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The goal of this study is to develop a computational model of the progression of changes in mitochondrial phenotype resulting from infection with pathogenic mycobacteria. This ultimately will enable a large-scale virulence screen of mutant…

Subcellular Processes · Quantitative Biology 2024-11-12 Shannon Quinn , Amr Abbadi , Seyed Alireza Vaezi , Russell K. Karls , Frederick D. Quinn

The magnetite/water interface is commonly found in nature and plays a crucial role in various technological applications. However, our understanding of its structural and dynamical properties at the molecular scale remains still limited. In…

Phototaxis is a light driven self-locomotion of mass and a common phenomenon in motile organisms with varieties of motility such as in bacteria, algae, etc. In naturally occurring organisms, mechanical force is generated utilising their…

Soft Condensed Matter · Physics 2023-08-11 Somnath Koley , Karuna Kar Nanda

Anaerobic processes (e.g., methanogenesis and fermentation) largely contribute to element cycling and natural contaminant attenuation/mobilization, even in well-oxygenated porous environments, such as shallow aquifers. This paradox is…

Biological Physics · Physics 2022-11-24 Giulia Ceriotti , Sergey M. Borisov , Jasmine Berg , Pietro de Anna

Bayesian methods are critical for quantifying the behaviors of systems. They capture our uncertainty about a system's behavior using probability distributions and update this understanding as new information becomes available. Probabilistic…

Computation · Statistics 2018-04-25 Thomas A. Catanach , James L. Beck

The marine environment is one of the most important sources for microbial biodiversity on the planet. These microbes are drivers for many biogeochemical processes, and their enormous genetic potential is still not fully explored or…

Distributed, Parallel, and Cluster Computing · Computer Science 2016-04-15 Espen Mikal Robertsen , Tim Kahlke , Inge Alexander Raknes , Edvard Pedersen , Erik Kjærner Semb , Martin Ernstsen , Lars Ailo Bongo , Nils Peder Willassen

Bacterial heterogeneity is pivotal for adaptation to diverse environments, posing significant challenges in microbial diagnostics and therapeutic interventions. Recent advancements in high-resolution optical microscopy have revolutionized…

Biological Physics · Physics 2025-01-06 Dohyeon Lee , Hyun-Seung Lee , Moosung Lee , Minhee Kang , Geon Kim , Tae Yeul Kim , Nam Yong Lee , YongKeun Park

The non-invasive spatiotemporal control of cellular functions, organization of tissues, and even the behavior of small animals has become paramount for advanced therapies. As magnetic fields do not interact with biological matter, their…

Biological Physics · Physics 2024-01-23 Peter Blümler , Fabian Raudzus , Friederike Schmid

Understanding flow and transport of bacteria in porous media is crucial to technologies such as bioremediation, biomineralization or enhanced oil recovery. While physicochemical bacteria filtration is well-documented, recent studies showed…

Soft Condensed Matter · Physics 2022-08-24 Marco Dentz , Adama Creppy , Carine Douarche , Eric Clément , Harold Auradou

A variety of bacterial species spontaneously assemble in aerotactic band, local accumulation at a fixed distance from the air-water interface. Although the phenomenon is long known, its modelling is so far limited to mesoscopic,…

Soft Condensed Matter · Physics 2025-07-23 F. Detcheverry

Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Among these mechanisms, interspecies recognition…

Populations and Evolution · Quantitative Biology 2025-12-01 Mattia Mattei , David Soriano Paños , Mahantesh Halappanavar , Alex Arenas

Organics, if they do exist on Europa, may only be present in trace amounts on the surface. NASA's upcoming mission Europa Clipper is going to provide global, high quality data of the surface of Europa in the near-infrared (NIR),…

Earth and Planetary Astrophysics · Physics 2025-06-03 Ishan Mishra , Nikole Lewis , Jonathan Lunine , Kevin P. Hand

Highly concentrated active agents tend to exhibit turbulent flows, reminiscent of classical hydrodynamic turbulence, which has attracted considerable attention lately. Controlling the so-called active turbulence has long been a challenge,…

Soft Condensed Matter · Physics 2023-07-13 Kazusa Beppu , Jaakko V. I. Timonen

Centrifugation is a widespread laboratory technique used to separate mixtures into fractions characterized by a specific size, weight or density. We demonstrate that centrifugation can be also used to separate swimming cells having…

Soft Condensed Matter · Physics 2014-11-07 Claudio Maggi , Alessia Lepore , Jacopo Solari , Alessandro Rizzo , Roberto Di Leonardo

Background: In the metagenome assembly of a microbiome community, we may think abundant species would be easier to assemble due to their deeper coverage. However, this conjucture is rarely tested. We often do not know how many abundant…

Genomics · Quantitative Biology 2022-11-23 Xiaowen Feng , Heng Li

The rapid advancement of environmental sequencing technologies, such as metagenomics, has significantly enhanced our ability to study microbial communities. The eubiotic composition of these communities is crucial for maintaining ecological…

Disordered Systems and Neural Networks · Physics 2025-08-27 Jacopo Pasqualini , Amos Maritan , Andrea Rinaldo , Sonia Facchin , Edoardo Savarino , Ada Altieri , Samir Suweis

Living systems continuously sense, integrate, and act on chemical information using multiscale biochemical networks whose dynamics are inherently nonlinear, adaptive, and energy-efficient. Yet, most attempts to harness such "wetware" for…

Emerging Technologies · Computer Science 2026-02-03 Ceylin Savas , Maryam Javed , Murat Kuscu

Magnetic particle imaging (MPI) is a non-invasive, non-ionizing imaging technique for the visualization and quantification of magnetic nanoparticles (MNPs). The technique is especially suitable for cell imaging as it offers zero background…

The ocean is filled with phytoplankton that contribute as much photosynthesis as all land plants combined, making them vital to the carbon cycle and climate system. Recent advances in flow cytometry allow oceanographers to measure the…

Methodology · Statistics 2026-03-09 Yik Lun Kei , Qi Wang , Paul Parker , Francois Ribalet , Sangwon Hyun

Increasing interest in the acquisition of biotic and abiotic resources from within the deep sea (e.g. fisheries, oil-gas extraction, and mining) urgently imposes the development of novel monitoring technologies, beyond the traditional…

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