Research

Bacterial Dyanamics in 3D Porous Media

While bacterial motility is well-studied for motion on flat surfaces or in unconfined liquid media, most bacteria are found in heterogeneous porous media, such as biological gels and tissues, soils, sediments, and subsurface formations. Understanding how confinement alters bacterial motility is therefore critical to model the progression of infections, apply beneficial bacteria for drug delivery, and bioremediation. Unconfined bacteria move via runs and tumbles, leading to random walk-like motion; in a porous medium, previous research has assumed bacteria still move via runs and tumbles, but with a reduced diffusivity due to collisions with obstacles. However, this assumption has never been directly tested due to the inability to visualize processes in opaque 3D media. Here, we directly visualize the motion of single E. coli cells inside a model 3D porous medium, having controlled pore structure. By analyzing the individual cell trajectories, we find that the bacteria do not move via a run and tumble process, but instead via intermittent hops and traps reminiscent of thermally-activated transport in disordered media. We will present how bacterial motility depends sensitively on pore-scale confinement. Our findings overturn standard assumptions made in the field and provide guidance for the development of more accurate macroscopic models of bacterial motion. Our recent work can be found in Nature Communications.

hopping

 

Jammed Microgel for Soft Matter Manufacturing

One of the major challenges of manufacturing soft delicate structures is to arrange them in complex 3D shape. We overcome this constain by using a packed system of polyelectrolyte hydrogel particles as a sacrificial support material in which we create soft delicate stuctures of cells, colloids, hydrogels and elastomers with an absolute high precision. We leverage the unique rheological properties of jammed microgels (low yield stress, short thixotropic time, and spontaneous reflow after yielding) to 3D print soft matter structures. Detailed work can be found in our recent work in Science Advances, MRS Bulletin and Science Advances.

 

Jammed MIcrogel as 3D Cell Growth Media

Cells grown on plates differ dramatically from cells in vivo or in 3D culture in terms of cell shape, structure, motion, and mechanical behavior. These physical properties of cells in 3D are, however, far less explored. By contrast, in terms of molecular biology, it is well known that gene expression profiles of cells grown in monolayers are anticorrelated with those of cells grown in 3D culture or xenograft animal models, whereas, our traditional approach towards cell biology majorly depends on the monolayer cell culture on 2D plates.Thus, to bridge this major gap between 2D in vitro culture and 3D in vivo biology we have created a combined 3D bioprinting and culture platform by directly packing microgel preswelled in liquid cell growth media. Our detailed work has been published in ACS Biomaterials Science and Engineering.

LLS

 

Scaling Laws for Polyelectrolyte Microgel Yielding Near Jamming

The phenomenology of microgel yielding near the jamming transition has not been studied with the perspective of polymer physics at the single chain level within microgels at low packing fractions. The currently eastablished scaling laws of hydrogel material and transport properties often depend on single chain structure and dynamics. A connection between current particle-scale descriptions of yielding and single chain dynamics would be a valuable tool in future experimental and industrial efforts. we use the established scaling laws of polymer gels to predict the yield stress and cross-over shear-rate in systems of packed microgels just above the jamming transition. This work has been recently pubished in Soft Matter.

 

3D T cell motility

Exploration of in vitro cell behavior in 3D space has revealed that cell morphology, cell generated forces, and the architecture of the intracellular mechanical machinery differ from their 2D counterparts, demonstrating the importance of investigation in 3D. However, current 3D methods employ continuous polymer networks to study cells in 3D which present numerous challenges associated with the need for transient pore-space to enable cell motion and the complexities of controlling the 3D cell distribution. To overcome these challenges, we have developed a 3D culture medium made from jammed microgels; the rheological properties of jammed microgels swelled in liquid cell growth media allow the dispersal of cells in into a 3D environment with well-defined structural and material properties. In this work, we explore the motility of T cells in systems of jammed microgel growth media prepared with different yield stresses, finding timescale and length-scale dependent dynamics that are correlated with the pore-space between the microgels. Jammed microgels represent a class of soft matter with unique properties that has not been leveraged for the study of cell motion or mechanics in 3D space; our observations of cell motion through jammed microgels demonstrate how T cells navigate porous environments and provide guidance for a multitude of future investigations in unexplored territory. To fing out more, please see our work published in Journal of Physics D

       cells and beads