Yielding behaviour of chemically treated <em>Pseudomonas fluorescens</em> biofilms

\ua9 2024 The Authors. The mechanics of biofilms are intrinsically shaped by their physicochemical environment. By understanding the influence of the extracellular matrix composition, pH and elevated levels of cationic species on the biofilm rheology, novel living materials with tuned properties can be formulated. In this study, we examine the role of a chaotropic agent (urea), two divalent cations and distilled deionized water on the nonlinear viscoelasticity of a model biofilm Pseudomonas fluorescens. The structural breakdown of each biofilm is quantified using tools of non-linear rheology. Our findings reveal that urea induced a softening response, and displayed strain overshoots comparable to distilled deionized water, without altering the microstructural packing fraction and macroscale morphology. The absorption of divalent ferrous and calcium cations into the biofilm matrix resulted in stiffening and a reduction in normalized elastic energy dissipation, accompanied by macroscale morphological wrinkling and moderate increases in the packing fraction. Notably, ferrous ions induced a predominance of rate dependent yielding, whereas the calcium ions resulted in equal contribution from both rate and strain dependent yielding and structural breakdown of the biofilms. Together, these results indicate that strain rate increasingly becomes an important factor controlling biofilm fluidity with cation-induced biofilm stiffening. The finding can help inform effective biofilm removal protocols and in development of bio-inks for additive manufacturing of biofilm derived materials

Precision Tuning of Silicon Nanophotonic Devices through Post-Fabrication Processes

This thesis investigates ways of improving the performance of fundamental silicon nanophotonic devices through post-fabrication processes. These devices include numerous optical resonator designs as well as slow-light waveguides. Optical resonators are used to confine photons both spatially and temporally. In recent years, there has been much research, both theoretical and experimental, into improving the design of optical resonators. Improving these devices through fabrication processes has generally been less studied. Optical waveguides are used to guide the flow of photons over chip-level distances. Slow-light waveguides have also been studied by many research groups in recent years and can applied to an increasingly wide-range of applications. The work can be divided into several parts: Chapter 1 is an introduction to the field of silicon photonics as well as an overview of the fabrication, experimental and computational techniques used throughout this work. Chapters 2, 3 and 4 describe our investigations into the precision tuning of nanophotonic devices using laser-assisted oxidation and atomic layer deposition. Chapters 5 and 6 describe our investigations into improving the sidewall roughness of silicon photonic devices using hydrogen annealing and excimer laser induced melting. Finally, Chapter 7 describes our investigations into the nonlinear properties of lead chalcogenide nanocrystals

Temperature-tuning of near-infrared monodisperse quantum dot solids at 1.5 um for controllable Forster energy transfer

We present the first time-resolved cryogenic observations of Forster energy transfer in large, monodisperse lead sulphide quantum dots with ground state transitions near 1.5 um (0.83 eV), in environments from 160 K to room temperature. The observed temperature-dependent dipole-dipole transfer rate occurs in the range of (30-50 ns)^(-1), measured with our confocal single-photon counting setup at 1.5 um wavelengths. By temperature-tuning the dots, 94% efficiency of resonant energy transfer can be achieved for donor dots. The resonant transfer rates match well with proposed theoretical models

Digital resonance tuning of high-Q/Vm silicon photonic crystal nanocavities by atomic layer deposition

We propose and demonstrate the digital resonance tuning of high-Q/Vm silicon photonic crystal nanocavities using a self-limiting atomic layer deposition technique. Control of resonances in discrete steps of 122 +/- 18 pm per hafnium oxide atomic layer is achieved through this post-fabrication process, nearly linear over a full 17 nm tuning range. The cavity Q is maintained in this perturbative process, and can reach up to its initial values of 49,000 or more. Our results are highly controllable, applicable to many material systems, and particularly critical to matching resonances and transitions involving mesoscopic optical cavities.Comment: 9 pages, 3 figure

The z = 0.0777 C III Absorber Towards PHL 1811 as a Case Study of a Low Redshift Weak Metal Line Absorber

We consider the physical conditions and origin of the z = 0.0777 absorption system observed in C III, C II, Si III, C IV, O VI, and H I absorption along the line of sight towards the quasar PHL 1811. We analysed the HST/STIS and FUSE spectra of this quasar and compared the results to Cloudy photoionization and collisional ionization models in order to derive densities, temperatures, and metallicities of the absorbing gas. The absorption can be explained by two C III clouds, offset by 35 km/s in velocity, with metallicities of ~one-tenth the solar value. One cloud has a density of order n_H = 1.2 +0.9 -0.5 * 10^-3 cm^-3 (thickness 0.4 +0.3 -0.2 kpc) and produces the observed C II and Si III absorption, while the other has a density of order n_H = 1.2 +0.9 -0.5 * 10^-5 cm^-3 (thickness 80 +70 -40 kpc) and gives rise to the observed weak C IV absorption. Cloud temperatures are ~14,000 +3000 -2000 K and ~34,000 -4000 +2000 K for photoionized models. Although collisionally ionized clouds with T ~ 70,000 K are possible, they are less likely because of the short cooling time-scales involved. Previous studies revealed no luminous galaxy at the absorber's redshift, so it is probably related to tidal debris, ejected material, a dwarf galaxy, or other halo material in a galaxy group. Our models also indicate that one of the two clouds would produce detectable weak Mg II absorption if spectral coverage of that transition existed. We predict what the system would look like at z ~ 1 when the ionizing background radiation was more intense. We find that at z ~ 1 the denser component resembles a C IV absorber. The second C III cloud in this z = 0.0777 absorber may be analogous to a subset of the more diffuse O VI absorbers at higher redshift.Comment: 15 pages, 6 figures, accepted by MNRA

Nonlinear rheological characteristics of single species bacterial biofilms

Bacterial biofilms in natural and artificial environments perform a wide array of beneficial or detrimental functions and exhibit resistance to physical as well as chemical perturbations. In dynamic environments, where periodic or aperiodic flows over surfaces are involved, biofilms can be subjected to large shear forces. The ability to withstand these forces, which is often attributed to the resilience of the extracellular matrix. This attribute of the extracellular matrix is referred to as viscoelasticity and is a result of self-assembly and cross-linking of multiple polymeric components that are secreted by the microbes. We aim to understand the viscoelastic characteristic of biofilms subjected to large shear forces by performing Large Amplitude Oscillatory Shear (LAOS) experiments on four species of bacterial biofilms: Bacillus subtilis, Comamonas denitrificans, Pseudomonas fluorescens and Pseudomonas aeruginosa. We find that nonlinear viscoelastic measures such as intracycle strain stiffening and intracycle shear thickening for each of the tested species, exhibit subtle or distinct differences in the plot of strain amplitude versus frequency (Pipkin diagram). The biofilms also exhibit variability in the onset of nonlinear behaviour and energy dissipation characteristics, which could be a result of heterogeneity of the extracellular matrix constituents of the different biofilms. The results provide insight into the nonlinear rheological behaviour of biofilms as they are subjected to large strains or strain rates; a situation that is commonly encountered in nature, but rarely investigated

Optical magnetic response in all-dielectric metamaterial

We experimentally demonstrate a new mechanism to achieve magnetic resonances at visible and near-infrared frequencies in purely dielectric metamaterials, realized through a coupling between pairs of closely spaced, dissimilar dielectric rods

A Hubble Space Telescope Study of Lyman Limit Systems: Census and Evolution

We present a survey for optically thick Lyman limit absorbers at z<2.6 using archival Hubble Space Telescope observations with the Faint Object Spectrograph and Space Telescope Imaging Spectrograph. We identify 206 Lyman limit systems (LLSs) increasing the number of catalogued LLSs at z<2.6 by a factor of ~10. We compile a statistical sample of 50 tau_LLS > 2 LLSs drawn from 249 QSO sight lines that avoid known targeting biases. The incidence of such LLSs per unit redshift, l(z)=dn/dz, at these redshifts is well described by a single power law, l(z) = C1 (1+z)^gamma, with gamma=1.33 +/- 0.61 at z<2.6, or with gamma=1.83 +/- 0.21 over the redshift range 0.2 < z < 4.9. The incidence of LLSs per absorption distance, l(X), decreases by a factor of ~1.5 over the ~0.6 Gyr from z=4.9 to 3.5; l(X) evolves much more slowly at low redshifts, decreasing by a similar factor over the ~8 Gyr from z=2.6 to 0.25. We show that the column density distribution function, f(N(HI)), at low redshift is not well fitted by a single power law index (f(N(HI)) = C2 N(HI)^(-beta)) over the column density range 13 17.2. While low and high redshift f(N(HI)) distributions are consistent for log N(HI)>19.0, there is some evidence that f(N(HI)) evolves with z for log N(HI) < 17.7, possibly due to the evolution of the UV background and galactic feedback. Assuming LLSs are associated with individual galaxies, we show that the physical cross section of the optically thick envelopes of galaxies decreased by a factor of ~9 from z~5 to 2 and has remained relatively constant since that time. We argue that a significant fraction of the observed population of LLSs arises in the circumgalactic gas of sub-L* galaxies.Comment: Accepted by Ap

Regulating, Measuring, and Modeling the Viscoelasticity of Bacterial Biofilms

Biofilms occur in a broad range of environments under heterogeneous physicochemical conditions, such as in bioremediation plants, on surfaces of biomedical implants, and in the lungs of cystic fibrosis patients. In these scenarios, biofilms are subjected to shear forces, but the mechanical integrity of these aggregates often prevents their disruption or dispersal. Biofilms' physical robustness is the result of the multiple biopolymers secreted by constituent microbial cells which are also responsible for numerous biological functions. A better understanding of the role of these biopolymers and their response to dynamic forces is therefore crucial for understanding the interplay between biofilm structure and function. In this paper, we review experimental techniques in rheology, which help quantify the viscoelasticity of biofilms, and modeling approaches from soft matter physics that can assist our understanding of the rheological properties. We describe how these methods could be combined with synthetic biology approaches to control and investigate the effects of secreted polymers on the physical properties of biofilms. We argue that without an integrated approach of the three disciplines, the links between genetics, composition, and interaction of matrix biopolymers and the viscoelastic properties of biofilms will be much harder to uncover

Deterministic tuning of slow-light in photonic-crystal waveguides through the C and L bands by atomic layer deposition

We demonstrate digital tuning of the slow-light regime in silicon photonic-crystal waveguides by performing atomic layer deposition of hafnium oxide. The high group-index regime was deterministically controlled (red-shift of 140 +/- 10 pm per atomic layer) without affecting the group-velocity dispersion and third-order dispersion. Additionally, differential tuning of 110 +/- 30 pm per monolayer of the slow-light TE-like and TM-like modes was observed. This passive post-fabrication process has potential applications including the tuning of chip-scale optical interconnects, as well as Raman and parametric amplification.Comment: 14 pages, 5 figure