Article
Astronomy & Astrophysics
Saee Dhawalikar, Christoph Federrath, Seth Davidovits, Romain Teyssier, Sabrina R. Nagel, Bruce A. Remington, David C. Collins
Summary: In this study, hydrodynamical simulations are used to investigate shock-induced turbulence, and the turbulence driving parameter is measured by analyzing the density and velocity distributions. The results show that shock-driven turbulence is consistent with strongly compressive driving.
MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY
(2022)
Article
Mechanics
S. Subbotin, N. Shmakova, V. Kozlov, E. Ermanyuk
Summary: This study experimentally investigates the fluid flow excited by inertial waves in a rotating annulus with a trapezoidal cross section. The experiment examines the interactions between inertial waves and zonal flows in the presence of the equivalent topographic beta-effect, and the dynamic behavior of the system under weak and strong forcing. The results show the generation of a zonal flow near a virtual axial cylinder at low wave intensity and the progression of non-linear regimes as forcing increases, leading to the emergence of additional discrete components and the development of a strong low-frequency component corresponding to Rossby waves.
Article
Physics, Multidisciplinary
Chaitanya Joshi, Sattvic Ray, Linnea M. Lemma, Minu Varghese, Graham Sharp, Zvonimir Dogic, Aparna Baskaran, Michael F. Hagan
Summary: This study identifies optimal continuum models for active nematics directly from experimental data using sparse regression method, and achieves important findings in microtubule-based active nematics experiments.
PHYSICAL REVIEW LETTERS
(2022)
Article
Mechanics
Snezhana I. Abarzhi
Summary: The study revealed that the dynamics of RT mixing can vary from superballistics to sub-diffusion depending on the acceleration, while still retaining memory of initial conditions. These findings have significant implications for understanding and controlling Rayleigh-Taylor relevant processes in fluids, plasmas, and materials.
Article
Mechanics
A. Chauhan, S. Gupta, C. Sasmal
Summary: This study presents a numerical investigation of viscoelastic fluid flows in porous media. It is found that geometric disorder increases chaotic fluctuations in the flow, which is attributed to the formation of preferential paths and highly curved streamlines. The chaotic flow behavior is strongly influenced by the competition between strain-hardening and shear-thinning behaviors of the viscoelastic fluid.
Article
Astronomy & Astrophysics
G. Bodo, G. Mamatsashvili, P. Rossi, A. Mignone
Summary: We analyze the evolution of current-driven kink instabilities in a highly magnetized relativistic plasma column and focus on its dissipation properties. The formation of thin current sheets where magnetic energy is dissipated occurs during the instability evolution. The dissipation occurs in two stages, with a peak stage characterized by the formation of a helicoidal current sheet and a weaker stage with turbulence development. The results have implications for high energy astrophysical sources.
MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY
(2022)
Article
Mechanics
A. F. Bonfils, Dhrubaditya Mitra, W. Moon, J. S. Wettlaufer
Summary: Motivated by wind blowing over water, this study uses asymptotic methods to investigate the evolution of short wavelength interfacial waves driven by the combined action of these flows. By solving the stability equation and constructing a valid approximation for the perturbed streamfunction, the real and imaginary parts of the eigenvalue are expanded and expressions for the growth rates of instabilities are obtained. The accuracy of the results is verified through a comparison with the exact solution.
JOURNAL OF FLUID MECHANICS
(2023)
Article
Astronomy & Astrophysics
Andrew Hillier, Ben Snow, Inigo Arregui
Summary: In many astrophysical systems, the mixing between cool and hot temperature gas/plasma creates an intermediate temperature phase with increased radiative losses, driving efficient cooling. This paper derives equations to model the evolution of this mixing layer, and predicts the cooling rate and the rate of condensation of coronal material due to mixing. These predictions are compared to simulations and applied to prominence threads and spicules, showing that the mixing process can explain the warm emission observed without the need for additional heating.
MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY
(2023)
Article
Mechanics
M. Tsoy, S. Skripkin, I. Litvinov
Summary: Two different scenarios of spiral vortex breakdown are experimentally observed and numerically investigated in a swirl flow into a conical diffuser. The primary spiral vortex breakdown occurs near the inlet of the conical diffuser when the cone angle beta is greater than 3 degrees. The secondary spiral vortex breakdown occurs at the exit of the cone when beta is less than or equal to 3 degrees. Additionally, the coexistence of two spiral vortices is observed, and their reasons are visualized and explained for the first time.
Article
Biochemical Research Methods
Shankarachary Ragi, Md Hafizur Rahman, Jamison Duckworth, Kalimuthu Jawaharraj, Parvathi Chundi, Venkataramana Gadhamshetty
Summary: The current study aims to use an artificial intelligence framework to measure the structural features of bacterial biofilms in microscopy images. The goal is to automate the extraction of geometrical properties of the cells, which can help understand how the biofilms adapt to the surface properties of the underlying metals and improve corrosion prevention solutions. Deep learning models are adapted to achieve semantic and instance segmentation of the cells, and these models are integrated with moment invariants approach to measure the geometric characteristics.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Eleonora Secchi, Giovanni Savorana, Alessandra Vitale, Leo Eberl, Roman Stocker, Roberto Rusconi
Summary: It has been found that the mechanical stability of Pseudomonas aeruginosa streamers mainly relies on the presence of extracellular DNA (eDNA) and the exopolysaccharide Pel. Controlling the composition of streamers can effectively control the formation of biofilm structures.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Astronomy & Astrophysics
Philip F. Hopkins, Anna L. Rosen, Jonathan Squire, Georgia Panopoulou, Nadine H. Soliman, Darryl Seligman, Ulrich P. Steinwandel
Summary: This study presents the first simulations of radiation-dust driven outflows in stratified, inhomogeneous media. The results show that dust plays a crucial role in the gas dynamics, leading to size-dependent dust clustering and unique nebular morphologies.
MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY
(2022)
Article
Mechanics
Yan Xia, Zhaosheng Yu, Zhaowu Lin, Yu Guo
Summary: This study establishes correlations between the interfacial terms and the fluid dissipation rate equation and Reynolds stress equations in particle-laden flows, providing an accurate mathematical model and method for simulating particle-induced turbulence.
JOURNAL OF FLUID MECHANICS
(2022)
Review
Engineering, Environmental
Ana C. Afonso, Ines B. Gomes, Maria Jose Saavedra, Efstathios Giaouris, Lucia C. Simoes, Manuel Simoes
Summary: Bacterial coaggregation is believed to be a key step in the formation of sessile communities in aquatic systems, with bacteria capable of autoaggregation and coaggregation being found in various aquatic systems. The coaggregation mechanism plays an important role in the development and stability of multispecies biofilms, particularly with potential implications for controlling undesirable biofilms in wastewater treatment plants.
Article
Multidisciplinary Sciences
Ge Liu, Bin Chen
Summary: In this study, the pressure signal of oil pulsating flow was decomposed using VMD, with the proposed center frequency slope criterion and energy value method successfully separating the signal into 9 components and identifying the beat vibration characteristics. The main components of the pressure signal were determined based on correlation and energy calculation, showing frequencies at multiples of the system spindle rotation frequency and exhibiting beat vibration properties.
SCIENTIFIC REPORTS
(2021)
Article
Biotechnology & Applied Microbiology
S. -Q. An, R. Hull, A. Metris, P. Barrett, J. S. Webb, P. Stoodley
Summary: Research on the oral microbiota has mainly focused on individual or a few cultivated species, lacking studies on more complex microbiota or multispecies biofilms. The CDC biofilm reactor has been shown to efficiently cultivate microbiota containing all six major phyla previously identified as the core saliva microbiota, making it a useful tool for studying the dynamics of microbial communities in the oral cavity.
LETTERS IN APPLIED MICROBIOLOGY
(2022)
Article
Immunology
Abigail Leggett, Da-Wei Li, Devin Sindeldecker, Amelia Staats, Nicholas Rigel, Lei Bruschweiler-Li, Rafael Brueschweiler, Paul Stoodley
Summary: This study reveals the metabolic differences of P. aeruginosa in different growth states using metabolomics approach. It shows that metabolites of the cadaverine branch of the lysine degradation pathway are significantly decreased in biofilm. Exogenous supplementation of cadaverine can promote planktonic growth, reduce biofilm accumulation, and alter biofilm morphology.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Yuqing Xia, Pahala G. Jayathilake, Bowen Li, Paolo Zuliani, David Deehan, Jennifer Longyear, Paul Stoodley, Jinju Chen
Summary: Understanding the mechanical properties and detachment mechanisms of bacterial biofilms is crucial for determining their stability and removal. The study of biofilm mechanics can provide insights into biofilm survival under shear stress and inform strategies for biofilm removal.
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Article
Orthopedics
Hanna H. Sorensen, Robert A. Magnussen, Alex C. DiBartola, Noah T. Mallory, Alan S. Litsky, Paul Stoodley, Steven D. Swinehart, Robert A. Duerr, Christopher C. Kaeding, David C. Flanigan
Summary: This study aimed to determine the impact of bacterial inoculation and length of exposure on the mechanical integrity of soft tissue tendon grafts. The presence of Staphylococcus epidermidis increased the elasticity and decreased the ultimate tensile strength of human cadaveric tendons, with a more significant effect observed with increasing bioburden.
JOURNAL OF ORTHOPAEDIC RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Mengfei Li, Yanina Nahum, Karel Matous, Paul Stoodley, Robert Nerenberg
Summary: This study investigates the effects of biofilm mechanical heterogeneity on the results obtained by rheometry. Both experiments and simulations show that the biofilm properties determined by rheometry are strongly influenced by the weakest portion of the biofilm. The findings suggest caution should be exercised when interpreting rheometry data, particularly when the mechanical properties are stratified.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Review
Microbiology
Hans-Curt Flemming, Eric D. van Hullebusch, Thomas R. Neu, Per H. Nielsen, Thomas Seviour, Paul Stoodley, Jost Wingender, Stefan Wuertz
Summary: In this review, the authors revisit the understanding of the biofilm matrix and discuss the diversity of its components and the novel aspects of their functional interactions. The biofilm matrix plays a crucial role in stabilizing microbial cells and fulfilling various functions. It is dynamic and influenced by physico-chemical and biological interactions as well as environmental conditions.
NATURE REVIEWS MICROBIOLOGY
(2023)
Article
Immunology
Jacob R. Brooks, Douglas J. Chonko, Matthew Pigott, Anne C. Sullivan, Kelly Moore, Paul Stoodley
Summary: This study aimed to investigate whether certain components and their surface features are more prone to biofilm formation in primary total joint arthroplasty. It was found that biofilm predominantly formed on the non-articulating surfaces between components and on ridges and edges. This has important implications for intraoperative debridement, retention choices, and implant design.
Article
Biotechnology & Applied Microbiology
Erum Razvi, Gregory B. Whitfield, Courtney Reichhardt, Julia E. Dreifus, Alexandra R. Willis, Oxana B. Gluscencova, Erin S. Gloag, Tarek S. Awad, Jacquelyn D. Rich, Daniel Passos da Silva, Whitney Bond, Francois Le Mauff, Donald C. Sheppard, Benjamin D. Hatton, Paul Stoodley, Aaron W. Reinke, Gabrielle L. Boulianne, Daniel J. Wozniak, Joe J. Harrison, Matthew R. Parsek, P. Lynne Howell
Summary: Pel exopolysaccharide biosynthetic loci are widespread biofilm matrix determinants in bacteria. In Pseudomonas aeruginosa, the glycoside hydrolase activity of PelA decreases adherent biofilm biomass and generates the low molecular weight secreted form of the Pel exopolysaccharide. Secreted Pel contributes to the biomechanical properties of the biofilm and decreases the virulence of P. aeruginosa in Caenorhabditis elegans and Drosophila melanogaster.
NPJ BIOFILMS AND MICROBIOMES
(2023)
Article
Microbiology
Erin S. Gloag, Yalda Khosravi, James G. Masters, Daniel J. Wozniak, Carlo Amorin Daep, Paul Stoodley
Summary: Mechanical removal of dental plaque is augmented with therapeutic compounds to promote oral health. A dentifrice containing the ingredients zinc and arginine has shown efficacy at reducing dental plaque both in vitro and in vivo. However, how these active compounds interact together to facilitate dental plaque removal is unclear. Here, we used a combination of biophysical analyses and microscopy to demonstrate that combined treatment with zinc and arginine targets the matrix of dental plaque biofilms, which destabilized the mechanical integrity of these microbial communities, making them more susceptible to removal by shear forces.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Amelia Staats, Peter W. W. Burback, Nadia N. N. Casillas-Ituarte, Daniel Li, Michaela R. R. Hostetler, Anne Sullivan, Alexander R. R. Horswill, Steven K. K. Lower, Paul Stoodley
Summary: The formation of a bacterial biofilm in the postsurgical joint environment significantly complicates the resolution of an infection. This study investigated the mechanisms of Staphylococcus aureus aggregation in synovial fluid and identified clumping factor A as the primary genetic determinant of aggregation. The study also found that the size and antibiotic tolerance of the aggregates formed under different conditions varied.
JOURNAL OF BACTERIOLOGY
(2023)
Article
Chemistry, Physical
Rui Han, Xi-Qiao Feng, Waldemar Vollmer, Paul Stoodley, Jinju Chen
Summary: Bacteria adapt the mechanical properties of their cell envelope, including cell wall stiffness, turgor, and cell wall tension and deformation, to grow and survive in harsh environments. This study quantified the mechanical properties and turgor of Staphylococcus epidermidis using theoretical modelling and experimental approaches. The results showed that high osmolarity leads to a decrease in both cell wall stiffness and turgor, and that the turgor change is associated with a change in bacterial cell viscosity. The study also found that cell wall tension is higher in deionized water and decreases with an increase in osmolality.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Review
Microbiology
Victor Choi, Jennifer L. Rohn, Paul Stoodley, Dario Carugo, Eleanor Stride
Summary: In this Review, emerging drug delivery strategies are discussed as a means to improve the clinical efficacy of antibiofilm agents in preventing and eliminating pathogenic biofilms. The potential benefits of these techniques include improved penetration of antimicrobials through biofilms, enhanced drug dispersal, and synergistic bactericidal effects. However, current limitations and future prospects for these therapies in the clinic are also highlighted.
NATURE REVIEWS MICROBIOLOGY
(2023)
Article
Microbiology
Kelly Moore, Anthony Li, Niraj Gupta, Tripti Thapa Gupta, Craig Delury, Sean S. Aiken, Phillip A. Laycock, Paul Stoodley
Summary: This in-vitro study found that high purity antibiotic-loaded calcium sulfate beads containing vancomycin and tobramycin in combination may be more effective in treating multispecies biofilm orthopedic infections than monotherapy alone.
Article
Chemistry, Physical
Alexandra A. Snowdon, Simon P. Dennington, Jennifer E. Longyear, Julian A. Wharton, Paul Stoodley
Summary: Marine biofilms on ship hulls increase frictional drag, which has economic and environmental consequences. The study aimed to characterise the rheological properties of ship-relevant marine biofilms. The results confirmed that surface treatment influences the structural and mechanical properties of marine biofilms, which could have implications for drag.
Article
Radiology, Nuclear Medicine & Medical Imaging
Monique Doran, Gemma Reemst, Kenny Ng, Courtney Shaw, Paul Stoodley