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Wen H, Zhu Y, Peng C, Kumar PBS, Laradji M. Collective vortical motion and vorticity reversals of self-propelled particles on circularly patterned substrates. Phys Rev E 2023; 107:024606. [PMID: 36932499 DOI: 10.1103/physreve.107.024606] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
The collective behavior of self-propelled particles (SPPs) under the combined effects of a circularly patterned substrate and circular confinement is investigated through coarse-grained molecular dynamics simulations of polarized and disjoint ring polymers. The study is performed over a wide range of values of the SPPs packing fraction ϕ[over ¯], motility force F_{D}, and area fraction of the patterned region. At low packing fractions, the SPPs are excluded from the system's center and exhibit a vortical motion that is dominated by the substrate at intermediate values of F_{D}. This exclusion zone is due to the coupling between the driving force and torque induced by the substrate, which induces an outward spiral motion of the SPPs. For high values of F_{D}, the SPPs exclusion from the center is dominated by the confining boundary. At high values of ϕ[over ¯], the substrate pattern leads to reversals in the vorticity, which become quasiperiodic with increasing ϕ[over ¯]. We also found that the substrate pattern is able to separate SPPs based on their motilities.
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Affiliation(s)
- Haosheng Wen
- Department of Physics and Materials Science, The University of Memphis, Memphis, Tennessee 38152, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, USA
| | - Yu Zhu
- Department of Physics and Materials Science, The University of Memphis, Memphis, Tennessee 38152, USA
| | - Chenhui Peng
- Department of Physics and Materials Science, The University of Memphis, Memphis, Tennessee 38152, USA
- Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - P B Sunil Kumar
- Department of Physics, Indian Institute of Technology Palakkad, Palakkad 668557, Kerala, India
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India
| | - Mohamed Laradji
- Department of Physics and Materials Science, The University of Memphis, Memphis, Tennessee 38152, USA
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Shi Y, Chen T, Shaw P, Wang PY. Manipulating Bacterial Biofilms Using Materiobiology and Synthetic Biology Approaches. Front Microbiol 2022; 13:844997. [PMID: 35875573 PMCID: PMC9301480 DOI: 10.3389/fmicb.2022.844997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 06/13/2022] [Indexed: 11/25/2022] Open
Abstract
Bacteria form biofilms on material surfaces within hours. Biofilms are often considered problematic substances in the fields such as biomedical devices and the food industry; however, they are beneficial in other fields such as fermentation, water remediation, and civil engineering. Biofilm properties depend on their genome and the extracellular environment, including pH, shear stress, and matrices topography, stiffness, wettability, and charges during biofilm formation. These surface properties have feedback effects on biofilm formation at different stages. Due to emerging technology such as synthetic biology and genome editing, many studies have focused on functionalizing biofilm for specific applications. Nevertheless, few studies combine these two approaches to produce or modify biofilms. This review summarizes up-to-date materials science and synthetic biology approaches to controlling biofilms. The review proposed a potential research direction in the future that can gain better control of bacteria and biofilms.
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Affiliation(s)
- Yue Shi
- Oujiang Laboratory, Key Laboratory of Alzheimer’s Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, China
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Tingli Chen
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Peter Shaw
- Oujiang Laboratory, Key Laboratory of Alzheimer’s Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, China
| | - Peng-Yuan Wang
- Oujiang Laboratory, Key Laboratory of Alzheimer’s Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, China
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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Biofilm viscoelasticity and nutrient source location control biofilm growth rate, migration rate, and morphology in shear flow. Sci Rep 2021; 11:16118. [PMID: 34373534 PMCID: PMC8352988 DOI: 10.1038/s41598-021-95542-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/27/2021] [Indexed: 02/07/2023] Open
Abstract
We present a numerical model to simulate the growth and deformation of a viscoelastic biofilm in shear flow under different nutrient conditions. The mechanical interaction between the biofilm and the fluid is computed using the Immersed Boundary Method with viscoelastic parameters determined a priori from measurements reported in the literature. Biofilm growth occurs at the biofilm-fluid interface by a stochastic rule that depends on the local nutrient concentration. We compare the growth, migration, and morphology of viscoelastic biofilms with a common relaxation time of 18 min over the range of elastic moduli 10-1000 Pa in different nearby nutrient source configurations. Simulations with shear flow and an upstream or a downstream nutrient source indicate that soft biofilms grow more if nutrients are downstream and stiff biofilms grow more if nutrients are upstream. Also, soft biofilms migrate faster than stiff biofilms toward a downstream nutrient source, and although stiff biofilms migrate toward an upstream nutrient source, soft biofilms do not. Simulations without nutrients show that on the time scale of several hours, soft biofilms develop irregular structures at the biofilm-fluid interface, but stiff biofilms deform little. Our results agree with the biophysical principle that biofilms can adapt to their mechanical and chemical environment by modulating their viscoelastic properties. We also compare the behavior of a purely elastic biofilm to a viscoelastic biofilm with the same elastic modulus of 50 Pa. We find that the elastic biofilm underestimates growth rates and downstream migration rates if the nutrient source is downstream, and it overestimates growth rates and upstream migration rates if the nutrient source is upstream. Future modeling can use our comparison to identify errors that can occur by simulating biofilms as purely elastic structures.
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Rhodeland B, Hoeger K, Ursell T. Bacterial surface motility is modulated by colony-scale flow and granular jamming. J R Soc Interface 2020; 17:20200147. [PMID: 32574537 DOI: 10.1098/rsif.2020.0147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Microbes routinely face the challenge of acquiring territory and resources on wet surfaces. Cells move in large groups inside thin, surface-bound water layers, often achieving speeds of 30 µm s-1 within this environment, where viscous forces dominate over inertial forces (low Reynolds number). The canonical Gram-positive bacterium Bacillus subtilis is a model organism for the study of collective migration over surfaces with groups exhibiting motility on length-scales three orders of magnitude larger than themselves within a few doubling times. Genetic and chemical studies clearly show that the secretion of endogenous surfactants and availability of free surface water are required for this fast group motility. Here, we show that: (i) water availability is a sensitive control parameter modulating an abiotic jamming-like transition that determines whether the group remains fluidized and therefore collectively motile, (ii) groups self-organize into discrete layers as they travel, (iii) group motility does not require proliferation, rather groups are pulled from the front, and (iv) flow within expanding groups is capable of moving material from the parent colony into the expanding tip of a cellular dendrite with implications for expansion into regions of varying nutrient content. Together, these findings illuminate the physical structure of surface-motile groups and demonstrate that physical properties, like cellular packing fraction and flow, regulate motion from the scale of individual cells up to length scales of centimetres.
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Affiliation(s)
- Ben Rhodeland
- Department of Physics, University of Oregon, Eugene OR 97403, USA
| | - Kentaro Hoeger
- Department of Physics, University of Oregon, Eugene OR 97403, USA
| | - Tristan Ursell
- Department of Physics, University of Oregon, Eugene OR 97403, USA.,Institute of Molecular Biology, University of Oregon, Eugene OR 97403, USA.,Materials Science Institute, University of Oregon, Eugene OR 97403, USA
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Zachreson C, Yap X, Gloag ES, Shimoni R, Whitchurch CB, Toth M. Network patterns in exponentially growing two-dimensional biofilms. Phys Rev E 2017; 96:042401. [PMID: 29347525 DOI: 10.1103/physreve.96.042401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Indexed: 06/07/2023]
Abstract
Anisotropic collective patterns occur frequently in the morphogenesis of two-dimensional biofilms. These patterns are often attributed to growth regulation mechanisms and differentiation based on gradients of diffusing nutrients and signaling molecules. Here, we employ a model of bacterial growth dynamics to show that even in the absence of growth regulation or differentiation, confinement by an enclosing medium such as agar can itself lead to stable pattern formation over time scales that are employed in experiments. The underlying mechanism relies on path formation through physical deformation of the enclosing environment.
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Affiliation(s)
- Cameron Zachreson
- School of Mathematical and Physical Sciences, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Xinhui Yap
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Erin S Gloag
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
- Center for Microbial Interface Biology, Ohio State University, 460 West 12th Avenue, Columbus, Ohio 43210, USA
| | - Raz Shimoni
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Cynthia B Whitchurch
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Milos Toth
- School of Mathematical and Physical Sciences, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
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