arXiv subjects

Wylie W. Ahmed

Publications and source records attributed to Wylie W. Ahmed.

11 recordsLinked to original sources

arXiv2026

Enhanced diffusion of colloidal tracers due to enzymatic activity

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.

cond-mat.soft↗

arXiv2026

Macroscopic active matter under confinement: dynamical heterogeneity, bursts, and glassy behavior in a few-body system of self-propelling camphor surfers

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.

cond-mat.soft↗

arXiv2025

A method for site-specifically tethering the enzyme urease to DNA origami with sustained activity

Attaching enzymes to nanostructures has proven useful to the study of enzyme functionality under controlled conditions and has led to new technologies. Often, the utility and interest of enzyme-tethered nanostructures lie in how the enzymatic activity is affected by how the enzymes are arranged in space. Therefore, being able to conjugate enzymes to nanostructures while preserving the enzymatic activity is essential. In this paper, we present a method to conjugate single-stranded DNA to the enzyme urease while maintaining enzymatic activity. We show evidence of successful conjugation and quantify the variables that affect the conjugation yield. We also show that the enzymatic activity is unchanged after conjugation compared to the enzyme in its native state. Finally, we demonstrate the tethering of urease to nanostructures made using DNA origami with high site-specificity. Decorating nanostructures with enzymatically-active urease may prove to be useful in studying, or even utilizing, the functionality of urease in disciplines ranging from biotechnology to soft-matter physics. The techniques we present in this paper will enable researchers across these fields to modify enzymes without disrupting their functionality, thus allowing for more insightful studies into their behavior and utility.

physics.bio-ph↗

arXiv2023

Inertia suppresses signatures of activity of active Brownian particles in a harmonic potential

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

cond-mat.soft↗

arXiv2022

Non-equilibrium fluctuations and nonlinear response of an active bath

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 $\sim 2$.

cond-mat.soft↗

arXiv2021

Stochastic force dynamics of the model microswimmer Chlamydomonas reinhardtii: Active forces and energetics

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)

physics.bio-ph↗

arXiv2020

Comparison of different approaches to single-molecule imaging of enhanced enzyme diffusion

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.

physics.bio-ph↗

arXiv2020

Surfing and crawling macroscopic active particles under strong confinement -- inertial dynamics

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.

cond-mat.soft↗

arXiv2018

Small-scale displacement fluctuations of vesicles in fibroblasts

The intracellular environment is a dynamic space filled with various organelles moving in all directions. Included in this diverse group of organelles are vesicles, which are involved in transport of molecular cargo throughout the cell. Vesicles move in either a directed or non-directed fashion, often depending on interactions with cytoskeletal proteins such as microtubules, actin filaments, and molecular motors. How these proteins affect the local fluctuations of vesicles in the cytoplasm is not clear since they have the potential to both facilitate and impede movement. Here we show that vesicle mobility is significantly affected by myosin-II, even though it is not a cargo transport motor. We find that myosin-II activity increases the effective diffusivity of vesicles and its inhibition facilitates longer states of non-directed motion. Our study suggests that altering myosin-II activity in the cytoplasm of cells can modulate the mobility of vesicles, providing a possible mechanism for cells to dynamically tune the cytoplasmic environment in space and time.

physics.bio-ph↗

arXiv2018

Active mechanics reveal molecular-scale force kinetics in living oocytes

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.

physics.bio-ph↗

arXiv2016

Nonequilibrium dissipation in living oocytes

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.

q-bio.SC↗