1
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Newman SA. Form, function, mind: What doesn't compute (and what might). Biochem Biophys Res Commun 2024; 721:150141. [PMID: 38781663 DOI: 10.1016/j.bbrc.2024.150141] [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: 10/24/2023] [Revised: 03/07/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
The applicability of computational and dynamical systems models to organisms is scrutinized, using examples from developmental biology and cognition. Developmental morphogenesis is dependent on the inherent material properties of developing animal (metazoan) tissues, a non-computational modality, but cell differentiation, which utilizes chromatin-based revisable memory banks and program-like function-calling, via the developmental gene co-expression system unique to the metazoans, has a quasi-computational basis. Multi-attractor dynamical models are argued to be misapplied to global properties of development, and it is suggested that along with computationalism, classic forms of dynamicism are similarly unsuitable to accounting for cognitive phenomena. Proposals are made for treating brains and other nervous tissues as novel forms of excitable matter with inherent properties which enable the intensification of cell-based basal cognition capabilities present throughout the tree of life. Finally, some connections are drawn between the viewpoint described here and active inference models of cognition, such as the Free Energy Principle.
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2
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Levin M. Self-Improvising Memory: A Perspective on Memories as Agential, Dynamically Reinterpreting Cognitive Glue. ENTROPY (BASEL, SWITZERLAND) 2024; 26:481. [PMID: 38920491 PMCID: PMC11203334 DOI: 10.3390/e26060481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 06/27/2024]
Abstract
Many studies on memory emphasize the material substrate and mechanisms by which data can be stored and reliably read out. Here, I focus on complementary aspects: the need for agents to dynamically reinterpret and modify memories to suit their ever-changing selves and environment. Using examples from developmental biology, evolution, and synthetic bioengineering, in addition to neuroscience, I propose that a perspective on memory as preserving salience, not fidelity, is applicable to many phenomena on scales from cells to societies. Continuous commitment to creative, adaptive confabulation, from the molecular to the behavioral levels, is the answer to the persistence paradox as it applies to individuals and whole lineages. I also speculate that a substrate-independent, processual view of life and mind suggests that memories, as patterns in the excitable medium of cognitive systems, could be seen as active agents in the sense-making process. I explore a view of life as a diverse set of embodied perspectives-nested agents who interpret each other's and their own past messages and actions as best as they can (polycomputation). This synthesis suggests unifying symmetries across scales and disciplines, which is of relevance to research programs in Diverse Intelligence and the engineering of novel embodied minds.
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Affiliation(s)
- Michael Levin
- Department of Biology, Allen Discovery Center, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155-4243, USA
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3
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Tajvidi Safa B, Huang C, Kabla A, Yang R. Active viscoelastic models for cell and tissue mechanics. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231074. [PMID: 38660600 PMCID: PMC11040246 DOI: 10.1098/rsos.231074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 02/01/2024] [Accepted: 02/25/2024] [Indexed: 04/26/2024]
Abstract
Living cells are out of equilibrium active materials. Cell-generated forces are transmitted across the cytoskeleton network and to the extracellular environment. These active force interactions shape cellular mechanical behaviour, trigger mechano-sensing, regulate cell adaptation to the microenvironment and can affect disease outcomes. In recent years, the mechanobiology community has witnessed the emergence of many experimental and theoretical approaches to study cells as mechanically active materials. In this review, we highlight recent advancements in incorporating active characteristics of cellular behaviour at different length scales into classic viscoelastic models by either adding an active tension-generating element or adjusting the resting length of an elastic element in the model. Summarizing the two groups of approaches, we will review the formulation and application of these models to understand cellular adaptation mechanisms in response to various types of mechanical stimuli, such as the effect of extracellular matrix properties and external loadings or deformations.
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Affiliation(s)
- Bahareh Tajvidi Safa
- Department of Mechanical and Materials Engineering, University of Nebraska-Lincoln, Lincoln, NE68588, USA
| | - Changjin Huang
- School of Mechanical & Aerospace Engineering, Nanyang Technological University, Singapore639798, Singapore
| | - Alexandre Kabla
- Department of Engineering, University of Cambridge, CambridgeCB2 1PZ, UK
| | - Ruiguo Yang
- Department of Mechanical and Materials Engineering, University of Nebraska-Lincoln, Lincoln, NE68588, USA
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI48824, USA
- Institute for Quantitative Health Science and Engineering (IQ), Michigan State University, East Lansing, MI48824, USA
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4
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Fu H, Cao N, Zeng W, Liao M, Yao S, Zhou J, Zhang W. Pumping Small Molecules Selectively through an Energy-Assisted Assembling Process at Nonequilibrium States. J Am Chem Soc 2024; 146:3323-3330. [PMID: 38273768 DOI: 10.1021/jacs.3c12228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
In living organisms, precise control over the spatial and temporal distribution of molecules, including pheromones, is crucial. This level of control is equally important for the development of artificial active materials. In this study, we successfully controlled the distribution of small molecules in the system at nonequilibrium states by actively transporting them, even against the apparent concentration gradient, with high selectivity. As a demonstration, in the aqueous solution of acid orange (AO7) and TMC10COOH, we found that AO7 molecules can coassemble with transient anhydride (TMC10CO)2O to form larger assemblies in the presence of chemical fuel 1-ethyl-3-(3-(dimethylamino)propyl) carbodiimide hydrochloride (EDC). This led to a decrease in local free AO7 concentration and caused AO7 molecules from other locations in the solution to move toward the assemblies. Consequently, AO7 accumulates at the location where EDC was injected. By continuously injecting EDC, we could maintain a stable high value of the apparent AO7 concentration at the injection point. We also observed that this process which operated at nonequilibrium states exhibited high selectivity.
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Affiliation(s)
- Huimin Fu
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, P. R. China
| | - Nengjie Cao
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, P. R. China
| | - Wang Zeng
- National Centre for Inorganic Mass Spectrometry in Shanghai, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050, P. R. China
| | - Min Liao
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, P. R. China
| | - Shenglin Yao
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, P. R. China
| | - Jiajia Zhou
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, P. R. China
| | - Wei Zhang
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, P. R. China
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5
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Livne G, Gat S, Armon S, Bernheim-Groswasser A. Self-assembled active actomyosin gels spontaneously curve and wrinkle similar to biological cells and tissues. Proc Natl Acad Sci U S A 2024; 121:e2309125121. [PMID: 38175871 PMCID: PMC10786314 DOI: 10.1073/pnas.2309125121] [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: 05/31/2023] [Accepted: 11/28/2023] [Indexed: 01/06/2024] Open
Abstract
Living systems adopt a diversity of curved and highly dynamic shapes. These diverse morphologies appear on many length scales, from cells to tissues and organismal scales. The common driving force for these dynamic shape changes are contractile stresses generated by myosin motors in the cell cytoskeleton, that converts chemical energy into mechanical work. A good understanding of how contractile stresses in the cytoskeleton arise into different three-dimensional (3D) shapes and what are the shape selection rules that determine their final configurations is still lacking. To obtain insight into the relevant physical mechanisms, we recreate the actomyosin cytoskeleton in vitro, with precisely controlled composition and initial geometry. A set of actomyosin gel discs, intrinsically identical but of variable initial geometry, dynamically self-organize into a family of 3D shapes, such as domes and wrinkled shapes, without the need for specific preprogramming or additional regulation. Shape deformation is driven by the spontaneous emergence of stress gradients driven by myosin and is encoded in the initial disc radius to thickness aspect ratio, which may indicate shaping scalability. Our results suggest that while the dynamical pathways may depend on the detailed interactions between the different microscopic components within the gel, the final selected shapes obey the general theory of elastic deformations of thin sheets. Altogether, our results emphasize the importance for the emergence of active stress gradients for buckling-driven shape deformations and provide insights on the mechanically induced spontaneous shape transitions in contractile active matter, revealing potential shared mechanisms with living systems across scales.
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Affiliation(s)
- Gefen Livne
- Department of Chemical Engineering, Ilse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer-Sheva84105, Israel
| | - Shachar Gat
- Department of Chemical Engineering, Ilse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer-Sheva84105, Israel
| | - Shahaf Armon
- Department of Physics, Weizmann Institute of Science, Rehovot76100, Israel
| | - Anne Bernheim-Groswasser
- Department of Chemical Engineering, Ilse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer-Sheva84105, Israel
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Bernheim-Groswasser A, Livne G, Nardinocchi P, Recrosi F, Teresi L. Interplay between activity, elasticity, and liquid transport in self-contractile biopolymer gels. Phys Rev E 2024; 109:014601. [PMID: 38366464 DOI: 10.1103/physreve.109.014601] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/29/2023] [Indexed: 02/18/2024]
Abstract
Active gels play an important role in biology and in inspiring biomimetic active materials, due to their ability to change shape, size, and create their own morphology. We study a particular class of active gels, generated by polymerizing actin in the presence of cross-linkers and clusters of myosin as molecular motors, which exhibit large contractions. The relevant mechanics for these highly swollen gels is the result of the interplay between activity and liquid flow: gel activity yields a structural reorganization of the gel network and produces a flow of liquid that eventually exits from the gel boundary. This dynamics inherits lengthscales that are typical of the liquid flow processes. The analyses we present provide insights into the contraction dynamics, and they focus on the effects of the geometry on both gel velocity and fluid flow.
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Affiliation(s)
| | - Gefen Livne
- Department of Chemical Engineering, Ben-Gurion University, Be'er Sheva 8774624, Israel
| | - Paola Nardinocchi
- Department of Structural Engineering & Geotechnic, Sapienza Università di Roma, 00184 Roma, Italy
| | - Filippo Recrosi
- Department of Structural Engineering & Geotechnic, Sapienza Università di Roma, 00184 Roma, Italy
| | - Luciano Teresi
- Department of Mathematics & Physics, Università Roma Tre, 00146 Roma, Italy
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7
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Abbasi A, Netz RR, Naji A. Non-Markovian Modeling of Nonequilibrium Fluctuations and Dissipation in Active Viscoelastic Biomatter. PHYSICAL REVIEW LETTERS 2023; 131:228202. [PMID: 38101355 DOI: 10.1103/physrevlett.131.228202] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/19/2023] [Indexed: 12/17/2023]
Abstract
Based on a Hamiltonian that incorporates the elastic coupling between a tracer particle and the embedding active viscoelastic biomatter, we derive a generalized non-Markovian Langevin model for the nonequilibrium mechanical tracer response. Our analytical expressions for the frequency-dependent tracer response function and the tracer positional autocorrelation function agree quantitatively with experimental data for red blood cells and actomyosin networks with and without adenosine triphosphate over the entire frequency range and in particular reproduce the low-frequency violation of the fluctuation-dissipation theorem. The viscoelastic power laws, the elastic constants and effective friction coefficients extracted from the experimental data allow straightforward physical interpretation.
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Affiliation(s)
- Amir Abbasi
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Roland R Netz
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Ali Naji
- School of Nano Science, Institute for Research in Fundamental Sciences (IPM), Tehran 19538-33511, Iran
- Department of Physics, College of Science, Sultan Qaboos University, Muscat 123, Oman
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8
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Maji A, Dasbiswas K, Rabin Y. Shape transitions in a network model of active elastic shells. SOFT MATTER 2023; 19:7216-7226. [PMID: 37724013 DOI: 10.1039/d3sm01041d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
Morphogenesis involves the transformation of initially simple shapes, such as multicellular spheroids, into more complex 3D shapes. These shape changes are governed by mechanical forces including molecular motor-generated forces as well as hydrostatic fluid pressure, both of which are actively regulated in living matter through mechano-chemical feedback. Inspired by autonomous, biophysical shape change, such as occurring in the model organism hydra, we introduce a minimal, active, elastic model featuring a network of springs in a globe-like spherical shell geometry. In this model there is coupling between activity and the shape of the shell: if the local curvature of a filament represented by a spring falls below a critical value, its elastic constant is actively changed. This results in deformation of the springs that changes the shape of the shell. By combining excitation of springs and pressure regulation, we show that the shell undergoes a transition from spheroidal to either elongated ellipsoidal or a different spheroidal shape, depending on pressure. There exists a critical pressure at which there is an abrupt change from ellipsoids to spheroids, showing that pressure is potentially a sensitive switch for material shape. We thus offer biologically inspired design principles for autonomous shape transitions in active elastic shells.
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Affiliation(s)
- Ajoy Maji
- Faculty of Biomedical Engineering, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Kinjal Dasbiswas
- Department of Physics, University of California, Merced, Merced, CA 95343, USA
| | - Yitzhak Rabin
- Department of Physics, Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel.
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9
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Paneru G, Tlusty T, Pak HK. Bona fide stochastic resonance under nonGaussian active fluctuations. SOFT MATTER 2023; 19:1356-1362. [PMID: 36723030 DOI: 10.1039/d2sm01449a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
We report on the experimental observation of stochastic resonance (SR) in a nonGaussian active bath without any periodic modulation. A Brownian particle hopping in a nanoscale double-well potential under the influence of nonGaussian correlated noise, with mean interval τP and correlation time τc, shows a series of equally-spaced peaks in the residence time distribution at integral multiples of τP. The strength of the first peak is found to be maximum when the mean residence time d matches the double condition, 4τc ≈ τP ≈ d/2, demonstrating a new type of bona fide SR. The experimental findings agree with a simple model that explains the emergence of SR without periodic modulation of the double-well potential. Additionally, we show that generic SR under periodic modulation, known to degrade in strongly correlated continuous noise, is recovered by the discrete nonGaussian kicks.
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Affiliation(s)
- Govind Paneru
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea.
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Tsvi Tlusty
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea.
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Hyuk Kyu Pak
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea.
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
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10
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Sun F, Zhao W, Shen H, Fan N, Zhang J, Liu Q, Xu C, Luo J, Zhao M, Chen Y, Lam KWK, Yang X, Kwok RTK, Lam JWY, Sun J, Zhang H, Tang BZ. Design of Smart Aggregates: Toward Rapid Clinical Diagnosis of Hyperlipidemia in Human Blood. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2207671. [PMID: 36134528 DOI: 10.1002/adma.202207671] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/10/2022] [Indexed: 06/16/2023]
Abstract
Molecular aggregates with environmental responsive properties are desired for their wide practical applications such as bioprobes. Here, a series of smart near-infrared (NIR) luminogens for hyperlipidemia (HLP) diagnosis is reported. The aggregates of these molecules exhibit a twisted intramolecular charge-transfer effect in aqueous media, but aggregation-induced emission in highly viscous media due to the restriction of the intramolecular motion. These aggregates, which can autonomously respond to different environments via switching the aggregation state without changing their chemical structures are described, as "smart aggregates". Intriguingly, these luminogens demonstrate NIR-II and NIR-III luminescence with ultralarge Stokes shifts (>950 nm). Both in vitro detection and in vivo imaging of HLP can be realized in a mouse model. Linear relationships exist between the emission intensity and multiple pathological parameters in blood samples of HLP patients. Thus, the design of smart aggregate facilitates rapid and accurate detection of HLP and provides a promising attempt in aggregate science.
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Affiliation(s)
- Feiyi Sun
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Guangdong-Hong Kong-Macau Joint Laboratory of Optoelectronic and Magnetic Functional Materials, Division of Life Science, and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, 999077, P. R. China
| | - Wei Zhao
- Department of Anesthesiology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, P. R. China
| | - Hanchen Shen
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Guangdong-Hong Kong-Macau Joint Laboratory of Optoelectronic and Magnetic Functional Materials, Division of Life Science, and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, 999077, P. R. China
| | - Ni Fan
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, 999077, P. R. China
| | - Jianyu Zhang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Guangdong-Hong Kong-Macau Joint Laboratory of Optoelectronic and Magnetic Functional Materials, Division of Life Science, and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, 999077, P. R. China
| | - Qingqing Liu
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, 999077, P. R. China
| | - Changhuo Xu
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Guangdong-Hong Kong-Macau Joint Laboratory of Optoelectronic and Magnetic Functional Materials, Division of Life Science, and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, 999077, P. R. China
| | - Jiaming Luo
- Department of Anesthesiology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, P. R. China
| | - Mengying Zhao
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Guangdong-Hong Kong-Macau Joint Laboratory of Optoelectronic and Magnetic Functional Materials, Division of Life Science, and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, 999077, P. R. China
| | - Yuyang Chen
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Guangdong-Hong Kong-Macau Joint Laboratory of Optoelectronic and Magnetic Functional Materials, Division of Life Science, and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, 999077, P. R. China
| | - Kristy W K Lam
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Guangdong-Hong Kong-Macau Joint Laboratory of Optoelectronic and Magnetic Functional Materials, Division of Life Science, and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, 999077, P. R. China
| | - Xueqin Yang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Guangdong-Hong Kong-Macau Joint Laboratory of Optoelectronic and Magnetic Functional Materials, Division of Life Science, and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, 999077, P. R. China
| | - Ryan T K Kwok
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Guangdong-Hong Kong-Macau Joint Laboratory of Optoelectronic and Magnetic Functional Materials, Division of Life Science, and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, 999077, P. R. China
| | - Jacky W Y Lam
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Guangdong-Hong Kong-Macau Joint Laboratory of Optoelectronic and Magnetic Functional Materials, Division of Life Science, and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, 999077, P. R. China
| | - Jianwei Sun
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Guangdong-Hong Kong-Macau Joint Laboratory of Optoelectronic and Magnetic Functional Materials, Division of Life Science, and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, 999077, P. R. China
| | - Hongfei Zhang
- Department of Anesthesiology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, P. R. China
| | - Ben Zhong Tang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Guangdong-Hong Kong-Macau Joint Laboratory of Optoelectronic and Magnetic Functional Materials, Division of Life Science, and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, 999077, P. R. China
- School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen, 518172, P. R. China
- Center of Aggregation-Induced Emission, South China University of Technology, Guangzhou, 510640, P. R. China
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11
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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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12
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Cytoplasmic forces functionally reorganize nuclear condensates in oocytes. Nat Commun 2022; 13:5070. [PMID: 36038550 PMCID: PMC9424315 DOI: 10.1038/s41467-022-32675-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/05/2022] [Indexed: 12/21/2022] Open
Abstract
Cells remodel their cytoplasm with force-generating cytoskeletal motors. Their activity generates random forces that stir the cytoplasm, agitating and displacing membrane-bound organelles like the nucleus in somatic and germ cells. These forces are transmitted inside the nucleus, yet their consequences on liquid-like biomolecular condensates residing in the nucleus remain unexplored. Here, we probe experimentally and computationally diverse nuclear condensates, that include nuclear speckles, Cajal bodies, and nucleoli, during cytoplasmic remodeling of female germ cells named oocytes. We discover that growing mammalian oocytes deploy cytoplasmic forces to timely impose multiscale reorganization of nuclear condensates for the success of meiotic divisions. These cytoplasmic forces accelerate nuclear condensate collision-coalescence and molecular kinetics within condensates. Disrupting the forces decelerates nuclear condensate reorganization on both scales, which correlates with compromised condensate-associated mRNA processing and hindered oocyte divisions that drive female fertility. We establish that cytoplasmic forces can reorganize nuclear condensates in an evolutionary conserved fashion in insects. Our work implies that cells evolved a mechanism, based on cytoplasmic force tuning, to functionally regulate a broad range of nuclear condensates across scales. This finding opens new perspectives when studying condensate-associated pathologies like cancer, neurodegeneration and viral infections. Cytoskeletal activity generates mechanical forces known to agitate and displace membrane-bound organelles in the cytoplasm. In oocytes, Al Jord et al. discover that these cytoplasmic forces functionally remodel nuclear RNA-processing condensates across scales for developmental success.
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13
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Mao DJ, Qin CR, Tian WD. Kick effect of enzymes causes filament compression. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:284003. [PMID: 35477158 DOI: 10.1088/1361-648x/ac6b09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 04/27/2022] [Indexed: 06/14/2023]
Abstract
We investigate the influence of enzymes on the structure and dynamics of a filament by dissipative particle dynamics simulations. Enzyme exerts a kick force on the filament monomer. We pay particular attention to two factors: the magnitude of kick force and enzyme concentration. Large kick force as well as high enzyme concentration prefers a remarkable compression of the filament reminiscent of the effective depletion interaction owing to an effective increase in enzyme size and the reduction of solvent quality. Additionally, the kick effect gives rise to an increase of enzyme density from the center-of-mass of the filament to its periphery. Moreover, the increase of enzyme concentration and kick force also causes a decrease in relaxation time. Our finding is helpful to understand the role of catalytic force in chemo-mechano-biological function and the filament behavior under chemical reaction via kick-induced change of solvent quality.
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Affiliation(s)
- Dan-Jian Mao
- Center for Soft Condensed Matter Physics & Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, People's Republic of China
| | - Chao-Ran Qin
- Center for Soft Condensed Matter Physics & Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, People's Republic of China
| | - Wen-de Tian
- Center for Soft Condensed Matter Physics & Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, People's Republic of China
- Department of Chemical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States of America
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14
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Abstract
Biological systems display a rich phenomenology of states that resemble the physical states of matter - solid, liquid and gas. These phases result from the interactions between the microscopic constituent components - the cells - that manifest in macroscopic properties such as fluidity, rigidity and resistance to changes in shape and volume. Looked at from such a perspective, phase transitions from a rigid to a flowing state or vice versa define much of what happens in many biological processes especially during early development and diseases such as cancer. Additionally, collectively moving confluent cells can also lead to kinematic phase transitions in biological systems similar to multi-particle systems where the particles can interact and show sub-populations characterised by specific velocities. In this Perspective we discuss the similarities and limitations of the analogy between biological and inert physical systems both from theoretical perspective as well as experimental evidence in biological systems. In understanding such transitions, it is crucial to acknowledge that the macroscopic properties of biological materials and their modifications result from the complex interplay between the microscopic properties of cells including growth or death, neighbour interactions and secretion of matrix, phenomena unique to biological systems. Detecting phase transitions in vivo is technically difficult. We present emerging approaches that address this challenge and may guide our understanding of the organization and macroscopic behaviour of biological tissues.
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Affiliation(s)
- Pierre-François Lenne
- Aix Marseille Univ, CNRS, UMR 7288, IBDM, Turing Center for Living Systems, Marseille, France.
| | - Vikas Trivedi
- European Molecular Biology Laboratory (EMBL), Barcelona, 08003, Spain.
- EMBL Heidelberg, Developmental Biology Unit, Heidelberg, 69117, Germany.
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15
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Digregorio P, Levis D, Cugliandolo LF, Gonnella G, Pagonabarraga I. Unified analysis of topological defects in 2D systems of active and passive disks. SOFT MATTER 2022; 18:566-591. [PMID: 34928290 DOI: 10.1039/d1sm01411k] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We provide a comprehensive quantitative analysis of localized and extended topological defects in the steady state of 2D passive and active repulsive Brownian disk systems. We show that, both in and out-of-equilibrium, the passage from the solid to the hexatic is driven by the unbinding of dislocations, in quantitative agreement with the KTHNY singularity. Instead, extended clusters of defects largely dominate below the solid-hexatic critical line. The latter percolate in the liquid phase very close to the hexatic-liquid transition, both for continuous and discontinuous transitions, in the homogeneous liquid regime. At critical percolation the clusters of defects are fractal with statistical and geometric properties that are independent of the activity and compatible with the universality class of uncorrelated critical percolation. We also characterize the spatial organization of point-like defects and we show that the disclinations are not free, but rather always very near more complex defect structures. At high activity, the bulk of the dense phase generated by Motility-Induced Phase Separation is characterized by a density of point-like defects, and statistics and morphology of defect clusters, set by the amount of activity and not the packing fraction. Hexatic domains within the dense phase are separated by grain-boundaries along which a finite network of topological defects resides, interrupted by gas bubbles in cavitation. This structure is dynamic in the sense that the defect network allows for an unzipping mechanism that leaves free space for gas bubbles to appear, close, and even be released into the dilute phase.
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Affiliation(s)
- Pasquale Digregorio
- Centre Européen de Calcul Atomique et Moléculaire (CECAM), Ecole Polytechnique Fédérale de Lausanne (EPFL), Batochimie, Avenue Forel 2, 1015 Lausanne, Switzerland
| | - Demian Levis
- Departament de Fisica de la Materia Condensada, Universitat de Barcelona, Marti i Franques 1, 08028 Barcelona, Spain
- UBICS University of Barcelona Institute of Complex Systems, Martí i Franquès 1, E08028 Barcelona, Spain
| | - Leticia F Cugliandolo
- Laboratoire de Physique Théorique et Hautes Energies, Sorbonne Université, CNRS UMR 7589, 4 Place Jussieu, 75252 Paris Cedex 05, France
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris Cedex 05, France
| | - Giuseppe Gonnella
- Dipartimento di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, Bari, I-70126, Italy
| | - Ignacio Pagonabarraga
- Centre Européen de Calcul Atomique et Moléculaire (CECAM), Ecole Polytechnique Fédérale de Lausanne (EPFL), Batochimie, Avenue Forel 2, 1015 Lausanne, Switzerland
- Departament de Fisica de la Materia Condensada, Universitat de Barcelona, Marti i Franques 1, 08028 Barcelona, Spain
- UBICS University of Barcelona Institute of Complex Systems, Martí i Franquès 1, E08028 Barcelona, Spain
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16
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Abramson CI, Levin M. Behaviorist approaches to investigating memory and learning: A primer for synthetic biology and bioengineering. Commun Integr Biol 2021; 14:230-247. [PMID: 34925687 PMCID: PMC8677006 DOI: 10.1080/19420889.2021.2005863] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The fields of developmental biology, biomedicine, and artificial life are being revolutionized by advances in synthetic morphology. The next phase of synthetic biology and bioengineering is resulting in the construction of novel organisms (biobots), which exhibit not only morphogenesis and physiology but functional behavior. It is now essential to begin to characterize the behavioral capacity of novel living constructs in terms of their ability to make decisions, form memories, learn from experience, and anticipate future stimuli. These synthetic organisms are highly diverse, and often do not resemble familiar model systems used in behavioral science. Thus, they represent an important context in which to begin to unify and standardize vocabulary and techniques across developmental biology, behavioral ecology, and neuroscience. To facilitate the study of behavior in novel living systems, we present a primer on techniques from the behaviorist tradition that can be used to probe the functions of any organism – natural, chimeric, or synthetic – regardless of the details of their construction or origin. These techniques provide a rich toolkit for advancing the fields of synthetic bioengineering, evolutionary developmental biology, basal cognition, exobiology, and robotics.
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Affiliation(s)
- Charles I Abramson
- Department of Psychology, Laboratory of Comparative Psychology and Behavioral Biology at Oklahoma State University, United States of America
| | - Michael Levin
- Department of Biology, Allen Discovery Center at Tufts University, United States of America
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17
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Matevosyan A, Allahverdyan AE. Nonequilibrium, weak-field-induced cyclotron motion: A mechanism for magnetobiology. Phys Rev E 2021; 104:064407. [PMID: 35030908 DOI: 10.1103/physreve.104.064407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/17/2021] [Indexed: 11/07/2022]
Abstract
There is a long-time quest for understanding physical mechanisms of weak magnetic field interaction with biological matter. Two factors impeded the development of such mechanisms: first, a high (room) temperature of a cellular environment, where a weak, static magnetic field induces a (classically) zero equilibrium response. Second, the friction in the cellular environment is large, preventing a weak field to alter nonequilibrium processes such as a free diffusion of charges. Here we study a class of nonequilibrium steady states of a cellular ion in a confining potential, where the response to a (weak, homogeneous, static) magnetic field survives strong friction and thermal fluctuations. The magnetic field induces a rotational motion of the ion that proceeds with the cyclotron frequency. Such nonequilibrium states are generated by a white noise acting on the ion additionally to the nonlocal (memory-containing) friction and noise generated by an equilibrium thermal bath. The intensity of this white noise can be weak, i.e., much smaller than the thermal noise intensity.
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Affiliation(s)
- Ashot Matevosyan
- University of Cambridge, Cavendish Laboratory, 19 J.J. Thompson Avenue, Cambridge CB3 0HE, United Kingdom.,Alikhanyan National Laboratory (Yerevan Physics Institute), 2 Alikhanyan Brothers street, Yerevan 0036, Armenia
| | - Armen E Allahverdyan
- Alikhanyan National Laboratory (Yerevan Physics Institute), 2 Alikhanyan Brothers street, Yerevan 0036, Armenia.,Yerevan State University, 1 A. Manoogian street, Yerevan 0025, Armenia
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18
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Paneru G, Park JT, Pak HK. Transport and Diffusion Enhancement in Experimentally Realized Non-Gaussian Correlated Ratchets. J Phys Chem Lett 2021; 12:11078-11084. [PMID: 34748337 DOI: 10.1021/acs.jpclett.1c03037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Living cells are known to generate non-Gaussian active fluctuations significantly larger than thermal fluctuations owing to various active processes. Understanding the effect of these active fluctuations on various physicochemical processes, such as the transport of molecular motors, is a fundamental problem in nonequilibrium physics. Therefore, we experimentally and numerically studied an active Brownian ratchet comprising a colloidal particle in an optically generated asymmetric periodic potential driven by non-Gaussian noise having finite-amplitude active bursts, each arriving at random and decaying exponentially. We find that the particle velocity is maximum for relatively sparse bursts with finite correlation time and non-Gaussian distribution. These occasional kicks, which produce Brownian yet non-Gaussian diffusion, are more efficient for transport and diffusion enhancement of the particle than the incessant kicks of active Ornstein-Uhlenbeck noise.
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Affiliation(s)
- Govind Paneru
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jin Tae Park
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Hyuk Kyu Pak
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
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19
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Sinha S, Malmi-Kakkada AN. Interparticle Adhesion Regulates the Surface Roughness of Growing Dense Three-Dimensional Active Particle Aggregates. J Phys Chem B 2021; 125:10445-10451. [PMID: 34499496 DOI: 10.1021/acs.jpcb.1c02758] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Activity and self-generated motion are fundamental features observed in many living and nonliving systems. Given that interparticle adhesive forces can regulate particle dynamics, we investigate how interparticle adhesion strength controls the boundary growth and roughness of active particle aggregates. Using particle based simulations incorporating both activity (birth, death, and growth) and systematic physical interactions (elasticity and adhesion), we establish that interparticle adhesion strength (fad) controls the surface roughness of a densely packed three-dimensional(3D) active particle aggregate expanding into a highly viscous medium. We discover that the surface roughness of a 3D active particle aggregate increases in proportion to the interparticle adhesion strength (fad) and show that asymmetry in the radial and transverse active particle mean-squared displacement (MSD) suppresses 3D surface roughness at lower adhesion strengths. By analyzing the statistical properties of particle displacements at the aggregate periphery, we determine that the 3D surface roughness is driven by the movement of active particle toward the core at high interparticle adhesion strengths. Our results elucidate the physics controlling the expansion of adhesive 3D active particle collectives into a highly viscous medium, with implications into understanding stochastic interface growth in active matter systems characterized by self-generation of particles.
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Affiliation(s)
- Sumit Sinha
- Department of Physics, University of Texas at Austin, Austin, Texas 78712, United States
| | - Abdul N Malmi-Kakkada
- Department of Chemistry and Physics, Augusta University, Augusta, Georgia 30912, United States
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20
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Liu T, Ou JY, Plum E, MacDonald KF, Zheludev NI. Visualization of Subatomic Movements in Nanostructures. NANO LETTERS 2021; 21:7746-7752. [PMID: 34469159 DOI: 10.1021/acs.nanolett.1c02644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Electron microscopy, scanning probe, and optical super-resolution imaging techniques with nanometric resolution are now routinely available but cannot capture the characteristically fast (MHz-GHz frequency) movements of micro-/nano-objects. Meanwhile, optical interferometric techniques can detect high-frequency picometric displacements but only with diffraction-limited lateral resolution. Here, we introduce a motion visualization technique, based on the spectrally resolved detection of secondary electron emission from moving objects, that combines picometric displacement sensitivity with the nanometric spatial (positional/imaging) resolution of electron microscopy. The sensitivity of the technique is quantitatively validated against the thermodynamically defined amplitude of a nanocantilever's Brownian motion. It is further demonstrated in visualizing externally driven modes of cantilever, nanomechanical photonic metamaterial, and MEMS device structures. With a noise floor reaching ∼1 pm/Hz1/2, it can provide for the study of oscillatory movements with subatomic amplitudes, presenting new opportunities for the interrogation of motion in functional structures across the materials, bio- and nanosciences.
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Affiliation(s)
- Tongjun Liu
- Optoelectronics Research Centre and Centre for Photonic Metamaterials, University of Southampton, Highfield, Southampton SO17 1BJ, U.K
| | - Jun-Yu Ou
- Optoelectronics Research Centre and Centre for Photonic Metamaterials, University of Southampton, Highfield, Southampton SO17 1BJ, U.K
| | - Eric Plum
- Optoelectronics Research Centre and Centre for Photonic Metamaterials, University of Southampton, Highfield, Southampton SO17 1BJ, U.K
| | - Kevin F MacDonald
- Optoelectronics Research Centre and Centre for Photonic Metamaterials, University of Southampton, Highfield, Southampton SO17 1BJ, U.K
| | - Nikolay I Zheludev
- Optoelectronics Research Centre and Centre for Photonic Metamaterials, University of Southampton, Highfield, Southampton SO17 1BJ, U.K
- Centre for Disruptive Photonic Technologies, School of Physical and Mathematical Sciences and The Photonics Institute, Nanyang Technological University, Singapore 637378, Singapore
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21
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Olsen KS. Diffusion of active particles with angular velocity reversal. Phys Rev E 2021; 103:052608. [PMID: 34134289 DOI: 10.1103/physreve.103.052608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/26/2021] [Indexed: 11/07/2022]
Abstract
Biological and synthetic microswimmers display a wide range of swimming trajectories depending on driving forces and torques. In this paper we consider a simple overdamped model of self-propelled particles with a constant self-propulsion speed but an angular velocity that varies in time. Specifically, we consider the case of both deterministic and stochastic angular velocity reversals, mimicking several synthetic active matter systems, such as propelled droplets. The orientational correlation function and effective diffusivity is studied using Langevin dynamics simulations and perturbative methods.
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22
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Liu T, Ou JY, MacDonald KF, Zheludev NI. Detection of sub-atomic movement in nanostructures. NANOSCALE ADVANCES 2021; 3:2213-2216. [PMID: 36133771 PMCID: PMC9419005 DOI: 10.1039/d0na01068e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/08/2021] [Indexed: 06/16/2023]
Abstract
Nanoscale objects move fast and oscillate billions of times per second. Such movements occur naturally in the form of thermal (Brownian) motion while stimulated movements underpin the functionality of nano-mechanical sensors and active nano-(electro/opto) mechanical devices. Here we introduce a methodology for detecting such movements, based on the spectral analysis of secondary electron emission from moving nanostructures, that is sensitive to displacements of sub-atomic amplitude. We demonstrate the detection of nanowire Brownian oscillations of ∼10 pm amplitude and hyperspectral mapping of stimulated oscillations of setae on the body of a common flea. The technique opens a range of opportunities for the study of dynamic processes in materials science, nanotechnology and biology.
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Affiliation(s)
- Tongjun Liu
- Optoelectronics Research Centre & Centre for Photonic Metamaterials, University of Southampton SO17 1BJ UK
| | - Jun-Yu Ou
- Optoelectronics Research Centre & Centre for Photonic Metamaterials, University of Southampton SO17 1BJ UK
| | - Kevin F MacDonald
- Optoelectronics Research Centre & Centre for Photonic Metamaterials, University of Southampton SO17 1BJ UK
| | - Nikolay I Zheludev
- Optoelectronics Research Centre & Centre for Photonic Metamaterials, University of Southampton SO17 1BJ UK
- Centre for Disruptive Photonic Technologies & the Photonics Institute, Nanyanag Technological University 637371 Singapore
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23
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Bongard J, Levin M. Living Things Are Not (20th Century) Machines: Updating Mechanism Metaphors in Light of the Modern Science of Machine Behavior. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.650726] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
One of the most useful metaphors for driving scientific and engineering progress has been that of the “machine.” Much controversy exists about the applicability of this concept in the life sciences. Advances in molecular biology have revealed numerous design principles that can be harnessed to understand cells from an engineering perspective, and build novel devices to rationally exploit the laws of chemistry, physics, and computation. At the same time, organicists point to the many unique features of life, especially at larger scales of organization, which have resisted decomposition analysis and artificial implementation. Here, we argue that much of this debate has focused on inessential aspects of machines – classical properties which have been surpassed by advances in modern Machine Behavior and no longer apply. This emerging multidisciplinary field, at the interface of artificial life, machine learning, and synthetic bioengineering, is highlighting the inadequacy of existing definitions. Key terms such as machine, robot, program, software, evolved, designed, etc., need to be revised in light of technological and theoretical advances that have moved past the dated philosophical conceptions that have limited our understanding of both evolved and designed systems. Moving beyond contingent aspects of historical and current machines will enable conceptual tools that embrace inevitable advances in synthetic and hybrid bioengineering and computer science, toward a framework that identifies essential distinctions between fundamental concepts of devices and living agents. Progress in both theory and practical applications requires the establishment of a novel conception of “machines as they could be,” based on the profound lessons of biology at all scales. We sketch a perspective that acknowledges the remarkable, unique aspects of life to help re-define key terms, and identify deep, essential features of concepts for a future in which sharp boundaries between evolved and designed systems will not exist.
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24
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Ferrer BR, Gomez-Solano JR, Arzola AV. Fluid Viscoelasticity Triggers Fast Transitions of a Brownian Particle in a Double Well Optical Potential. PHYSICAL REVIEW LETTERS 2021; 126:108001. [PMID: 33784172 DOI: 10.1103/physrevlett.126.108001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/03/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Thermally activated transitions are ubiquitous in nature, occurring in complex environments which are typically conceived as ideal viscous fluids. We report the first direct observations of a Brownian bead transiting between the wells of a bistable optical potential in a viscoelastic fluid with a single long relaxation time. We precisely characterize both the potential and the fluid, thus enabling a neat comparison between our experimental results and a theoretical model based on the generalized Langevin equation. Our findings reveal a drastic amplification of the transition rates compared to those in a Newtonian fluid, stemming from the relaxation of the fluid during the particle crossing events.
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Affiliation(s)
- Brandon R Ferrer
- Instituto de Física, Universidad Nacional Autónoma de México, Ciudad de México, Codigo Postal 04510, México
| | - Juan Ruben Gomez-Solano
- Instituto de Física, Universidad Nacional Autónoma de México, Ciudad de México, Codigo Postal 04510, México
| | - Alejandro V Arzola
- Instituto de Física, Universidad Nacional Autónoma de México, Ciudad de México, Codigo Postal 04510, México
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25
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Petrelli I, Cugliandolo LF, Gonnella G, Suma A. Effective temperatures in inhomogeneous passive and active bidimensional Brownian particle systems. Phys Rev E 2020; 102:012609. [PMID: 32794963 DOI: 10.1103/physreve.102.012609] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/25/2020] [Indexed: 05/15/2023]
Abstract
We study the stationary dynamics of an active interacting Brownian particle system. We measure the violations of the fluctuation dissipation theorem, and the corresponding effective temperature, in a locally resolved way. Quite naturally, in the homogeneous phases the diffusive properties and effective temperature are also homogeneous. Instead, in the inhomogeneous phases (close to equilibrium and within the MIPS sector) the particles can be separated in two groups with different diffusion properties and effective temperatures. Notably, at fixed activity strength the effective temperatures in the two phases remain distinct and approximately constant within the MIPS region, with values corresponding to the ones of the whole system at the boundaries of this sector of the phase diagram. We complement the study of the globally averaged properties with the theoretical and numerical characterization of the fluctuation distributions of the single-particle diffusion, linear response, and effective temperature in the homogeneous and inhomogeneous phases. We also distinguish the behavior of the (time-delayed) effective temperature from the (instantaneous) kinetic temperature, showing that the former is independent of the friction coefficient.
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Affiliation(s)
- Isabella Petrelli
- Dipartimento di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, Bari, I-70126, Italy
| | - Leticia F Cugliandolo
- Sorbonne Université, Laboratoire de Physique Théorique et Hautes Energies, CNRS UMR 7589, 4 Place Jussieu, 75252 Paris Cedex 05, France
- Institut Universitaire de France, 1 rue Descartes, 75005 Paris, France
| | - Giuseppe Gonnella
- Dipartimento di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, Bari, I-70126, Italy
| | - Antonio Suma
- Dipartimento di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, Bari, I-70126, Italy
- Institute for Computational Molecular Science, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA
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26
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Cao X, Zhang B, Zhao N. Contrastive factors of activity and crowding on conformational properties of a flexible polymer. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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27
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Zhao S, Ren W, Gao W, Tian G, Zhao C, Bao Y, Cui J, Lian Y, Zheng J. Effect of mesoscopic structure of citrus pectin on its emulsifying properties: Compactness is more important than size. J Colloid Interface Sci 2020; 570:80-88. [PMID: 32142905 DOI: 10.1016/j.jcis.2020.02.113] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 02/24/2020] [Accepted: 02/27/2020] [Indexed: 01/29/2023]
Abstract
We previously explored citrus oil emulsion stabilized by citrus pectin. In this report, we characterized key parameters of the citrus pectin mesoscopic structure and their effect on emulsifying capacity, and explored the underlying mechanism by determining the interfacial properties, emulsifying ability, and micromorphology. To generate different mesoscopic structure, citrus pectins were hydrolyzed or regulated by pH and NaCl. Hydrolysis decreased the size of citrus pectin mesoscopic structure with constant compactness, leading to superior interfacial properties but inferior emulsifying ability. In contrast, pH and NaCl regulation decreased the mesoscopic structure size and increased the compactness, and pH- and NaCl-regulated citrus pectin formed a compact absorbed layer at the interface to resist droplet coalescence/flocculation during homogenization. Our results support the importance of compactness of the citrus pectin mesoscopic structure on emulsifying capacity. This study increased our understanding on the relationship between the mesoscopic structures of polysaccharide emulsifier and emulsifying ability.
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Affiliation(s)
- Shaojie Zhao
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wenbo Ren
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wei Gao
- Chenguang Biotech Group Co., Ltd., Hebei 057250, China
| | - Guifang Tian
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chengying Zhao
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuming Bao
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiefen Cui
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yunhe Lian
- Chenguang Biotech Group Co., Ltd., Hebei 057250, China
| | - Jinkai Zheng
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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28
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Cao X, Zhang B, Zhao N. Effective temperature scaled dynamics of a flexible polymer in an active bath. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1730992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Xiuli Cao
- College of Chemistry, Sichuan University, Chengdu, China
| | - Bingjie Zhang
- College of Chemistry, Sichuan University, Chengdu, China
| | - Nanrong Zhao
- College of Chemistry, Sichuan University, Chengdu, China
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29
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Salman OU, Vitale G, Truskinovsky L. Continuum theory of bending-to-stretching transition. Phys Rev E 2019; 100:051001. [PMID: 31869905 DOI: 10.1103/physreve.100.051001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Indexed: 11/07/2022]
Abstract
Transition from bending-dominated to stretching-dominated elastic response in semiflexible fibrous networks plays an important role in the mechanical behavior of cells and tissues. It is induced by changes in network connectivity and relies on the construction of new cross-links. We propose a simple continuum model of this transition with macroscopic strain playing the role of order parameter. An unusual feature of this Landau-type theory is that it is based on a single-well potential. The theory predicts that bending-to-stretching transition should proceed through propagation of the fronts separating domains with affine and nonaffine elastic response.
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Affiliation(s)
- O U Salman
- CNRS, LSPM UPR3407, Université Paris 13, Sorbonne Paris Cité, 93430 Villetaneuse, France
| | - G Vitale
- Laboratoire de Mécanique des Solides, CNRS-UMR 7649, Ecole Polytechnique, Route de Saclay, F-91128 Palaiseau Cedex, France
| | - L Truskinovsky
- PMMH, CNRS-UMR 7636 PSL-ESPCI, 10 Rue Vauquelin, 75005 Paris, France
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Affiliation(s)
- S. Mahdiyeh Mousavi
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Gerhard Gompper
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Roland G. Winkler
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
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