Optical coherence tomography (OCT) has become an indispensable tool for investigating mesoscopic features in soft matter and fluid mechanics. Its ability to provide high-resolution, non-invasive measurements in both spatial and temporal domains bridges critical gaps in experimental instrumentation, enabling the study of complex, confined, and dynamic systems. This review serves as both an introduction to OCT and a practical guide for researchers seeking to adopt this technology. A set of tutorials, complemented by Python scripts, is provided for both intensity- and Doppler-based techniques. The versatility of OCT is illustrated through case studies, including time-resolved velocimetry, particle-based velocity measurements, slip velocity characterization, detection of shear-induced structures, and analysis of fluid-fluid and fluid-structure interactions. Drawing on our experiences, we also present a set of practical guidelines for avoiding common pitfalls.

Biofilms constitute one of the most common forms of living matter, playing an increasingly important role in technology, health, and ecology. While it is well established that biofilm growth and morphology are highly dependent on the external flow environment, the precise role of fluid friction has remained elusive. We grew Bacillus subtilis biofilms on flat surfaces of a channel in a laminar flow at wall shear stresses spanning one order of magnitude (τw = 0.068 Pa to τw = 0.67 Pa). By monitoring the three-dimensional distribution of biofilm over seven days, we found that the biofilms consist of smaller microcolonies, shaped like leaning pillars, many of which feature a streamer in the form of a thin filament that originates near the tip of the pillar. While the shape, size, and distribution of these microcolonies depend on the imposed shear stress, the same structural features appear consistently for all shear stress values. The formation of streamers occurs after the development of a base structure, suggesting that the latter induces a secondary flow that triggers streamer formation. Moreover, we observed that the biofilm volume grows approximately linearly over seven days for all shear stress values, with a growth rate inversely proportional to the wall shear stress. We develop a scaling model, providing insight into the mechanisms by which friction limits biofilm growth.

The interaction between fluid dynamics and biofilm growth plays a key role in both medical and industrial applications. Biofilms, or bacteria that are embedded in a protective matrix of extracellular polymeric substances, settle on interfaces such as on implanted devices or ship hulls. These biofilms canthen cause infectious diseases or significantly increase drag. In this thesis, we investigate the influence of flow, specifically shear stress, on the development of biofilm.

The first paper presents a new facility to investigate biofilm growth in laminar flow cells over extended periods of up to several weeks. Optical coherence tomography is used to obtain three-dimensional scans of the biofilm structure at regular intervals. From these time series, we derive a simple model that relates the growth of an individual microcolony to the growth of the full biofilm depending on the wall shear stress. Additionally, we show that biofilm streamers, thin, flexible filaments that extend into the bulk flow, can form on sharp biofilm structures in laminar flow, even if the substratum is a flat surface.

The second contribution is a report detailing preliminary studies on biofilm experiments. We investigate the formation of biofilm in the shear layer behinda backward-facing step. The results indicate a maximum shear stress, beyond which biofilm growth is inhibited. We also provide guidelines for the design of experimental setups for the investigation of the influence of fluid dynamics on biofilm and vice-versa.

Samspelet mellan fluiddynamik och biofilmtillväxt spelar en nyckelroll i både medicinska och industriella tillämpningar. Biofilmer, eller bakterier som är inbäddade i en skyddande matris av extracellulära polymera substanser, sätter sig på ytor som på implanterade enheter eller fartygsskrov. Dessa biofilmer kan sedan orsaka infektionssjukdomar eller avsevärt öka vattenmotståndet. I den här avhandlingen undersöker vi hur flöde, speciellt skjuvspänning, påverkar utvecklingen av biofilm.

I den första artikeln presenteras en ny uppställning för att undersöka biofilmstillväxt i flödesceller med laminärt flöde under längre perioder på upp till flera veckor. Optisk koherenstomografi används för att få tredimensionella skanningar av biofilmstrukturen vid regelbundna intervall. Från dessa tidsserier härleder vi en enkel modell som relaterar tillväxten av en enskild mikrokoloni till tillväxten av hela biofilmen beroende på väggskjuvspänning. Dessutom visar vi att biofilm filament som sträcker sig in i bulkflödet, kan bildas på skarpa biofilmstrukturer i laminärt flöde, även om substratum är en plan yta. 

Det andra bidraget är en rapport som beskriver preliminära studier av biofilmsexperiment. Vi undersöker bildandet av biofilm i skjuvskiktet bakom ett bakåtvänt steg. Resultaten indikerar en maximal skjuvspänning, bortom vilken biofilmstillväxt hämmas. 

Optical Coherence Tomography (OCT) has become an indispensable tool for investigating mesoscopic features in soft matter and fluid mechanics. Its ability to provide high-resolution, non-invasive measurements in both spatial and temporal domains bridges critical gaps in experimental instrumentation, enabling the study of complex, confined, and dynamic systems. This review serves as both an introduction to OCT and a practical guide for researchers seeking to adopt this technology. A set of tutorials, complemented by Python scripts, are provided for both intensity- and Doppler-based techniques. TheversatilityofOCTisillustratedthroughcasestudies, includingtime-resolvedvelocimetry, particle-based velocity measurements, slip velocity characterization, detection of shear-induced structures, and analysis of fluid-fluid and fluid-structure interactions. Drawing on our experiences, we also present a set of practical guidelines for avoiding common pitfalls.

Bacillus subtilis biofilms were grown in laminar channel flow at wall shear stress spanning one order of magnitude (tau_w = 0.068 Pa to tau_w = 0.67 Pa). We monitor, non-invasively, the evolution of the three-dimensional distribution of biofilm over seven days using optical coherence tomography (OCT). The obtained biofilms consist of many microcolonies where the characteristic colony has a base structure in the form of a leaning pillar and a streamer in the form of a thin filament that originates near the tip of the pillar. While the shape, size and distribution of these microcolonies depend on the imposed shear stress, the same structural features appear consistently for all shear stress values. The formation of streamers seems to occur after the development of a base structure, suggesting that the latter induces a curved secondary flow that triggers the formation of the streamers. Moreover, we observe that the biofilm volume grows approximately linearly over seven days for all the shear stress values, with a growth rate that is inversely proportional to the wall shear stress. We develop a simple model of friction-limited growth, which agrees with the experimental observations. The model provides physical insight into growth mechanisms and can be used to develop accurate continuum models of bacterial biofilm growth.