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Salvadori A, Bonanno C, Serpelloni M, McMeeking RM. On the generation of force required for actin-based motility. Sci Rep 2024; 14:18384. [PMID: 39117762 PMCID: PMC11310465 DOI: 10.1038/s41598-024-69422-3] [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] [Received: 02/27/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024] Open
Abstract
The fundamental question of how forces are generated in a motile cell, a lamellipodium, and a comet tail is the subject of this note. It is now well established that cellular motility results from the polymerization of actin, the most abundant protein in eukaryotic cells, into an interconnected set of filaments. We portray this process in a continuum mechanics framework, claiming that polymerization promotes a mechanical swelling in a narrow zone around the nucleation loci, which ultimately results in cellular or bacterial motility. To this aim, a new paradigm in continuum multi-physics has been designed, departing from the well-known theory of Larché-Cahn chemo-transport-mechanics. In this note, we set up the theory of network growth and compare the outcomes of numerical simulations with experimental evidence.
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Affiliation(s)
- Alberto Salvadori
- The Mechanobiology Research Center, UNIBS, 25123, Brescia, Italy.
- Department of Mechanical and Industrial Engineering, Università degli Studi di Brescia, via Branze 38, 25123, Brescia, Italy.
| | - Claudia Bonanno
- The Mechanobiology Research Center, UNIBS, 25123, Brescia, Italy
| | - Mattia Serpelloni
- The Mechanobiology Research Center, UNIBS, 25123, Brescia, Italy
- Department of Mechanical and Industrial Engineering, Università degli Studi di Brescia, via Branze 38, 25123, Brescia, Italy
| | - Robert M McMeeking
- The Mechanobiology Research Center, UNIBS, 25123, Brescia, Italy
- Materials and Mechanical Engineering Departments, University of California, Santa Barbara, CA, 93106, USA
- School of Engineering, University of Aberdeen, King's College, Aberdeen, AB24 3UE, UK
- INM - Leibniz Institute for New Materials, Campus D2 2, Saarbruecken, Germany
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2
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Lee CT, Bell M, Bonilla-Quintana M, Rangamani P. Biophysical Modeling of Synaptic Plasticity. Annu Rev Biophys 2024; 53:397-426. [PMID: 38382115 DOI: 10.1146/annurev-biophys-072123-124954] [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
Dendritic spines are small, bulbous compartments that function as postsynaptic sites and undergo intense biochemical and biophysical activity. The role of the myriad signaling pathways that are implicated in synaptic plasticity is well studied. A recent abundance of quantitative experimental data has made the events associated with synaptic plasticity amenable to quantitative biophysical modeling. Spines are also fascinating biophysical computational units because spine geometry, signal transduction, and mechanics work in a complex feedback loop to tune synaptic plasticity. In this sense, ideas from modeling cell motility can inspire us to develop multiscale approaches for predictive modeling of synaptic plasticity. In this article, we review the key steps in postsynaptic plasticity with a specific focus on the impact of spine geometry on signaling, cytoskeleton rearrangement, and membrane mechanics. We summarize the main experimental observations and highlight how theory and computation can aid our understanding of these complex processes.
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Affiliation(s)
- Christopher T Lee
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
| | - Miriam Bell
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
| | - Mayte Bonilla-Quintana
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
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3
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Zhu K, Guo X, Chandrasekaran A, Miao X, Rangamani P, Zhao W, Miao Y. Membrane curvature catalyzes actin nucleation through nano-scale condensation of N-WASP-FBP17. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591054. [PMID: 38712166 PMCID: PMC11071460 DOI: 10.1101/2024.04.25.591054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Actin remodeling is spatiotemporally regulated by surface topographical cues on the membrane for signaling across diverse biological processes. Yet, the mechanism dynamic membrane curvature prompts quick actin cytoskeletal changes in signaling remain elusive. Leveraging the precision of nanolithography to control membrane curvature, we reconstructed catalytic reactions from the detection of nano-scale curvature by sensing molecules to the initiation of actin polymerization, which is challenging to study quantitatively in living cells. We show that this process occurs via topographical signal-triggered condensation and activation of the actin nucleation-promoting factor (NPF), Neuronal Wiskott-Aldrich Syndrome protein (N-WASP), which is orchestrated by curvature-sensing BAR-domain protein FBP17. Such N-WASP activation is fine-tuned by optimizing FBP17 to N-WASP stoichiometry over different curvature radii, allowing a curvature-guided macromolecular assembly pattern for polymerizing actin network locally. Our findings shed light on the intricate relationship between changes in curvature and actin remodeling via spatiotemporal regulation of NPF/BAR complex condensation.
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4
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Pezeshkian W, Ipsen JH. Mesoscale simulation of biomembranes with FreeDTS. Nat Commun 2024; 15:548. [PMID: 38228588 PMCID: PMC10792169 DOI: 10.1038/s41467-024-44819-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 01/05/2024] [Indexed: 01/18/2024] Open
Abstract
We present FreeDTS software for performing computational research on biomembranes at the mesoscale. In this software, a membrane is represented by a dynamically triangulated surface equipped with vertex-based inclusions to integrate the effects of integral and peripheral membrane proteins. Several algorithms are included in the software to simulate complex membranes at different conditions such as framed membranes with constant tension, vesicles and high-genus membranes with various fixed volumes or constant pressure differences and applying external forces to membrane regions. Furthermore, the software allows the user to turn off the shape evolution of the membrane and focus solely on the organization of proteins. As a result, we can take realistic membrane shapes obtained from, for example, cryo-electron tomography and backmap them into a finer simulation model. In addition to many biomembrane applications, this software brings us a step closer to simulating realistic biomembranes with molecular resolution. Here we provide several interesting showcases of the power of the software but leave a wide range of potential applications for interested users.
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Affiliation(s)
- Weria Pezeshkian
- Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100, Copenhagen, Denmark.
| | - John H Ipsen
- MEMPHYS/PhyLife, Department of Physics, Chemistry and Pharmacy (FKF), University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
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5
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Johnson GT, Agmon E, Akamatsu M, Lundberg E, Lyons B, Ouyang W, Quintero-Carmona OA, Riel-Mehan M, Rafelski S, Horwitz R. Building the next generation of virtual cells to understand cellular biology. Biophys J 2023; 122:3560-3569. [PMID: 37050874 PMCID: PMC10541477 DOI: 10.1016/j.bpj.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/19/2023] [Accepted: 04/06/2023] [Indexed: 04/14/2023] Open
Abstract
Cell science has made significant progress by focusing on understanding individual cellular processes through reductionist approaches. However, the sheer volume of knowledge collected presents challenges in integrating this information across different scales of space and time to comprehend cellular behaviors, as well as making the data and methods more accessible for the community to tackle complex biological questions. This perspective proposes the creation of next-generation virtual cells, which are dynamic 3D models that integrate information from diverse sources, including simulations, biophysical models, image-based models, and evidence-based knowledge graphs. These virtual cells would provide statistically accurate and holistic views of real cells, bridging the gap between theoretical concepts and experimental data, and facilitating productive new collaborations among researchers across related fields.
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Affiliation(s)
| | - Eran Agmon
- Center for Cell Analysis and Modeling, University of Connecticut Health, Farmington, Connecticut
| | - Matthew Akamatsu
- Department of Biology, University of Washington, Seattle, Washington
| | - Emma Lundberg
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden; Department of Bioengineering, Stanford University, Stanford, California; Department of Pathology, Stanford University, Stanford, California; Chan Zuckerberg Biohub, San Francisco, California
| | - Blair Lyons
- Allen Institute for Cell Science, Seattle, Washington
| | - Wei Ouyang
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | | | | | - Rick Horwitz
- Allen Institute for Cell Science, Seattle, Washington.
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6
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Ni H, Ni Q, Papoian GA, Trache A, Jiang Y. Myosin and [Formula: see text]-actinin regulation of stress fiber contractility under tensile stress. Sci Rep 2023; 13:8662. [PMID: 37248294 PMCID: PMC10227020 DOI: 10.1038/s41598-023-35675-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/19/2023] [Indexed: 05/31/2023] Open
Abstract
Stress fibers are actomyosin bundles that regulate cellular mechanosensation and force transduction. Interacting with the extracellular matrix through focal adhesion complexes, stress fibers are highly dynamic structures regulated by myosin motors and crosslinking proteins. Under external mechanical stimuli such as tensile forces, the stress fiber remodels its architecture to adapt to external cues, displaying properties of viscoelastic materials. How the structural remodeling of stress fibers is related to the generation of contractile force is not well understood. In this work, we simulate mechanochemical dynamics and force generation of stress fibers using the molecular simulation platform MEDYAN. We model stress fiber as two connecting bipolar bundles attached at the ends to focal adhesion complexes. The simulated stress fibers generate contractile force that is regulated by myosin motors and [Formula: see text]-actinin crosslinkers. We find that stress fibers enhance contractility by reducing the distance between actin filaments to increase crosslinker binding, and this structural remodeling ability depends on the crosslinker turnover rate. Under tensile pulling force, the stress fiber shows an instantaneous increase of the contractile forces followed by a slow relaxation into a new steady state. While the new steady state contractility after pulling depends only on the overlap between actin bundles, the short-term contractility enhancement is sensitive to the tensile pulling distance. We further show that this mechanical response is also sensitive to the crosslinker turnover rate. Our results provide new insights into the stress fiber mechanics that have significant implications for understanding cellular adaptation to mechanical signaling.
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Affiliation(s)
- Haoran Ni
- Institute for Physical Science and Technology, University of Maryland, College Park, MD, USA
| | - Qin Ni
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA
| | - Garegin A. Papoian
- Institute for Physical Science and Technology, University of Maryland, College Park, MD, USA
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Andreea Trache
- Department of Medical Physiology, Texas A &M University Health Science Center, Bryan, TX, USA
- Department of Biomedical Engineering, Texas A &M University, College Station, TX, USA
| | - Yi Jiang
- Department of Mathematics and Statistics, Georgia State University, Atlanta, GA, USA
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7
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Fu Y, Johnson ME. Modeling membrane reshaping driven by dynamic protein assemblies. Curr Opin Struct Biol 2023; 78:102505. [PMID: 36528994 PMCID: PMC9908840 DOI: 10.1016/j.sbi.2022.102505] [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: 08/23/2022] [Revised: 11/02/2022] [Accepted: 11/07/2022] [Indexed: 12/23/2022]
Abstract
Remodeling of membranes in living systems is almost universally coupled to self-assembly of soluble proteins. Proteins assemble into semi-rigid shells that reshape attached membranes, and into filaments that protrude membranes. These assemblies are temporary, building from reversible protein and membrane interactions that must nucleate in the proper location. The interactions are strongly influenced by the nonequilibrium environment of the cell, such as gradients of components or active modifications by kinases. From a modeling perspective, understanding mechanisms and control thus requires 1. time-dependent approaches that ideally incorporate 2. macromolecular structure, 3. out-of-equilibrium processes, and 4. deformable membranes over microns and seconds. Realistically, tradeoffs must be made with these last three features. However, we see recent developments from the highly coarsened molecule-based scale, the continuum reaction-diffusion scale, and hybrid approaches as stimulating efforts in diverse applications. We discuss here methodological advances and progress towards simulating these processes as they occur physiologically.
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Affiliation(s)
- Yiben Fu
- T. C. Jenkins Department of Biophysics, The Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Margaret E Johnson
- T. C. Jenkins Department of Biophysics, The Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA.
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8
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Cockerell A, Wright L, Dattani A, Guo G, Smith A, Tsaneva-Atanasova K, Richards DM. Biophysical models of early mammalian embryogenesis. Stem Cell Reports 2023; 18:26-46. [PMID: 36630902 PMCID: PMC9860129 DOI: 10.1016/j.stemcr.2022.11.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 11/02/2022] [Accepted: 11/24/2022] [Indexed: 01/12/2023] Open
Abstract
Embryo development is a critical and fascinating stage in the life cycle of many organisms. Despite decades of research, the earliest stages of mammalian embryogenesis are still poorly understood, caused by a scarcity of high-resolution spatial and temporal data, the use of only a few model organisms, and a paucity of truly multidisciplinary approaches that combine biological research with biophysical modeling and computational simulation. Here, we explain the theoretical frameworks and biophysical processes that are best suited to modeling the early mammalian embryo, review a comprehensive list of previous models, and discuss the most promising avenues for future work.
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Affiliation(s)
- Alaina Cockerell
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Liam Wright
- Department of Mathematics, University of Exeter, North Park Road, Exeter EX4 4QF, UK
| | - Anish Dattani
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Ge Guo
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Austin Smith
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Krasimira Tsaneva-Atanasova
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK; Department of Mathematics, University of Exeter, North Park Road, Exeter EX4 4QF, UK; EPSRC Hub for Quantitative Modelling in Healthcare, University of Exeter, Exeter EX4 4QJ, UK; Department of Bioinformatics and Mathematical Modelling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 105 Acad. G. Bonchev Street, 1113 Sofia, Bulgaria
| | - David M Richards
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK; Department of Physics and Astronomy, University of Exeter, North Park Road, Exeter EX4 4QL, UK.
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9
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Iyer P, Gompper G, Fedosov DA. Non-equilibrium shapes and dynamics of active vesicles. SOFT MATTER 2022; 18:6868-6881. [PMID: 36043635 DOI: 10.1039/d2sm00622g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Active vesicles, constructed through the confinement of self-propelled particles (SPPs) inside a lipid membrane shell, exhibit a large variety of non-equilibrium shapes, ranging from the formation of local tethers and dendritic conformations, to prolate and bola-like structures. To better understand the behavior of active vesicles, we perform simulations of membranes modelled as dynamically triangulated surfaces enclosing active Brownian particles. A systematic analysis of membrane deformations and SPP clustering, as a function of SPP activity and volume fraction inside the vesicle is carried out. Distributions of membrane local curvature, and the clustering and mobility of SPPs obtained from simulations of active vesicles are analysed. There exists a feedback mechanism between the enhancement of membrane curvature, the formation of clusters of active particles, and local or global changes in vesicle shape. The emergence of active tension due to the activity of SPPs can well be captured by the Young-Laplace equation. Furthermore, a simple numerical method for tether detection is presented and used to determine correlations between the number of tethers, their length, and local curvature. We also provide several geometrical arguments to explain different tether characteristics for various conditions. These results contribute to the future development of steerable active vesicles or soft micro-robots whose behaviour can be controlled and used for potential applications.
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Affiliation(s)
- Priyanka Iyer
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany.
| | - Gerhard Gompper
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany.
| | - Dmitry A Fedosov
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany.
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10
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Mondal A, Morrison G. Compression-induced buckling of a semiflexible filament in two and three dimensions. J Chem Phys 2022; 157:104903. [DOI: 10.1063/5.0104910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The ability of biomolecules to exert forces on their surroundings or resist compression from the environment is essential in a variety of biologically relevant contexts. For filaments in the low-temperature limit and under a constant compressive force, Euler buckling theory predicts a sudden transition from a compressed to a bent state in these slender rods. In this paper, we use a mean-field theory to show that if a semiflexible chain is compressed at a finite temperature with a fixed end-to-end distance (permitting fluctuations in the compressive forces), it exhibits a continuous phase transition to a buckled state at a critical level of compression. We determine a quantitatively accurate prediction of the transverse position distribution function of the midpoint of the chain that indicates this transition. We find the mean compressive forces are non-monotonic as the extension of the filament varies, consistent with the observation that strongly buckled filaments are less able to bear an external load. We also find that for the fixed extension (isometric) ensemble, the buckling transition does not coincide with the local minimum of the mean force (in contrast to Euler buckling). We also show the theory is highly sensitive to fluctuations in length in two dimensions, and that the buckling transition can still be accurately recovered by accounting for those fluctuations. These predictions may be useful in understanding the behavior of filamentous biomolecules compressed by fluctuating forces, relevant in a variety of biological contexts.
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Affiliation(s)
- Ananya Mondal
- Physics, University of Houston, United States of America
| | - Greg Morrison
- Physics, University of Houston, United States of America
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11
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Okuda S, Sato K, Hiraiwa T. Continuum modeling of non-conservative fluid membrane for simulating long-term cell dynamics. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2022; 45:69. [PMID: 35984568 DOI: 10.1140/epje/s10189-022-00223-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/30/2022] [Indexed: 06/15/2023]
Abstract
Living cells actively deform and move by their force generations in three-dimensional (3D) space. These 3D cell dynamics occur over a long-term time scale, ranging from tens of minutes to days. On such a time scale, turnover of cell membrane constituents due to endocytosis and exocytosis cannot be ignored, i.e., the surface membrane dynamically deforms without mass conservation. Although membrane turnover is essential for large deformation of cells, there is no computational framework yet to simulate long-term cell dynamics with a non-conservative fluidic membrane. In this paper, we proposed a computational framework for simulating the long-term dynamics of a cell membrane in 3D space. For this purpose, in the proposed framework, the cell surface membrane is treated as a viscous fluid membrane without mass conservation. Cell shape is discretized by a triangular mesh, and its dynamics are expressed by effective energy and dissipation function. The mesh structure, distorted by membrane motion, is dynamically optimized by introducing a modified dynamic remeshing method. To validate the proposed framework, numerical simulations were performed, showing that the membrane flow is reproduced in a physically consistent manner and that the artificial effects of the remeshing method were negligible. To further demonstrate the applicability of the proposed framework, numerical simulations of cell migration induced by a mechanism similar to the Marangoni effect, i.e., the polarized surface tension actively generated by the cell, were performed. The observed cell behaviors agreed with existing analytical solutions, indicating that the proposed computational framework can quantitatively reproduce long-term active cell dynamics with membrane turnover. Based on the simple description of cell membrane dynamics, this framework provides a useful basis for analyzing various cell shaping and movement.
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Affiliation(s)
- Satoru Okuda
- Nano Life Science Institute, Kakuma-machi, Kanazawa, Japan.
| | - Katsuhiko Sato
- Research Institute for Electronic Science, Hokkaido University, Sapporo, Japan
- Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Tetsuya Hiraiwa
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
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12
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Natsume Y. Thermo-Statistical Effects of Inclusions on Vesicles: Division into Multispheres and Polyhedral Deformation. MEMBRANES 2022; 12:608. [PMID: 35736315 PMCID: PMC9229943 DOI: 10.3390/membranes12060608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 12/10/2022]
Abstract
The construction of simple cellular models has attracted much attention as a way to explore the origin of life or elucidate the mechanisms of cell division. In the absence of complex regulatory systems, some bacteria spontaneously divide through thermostatistically elucidated mechanisms, and incorporating these simple physical principles could help to construct primitive or artificial cells. Because thermodynamic interactions play an essential role in such mechanisms, this review discusses the thermodynamic aspects of spontaneous division models of vesicles that contain a high density of inclusions, with their membrane serving as a boundary. Vesicles with highly dense inclusions are deformed according to the volume-to-area ratio. The phase separation of beads at specific intermediate volume fractions and the associated polyhedral deformation of the membrane are considered in relation to the Alder transition. Current advances in the development of a membrane-growth vesicular model are summarized. The thermostatistical understanding of these mechanisms could become a cornerstone for the construction of vesicular models that display spontaneous cell division.
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Affiliation(s)
- Yuno Natsume
- Schoolteacher Training Course/Natural Sciences, Cooperative Faculty of Education, Utsunomiya University, Mine-machi 350, Utsunomiya 321-8505, Japan;
- Institute for Promotion of Research Center for Bioscience Research and Education, Utsunomiya University, Mine-machi 350, Utsunomiya 321-8505, Japan
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13
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Luthey-Schulten Z, Thornburg ZR, Gilbert BR. Integrating cellular and molecular structures and dynamics into whole-cell models. Curr Opin Struct Biol 2022; 75:102392. [PMID: 35623188 DOI: 10.1016/j.sbi.2022.102392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 11/03/2022]
Abstract
A complete description of the state of the cell requires knowledge of its size, shape, components, intracellular reactions, and interactions with its environment-all of these as a function of time and cell growth. Adding to this list is the need for theoretical models and simulations that integrate and help to interpret this daunting amount of experimental data. It seems like an overwhelming list of requirements, but progress is being made on many fronts. In this review, we discuss the current challenges and problems in obtaining sufficient information about each aspect of a dynamical whole-cell model (DWCM) for simple and well-studied bacterial systems.
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Affiliation(s)
- Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, USA; Center for the Physics of the Living Cell, University of Illinois at Urbana-Champaign, USA.
| | - Zane R Thornburg
- Department of Chemistry, University of Illinois at Urbana-Champaign, USA
| | - Benjamin R Gilbert
- Department of Chemistry, University of Illinois at Urbana-Champaign, USA
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14
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Peterson MSE, Baskaran A, Hagan MF. Vesicle shape transformations driven by confined active filaments. Nat Commun 2021; 12:7247. [PMID: 34903731 PMCID: PMC8668962 DOI: 10.1038/s41467-021-27310-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 11/12/2021] [Indexed: 12/02/2022] Open
Abstract
In active matter systems, deformable boundaries provide a mechanism to organize internal active stresses. To study a minimal model of such a system, we perform particle-based simulations of an elastic vesicle containing a collection of polar active filaments. The interplay between the active stress organization due to interparticle interactions and that due to the deformability of the confinement leads to a variety of filament spatiotemporal organizations that have not been observed in bulk systems or under rigid confinement, including highly-aligned rings and caps. In turn, these filament assemblies drive dramatic and tunable transformations of the vesicle shape and its dynamics. We present simple scaling models that reveal the mechanisms underlying these emergent behaviors and yield design principles for engineering active materials with targeted shape dynamics.
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Affiliation(s)
- Matthew S E Peterson
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA, 02453, United States
| | - Aparna Baskaran
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA, 02453, United States.
| | - Michael F Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA, 02453, United States.
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