arXiv subjects

Xin Yong

Publications and source records attributed to Xin Yong.

7 recordsLinked to original sources

arXiv2026

Self-Assembly of Crowded Semiflexible Polymers under Dynamic and Deformable Confinement

Semiflexible polymers are ubiquitous in natural and artificial systems, where their intermediate rigidity gives rise to rich structural and dynamical behavior. Confinement plays a central role in these behaviors, as spatial restrictions can promote chain alignment, induce structural rearrangements, and enable complex self-assembly. While the organization of semiflexible polymers under rigid confinement has been extensively investigated, their behavior within deformable and dynamically evolving microenvironments, such as drying droplets or intracellular compartments, remains poorly understood. In this study, we use dissipative particle dynamics simulations to investigate the self-assembly of crowded semiflexible polymers confined within a deformable droplet, whose size may also change over time. By systematically varying polymer contour length, concentration, and degree of confinement, we identify distinct assembly regimes. Increasing polymer concentration promotes the formation of ordered fibrillar domains, with orientational alignment strongest near the droplet interface. Chain length critically dictates the morphology of assembled structures: short chains remain largely disordered, chains with intermediate lengths form linear fibrillar structures with maximal nematic order, and long chains assemble into circular bundles. Dynamic confinement further modulates the assembly through the competition between the rate of confinement change and polymer mobility. Slow increase in the degree of confinement allows polymers to reorganize into highly ordered structures, while rapid crowding kinetically traps the system in disordered states. Our findings elucidate how polymer mechanics and time-dependent confinement jointly govern the organization of semiflexible polymers in deformable, dynamic, and crowded environments.

cond-mat.soft↗

arXiv2026

Seeing new depths: Three-dimensional flow of a free-swimming alga

A swimming microorganism stirs the surrounding fluid, creating a flow field that governs not only its locomotion and nutrient uptake, but also its interactions with other microorganisms and the environment. Despite its fundamental importance, capturing this flow field and unraveling its biological implications remains a challenge. Here, we report the first direct, time-resolved measurements of the three-dimensional (3D) flow field generated by a single, free-swimming microalga, Chlamydomonas reinhardtii, a model organism for microbial locomotion and flagellar dynamics. Supported by hydrodynamic modeling and simulations, our measurements resolve how established two-dimensional (2D) flow features such as in-plane vortices and the stagnation point emerge from and shape the full algal flow in 3D. Moreover, we reveal unexpected low-Reynolds-number flow phenomena including micron-sized vortex rings and periodically recurring translating vortices and uncover topological changes in the underlying flow structure associated with the puller-to-pusher transition of an alga. Biologically, access to the 3D flow field enables rigorous quantification of the alga's energy expenditure, as well as its swimming and feeding efficiency, improving the precision of these physiological metrics. Taken together, our study demonstrates rich vortex dynamics in inertialess flows and shows their influence on microbial motility. The work also introduces a new experimental method for mapping the fluid environment sculpted by beating flagella.

physics.flu-dyn↗

arXiv2026

Improving Hydrodynamic Modeling of Free-Swimming Algae Using a Modified Three-Sphere Approach

The beating flagella of the green alga Chlamydomonas reinhardtii play a prominent role in cellular mechanics, enabling cells to both displace and sense surrounding fluid. Specifically, flagellum-induced fluid transport enables microalgae to swim through fluid media and interact with other microorganisms. Minimal models, such as the three-sphere model with one sphere representing the cell body and two orbiting spheres mimicking the flagella, have been widely adopted to study various aspects of algal motility, including the synchronization of flagellar beating, run-and-tumble swimming, responses to shear flow, cell-body rolling, and helical navigation. However, detailed investigation of the algal flow fields generated by this minimal model remains limited. In this study, we systematically examine the time-averaged and time-resolved fluid flows generated by the three-sphere algae model and compare the numerical predictions with experimental data. Our findings reveal that the standard three-sphere model fails to produce key flow characteristics observed experimentally. To address this discrepancy, we explore a modified three-sphere model with refined flagellar beating dynamics and identify that differential drag acting on the flagellar spheres is the dominant factor influencing the fidelity of the modeled flow fields. These results advance the fundamental understanding of the flagellum-fluid interactions and algal flow and enhance our ability to accurately simulate microswimmer dynamics.

physics.flu-dyn↗

arXiv2025

Cell-Scale Dynamic Modeling of Membrane Interactions with Arbitrarily Shaped Particles

Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to resolve fully coupled translational and rotational dynamics. Here, we present a force-based computational framework capable of capturing dynamic interactions between deformable lipid vesicles and rigid particles of irregular shapes. Both vesicle and particle surfaces are represented using triangulated meshes, and Langevin dynamics resolves membrane deformation alongside rigid-body particle motion. Adhesive interactions between the particle and membrane surfaces are modeled using two numerical schemes: a vertex-to-vertex mapping and a vertex-to-surface projection. The latter yields more accurate wrapping energetics, as demonstrated by benchmark comparisons against ideal spheres. The dynamic simulations reveal that lower particle-to-vesicle mass ratios facilitate frequent particle reorientation and complete membrane wrapping, while higher mass ratios limit orientation changes and stabilize partial wrapping. To illustrate the framework's versatility, we simulate interactions involving cubical, rod-like, bowl-shaped, and tetrahedral particles with spherical, cigar-shaped, or biconcave vesicles. This generalizable modeling approach enables predictive, cell-scale studies of membrane-particle interactions across a wide range of geometries, with applications in environmental biophysics and nanomedicine.

cond-mat.soft↗

arXiv2023

Effects of Shape on Interaction Dynamics of Tetrahedral Nanoplastics and the Cell Membrane

Cellular uptake of nanoplastics is instrumental in their environmental accumulation and transfer to humans through the food chain. Despite extensive studies using spherical plastic nanoparticles, the influence of the morphological characteristics of environmentally released nanoplastics is understudied. Using dissipative particle dynamics simulations, we modeled the interactions between a cell membrane and hydrophobic nanotetrahedra, which feature high shape anisotropy and large surface curvature seen for environmental nanoplastics. We observe robust uptake of nanotetrahedra with sharp vertices and edges by the lipid membrane. Two local energy minimum configurations of nanotetrahedra embedded in the membrane bilayer were identified for particles of large sizes. Further analysis of particle dynamics within the membrane shows that the two interaction states exhibit distinct translational and rotational dynamics in the directions normal and parallel to the plane of the membrane. The membrane confinement significantly arrests the out-of-plane motion, resulting in caged translation and subdiffusive rotation. While the in-plane diffusion remains Brownian, we find that the translational and rotational modes decouple from each other as the particle size increases. The rotational diffusion decreases by a greater extent compared to the translational diffusion, deviating from the continuum theory predictions. These results provide fundamental insights into the shape effect on the nanoparticle dynamics in crowded lipid membranes.

cond-mat.soft↗

arXiv2022

Effect of local stress on accurate modeling of bacterial outer membranes using all-atom molecular dynamics

Biological membranes are fundamental components of living organisms that play an undeniable role in their survival. Molecular dynamics (MD) serves as an essential computational tool for studying biomembranes on molecular and atomistic scales. The status quo of MD simulations of biomembranes studies a nanometer-sized membrane patch periodically extended under periodic boundary conditions (PBC). In nature, membranes are usually composed of different lipids in their two layers (referred to as leaflets). This compositional asymmetry imposes a fixed ratio of lipid numbers between the two leaflets in a periodically constrained membrane, which needs to be set appropriately. The widely adopted methods of defining leaflet lipid ratio suffer from the lack of control over the mechanical tension of each leaflet, which could significantly influence research findings. In this study, we investigate the role of membrane-building protocol and the resulting initial stress state on the interaction between small molecules and asymmetric membranes. We model the outer membrane of Pseudomonas aeruginosa bacteria using two different building protocols and probe their interactions with the Pseudomonas Quinolone Signal (PQS). Our results show that differential stress could shift the position of free energy minimum for the PQS molecule between the two leaflets of the asymmetric membrane. This work provides critical insights into the relationship between the initial per-leaflet tension and the spontaneous intercalation of PQS.

cond-mat.soft↗

arXiv2021

Numerical and Theoretical Modeling of Droplet Impact on Spherical Surfaces

Droplet impact on solid surfaces is a fluid phenomenon widely involved in additive manufacturing, heat management, and coating, in which the ability to exert control over the impact dynamics and duration is critical. While past studies have established a comprehensive understanding of the impact on flat substrates, what we know about the impact dynamics on curved solid surfaces is still limited. This work aims to elucidate the physics of droplet impact on spherical surfaces with different Weber numbers ($We$), radii ($R_s$), and surface wettability ($θ^{eq}$) using a combination of axisymmetric lattice Boltzmann method (LBM) and theoretical analysis. The model developed in our previous work [H. Dalgamoni and X. Yong, Phys. Rev. E 98, 13102 (2018)] was extended and modified for simulating the normal impact of droplet on curved substrates in the low Weber number regime (i.e., $We \leq 15$), in which axisymmetric assumption of droplet deformation holds. The LBM simulations show that $We$, $R_s$, and $θ^{eq}$ significantly affect the spreading and recoiling of droplet during impact. The parametric studies uncover five outcomes of impact, which range from complete deposition to total rebound. A simulation-predicted phase diagram was constructed and correlated with the total time that the droplet was in contact with the solid. In addition, a theoretical model based on energy budget during impact was developed to predict the rebound threshold for impact on spherical targets when varying We, and independently, which agrees well with simulation observations. These findings provide fundamental insight into surface structure design for controlling droplet hydrodynamics and the contact time during impact.

physics.flu-dyn↗