of the active bath shows a decreased effect of thickening and plateaus. These results are in agreement with recent modeling and simulations of the nonlinear rheology of an isotropic active bath, providing experimental verification, and suggesting the model predictions extends to moderately dense suspensions. Further, we observe that the distribution of force fluctuations depends on Pe, unlike in passive equilibrium baths. Lastly, we measure the energy transfer rate from the active bath to the probe to be $\langle J \rangle \approx 10^3$ $k_B T/$s, which leads to an increase in the effective diffusion of the probe by a factor of $\sim 2$.
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Submitted 21 March, 2022; v1 submitted 29 October, 2021;
originally announced October 2021.
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Comparison of different approaches to single-molecule imaging of enhanced enzyme diffusion
Authors:
Mengqi Xu,
W. Benjamin Rogers,
Wylie W. Ahmed,
Jennifer L. Ross
Abstract:
Enzymes have been shown to diffuse faster in the presence of their reactants. Recently, we revealed new insights into this process of enhanced diffusion using single-particle tracking (SPT) with total internal reflection fluorescence (TIRF) microscopy. We found that the mobility of individual enzymes was enhanced three fold in the presence of the substrate, and the motion remained Brownian. In thi…
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Enzymes have been shown to diffuse faster in the presence of their reactants. Recently, we revealed new insights into this process of enhanced diffusion using single-particle tracking (SPT) with total internal reflection fluorescence (TIRF) microscopy. We found that the mobility of individual enzymes was enhanced three fold in the presence of the substrate, and the motion remained Brownian. In this work, we compare different experimental designs, as well as different data analysis approaches, for studying single enzyme diffusion. We first tether enzymes directly on supported lipid bilayers (SLBs) to constrain the diffusion of enzymes to two dimensions. This experimental design recovers the 3-fold enhancement in enzyme diffusion in the presence of the substrate, as we observed before. We also simplify our system by replacing the bulky polymers used in the prior chamber design with a SLB-coated surface and glycerol. Using this newly-designed SLB/glycerol chamber, we compare two different analysis approaches for SPT: the mean-squared displacement (MSD) analysis and the jump-length analysis. We find that the MSD analysis requires high viscosity and large particles to accurately report the diffusion coefficient, while jump-length analysis depends less on the viscosity or size. Furthermore, the SLB-glycerol chamber fails to reproduce the enhanced diffusion of enzymes because glycerol inhibits enzyme activity.
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Submitted 30 December, 2020;
originally announced December 2020.
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Stochastic force dynamics of the model microswimmer Chlamydomonas reinhardtii: Active forces and energetics
Authors:
Corbyn Jones,
Mauricio Gomez,
Ryan M. Muoio,
Alex Vidal,
Anthony Mcknight,
Nicholas D. Brubaker,
Wylie W. Ahmed
Abstract:
We study the stochastic force dynamics of a model microswimmer (Chlamydomonas reinhardtii), using a combined experimental, theoretical, and numerical approach. While swimming dynamics have been extensively studied using hydrodynamic approaches, which infer forces from the viscous flow field, we directly measure the stochastic forces generated by the microswimmer using an optical trap via the photo…
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We study the stochastic force dynamics of a model microswimmer (Chlamydomonas reinhardtii), using a combined experimental, theoretical, and numerical approach. While swimming dynamics have been extensively studied using hydrodynamic approaches, which infer forces from the viscous flow field, we directly measure the stochastic forces generated by the microswimmer using an optical trap via the photon momentum method. We analyze the force dynamics by modeling the microswimmer as a self-propelled particle, a la active matter, and analyze it's energetics using methods from stochastic thermodynamics. We find complex oscillatory force dynamics and power dissipation on the order of $10^6$ $k_B T / s$ ($\sim$ fW)
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Submitted 5 February, 2021; v1 submitted 24 November, 2020;
originally announced November 2020.
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Surfing and crawling macroscopic active particles under strong confinement -- inertial dynamics
Authors:
Marco Leoni,
Matteo Paoluzzi,
Sarah Eldeen,
Anthony Estrada,
Lauren Nguyen,
Maria Alexandrescu,
Karin Sherb,
Wylie W. Ahmed
Abstract:
We study two types of active (self-propelled) macroscopic particles under confinement: camphor surfers and hexbug crawlers, using a combined experimental, theoretical, and numerical approach. Unlike widely studied microscopic active particles and swimmers, where thermal forces are often important and inertia is negligible, our macroscopic particles exhibit complex dynamics due expressly to active…
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We study two types of active (self-propelled) macroscopic particles under confinement: camphor surfers and hexbug crawlers, using a combined experimental, theoretical, and numerical approach. Unlike widely studied microscopic active particles and swimmers, where thermal forces are often important and inertia is negligible, our macroscopic particles exhibit complex dynamics due expressly to active non-thermal noise combined with inertial effects. Strong confinement induces accumulation at a finite distance within the boundary and gives rise to three distinguishable dynamical states; both depending on activity and inertia. These surprisingly complex dynamics arise already at the single particle level -- highlighting the importance of inertia in macroscopic active matter.
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Submitted 21 October, 2020; v1 submitted 21 May, 2020;
originally announced May 2020.
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Quantifying the non-equilibrium activity of an active colloid
Authors:
Sarah Eldeen,
Ryan Muoio,
Paris Blaisdell-Pijuan,
Ngoc La,
Mauricio Gomez,
Alex Vidal,
Wylie Ahmed
Abstract:
Active matter systems exhibit rich emergent behavior due to constant injection and dissipation of energy at the level of individual agents. Since these systems are far from equilibrium, their dynamics and energetics cannot be understood using the framework of equilibrium statistical mechanics. Recent developments in stochastic thermodynamics extend classical concepts of work, heat, and energy diss…
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Active matter systems exhibit rich emergent behavior due to constant injection and dissipation of energy at the level of individual agents. Since these systems are far from equilibrium, their dynamics and energetics cannot be understood using the framework of equilibrium statistical mechanics. Recent developments in stochastic thermodynamics extend classical concepts of work, heat, and energy dissipation to fluctuating non-equilibrium systems. We use recent advances in experiment and theory to study the non-thermal dissipation of individual light-activated self-propelled colloidal particles. We focus on characterizing the transition from thermal to non-thermal fluctuations and show that energy dissipation rates on the order of $\sim k_BT/$s are measurable from finite time series data.
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Submitted 9 April, 2020;
originally announced April 2020.
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Noncommutative scalar fields in compact spaces: quantisation and implications
Authors:
Mir Mehedi Faruk,
Mishkat Al Alvi,
Wasif Ahmed,
Md Muktadir Rahman,
Arup Barua Apu
Abstract:
In this paper we consider a two component scalar field theory, with noncommutativity in its conjugate momentum space. We quantize such a theory in a compact space with the help of dressing transformations and we reveal a significant effect of introducing such noncommutativity as the splitting of the energy levels of each individual mode that constitutes the whole system. We further compute the the…
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In this paper we consider a two component scalar field theory, with noncommutativity in its conjugate momentum space. We quantize such a theory in a compact space with the help of dressing transformations and we reveal a significant effect of introducing such noncommutativity as the splitting of the energy levels of each individual mode that constitutes the whole system. We further compute the thermal partition function exactly with predicted deformed dispersion relations from noncommutative theories and compare the results with usual results. It is found that thermodynamic quantities in noncommutative models, irrespective of whether the model is more deformed in infrared/UV region, show deviation from standard results in high temperature region.
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Submitted 30 August, 2017; v1 submitted 6 July, 2017;
originally announced July 2017.
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Nonequilibrium dissipation in living oocytes
Authors:
Étienne Fodor,
Wylie W. Ahmed,
Maria Almonacid,
Matthias Bussonnier,
Nir S. Gov,
Marie-Hélène Verlhac,
Timo Betz,
Paolo Visco,
Frédéric van Wijland
Abstract:
Living organisms are inherently out-of-equilibrium systems. We employ new developments in stochastic energetics and rely on a minimal microscopic model to predict the amount of mechanical energy dissipated by such dynamics. Our model includes complex rheological effects and nonequilibrium stochastic forces. By performing active microrheology and tracking micron-sized vesicles in the cytoplasm of l…
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Living organisms are inherently out-of-equilibrium systems. We employ new developments in stochastic energetics and rely on a minimal microscopic model to predict the amount of mechanical energy dissipated by such dynamics. Our model includes complex rheological effects and nonequilibrium stochastic forces. By performing active microrheology and tracking micron-sized vesicles in the cytoplasm of living oocytes, we provide unprecedented measurements of the spectrum of dissipated energy. We show that our model is fully consistent with the experimental data, and we use it to offer predictions for the injection and dissipation energy scales involved in active fluctuations.
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Submitted 22 December, 2016; v1 submitted 3 November, 2015;
originally announced November 2015.
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Active mechanics reveal molecular-scale force kinetics in living oocytes
Authors:
Wylie W. Ahmed,
Etienne Fodor,
Maria Almonacid,
Matthias Bussonnier,
Marie-Helene Verlhac,
Nir S. Gov,
Paolo Visco,
Frederic van Wijland,
Timo Betz
Abstract:
Active diffusion of intracellular components is emerging as an important process in cell biology. This process is mediated by complex assemblies of molecular motors and cytoskeletal filaments that drive force generation in the cytoplasm and facilitate enhanced motion. The kinetics of molecular motors have been precisely characterized in-vitro by single molecule approaches, however, their in-vivo b…
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Active diffusion of intracellular components is emerging as an important process in cell biology. This process is mediated by complex assemblies of molecular motors and cytoskeletal filaments that drive force generation in the cytoplasm and facilitate enhanced motion. The kinetics of molecular motors have been precisely characterized in-vitro by single molecule approaches, however, their in-vivo behavior remains elusive. Here, we study the active diffusion of vesicles in mouse oocytes, where this process plays a key role in nuclear positioning during development, and combine an experimental and theoretical framework to extract molecular-scale force kinetics (force, power-stroke, and velocity) of the in-vivo active process. Assuming a single dominant process, we find that the nonequilibrium activity induces rapid kicks of duration $τ\sim$ 300 $μ$s resulting in an average force of $F \sim$ 0.4 pN on vesicles in in-vivo oocytes, remarkably similar to the kinetics of in-vitro myosin-V. Our results reveal that measuring in-vivo active fluctuations allows extraction of the molecular-scale activity in agreement with single-molecule studies and demonstrates a mesoscopic framework to access force kinetics.
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Submitted 8 February, 2018; v1 submitted 28 October, 2015;
originally announced October 2015.