Discrete element method to study biofilm deformation in fluid flow

Ph. D. Thesis.Biofilms are the assemblage of one or more types of microorganisms, which are usually found attached and grew on surfaces, embedded in their extracellular polymeric substances (EPS). They could form diverse morphologies to adapt to different environments, especially in a flow system such as water filtration. Hydrodynamic conditions have a significant impact on the deformation and detachment of biofilm, which has been primarily investigated by the experiments. However, relevant modelling research is lacking. Therefore, the individual based model (IbM) is adopted to study the biofilm-fluid interaction in present work. In the first part of this work, the discrete element method was utilized to simulate the biofilm growth, deformation and detachment, where the fluid was mimicked by applying a simple shear force. Due to the fact that the biofilms would also affect the flow pattern in return, the simply one-way approach was then extended to a two-way coupled computational fluid dynamic – discrete element method (CFD-DEM) model. Biofilm deformation and detachment was investigated at varied inlet flow velocity. We have also studied the effect of the EPS content on the deformation and detachment of biofilms. Furthermore, the strain-stress curves during biofilm deformation have been captured by loading and unloading the fluid shear stress. Biofilm streamer (filamentous structure of biofilm) motion under different flow conditions is important for a wide range of industries as well. The flow-induced oscillations and cohesive failure of single and multiple biofilm streamers have been investigated based on the CFD-DEM model. In this section, we have studied the effect of streamer length on the oscillation at varied flow rates. The predicted single biofilm streamer oscillations in various flow rates agreed well with experimental measurements. We have also investigated the effect of the spatial arrangement of streamers on interactions between two oscillating streamers in parallel and tandem arrangements. Besides, cohesive failure of streamers was studied in an accelerating fluid flow, which is important for slowing down biofilm induced cloggingEPSRC, BBSR

Magneto-mechanically actuated microstructures to efficiently prevent bacterial biofilm formation

Abstract: Biofilm colonisation of surfaces is of critical importance in various areas ranging from indwelling medical devices to industrial setups. Of particular importance is the reduced susceptibility of bacteria embedded in a biofilm to existing antimicrobial agents. In this paper, we demonstrate that remotely actuated magnetic cantilevers grafted on a substrate act efficiently in preventing bacterial biofilm formation. When exposed to an alternating magnetic field, the flexible magnetic cantilevers vertically deflect from their initial position periodically, with an extremely low frequency (0.16 Hz). The cantilevers’ beating prevents the initial stage of bacterial adhesion to the substrate surface and the subsequent biofilm growth. Our experimental data on E. coli liquid cultures demonstrate up to a 70% reduction in biofilm formation. A theoretical model has been developed to predict the amplitude of the cantilevers vertical deflection. Our results demonstrate proof-of-concept for a device that can magneto-mechanically prevent the first stage in bacterial biofilm formation, acting as on-demand fouling release active surfaces

PROGRAM and PROCEEDINGS THE NEBRASKA ACADEMY OF SCIENCES: 139th Anniversary Year, One Hundred-Twenty-Ninth Annual Meeting, April 12, 2019, NEBRASKA WESLEYAN UNIVERSITY, LINCOLN, NEBRASKA

PROGRAM AT-A-GLANCE FRIDAY, APRIL 12, 2019 7:30 a.m. REGISTRATION OPENS - Lobby of Lecture Wing, Olin Hall 8:00 Aeronautics and Space Science, Session A – Acklie 109 Aeronautics and Space Science, Session B – Acklie 111 Collegiate Academy; Biology, Session B - Olin B Biological and Medical Sciences, Session A - Olin 112 Biological and Medical Sciences, Session B - Smith Callen Conference Center Chemistry and Physics; Chemistry - Olin A 8:00 “Teaching and Learning the Dynamics of Cellular Respiration Using Interactive Computer Simulations” Workshop – Olin 110 9:30 “Life After College: Building Your Resume for the Future” Workshop – Acklie 218 8:25 Collegiate Academy; Chemistry and Physics, Session A – Acklie 007 8:36 Collegiate Academy; Biology, Session A - Olin 111 9:00 Chemistry and Physics; Physics – Acklie 320 9:10 Aeronautics and Space Science, Poster Session – Acklie 109 & 111 10:30 Aeronautics and Space Science, Poster Session – Acklie 109 & 111 11:00 MAIBEN MEMORIAL LECTURE: Dr David Swanson - OLIN B Scholarship and Friend of Science Award announcements 12:00 p.m. LUNCH – WESLEYAN CAFETERIA Round-Table Discussion – “Assessing the Academy: Current Issues and Avenues for Growth” led by Todd Young – Sunflower Room 12:50 Anthropology – Acklie 109 1:00 Applied Science and Technology - Olin 111 Biological and Medical Sciences, Session C - Olin 112 Biological and Medical Sciences, Session D - Smith Callen Conference Center Chemistry and Physics; Chemistry - Olin A Collegiate Academy; Biology, Session B - Olin B Earth Science – Acklie 007 Environmental Sciences – Acklie 111 Teaching of Science and Math – Acklie 218 1:20 Chemistry and Physics; Physics – Acklie 320 4:30 BUSINESS MEETING - OLIN B NEBRASKA ASSOCIATION OF TEACHERS OF SCIENCE (NATS) The 2019 Fall Conference of the Nebraska Association of Teachers of Science (NATS) will be held at the Younes Conference Center, Kearney, NE, September 19-21, 2019. President: Betsy Barent, Norris Public Schools, Firth, NE President-Elect: Anya Covarrubias, Grand Island Public Schools, Grand Island, NE AFFILIATED SOCIETIES OF THE NEBRASKA ACADEMY OF SCIENCES, INC. 1. American Association of Physics Teachers, Nebraska Section Web site: http://www.aapt.org/sections/officers.cfm?section=Nebraska 2. Friends of Loren Eiseley Web site: http://www.eiseley.org/ 3. Lincoln Gem & Mineral Club Web site: http://www.lincolngemmineralclub.org/ 4. Nebraska Chapter, National Council for Geographic Education 5. Nebraska Geological Society Web site: http://www.nebraskageologicalsociety.org Sponsors of a $50 award to the outstanding student paper presented at the Nebraska Academy of Sciences Annual Meeting, Earth Science /Nebraska Chapter, Nat\u27l Council Sections 6. Nebraska Graduate Women in Science 7. Nebraska Junior Academy of Sciences Web site: http://www.nebraskajunioracademyofsciences.org/ 8. Nebraska Ornithologists’ Union Web site: http://www.noubirds.org/ 9. Nebraska Psychological Association http://www.nebpsych.org/ 10. Nebraska-Southeast South Dakota Section Mathematical Association of America Web site: http://sections.maa.org/nesesd/ 11. Nebraska Space Grant Consortium Web site: http://www.ne.spacegrant.org

Rheological characterisation of biofilms in both linear and nonlinear viscoelastic regimes

Ph. D. ThesisBiofilms are a ubiquitous mode of bacteria proliferation found within aqueous environments. The structure and architecture that a biofilm self assembles into confers mechanical resistance against shear forces. A characteristic trait of biofilm is the production of extra cellular materials which act as the “glue” in the ECM/bacteria composite. The myriad physical properties of biofilm systems result in highly variable mechanical properties, which are studied using rheology. Previous studies about biofilm mechanics were mainly focused on linear viscoelastic regions. However the linear region is unable to provide information regarding the dynamics of deformation and structural rearrangement. Probing the biofilm nonlinear viscoelastic regime and yielding dynamics opens a window to access how the rearrangement behaviour of the EPS network and bacterium network are impacted by EPS composition and bacterial network topology. In addition, to determine the rheological properties of biofilms within the linear viscoelastic regime using the rotational rheometer, this thesis sheds light on utilising high fidelity non-linear rheological techniques and advanced imaging techniques to produce a framework explaining the emergence of characteristic biofilm mechanical behaviours across an array of species, chemical environments and genetic mutations. I have demonstrated the applicability of three types of large amplitude oscillatory shear (LAOS) analysis methodologies to Pseudomonas fluorescens biofilms and the rheological effects of divalent cations and a chaotropic compound. It was shown that by increasing ionic concentration the characteristic behaviour changes from a repulsive glass to an attractive glass. To understand the rheological and architectural effects of capsular polysaccharide secretion in biofilms, I selected the bacterium Pantoea sp. I revealed how the secretion of amylovoren and stewartin causes a characteristic rheological change from viscoelastic liquid to glass and how this is primarily driven by changes in EPS polymer concentration and packing fraction. Finally, I investigated the yielding behaviours across a range of bacteria with different geometries (rods/cocci) and EPS compositions. I identified four different types of yielding behaviour across the tested bacterial strains and used a range of rheological and microscopy data to identify the extent of short- and long-range polymer networks which determine the viscoelastic response of bacterial biofilms. Biofilms are a ubiquitous mode of bacteria proliferation found within aqueous environments. The structure and architecture that a biofilm self assembles into confers mechanical resistance against shear forces. A characteristic trait of biofilm is the production of extra cellular materials which act as the “glue” in the ECM/bacteria composite. The myriad physical properties of biofilm systems result in highly variable mechanical properties, which are studied using rheology. Previous studies about biofilm mechanics were mainly focused on linear viscoelastic regions. However the linear region is unable to provide information regarding the dynamics of deformation and structural rearrangement. Probing the biofilm nonlinear viscoelastic regime and yielding dynamics opens a window to access how the rearrangement behaviour of the EPS network and bacterium network are impacted by EPS composition and bacterial network topology. In addition, to determine the rheological properties of biofilms within the linear viscoelastic regime using the rotational rheometer, this thesis sheds light on utilising high fidelity non-linear rheological techniques and advanced imaging techniques to produce a framework explaining the emergence of characteristic biofilm mechanical behaviours across an array of species, chemical environments and genetic mutations. I have demonstrated the applicability of three types of large amplitude oscillatory shear (LAOS) analysis methodologies to Pseudomonas fluorescens biofilms and the rheological effects of divalent cations and a chaotropic compound. It was shown that by increasing ionic concentration the characteristic behaviour changes from a repulsive glass to an attractive glass. To understand the rheological and architectural effects of capsular polysaccharide secretion in biofilms, I selected the bacterium Pantoea sp. I revealed how the secretion of amylovoren and stewartin causes a characteristic rheological change from viscoelastic liquid to glass and how this is primarily driven by changes in EPS polymer concentration and packing fraction. Finally, I investigated the yielding behaviours across a range of bacteria with different geometries (rods/cocci) and EPS compositions. I identified four different types of yielding behaviour across the tested bacterial strains and used a range of rheological and microscopy data to identify the extent of short- and long-range polymer networks which determine the viscoelastic response of bacterial biofilms. In summary, this thesis demonstrates how contemporary rheological methods and soft matter physics can be used in a reductive approach towards linking biofilm mechanics, microstructure and phenomenology.EPSRC DT

High-speed imaging in fluids

High-speed imaging is in popular demand for a broad range of experiments in fluids. It allows for a detailed visualization of the event under study by acquiring a series of image frames captured at high temporal and spatial resolution. This review covers high-speed imaging basics, by defining criteria for high-speed imaging experiments in fluids and to give rule-of-thumbs for a series of cases. It also considers stroboscopic imaging, triggering and illumination, and scaling issues. It provides guidelines for testing and calibration. Ultra high-speed imaging at frame rates exceeding 1 million frames per second is reviewed, and the combination of conventional experiments in fluids techniques with high-speed imaging techniques are discussed. The review is concluded with a high-speed imaging chart, which summarizes criteria for temporal scale and spatial scale and which facilitates the selection of a high-speed imaging system for the applicatio

Consequences of biofilm architecture on Vibrio cholerae ecology and life history

The diversity of microbes and the environments they inhabit are staggering. In many of these environments, bacteria have evolved to form sessile surface attached communities called biofilms. These biofilms have wide reaching impacts from importance in global carbon cycling, to persistent catheter infections, to biofouling and wastewater treatment. While many species of microbes form biofilms to survive in their environment, the architectures of these structures vary widely between organisms. Even though a great deal of work has been done to understand bacterial communities and their functions, little work has examined how the spatial aspects of biofilm architecture can affect the ecology of a species. Vibrio cholerae is a marine bacterium that has been at the forefront of understanding biofilm architecture at the single cell level. Here, we use confocal microscopy and microfluidics to understand the impacts that biofilm architecture have on V. cholerae’s ability to exist in a wealth of environments. We examine its capacity for intra-strain competition, predation protection, and multispecies community assembly through the lens of biofilm architecture. This thesis establishes how the architecture of a biofilm is a critical component when understanding the ecology of a microbe and should be considered along with more conventional traits

Dielectric barrier discharges : a promising tool for the fabrication of anti-fogging coatings

La « vue floue » typique des surfaces embuées peut être extrêmement frustrante. Des exemples tels que les lunettes qui s’embuent pendant l’activité physique, la condensation qui se forme à l’intérieur des fenêtres pendant l’hiver ou les miroirs qui se couvrent de buée pendant la douche le démontrent. En outre, la présence de buée sur les surfaces cause des effets néfastes dans certains secteurs d’activité comme l’industrie automobile (pare-brise et rétroviseurs), l’industrie optique (objectifs, caméras, télescopes et capteurs), l’industrie solaire (modules photovoltaïques), l’industrie alimentaire (emballages d’aliments) et le secteur médical (lunettes et endoscopes). Au cours de la dernière décennie, l’application de revêtements (super)hydrophiles a suscité un intérêt croissant, en raison de leur capacité d’atténuer les effets de la buée. Leur principe de fonctionnement repose sur l’utilisation de matériaux interagissant avec les gouttes d’eau pour en modifier leur morphologie, générant une couche mince d’eau sur la surface. Ainsi, la lumière incidente n’est pas dispersée et les effets de la buée sont amoindris. Jusqu’à présent, la plupart des techniques de dépôt explorées pour produire des revêtements (super) hydrophiles sont inaccessibles à la production de masse en raison de leur nature multiétape. Pour cette raison, l’exploration de techniques adaptées à ce type de production, telles que les décharges à barrière diélectrique à pression atmosphérique (AP-DBD), un type de procédé de dépôt chimique en phase vapeur assisté par plasma (AP-PECVD), est cruciale afin d’élargir l’utilisation des revêtements antibuée au-delà du laboratoire. Dans un procédé AP-PECVD contrôlé par des barrières diélectriques (AP-DBD), certains précurseurs inorganiques ou organométalliques (e.g., TiCl4, TiN, SiH4, Si2O(CH3)2) sont introduits entre deux électrodes parallèles avec un gaz vecteur (e.g., N2, Ar, He) à la pression atmosphérique, où ils se fragmentent à la suite d’interactions avec les espèces du plasma. Les fragments résultants réagissent les uns avec les autres ou avec le substrat afin de produire les espèces réactives requises au dépôt du revêtement. Les caractéristiques structurelles et fonctionnelles des revêtements PECVD (e.g., la rugosité de surface, la biocompatibilité, les propriétés optiques et de mouillage) dépendent des certains paramètres de dépôt, tels que la puissance dissipée dans la décharge, le type de décharge, la concentration de précurseurs et le débit de gaz. La possibilité de se procurer des échantillons de verre dotés de la propriété antibuée via APPECVD a été démontrée dans cette thèse. En contrôlant les paramètres de dépôt, les revêtements antibuée ont été préparés en utilisant du 1,3,5,7-tétraméthylcyclotétrasiloxane (Si4O4H4(CH3)4) et de l’oxyde nitreux (N2O) au moyen d’une DBD fonctionnant en N2 à la pression atmosphérique. Dans le cas des revêtements fabriqués dans des conditions statiques (aucun mouvement entre l’échantillon de verre et les électrodes), l’évaluation quantitative de la résistance à la buée (ASTM F 659-06) a révélé que les revêtements obtenus avec un rapport [N2O]/[TMCTS] ³ 30 ou avec une puissance dissipée ³ 0,25 W cm-2 sont antibuée (transmittance > 80%) en raison de leur nature hydrophile. La quantité de précurseur et d’oxydant injectée dans la décharge, exprimée par la somme « [N2O] + [TMCTS] », n’agissait que peu sur la performance antibuée. En l’absence de changements significatifs dans la rugosité de surface (Rrms et Ra étant compris entre 3 et 6 nm), l’origine de la performance antibuée a été attribuée à la chimie de surface. Couplé aux rapports O/Si (résultats XPS), un paramètre arbitraire, appelé « rapport d’embuage » a été défini en considérant les résultats FTIR pour expliquer les performances antibuée observées. On a pu constater qu’un rapport O/Si ≥ 2,3 couplé à un rapport d’embuage dans l’intervalle de 0-0,10, résultant de la présence de fonctionnalités hydrophiles, telles que les groupes silanol, hydroxyle, carboxyle or ester à la surface étaient nécessaires pour atteindre la propriété antibuée. Par ailleurs, les revêtements préparés dans des conditions dynamiques utilisant trois autres précurseurs aux structures différentes quant à la présence d’un cycle et au nombre de groupes Si-H et Si-CH3 (l’octaméthylcyclotétrasiloxane, le 1,1,3,3-tétraméthyldisiloxane et l’hexaméthyldisiloxane) n’étaient pas antibuée. Ce résultat porte à croire que la structure cyclique du TMCTS et la forte réactivité des liaisons Si-H est à l’origine de la formation de ces fonctionnalités hydrophiles et par conséquent, à la performance antibuée observée dans les verres traités en injectant du TMCTS dans la décharge plasma.Experience shows that the “blurred view” typical of fogged surfaces can be incredibly frustrating. Eyewear fogging up during physical activity, condensation forming on the inside of windows during the winter, or bathroom mirrors steaming up when taking a shower are some obvious examples. In addition to being upsetting, the fogging of surfaces has been reported to cause adverse effects on sectors of activity as diverse as the automotive industry (e.g., windshield glass and rearview mirrors), the optical industry (e.g., lenses, cameras, telescopes, and sensors), the solar industry (e.g., photovoltaic modules), the food industry (e.g., food packaging), and medicine (e.g., goggles and endoscopes). Over the last decade, interest has been growing in the application of hydrophilic and superhydrophilic coatings, as they can efficiently mitigate the effects of fogging by changing the morphology of fog drops. The working principle of a (super)hydrophilic surface is based on the use of materials producing a thin film of water on the solid surface on interaction with fog drops. As a result, incident light transmits without being scattered and the effects of fogging are minimized. Unfortunately, most of the deposition techniques used thus far for the fabrication of (super)hydrophilic coatings involves multiple steps, thus making their integration into mass production a challenging task. For this reason, the exploration of deposition techniques adapted for large-scale production is crucial to broaden the range of application of antifogging coatings beyond the laboratory. In this regard, numerous studies on the use of dielectric barriers in plasma enhanced chemical vapor deposition at atmospheric pressure (AP-PECVD) are strongly emerging to address this issue. In a typical AP-PECVD controlled by dielectric barriers, inorganic or organometallic precursors (e.g., TiCl4, TiN, SiH4, Si2O(CH3)2) are introduced between two parallel electrodes along with a carrier gas (e.g., N2, Ar, He) at atmospheric pressure where, on interaction with plasma species, undergo fragmentation. The resulting fragments can react with the substrate or with each other to produce short-lived species required for coating deposition. The structural and functional features of PECVD coatings (e.g., surface roughness, biocompatibility, wetting and optical properties) depend on several deposition parameters, including the power dissipated in the discharge, type of plasma discharge, precursor concentration, and the flow rate of gases. With this in mind, the feasibility of conferring fogging resistance to commercial glass samples via AP-PECVD has been demonstrated in this doctoral thesis. By appropriately controlling the deposition parameters, anti-fogging coatings were prepared using 1,3,5,7- tetramethylcyclotetrasiloxane (Si4O4H4(CH3)4) and nitrous oxide (N2O) by a dielectric barrier discharge operated in N2 at atmospheric pressure (AP-DBD). When coating deposition was conducted in static conditions, that is, with no relative movement between the glass sample and the electrodes, quantitative assessment of the fogging resistance (ASTM F 659-06 standard) revealed that coatings obtained under [N2O]/[TMCTS] ratios ³ 30 or under a dissipated power ³ 0.25 W cm-2 endowed glass samples with the anti-fogging property (transmittance > 80%), because of their hydrophilic nature. In terms of the [N2O] + [TMCTS] sum, the amount of TMCTS and N2O injected into the discharge did not appear to have a great impact on the anti-fogging performance. Indeed, as no significant changes in surface roughness were observed (Rrms and Ra were between 3 and 6 nm), the origin of the anti-fogging performance was attributed to the surface chemistry. To this end, an arbitrary parameter, called “fogging ratio”, was defined considering FTIR results to account for, along with O/Si ratios (XPS results), the observed anti-fogging performance. Fogging ratios in the 0-0.10 range coupled with O/Si ratios ³ 2.3, resulting from the presence of hydrophilic functionalities, such as silanol (Si-OH), hydroxyl (C-OH) carboxyl (COOH), and ester (COOR) groups at the coating surface were necessary to attain the anti-fogging property. Interestingly, coatings prepared in dynamic conditions using three other precursors with different structures and different number of Si-H and Si-CH3 groups; namely, octamethylcyclotetrasiloxane (OMCTS), 1,1,3,3-tetramethyldisiloxane (TMDSO), and hexamethyldisiloxane (HMDSO) were not fogging-resistant. This result leads us to believe that the cyclic structure of TMCTS in conjunction with the high reactivity of Si-H bonds is behind the formation of the above-mentioned hydrophilic functionalities, and thus the antifogging performance of TMCTS-coated glasses