arXiv subjects

Xinliang Xu

Publications and source records attributed to Xinliang Xu.

17 recordsLinked to original sources

arXiv2026

Flow-polarity decoupling and universal mobility enhancement in dense bacterial active fluids with mesoscale order

Active fluids consisting of living cells or synthetic microswimmers display rich emergent behavior and nonequilibrium mechanical properties, which not only shed light on various biological processes but also inform the engineering of autonomous fluidics and self-driven materials. The individual behavior of microswimmers and their interaction with self-generated mesoscale solvent flows underlie the emergent properties of active fluids. Here we studied the microscopic dynamics in dense 3D bacterial active fluids by simultaneous imaging of cell body, flagella, and flow field. A surprising finding is that the polarity of cells was randomly distributed in mesoscale flow regimes, and yet the system displays mesoscale order in the self-generated solvent flows. Despite the apparent flow-polarity decoupling, the motion of cells relative to local solvent flows predominantly navigated upstream, with the self-advection speed universally enhanced by a flow-controlled constant. Numerical modeling with full hydrodynamic interactions reveals that the observed flow-polarity decoupling arises from the breakdown of the commonly held force-dipole assumption for anisotropic microswimmers: in the presence of flow gradient and near-field hydrodynamic interactions, the direction of total active forcing exerted by a swimming bacterium to the surrounding fluid no longer aligns with its polarity. The simulations suggest that near-field interactions serve as a new type of emergent, configuration-dependent active forcing, which profoundly impact self-organization and transport in dense bacterial suspensions. Taken together, our work establishes fundamental knowledge for faithfully understanding the collective behavior of dense polar active fluids.

physics.bio-ph↗

arXiv2025

Bacterial dimensions sensitively regulate surface diffusivity and residence time

Run-and-tumble is a common but vital strategy that bacteria employ to explore environment suffused with boundaries, as well as to escape from entrapment. In this study we reveal how this strategy and the resulting dynamical behavior can be sensitively regulated by bacterial dimensions. Our results demonstrate that the logarithm of the surface residence time for bacteria with constant tumble bias is linearly related to a dimensionless parameter of bacterial intrinsic size characteristics, where a small variation in bacterial dimensions, which is natural in a suspension, reproduces well the experimentally observed large variation in bacterial residence time. Furthermore, our results predict that the optimal tumble bias corresponding to the maximum surface diffusivity depends strongly on bacterial dimensions, where the same small variation in bacterial dimensions gives rise to a strongly diversified optimal tumble bias and an order of magnitude change in surface diffusivity.

cond-mat.soft↗

arXiv2024

Cell aspect ratio important for bacterial rheotaxis

When placed in flows with local shear, flagellated bacteria commonly display reorientations towards the local vorticity direction, a chirality-induced rheotactic behavior of great importance for many biological functions. As the observed reorientational dynamics arises from the interplay between the Jeffery dynamics controlled by the cell aspect ratio and the chirality-induced reorientation controlled by the chiral strength, in this work we quantitatively study how cell aspect ratio can become a key factor in tuning the reorientational dynamics, through numerical and theoretical analysis. Our results reveal that, for sphere-like bacteria the rheotactic behavior sensitively depends on the cell aspect ratio and totally disappears in the limiting case with cell aspect ratio being 1, in very good agreement with our predicted analytic functional form. For needle-like bacteria with cell aspect ratio much larger than 1, the rheotactic behavior becomes insensitive to cell aspect ratio, in agreement with previous experimental observations.

cond-mat.soft↗

arXiv2023

An entropic effect essential for surface entrapment of bacteria

The entrapment of bacteria near boundary surfaces is of biological and practical importance, yet the underlying physics is still not well understood. We demonstrate that it is crucial to include a commonly neglected entropic effect arising from the spatial variation of hydrodynamic interactions, through a model that provides analytic explanation of bacterial entrapment in two dimensionless parameters: $α_1$ the ratio of thermal energy to self-propulsion, and $α_2$ an intrinsic shape factor. For $α_1$ and $α_2$ that match an {\it Escherichia coli} at room temperature, our model quantitatively reproduces existing experimental observations, including two key features that have not been previously resolved: The bacterial "nose-down" configuration, and the anticorrelation between the pitch angle and the wobbling angle. Furthermore, our model analytically predicts the existence of an entrapment zone in the parameter space defined by $\{α_1,α_2\}$.

cond-mat.soft↗

arXiv2023

Molecular chaos in dense active systems

The hypothesis of molecular chaos plays the central role in kinetic theory, which provides a closure leading to the Boltzmann equation for quantitative description of classic fluids. Yet how to properly extend it to active systems is still an open question in nonequilibrium physics. Combining experiment, simulation, and theory, we investigate the emergent collective behaviors of self-propelled particles that exhibit collision avoidance, a moving strategy commonly adopted in natural and engineering active systems. This dense active system shows unusual phase dynamics strongly regulated by many-body interactions, which cannot be explained by theories assuming molecular chaos. To rationalize the interplay between different emergent phases, a simple kinetic model is proposed with a revised molecular chaos hypothesis, which treats the many-body effect implicitly via categorizing different types of particle pair collisions. Our model predicts an optimal growth rate of flocking and illustrates a generic approach for understanding dense active systems.

cond-mat.soft↗

arXiv2022

The colloidal nature of complex fluids leads to enhanced motility of flagellated bacteria

The natural habitats of microorganisms in the human microbiome and ocean and soil ecosystems are full of colloids and macromolecules, which impart non-Newtonian flow properties drastically affecting the locomotion of swimming microorganisms. Although the low-Reynolds-number hydrodynamics of the swimming of flagellated bacteria in simple Newtonian fluids has been well developed, our understanding of bacterial motility in complex non-Newtonian fluids is still primitive. Even after six decades of research, fundamental questions about the nature and origin of bacterial motility enhancement in polymer solutions are still under debate. Here, we study the motility of flagellated bacteria in colloidal suspensions of varying sizes and volume fractions. We find that bacteria in dilute colloidal suspensions display quantitatively the same motile behaviors as those in dilute polymer solutions, where a universal particle-size-dependent motility enhancement up to 80% is uncovered, accompanied by strong suppression of bacterial wobbling. By virtue of the well-controlled size and the hard-sphere nature of colloids, the finding not only resolves the long-standing controversy over bacterial motility enhancement in complex fluids but also challenges all the existing theories using polymer dynamics to address the swimming of flagellated bacteria in dilute polymer solutions. We further develop a simple physical model incorporating the colloidal nature of complex fluids, which quantitatively explains bacterial wobbling dynamics and mobility enhancement in both colloidal and polymeric fluids. Our study sheds light on the puzzling motile behaviors of bacteria in complex fluids relevant to a wide range of microbiological processes and provides a cornerstone in engineering bacterial swimming in complex environments.

cond-mat.soft↗

arXiv2021

Achieving adjustable elasticity with non-affine to affine transition

For various engineering and industrial applications it is desirable to realize mechanical systems with broadly adjustable elasticity to respond flexibly to the external environment. Here we discover a topology-correlated transition between affine and non-affine regimes in elasticity in both two- and three-dimensional packing-derived networks. Based on this transition, we numerically design and experimentally realize multifunctional systems with adjustable elasticity. Within one system, we achieve solid-like affine response, liquid-like non-affine response and a continuous tunability in between. Moreover, the system also exhibits a broadly tunable Poisson's ratio from positive to negative values, which is of practical interest for energy absorption and for fracture-resistant materials. Our study reveals a fundamental connection between elasticity and network topology, and demonstrates its practical potential for designing mechanical systems and metamaterials.

cond-mat.mtrl-sci↗

arXiv2020

Active suspensions of bacteria and passive objects: a model for the near field pair dynamics

Near field hydrodynamic interactions are essential to determine many important emergent behaviors observed in active suspensions, but have not been successfully modeled so far. In this work we propose an effective model capable of efficiently capturing the essence of the near field hydrodynamic interactions, validated numerically by a pedagogic model system consisting of an E. coli and a spherical tracer. The proposed model effectively captures all the details of near field hydrodynamics through only a tensorial coefficient of resistance, which is fundamentally different from, and thus cannot be replaced by, an effective interaction of conservative nature. In a critical test case that studies the scattering angle of the bacterium-tracer pair dynamics, calculations based on the proposed model reveals a region in parameter space where the bacterium is trapped by the spherical tracer, a phenomenon that is regularly observed in experiments but cannot be explained by any existing model.

cond-mat.soft↗

arXiv2018

Symmetric shear banding and swarming vortices in bacterial "superfluids"

Bacterial suspensions--a premier example of active fluids--show an unusual response to shear stresses. Instead of increasing the viscosity of the suspending fluid, the emergent collective motions of swimming bacteria can turn a suspension into a "superfluid" with zero apparent viscosity. Although the existence of active "superfluids" has been demonstrated in bulk rheological measurements, the microscopic origin and dynamics of such an exotic phase have not been experimentally probed. Here, using high-speed confocal rheometry, we study the dynamics of concentrated bacterial suspensions under simple planar shear. We find that bacterial "superfluids" under shear exhibit unusual symmetric shear bands, defying the conventional wisdom on shear-banding of complex fluids, where the formation of steady shear bands necessarily breaks the symmetry of unsheared samples. We propose a simple hydrodynamic model based on the local stress balance and the ergodic sampling of nonequilibrium shear configurations, which quantitatively describes the observed symmetric shear-banding structure. The model also successfully predicts various interesting features of swarming vortices in stationary bacterial suspensions. Our study provides new insights into the physical properties of collective swarming in active fluids and illustrates their profound influences on transport processes.

cond-mat.soft↗

arXiv2016

Analytic Solution of the Ornstein-Zernike Relation for Inhomogeneous Liquids

The properties of a classical simple liquid can be strongly affected by application of an external potential that supports inhomogeneity. To understand the nature of these property changes the equilibrium particle distribution functions of the liquid have, typically, been evaluated individually as functions of system control parameters, such as the packing fraction of a hard sphere liquid. In this study we focus attention on two distribution functions that characterize the inhomogeneous liquid: the pair direct correlation function $c(\mathbf{r}_1,\mathbf{r}_2)$ and the pair correlation function $g(\mathbf{r}_1,\mathbf{r}_2)$. We solve the Ornstein-Zernike equation for the inhomogeneous liquid to obtain $c(\mathbf{r}_1,\mathbf{r}_2)$ as an explicit function of $g(\mathbf{r}_1,\mathbf{r}_2)$, with the latter considered to be an experimental observable, using information about the well studied and resolved $g^0(\mathbf{r}_1-\mathbf{r}_2)$ and $c^0(\mathbf{r}_1-\mathbf{r}_2)$ for the parent homogeneous ($^0$) system. The result obtained with our formulation is tested against the exact solutions for the correlation and distribution functions of a one-dimensional inhomogeneous hard rod liquid. Following the success of that test the formalism is extended to obtain $c(\mathbf{r}_1,\mathbf{r}_2)$ as an explicit function of $g(\mathbf{r}_1,\mathbf{r}_2)$ in a three dimensional liquid.

cond-mat.soft↗

arXiv2016

Dynamics of ellipsoidal tracers in swimming algal suspensions

Enhanced diffusion of passive tracers immersed in active fluids is a universal feature of active fluids and has been extensively studied in recent years. Similar to microrheology for equilibrium complex fluids, the unusual enhanced particle dynamics reveal intrinsic properties of active fluids. Nevertheless, previous studies have shown that the translational dynamics of spherical tracers are qualitatively similar, independent of whether active particles are pushers or pullers---the two fundamental classes of active fluids. Is it possible to distinguish pushers from pullers by simply imaging the dynamics of passive tracers? Here, we investigated the diffusion of isolated ellipsoids in algal C. reinhardtii suspensions---a model for puller-type active fluids. In combination with our previous results on pusher-type E. coli suspensions [Peng et al., Phys. Rev. Lett. 116, 068303 (2016)], we showed that the dynamics of asymmetric tracers show a profound difference in pushers and pullers due to their rotational degree of freedom. Although the laboratory-frame translation and rotation of ellipsoids are enhanced in both pushers and pullers, similar to spherical tracers, the anisotropic diffusion in the body frame of ellipsoids shows opposite trends in the two classes of active fluids. An ellipsoid diffuses fastest along its major axis when immersed in pullers, whereas it diffuses slowest along the major axis in pushers. This striking difference can be qualitatively explained using a simple hydrodynamic model. In addition, our study on algal suspensions reveals that the influence of the near-field advection of algal swimming flows on the translation and rotation of ellipsoids shows different ranges and strengths. Our work provides not only new insights into universal organizing principles of active fluids, but also a convenient tool for detecting the class of active particles.

cond-mat.soft↗

arXiv2016

Diffusion of an ellipsoid in bacterial suspensions

Active matter such as swarming bacteria and motile colloids exhibits exotic properties different from conventional equilibrium materials. Among these properties, the enhanced diffusion of tracer particles is generally deemed as a hallmark of active matter. Here, rather than spherical tracers, we investigate the diffusion of isolated ellipsoids in quasi-two-dimensional bacterial bath. Our study reveals a nonlinear enhancement of both translational and rotational diffusions. More importantly, we uncover an anomalous coupling between translation and rotation that is strictly prohibited in the classic Brownian diffusion. Combining experiments with theoretical modeling, we show that such an anomaly arises from generic stretching flows induced by swimming bacteria. Our work illustrates a universal organizing principle of active matter and sheds new light on fundamental transport processes in microbiological systems.

cond-mat.soft↗

arXiv2013

Influence of Inter-Layer Exchanges on Vorticity-Aligned Colloidal String Assembly in a Simple Shear Flow

Hard spheres in Newtonian fluids serve as paradigms for Non-Newtonian materials phenomena exhibited by colloidal suspensions. A recent experimental study (Cheng et al. 2011 Science, 333, 1276) showed that upon application of shear to such a system, the particles form string-like structures aligned in the vorticity direction. We explore the mechanism underlying this out-of-equilibrium organization with Steered Transition Path Sampling, which allows us to bias the Brownian contribution to rotations of close pairs of particles and alter the dynamics of the suspension in a controlled fashion. Our results show a strong correlation between the string structures and the rotation dynamics. Specifically, the simulations show that accelerating the rotations of close pairs of particles, not increasing their frequency, favors formation of the strings. This insight delineates the roles of hydrodynamics, Brownian motion, and particle packing, and, in turn, informs design strategies for controlling the assembly of large-scale particle structures.

cond-mat.soft↗

arXiv2013

Correlated local bending of DNA double helix and its effect on the cyclization of short DNA fragments

We report a theoretical study of DNA flexibility and quantitatively predict the ring closure probability as a function of DNA contour length. Recent experimental studies show that the flexibility of short DNA fragments (as compared to the persistence length of DNA l_P~150 base pairs) cannot be described by the traditional worm-like chain (WLC) model, e.g., the observed ring closure probability is much higher than predicted. To explain these observations, DNA flexibility is investigated with explicit considerations of a new length scale l_D~10 base pairs, over which DNA local bend angles are correlated. In this correlated worm-like chain (C-WLC) model, a finite length correction term is analytically derived and the persistence length is found to be contour length dependent. While our model reduces to the traditional worm-like chain model when treating long DNA at length scales much larger than l_P, it predicts that DNA becomes much more flexible at shorter sizes, which helps explain recent cyclization measurements of short DNA fragments around 100 base pairs.

cond-mat.soft↗

arXiv2013

Divergence of the Long Wavelength Collective Diffusion Coefficient in Quasi-one and Quasi-two Dimensional Colloid Suspensions

We report the results of experimental studies of the short time-long wavelength behavior of collective particle displacements in quasi-one-dimensional and quasi-two-dimensional colloid suspensions. Our results are represented by the behavior of the hydrodynamic function H(q) that relates the effective collective diffusion coefficient, D_e(q) with the static structure factor S(q) and the self-diffusion coefficient of isolated particles D_0: H(q)=D_e(q)S(q)/D_0. We find an apparent divergence of H(q) as q->0 with the form H(q) proportional to q^-gamma, 1.7 0 we infer that D_e(q) does. We provide evidence that this divergence arises from the interplay of boundary conditions on the flow of the carrier liquid and many-body hydrodynamic interactions between colloid particles that affect the long wavelength behavior of the particle collective diffusion coefficient in the suspension. We speculate that in the q1D and q2D systems studied the divergence of H(q) might be associated with a q-dependent partial slip boundary condition, specifically an effective slip length that increases with decreasing q. We also verify, using data from the work of Lin, Rice and Weitz (J. Chem. Phys. 99, 9585 (1993)), the prediction by Bleibel et al (arXiv:1305.3715), that D_e(q) for a monolayer of colloid particles constrained to lie in the interface between two fluids diverges as 1/q as q->0. The verification of that prediction, which is based on an analysis that allows two-dimensional colloid motion embedded in three-dimensional suspending fluid motion, supports the contention that the boundary conditions that define a q2D system play a very important role in determining the long wavelength behavior of the collective diffusion coefficient.

cond-mat.soft↗

arXiv2012

Structural Responses of Quasi-2D Colloid Fluids to Excitations Elicited by Nonequilibrium Perturbations

We investigate the response of a dense monodisperse quasi-two-dimensional (q2D) colloid suspension when a particle is dragged by a constant velocity optical trap. Consistent with microrheological studies of other geometries, the perturbation induces a leading density wave and trailing wake, and we use Stokesian Dynamics (SD) simulations to parse direct colloid-colloid and hydrodynamic interactions. We go on to analyze the underlying individual particle-particle collisions in the experimental images. The displacements of particles form chains reminiscent of stress propagation in sheared granular materials. From these data, we can reconstruct steady-state dipolar flow patterns that were predicted for dilute suspensions and previously observed in granular analogs to our system. The decay of this field differs, however, from point Stokeslet calculations, indicating that the finite size of the colloids is important. Moreover, there is a pronounced angular dependence that corresponds to the surrounding colloid structure, which evolves in response to the perturbation. Put together, our results show that the response of the complex fluid is highly anisotropic owing to the fact that the effects of the perturbation propagate through the structured medium via chains of colloid-colloid collisions.

cond-mat.soft↗

arXiv2010

Maximally Random Jamming of Two-Dimensional One-Component and Binary Hard Disc Fluids

We report calculations of the density of maximally random jamming (aka random close packing) of one-component and binary hard disc fluids. The theoretical structure used provides a common framework for description of the hard disc liquid to hexatic, the liquid to hexagonal crystal and the liquid-to-maximally random jammed state transitions. Our analysis is based on locating a particular bifurcation of the solutions of the integral equation for the inhomogeneous single particle density at the transition between different spatial structures. The bifurcation of solutions we study is initiated from the dense metastable fluid, and we associate it with the limit of stability of the fluid, which we identify with the transition from the metastable fluid to a maximally random jammed state. For the one-component hard disc fluid the predicted packing fraction at which the metastable fluid to maximally random jammed state transition occurs is 0.84, in excellent agreement with the experimental value 0.84 \pm 0.02. The corresponding analysis of the limit of stability of a binary hard disc fluid with specified disc diameter ratio and disc composition requires extra approximations in the representations of the direct correlation function, the equation of state, and the number of order parameters accounted for. Keeping only the order parameter identified with the largest peak in the structure factor of the highest density regular lattice with the same disc diameter ratio and disc composition as the binary fluid, the predicted density of maximally random jamming is found to be 0.84 to 0.87, depending on the equation of state used, and very weakly dependent on the ratio of disc diameters and the fluid composition, in agreement with both experimental data and computer simulation data.

cond-mat.soft↗