1
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Lo WC, Krasnopeeva E, Pilizota T. Bacterial Electrophysiology. Annu Rev Biophys 2024; 53:487-510. [PMID: 38382113 DOI: 10.1146/annurev-biophys-030822-032215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Bacterial ion fluxes are involved in the generation of energy, transport, and motility. As such, bacterial electrophysiology is fundamentally important for the bacterial life cycle, but it is often neglected and consequently, by and large, not understood. Arguably, the two main reasons for this are the complexity of measuring relevant variables in small cells with a cell envelope that contains the cell wall and the fact that, in a unicellular organism, relevant variables become intertwined in a nontrivial manner. To help give bacterial electrophysiology studies a firm footing, in this review, we go back to basics. We look first at the biophysics of bacterial membrane potential, and then at the approaches and models developed mostly for the study of neurons and eukaryotic mitochondria. We discuss their applicability to bacterial cells. Finally, we connect bacterial membrane potential with other relevant (electro)physiological variables and summarize methods that can be used to both measure and influence bacterial electrophysiology.
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Affiliation(s)
- Wei-Chang Lo
- Institute of Physics, Academia Sinica, Taipei, Taiwan
| | | | - Teuta Pilizota
- School of Biological Sciences, Centre for Engineering Biology, University of Edinburgh, Edinburgh, United Kingdom;
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2
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Lohrmann C, Holm C, Datta SS. Influence of bacterial swimming and hydrodynamics on attachment of phages. SOFT MATTER 2024; 20:4795-4805. [PMID: 38847805 DOI: 10.1039/d4sm00060a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Bacteriophages ("phages") are viruses that infect bacteria. Since they do not actively self-propel, phages rely on thermal diffusion to find target cells-but can also be advected by fluid flows, such as those generated by motile bacteria themselves in bulk fluids. How does the flow field generated by a swimming bacterium influence how it encounters phages? Here, we address this question using coupled molecular dynamics and lattice Boltzmann simulations of flagellated bacteria swimming through a bulk fluid containing uniformly-dispersed phages. We find that while swimming increases the rate at which phages attach to both the cell body and flagellar propeller, hydrodynamic interactions strongly suppress this increase at the cell body, but conversely enhance this increase at the flagellar bundle. Our results highlight the pivotal influence of hydrodynamics on the interactions between bacteria and phages, as well as other diffusible species, in microbial environments.
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Affiliation(s)
- Christoph Lohrmann
- Institute for Computational Physics, University of Stuttgart, 70569 Stuttgart, Germany.
| | - Christian Holm
- Institute for Computational Physics, University of Stuttgart, 70569 Stuttgart, Germany.
| | - Sujit S Datta
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA.
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3
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Jakuszeit T, Croze OA. Role of tumbling in bacterial scattering at convex obstacles. Phys Rev E 2024; 109:044405. [PMID: 38755868 DOI: 10.1103/physreve.109.044405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/15/2024] [Indexed: 05/18/2024]
Abstract
Active propulsion, as performed by bacteria and Janus particles, in combination with hydrodynamic interaction results in the accumulation of bacteria at a flat wall. However, in microfluidic devices with cylindrical pillars of sufficiently small radius, self-propelled particles can slide along and scatter off the surface of a pillar, without becoming trapped over long times. This nonequilibrium scattering process has been predicted to result in large diffusivities, even at high obstacle density, unlike particles that undergo classical specular reflection. Here, we test this prediction by experimentally studying the nonequilibrium scattering of pusherlike swimmers in microfluidic obstacle lattices. To explore the role of tumbles in the scattering process, we microscopically tracked wild-type (run and tumble) and smooth-swimming (run only) mutants of the bacterium Escherichia coli scattering off microfluidic pillars. We quantified key scattering parameters and related them to previously proposed models that included a prediction for the diffusivity, discussing their relevance. Finally, we discuss potential interpretations of the role of tumbles in the scattering process and connect our work to the broader study of swimmers in porous media.
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Affiliation(s)
- Theresa Jakuszeit
- Institut Curie and Institut Pierre Gilles de Gennes, PSL Research University, CNRS UMR 144, 75005 Paris, France
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Ottavio A Croze
- School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
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4
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Kurzthaler C, Zhao Y, Zhou N, Schwarz-Linek J, Devailly C, Arlt J, Huang JD, Poon WCK, Franosch T, Tailleur J, Martinez VA. Characterization and Control of the Run-and-Tumble Dynamics of Escherichia Coli. PHYSICAL REVIEW LETTERS 2024; 132:038302. [PMID: 38307047 DOI: 10.1103/physrevlett.132.038302] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 11/29/2023] [Accepted: 12/01/2023] [Indexed: 02/04/2024]
Abstract
We characterize the full spatiotemporal gait of populations of swimming Escherichia coli using renewal processes to analyze the measurements of intermediate scattering functions. This allows us to demonstrate quantitatively how the persistence length of an engineered strain can be controlled by a chemical inducer and to report a controlled transition from perpetual tumbling to smooth swimming. For wild-type E. coli, we measure simultaneously the microscopic motility parameters and the large-scale effective diffusivity, hence quantitatively bridging for the first time small-scale directed swimming and macroscopic diffusion.
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Affiliation(s)
- Christina Kurzthaler
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey 08544, USA
- Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria
| | - Yongfeng Zhao
- Center for Soft Condensed Matter Physics and Interdisciplinary Research and School of Physical Science and Technology, Soochow University, Suzhou 215006, China
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pok Fu Lam, Hong Kong, China
- Université de Paris, MSC, UMR 7057 CNRS, 75205 Paris, France
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Nan Zhou
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Jana Schwarz-Linek
- School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Clemence Devailly
- School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Jochen Arlt
- School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Jian-Dong Huang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pok Fu Lam, Hong Kong, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wilson C K Poon
- School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Thomas Franosch
- Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria
| | - Julien Tailleur
- Université de Paris, MSC, UMR 7057 CNRS, 75205 Paris, France
| | - Vincent A Martinez
- School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
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5
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Bradley JJ, Martinez VA, Arlt J, Royer JR, Poon WCK. Sizing multimodal suspensions with differential dynamic microscopy. SOFT MATTER 2023; 19:8179-8192. [PMID: 37850499 PMCID: PMC10619199 DOI: 10.1039/d3sm00593c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 10/10/2023] [Indexed: 10/19/2023]
Abstract
Differential dynamic microscopy (DDM) can be used to extract the mean particle size from videos of suspensions. However, many suspensions have multimodal particle size distributions, for which a single 'mean' is not a sufficient description. After clarifying how different particle sizes contribute to the signal in DDM, we show that standard DDM analysis can extract the mean sizes of two populations in a bimodal suspension given prior knowledge of the sample's bimodality. Further, the use of the CONTIN algorithm obviates the need for such prior knowledge. Finally, we show that by selectively analysing portions of the DDM images, we can size a trimodal suspension where the large particles would otherwise dominate the signal, again without prior knowledge of the trimodality.
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Affiliation(s)
- Joe J Bradley
- School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Vincent A Martinez
- School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Jochen Arlt
- School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - John R Royer
- School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Wilson C K Poon
- School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
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6
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Lohrmann C, Holm C. Optimal motility strategies for self-propelled agents to explore porous media. Phys Rev E 2023; 108:054401. [PMID: 38115480 DOI: 10.1103/physreve.108.054401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 10/12/2023] [Indexed: 12/21/2023]
Abstract
Microrobots for, e.g., biomedical applications, need to be equipped with motility strategies that enable them to navigate through complex environments. Inspired by biological microorganisms we re-create motility patterns such as run-and-reverse, run-and-tumble, or run-reverse-flick applied to active rodlike particles in silico. We investigate their capability to efficiently explore disordered porous environments with various porosities and mean pore sizes ranging down to the scale of the active particle. By calculating the effective diffusivity for the different patterns, we can predict the optimal one for each porous sample geometry. We find that providing the agent with very basic sensing and decision-making capabilities yields a motility pattern outperforming the biologically inspired patterns for all investigated porous samples.
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Affiliation(s)
- Christoph Lohrmann
- Institute for Computational Physics, University of Stuttgart, 70569 Stuttgart, Germany
| | - Christian Holm
- Institute for Computational Physics, University of Stuttgart, 70569 Stuttgart, Germany
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7
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Bickmann J, Bröker S, Te Vrugt M, Wittkowski R. Active Brownian particles in external force fields: Field-theoretical models, generalized barometric law, and programmable density patterns. Phys Rev E 2023; 108:044601. [PMID: 37978644 DOI: 10.1103/physreve.108.044601] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 08/24/2023] [Indexed: 11/19/2023]
Abstract
We investigate the influence of external forces on the collective dynamics of interacting active Brownian particles in two as well as three spatial dimensions. Via explicit coarse graining, we derive predictive models, i.e., models that give a direct relation between the models' coefficients and the bare parameters of the system, that are applicable for space- and time-dependent external force fields. We study these models for the cases of gravity and harmonic traps. In particular, we derive a generalized barometric formula for interacting active Brownian particles under gravity that is valid for low to high concentrations and activities of the particles. Furthermore, we show that one can use an external harmonic trap to induce motility-induced phase separation in systems that, without external fields, remain in a homogeneous state. This finding makes it possible to realize programmable density patterns in systems of active Brownian particles. Our analytic predictions are found to be in very good agreement with Brownian dynamics simulations.
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Affiliation(s)
- Jens Bickmann
- Institut für Theoretische Physik, Center for Soft Nanoscience, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Stephan Bröker
- Institut für Theoretische Physik, Center for Soft Nanoscience, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Michael Te Vrugt
- Institut für Theoretische Physik, Center for Soft Nanoscience, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Raphael Wittkowski
- Institut für Theoretische Physik, Center for Soft Nanoscience, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
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8
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Sharan P, Daddi-Moussa-Ider A, Agudo-Canalejo J, Golestanian R, Simmchen J. Pair Interaction between Two Catalytically Active Colloids. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300817. [PMID: 37165719 DOI: 10.1002/smll.202300817] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/16/2023] [Indexed: 05/12/2023]
Abstract
Due to the intrinsically complex non-equilibrium behavior of the constituents of active matter systems, a comprehensive understanding of their collective properties is a challenge that requires systematic bottom-up characterization of the individual components and their interactions. For self-propelled particles, intrinsic complexity stems from the fact that the polar nature of the colloids necessitates that the interactions depend on positions and orientations of the particles, leading to a 2d - 1 dimensional configuration space for each particle, in d dimensions. Moreover, the interactions between such non-equilibrium colloids are generically non-reciprocal, which makes the characterization even more complex. Therefore, derivation of generic rules that enable us to predict the outcomes of individual encounters as well as the ensuing collective behavior will be an important step forward. While significant advances have been made on the theoretical front, such systematic experimental characterizations using simple artificial systems with measurable parameters are scarce. Here, two different contrasting types of colloidal microswimmers are studied, which move in opposite directions and show distinctly different interactions. To facilitate the extraction of parameters, an experimental platform is introduced in which these parameters are confined on a 1D track. Furthermore, a theoretical model for interparticle interactions near a substrate is developed, including both phoretic and hydrodynamic effects, which reproduces their behavior. For subsequent validation, the degrees of freedom are increased to 2D motion and resulting trajectories are predicted, finding remarkable agreement. These results may prove useful in characterizing the overall alignment behavior of interacting self-propelling active swimmer and may find direct applications in guiding the design of active-matter systems involving phoretic and hydrodynamic interactions.
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Affiliation(s)
- Priyanka Sharan
- Chair of Physical Chemistry, TU Dresden, 01062, Dresden, Germany
| | | | - Jaime Agudo-Canalejo
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), 37077, Göttingen, Germany
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), 37077, Göttingen, Germany
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Juliane Simmchen
- Chair of Physical Chemistry, TU Dresden, 01062, Dresden, Germany
- Pure and applied chemistry, University of Strathclyde, G11XL, Glasgow
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9
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Pellicciotta N, Paoluzzi M, Buonomo D, Frangipane G, Angelani L, Di Leonardo R. Colloidal transport by light induced gradients of active pressure. Nat Commun 2023; 14:4191. [PMID: 37443155 DOI: 10.1038/s41467-023-39974-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 07/06/2023] [Indexed: 07/15/2023] Open
Abstract
Active fluids, like all other fluids, exert mechanical pressure on confining walls. Unlike equilibrium, this pressure is generally not a function of the fluid state in the bulk and displays some peculiar properties. For example, when activity is not uniform, fluid regions with different activity may exert different pressures on the container walls but they can coexist side by side in mechanical equilibrium. Here we show that by spatially modulating bacterial motility with light, we can generate active pressure gradients capable of transporting passive probe particles in controlled directions. Although bacteria swim faster in the brighter side, we find that bacteria in the dark side apply a stronger pressure resulting in a net drift motion that points away from the low activity region. Using a combination of experiments and numerical simulations, we show that this drift originates mainly from an interaction pressure term that builds up due to the compression exerted by a layer of polarized cells surrounding the slow region. In addition to providing new insights into the generalization of pressure for interacting systems with non-uniform activity, our results demonstrate the possibility of exploiting active pressure for the controlled transport of microscopic objects.
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Affiliation(s)
- Nicola Pellicciotta
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185, Roma, Italy.
- NANOTEC-CNR, Soft and Living Matter Laboratory, Institute of Nanotechnology, Piazzale A. Moro 5, 00185, Roma, Italy.
| | - Matteo Paoluzzi
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, C. Martí Franquès 1, 08028, Barcelona, Spain
| | - Dario Buonomo
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185, Roma, Italy
| | - Giacomo Frangipane
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185, Roma, Italy
- NANOTEC-CNR, Soft and Living Matter Laboratory, Institute of Nanotechnology, Piazzale A. Moro 5, 00185, Roma, Italy
| | - Luca Angelani
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185, Roma, Italy
- ISC-CNR, Institute for Complex Systems, Piazzale A. Moro 5, 00185, Roma, Italy
| | - Roberto Di Leonardo
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185, Roma, Italy.
- NANOTEC-CNR, Soft and Living Matter Laboratory, Institute of Nanotechnology, Piazzale A. Moro 5, 00185, Roma, Italy.
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10
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Hallatschek O, Datta SS, Drescher K, Dunkel J, Elgeti J, Waclaw B, Wingreen NS. Proliferating active matter. NATURE REVIEWS. PHYSICS 2023; 5:1-13. [PMID: 37360681 PMCID: PMC10230499 DOI: 10.1038/s42254-023-00593-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 05/02/2023] [Indexed: 06/28/2023]
Abstract
The fascinating patterns of collective motion created by autonomously driven particles have fuelled active-matter research for over two decades. So far, theoretical active-matter research has often focused on systems with a fixed number of particles. This constraint imposes strict limitations on what behaviours can and cannot emerge. However, a hallmark of life is the breaking of local cell number conservation by replication and death. Birth and death processes must be taken into account, for example, to predict the growth and evolution of a microbial biofilm, the expansion of a tumour, or the development from a fertilized egg into an embryo and beyond. In this Perspective, we argue that unique features emerge in these systems because proliferation represents a distinct form of activity: not only do the proliferating entities consume and dissipate energy, they also inject biomass and degrees of freedom capable of further self-proliferation, leading to myriad dynamic scenarios. Despite this complexity, a growing number of studies document common collective phenomena in various proliferating soft-matter systems. This generality leads us to propose proliferation as another direction of active-matter physics, worthy of a dedicated search for new dynamical universality classes. Conceptual challenges abound, from identifying control parameters and understanding large fluctuations and nonlinear feedback mechanisms to exploring the dynamics and limits of information flow in self-replicating systems. We believe that, by extending the rich conceptual framework developed for conventional active matter to proliferating active matter, researchers can have a profound impact on quantitative biology and reveal fascinating emergent physics along the way.
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Affiliation(s)
- Oskar Hallatschek
- Departments of Physics and Integrative Biology, University of California, Berkeley, CA US
- Peter Debye Institute for Soft Matter Physics, Leipzig University, Leipzig, Germany
| | - Sujit S. Datta
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ USA
| | | | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Jens Elgeti
- Theoretical Physics of Living Matter, Institute of Biological Information Processing, Forschungszentrum Jülich, Jülich, Germany
| | - Bartek Waclaw
- Dioscuri Centre for Physics and Chemistry of Bacteria, Institute of Physical Chemistry PAN, Warsaw, Poland
- School of Physics and Astronomy, The University of Edinburgh, JCMB, Edinburgh, UK
| | - Ned S. Wingreen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ USA
- Department of Molecular Biology, Princeton University, Princeton, NJ USA
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11
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Pal A, Gope A, Sengupta A. Drying of bio-colloidal sessile droplets: Advances, applications, and perspectives. Adv Colloid Interface Sci 2023; 314:102870. [PMID: 37002959 DOI: 10.1016/j.cis.2023.102870] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 04/03/2023]
Abstract
Drying of biologically-relevant sessile droplets, including passive systems such as DNA, proteins, plasma, and blood, as well as active microbial systems comprising bacterial and algal dispersions, has garnered considerable attention over the last decades. Distinct morphological patterns emerge when bio-colloids undergo evaporative drying, with significant potential in a wide range of biomedical applications, spanning bio-sensing, medical diagnostics, drug delivery, and antimicrobial resistance. Consequently, the prospects of novel and thrifty bio-medical toolkits based on drying bio-colloids have driven tremendous progress in the science of morphological patterns and advanced quantitative image-based analysis. This review presents a comprehensive overview of bio-colloidal droplets drying on solid substrates, focusing on the experimental progress during the last ten years. We provide a summary of the physical and material properties of relevant bio-colloids and link their native composition (constituent particles, solvent, and concentrations) to the patterns emerging due to drying. We specifically examined the drying patterns generated by passive bio-colloids (e.g., DNA, globular, fibrous, composite proteins, plasma, serum, blood, urine, tears, and saliva). This article highlights how the emerging morphological patterns are influenced by the nature of the biological entities and the solvent, micro- and global environmental conditions (temperature and relative humidity), and substrate attributes like wettability. Crucially, correlations between emergent patterns and the initial droplet compositions enable the detection of potential clinical abnormalities when compared with the patterns of drying droplets of healthy control samples, offering a blueprint for the diagnosis of the type and stage of a specific disease (or disorder). Recent experimental investigations of pattern formation in the bio-mimetic and salivary drying droplets in the context of COVID-19 are also presented. We further summarized the role of biologically active agents in the drying process, including bacteria, algae, spermatozoa, and nematodes, and discussed the coupling between self-propulsion and hydrodynamics during the drying process. We wrap up the review by highlighting the role of cross-scale in situ experimental techniques for quantifying sub-micron to micro-scale features and the critical role of cross-disciplinary approaches (e.g., experimental and image processing techniques with machine learning algorithms) to quantify and predict the drying-induced features. We conclude the review with a perspective on the next generation of research and applications based on drying droplets, ultimately enabling innovative solutions and quantitative tools to investigate this exciting interface of physics, biology, data sciences, and machine learning.
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Affiliation(s)
- Anusuya Pal
- University of Warwick, Department of Physics, Coventry CV47AL, West Midlands, UK; Worcester Polytechnic Institute, Department of Physics, Worcester 01609, MA, USA.
| | - Amalesh Gope
- Tezpur University, Department of Linguistics and Language Technology, Tezpur 784028, Assam, India
| | - Anupam Sengupta
- University of Luxembourg, Physics of Living Matter, Department of Physics and Materials Science, Luxembourg L-1511, Luxembourg
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12
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Green Fabrication, Characterization of Zinc Oxide Nanoparticles Using Plant Extract of Momordica charantia and Curcuma zedoaria and Their Antibacterial and Antioxidant Activities. Appl Biochem Biotechnol 2023; 195:3546-3565. [PMID: 36622631 DOI: 10.1007/s12010-022-04309-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2022] [Indexed: 01/10/2023]
Abstract
In recent years, the rapid increase in the resistance of microorganisms to antibiotics has produced major health issues. Novel applications for these compounds have been developed by integrating modern technologies such as nanotechnology and material science with the innate antibacterial activity of metals. The current study demonstrated the synthesis of zinc oxide nanoparticles (ZnO NPs) from Momordica charantia and Curcuma zedoaria plant extracts, as well as their antibacterial properties. The synthesis of ZnO NPs was confirmed via UV-visible spectroscopy, showing clear peaks at 375 and 350 nm for M. charantia and C. zedoaria, respectively. Scanning electron microscopy (SEM) analysis revealed crystals of irregular shapes for the majority of the nanoparticles synthesized from both plants. The existence of ZnO NPs was confirmed using X-ray diffraction while the particle size was calculated using Scherrer's equation, which was 19.65 for C. zedoaria and 17.02 for M. charantia. Different functional groups were detected through Fourier transform infrared spectroscopy analysis. The antibacterial activity of the ZnO NPs at three different concentrations (250, 500, and 1000 µg/ml) was assessed against three different bacterial strains, i.e., Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), and Pseudomonas aeruginosa (P. aeruginosa), using disc diffusion methods. The ZnO nanoparticles showed promising antibacterial activity against bacterial strains. For C. zedoaria, the highest growth inhibition was observed at a concentration of 1000 µg/ml, which was 18, 19, and 18 mm as compared to antibiotics (15, 11, and 15.6 mm) against E. coli, P. aeruginosa, and S. aureus, respectively. Similarly, at 1000 µg/ml of NPs, M. charantia showed the highest growth inhibition (18, 15, and 17 mm) as compared to antibiotics (15, 11, and 14.6 mm) against E. coli, P. aeruginosa, and S. aureus, respectively. In conclusion, compared to pure plant extract and antibiotics, ZnO NPs at a higher concentration (1000 µg/ml) exhibited a significant difference in zone of inhibition against all the bacterial strains. Different concentrations of ZnO using M. charantia and C. zedoaria caused increments in the scavenging of 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals and 2,2-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS). The nanoparticles extracted using C. zedoaria exhibited higher antioxidant activity than M. charantia. Greenly synthesized ZnO nanoparticles have remarkable antibacterial properties and antioxidant activity, making them a promising contender for future pharmaceutical application.
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13
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Goral M, Clement E, Darnige T, Lopez-Leon T, Lindner A. Frustrated 'run and tumble' of swimming Escherichia coli bacteria in nematic liquid crystals. Interface Focus 2022; 12:20220039. [PMID: 36330319 PMCID: PMC9560793 DOI: 10.1098/rsfs.2022.0039] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 09/05/2022] [Indexed: 10/16/2023] Open
Abstract
In many situations, bacteria move in complex environments, as soils, oceans or the human gut-track, where carrier fluids show complex structures associated with non-Newtonian rheology. Many fundamental questions concerning the ability to navigate in such environments remain unsolved. Recently, it has been shown that the kinetics of bacterial motion in structured fluids as liquid crystals (LCs) is constrained by the orientational molecular order (or director field) and that novel spatio-temporal patterns arise. A question unaddressed so far is how bacteria change swimming direction in such an environment. In this work, we study the swimming mechanism of a single bacterium, Esherichia coli, constrained to move along the director field of a lyotropic chromonic liquid crystal confined to a planar cell. Here, the spontaneous 'run and tumble' motion of the bacterium gets frustrated: the elasticity of the LC prevents flagella from unbundling. Interestingly, to change direction, bacteria execute a reversal motion along the director field, driven by the relocation of a single flagellum, a 'frustrated tumble'. We characterize this phenomenon in detail experimentally, exploiting exceptional spatial and temporal resolution of bacterial and flagellar dynamics, using a two colour Lagrangian tracking technique. We suggest a possible mechanism accounting for these observations.
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Affiliation(s)
- Martyna Goral
- Laboratoire de Physique et Mécanique des Milieux Hétérogènes, UMR 7636, CNRS, ESPCI Paris-PSL, Sorbonne Université, Université Paris Cité, 75005 Paris, France
- Laboratoire Gulliver, UMR 7083, CNRS, ESPCI Paris-PSL, 75005 Paris, France
| | - Eric Clement
- Laboratoire de Physique et Mécanique des Milieux Hétérogènes, UMR 7636, CNRS, ESPCI Paris-PSL, Sorbonne Université, Université Paris Cité, 75005 Paris, France
- Institut Universitaire de France (IUF), Paris, France
| | - Thierry Darnige
- Laboratoire de Physique et Mécanique des Milieux Hétérogènes, UMR 7636, CNRS, ESPCI Paris-PSL, Sorbonne Université, Université Paris Cité, 75005 Paris, France
| | - Teresa Lopez-Leon
- Laboratoire Gulliver, UMR 7083, CNRS, ESPCI Paris-PSL, 75005 Paris, France
| | - Anke Lindner
- Laboratoire de Physique et Mécanique des Milieux Hétérogènes, UMR 7636, CNRS, ESPCI Paris-PSL, Sorbonne Université, Université Paris Cité, 75005 Paris, France
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14
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Gomez-Solano JR, Rodríguez RF, Salinas-Rodríguez E. Nonequilibrium dynamical structure factor of a dilute suspension of active particles in a viscoelastic fluid. Phys Rev E 2022; 106:054602. [PMID: 36559383 DOI: 10.1103/physreve.106.054602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
Abstract
In this work we investigate the dynamics of the number-density fluctuations of a dilute suspension of active particles in a linear viscoelastic fluid. We propose a model for the frequency-dependent diffusion coefficient of the active particles which captures the effect of rotational diffusion on the persistence of their self-propelled motion and the viscoelasticity of the medium. Using fluctuating hydrodynamics, the linearized equations for the active suspension are derived, from which we calculate its dynamic structure factor and the corresponding intermediate scattering function. For a Maxwell-type rheological model, we find an intricate dependence of these functions on the parameters that characterize the viscoelasticity of the solvent and the activity of the particles, which can significantly deviate from those of an inert suspension of passive particles and of an active suspension in a Newtonian solvent. In particular, in some regions of the parameter space we uncover the emergence of oscillations in the intermediate scattering function at certain wave numbers which represent the hallmark of the nonequilibrium particle activity in the dynamical structure of the suspension and also encode the viscoelastic properties of the medium.
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Affiliation(s)
- Juan Ruben Gomez-Solano
- Instituto de Física, Universidad Nacional Autónoma de México, Ciudad de México, Código Postal 04510, Mexico
| | - Rosalío F Rodríguez
- Instituto de Física, Universidad Nacional Autónoma de México, Ciudad de México, Código Postal 04510, Mexico.,FENOMEC, Universidad Nacional Autónoma de México, Apdo. Postal 20-726, 01000 Ciudad de México, Mexico
| | - Elizabeth Salinas-Rodríguez
- Departamento I. P. H., Universidad Autónoma Metropolitana, Iztapalapa, Apdo. Postal 55-534, 09340 Ciudad de México, Mexico
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15
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Voliotis M, Rosko J, Pilizota T, Liverpool TB. Steady-state running rate sets the speed and accuracy of accumulation of swimming bacteria. Biophys J 2022; 121:3435-3444. [PMID: 36045575 PMCID: PMC9515231 DOI: 10.1016/j.bpj.2022.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 07/31/2022] [Accepted: 08/15/2022] [Indexed: 11/21/2022] Open
Abstract
We study the chemotaxis of a population of genetically identical swimming bacteria undergoing run and tumble dynamics driven by stochastic switching between clockwise and counterclockwise rotation of the flagellar rotary system, where the steady-state rate of the switching changes in different environments. Understanding chemotaxis quantitatively requires that one links the measured steady-state switching rates of the rotary system, as well as the directional changes of individual swimming bacteria in a gradient of chemoattractant/repellant, to the efficiency of a population of bacteria in moving up/down the gradient. Here we achieve this by using a probabilistic model, parametrized with our experimental data, and show that the response of a population to the gradient is complex. We find the changes to the steady-state switching rate in the absence of gradients affect the average speed of the swimming bacterial population response as well as the width of the distribution. Both must be taken into account when optimizing the overall response of the population in complex environments.
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Affiliation(s)
- Margaritis Voliotis
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, United Kingdom.
| | - Jerko Rosko
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Teuta Pilizota
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom.
| | - Tanniemola B Liverpool
- School of Mathematics, University of Bristol, Bristol, United Kingdom; BrisSynBio, Life Sciences Building, University of Bristol, Bristol, United Kingdom.
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16
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Al-Shahrani M, Bryant G. Differential dynamic microscopy for the characterisation of motility in biological systems. Phys Chem Chem Phys 2022; 24:20616-20623. [PMID: 36048134 DOI: 10.1039/d2cp02034c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Differential Dynamic Microscopy (DDM) is a relatively new technique which measures the dynamics of suspended particles using a dynamic light scattering formalism. Videos are recorded using standard light microscopy at moderate frame rates, and fluctuations in pixel intensity are measured as a function of time. As only pixel intensity is analysed, it is not necessary to resolve individual particles. This allows for low magnifications and wide fields of view, and therefore dynamics can be measured on tens of thousands of scattering objects, providing robust statistics. A decade ago the technique was successfully applied to measure bacterial motility. Since then, it has been applied to a range of motile systems, but has not yet reached the wider biological community. This perspective reviews the work done so far, and provides the basic background to enable the broader application of this promising technique.
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Affiliation(s)
- Monerh Al-Shahrani
- Physics, School of Science, RMIT University, Melbourne, Australia. .,Department of Physics, College of Science, University of Bisha, Bisha, Saudi Arabia
| | - Gary Bryant
- Physics, School of Science, RMIT University, Melbourne, Australia.
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17
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Abstract
Swimming bacterial pathogens can penetrate and shape the membranes of their host cells. We study an artificial model system of this kind comprising Escherichia coli enclosed inside vesicles, which consist of nothing more than a spherical membrane bag. The bacteria push out membrane tubes, and the tubes propel the vesicles. This phenomenon is intriguing because motion cannot be generated by pushing the vesicles from within. We explain the motility of our artificial cell by a shape coupling between the flagella of each bacterium and the enclosing membrane tube. This constitutes a design principle for conferring motility to cell-sized vesicles and demonstrates the universality of lipid membranes as a building block in the development of new biohybrid systems. We study a synthetic system of motile Escherichia coli bacteria encapsulated inside giant lipid vesicles. Forces exerted by the bacteria on the inner side of the membrane are sufficient to extrude membrane tubes filled with one or several bacteria. We show that a physical coupling between the membrane tube and the flagella of the enclosed cells transforms the tube into an effective helical flagellum propelling the vesicle. We develop a simple theoretical model to estimate the propulsive force from the speed of the vesicles and demonstrate the good efficiency of this coupling mechanism. Together, these results point to design principles for conferring motility to synthetic cells.
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18
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Junot G, Darnige T, Lindner A, Martinez VA, Arlt J, Dawson A, Poon WCK, Auradou H, Clément E. Run-to-Tumble Variability Controls the Surface Residence Times of E. coli Bacteria. PHYSICAL REVIEW LETTERS 2022; 128:248101. [PMID: 35776449 DOI: 10.1103/physrevlett.128.248101] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
Motile bacteria are known to accumulate at surfaces, eventually leading to changes in bacterial motility and biofilm formation. We use a novel two-color, three-dimensional Lagrangian tracking technique to follow simultaneously the body and the flagella of a wild-type Escherichia coli. We observe long surface residence times and surface escape corresponding mostly to immediately antecedent tumbling. A motility model accounting for a large behavioral variability in run-time duration reproduces all experimental findings and gives new insights into surface trapping efficiency.
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Affiliation(s)
- Gaspard Junot
- PMMH, UMR 7636 CNRS, ESPCI Paris, PSL Research University, Sorbonne Université and Université Paris Cité, 7-9 quai Saint-Bernard, Paris, 75005, France
| | - Thierry Darnige
- PMMH, UMR 7636 CNRS, ESPCI Paris, PSL Research University, Sorbonne Université and Université Paris Cité, 7-9 quai Saint-Bernard, Paris, 75005, France
| | - Anke Lindner
- PMMH, UMR 7636 CNRS, ESPCI Paris, PSL Research University, Sorbonne Université and Université Paris Cité, 7-9 quai Saint-Bernard, Paris, 75005, France
| | - Vincent A Martinez
- SUPA and the School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Jochen Arlt
- SUPA and the School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Angela Dawson
- SUPA and the School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Wilson C K Poon
- SUPA and the School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Harold Auradou
- Université Paris-Saclay, CNRS, FAST, 91405 Orsay, France
| | - Eric Clément
- PMMH, UMR 7636 CNRS, ESPCI Paris, PSL Research University, Sorbonne Université and Université Paris Cité, 7-9 quai Saint-Bernard, Paris, 75005, France
- Institut Universitaire de France (IUF)
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19
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Zunke C, Bewerunge J, Platten F, Egelhaaf SU, Godec A. First-passage statistics of colloids on fractals: Theory and experimental realization. SCIENCE ADVANCES 2022; 8:eabk0627. [PMID: 35061533 PMCID: PMC8782457 DOI: 10.1126/sciadv.abk0627] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 11/29/2021] [Indexed: 05/30/2023]
Abstract
In nature and technology, particle dynamics frequently occur in complex environments, for example in restricted geometries or crowded media. These dynamics have often been modeled invoking a fractal structure of the medium although the fractal structure was only indirectly inferred through the dynamics. Moreover, systematic studies have not yet been performed. Here, colloidal particles moving in a laser speckle pattern are used as a model system. In this case, the experimental observations can be reliably traced to the fractal structure of the underlying medium with an adjustable fractal dimension. First-passage time statistics reveal that the particles explore the speckle in a self-similar, fractal manner at least over four decades in time and on length scales up to 20 times the particle radius. The requirements for fractal diffusion to be applicable are laid out, and methods to extract the fractal dimension are established.
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Affiliation(s)
- Christoph Zunke
- Condensed Matter Physics Laboratory, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Jörg Bewerunge
- Condensed Matter Physics Laboratory, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Florian Platten
- Condensed Matter Physics Laboratory, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
- Institute of Biological Information Processing, Biomacromolecular Systems and Processes (IBI-4), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Stefan U. Egelhaaf
- Condensed Matter Physics Laboratory, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Aljaž Godec
- Mathematical bioPhysics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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20
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Bellotto N, Agudo-Canalejo J, Colin R, Golestanian R, Malengo G, Sourjik V. Dependence of diffusion in Escherichia coli cytoplasm on protein size, environmental conditions, and cell growth. eLife 2022; 11:82654. [PMID: 36468683 PMCID: PMC9810338 DOI: 10.7554/elife.82654] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Inside prokaryotic cells, passive translational diffusion typically limits the rates with which cytoplasmic proteins can reach their locations. Diffusion is thus fundamental to most cellular processes, but the understanding of protein mobility in the highly crowded and non-homogeneous environment of a bacterial cell is still limited. Here, we investigated the mobility of a large set of proteins in the cytoplasm of Escherichia coli, by employing fluorescence correlation spectroscopy (FCS) combined with simulations and theoretical modeling. We conclude that cytoplasmic protein mobility could be well described by Brownian diffusion in the confined geometry of the bacterial cell and at the high viscosity imposed by macromolecular crowding. We observed similar size dependence of protein diffusion for the majority of tested proteins, whether native or foreign to E. coli. For the faster-diffusing proteins, this size dependence is well consistent with the Stokes-Einstein relation once taking into account the specific dumbbell shape of protein fusions. Pronounced subdiffusion and hindered mobility are only observed for proteins with extensive interactions within the cytoplasm. Finally, while protein diffusion becomes markedly faster in actively growing cells, at high temperature, or upon treatment with rifampicin, and slower at high osmolarity, all of these perturbations affect proteins of different sizes in the same proportions, which could thus be described as changes of a well-defined cytoplasmic viscosity.
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Affiliation(s)
- Nicola Bellotto
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | | | - Remy Colin
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-OrganizationGöttingenGermany,Rudolf Peierls Centre for Theoretical Physics, University of OxfordOxfordUnited Kingdom
| | - Gabriele Malengo
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
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21
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Griffiths SE, Koumakis N, Brown AT, Vissers T, Warren PB, Poon WCK. Diffusion, phase behavior, and gelation in a two-dimensional layer of colloids in osmotic equilibrium with a polymer reservoir. J Chem Phys 2021; 155:074903. [PMID: 34418940 DOI: 10.1063/5.0058172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The addition of enough non-adsorbing polymers to an otherwise stable colloidal suspension gives rise to a variety of phase behaviors and kinetic arrest due to the depletion attraction induced between the colloids by the polymers. We report a study of these phenomena in a two-dimensional layer of colloids. The three-dimensional phenomenology of crystal-fluid coexistence is reproduced, but gelation takes a novel form, in which the strands in the gel structure are locally crystalline. We compare our findings with a previous simulation and theory and find substantial agreement.
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Affiliation(s)
- Sam E Griffiths
- School of Physics and Astronomy, The University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - Nick Koumakis
- School of Physics and Astronomy, The University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - Aidan T Brown
- School of Physics and Astronomy, The University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - Teun Vissers
- School of Physics and Astronomy, The University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - Patrick B Warren
- Hartree Centre, Science and Technology Facilities Council (STFC), Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - Wilson C K Poon
- School of Physics and Astronomy, The University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
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22
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Kubacka A, Rojo D, Muñoz-Batista MJ, Barbas C, Fernández-García M, Ferrer M. Metabolomics reveals synergy between Ag and g-C 3N 4 in Ag/g-C 3N 4 composite photocatalysts: a unique feature among Ag-doped biocidal materials. Metabolomics 2021; 17:53. [PMID: 34061256 DOI: 10.1007/s11306-021-01804-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/24/2021] [Indexed: 10/21/2022]
Abstract
INTRODUCTION The silver/graphitic carbon nitride (Ag/g-C3N4) composite system exerts biocidal activity against the pathogenic bacterium Escherichia coli 1337-H that is stronger than that of well-known silver and titanium oxide (TiO2)-based composites. However, whether the Ag/g-C3N4 composite system has biocidal properties that the parent components do or do not have as separate chemical entities and whether they differ from those in Ag/TiO2 composite photocatalysts have not been clarified. OBJECTIVE We investigated the chemical (cooperative charge handling and electronic properties) and biological (metabolic) effects exerted by the addition of Ag to g-C3N4 and to TiO2. METHODS In this work, we undertook metabolome-wide analysis by liquid chromatography-electrospray ionization-quadrupole-time of flight-mass spectrometry to compare the metabolite profiles of untreated E. coli 1337-H cells or those subjected to disinfection with Ag, g-C3N4, 2Ag/g-C3N4, TiO2 and 2Ag/TiO2. RESULTS While Ag or g-C3N4 moderately affected microbial metabolism according to the mean of the altered metabolites, multiple cell systems contributing to rapid cell death were immediately affected by the light-triggered radical species produced when Ag and g-C3N4 were as xAg/g-C3N4. The effects include drastically reduced production of small metabolites essential for detoxifying reactive oxygen species and those that regulate DNA replication fidelity, cell morphology and energy status. These biological consequences were different from those caused by Ag/TiO2-based biocides, demonstrating the uniqueness of the Ag/g-C3N4 system. CONCLUSIONS Our results support the idea that the unique Ag/g-C3N4 biocidal properties are based on synergistic action and reveal new directions for designing future photocatalysts for use in disinfection and microbial control.
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Affiliation(s)
- Anna Kubacka
- Institute of Catalysis and Petrochemistry, Consejo Superior de Investigaciones Científicas, c/Marie Curie 2, 28049, Madrid, Spain
| | - David Rojo
- Department of Chemistry and Biochemistry, Facultad de Farmacia, Centre for Metabolomics and Bioanalysis (CEMBIO), Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Mario J Muñoz-Batista
- Institute of Catalysis and Petrochemistry, Consejo Superior de Investigaciones Científicas, c/Marie Curie 2, 28049, Madrid, Spain
- Department of Chemical Engineering, University of Granada, Av. de La Fuente Nueva S/N, 18071, Granada, Spain
| | - Coral Barbas
- Department of Chemistry and Biochemistry, Facultad de Farmacia, Centre for Metabolomics and Bioanalysis (CEMBIO), Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Marcos Fernández-García
- Institute of Catalysis and Petrochemistry, Consejo Superior de Investigaciones Científicas, c/Marie Curie 2, 28049, Madrid, Spain.
| | - Manuel Ferrer
- Institute of Catalysis and Petrochemistry, Consejo Superior de Investigaciones Científicas, c/Marie Curie 2, 28049, Madrid, Spain.
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23
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Bhattacharjee T, Amchin DB, Ott JA, Kratz F, Datta SS. Chemotactic migration of bacteria in porous media. Biophys J 2021; 120:3483-3497. [PMID: 34022238 DOI: 10.1016/j.bpj.2021.05.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 03/11/2021] [Accepted: 05/06/2021] [Indexed: 11/16/2022] Open
Abstract
Chemotactic migration of bacteria-their ability to direct multicellular motion along chemical gradients-is central to processes in agriculture, the environment, and medicine. However, current understanding of migration is based on studies performed in bulk liquid, despite the fact that many bacteria inhabit tight porous media such as soils, sediments, and biological gels. Here, we directly visualize the chemotactic migration of Escherichia coli populations in well-defined 3D porous media in the absence of any other imposed external forcing (e.g., flow). We find that pore-scale confinement is a strong regulator of migration. Strikingly, cells use a different primary mechanism to direct their motion in confinement than in bulk liquid. Furthermore, confinement markedly alters the dynamics and morphology of the migrating population-features that can be described by a continuum model, but only when standard motility parameters are substantially altered from their bulk liquid values to reflect the influence of pore-scale confinement. Our work thus provides a framework to predict and control the migration of bacteria, and active matter in general, in complex environments.
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Affiliation(s)
- Tapomoy Bhattacharjee
- Andlinger Center for Energy and the Environment, Princeton University, Princeton, New Jersey
| | - Daniel B Amchin
- Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
| | - Jenna A Ott
- Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
| | - Felix Kratz
- Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
| | - Sujit S Datta
- Chemical and Biological Engineering, Princeton University, Princeton, New Jersey.
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24
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Photocatalytic Bactericidal Performance of LaFeO3 under Solar Light: Kinetics, Spectroscopic and Mechanistic Evaluation. WATER 2021. [DOI: 10.3390/w13091135] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Lanthanum orthoferrites are a versatile class of catalysts. Here, the photocatalytic bactericidal performance of LaFeO3 (LF) to inactivate pathogenic microorganisms, i.e., Escherichia coli (E. coli), in water under simulated solar irradiation conditions was investigated. Various competing and contributing factors were covered to visualize the reaction medium consisting of E. coli K12 cells, organic sub-fractions formed by cell destruction, and LF surface. LF solar photocatalytic inactivation (SPCI) kinetics revealed the highest inactivation rate in ultrapure water as expected, followed by distilled water (DW), aqueous solution containing anions and cations (WM) and saline solution (SS). Characterization of the released organic matter was achieved by UV-vis and fluorescence spectroscopic techniques as well as organic carbon contents (DOC). Upon SPCI, significant amounts of K+ along with released protein contents were detected expressing cell wall destruction and lysis. Under the specified experimental conditions, in the presence of released intracellular organic and inorganic components via cell lysis, a significant count of E. coli was still present in SS, whereas almost all bacteria were removed in other matrices due to various challenging reasons. Based on the presented data, SPCI of E. coli using LF as a novel photocatalyst was successfully demonstrated as an alternative and promising method for disinfection purposes.
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25
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Singh J, Patteson AE, Torres Maldonado BO, Purohit PK, Arratia PE. Bacterial activity hinders particle sedimentation. SOFT MATTER 2021; 17:4151-4160. [PMID: 33881035 DOI: 10.1039/d0sm02115f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Sedimentation in active fluids has come into focus due to the ubiquity of swimming micro-organisms in natural and industrial processes. Here, we investigate sedimentation dynamics of passive particles in a fluid as a function of bacteria E. coli concentration. Results show that the presence of swimming bacteria significantly reduces the speed of the sedimentation front even in the dilute regime, in which the sedimentation speed is expected to be independent of particle concentration. Furthermore, bacteria increase the dispersion of the passive particles, which determines the width of the sedimentation front. For short times, particle sedimentation speed has a linear dependence on bacterial concentration. Mean square displacement data shows, however, that bacterial activity decays over long experimental (sedimentation) times. An advection-diffusion equation coupled to bacteria population dynamics seems to capture concentration profiles relatively well. A single parameter, the ratio of single particle speed to the bacteria flow speed can be used to predict front sedimentation speed.
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Affiliation(s)
- Jaspreet Singh
- Department of Mechanical Engineering & Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | | | - Bryan O Torres Maldonado
- Department of Mechanical Engineering & Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Prashant K Purohit
- Department of Mechanical Engineering & Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Paulo E Arratia
- Department of Mechanical Engineering & Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA.
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26
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Naaz F, Agrawal M, Chakraborty S, Tirumkudulu MS, Venkatesh KV. Ligand sensing enhances bacterial flagellar motor output via stator recruitment. eLife 2021; 10:62848. [PMID: 33821791 PMCID: PMC8062133 DOI: 10.7554/elife.62848] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 04/03/2021] [Indexed: 11/13/2022] Open
Abstract
It is well known that flagellated bacteria, such as Escherichia coli, sense chemicals in their environment by a chemoreceptor and relay the signals via a well-characterized signaling pathway to the flagellar motor. It is widely accepted that the signals change the rotation bias of the motor without influencing the motor speed. Here, we present results to the contrary and show that the bacteria is also capable of modulating motor speed on merely sensing a ligand. Step changes in concentration of non-metabolizable ligand cause temporary recruitment of stator units leading to a momentary increase in motor speeds. For metabolizable ligand, the combined effect of sensing and metabolism leads to higher motor speeds for longer durations. Experiments performed with mutant strains delineate the role of metabolism and sensing in the modulation of motor speed and show how speed changes along with changes in bias can significantly enhance response to changes in its environment.
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Affiliation(s)
- Farha Naaz
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Megha Agrawal
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Soumyadeep Chakraborty
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Mahesh S Tirumkudulu
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - K V Venkatesh
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
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27
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Semeraro EF, Marx L, Mandl J, Frewein MPK, Scott HL, Prévost S, Bergler H, Lohner K, Pabst G. Evolution of the analytical scattering model of live Escherichia coli. J Appl Crystallogr 2021; 54:473-485. [PMID: 33953653 PMCID: PMC8056759 DOI: 10.1107/s1600576721000169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/05/2021] [Indexed: 11/10/2022] Open
Abstract
A previously reported multi-scale model for (ultra-)small-angle X-ray (USAXS/SAXS) and (very) small-angle neutron scattering (VSANS/SANS) of live Escherichia coli was revised on the basis of compositional/metabolomic and ultrastructural constraints. The cellular body is modeled, as previously described, by an ellipsoid with multiple shells. However, scattering originating from flagella was replaced by a term accounting for the oligosaccharide cores of the lipopolysaccharide leaflet of the outer membrane including its cross-term with the cellular body. This was mainly motivated by (U)SAXS experiments showing indistinguishable scattering for bacteria in the presence and absence of flagella or fimbrae. The revised model succeeded in fitting USAXS/SAXS and differently contrasted VSANS/SANS data of E. coli ATCC 25922 over four orders of magnitude in length scale. Specifically, this approach provides detailed insight into structural features of the cellular envelope, including the distance of the inner and outer membranes, as well as the scattering length densities of all bacterial compartments. The model was also successfully applied to E. coli K12, used for the authors' original modeling, as well as for two other E. coli strains. Significant differences were detected between the different strains in terms of bacterial size, intermembrane distance and its positional fluctuations. These findings corroborate the general applicability of the approach outlined here to quantitatively study the effect of bactericidal compounds on ultrastructural features of Gram-negative bacteria without the need to resort to any invasive staining or labeling agents.
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Affiliation(s)
- Enrico F Semeraro
- University of Graz, Institute of Molecular Biosciences, NAWI Graz, 8010 Graz, Austria.,BioTechMed Graz, 8010 Graz, Austria.,Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Lisa Marx
- University of Graz, Institute of Molecular Biosciences, NAWI Graz, 8010 Graz, Austria.,BioTechMed Graz, 8010 Graz, Austria.,Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Johannes Mandl
- University of Graz, Institute of Molecular Biosciences, NAWI Graz, 8010 Graz, Austria.,BioTechMed Graz, 8010 Graz, Austria.,Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Moritz P K Frewein
- University of Graz, Institute of Molecular Biosciences, NAWI Graz, 8010 Graz, Austria.,BioTechMed Graz, 8010 Graz, Austria.,Field of Excellence BioHealth - University of Graz, Graz, Austria.,Institut Laue-Langevin, 38043 Grenoble, France
| | - Haden L Scott
- University of Tennessee, Center for Environmental Biotechnology, Knoxville, Tennessee, USA
| | | | - Helmut Bergler
- University of Graz, Institute of Molecular Biosciences, NAWI Graz, 8010 Graz, Austria.,BioTechMed Graz, 8010 Graz, Austria.,Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Karl Lohner
- University of Graz, Institute of Molecular Biosciences, NAWI Graz, 8010 Graz, Austria.,BioTechMed Graz, 8010 Graz, Austria.,Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Georg Pabst
- University of Graz, Institute of Molecular Biosciences, NAWI Graz, 8010 Graz, Austria.,BioTechMed Graz, 8010 Graz, Austria.,Field of Excellence BioHealth - University of Graz, Graz, Austria
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28
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Malvar S, Cardoso LOB, Karolski B, Perpetuo EA, Carmo BS, Meneghini JR. A rheological approach to identify efficient biopolymer producing bacteria. Biotechnol Bioeng 2020; 118:622-632. [PMID: 33090455 DOI: 10.1002/bit.27595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/22/2020] [Accepted: 09/28/2020] [Indexed: 11/09/2022]
Abstract
This study investigates the relationship between collective motion and propulsion of bacterial consortia and their biopolymer production efficiency. Rheological tests were conducted for suspensions of two different methanotrophic bacterial consortia obtained after enrichment of sediment samples from mangrove sites in Brazil. We considered the linear viscoelasticity region and analyzed the values of storage and loss moduli as functions of days of cultivation, for different values of the volume fraction. The suspensions' rheological behaviors reflected the bacterial growth stage. We found that the formation of structures over time in some types of consortia can hinder the movement of bacteria in the search for nutrients. The change in complex viscosity of the two consortia followed a different and rich behavior that appears to be closely related to their capacity to capture methane. Our analysis showed a possible correlation between collective motion, viscosity reduction, and biopolymer production. The pieces of evidence from this study suggest that the efficiency of bacterial motion is directly related to biopolymer production, and this could facilitate the process of identifying the best consortium of biopolymer producing bacteria.
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Affiliation(s)
- Sara Malvar
- Department of Mechanical Engineering, Escola Politécnica, University of São Paulo, São Paulo, SP, Brazil
| | - Letícia O B Cardoso
- The Interunit Program in Biotechnology, University of São Paulo, São Paulo, SP, Brazil.,Environmental Research and Education Center - CEPEMA, Escola Politécnica, University of São Paulo, Cubatão, SP, Brazil
| | - Bruno Karolski
- Environmental Research and Education Center - CEPEMA, Escola Politécnica, University of São Paulo, Cubatão, SP, Brazil
| | - Elen A Perpetuo
- Environmental Research and Education Center - CEPEMA, Escola Politécnica, University of São Paulo, Cubatão, SP, Brazil.,Institute of Marine Sciences, Federal University of São Paulo, Santos, SP, Brazil
| | - Bruno S Carmo
- Department of Mechanical Engineering, Escola Politécnica, University of São Paulo, São Paulo, SP, Brazil
| | - Julio R Meneghini
- Department of Mechanical Engineering, Escola Politécnica, University of São Paulo, São Paulo, SP, Brazil
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29
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Sprenger AR, Shaik VA, Ardekani AM, Lisicki M, Mathijssen AJTM, Guzmán-Lastra F, Löwen H, Menzel AM, Daddi-Moussa-Ider A. Towards an analytical description of active microswimmers in clean and in surfactant-covered drops. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2020; 43:58. [PMID: 32920676 DOI: 10.1140/epje/i2020-11980-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/10/2020] [Indexed: 05/24/2023]
Abstract
Geometric confinements are frequently encountered in the biological world and strongly affect the stability, topology, and transport properties of active suspensions in viscous flow. Based on a far-field analytical model, the low-Reynolds-number locomotion of a self-propelled microswimmer moving inside a clean viscous drop or a drop covered with a homogeneously distributed surfactant, is theoretically examined. The interfacial viscous stresses induced by the surfactant are described by the well-established Boussinesq-Scriven constitutive rheological model. Moreover, the active agent is represented by a force dipole and the resulting fluid-mediated hydrodynamic couplings between the swimmer and the confining drop are investigated. We find that the presence of the surfactant significantly alters the dynamics of the encapsulated swimmer by enhancing its reorientation. Exact solutions for the velocity images for the Stokeslet and dipolar flow singularities inside the drop are introduced and expressed in terms of infinite series of harmonic components. Our results offer useful insights into guiding principles for the control of confined active matter systems and support the objective of utilizing synthetic microswimmers to drive drops for targeted drug delivery applications.
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Affiliation(s)
- Alexander R Sprenger
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225, Düsseldorf, Germany.
| | - Vaseem A Shaik
- School of Mechanical Engineering, Purdue University, 47907, West Lafayette, IN, USA
| | - Arezoo M Ardekani
- School of Mechanical Engineering, Purdue University, 47907, West Lafayette, IN, USA
| | - Maciej Lisicki
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Arnold J T M Mathijssen
- Department of Bioengineering, Stanford University, 443 Via Ortega, 94305, Stanford, CA, USA
- Department of Physics and Astronomy, University of Pennsylvania, 209 South 33rd Street, 19104, Philadelphia, PA, USA
| | - Francisca Guzmán-Lastra
- Centro de Investigación DAiTA Lab, Facultad de Estudios Interdisciplinarios, Universidad Mayor, Av. Manuel Montt 367, Providencia, Santiago de Chile, Chile
| | - Hartmut Löwen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225, Düsseldorf, Germany
| | - Andreas M Menzel
- Institut für Physik, Otto-von-Guericke-Universität Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany
| | - Abdallah Daddi-Moussa-Ider
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225, Düsseldorf, Germany
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30
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Lagarde A, Dagès N, Nemoto T, Démery V, Bartolo D, Gibaud T. Colloidal transport in bacteria suspensions: from bacteria collision to anomalous and enhanced diffusion. SOFT MATTER 2020; 16:7503-7512. [PMID: 32725023 DOI: 10.1039/d0sm00309c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Swimming microorganisms interact and alter the dynamics of Brownian particles and tend to modify their transport properties. In particular, dilute colloids coupled to a bath of swimming cells generically display enhanced diffusion on long time scales. This transport dynamics stems from a subtle interplay between the active and passive particles that still resists our understanding despite decades of intense research. Here, we tackle the root of the problem by providing a quantitative characterisation of the single scattering events between a colloid and a bacterium, a smooth running E. coli. Based on our experiments, we build a minimal model that quantitatively predicts the geometry of the scattering trajectories, and enhanced colloidal diffusion at long times. This quantitative confrontation between theory and experiments elucidates the microscopic origin of enhanced transport. Collisions are solely ruled by stochastic contact interactions and the ratio of the drag coefficients of the colloid and the bacteria. Such description accounts both for genuine anomalous diffusion at short times and enhanced diffusion at long times with no ballistic regime at any scale.
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Affiliation(s)
- Antoine Lagarde
- Univ Lyon, Ens de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Physique, F-69342 Lyon, France.
| | - Noémie Dagès
- Univ Lyon, Ens de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Physique, F-69342 Lyon, France.
| | - Takahiro Nemoto
- Philippe Meyer Institute for Theoretical Physics, Physics Department, École Normale Supérieure & PSL Research University, 24 rue Lhomond, F-75231 Paris Cedex 05, France
| | - Vincent Démery
- Univ Lyon, Ens de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Physique, F-69342 Lyon, France. and Gulliver, UMR CNRS 7083, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
| | - Denis Bartolo
- Univ Lyon, Ens de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Physique, F-69342 Lyon, France.
| | - Thomas Gibaud
- Univ Lyon, Ens de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Physique, F-69342 Lyon, France.
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31
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Bacterial flagellar motor as a multimodal biosensor. Methods 2020; 193:5-15. [PMID: 32640316 DOI: 10.1016/j.ymeth.2020.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/04/2020] [Accepted: 06/22/2020] [Indexed: 01/05/2023] Open
Abstract
Bacterial Flagellar Motor is one of nature's rare rotary molecular machines. It enables bacterial swimming and it is the key part of the bacterial chemotactic network, one of the best studied chemical signalling networks in biology, which enables bacteria to direct its movement in accordance with the chemical environment. The network can sense down to nanomolar concentrations of specific chemicals on the time scale of seconds. Motor's rotational speed is linearly proportional to the electrochemical gradients of either proton or sodium driving ions, while its direction is regulated by the chemotactic network. Recently, it has been discovered that motor is also a mechanosensor. Given these properties, we discuss the motor's potential to serve as a multifunctional biosensor and a tool for characterising and studying the external environment, the bacterial physiology itself and single molecular motor biophysics.
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32
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Dulaney AR, Brady JF. Waves in active matter: The transition from ballistic to diffusive behavior. Phys Rev E 2020; 101:052609. [PMID: 32575299 DOI: 10.1103/physreve.101.052609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/23/2020] [Indexed: 01/19/2023]
Abstract
We highlight the unique wavelike character observed in the relaxation dynamics of active systems via a Smoluchowski based theoretical framework and Brownian dynamic simulations. Persistent swimming motion results in wavelike dynamics until the advective swim displacements become sufficiently uncorrelated, at which point the motion becomes a random walk process characterized by a swim diffusivity, D^{swim}=U_{0}^{2}τ_{R}/[d(d-1)], dependent on the speed of swimming U_{0}, reorientation time τ_{R}, and reorientation dimension d. This change in behavior is described by a telegraph equation, which governs the transition from ballistic wavelike motion to long-time diffusive motion. We study the relaxation of active Brownian particles from an instantaneous source, and provide an explanation for the nonmonotonicity observed in the intermediate scattering function. Using our simple kinetic model we provide the density distribution for the diffusion of active particles released from a line source as a function of time, position, and the ratio of the activity to thermal energy. We extend our analysis to include the effects of an external field on particle spreading to further understand how reorientation events in the active force vector affect relaxation. The strength of the applied external field is shown to be inversely proportional to the decay of the wavelike structure. Our theoretical description for the evolution of the number density agrees with Brownian dynamic simulation data.
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Affiliation(s)
- A R Dulaney
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - J F Brady
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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33
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Bickmann J, Wittkowski R. Predictive local field theory for interacting active Brownian spheres in two spatial dimensions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:214001. [PMID: 31791019 DOI: 10.1088/1361-648x/ab5e0e] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We present a predictive local field theory for the nonequilibrium dynamics of interacting active Brownian particles with a spherical shape in two spatial dimensions. The theory is derived by a rigorous coarse-graining starting from the Langevin equations that describe the trajectories of the individual particles. For high accuracy and generality of the theory, it includes configurational order parameters and derivatives up to infinite order. In addition, we discuss possible approximations of the theory and present reduced models that are easier to apply. We show that our theory contains popular models such as Active Model B+ as special cases and that it provides explicit expressions for the coefficients occurring in these and other, often phenomenological, models. As a further outcome, the theory yields an analytical expression for the density-dependent mean swimming speed of the particles. To demonstrate an application of the new theory, we analyze a simple reduced model of the lowest nontrivial order in derivatives, which is able to predict the onset of motility-induced phase separation of the particles. By a linear stability analysis, an analytical expression for the spinodal corresponding to motility-induced phase separation is obtained. This expression is evaluated for the case of particles interacting repulsively by a Weeks-Chandler-Andersen potential. The analytical predictions for the spinodal associated with these particles are found to be in very good agreement with the results of Brownian dynamics simulations that are based on the same Langevin equations as our theory. Furthermore, the critical point predicted by our analytical results agrees excellently with recent computational results from the literature.
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Affiliation(s)
- Jens Bickmann
- Institut für Theoretische Physik, Center for Soft Nanoscience, Westfälische Wilhelms-Universität Münster, D-48149 Münster, Germany
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34
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Vizsnyiczai G, Frangipane G, Bianchi S, Saglimbeni F, Dell'Arciprete D, Di Leonardo R. A transition to stable one-dimensional swimming enhances E. coli motility through narrow channels. Nat Commun 2020; 11:2340. [PMID: 32393772 PMCID: PMC7214458 DOI: 10.1038/s41467-020-15711-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/20/2020] [Indexed: 01/16/2023] Open
Abstract
Living organisms often display adaptive strategies that allow them to move efficiently even in strong confinement. With one single degree of freedom, the angle of a rotating bundle of flagella, bacteria provide one of the simplest examples of locomotion in the living world. Here we show that a purely physical mechanism, depending on a hydrodynamic stability condition, is responsible for a confinement induced transition between two swimming states in E. coli. While in large channels bacteria always crash onto confining walls, when the cross section falls below a threshold, they leave the walls to move swiftly on a stable swimming trajectory along the channel axis. We investigate this phenomenon for individual cells that are guided through a sequence of micro-fabricated tunnels of decreasing cross section. Our results challenge current theoretical predictions and suggest effective design principles for microrobots by showing that motility based on helical propellers provides a robust swimming strategy for exploring narrow spaces.
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Affiliation(s)
- Gaszton Vizsnyiczai
- Department of Physics, Sapienza University of Rome, 00185, Rome, Italy.,Biological Research Centre, Institute of Biophysics, Szeged, 6726, Hungary
| | - Giacomo Frangipane
- Department of Physics, Sapienza University of Rome, 00185, Rome, Italy.,NANOTEC-CNR, Institute of Nanotechnology, Soft and Living Matter Laboratory, 00185, Rome, Italy
| | - Silvio Bianchi
- NANOTEC-CNR, Institute of Nanotechnology, Soft and Living Matter Laboratory, 00185, Rome, Italy
| | - Filippo Saglimbeni
- NANOTEC-CNR, Institute of Nanotechnology, Soft and Living Matter Laboratory, 00185, Rome, Italy
| | - Dario Dell'Arciprete
- Department of Physics, Sapienza University of Rome, 00185, Rome, Italy.,CNRS-Laboratoire de Physique de l'École Normale Supérieure, 75005, Paris, France
| | - Roberto Di Leonardo
- Department of Physics, Sapienza University of Rome, 00185, Rome, Italy. .,NANOTEC-CNR, Institute of Nanotechnology, Soft and Living Matter Laboratory, 00185, Rome, Italy.
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35
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Gompper G, Winkler RG, Speck T, Solon A, Nardini C, Peruani F, Löwen H, Golestanian R, Kaupp UB, Alvarez L, Kiørboe T, Lauga E, Poon WCK, DeSimone A, Muiños-Landin S, Fischer A, Söker NA, Cichos F, Kapral R, Gaspard P, Ripoll M, Sagues F, Doostmohammadi A, Yeomans JM, Aranson IS, Bechinger C, Stark H, Hemelrijk CK, Nedelec FJ, Sarkar T, Aryaksama T, Lacroix M, Duclos G, Yashunsky V, Silberzan P, Arroyo M, Kale S. The 2020 motile active matter roadmap. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:193001. [PMID: 32058979 DOI: 10.1088/1361-648x/ab6348] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Activity and autonomous motion are fundamental in living and engineering systems. This has stimulated the new field of 'active matter' in recent years, which focuses on the physical aspects of propulsion mechanisms, and on motility-induced emergent collective behavior of a larger number of identical agents. The scale of agents ranges from nanomotors and microswimmers, to cells, fish, birds, and people. Inspired by biological microswimmers, various designs of autonomous synthetic nano- and micromachines have been proposed. Such machines provide the basis for multifunctional, highly responsive, intelligent (artificial) active materials, which exhibit emergent behavior and the ability to perform tasks in response to external stimuli. A major challenge for understanding and designing active matter is their inherent nonequilibrium nature due to persistent energy consumption, which invalidates equilibrium concepts such as free energy, detailed balance, and time-reversal symmetry. Unraveling, predicting, and controlling the behavior of active matter is a truly interdisciplinary endeavor at the interface of biology, chemistry, ecology, engineering, mathematics, and physics. The vast complexity of phenomena and mechanisms involved in the self-organization and dynamics of motile active matter comprises a major challenge. Hence, to advance, and eventually reach a comprehensive understanding, this important research area requires a concerted, synergetic approach of the various disciplines. The 2020 motile active matter roadmap of Journal of Physics: Condensed Matter addresses the current state of the art of the field and provides guidance for both students as well as established scientists in their efforts to advance this fascinating area.
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Affiliation(s)
- Gerhard Gompper
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany
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36
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Hong SH, Gorce JB, Punzmann H, Francois N, Shats M, Xia H. Surface waves control bacterial attachment and formation of biofilms in thin layers. SCIENCE ADVANCES 2020; 6:eaaz9386. [PMID: 32766446 PMCID: PMC7385439 DOI: 10.1126/sciadv.aaz9386] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/19/2020] [Indexed: 05/06/2023]
Abstract
Formation of bacterial biofilms on solid surfaces within a fluid starts when bacteria attach to the substrate. Understanding environmental factors affecting the attachment and the early stages of the biofilm development will help develop methods of controlling the biofilm growth. Here, we show that biofilm formation is strongly affected by the flows in thin layers of bacterial suspensions controlled by surface waves. Deterministic wave patterns promote the growth of patterned biofilms, while wave-driven turbulent motion discourages patterned attachment of bacteria. Strong biofilms form under the wave antinodes, while inactive bacteria and passive particles settle under nodal points. By controlling the wavelength, its amplitude, and horizontal mobility of the wave patterns, one can shape the biofilm and either enhance the growth or discourage the formation of the biofilm. The results suggest that the deterministic wave-driven transport channels, rather than hydrodynamic forces acting on microorganisms, determine the preferred location for the bacterial attachment.
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Affiliation(s)
- Sung-Ha Hong
- Research School of Physics, The Australian National University, Canberra, ACT 2601, Australia
| | - Jean-Baptiste Gorce
- Research School of Physics, The Australian National University, Canberra, ACT 2601, Australia
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37
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A combined rheometry and imaging study of viscosity reduction in bacterial suspensions. Proc Natl Acad Sci U S A 2020; 117:2326-2331. [PMID: 31964833 PMCID: PMC7007524 DOI: 10.1073/pnas.1912690117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Suspending self-propelled "pushers" in a liquid lowers its viscosity. We study how this phenomenon depends on system size in bacterial suspensions using bulk rheometry and particle-tracking rheoimaging. Above the critical bacterial volume fraction needed to decrease the viscosity to zero, [Formula: see text], large-scale collective motion emerges in the quiescent state, and the flow becomes nonlinear. We confirm a theoretical prediction that such instability should be suppressed by confinement. Our results also show that a recent application of active liquid-crystal theory to such systems is untenable.
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38
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Lucidi M, Marsan M, Pudda F, Pirolo M, Frangipani E, Visca P, Cincotti G. Geometrical-optics approach to measure the optical density of bacterial cultures using a LED-based photometer. BIOMEDICAL OPTICS EXPRESS 2019; 10:5600-5610. [PMID: 31799033 PMCID: PMC6865109 DOI: 10.1364/boe.10.005600] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/09/2019] [Accepted: 10/02/2019] [Indexed: 05/11/2023]
Abstract
We develop a suitable geometrical-optics approach and demonstrate that it is possible to measure the optical density (OD) of bacterial cultures using a light emitting diode (LED)-based photometer. We measure both attenuation and spot-size variation, and we compensate for diffraction and stray-light impairment related to the incoherent source and large detection area. The approach is validated for different concentrations of two bacterial species, Escherichia coli and Staphylococcus aureus, that present different shapes and clustering organization.
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Affiliation(s)
- Massimiliano Lucidi
- Engineering Department, University Roma Tre, via Vito Volterra 62, 00146 Rome, Italy
| | - Marco Marsan
- Engineering Department, University Roma Tre, via Vito Volterra 62, 00146 Rome, Italy
| | - Francesco Pudda
- Engineering Department, University Roma Tre, via Vito Volterra 62, 00146 Rome, Italy
| | - Mattia Pirolo
- Department of Science, University Roma Tre, viale Marconi 446, 00146 Rome, Italy
| | - Emanuela Frangipani
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Paolo Visca
- Department of Science, University Roma Tre, viale Marconi 446, 00146 Rome, Italy
| | - Gabriella Cincotti
- Engineering Department, University Roma Tre, via Vito Volterra 62, 00146 Rome, Italy
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39
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LEDAS ŽILVINAS, ŠIMKUS REMIGIJUS, BARONAS ROMAS. COMPUTATIONAL MODELING OF SELF-ORGANIZATION OF BACTERIAL POPULATION CONSISTING OF SUBPOPULATIONS OF ACTIVE AND PASSIVE CELLS. J BIOL SYST 2019. [DOI: 10.1142/s0218339019500153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
This paper deals with the computational modeling of the bioluminescence pattern formation in suspensions of Escherichia coli bacteria. The aim was to develop a computational model for simulating the bacterial populations consisting of two subpopulations of active and passive cells. A suitable model based on Keller–Segel and Fisher equations was proposed and the spatiotemporal patterns were simulated using the finite difference technique. The influence of cell activation, deactivation, chemotactic sensitivity, growth rate and saturating signal production parameter values on the pattern formation was investigated. The proposed model can be used to effectively simulate quasi-one-dimensional spatiotemporal patterns. We provide a simple qualitative explanation of the experimental results and estimated model parameters. In particular, it is argued that the effective model simulates patterns of evaporation-driven convection in open-to-air suspensions of cells that can be either active or passive.
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Affiliation(s)
- ŽILVINAS LEDAS
- Vilnius University Institute of Computer Science, Didlaukio g. 47, LT-08303 Vilnius, Lithuania
| | - REMIGIJUS ŠIMKUS
- Vilnius University Life Sciences Center Institute of Biochemistry, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania
| | - ROMAS BARONAS
- Vilnius University Institute of Computer Science, Didlaukio g. 47, LT-08303 Vilnius, Lithuania
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40
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Koumakis N, Brown AT, Arlt J, Griffiths SE, Martinez VA, Poon WCK. Dynamic optical rectification and delivery of active particles. SOFT MATTER 2019; 15:7026-7032. [PMID: 31435632 DOI: 10.1039/c9sm00799g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We use moving light patterns to control the motion of Escherichia coli bacteria whose motility is photo-activated. Varying the pattern speed controls the magnitude and direction of the bacterial flux, and therefore the accumulation of cells in up- and down-stream reservoirs. We validate our results with two-dimensional simulations and a 1-dimensional analytic model, and use these to explore parameter space. We find that cell accumulation is controlled by a competition between directed flux and undirected, stochastic transport. Our results point to a number of design principles for using moving light patterns and light-activated micro-swimmers in a range of practical applications.
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Affiliation(s)
- Nick Koumakis
- SUPA and School of Physics & Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, UK.
| | - Aidan T Brown
- SUPA and School of Physics & Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, UK.
| | - Jochen Arlt
- SUPA and School of Physics & Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, UK.
| | - Samuel E Griffiths
- SUPA and School of Physics & Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, UK.
| | - Vincent A Martinez
- SUPA and School of Physics & Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, UK.
| | - Wilson C K Poon
- SUPA and School of Physics & Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, UK.
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41
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Mathijssen AJTM, Figueroa-Morales N, Junot G, Clément É, Lindner A, Zöttl A. Oscillatory surface rheotaxis of swimming E. coli bacteria. Nat Commun 2019; 10:3434. [PMID: 31366920 PMCID: PMC6668461 DOI: 10.1038/s41467-019-11360-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 07/08/2019] [Indexed: 11/19/2022] Open
Abstract
Bacterial contamination of biological channels, catheters or water resources is a major threat to public health, which can be amplified by the ability of bacteria to swim upstream. The mechanisms of this 'rheotaxis', the reorientation with respect to flow gradients, are still poorly understood. Here, we follow individual E. coli bacteria swimming at surfaces under shear flow using 3D Lagrangian tracking and fluorescent flagellar labelling. Three transitions are identified with increasing shear rate: Above a first critical shear rate, bacteria shift to swimming upstream. After a second threshold, we report the discovery of an oscillatory rheotaxis. Beyond a third transition, we further observe coexistence of rheotaxis along the positive and negative vorticity directions. A theoretical analysis explains these rheotaxis regimes and predicts the corresponding critical shear rates. Our results shed light on bacterial transport and reveal strategies for contamination prevention, rheotactic cell sorting, and microswimmer navigation in complex flow environments.
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Affiliation(s)
- Arnold J T M Mathijssen
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, CA, 94305, USA
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, 1 Keble Road, OX1 3NP, UK
| | - Nuris Figueroa-Morales
- PMMH, UMR 7636 CNRS-ESPCI-PSL Research University, Sorbonne University, University Paris Diderot, 7-9 quai Saint-Bernard, 75005, Paris, France
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Gaspard Junot
- PMMH, UMR 7636 CNRS-ESPCI-PSL Research University, Sorbonne University, University Paris Diderot, 7-9 quai Saint-Bernard, 75005, Paris, France
| | - Éric Clément
- PMMH, UMR 7636 CNRS-ESPCI-PSL Research University, Sorbonne University, University Paris Diderot, 7-9 quai Saint-Bernard, 75005, Paris, France
| | - Anke Lindner
- PMMH, UMR 7636 CNRS-ESPCI-PSL Research University, Sorbonne University, University Paris Diderot, 7-9 quai Saint-Bernard, 75005, Paris, France.
| | - Andreas Zöttl
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, 1 Keble Road, OX1 3NP, UK.
- PMMH, UMR 7636 CNRS-ESPCI-PSL Research University, Sorbonne University, University Paris Diderot, 7-9 quai Saint-Bernard, 75005, Paris, France.
- Institute for Theoretical Physics, TU Wien, Wiedner Hauptstraße 8-10, Wien, Austria.
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42
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Vissers T, Koumakis N, Hermes M, Brown AT, Schwarz-Linek J, Dawson A, Poon WCK. Dynamical analysis of bacteria in microscopy movies. PLoS One 2019; 14:e0217823. [PMID: 31170194 PMCID: PMC6553751 DOI: 10.1371/journal.pone.0217823] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 05/21/2019] [Indexed: 01/12/2023] Open
Abstract
Recent advances in microscopy, computing power and image processing have enabled the analysis of ever larger datasets of movies of microorganisms to study their behaviour. However, techniques for analysing the dynamics of individual cells from such datasets are not yet widely available in the public domain. We recently demonstrated significant phenotypic heterogeneity in the adhesion of Escherichia coli bacteria to glass surfaces using a new method for the high-throughput analysis of video microscopy data. Here, we present an in-depth analysis of this method and its limitations, and make public our algorithms for following the positions and orientations of individual rod-shaped bacteria from time-series of 2D images to reconstruct their trajectories and characterise their dynamics. We demonstrate in detail how to use these algorithms to identify different types of adhesive dynamics within a clonal population of bacteria sedimenting onto a surface. The effects of measurement errors in cell positions and of limited trajectory durations on our results are discussed.
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Affiliation(s)
- Teun Vissers
- SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, United Kingdom
- * E-mail:
| | - Nick Koumakis
- SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, United Kingdom
| | - Michiel Hermes
- SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, United Kingdom
- Department of Physics, Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, Netherlands
| | - Aidan T. Brown
- SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, United Kingdom
| | - Jana Schwarz-Linek
- SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, United Kingdom
| | - Angela Dawson
- SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, United Kingdom
| | - Wilson C. K. Poon
- SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, United Kingdom
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43
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Invariance properties of bacterial random walks in complex structures. Nat Commun 2019; 10:2442. [PMID: 31164651 PMCID: PMC6547659 DOI: 10.1038/s41467-019-10455-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 05/09/2019] [Indexed: 11/30/2022] Open
Abstract
Motile cells often explore natural environments characterized by a high degree of structural complexity. Moreover cell motility is also intrinsically noisy due to spontaneous random reorientations and speed fluctuations. This interplay of internal and external noise sources gives rise to a complex dynamical behavior that can be strongly sensitive to details and hard to model quantitatively. In striking contrast to this general picture we show that the mean residence time of swimming bacteria inside artificial complex microstructures is quantitatively predicted by a generic invariance property of random walks. We find that while external shape and internal disorder have dramatic effects on the distributions of path lengths and residence times, the corresponding mean values are constrained by the sole free surface to perimeter ratio. As a counterintuitive consequence, bacteria escape faster from structures with higher density of obstacles due to the lower accessible surface. It has been previously shown theoretically that the average path length of random walks inside a closed domain is invariant. Here the authors demonstrate that this invariance property can be used to predict the mean residence time of swimming bacteria exploring structured micro-environments.
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Arlt J, Martinez VA, Dawson A, Pilizota T, Poon WCK. Dynamics-dependent density distribution in active suspensions. Nat Commun 2019; 10:2321. [PMID: 31127122 PMCID: PMC6534614 DOI: 10.1038/s41467-019-10283-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/26/2019] [Indexed: 12/04/2022] Open
Abstract
Self-propelled colloids constitute an important class of intrinsically non-equilibrium matter. Typically, such a particle moves ballistically at short times, but eventually changes its orientation, and displays random-walk behaviour in the long-time limit. Theory predicts that if the velocity of non-interacting swimmers varies spatially in 1D, v(x), then their density ρ(x) satisfies ρ(x) = ρ(0)v(0)/v(x), where x = 0 is an arbitrary reference point. Such a dependence of steady-state ρ(x) on the particle dynamics, which was the qualitative basis of recent work demonstrating how to 'paint' with bacteria, is forbidden in thermal equilibrium. Here we verify this prediction quantitatively by constructing bacteria that swim with an intensity-dependent speed when illuminated and implementing spatially-resolved differential dynamic microscopy (sDDM) for quantitative analysis over millimeter length scales. Applying a spatial light pattern therefore creates a speed profile, along which we find that, indeed, ρ(x)v(x) = constant, provided that steady state is reached.
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Affiliation(s)
- Jochen Arlt
- School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD UK
| | - Vincent A. Martinez
- School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD UK
| | - Angela Dawson
- School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD UK
| | - Teuta Pilizota
- School of Biological Sciences and Centre for Synthetic and Systems Biology, The University of Edinburgh, Alexander Crum Brown Road, Edinburgh, EH9 3FF UK
| | - Wilson C. K. Poon
- School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD UK
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45
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Jepson A, Arlt J, Statham J, Spilman M, Burton K, Wood T, Poon WCK, Martinez VA. High-throughput characterisation of bull semen motility using differential dynamic microscopy. PLoS One 2019; 14:e0202720. [PMID: 30969959 PMCID: PMC6457493 DOI: 10.1371/journal.pone.0202720] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 01/29/2019] [Indexed: 01/21/2023] Open
Abstract
We report a high-throughput technique for characterising the motility of spermatozoa using differential dynamic microscopy. A movie with large field of view (∼10mm2) records thousands of cells (e.g. ≈ 5000 cells even at a low cell density of 20 × 106 cells/ml) at once and yields averaged measurements of the mean ([Formula: see text]) and standard deviation (σ) of the swimming speed, head oscillation amplitude (A0) and frequency (f0), and the fraction of motile spermatozoa (α). Interestingly, we found that the measurement of α is facilitated because the swimming spermatozoa enhance the motion of the non-swimming population. We demonstrate the ease and rapidity of our method by performing on-farm characterisation of bull spermatozoa motility, and validate the technique by comparing laboratory measurements with tracking. Our results confirm the long-standing theoretical prediction that [Formula: see text] for swimming spermatozoa.
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Affiliation(s)
- Alys Jepson
- SUPA, School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
- School of Biosciences, University of Exeter, Exeter, United Kingdom
- * E-mail: (AJ); (VAM)
| | - Jochen Arlt
- SUPA, School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Jonathan Statham
- RAFT Solutions Ltd., Mill Farm, Studley Road, Ripon, HG4 2QR, United Kingdom
| | - Mark Spilman
- RAFT Solutions Ltd., Mill Farm, Studley Road, Ripon, HG4 2QR, United Kingdom
| | - Katie Burton
- RAFT Solutions Ltd., Mill Farm, Studley Road, Ripon, HG4 2QR, United Kingdom
| | - Tiffany Wood
- SUPA, School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Wilson C. K. Poon
- SUPA, School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Vincent A. Martinez
- SUPA, School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
- * E-mail: (AJ); (VAM)
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Sun H, Wang J, Jiang Y, Shen W, Jia F, Wang S, Liao X, Zhang L. Rapid Aerobic Inactivation and Facile Removal of Escherichia coli with Amorphous Zero-Valent Iron Microspheres: Indispensable Roles of Reactive Oxygen Species and Iron Corrosion Products. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:3707-3717. [PMID: 30817131 DOI: 10.1021/acs.est.8b06499] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Zero valent iron (ZVI) is recently regarded as a promising alternative for water disinfection, but still suffers from low efficiency. Herein we demonstrate that amorphous zerovalent iron microspheres (A-mZVI) exhibit both higher inactivation rate and physical removal efficiency for the disinfection of Escherichia coli than conventional crystalline nanoscale ZVI (C-nZVI) under aerobic condition. The enhanced E. coli inactivation performance of A-mZVI was mainly attributed to more reactive oxygen species (ROSs), especially free •OH, generated by the accelerated iron dissolution and molecular oxygen activation in bulk solution. In contrast, C-nZVI preferred to produce surface bound •OH, and its bactericidal ability was thus hampered by the limited physical contact between C-nZVI and E. coli. More importantly, hydrolysis of dissolved iron released from A-mZVI produced plenty of loose FeOOH to wrap E. coli, increasing the dysfunction of E. coli membrane. Meanwhile, this hydrolysis process lowered the stability of E. coli colloid and caused its rapid coagulation and sedimentation, favoring its physical removal. These findings clarify the indispensable roles of ROSs and iron corrosion products during the ZVI disinfection, and also provide a promising disinfection material for water treatment.
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Affiliation(s)
- Hongwei Sun
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, Institute of Environmental & Applied Chemistry, College of Chemistry , Central China Normal University , Wuhan 430079 , P. R. China
| | - Jian Wang
- Hubei Key Lab of Genetic Regulation and Integrative Biology, School of Life Sciences , Central China Normal University , Wuhan 430079 , P. R. China
| | - Yao Jiang
- Hubei Key Lab of Genetic Regulation and Integrative Biology, School of Life Sciences , Central China Normal University , Wuhan 430079 , P. R. China
| | - Wenjuan Shen
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, Institute of Environmental & Applied Chemistry, College of Chemistry , Central China Normal University , Wuhan 430079 , P. R. China
| | - Falong Jia
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, Institute of Environmental & Applied Chemistry, College of Chemistry , Central China Normal University , Wuhan 430079 , P. R. China
| | - Shaohui Wang
- Hubei Key Lab of Genetic Regulation and Integrative Biology, School of Life Sciences , Central China Normal University , Wuhan 430079 , P. R. China
| | - Xiaomei Liao
- Hubei Key Lab of Genetic Regulation and Integrative Biology, School of Life Sciences , Central China Normal University , Wuhan 430079 , P. R. China
| | - Lizhi Zhang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, Institute of Environmental & Applied Chemistry, College of Chemistry , Central China Normal University , Wuhan 430079 , P. R. China
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47
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Colloid Transport in Porous Media: A Review of Classical Mechanisms and Emerging Topics. Transp Porous Media 2019. [DOI: 10.1007/s11242-019-01270-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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48
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Andac T, Weigmann P, Velu SKP, Pinçe E, Volpe G, Volpe G, Callegari A. Active matter alters the growth dynamics of coffee rings. SOFT MATTER 2019; 15:1488-1496. [PMID: 30570633 DOI: 10.1039/c8sm01350k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
How particles are deposited at the edge of evaporating droplets, i.e. the coffee ring effect, plays a crucial role in phenomena as diverse as thin-film deposition, self-assembly, and biofilm formation. Recently, microorganisms have been shown to passively exploit and alter these deposition dynamics to increase their survival chances under harshening conditions. Here, we show that, as the droplet evaporation rate slows down, bacterial mobility starts playing a major role in determining the growth dynamics of the edge of drying droplets. Such motility-induced dynamics can influence several biophysical phenomena, from the formation of biofilms to the spreading of pathogens in humid environments and on surfaces subject to periodic drying. Analogous dynamics in other active matter systems can be exploited for technological applications in printing, coating, and self-assembly, where the standard coffee-ring effect is often a nuisance.
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Affiliation(s)
- Tugba Andac
- Soft Matter Lab, Department of Physics, Bilkent University, Ankara, Turkey.
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49
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Allen RJ, Waclaw B. Bacterial growth: a statistical physicist's guide. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2019; 82:016601. [PMID: 30270850 PMCID: PMC6330087 DOI: 10.1088/1361-6633/aae546] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Bacterial growth presents many beautiful phenomena that pose new theoretical challenges to statistical physicists, and are also amenable to laboratory experimentation. This review provides some of the essential biological background, discusses recent applications of statistical physics in this field, and highlights the potential for future research.
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Affiliation(s)
- Rosalind J Allen
- School of Physics and Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
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50
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Rodenburg J, Paliwal S, de Jager M, Bolhuis PG, Dijkstra M, van Roij R. Ratchet-induced variations in bulk states of an active ideal gas. J Chem Phys 2018; 149:174910. [DOI: 10.1063/1.5048698] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Jeroen Rodenburg
- Institute for Theoretical Physics, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
| | - Siddharth Paliwal
- Soft Condensed Matter Group, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - Marjolein de Jager
- Institute for Theoretical Physics, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
| | - Peter G. Bolhuis
- Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Marjolein Dijkstra
- Soft Condensed Matter Group, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - René van Roij
- Institute for Theoretical Physics, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
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