Article
Physics, Fluids & Plasmas
Cesar Nieto, Cesar Vargas-Garcia, Juan M. Pedraza
Summary: This study presents a theoretical approach based on the Chapman-Kolmogorov equation to discuss the stochastic effects of bacterial division on cell size dynamics, predicting oscillations in the size distribution. The results illustrate the importance of incorporating inherent stochasticity in mathematical descriptions of biological processes.
Article
Engineering, Biomedical
Mandeep Chhajer Jain, Anupama Vijaya Nadaraja, Sevda Mohammadi, Bianca Marjan Vizcaino, Mohammad Hossein Zarifi
Summary: The study presents a real-time and label-free microstrip sensor for detecting and monitoring subsurface growth of Escherichia coli on solid growth media, demonstrating high efficiency in this aspect.
IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS
(2021)
Article
Environmental Sciences
John Greenman, Buddhi Arjuna Mendis, Iwona Gajda, Ioannis A. Ieropoulos
Summary: This review focuses on a novel exploratory model of microbial fuel cells in which thin biofilms form on highly perfusable anodes in small-scale, continuous flow setups. The model exhibits chemostat-like behavior and multiple steady states.
Article
Mechanics
Yuan-Jung Chang, Rong-Yeu Chang, Tim A. Osswald
Summary: Bulk viscosity, which has been ignored in polymer processing for decades, plays an important role in preventing material size changes and reducing mechanical pressure variations during injection molding. A new model was developed to obtain smooth and reliable bulk viscosity results for amorphous Polystyrene melt, which was verified and implemented in an injection molding simulation. The study demonstrated the significance of bulk viscosity in compressible polymer melts undergoing strong compression.
Article
Microbiology
Mark T. Anderson, Aric N. Brown, Ali Pirani, Sara N. Smith, Amanda L. Photenhauer, Yuang Sun, Evan S. Snitkin, Michael A. Bachman, Harry L. T. Mobley
Summary: Bloodstream infections, caused by Gram-negative species, are a significant public health burden due to high mortality rates and treatment costs. A study characterizing infection kinetics and bacterial replication rates of six common pathogens in a murine model revealed different colonization abilities in major organs. While some species replicated rapidly in the liver or kidney, others were steadily cleared from targeted organs during infection, highlighting the complex dynamics of bacterial replication and immune-mediated clearance. Insights from this study may aid in developing strategies to combat bloodstream infections in the future.
Article
Agricultural Engineering
Jianke Huang, Ruirui Chu, Ting Chang, Pengfei Cheng, Jingshun Jiang, Ting Yao, Chengxu Zhou, Tianzhong Liu, Roger Ruan
Summary: The microalgal biofilm-attached-system offers advantages of improved biomass productivity, efficient harvesting, and water saving. A growth model for the biofilm attached culture system has been developed and validated, showing its capability to describe microalgae growth accurately. System structural parameters, light dilution rate, and light intensity significantly affect the culture performance, and this model will be helpful in design, improvement, optimization, and evaluation of biofilm-attached-systems.
BIORESOURCE TECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Yang Xi, Qifan Wu, Yutian Zeng, Jingjing Qi, Junpeng Li, Hua He, Hengyong Xu, Jiwei Hu, Xiping Yan, Lili Bai, Chunchun Han, Shenqiang Hu, Jiwen Wang, Hehe Liu, Liang Li
Summary: This study performed a genome wide association study to identify the genetic basis of growth rate in ducks. They found 41 significant SNPs related to growth rate, with ASAP1 and LYN genes being important candidate genes. The study also showed that growth rate can be used as a reliable predictor of adult weight.
Article
Environmental Sciences
Javiera Collao, Maria del Mar Morales-Amaral, Francisco Gabriel Acien-Fernandez, Silvia Bolado-Rodriguez, Nuria Fernandez-Gonzalez
Summary: The study showed that biomass productivity in photobioreactors increased as water depth decreased, but a decrease in bacterial community evenness may lead to a reduction in nutrient removal. Heterotrophs and phototrophs, mainly from the family Rhodobacteraceae, dominated bacterial diversity, and community changes were driven by various environmental factors and biological interactions.
Article
Biotechnology & Applied Microbiology
M. Luisa Navarro-Perez, M. Coronada Fernandez-Calderon, Virginia Vadillo-Rodriguez
Summary: This paper presents a simple numerical procedure for monitoring the growth of Streptococcus sanguinis. Through the decomposition of growth curves, it provides precise data on key parameters and allows a comprehensive description of growth over time. The procedure has important implications for evaluating antimicrobial agents and predictive microbiology.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Astronomy & Astrophysics
Joseph DeRose, Matthew R. Becker, Risa H. Wechsler
Summary: This study explores the degrees of freedom needed to fit the clustering of galaxies in both projected and redshift-space using a subhalo abundance matching (SHAM) model. By employing emulators for clustering statistics, the analysis gains speed with minimal loss of accuracy. The results show that fitting the clustering of the most massive galaxy samples can be achieved with just two free parameters. The study also models the clustering signals of star formation rate selected samples using conditional abundance matching (CAM) variants. Incorporating nonunity correlations between the CAM proxy and star formation rate helps resolve previously identified discrepancies.
ASTROPHYSICAL JOURNAL
(2022)
Article
Soil Science
Yuqian Tang, Sara Winterfeldt, Albert C. Brangari, Lettice C. Hicks, Johannes Rousk
Summary: Climate change is expected to change precipitation patterns, resulting in longer drought periods and heavier rainfall. We investigated how the history of precipitation influenced microbial resistance and resilience to drought using soils from a natural precipitation gradient. Our results showed that bacterial growth was more resistant and resilient to drought in areas with lower precipitation. The variations in microbial resistance and resilience were linked to the microbial community structure.
SOIL BIOLOGY & BIOCHEMISTRY
(2023)
Article
Thermodynamics
Jonathan M. Bonebrake, Viswanath R. Katta, Timothy M. Ombrello, David L. Blunck
Summary: Ignition of fuel/oxidizer mixtures is essential for advanced combustor operation. The presence of NO can decrease ignition delay times, but its influence on forced ignition is unclear. This study investigates ignition kernels generated by spark discharges in CH4/air flows diluted with NO and N2. It is found that the presence of NO increases the size of ignition kernels compared to mixtures diluted with N2. Numerical modeling reveals that low-temperature chemistry plays a role in this sensitivity. (c) 2023 The Combustion Institute. Published by Elsevier Inc. All rights reserved.
COMBUSTION AND FLAME
(2023)
Article
Biology
Valentina Baldazzi, Delphine Ropers, Jean-Luc Gouze, Tomas Gedeon, Hidde de Jong
Summary: Different strains of a microorganism exhibit variability in growth rates and yields, which can be explained by different resource allocation strategies. A coarse-grained model was developed to test this hypothesis and was validated using a database of E. coli strains grown in standard laboratory conditions. The model accurately predicted the range of growth rates, growth yields, and nutrient uptake and secretion rates, supporting the idea that resource allocation is a major factor in growth variability. The model also suggests that high growth rates can be achieved without sacrificing growth yields.
Article
Agriculture, Dairy & Animal Science
Khama R. Kelman, Clair Alston-Knox, David W. Pethick, Graham E. Gardner
Summary: This study demonstrates that factors such as poor ewe nutrition, birth type, rear type, and sire breed can have a significant impact on lamb growth. It suggests that genetic potential for lamb growth can be moderated by environment, multiple births, and sire type. The study highlights the need for lamb producers to have realistic expectations of lamb growth and consider mitigation strategies such as precision feeding or alternate breeds.
Article
Ecology
Thomas P. Smith, Tom Clegg, Thomas Bell, Samrat Pawar
Summary: Microbial CUE varies in response to temperature in a taxonomically structured manner, with population growth rates of bacteria typically responding more strongly to temperature than respiration rates. This insight provides a basis for accurately modeling the effects of thermal fluctuations on complex microbial communities.
Meeting Abstract
Biophysics
Valentino Lepro, Oliver Nagel, Stefan Klumpp, Reinhard Lipowsky, Carsten Beta
BIOPHYSICAL JOURNAL
(2019)
Review
Physics, Multidisciplinary
Stefan Klumpp, William Bode, Palka Puri
EUROPEAN PHYSICAL JOURNAL-SPECIAL TOPICS
(2019)
Article
Biology
Klaas Bente, Sarah Mohammadinejad, Mohammad Avalin Charsooghi, Felix Bachmann, Agnese Codutti, Christopher T. Lefevre, Stefan Klumpp, Damien Faivre
Article
Physics, Applied
Felix Bachmann, Joshua Giltinan, Agnese Codutti, Stefan Klumpp, Metin Sitti, Damien Faivre
Summary: Microswimmers are smart devices with potential applications in medicine and biotechnology at the micrometer-scale. Magnetic micropropellers are particularly promising due to their remote control capabilities via rotating magnetic fields. However, deviations in shape and swimming behavior have led to the emergence of propellers with nonlinear velocity-frequency relationships, posing different challenges and offering advanced possibilities. The most critical nonlinearities include wobbling behavior with its solution branching and swimming characteristics in the step-out regime, both essential for selection and swarm control.
APPLIED PHYSICS LETTERS
(2021)
Article
Multidisciplinary Sciences
Anna Schepers, Charlotta Lorenz, Peter Nietmann, Andreas Janshoff, Stefan Klumpp, Sarah Koster
Summary: The mechanical properties of cells are largely determined by the cytoskeleton, with the intermediate filament network being the most extensible and stress-resilient. A multiscale approach is used to analyze the contributions of single-filament mechanics, filament length, and interactions between filaments to vimentin IF network mechanics. Hydrophobic contributions primarily affect filament elongation kinetics, while electrostatics influence filament-filament interactions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Laura Schaedel, Charlotta Lorenz, Anna V. Schepers, Stefan Klumpp, Sarah Koester
Summary: The study demonstrates that vimentin intermediate filaments stabilize microtubules against depolymerization and support microtubule rescue through direct interactions in a reconstituted in vitro system. By measuring interaction forces and numerical simulations, insights into the physical nature of these interactions and their effects on microtubule dynamics are provided.
NATURE COMMUNICATIONS
(2021)
Article
Physics, Multidisciplinary
Gabriel Knotz, Ulrich Parlitz, Stefan Klumpp
Summary: The cell cycle has a significant impact on the dynamics of oscillatory gene circuits, leading to quasiperiodic motion and the formation of synchronization windows. The size of these windows is influenced by the timing of gene doubling and the location of the genes.
NEW JOURNAL OF PHYSICS
(2022)
Article
Biology
Agnese Codutti, Mohammad A. Charsooghi, Elisa Cerda-Donate, Hubert M. Taieb, Tom Robinson, Damien Faivre, Stefan Klumpp, Raymond E. Goldstein
Summary: In this study, magnetically steerable microswimmers, specifically magnetotactic bacteria, were trapped in micrometer-sized microfluidic chambers and their motion was tracked and analyzed. The researchers observed a variety of different trajectories, depending on the chamber size and the strength of the magnetic field. Combining experimental observations with simulations, they explained the diversity of trajectories by the interplay between wall interactions and the magnetic torque. The study also highlighted the importance of single-cell tracking for understanding motility patterns and established a basis for analyzing and predicting microswimmer motility in more complex environments.
Article
Chemistry, Physical
Omar Munoz, Stefan Klumpp
Summary: This study proposes a model that extends the tug-of-war model by incorporating a mechanism of motor activation and inactivation. The model successfully explains some observations that are inconsistent with a simple tug-of-war scenario, including long unidirectional runs and a directional memory after unbinding from the filament.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Editorial Material
Biophysics
Stefan Klumpp
BIOPHYSICAL JOURNAL
(2023)
Article
Physics, Fluids & Plasmas
M. Sahoo, N. Arsha, P. R. Baral, S. Klumpp
Summary: DNA polymerase, a dual purpose enzyme, is responsible for elongating newly formed DNA strands and cleaving erroneous growth. Replication efficiency relies on the coordination between polymerization and exonuclease activities. The accuracy and speed of replication are influenced by the kinetic parameters of the model and the crucial role of stepping after erroneous incorporation.
Article
Physics, Fluids & Plasmas
Pintu Patra, Stefan Klumpp
Summary: Bacterial persistence through stochastic phenotype switching against antibiotics is a survival strategy, with benefits in spatially varying environments. The presence of persister cells affects the expansion speed of the population, allowing for deeper spread into antibiotic regions. Optimal switching rates maximize population expansion in environments with alternating growth conditions and antibiotics.
Article
Physics, Fluids & Plasmas
Leila Abbaspour, Stefan Klumpp
Summary: Living systems contain active particles that can enhance the diffusion of passive particles through their active motion. The density and activity of active particles affect the passive tracer particle diffusion. Additionally, clustering of active particles can suppress the enhanced diffusion of passive particles.
Article
Physics, Fluids & Plasmas
David Seiferth, Peter Sollich, Stefan Klumpp
Article
Chemistry, Physical
Vitali Telezki, Stefan Klumpp
