arXiv subjects

Zijie Qu

Publications and source records attributed to Zijie Qu.

15 recordsLinked to original sources

arXiv2026

Rheologically tuned diffusion modulates quorum sensing in Vibrio fischeri

Understanding how the physical properties of a fluid influence bacterial behavior is essential for explaining how microorganisms interact with their environment and with animal hosts. Here, we examine how changes in fluid viscosity and rheological properties affect the locomotion of the marine bacterium Vibrio fischeri and its ability to produce luminescence through cell--cell communication. We track the three-dimensional motion of single cells in well-defined fluids with different physical properties and measure the luminescence emitted by cell populations. We find that fluids with higher viscosity cause V. fischeri to spend more time in a slower, turning-focused swimming mode, which reduces how effectively cells spread out and encounter the chemical signals required to activate luminescence. As a result, luminescence first increases and then decreases in Newtonian fluids, but decreases monotonically in fluids that exhibit non-Newtonian rheological behavior. Computer simulations based on our measurements confirm that the ability of cells to explore their surroundings plays a central role in determining when and how strongly they communicate. These findings reveal a direct link between the physical environment, bacterial movement, and collective behavior, and offer new insight into how microorganisms adapt to complex fluid habitats, including those found inside animal hosts.

cond-mat.soft↗

arXiv2026

Population-Scale Advancing Interface Modeling Reveals How Bacterial Swarms Encode Future Spatial Architecture

Motile bacteria shape microbial function by occupying space, yet how collective motion becomes population-scale architecture remains poorly resolved. Bacterial swarming is not merely surface motion, but a process by which motile populations commit to future macroscopic form. Here, in Enterobacter sp. SM3, a gut-associated swarmer linked to mucosal repair, we treat the advancing colony--environment interface as a morphodynamic state through which local motility becomes spatial order. We built SwarmEvo across thermal, hydration, and substrate-mechanical conditions and developed Morpher to resolve and propagate interface states. Counterintuitively, within the permissive assay range, condition labels only weakly separated future trajectories, whereas colony-specific interface geometry constrained later expansion, indicating that swarm fate is written into the interface rather than prescribed by condition identity. Boundary fidelity was decisive: a 0.67 percentage-point segmentation gap expanded into a 2.4--3.1 IoU-point forecasting loss. Preserving front displacement, protrusion continuity, and branch memory, Morpher predicted late-stage expansion with 95.42% mIoU, 10.61 px HD$_{95}$, and 3.93 px ASSD. These results identify the advancing interface as a state-bearing layer through which motility and environmental constraint are converted into future spatial form, enabling disease-relevant microbial organization to be read before endpoint architecture emerges.

cond-mat.soft↗

arXiv2025

Phase separation dynamics and active turbulence in a binary fluid mixture

Active matter, encompassing natural systems, converts surrounding energy to sustain autonomous motion, exhibiting unique non-equilibrium behaviors such as active turbulence and phase separation. In this study, we develop a continuum two-fluid model for a binary mixture of an active nematic and a passive Newtonian fluid, coupling Cahn-Hilliard dynamics for phase separation with Beris-Edwards nematohydrodynamics and two distinct momentum equations connected by viscous drag. A phase field-based lattice Boltzmann method is used to investigate the existence of active turbulence and phase separation in the binary mixture. We find that active stress enhances velocity and vorticity differences between phases, and that increased active concentration promotes stronger inter-fluid coupling. Activity not only amplifies turbulent fluctuations but also arrests domain coarsening, leading to a finite characteristic length scale that decreases with increasing activity. Key parameters, like active parameter, tumbling parameter and Frank elastic constant, affect the characteristic scale of flow. These results highlight the role of relative motion and drag-mediated momentum transfer in active binary mixtures, providing a framework for studying systems such as bacterial suspensions in polymeric fluids or active emulsions.

cond-mat.soft↗

arXiv2025

Boundaries Program Deformation in Isolated Active Networks

Cellular structures must organize themselves within strict physical constraints, operating with finite resources and well-defined boundaries. Classical systems demonstrate only passive responses to boundaries, from surface energy minimization in soap films to strain distributions in elastic networks. Active matter fundamentally alters this paradigm - internally generated stresses create a bidirectional coupling between boundary geometry and mass conservation that enables dynamic control over network organization. Here we demonstrate boundary geometry actively directs network deformation in reconstituted microtubule-kinesin systems, revealing a programmable regime of shape transformation through controlled boundary manipulation. A coarse-grained theoretical framework reveals how boundary geometry couples to internal stress fields via mass conservation, producing distinct dynamical modes that enable engineered deformations. The emergence of shape-preserving and shape-changing regimes, predicted by theory and confirmed through experiments, establishes boundary geometry as a fundamental control parameter for active materials. The control principle based on boundaries advances both the understanding of biological organization and enables design of synthetic active matter devices with programmable deformation.

cond-mat.soft↗

arXiv2025

Hydrodynamic Interaction and Geometric Memory Effect Drive Directed Swimming of Chlamydomonas reinhardtii near Periodic Microstructures

The movement of microorganisms near solid-liquid interfaces is a topic of significant scientific interest due to its relevance in various natural and industrial contexts, such as biofilm formation and marine biofouling. In this study, we investigate the swimming behavior of C. reinhardtii near a sinusoidal periodic microstructure (SPM). Using fluorescence microscopy and three-dimensional tracking, we observe that the swimming direction of C. reinhardtii is strongly influenced by the geometric constraints of the SPM. Our results show that cells tend to aggregate at the bottom of the SPM rather than the top, and exhibit a speed orientation tendency near the microstructure. We attribute this behavior to a combination of the "memory effect" and hydrodynamic attraction. By altering the shape of the periodic microstructure, we successfully achieve directed induction of cell swimming, which has potential applications in micro-nano robot control and biofouling prevention. This work provides new insights into the movement mechanisms of microorganisms near solid-liquid surfaces and highlights the potential for manipulating their behavior through microstructure design.

cond-mat.soft↗

arXiv2025

Active Turbulence in Shear Thinning Fluid

The study of active matter system has critical importance in revealing the physical essence of biological collective behavior. Dense bacterial suspension - a typical biological active matter, exhibits a wide range of phenomenons, among which bacterial turbulence has received extensive interest in recent years. This seemingly chaotic motion is widely studied in Newtonian fluid. However, studies based on complex fluids have predominantly focused on viscoelastic effects, leaving the role of shear-thinning viscosity largely unexplored despite its prevalence in natural bacterial environments like mucus and gastric fluids. Here, we experimentally employed Ficoll and Methocel polymers to study the impacts of various viscosities by Newtonian fluid and shear-thinning effects by Non-Newtonian fluids on bacterial turbulence. We analyzed various physical properties, including energy, enstrophy, etc., and observed that the shear-thinning effect is significantly suppressed in high-concentration bacterial suspensions. While the ordered arrangement of polymer chains under shear flow leads to the microscopic anisotropic viscosity, the suppression is largely attributed to the disruption of polymer chains caused by strong inter bacterial interactions in dense suspensions. To validate this hypothesis, we conducted experiments at a lower bacterial concentration and verified the findings using theoretical calculations based on the modified Resistive Force Theory.

cond-mat.soft↗

arXiv2024

Hydrodynamic interaction leads to the accumulation of Chlamydomonas reinhardtii near a solid-liquid interface

The physical mechanism of microbial motion near solid-liquid interfaces is crucial for understanding various biological phenomena and developing ecological applications. However, limited works have been conducted on the swimming behavior of C. reinhardtii, a typical "puller" type cell, near solid surfaces, particularly with varying and conflicting experimental observations. Here, we investigate the swimming behavior of C.reinhardtii using a three-dimensional real-time tracking microscopy system both near a solid-liquid interface and in the fluid bulk region. We explore the relationships between the cell density, swimming speed and orientation with respect to the distance from the solid-liquid interface, confirming the phenomenon of C. reinhardtii accumulation near the solid-liquid interface. Based on the traditional definitions of "pusher" and "puller" cells, we propose a simplified model consisting of two pairs of mutually perpendicular force dipoles for C. reinhardtii. This model is employed to analyze the complex hydrodynamic interactions between C. reinhardtii and the solid surface, providing a potential theoretical explanation for the observed accumulation phenomenon at the solid-liquid interface.

physics.bio-ph↗

arXiv2024

Propulsion Contribution from Individual Filament in Flagellar Bundle

Flagellated microorganisms overcome the low-Reynolds-number time reversibility by rotating helical flagella. For peritrichous bacteria, such as Escherichia coli, the randomly distributed flagellar filaments align along the same direction to form a bundle, facilitating complex locomotive strategies. To understand the process of flagella bundling, especially the propulsion force, we develop a multi-functional macroscopic experimental system and employ advanced numerical simulations for verification. Flagella arrangements and phase differences between helices are investigated, revealing the variation in propulsion contribution from the individual helix. Numerically, we build a time-dependent model to match the bundling process and study the influence of hydrodynamic interactions. Surprisingly, it is found that the total propulsion generated by a bundle of two filaments is constant at various phase differences between the helices. However, the difference between the propulsion from each helix is significantly affected by the phase difference, and only one of the helices is responsible for the total propulsion at a phase difference equals to pi. Through our experimental and computational results, we provide a new model considering the propulsion contribution of each filament to better understand microbial locomotion mechanisms, especially on the wobbling behavior of the cell. Our work also sheds light on the design and control of artificial microswimmers.

cond-mat.soft↗

arXiv2024

Force Propagation in Active Cytoskeletal Networks

In biological systems, molecular-scale forces and motions are pivotal for enabling processes like motility, shape change, and replication. These forces and motions are organized, amplified, and transmitted across macroscopic scales by active materials such as the cytoskeleton, which drives micron-scale cellular movement and re-organization. Despite the integral role of active materials, understanding how molecular-scale interactions alter macroscopic structure and force propagation remains elusive. This knowledge gap presents challenges to the harnessing and regulation of such dynamics across diverse length scales. Here, we demonstrate how mediating the bundling of microtubules can shift active matter between a global force-transmitting phase and a local force-dissipating phase. A fivefold increase in microtubule effective length results in the transition from local to global phase with a hundredfold increase in velocity autocorrelation. Through theory and simulation, we identify signatures of a percolation-driven transition between the two phases. This provides evidence for how force propagation can be generated when local molecular interactions reach a sufficient length scale. We show that force propagation in the active matter system enables material transport. Consequently, we demonstrate that the global phase is capable of facilitating millimeter-scale human cell transport and manipulation, as well as powering the movement of aqueous droplets. These findings underscore the potential for designing active materials capable of force organization and transmission. Our results lay the foundation for further exploration into the organization and propagation of forces/stresses in biological systems, thereby paving the way for the engineering of active materials in synthetic biology and soft robotics.

cond-mat.soft↗

arXiv2021

Programming Boundary Deformation Patterns in Active Networks

Active materials take advantage of their internal sources of energy to self-organize in an automated manner. This feature provides a novel opportunity to design micron-scale machines with minimal required control. However, self-organization goes hand in hand with predetermined dynamics that are hardly susceptible to environmental perturbations. Therefore utilizing this feature of active systems requires harnessing and directing the macroscopic dynamics to achieve specific functions; which in turn necessitates understanding the underlying mechanisms of active forces. Here we devise an optical control protocol to engineer the dynamics of active networks composed of microtubules and light-activatable motor proteins. The protocol enables carving activated networks of different shapes, and isolating them from the embedding solution. Studying a large set of shapes, we observe that the active networks contract in a shape-preserving manner that persists over the course of contraction. We formulate a coarse-grained theory and demonstrate that self-similarity of contraction is associated with viscous-like active stresses. These findings help us program the dynamics of the network through manipulating the light intensity in space and time, and maneuver the network into bending in specific directions, as well as temporally alternating directions. Our work improves understanding the active dynamics in contractile networks, and paves a new path towards engineering the dynamics of a large class of active materials.

cond-mat.soft↗

arXiv2020

Persistent fluid flows defined by active matter boundaries

Biological systems achieve precise control over ambient fluids through the self-organization of active protein structures including flagella, cilia, and cytoskeletal networks. In active structures individual proteins consume chemical energy to generate force and motion at molecular length scales. Self-organization of protein components enables the control and modulation of fluid flow fields on micron scales. The physical principles underlying the organization and control of active-matter driven fluid flows are poorly understood. Here, we apply an optically-controlled active-matter system composed of microtubule filaments and light-switchable kinesin motor proteins to analyze the emergence of persistent flow fields in a model active matter system. Using light, we form contractile microtubule networks of varying shape. We analyze the fluid flow fields generated by a wide range of microtubule network geometries and explain the resulting flow fields within a unified theoretical framework. We specifically demonstrate that the geometry of microtubule flux at the boundary of contracting microtubule networks predicts the steady-state fluid flow fields across polygonal network geometries through finite-element simulations. Our work provides a foundation for programming microscopic fluid-flows with controllable active matter and could enable the engineering of versatile and dynamic microfluidic devices.

cond-mat.soft↗

arXiv2020

Measuring the viscoelastic behavior of dilute polymer solutions using high-speed statistical particle microrheology

The viscoelastic behavior of polymer solutions is commonly measured using oscillating shear rheometry, however, the accuracy of such methods is limited by the oscillating frequency of the equipment and since the relaxation time of the dilute polymer solutions is short, this requires measurement at very high frequencies. Microrheology has been proposed to overcome this technical challenge. Yet the equipment for resolving the statistics of particle displacements in microrheology is expensive. In this work, we measured the viscoelastic behavior of Methocel solutions at various concentrations using a conventional epi-fluorescence microscope coupled to a high-speed intensified camera. Statistical Particle Tracking is used in analyzing the mean-squared displacement of the dispersive particles. Relaxation times ranging from 0.76 - 9.00 ms and viscoelastic moduli, G' between 11.34 and 3.39 are reported for Methocel solutions of concentrations between 0.063 - 0.5%

physics.flu-dyn↗

arXiv2020

Effects of shear thinning viscosity and viscoelastic stresses on flagellated bacteria motility

The behavior of flagellated bacteria swimming in non-Newtonian media remains an area with contradictory and conflicting results. We report on the behavior of wild-type and smooth-swimming E. coli in Newtonian, shear thinning and viscoelastic media, measuring their trajectories and swimming speed using a three dimensional real-time tracking microscope. We conclude that the speed enhancement in Methocel solution at higher concentration is due to shear-thinning and an analytical model is used to support our experimental result. We argue that shear-induced normal stresses reduce the wobbling behavior during cell swimming but do not significantly affect swimming speed. However, the normal stresses play an important role in decreasing the flagellar bundling time which changes the swimming speed distribution. A dimensionless number, the "Strangulation number" (Str) is proposed and used to characterize this effect.

physics.bio-ph↗

arXiv2019

Controlling Organization and Forces in Active Matter Through Optically-Defined Boundaries

Living systems are capable of locomotion, reconfiguration, and replication. To perform these tasks, cells spatiotemporally coordinate the interactions of force-generating, "active" molecules that create and manipulate non-equilibrium structures and force fields that span up to millimeter length scales [1-3]. Experimental active matter systems of biological or synthetic molecules are capable of spontaneously organizing into structures [4,5] and generating global flows [6-9]. However, these experimental systems lack the spatiotemporal control found in cells, limiting their utility for studying non-equilibrium phenomena and bioinspired engineering. Here, we uncover non-equilibrium phenomena and principles by optically controlling structures and fluid flow in an engineered system of active biomolecules. Our engineered system consists of purified microtubules and light-activatable motor proteins that crosslink and organize microtubules into distinct structures upon illumination. We develop basic operations, defined as sets of light patterns, to create, move, and merge microtubule structures. By composing these basic operations, we are able to create microtubule networks that span several hundred microns in length and contract at speeds up to an order of magnitude faster than the speed of an individual motor. We manipulate these contractile networks to generate and sculpt persistent fluid flows. The principles of boundary-mediated control we uncover may be used to study emergent cellular structures and forces and to develop programmable active matter devices.

cond-mat.soft↗

arXiv2017

Changes in the flagellar bundling time account for variations in swimming behavior of flagellated bacteria in viscous media

Although the motility of the flagellated bacteria, Escherichia coli, has been widely studied, the effect of viscosity on swimming speed remains controversial. The swimming mode of wild-type E.coli is often idealized as a "run-and- tumble" sequence in which periods of swimming at a constant speed are randomly interrupted by a sudden change of direction at a very low speed. Using a tracking microscope, we follow cells for extended periods of time in Newtonian liquids of varying viscosity, and find that the swimming behavior of a single cell can exhibit a variety of behaviors including run-and-tumble and "slow-random-walk" in which the cells move at relatively low speed. Although the characteristic swimming speed varies between individuals and in different polymer solutions, we find that the skewness of the speed distribution is solely a function of viscosity and can be used, in concert with the measured average swimming speed, to determine the effective running speed of each cell. We hypothesize that differences in the swimming behavior observed in solutions of different viscosity are due to changes in the flagellar bundling time, which increases as the viscosity rises, due to the lower rotation rate of the flagellar motor. A numerical simulation and the use of Resistive Force theory provide support for this hypothesis.

physics.bio-ph↗