Date of Award




Document Type


Degree Name

Doctor of Philosophy (PhD)


Department of Nanoscale Science and Engineering


Nanoscale Sciences

Content Description

1 online resource (xii, 170 pages) : illustrations (some color)

Dissertation/Thesis Chair

Nathaniel C Cady

Committee Members

Thomas Begley, Scott Tenenbaum, Rebecca Cortez, Robert Geer


Atomic force microscopy (AFM), Biofilm, Elasticity, Microfluidics, Biofilms, Atomic force microscopy

Subject Categories

Materials Science and Engineering | Microbiology | Nanoscience and Nanotechnology


Viable methods for bacterial biofilm remediation require a fundamental understanding of biofilm mechanical properties and their dependence on dynamic environmental conditions. Mechanical test data, quantifying elasticity or adhesion, may be used to perform physical modeling of biofilm behavior, thus enabling the development of novel remediation strategies. To achieve real-time, dynamic measurements of these properties, a novel analysis platform consisting of a microfluidic flowcell device has been designed and fabricated for in situ analysis using atomic force microscopy (AFM) and confocal laser scanning microscopy (CLSM). The flowcell consists of microfluidic channels for biofilm establishment that are then converted into an open architecture, laminar flow channel for AFM measurement in a liquid environment. Computational fluid dynamics (CFD) was used to profile fluid conditions within the device during biofilm establishment. The validity of the AFM nanoindentation measurement mechanism was confirmed in the context of the system through the elastic characterization of several non-living reference materials. Force-mode AFM was used to measure the elastic properties of mature Pseudomonas aeruginosa PAO1 biofilms and observe a dynamic response to a chemical antagonist. Elastic moduli ranging from 0.58 to 2.61 kPa were determined for the mature biofilm, which fall within the range of moduli previously reported by optical, rheometric, and microindentation techniques. A modified version of the flowcell was employed to perform similar elastic characterization of mouse submandibular glands (SMGs), demonstrating the adaptability of the system to perform ex situ analyses of a broader set of biological materials. These results demonstrate the validity of the microfluidic flowcell system as an effective platform for future investigations of the mechanical and morphological response of biofilms and other soft biomaterials to dynamic environmental conditions.