1
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Zhu G, Gao L, Sun Y, Wei W, Yan LT. Non-equilibrium structural and dynamic behaviors of active polymers in complex and crowded environments. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2024; 87:054601. [PMID: 38608453 DOI: 10.1088/1361-6633/ad3e11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/12/2024] [Indexed: 04/14/2024]
Abstract
Active matter systems, which convert internal chemical energy or energy from the environment into directed motion, are ubiquitous in nature and exhibit a range of emerging non-equilibrium behaviors. However, most of the current works on active matter have been devoted to particles, and the study of active polymers has only recently come into the spotlight due to their prevalence within living organisms. The intricate interplay between activity and conformational degrees of freedom gives rise to novel structural and dynamical behaviors of active polymers. Research in active polymers remarkably broadens diverse concepts of polymer physics, such as molecular architecture, dynamics, scaling and so on, which is of significant importance for the development of new polymer materials with unique performance. Furthermore, active polymers are often found in strongly interacting and crowded systems and in complex environments, so that the understanding of this behavior is essential for future developments of novel polymer-based biomaterials. This review thereby focuses on the study of active polymers in complex and crowded environments, and aims to provide insights into the fundamental physics underlying the adaptive and collective behaviors far from equilibrium, as well as the open challenges that the field is currently facing.
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Affiliation(s)
- Guolong Zhu
- School of Physics and Electronics, Hunan University, Changsha 410082, People's Republic of China
| | - Lijuan Gao
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, People's Republic of China
| | - Yihang Sun
- School of Physics and Electronics, Hunan University, Changsha 410082, People's Republic of China
| | - Wenjie Wei
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, People's Republic of China
| | - Li-Tang Yan
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, People's Republic of China
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2
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Zhang Z, Ou L, Yang K, Yuan B. Energy and Speed Landscapes of the Membrane Internalization Behavior of Soft Nanoparticles. J Phys Chem B 2024; 128:2632-2639. [PMID: 38467492 DOI: 10.1021/acs.jpcb.3c07177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
The cellular endocytosis of nanoparticles (NPs) is a fundamental biological process with significant potential in biomedical applications. However, a comprehensive understanding of the mechanistic aspects of endocytosis and the impact of particle properties on this process remains elusive. In this study, we investigated the membrane-wrapping behavior of soft NPs (SNPs) with varying rigidities using theoretical calculations. Our findings reveal that the membrane-wrapping process of SNPs involves a complex energy change including the possible existence of an energy barrier; moreover, it is found that the location and height of this barrier strongly depend on the mechanistic properties of the NPs and membranes. Additionally, by considering force balance in the membrane-wrapping process, we calculated the speed at which NP is internalized by the membrane, showing a nonmonotonic dependence on particle rigidity and/or wrapping degree. These phenomena can be attributed to competition between different energy components associated with NP-membrane binding, membrane tension, and deformations occurring during SNP-membrane interaction processes. Our results contribute to a deeper understanding of cellular-level endocytosis mechanisms and offer potential applications for soft NPs in biomedicine.
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Affiliation(s)
- Zhenyu Zhang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, Jiangsu,China
| | - Luping Ou
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, Jiangsu,China
| | - Kai Yang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, Jiangsu,China
- Songshan Lake Materials Laboratory, Dongguan 523808, Guangdong,China
| | - Bing Yuan
- Songshan Lake Materials Laboratory, Dongguan 523808, Guangdong,China
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3
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Zhang X, Dai X, Gao L, Xu D, Wan H, Wang Y, Yan LT. The entropy-controlled strategy in self-assembling systems. Chem Soc Rev 2023; 52:6806-6837. [PMID: 37743794 DOI: 10.1039/d3cs00347g] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Self-assembly of various building blocks has been considered as a powerful approach to generate novel materials with tailorable structures and optimal properties. Understanding physicochemical interactions and mechanisms related to structural formation and transitions is of essential importance for this approach. Although it is well-known that diverse forces and energies can significantly contribute to the structures and properties of self-assembling systems, the potential entropic contribution remains less well understood. The past few years have witnessed rapid progress in addressing the entropic effects on the structures, responses, and functions in the self-assembling systems, and many breakthroughs have been achieved. This review provides a framework regarding the entropy-controlled strategy of self-assembly, through which the structures and properties can be tailored by effectively tuning the entropic contribution and its interplay with the enthalpic counterpart. First, we focus on the fundamentals of entropy in thermodynamics and the entropy types that can be explored for self-assembly. Second, we discuss the rules of entropy in regulating the structural organization in self-assembly and delineate the entropic force and superentropic effect. Third, we introduce the basic principles, significance and approaches of the entropy-controlled strategy in self-assembly. Finally, we present the applications where this strategy has been employed in fields like colloids, macromolecular systems and nonequilibrium assembly. This review concludes with a discussion on future directions and future research opportunities for developing and applying the entropy-controlled strategy in complex self-assembling systems.
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Affiliation(s)
- Xuanyu Zhang
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.
| | - Xiaobin Dai
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.
| | - Lijuan Gao
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.
| | - Duo Xu
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.
| | - Haixiao Wan
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.
| | - Yuming Wang
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.
| | - Li-Tang Yan
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.
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4
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Chen H, Dong X, Ou L, Ma C, Yuan B, Yang K. Thermal-controlled cellular uptake of "hot" nanoparticles. NANOSCALE 2023; 15:12718-12727. [PMID: 37470374 DOI: 10.1039/d3nr02449k] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Nanoparticles (NPs) have shown immense potential in the field of biomedical applications, particularly in NP-based photothermal therapy, which offers a remote-controlled approach to achieve precise temperature control for site-specific heating and sub-cellular tumor treatment. However, the molecular mechanisms underlying related cellular activities, such as the cellular uptake behavior of irradiated NPs in photothermal effects, remain elusive. In this study, we conducted a thorough investigation of the interaction between an irradiated NP with elevated temperature (ranging from 270 to 360 K) and a model bilayer membrane composed of DPPC or DOPC using nonequilibrium coarse-grained molecular dynamics simulations with the implicit-solvent Dry Martini force field. We observe that the interaction between a "hot" NP and a membrane is thermally regulated. In addition, the wrapping of membranes around NPs exhibits a strong dependence on the temperature of the irradiated NP, demonstrating a step-like change in behavior. This membrane wrapping effect is attributed to the heat conduction between NPs and membrane lipids, which occurs almost simultaneously with the membrane deformation and wrapping of NPs during the NP-membrane interaction process. Especially, during the process of heat conduction, a gel-to-fluid phase transition of the membrane may occur, which plays a crucial role in determining the deformation behavior of the membrane. Moreover, it is found that the membrane lipids in the two leaflets exhibit obvious and asymmetric molecular-level responses to heat flux, characterized by significant changes in packing states (e.g., the order parameter of lipid tails and area per lipid) and possible interdigitation between lipids. Furthermore, the thermal-controlled wrapping effect is tightly linked to the properties of NPs (e.g., size, NP-lipid affinity) and lipid species. Our findings are valuable for comprehending the thermal-regulated cellular internalization of NPs and offer insights into devising strategies to precisely modulate NP endocytosis by exploiting the interplay between heating and NP properties.
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Affiliation(s)
- Haibo Chen
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, Jiangsu, China.
| | - Xuewei Dong
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, Jiangsu, China.
| | - Luping Ou
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, Jiangsu, China.
| | - Chiyun Ma
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, Jiangsu, China.
| | - Bing Yuan
- Songshan Lake Materials Laboratory, Dongguan 523808, Guangdong, China
| | - Kai Yang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, Jiangsu, China.
- Songshan Lake Materials Laboratory, Dongguan 523808, Guangdong, China
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5
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Xiao K, Ma R, Wu CX. Wrapping dynamics and critical conditions for active nonspherical nanoparticle uptake. Phys Rev E 2023; 107:054401. [PMID: 37329073 DOI: 10.1103/physreve.107.054401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 04/17/2023] [Indexed: 06/18/2023]
Abstract
The cellular uptake of self-propelled nonspherical nanoparticles (NPs) or viruses by cell membrane is crucial in many biological processes, but its universal dynamics have yet to be elucidated. In this study, using the Onsager variational principle, we obtain a general wrapping equation for nonspherical self-propelled nanoparticles. Two analytical critical conditions are theoretically found, indicating a continuous full uptake for prolate particles and a snapthrough full uptake for oblate particles. They precisely capture the full uptake critical boundaries in the phase diagrams numerically constructed in terms of active force, aspect ratio, adhesion energy density, and membrane tension. It is found that enhancing activity (active force), reducing effective dynamic viscosity, increasing adhesion energy density, and decreasing membrane tension can significantly improve the wrapping efficiency of the self-propelled nonspherical nanoparticles. These results give a panoramic view of the uptake dynamics of active nonspherical nanoparticles, and may offer instructions for designing an effective active NP-based vehicle for controlled drug delivery.
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Affiliation(s)
- Ke Xiao
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325016, People's Republic of China and Department of Physics, College of Physical Science and Technology, Xiamen University, Xiamen 361005, People's Republic of China
| | - Rui Ma
- Fujian Provincial Key Lab for Soft Functional Materials Research, Research Institute for Biomimetics and Soft Matter, Department of Physics, College of Physical Science and Technology, Xiamen University, Xiamen 361005, People's Republic of China
| | - Chen-Xu Wu
- Fujian Provincial Key Lab for Soft Functional Materials Research, Research Institute for Biomimetics and Soft Matter, Department of Physics, College of Physical Science and Technology, Xiamen University, Xiamen 361005, People's Republic of China
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6
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Ou L, Chen H, Yuan B, Yang K. Membrane-Specific Binding of 4 nm Lipid Nanoparticles Mediated by an Entropy-Driven Interaction Mechanism. ACS NANO 2022; 16:18090-18100. [PMID: 36278503 DOI: 10.1021/acsnano.2c04774] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Lipid nanoparticles (LNPs) are a leading biomimetic drug delivery platform due to their distinctive advantages and highly tunable formulations. A mechanistic understanding of the interaction between LNPs and cell membranes is essential for developing the cell-targeted carriers for precision medicine. Here the interactions between sub 10 nm cationic LNPs (cLNPs; e.g., 4 nm in size) and varying model cell membranes are systematically investigated using molecular dynamics simulations. We find that the membrane-binding behavior of cLNPs is governed by a two-step mechanism that is initiated by direct contact followed by a more crucial lipid exchange (dissociation of cLNP's coating lipids and subsequent flip and intercalation into the membrane). Importantly, our simulations demonstrate that the membrane binding of cLNPs is an entropy-driven process, which thus enables cLNPs to differentiate between membranes having different lipid compositions (e.g., the outer and inner membranes of bacteria vs the red blood cell membranes). Accordingly, the possible strategies to drive the membrane-targeting behaviors of cLNPs, which mainly depend on the entropy change in the complicated entropy-enthalpy competition of the cLNP-membrane interaction process, are investigated. Our work unveils the molecular mechanism underlying the membrane selectivity of cLNPs and provides useful hints to develop cLNPs as membrane-targeting agents for precision medicine.
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Affiliation(s)
- Luping Ou
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou215006, Jiangsu, People's Republic of China
| | - Haibo Chen
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou215006, Jiangsu, People's Republic of China
| | - Bing Yuan
- Songshan Lake Materials Laboratory, Dongguan523808, Guangdong, People's Republic of China
| | - Kai Yang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou215006, Jiangsu, People's Republic of China
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7
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Xiao K, Ma R, Wu CX. Force-induced wrapping phase transition in activated cellular uptake. Phys Rev E 2022; 106:044411. [PMID: 36397463 DOI: 10.1103/physreve.106.044411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Intracellular pathogens, including all viruses and many bacteria, enter a host cell through either passive endocytosis or active self-propulsion. Though the cellular uptake of passive particles via endocytic process has been studied extensively, little work has been done on the active entry of self-propelled pathogens, such as Listeria monocytogenes. Here, we present a theoretical model to investigate the adhesive wrapping of a self-propelled particle by a plasma membrane, and find a type of first-order wrapping transition from a small partial wrapping state to a large partial wrapping state triggered by the active force. The phase diagram displays more complex behaviors compared with the passive wrapping mediated merely by adhesion. We also find that a tubular protrusion can be formed if the active force exceeds a force barrier. These results may provide a useful guidance to the study of activity-driven cellular entry of active particles into cells.
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Affiliation(s)
- Ke Xiao
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325016, People's Republic of China and Department of Physics, College of Physical Science and Technology, Xiamen University, Xiamen 361005, People's Republic of China
| | - Rui Ma
- Fujian Provincial Key Lab for Soft Functional Materials Research, Research Institute for Biomimetics and Soft Matter, Department of Physics, College of Physical Science and Technology, Xiamen University, Xiamen 361005, People's Republic of China
| | - Chen-Xu Wu
- Fujian Provincial Key Lab for Soft Functional Materials Research, Research Institute for Biomimetics and Soft Matter, Department of Physics, College of Physical Science and Technology, Xiamen University, Xiamen 361005, People's Republic of China
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8
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Gao L, Xu D, Wan H, Zhang X, Dai X, Yan LT. Understanding Interfacial Nanoparticle Organization through Simulation and Theory: A Review. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:11137-11148. [PMID: 36070512 DOI: 10.1021/acs.langmuir.2c01192] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Understanding the behaviors of nanoparticles at interfaces is crucial not only for the design of novel nanostructured materials with superior properties but also for a better understanding of many biological systems where nanoscale objects such as drug molecules, viruses, and proteins can interact with various interfaces. Theoretical studies and tailored computer simulations offer unique approaches to investigating the evolution and formation of structures as well as to determining structure-property relationships regarding the interfacial nanostructures. In this feature article, we summarize our efforts to exploit computational approaches as well as theoretical modeling in understanding the organization of nanoscale objects at the interfaces of various systems. First, we present the latest research advances and state-of-the-art computational techniques for the simulation of nanoparticles at interfaces. Then we introduce the applications of multiscale modeling and simulation methods as well as theoretical analysis to explore the basic science and the fundamental principles in the interfacial nanoparticle organization, covering the interfaces of polymer, nanoscience, biomacromolecules, and biomembranes. Finally, we discuss future directions to signify the framework in tailoring the interfacial organization of nanoparticles based on the computational design. This feature article could promote further efforts toward fundamental research and the wide applications of theoretical approaches in designing interfacial assemblies for new types of functional nanomaterials and beyond.
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Affiliation(s)
- Lijuan Gao
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
| | - Duo Xu
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
| | - Haixiao Wan
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
| | - Xuanyu Zhang
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
| | - Xiaobin Dai
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
| | - Li-Tang Yan
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
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9
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Cagnetta F, Škultéty V, Evans MR, Marenduzzo D. Renormalization group study of the dynamics of active membranes: Universality classes and scaling laws. Phys Rev E 2022; 105:014610. [PMID: 35193300 DOI: 10.1103/physreve.105.014610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 11/24/2021] [Indexed: 06/14/2023]
Abstract
Motivated by experimental observations of patterning at the leading edge of motile eukaryotic cells, we introduce a general model for the dynamics of nearly-flat fluid membranes driven from within by an ensemble of activators. We include, in particular, a kinematic coupling between activator density and membrane slope which generically arises whenever the membrane has a nonvanishing normal speed. We unveil the phase diagram of the model by means of a perturbative field-theoretical renormalization group analysis. Due to the aforementioned kinematic coupling the natural early-time dynamical scaling is acoustic, that is the dynamical critical exponent is 1. However, as soon as the the normal velocity of the membrane is tuned to zero, the system crosses over to diffusive dynamic scaling in mean field. Distinct critical points can be reached depending on how the limit of vanishing velocity is realized: in each of them corrections to scaling due to nonlinear coupling terms must be taken into account. The detailed analysis of these critical points reveals novel scaling regimes which can be accessed with perturbative methods, together with signs of strong coupling behavior, which establishes a promising ground for further nonperturbative calculations. Our results unify several previous studies on the dynamics of active membrane, while also identifying nontrivial scaling regimes which cannot be captured by passive theories of fluctuating interfaces and are relevant for the physics of living membranes.
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Affiliation(s)
- Francesco Cagnetta
- SUPA, School of Physics and Astronomy, The University of Edinburgh, Edinburgh, EH9 3FD Scotland, United Kingdom
| | - Viktor Škultéty
- SUPA, School of Physics and Astronomy, The University of Edinburgh, Edinburgh, EH9 3FD Scotland, United Kingdom
| | - Martin R Evans
- SUPA, School of Physics and Astronomy, The University of Edinburgh, Edinburgh, EH9 3FD Scotland, United Kingdom
| | - Davide Marenduzzo
- SUPA, School of Physics and Astronomy, The University of Edinburgh, Edinburgh, EH9 3FD Scotland, United Kingdom
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10
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Poblete S, Božič A, Kanduč M, Podgornik R, Guzman HV. RNA Secondary Structures Regulate Adsorption of Fragments onto Flat Substrates. ACS OMEGA 2021; 6:32823-32831. [PMID: 34901632 PMCID: PMC8655909 DOI: 10.1021/acsomega.1c04774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/04/2021] [Indexed: 06/14/2023]
Abstract
RNA is a functionally rich molecule with multilevel, hierarchical structures whose role in the adsorption to molecular substrates is only beginning to be elucidated. Here, we introduce a multiscale simulation approach that combines a tractable coarse-grained RNA structural model with an interaction potential of a structureless flat adsorbing substrate. Within this approach, we study the specific role of stem-hairpin and multibranch RNA secondary structure motifs on its adsorption phenomenology. Our findings identify a dual regime of adsorption for short RNA fragments with and without the secondary structure and underline the adsorption efficiency in both cases as a function of the surface interaction strength. The observed behavior results from an interplay between the number of contacts formed at the surface and the conformational entropy of the RNA molecule. The adsorption phenomenology of RNA seems to persist also for much longer RNAs as qualitatively observed by comparing the trends of our simulations with a theoretical approach based on an ideal semiflexible polymer chain.
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Affiliation(s)
- Simón Poblete
- Instituto
de Ciencias Físicas y Matemáticas, Universidad Austral de Chile, Valdivia 5091000, Chile
- Computational
Biology Lab, Fundación Ciencia &
Vida, Santiago 7780272, Chile
| | - Anže Božič
- Department
of Theoretical Physics, Jožef Stefan
Institute, SI-1000 Ljubljana, Slovenia
| | - Matej Kanduč
- Department
of Theoretical Physics, Jožef Stefan
Institute, SI-1000 Ljubljana, Slovenia
| | - Rudolf Podgornik
- School
of Physical Sciences and Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute
of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Wenzhou
Institute of the University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- Department
of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Horacio V. Guzman
- Department
of Theoretical Physics, Jožef Stefan
Institute, SI-1000 Ljubljana, Slovenia
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11
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Makvandi P, Chen M, Sartorius R, Zarrabi A, Ashrafizadeh M, Dabbagh Moghaddam F, Ma J, Mattoli V, Tay FR. Endocytosis of abiotic nanomaterials and nanobiovectors: Inhibition of membrane trafficking. NANO TODAY 2021; 40:101279. [PMID: 34518771 PMCID: PMC8425779 DOI: 10.1016/j.nantod.2021.101279] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 08/05/2021] [Accepted: 08/19/2021] [Indexed: 05/04/2023]
Abstract
Humans are exposed to nanoscopical nanobiovectors (e.g. coronavirus SARS-CoV-2) as well as abiotic metal/carbon-based nanomaterials that enter cells serendipitously or intentionally. Understanding the interactions of cell membranes with these abiotic and biotic nanostructures will facilitate scientists to design better functional nanomaterials for biomedical applications. Such knowledge will also provide important clues for the control of viral infections and the treatment of virus-induced infectious diseases. In the present review, the mechanisms of endocytosis are reviewed in the context of how nanomaterials are uptaken into cells. This is followed by a detailed discussion of the attributes of man-made nanomaterials (e.g. size, shape, surface functional groups and elasticity) that affect endocytosis, as well as the different human cell types that participate in the endocytosis of nanomaterials. Readers are then introduced to the concept of viruses as nature-derived nanoparticles. The mechanisms in which different classes of viruses interact with various cell types to gain entry into the human body are reviewed with examples published over the last five years. These basic tenets will enable the avid reader to design advanced drug delivery and gene transfer nanoplatforms that harness the knowledge acquired from endocytosis to improve their biomedical efficacy. The review winds up with a discussion on the hurdles to be addressed in mimicking the natural mechanisms of endocytosis in nanomaterials design.
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Affiliation(s)
- Pooyan Makvandi
- Istituto Italiano di Tecnologia, Centre for Materials Interfaces, Viale Rinaldo Piaggio 34, 56025 Pontedera, Pisa, Italy
| | - Meiling Chen
- Department of Stomatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rossella Sartorius
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Naples 80131, Italy
| | - Ali Zarrabi
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, Istanbul 34956, Turkey
| | - Milad Ashrafizadeh
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, Istanbul 34956, Turkey
- Faculty of Engineering and Natural Sciences, Sabanci University, Orta Mahalle, Üniversite Caddesi No. 27, Orhanlı, Tuzla, 34956 Istanbul, Turkey
| | - Farnaz Dabbagh Moghaddam
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran 1477893855, Iran
| | - Jingzhi Ma
- Department of Stomatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Virgilio Mattoli
- Istituto Italiano di Tecnologia, Centre for Materials Interfaces, Viale Rinaldo Piaggio 34, 56025 Pontedera, Pisa, Italy
| | - Franklin R Tay
- The Graduate School, Augusta University, Augusta, GA 30912, United States
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12
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He K, Wei Y, Zhang Z, Chen H, Yuan B, Pang HB, Yang K. Membrane-curvature-mediated co-endocytosis of bystander and functional nanoparticles. NANOSCALE 2021; 13:9626-9633. [PMID: 34008687 PMCID: PMC8177723 DOI: 10.1039/d1nr01443a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Efficient cellular uptake of nanoparticles (NPs) is necessary for the development of nanomedicine in biomedical applications. Recently, the coadministration of functionalized NPs (FNPs) was shown to stimulate the cellular uptake of nonfunctionalized NPs (termed bystander NPs, BNPs), which presents a new strategy to achieve synergistic delivery. However, a mechanistic understanding of the underlying mechanism is still lacking. In this work, the bystander uptake effect was investigated at the cell membrane level by combining the coarse-grained molecular dynamics, potential of mean force calculation and theoretical energy analysis methods. The membrane internalization efficiency of BNPs was enhanced by co-administered FNPs, and such activity depends on the affinity of both NPs to the membrane and the resultant membrane deformation. The membrane-curvature-mediated attraction and aggregation of NPs facilitated the membrane uptake of BNPs. Furthermore, quantitative suggestions were given to modulate the BNP internalization through controlling the FNP properties such as size, concentration and surface-ligand density. Our results provide insight into the molecular mechanism of the bystander uptake effect, and offer a practical guide to regulate the cellular internalization of NPs for targeted and efficient delivery to cells.
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Affiliation(s)
- Kejie He
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou, 215006, P. R. China.
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13
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Cao XZ, Merlitz H, Wu CX, Forest MG. Chain stiffness boosts active nanoparticle transport in polymer networks. Phys Rev E 2021; 103:052501. [PMID: 34134347 DOI: 10.1103/physreve.103.052501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/27/2021] [Indexed: 11/07/2022]
Abstract
Recent advances in technologies such as nanomanufacturing and nanorobotics have opened new pathways for the design of active nanoparticles (NPs) capable of penetrating biolayers for biomedical applications, e.g., for drug delivery. The coupling and feedback between active NP motility (with large stochastic increments relative to passive NPs) and the induced nonequilibrium deformation and relaxation responses of the polymer network, spanning scales from the NP to the local structure of the network, remain to be clarified. Using molecular dynamics simulations, combined with a Rouse mode analysis of network chains and position and velocity autocorrelation functions of the NPs, we demonstrate that the mobility of active NPs within cross-linked, concentrated polymer networks is a monotonically increasing function of chain stiffness, contrary to passive NPs, for which chain stiffness suppresses mobility. In flexible networks, active NPs exhibit a behavior similar to passive NPs, with a boost in mobility proportional to the self-propulsion force. These results are suggestive of design strategies for active NP penetration of stiff biopolymer matrices.
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Affiliation(s)
- Xue-Zheng Cao
- Department of Physics, Xiamen University, Xiamen 361005, People's Republic of China
| | - Holger Merlitz
- Leibniz-Institut für Polymerforschung Dresden, 01069 Dresden, Germany
| | - Chen-Xu Wu
- Department of Physics, Xiamen University, Xiamen 361005, People's Republic of China
| | - M Gregory Forest
- Departments of Mathematics, Applied Physical Sciences, Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3250, USA
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14
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Ghosh R, Satarifard V, Grafmüller A, Lipowsky R. Budding and Fission of Nanovesicles Induced by Membrane Adsorption of Small Solutes. ACS NANO 2021; 15:7237-7248. [PMID: 33819031 PMCID: PMC8155335 DOI: 10.1021/acsnano.1c00525] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Membrane budding and fission are essential cellular processes that produce new membrane compartments during cell and organelle division, for intracellular vesicle trafficking as well as during endo- and exocytosis. Such morphological transformations have also been observed for giant lipid vesicles with a size of many micrometers. Here, we report budding and fission processes of lipid nanovesicles with a size below 50 nm. We use coarse-grained molecular dynamics simulations, by which we can visualize the morphological transformations of individual vesicles. The budding and fission processes are induced by low concentrations of small solutes that absorb onto the outer leaflets of the vesicle membranes. In addition to the solute concentration, we identify the solvent conditions as a second key parameter for these processes. For good solvent conditions, the budding of a nanovesicle can be controlled by reducing the vesicle volume for constant solute concentration or by increasing the solute concentration for constant vesicle volume. After the budding process is completed, the budded vesicle consists of two membrane subcompartments which are connected by a closed membrane neck. The budding process is reversible as we demonstrate explicitly by reopening the closed neck. For poor solvent conditions, on the other hand, we observe two unexpected morphological transformations of nanovesicles. Close to the binodal line, at which the aqueous solution undergoes phase separation, the vesicle exhibits recurrent shape changes with closed and open membrane necks, reminiscent of flickering fusion pores (kiss-and-run) as observed for synaptic vesicles. As we approach the binodal line even closer, the recurrent shape changes are truncated by the fission of the membrane neck which leads to the division of the nanovesicle into two daughter vesicles. In this way, our simulations reveal a nanoscale mechanism for the budding and fission of nanovesicles, a mechanism that arises from the interplay between membrane elasticity and solute-mediated membrane adhesion.
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15
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Frey F, Idema T. More than just a barrier: using physical models to couple membrane shape to cell function. SOFT MATTER 2021; 17:3533-3549. [PMID: 33503097 DOI: 10.1039/d0sm01758b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The correct execution of many cellular processes, such as division and motility, requires the cell to adopt a specific shape. Physically, these shapes are determined by the interplay of the plasma membrane and internal cellular driving factors. While the plasma membrane defines the boundary of the cell, processes inside the cell can result in the generation of forces that deform the membrane. These processes include protein binding, the assembly of protein superstructures, and the growth and contraction of cytoskeletal networks. Due to the complexity of the cell, relating observed membrane deformations back to internal processes is a challenging problem. Here, we review cell shape changes in endocytosis, cell adhesion, cell migration and cell division and discuss how by modeling membrane deformations we can investigate the inner working principles of the cell.
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Affiliation(s)
- Felix Frey
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands.
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16
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Li SJ, Shi X. Tailoring Antifouling Properties of Nanocarriers via Entropic Collision of Polymer Grafting. ACS NANO 2021; 15:5725-5734. [PMID: 33710849 DOI: 10.1021/acsnano.1c01173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Polymer graftings (PGs) are widely employed in antifouling surfaces and drug delivery systems to regulate the interaction with a foreign environment. Through molecular dynamics simulations and scaling theory analysis, we investigate the physical antifouling properties of PGs via their collision behaviors. Compared with mushroom-like PGs with low grafting density, we find brush-like PGs with high grafting density could generate large deformation-induced entropic repulsive force during a collision, revealing a microscopic mechanism for the hop motions of polymer-grafted nanoparticles for drug delivery observed in experiment. In addition, the collision elasticity of PGs is found to decay with the collision velocity by a power law, i.e., a concise dynamic scaling despite the complex process involved, which is beyond expectation. These results elucidate the dynamic interacting mechanism of PGs, which are of immediate interest for a fundamental understanding of the antifouling performance of PGs and the rational design of PG-coated nanoparticles in nanomedicine for drug delivery.
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Affiliation(s)
- Shu-Jia Li
- Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Chinese Academy of Sciences, No. 11 ZhongGuanCun BeiYiTiao, Beijing 100190, China
| | - Xinghua Shi
- Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Chinese Academy of Sciences, No. 11 ZhongGuanCun BeiYiTiao, Beijing 100190, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
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17
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Baranov MV, Kumar M, Sacanna S, Thutupalli S, van den Bogaart G. Modulation of Immune Responses by Particle Size and Shape. Front Immunol 2021; 11:607945. [PMID: 33679696 PMCID: PMC7927956 DOI: 10.3389/fimmu.2020.607945] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/23/2020] [Indexed: 12/12/2022] Open
Abstract
The immune system has to cope with a wide range of irregularly shaped pathogens that can actively move (e.g., by flagella) and also dynamically remodel their shape (e.g., transition from yeast-shaped to hyphal fungi). The goal of this review is to draw general conclusions of how the size and geometry of a pathogen affect its uptake and processing by phagocytes of the immune system. We compared both theoretical and experimental studies with different cells, model particles, and pathogenic microbes (particularly fungi) showing that particle size, shape, rigidity, and surface roughness are important parameters for cellular uptake and subsequent immune responses, particularly inflammasome activation and T cell activation. Understanding how the physical properties of particles affect immune responses can aid the design of better vaccines.
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Affiliation(s)
- Maksim V. Baranov
- Department of Molecular Immunology and Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Manoj Kumar
- Simons Center for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, India
| | - Stefano Sacanna
- Molecular Design Institute, Department of Chemistry, New York University, New York, NY, United States
| | - Shashi Thutupalli
- Simons Center for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, India
- International Centre for Theoretical Sciences, Tata Institute for Fundamental Research, Bangalore, India
| | - Geert van den Bogaart
- Department of Molecular Immunology and Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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18
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Chen G, Shen Z, Li Y. A machine-learning-assisted study of the permeability of small drug-like molecules across lipid membranes. Phys Chem Chem Phys 2021; 22:19687-19696. [PMID: 32830206 DOI: 10.1039/d0cp03243c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Study of the permeability of small organic molecules across lipid membranes plays a significant role in designing potential drugs in the field of drug discovery. Approaches to design promising drug molecules have gone through many stages, from experiment-based trail-and-error approaches, to the well-established avenue of the quantitative structure-activity relationship, and currently to the stage guided by machine learning (ML) and artificial intelligence techniques. In this work, we present a study of the permeability of small drug-like molecules across lipid membranes by two types of ML models, namely the least absolute shrinkage and selection operator (LASSO) and deep neural network (DNN) models. Molecular descriptors and fingerprints are used for featurization of organic molecules. Using molecular descriptors, the LASSO model uncovers that the electro-topological, electrostatic, polarizability, and hydrophobicity/hydrophilicity properties are the most important physical properties to determine the membrane permeability of small drug-like molecules. Additionally, with molecular fingerprints, the LASSO model suggests that certain chemical substructures can significantly affect the permeability of organic molecules, which closely connects to the identified main physical properties. Moreover, the DNN model using molecular fingerprints can help develop a more accurate mapping between molecular structures and their membrane permeability than LASSO models. Our results provide deep understanding of drug-membrane interactions and useful guidance for the inverse molecular design of drug-like molecules. Last but not least, while the current focus is on the permeability of drug-like molecules, the methodology of this work is general and can be applied for other complex physical chemistry problems to gain molecular insights.
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Affiliation(s)
- Guang Chen
- Department of Mechanical Engineering and Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA.
| | - Zhiqiang Shen
- Department of Mechanical Engineering and Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA.
| | - Ying Li
- Department of Mechanical Engineering and Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA.
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19
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Wiemann JT, Shen Z, Ye H, Li Y, Yu Y. Membrane poration, wrinkling, and compression: deformations of lipid vesicles induced by amphiphilic Janus nanoparticles. NANOSCALE 2020; 12:20326-20336. [PMID: 33006360 DOI: 10.1039/d0nr05355d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Building upon our previous studies on interactions of amphiphilic Janus nanoparticles with glass-supported lipid bilayers, we study here how these Janus nanoparticles perturb the structural integrity and induce shape instabilities of membranes of giant unilamellar vesicles (GUVs). We show that 100 nm amphiphilic Janus nanoparticles disrupt GUV membranes at a threshold particle concentration similar to that in supported lipid bilayers, but cause drastically different membrane deformations, including membrane wrinkling, protrusion, poration, and even collapse of entire vesicles. By combining experiments with molecular simulations, we reveal how Janus nanoparticles alter local membrane curvature and collectively compress the membrane to induce shape transformation of vesicles. Our study demonstrates that amphiphilic Janus nanoparticles disrupt vesicle membranes differently and more effectively than uniform amphiphilic particles.
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Affiliation(s)
- Jared T Wiemann
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
| | - Zhiqiang Shen
- Department of Mechanical Engineering, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Huilin Ye
- Department of Mechanical Engineering, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Ying Li
- Department of Mechanical Engineering and Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, USA.
| | - Yan Yu
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
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20
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Yang Y, Bu X, Zhang X. Regulation Mechanism of Bubbling Deformation and Fracture Toughness of the Membrane by Asymmetric Phospholipids: A Model System Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:10138-10146. [PMID: 32787040 DOI: 10.1021/acs.langmuir.0c01580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Dynamic regulation of the deformation modulus and fracture toughness of a membrane is critical to organelles and cells for matching their conflicting needs of resilient and fractured behaviors. These properties implement the protection of the function in the normal condition and the fission function in the endocytosis condition of a membrane. Naturally, a membrane contains phospholipids that have different hydrophilic and hydrophobic group length. The diffusion and aggregation of the phospholipids with asymmetry of the hydrophilic-hydrophobic ratio on the membrane play a key role in regulating the mechanical behaviors passively to the external force. In present work, the effects of the asymmetry of phospholipids on the bubbling deformation and fracture toughness of the membrane to external stretching are investigated in a model system. A disk-shaped micelle formed from the blend of symmetric and asymmetric diblock copolymers in a selective solvent is considered as the membrane sheet. Its mechanically responsive behaviors are investigated by self-consistent field theory. By analyzing the evolution of different components during the stretching process, the mechanism of formation of the bubbling structure is revealed. Moreover, the fracture toughness depending on the asymmetry of the phospholipids is determined quantitatively.
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Affiliation(s)
- Yang Yang
- School of Science, Beijing Jiaotong University, Beijing 100044, PR China
| | - Xiangyu Bu
- School of Science, Beijing Jiaotong University, Beijing 100044, PR China
| | - Xinghua Zhang
- School of Science, Beijing Jiaotong University, Beijing 100044, PR China
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21
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Abstract
Entropy, one of the central concepts of thermodynamics, can be a predominant contribution to structural formation and transition. Although it is well-known that diverse forces and energies can significantly contribute to the structures and activities at bio-nano interfaces, the potential entropic contribution remains less well understood. Therefore, this review article seeks to provide a conceptual framework demonstrating that entropy can be exploited to shape the physicochemical properties of bio-nano interfaces and thereby regulate the structures, responses, and functions of biological systems. We introduce the typical types of entropy that matter at bio-nano interfaces. Moreover, some key characteristics featuring entropy at bio-nano interfaces, such as the difference between entropic force and energetic interaction and the associated implications for biomimetic research, are discussed. We expect that this review could stimulate further effort in the fundamental research of entropy in biology and in the biological applications of entropic effects in designer biomaterials.
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Affiliation(s)
- Guolong Zhu
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
| | - Ziyang Xu
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
| | - Li-Tang Yan
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
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