arXiv subjects

Albert Bae

Publications and source records attributed to Albert Bae.

4 recordsLinked to original sources

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

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↗

arXiv2010

On the Swimming of \textit{Dictyostelium} amoebae

Traditionally, the primary mode for locomotion of amoeboid cells was thought to be crawling on a substrate. Recently, it has been experimentally shown that \textit{Dictostelium} amoeba and neutrophils can also swim in a directed fashion. The mechanisms for amoeboid crawling and swimming were hypothesized to be similar. In this letter, we show that the shape changes generated by a crawling \textit{D. discoideum} cell are consistent with swimming.

physics.bio-ph↗