Shanghai Jiaotong Univeristy Institute of Natural Sciences Physics Department 
Zhang Group @ SJTU
Research


Unraveling the physiochemical nature of colloidal motion waves among silver colloids

Traveling waves are common in biological and synthetic systems, including the recent discovery that silver (Ag) colloids form traveling motion waves in H2O2 and under light. Here, we show that this colloidal motion wave is a heterogeneous excitable system. The Ag colloids generate traveling chemical waves via reaction-diffusion, and either self-propel through self-diffusiophoresis ("ballistic waves") or are advected by diffusio-osmotic flows from gradients of neutral molecules ("swarming waves"). Key results include the experimental observation of traveling waves of OH− with pH-sensitive fluorescent dyes and a Rogers-McCulloch model that qualitatively and quantitatively reproduces the key features of colloidal waves. These results are a step forward in elucidating the Ag-H2O2-light oscillatory system at individual and collective levels. In addition, they pave the way for using colloidal waves either as a platform for studying nonlinear phenomena, or as a tool for colloidal transport and for information transmission in microrobot ensembles.

Publication: 
   Xi Chen^, Yankai Xu^, Chao Zhou, Kai Lou, Yixin Peng, H. P. Zhang*, Wei Wang*
   "Unraveling the physiochemical nature of colloidal motion waves among silver colloids
"
   
Science Advances , 8, eabn9130 (2022). [Journal URL], [pdf].   


Circular swimming motility and disordered hyperuniform state in an algae system

Active matter comprises individually driven units that convert locally stored energy into mechanical motion. Interactions between driven units lead to a variety of nonequilibrium collective phenomena in active matter. One of such phenomena is anomalously large density fluctuations, which have been observed in both experiments and theories. Here we show that, on the contrary, density fluctuations in active matter can also be greatly suppressed. Our experiments are carried out with marine algae (Effrenium voratum), which swim in circles at the air-liquid interfaces with two different eukaryotic flagella. Cell swimming generates fluid flow that leads to effective repulsions between cells in the far field. The long-range nature of such repulsive interactions suppresses density fluctuations and generates disordered hyperuniform states under a wide range of density conditions. Emergence of hyperuniformity and associated scaling exponent are quantitatively reproduced in a numerical model whose main ingredients are effective hydrodynamic interactions and uncorrelated random cell motion. Our results demonstrate the existence of disordered hyperuniform states in active matter and suggest the possibility of using hydrodynamic flow for self-assembly in active matter.

Publication: 
   M Huang, W Hu,  S Yang, Q-X Liu, H. P. Zhang
    "Circular swimming motility and disordered hyperuniform state in an algae system"
   
Proceedings of the National Academy of Sciences, 118, (2021). [Journal URL], [pdf].        


Controlling Cell Motion and Microscale Flow with Polarized Light Fields

We investigate how light polarization affects the motion of photoresponsive algae, Euglena gracilis. In a uniformly polarized field, cells swim approximately perpendicular to the polarization direction and form a nematic state with zero mean velocity. When light polarization varies spatially, cell motion is modulated by local polarization. In such light fields, cells exhibit complex spatial distribution and motion patterns which are controlled by topological properties of the underlying fields; we further show that ordered cell swimming can generate directed transporting fluid flow. Experimental results are quantitatively reproduced by an active Brownian particle model in which particle motion direction is nematically coupled to local light polarization.

Publication: 
  S Yang, M Huang, Y Zhao, H. P. Zhang
   "
Controlling Cell Motion and Microscale Flow with Polarized Light Fields"
  
Physical Review Letters, 126, 058001 (2021). [Journal URL], [pdf].   


Data-driven quantitative modeling of bacterial active nematics

Active nematics are nonequilibrium fluids consisting of elongated units driven at the individual scale. They spontaneously exhibit complex spatiotemporal dynamics and have attracted the attention of scientists from many disciplines. Here, we introduce an experimental system (made of filamentous bacteria) and a type of microscopic model for active nematics. Simultaneous measurements of orientation and velocity fields yield comprehensive experimental data that can be used to identify optimal values for all important parameters in the model. At these optimal parameters, the model quantitatively reproduces all experimentally measured features. This, in turn, reveals key processes governing active nematics. Our versatile approach successfully combines quantitative experiments and data-driven modeling; it can be used to study other dense active systems.Active matter comprises individual units that convert energy into mechanical motion. In many examples, such as bacterial systems and biofilament assays, constituent units are elongated and can give rise to local nematic orientational order. Such "active nematics" systems have attracted much attention from both theorists and experimentalists. However, despite intense research efforts, data-driven quantitative modeling has not been achieved, a situation mainly due to the lack of systematic experimental data and to the large number of parameters of current models. Here, we introduce an active nematics system made of swarming filamentous bacteria. We simultaneously measure orientation and velocity fields and show that the complex spatiotemporal dynamics of our system can be quantitatively reproduced by a type of microscopic model for active suspensions whose important parameters are all estimated from comprehensive experimental data. This provides unprecedented access to key effective parameters and mechanisms governing active nematics. Our approach is applicable to different types of dense suspensions and shows a path toward more quantitative active matter research.

Publication: 
   He Li, Xia-qing Shi, Mingji Huang, Xiao Chen, Mingfeng Xiao, Chenli Liu, Hugues, Chate, H. P. Zhang ,
    "Data-driven quantitative modeling of bacterial active nematics
"
   
Proceedings of the National Academy of Sciences, 116777-785 , (2019). [Journal URL], [pdf].         



Hydrodynamic and entropic effects on colloidal diffusion in corrugated channels          

3D printed corrugated channel.
Collective cell
                                    motioninacolony

        In the absence of advection, confined diffusion characterizes transport in many natural and artificial devices, such as ionic channels, zeolites, and nanopores. While extensive theoretical and numerical studies on this subject have produced many important predictions, experimental verifications of the predictions are rare. Here, we experimentally measure colloidal diffusion times in microchannels with periodically varying width and contrast results with predictions from the Fick–Jacobs theory and Brownian dynamics simulation. While the theory and simulation correctly predict the entropic effect of the varying channel width, they fail to account for hydrodynamic effects, which include both an overall decrease and a spatial variation of diffusivity in channels. Neglecting such hydrodynamic effects, the theory and simulation underestimate the mean and standard deviation of first passage times by 40% in channels with a neck width twice the particle diameter. We further show that the validity of the Fick–Jacobs theory can be restored by reformulating it in terms of the experimentally measured diffusivity. Our work thus shows that hydrodynamic effects play a key role in diffusive transport through narrow channels and should be included in theoretical and numerical models.


Publication: 
   Xiang Yang, Chang Liu, Yunyun Li,  Fabio Marchesoni, Peter Hänggi, and H. P. Zhang,
    "Hydrodynamic and entropic effects on colloidal diffusion in corrugated channels"
   
Proceedings of the National Academy of Sciences,  In Press, (2017). [Journal URL], [pdf]. 
       


Bimetallic Microswimmers Speed Up in Confining Channels           

Microswimmer swims through a channel.
Collective cell motion
                                    inacolony

        Synthetic microswimmers are envisioned to be useful in numerous applications, many of which occur in tightly confined spaces. It is therefore important to understand how confinement influences swimmer dynamics. Here we study the motility of bimetallic microswimmers in linear and curved channels. Our experiments show swimmer velocities increase, up to 5 times, with the degree of confinement, and the relative velocity increase depends weakly on the fuel concentration and ionic strength in solution. Experimental results are reproduced in a numerical model which attributes the swimmer velocity increase to electrostatic and electrohydrodynamic boundary effects. Our work not only helps to elucidate the confinement effect of phoretic swimmers, but also suggests that spatial confinement may be used as an effective control method for them.


Publication: 
     Chang Liu, Chao Zhou, Wei Wang, and H. P. Zhang,
    "Bimetallic Microswimmers Speed Up in Confining Channels"
   
Physical Review Letters, 117, 198001 (2016). [Journal URL], [pdf].       


Using confined bacteria as building blocks to generate fluid flow            

Bacteria trapped along
a spiral.

Collective cell motion in
                                    acolony

        In many technological applications, materials are transported by fluid flow at micro/nanometer scales. Conventionally, macroscopic apparatuses, such as syringe pumps, are used to drive the flow. This work explores the possibility of utilizing motile bacteria as microscopic pumps. We used micro-fabricated structures to confine smooth-swimming bacteria in a prescribed configuration. The flagella of confined bacteria rotate to collectively generate flow that can transport materials along designed trajectories. Different structures are combined to realize complex functions, such as collection or dispersion of particles. Experimental findings are reproduced in numerical simulations. Our method opens new ways to generate transport flow at the micrometer scale and to drive bio-hybrid devices.


Publication: 
       Z. Gao, H. Li, X Chen, and H. P. Zhang,
    "Using confined bacteria as building blocks to generate fluid flow"
    Lab on a Chip
, 15, 4555 (2015). [Journal URL], [pdf].


Dynamic clustering in suspension of motile bacteria 
           
Bacterial Clusters at an air-liquid interface.
Collective cell motion in a
                                    colony

        Bacteria suspension exhibits a wide range of collective phenomena, arising from interactions between individual cells. Here we show Serratia marcescens cells near an air-liquid interface spontaneously aggregate into dynamic clusters through surface-mediated hydrodynamic interactions. These long-lived clusters translate randomly and rotate in the counterclockwise direction; they continuously evolve, merge with others and split into smaller ones. Measurements indicate that long-ranged hydrodynamic interactions have strong influences on cluster properties. Bacterial clusters change material and fluid transport near the interface and hence may have environmental and biological consequences.



Publication: 
        X. Chen, X. Yang, M. Yang and H. P. Zhang
       "Dynamic clustering in suspension of motile bacteria "
        EPL (Europhysics Letters), 111, 54002 (2015).  [Journal URL], [pdf].




Scale-Invariant Correlations in Dynamic Bacterial Clusters
             with: Avraham Be’er and Harry L. Swinney   

Four Dynamic Bacterial Clusters in a colony.
Collective cell motion in a
                                      colony

        In Bacillus subtilis colonies, motile bacteria move collectively, spontaneously forming dynamic clusters. These bacterial clusters share similarities with other systems exhibiting polarized collective motion, such as bird flocks or fish schools. Here we study experimentally how velocity and orientation fluctuations within clusters are spatially correlated. For a range of cell density and cluster size, the correlation length is shown to be 30% of the spatial size of clusters, and the correlation functions collapse onto a master curve after rescaling the separation with correlation length. Our results demonstrate that correlations of velocity and orientation fluctuations are scale invariant in dynamic bacterial clusters.


Publication:
  •  X. Chen, X. Dong, A. Be’er, H. L. Swinney, and H. P. Zhang
     "Scale-invariant correlations in dynamic bacterial clusters"
      Physical Review Letters, 108, 148101 (2012).  [Journal URL], [pdf].

    See also
    Physics Synopsis  and a PRL cover image .

Collective motion and density fluctuations in bacterial colonies
             with: Avraham Be’er,  E.-L. Florin, and Harry L. Swinney   

Collective bacterial cell motion observed in a colony.
Collective cell motion in a
                                      colony

        Flocking birds, fish schools, and insect swarms are familiar examplesof collective motion that plays a role in a range of problems, such as spreading of diseases. Models have provided a qualitative understanding of the collective motion, but progress has been hindered by the lack of detailed experimental data. Here we report simultaneous measurements of the positions, velocities, and orientations as a function of time for up to a thousand wild-type Bacillus subtilis bacteria in a colony. The bacteria spontaneously form closely packed dynamic clusters within which they move cooperatively. The number of bacteria in a cluster exhibits a power-law distribution truncated by an exponential tail. The probability of finding clusters with large numbers of bacteria grows markedly as the bacterial density increases. The number of bacteria per unit area exhibits fluctuations far larger than those for populations in thermal equilibrium. Such “giant number fluctuations” have been found in models and in experiments on inert systems but not observed previously in a biological system. Our results demonstrate that bacteria are an excellent system to study the general phenomenon of collective motion.


Movies:


Collective motion under low cell
density condition
Single
                                      growing colony
Collective motion under high cell
 density condition
Two competing colonies

Publications:
  • H. P. Zhang, Avraham Be’er, E.-L. Florin, and Harry L. Swinney
    "Collective motion and density uctuations in bacterial colonies"
    Proceedings of the National Academy of Sciences 107, 13626–13630 (2010).  [Journal URL], [pdf].


Deadly competition between sibling bacterial colonies
             with: Avraham Be’er, E.-L. Florin, Shelley M. Payne, Eshel Ben-Jacob, and Harry L. Swinney   

Bacterial colony grown from a C-shape inoculation.
Colony grown from a C-shape
                                      inoculation

        Bacteria are not the simple solitary creatures of limited capabilities they were long believed to be. When exposed to harsh environmental conditions such as starvation, extreme heat, and hazardous chemicals, the bacteria can collectively develop sophisticated strategies for adaptation and survival. To coordinate such cooperative ventures, bacteria have developed methods of cell-to-cell signaling. One of these methods is by secretion of extracellular materials. Recently, researchers have found chemical secretions capable of attacking sibling cells within the same colony.

        Here, we present experimental observations of competition between two sibling colonies of Paenibacillus dendritiformis grown on a low-nutrient agar gel. We find that neighboring colonies (growing from droplet inoculation) mutually inhibit growth through secretions that become lethal if the level exceeds a well-defined threshold. In contrast, within a single colony developing from a droplet inoculation, no growth inhibition is observed. However, growth inhibition and cell death are observed if material extracted from the agar between two growing colonies is introduced outside a growing single colony. To interpret the observations, we devised a simple mathematical model for the secretion of an antibacterial compound. Simulations of this model illustrate how secretions from neighboring colonies can be deadly, whereas secretions from a single colony growing from a droplet are not.


Movies:


Single colony growing on an agar substrate
Single
                                      growing colony
Two competing colonies growing on an agar substrate
Two competing colonies

Publications:
  • Avraham Be’er, H. P. Zhang, E.-L. Florin, Shelley M. Payne, Eshel Ben-Jacob, and Harry L. Swinney
    "Deadly competition between sibling bacterial colonies"
    Proceedings of the National Academy of Sciences 106, 428-433 (2009).  [Journal URL], [pdf].
  • A. Be'er, G. Ariel, O. Kalisman, Y. Helmanc, A. Sirota-Madi, H. P. Zhang, E. L. Florin, S. M. Payne, E. Ben-Jacob and H. L. Swinney
    "Lethal protein produced in response to competition between sibling bacterial colonies"
    Proceedings of the National Academy of Sciences, 107, 6258-6263 (2010).  [Journal URL], [pdf].
Press Coverage:

Swarming Dynamics
             with: Avraham Be’er, Rachel S. Smith, E. L. Florin and Harry L. Swinney

Trajectories of numerical tracers in a swarming colony
numerical tracers

         Collective motion with extended spatiotemporal coherence can be found in systems of self-propelled objects at almost every length scale, from flocking birds and fish schools, to bacterial swarming  and cooperative behavior of molecular motors in the cell. This biologically originated phenomenon has been studied from perspectives of nonequilibrium statistical mechanics and nonlinear dynamics. The studies have used discrete-particle dynamics based on simple local-interaction laws, continuum ideas from liquid crystal physics, two-fluid models, and hydrodynamics, and have simulated numerically idealized swimmers.

     We determine and relate the characteristic velocity, length, and time scales for bacterial motion in swarming colonies of Paenibacillus dendritiformis growing on semi-solid agar substrates. The bacteria swim within a thin fluid layer, and they form long-lived jets and vortices. These coherent structures lead to anisotropy in velocity spatial correlations and to a two-step relaxation in velocity temporal correlations. The mean squared displacement of passive tracers exhibits a short-time regime with nearly ballistic transport and a diffusive long-time regime. We find that various definitions of the correlation length all lead to length scales that are, surprisingly, essentially independent of the mean bacterial speed, while the correlation time is linearly proportional to the ratio of the correlation length to the mean speed.

Movies:

Instantaneous velocity fields measured in a swarming colony
Swarming PIV results
Complex motion of micron-beads in a swarming colony
Trajectories of physical
                                    tracer

Publications:
  • H. P. Zhang, Avraham Be’er, Rachel S. Smith, E. L. Florin and Harry L. Swinney
    "Swarming dynamics in bacterial colonies"
    Europhysics Letters, 87, 48011 (2009). [Journal URL], [pdf].
  • Avraham Be’er, Rachel S. Smith, H. P. Zhang, E. L. Florin and Harry L. Swinney
    "Paenibacillus dendritiformis bacterial colony growth depends on surfactant but not on bacterial motion "
    Journal of Bacteriology, 191, 5758 (2009). [Journal URL], [pdf].

Internal Gravity Waves
             with: Ben King and Harry Swinney  

Kelvin-Helmholtz bellows created by internal waves
Delamination blisters

        Internal waves are a special kind of wave that can arise in any fluid that is stratified, meaning that the density of the fluid varies with height. The ocean is a classic example of a naturally occurring stratified fluid, being warmer and less salty near the surface, and colder and saltier in the deep sea. The ocean is stably stratified, meaning that a fluid parcel has a strong tendency to remain at its equilibrium height. Whenever a disturbance of any kind causes vertical motion of fluid, the fluid oscillates around its equilibrium height. This oscillatory disturbance propagates through the fluid as an internal wave. These waves are generally not visible from the surface, but are nearly ubiquitous throughout the ocean. Internal waves can generate turbulences at very small scales, which are extremely important for sustaining the global ocean circulation.

        We study internal wave generation by tidal flow over topography on the ocean floor in laboratory and numerical experiments. Waves are found to be generated most efficiently in a near-critical region where the slope of the bottom topography matches that of internal waves. If the near-critical region is sufficiently long, fluid motion with a velocity an order of magnitude larger than that of the forcing occurs within a thin boundary layer above the bottom surface. The resonant wave is unstable because of strong shear; Kelvin-Helmholtz billows (see figure on the left) precede wave breaking. Our work provides a new explanation for the intense boundary flows on continental slopes and how these flow may shape continental margins. We are currently investigating internal wave generation from a 3-D topography and nonlinear reflection of internal wave from a slope.

Movies:

Raw data of tracer particles demonstrating a resonant wave
Slope
                                      PIV Experiments
Instantaneous velocity field measured from the left movie
PIV results of a resonant wave

Publications:
  • H. P. Zhang, B. King, and Harry L. Swinney
    "Resonant Generation of Internal Waves on a Model Continental Slope"
    Physical Review Letters 100, 244504 (2008). [Journal URL], [pdf], [ps].
  • H. P. Zhang, B. King, and Harry L. Swinney
    "Experimental study of internal gravity waves generated by supercritical topography"
    Physics of Fluids 19, 096602 (2007).  [Journal URL], [pdf].
  • B. King, H. P. Zhang, and Harry L. Swinney
    "Tidal flow over three-dimensional topography in a stratified fluid"
    Physics of Fluids, 21, 116601 (2009).  [Journal URL], [pdf]
  • B. King, H. P. Zhang, and Harry L. Swinney
    "Tidal ow over three-dimensional topography generates out-of-forcing-plane harmonics"
    Geophysical Research Letters, 37,  L14606 (2010). [Journal URL], [pdf]
Press Coverage:

Toughening Crystallites
             with: J. Niemczura, G. Dennis, K. Ravi-Chandar, and M. Marder

Instantaneous openings and particle velocity fields under two stretching conditions
Delamination blisters

     Fracture resistance is the property of materials that determines when and how they break. It can be defined as the energy per area required to create a new fracture surface. A very simple view would be that fracture resistance is essentially equal to the surface energy. However, this viewpoint is a severe over-simplification; studies have shown that adding small amounts, ~1% in volume fraction, of nanometer-sized fillers, such as rubber particles or nanotubes, can greatly improve the fracture resistance of a polymeric matrix. Many tough natural materials (usually of biological origin), such as nacre, bone, and spider silk, also contain nanostructures embedded in an amorphous matrix. Like their man-made counterparts, all these biological materials show greater resistance to fracture than one might expect from the mechanical properties of the component parts.

      We study fracture propagation in stretched natural rubber sheets. Experimental results in specimens stretched less than 3.8 times show a monotonic increase in the crack speed with stretch and can be explained by a numerical model based on neo-Hookean theory and Kelvin dissipation. In specimens stretched more than 3.8 times, strain-induced crystallites act as reinforcing and toughening fillers and significantly increase fracture resistance, like nanostructures in other polymeric or biological materials. Consequently, as we increase the amount of stretch, fractures travel slower and slower, and eventually halt altogether.

Movies:

Fracture propagations at three stretching conditions. Data were collected with a high-speed camera running at 48000 frames/sec. Particle velocities of the left two pannels are shown in the figure above.
Fracture propagation at three
                                      conditions at room temperature
Publications:
  • H. P. Zhang, J. Niemczura, G. Dennis, K. Ravi-Chandar, and M. Marder
    "Toughening Effect of Strain-Induced Crystallites in Natural Rubber"
    Physical Review Letters 102, 245503 (2009). [Journal URL], [pdf].

Dynamics of Static Friction
             with: Zhiping, Yang and Marder, M. 

Experimental apparatus for friction studies
Experiments

     The understanding of friction has evolved greatly in the last 70 years. Bowden and Tabor established that friction is due to populations of asperities and that the actual contact area of two solids in frictional sliding is much less than apparent. Dieterich showed that the population of frictional contacts evolves during dynamic sliding, and measured changes in force over time and at different steady speeds. Rice and Ruina  developed a standard theory for this phenomenon, known as ‘‘rate and state friction’’ in which a single state variable accounts for the population of asperities and its evolution in time. Baumberger and collaborators showed that the rate and state equations extend to low velocities, on the order of 1 µm/s, as a sliding object comes to a halt. During stick-slip motion, samples of Plexiglas and paper continue to creep during the ‘‘stick’’ phase.

    Here, we describe experiments where silicon and quartz are clamped on steel, motion is measured down to the nanometer scale, and velocities are measured down to 0.00001 µm/s. We see that static friction is not really static. Under conditions where objects are pressed into each other and are not normally expected to slide, the asperity population gives way a little bit and evolves before the contacts lock up and become motionless. The characteristic sliding distance is a fraction of a micrometer, which is the characteristic scale of asperities, and the motion remains regular down to the scale of nanometers. We show that the observations are described quantitatively by modifications of the standard equations of rate and state friction

Publications:
  • Zhiping, Yang, H. P. Zhang and Mike Marder
    "Dynamics of static friction between steel and silicon"
    Proceedings of the National Academy of Sciences 105, 13264-13268 (2008).  [Journal URL], [pdf].
Press Coverage:
  • A commentary by Martin H. Müser in PNAS.

Granular and Glassy Materials 
           with: Herman Cummins and Hernan Makse

Dynamic light-scattering
spectra measure in salol

Delamination blisters

      In the period of my graduate study, I worked on the glass transition in molecular liquids  and the jamming transition in granular matter. I did extensive lightscattering experiments, including Brillouin, Raman and photon correlation spectroscopies, primarily to study rotational and translational dynamics in glassforming liquids of anisotropic molecules. We observed a new phenomenon due to the coupling between rotational and translational dynamics in polarized spectrum, which had been predicted theoretically by Pick et al.  but not observed before.

     I carried out numerical simulations to study the rigidity and jamming transition in granular packings generated by compressing a granular gas. The construction history parametrized by the compression rate during the preparation protocol was found to have a strong effect on the micromechanical properties of frictional granular materials. This leads the frictional granular system to jam at different volume fractions, depending on the history. Isostaticity, which means the number of inter-grain contact forces equals the number of force balance equations of grains, was found in the packings close to the jamming transition in frictionless packings and in frictional packing at slow compression rates and infinite friction. Multiple scaling laws are identified in system near the jamming transition.


Publications:
  •  H. P. Zhang, A. Brodin, H. C. Barshilia, G. Q. Shen, and H. Z. Cummins
    "Brillouin scattering study of Salol: effects of Rotation-Translation Coupling"
    Physical Review E, 70, 011502 (2004).   [Journal URL], [pdf].
  •  H. P. Zhang and H. A. Makse
    "Jamming transition in emulsions and granular materials"
    Physical Review E, 72, 011301 (2005). [Journal URL], [pdf].
  •  H. Z. Cummins, H. P. Zhang, J. Oh, J. A. Seo, H. K. Kim, Y-H Hwang, Y.S. Yang, Y. S. Yu, Y. Inn
    "The liquid-glass transition in sugars: Relaxation dynamics in trehalose"
    Journal of Non-Crystalline Solids, 352, 4464-4474 (2006). [Journal URL], [pdf].
© 2016 Institute of Natural Sciences and  Dept. of Physics, Shanghai Jiao Tong University, Shanghai China