arXiv subjects

Azam Gholami

Publications and source records attributed to Azam Gholami.

10 recordsLinked to original sources

arXiv2026

Spontaneous flows and interfacial instabilities in oxygen-sensitive living active matter

Active fluids generate motion and stress internally, but in living systems their activity is often regulated by environmental fields that organisms consume or produce. How such fields localise active stresses and create flow-generating interfaces remains unclear. Here we show that oxygen organises suspensions of the flagellated microswimmer \textit{Euglena gracilis} into an annular living interface. In circular chambers with an air-exposed periphery, a labyrinthine bioconvective pattern and an annular cellular accumulation emerge nearly simultaneously, whereas sealing the periphery suppresses the annulus. The accumulation then sharpens, develops finite-wavelength protrusions and forms a long-lived, collectively rotating corona. An oxygen-coupled polar active-fluid model qualitatively recapitulates this progression: oxygen transport, cellular consumption and oxygen-regulated swimming and reorientation assemble and position the annulus, whereas dipolar active stresses destabilise it and generate collective flow. These results show how a metabolically shaped chemical field can create and activate a living interface, linking taxis, bioconvection and active interfacial hydrodynamics.

cond-mat.soft↗

arXiv2025

Multiparticle Collision Dynamics Simulations of the Flagellar Apparatus in Chlamydomonas reinhardtii

Using multiparticle collision dynamics simulations, we investigate the swimming dynamics, orientational behavior, and hydrodynamic interactions of a model swimmer designed to mimic the isolated flagellar apparatus ($FA$) of Chlamydomonas reinhardtii. We represent the $FA$ as a chain of monomers connected by elastic springs, with two traveling waves originating at its center and propagating in opposite directions along the chain. Our simulations show that an $FA$ whose beat pattern has non-zero mean curvature sustains ballistic motion for several hundred beats before transitioning to a diffusion-dominated regime via rotational diffusion. In contrast, a flagellar apparatus with zero mean curvature ($FA_0$) -- generates mirror-symmetric deformations and fails to achieve net propulsion. Both the active $FA$ and $FA_0$ exhibit orientational autocorrelation functions that decay exponentially -- matching those of their inactive counterparts -- indicating that active beating does not influence the FA's rotational diffusion. Driving the two flagellar arms at different frequencies reproduces the epitrochoid-like trajectory observed experimentally. Finally, hydrodynamic interactions between two $FA$s give rise to co-moving bound pairs in either parallel or antiparallel configurations, with their stability governed by the phase difference of the curvature waves. Together, our results establish a versatile model microswimmer with tunable dynamics -- offering a blueprint for the rational design of artificial, flagella-driven microswimmers.

physics.bio-ph↗

arXiv2024

Symmetry Breaking in Chemical Systems: Engineering Complexity through Self-Organization and Marangoni Flows

Far from equilibrium, chemical and biological systems can form complex patterns and waves through reaction-diffusion coupling. Fluid motion often interferes with these self-organized concentration patterns. In this study, we investigate the influence of Marangoni-driven flows inside a thin layer of fluid ascending the outer surfaces of hydrophilic obstacles on the spatio-temporal dynamics of chemical waves in the modified Belousov-Zhabotinsky reaction. Our observations reveal that circular waves originate nearly simultaneously at the obstacles and propagate outward. In a covered setup, where evaporation is minimal, the wavefronts maintain their circular shape. However, in an uncovered setup with significant evaporation and resulting Marangoni flows, the interplay between surface tension-driven Marangoni flows and gravity destabilizes the wavefronts, creating distinctive flower-like patterns around the obstacles. Our analysis shows that here solutal Marangoni forces are more relevant than thermal ones. Our experiments further show that the number of petals formed increases linearly with the obstacle's diameter, though a minimum diameter is required for these instabilities to appear. These findings demonstrate the potential to 'engineer' specific wave patterns, offering a method to control and direct reaction dynamics. This capability is especially important for developing microfluidic devices requiring precise control over chemical wave propagation.

physics.flu-dyn↗

arXiv2018

Spontaneous center formation in Dictyostelium discoideum

Dictyostelium discoideum (D.d.) is a widely studied amoeba due to its capabilities of development, survival, and self-organization. During aggregation it produces and relays a chemical signal (cAMP) which shows spirals and target centers. Nevertheless, the natural emergence of these structures is still not well understood. We present a mechanism for creation of centers and target waves of cAMP in D.d. by adding cell inhomogeneity to a well known reaction-diffusion model of cAMP waves and we characterize its properties. We show how stable activity centers appear spontaneously in areas of higher cell density with the oscillation frequency of these centers depending on their density. The cAMP waves have the characteristic dispersion relation of trigger waves and a velocity which increases with cell density. Chemotactically competent cells react to these waves and create aggregation streams even with very simple movement rules. Finally we argue in favor of the existence of bounded phosphodiesterase to maintain the wave properties once small cell clusters appear.

nlin.PS↗

arXiv2018

Spatial heterogeneities shape collective behavior of signaling amoeboid cells

We present novel experimental results on pattern formation of signaling Dictyostelium discoideum amoeba in the presence of a periodic array of millimeter-sized pillars. We observe concentric cAMP waves that initiate almost synchronously at the pillars and propagate outwards. These waves have higher frequency than the other firing centers and dominate the system dynamics. The cells respond chemotactically to these circular waves and stream towards the pillars, forming periodic Voronoi domains that reflect the periodicity of the underlying lattice. We performed comprehensive numerical simulations of a reaction-diffusion model to study the characteristics of the boundary conditions given by the obstacles. Our simulations show that, the obstacles can act as the wave source depending on the imposed boundary condition. Interestingly, a critical minimum accumulation of cAMP around the obstacles is needed for the pillars to act as the wave source. This critical value is lower at smaller production rates of the intracellular cAMP which can be controlled in our experiments using caffeine. Experiments and simulations also show that in the presence of caffeine the number of firing centers is reduced which is crucial in our system for circular waves emitted from the pillars to successfully take over the dynamics. These results are crucial to understand the signaling mechanism of Dictyostelium cells that experience spatial heterogeneities in its natural habitat.

physics.bio-ph↗

arXiv2018

Modelling of Dictyostelium Discoideum Movement in Linear Gradient of Chemoattractant

Chemotaxis is a ubiquitous biological phenomenon in which cells detect a spatial gradient of chemoattractant, and then move towards the source. Here we present a position-dependent advection-diffusion model that quantitatively describes the statistical features of the chemotactic motion of the social amoeba {\it Dictyostelium discoideum} in a linear gradient of cAMP (cyclic adenosine monophosphate). We fit the model to experimental trajectories that are recorded in a microfluidic setup with stationary cAMP gradients and extract the diffusion and drift coefficients in the gradient direction. Our analysis shows that for the majority of gradients, both coefficients decrease in time and become negative as the cells crawl up the gradient. The extracted model parameters also show that besides the expected drift in the direction of chemoattractant gradient, we observe a nonlinear dependency of the corresponding variance in time, which can be explained by the model. Furthermore, the results of the model show that the non-linear term in the mean squared displacement of the cell trajectories can dominate the linear term on large time scales.

physics.bio-ph↗

arXiv2017

Effects of developmental variability on the dynamics and self-organization of cell populations

We report experimental and theoretical results on spatiotemporal pattern formation in cell populations, where the parameters vary in space and time due to mechanisms intrinsic to the system, namely Dictyostelium discoideum (D.d.) in the starvation phase. We find that different patterns are formed when the populations are initialized at different developmental stages, or, when populations at different initial developmental stages are mixed. The experimentally observed patterns can be understood with a modified Kessler-Levine model that takes into account the initial spatial heterogeneity of the cell populations and a developmental path introduced by us, i.e., the time dependence of the various biochemical parameters. The dynamics of the parameter agree with known biochemical studies. Most importantly the modified model reproduces not only our results, but also the observations of an independent experiment published earlier. This shows that pattern formation can be used to understand and quantify the temporal evolution of the system parameters.

physics.bio-ph↗

arXiv2017

Convective Instability and Boundary Driven Oscillations in a Reaction-Diffusion-Advection Model

In a reaction-diffusion-advection system, with a convectively unstable regime, a perturbation creates a wave train that is advected downstream and eventually leaves the system. We show that the convective instability coexists with a local absolute instability when a fixed boundary condition upstream is imposed. This boundary induced instability acts as a continuous wave source, creating a local periodic excitation near the boundary, which initiates waves traveling both up and downstream. To confirm this, we performed analytical analysis and numerical simulations of a modified Martiel-Goldbeter reaction-diffusion model with the addition of an advection term. We provide a quantitative description of the wave packet appearing in the convectively unstable regime, which we found to be in excellent agreement with the numerical simulations. We characterize this new instability and show that in the limit of high advection speed, it is suppressed. This type of instability can be expected for reaction-diffusion systems that present both a convective instability and an excitable regime. In particular, it can be relevant to understand the signaling mechanism of the social amoeba Dictyostelium discoideum that may experience fluid flows in its natural habitat.

nlin.PS↗

arXiv2007

Velocity oscillations in actin-based motility

We present a simple and generic theoretical description of actin-based motility, where polymerization of filaments maintains propulsion. The dynamics is driven by polymerization kinetics at the filaments' free ends, crosslinking of the actin network, attachment and detachment of filaments to the obstacle interfaces and entropic forces. We show that spontaneous oscillations in the velocity emerge in a broad range of parameter values, and compare our findings with experiments.

q-bio.CB↗

arXiv2006

Entropic forces generated by grafted semiflexible polymers

The entropic force exerted by the Brownian fluctuations of a grafted semiflexible polymer upon a rigid smooth wall are calculated both analytically and by Monte Carlo simulations. Such forces are thought to play an important role for several cellular phenomena, in particular, the physics of actin-polymerization-driven cell motility and movement of bacteria like Listeria. In the stiff limit, where the persistence length of the polymer is larger than its contour length, we find that the entropic force shows scaling behavior. We identify the characteristic length scales and the explicit form of the scaling functions. In certain asymptotic regimes we give simple analytical expressions which describe the full results to a very high numerical accuracy. Depending on the constraints imposed on the transverse fluctuations of the filament there are characteristic differences in the functional form of the entropic forces; in a two-dimensional geometry the entropic force exhibits a marked peak.

cond-mat.soft↗