Yingjie Du

Localized cell death focuses mechanical forces during 3D patterning in a biofilm

From microbial biofilm communities to multicellular organisms, 3D macroscopic structures develop through poorly understood interplay between cellular processes and mechanical forces. Investigating wrinkled biofilms of Bacillus subtilis, we discovered a pattern of localized cell death that spatially focuses mechanical forces, and thereby initiates wrinkle formation. Deletion of genes implicated in biofilm development, together with mathematical modeling, revealed that ECM production underlies the localization of cell death. Simultaneously with cell death, we quantitatively measured mechanical stiffness and movement in WT and mutant biofilms. Results suggest that localized cell death provides an outlet for lateral compressive forces, thereby promoting vertical mechanical buckling, which subsequently leads to wrinkle formation. Guided by these findings, we were able to generate artificial wrinkle patterns within biofilms. Formation of 3D structures facilitated by cell death may underlie self-organization in other developmental systems, and could enable engineering of macroscopic structures from cell populations.

Fluorescent stereo microscopy for 3D surface profilometry and deformation mapping

Recently, mechanobiology has received increased attention. For investigation of biofilm and cellular tissue, measurements of the surface topography and deformation in real-time are a pre-requisite for understanding the growth mechanisms. In this paper, a novel three-dimensional (3D) fluorescent microscopic method for surface profilometry and deformation measurements is developed. In this technique a pair of cameras are connected to a binocular fluorescent microscope to acquire micrographs from two different viewing angles of a sample surface doped or sprayed with fluorescent microparticles. Digital image correlation technique is used to search for matching points in the pairing fluorescence micrographs. After calibration of the system, the 3D surface topography is reconstructed from the pair of planar images. When the deformed surface topography is compared with undeformed topography using fluorescent microparticles for movement tracking of individual material points, the full field deformation of the surface is determined. The technique is demonstrated on topography measurement of a biofilm, and also on surface deformation measurement of the biofilm during growth. The use of 3D imaging of the fluorescent microparticles eliminates the formation of bright parts in an image caused by specular reflections. The technique is appropriate for non-contact, full-field and real-time 3D surface profilometry and deformation measurements of materials and structures at the microscale.

Structural, elastic, thermal, and electronic responses of small-molecule-loaded metal–organic framework materials

We combine infrared spectroscopy, nano-indentation measurements, and ab initio simulations to study the evolution of structural, elastic, thermal, and electronic responses of the metal–organic framework MOF-74-Zn when loaded with H2, CO2, CH4, and H2O. We find that molecular adsorption in this MOF triggers remarkable responses in all these properties of the host material, with specific signatures for each of the guest molecules. With this comprehensive study, we are able to clarify and correlate the underlying mechanisms regulating these responses with changes of physical and chemical environments. Our findings suggest that metal–organic framework materials in general, and MOF-74-Zn in particular, can be very promising materials for novel transducers and sensor applications, including highly selective small-molecule detection in gas mixtures.

Nanoindentation of Pseudomonas aeruginosa bacterial biofilm using atomic force microscopy

Bacterial biofilms are a source of many chronic infections. Biofilms and their inherent resistance to antibiotics are attributable to a range of health issues including affecting prosthetic implants, hospital-acquired infections, and wound infection. Mechanical properties of biofilm, in particular, at micro- and nano-scales, are governed by microstructures and porosity of the biofilm, which in turn may contribute to their inherent antibiotic resistance. We utilize atomic force microscopy (AFM)-based nanoindentation and finite element simulation to investigate the nanoscale mechanical properties of Pseudomonas aeruginosa bacterial biofilm. This biofilm was derived from human samples and represents a medically relevant model.

High-Strain Rate Compressive Behavior of Dry Mason Sand Under Confinement

Uniaxial compressive behavior of Mason sand, a poorly-graded local sand supplied by Colorado Materials (Longmont, CO), was investigated on a long split Hopkinson pressure bar. Sand grains were confined inside a hardened steel tube and capped by tungsten carbide rods. This assembly was subjected to repeat shaking to consolidate sand to attain desired bulk mass density, then sandwiched between incident and transmission bar ends for dynamic compression. Unsorted dry sand was characterized at high strain rates to determine the volumetric and deviatoric behavior through measurements of both axial and transverse response of cylindrical sand sample under confinement. Effects of sand mass density on the constitutive behavior were investigated. The stress–strain relationship was found to follow a power law relationship with the initial bulk density. The Young’s modulus and hardness of individual sand grains were determined by nanoindentation. The sand deformation was observed through sapphire tube using ultra-high speed photography to determine the elastic deformation and compaction behavior. The energy absorption density and compressibility were determined as a function of axial stress. These results can be analyzed further for constitutive modeling and for mesoscale simulations to understand the soil behavior under blast subject to high pressure and high rate deformations.

Correlation of Microscale Deformations to Macroscopic Mechanical Behavior Using Incremental Digital Volume Correlation of In-Situ Tomography

An incremental digital volume correlation (DVC) technique was developed to measure large nonlinear deformations on volumetric images acquired using X-ray micro-computed tomography (μ-CT). A series of bridging volumetric images are acquired during the loading of a specimen. The deformation in the neighboring images is sufficiently small to allow DVC calculation. The displacements are accumulated, and analyzed to determine their gradients for deformation measurements. The technique was applied for observation of internal deformations of Polymethacrylimide (PMI) foam, polymer bonded sugar (PBS), and granular materials in compression experiencing large nonlinear deformations. When PMI foam underwent compression, 17 states of the PMI were captured and large nonlinear deformations were observed. The PBS cylindrical specimen, in which sugar grains are embedded in hydroxylterminated polybutadiene (HTPB) binder matrix, was compressed up to 32 % of compressive strain without confinement. The debonding evolution was observed and discussed. On granular materials, a methodology was developed to determine for the force chains. These applications demonstrate that incremental DVC is a powerful technique for linking the microstructure with macroscopic mechanical behavior.

Tri-layer nanoindentation for mechanical characterization of ultra-low-k dielectrics

Recently the mechanical properties of nano-porous ultra-low-k (ULK) dielectric thin films have been characterized by nanoindentation using a tri-layer sample configuration. Tetraethyl orthosilicate (TEOS) silica was coated on the fragile ULK thin film to protect it from direct contact with nanoindenter tip. In this paper, the finite element method (FEM) simulations are conducted to investigate the effect of TEOS thickness, and to propose rules to design the tri-layer sample.