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Zhang F, Yang R, Lu D. Investigation of Polymer Aging Mechanisms Using Molecular Simulations: A Review. Polymers (Basel) 2023; 15:polym15081928. [PMID: 37112075 PMCID: PMC10145009 DOI: 10.3390/polym15081928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/03/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Aging has a serious impact on the properties of functional polymers. Therefore, it is necessary to study the aging mechanism to prolong the service and storage life of polymer-based devices and materials. Due to the limitations of traditional experimental methods, more and more studies have adopted molecular simulations to analyze the intrinsic mechanisms of aging. In this paper, recent advances in molecular simulations of the aging of polymers and their composites are reviewed. The characteristics and applications of commonly used simulation methods in the study of the aging mechanisms (traditional molecular dynamics simulation, quantum mechanics, and reactive molecular dynamics simulation) are outlined. The current simulation research progress of physical aging, aging under mechanical stress, thermal aging, hydrothermal aging, thermo-oxidative aging, electric aging, aging under high-energy particle impact, and radiation aging is introduced in detail. Finally, the current research status of the aging simulations of polymers and their composites is summarized, and the future development trend has been prospected.
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Affiliation(s)
- Fan Zhang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Rui Yang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Diannan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
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Mima T, Kinjo T, Yamakawa S, Asahi R. Study of the conformation of polyelectrolyte aggregates using coarse-grained molecular dynamics simulations. SOFT MATTER 2017; 13:5991-5999. [PMID: 28776057 DOI: 10.1039/c7sm01196b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The conformation of polyelectrolyte aggregates as a function of the backbone rigidity is investigated by coarse-grained molecular dynamics simulation. The polyelectrolyte is represented by a bead-spring chain with charged side chains. The simulations start from the uniform distributions of the polyelectrolytes, and the resultant polyelectrolyte conformation after a few microseconds exhibits spherical self-aggregates, clusters, or bending bundle-like aggregates, depending on the backbone rigidity. The interaggregate structures on a large scale are featured by the static structure factor (SSF). The simulated SSFs of the bending bundle-like aggregates are consistent with those of the small angle X-ray scattering (SAXS) measurement so we successfully assign the microscopic structures of polyelectrolytes to the SAXS measurement. The power-law of the SSFs for the bundle conditions is steeper than that of the conventional cylinder model. The present study finds that such discrepancy in the power-law results from the bending of the bundle-like aggregates. In addition, the relaxation behavior includes slow dynamics. The present study proposes that such slow dynamics results from diffusion-limited aggregation and from gliding processes to reduce local metastable folding within the aggregates.
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Affiliation(s)
- Toshiki Mima
- Toyota Central R&D Labs., Inc., 41-1, Yokomichi, Nagakute, Aichi, Japan.
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Das S, Chakraborty S. Probing solvation decay length in order to characterize hydrophobicity-induced bead-bead attractive interactions in polymer chains. J Mol Model 2010; 17:1911-8. [PMID: 21110052 DOI: 10.1007/s00894-010-0899-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Accepted: 11/09/2010] [Indexed: 11/24/2022]
Abstract
In this paper, we quantitatively demonstrate that exponentially decaying attractive potentials can effectively mimic strong hydrophobic interactions between monomer units of a polymer chain dissolved in aqueous solvent. Classical approaches to modeling hydrophobic solvation interactions are based on invariant attractive length scales. However, we demonstrate here that the solvation interaction decay length may need to be posed as a function of the relative separation distances and the sizes of the interacting species (or beads or monomers) to replicate the necessary physical interactions. As an illustrative example, we derive a universal scaling relationship for a given solute-solvent combination between the solvation decay length, the bead radius, and the distance between the interacting beads. With our formalism, the hydrophobic component of the net attractive interaction between monomer units can be synergistically accounted for within the unified framework of a simple exponentially decaying potential law, where the characteristic decay length incorporates the distinctive and critical physical features of the underlying interaction. The present formalism, even in a mesoscopic computational framework, is capable of incorporating the essential physics of the appropriate solute-size dependence and solvent-interaction dependence in the hydrophobic force estimation, without explicitly resolving the underlying molecular level details.
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Affiliation(s)
- Siddhartha Das
- Department of Mechanical Engineering, Indian Institute of Technology, Kharagpur 721302, India
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Hu J, Wang D, Xu J, Zhu Z, Liu S. Contraction and Collapsing Kinetics of Single Synthetic Polymer Chains at Small Quench Depths. MACROMOL CHEM PHYS 2010. [DOI: 10.1002/macp.201000476] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Vitalis A, Pappu RV. Methods for Monte Carlo simulations of biomacromolecules. ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY 2009; 5:49-76. [PMID: 20428473 PMCID: PMC2860296 DOI: 10.1016/s1574-1400(09)00503-9] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The state-of-the-art for Monte Carlo (MC) simulations of biomacromolecules is reviewed. Available methodologies for sampling conformational equilibria and associations of biomacromolecules in the canonical ensemble, given a continuum description of the solvent environment, are reviewed. Detailed sections are provided dealing with the choice of degrees of freedom, the efficiencies of MC algorithms and algorithmic peculiarities, as well as the optimization of simple movesets. The issue of introducing correlations into elementary MC moves, and the applicability of such methods to simulations of biomacromolecules is discussed. A brief discussion of multicanonical methods and an overview of recent simulation work highlighting the potential of MC methods are also provided. It is argued that MC simulations, while underutilized biomacromolecular simulation community, hold promise for simulations of complex systems and phenomena that span multiple length scales, especially when used in conjunction with implicit solvation models or other coarse graining strategies.
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Affiliation(s)
- Andreas Vitalis
- Department of Biomedical Engineering, Molecular Biophysics Program, Center for Computational Biology, Washington University in St. Louis, One Brookings Drive, Campus Box 1097, St. Louis, MO 63130-4899, USA
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Steppich DM, Angerer JI, Opfer J, Sritharan K, Schneider SW, Thalhammer S, Wixforth A, Alexander-Katz A, Schneider MF. Relaxation of ultralarge VWF bundles in a microfluidic-AFM hybrid reactor. Biochem Biophys Res Commun 2008; 369:507-12. [PMID: 18298947 DOI: 10.1016/j.bbrc.2008.02.062] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Accepted: 02/12/2008] [Indexed: 11/17/2022]
Abstract
The crucial role of the biopolymer "Von Willebrand factor" (VWF) in blood platelet binding is tightly regulated by the shear forces to which the protein is exposed in the blood flow. Under high-shear conditions, VWFs ability to immobilize blood platelets is strongly increased due to a change in conformation which at sufficient concentration is accompanied by the formation of ultra large VWF bundles (ULVWF). However, little is known about the dynamic and mechanical properties of such bundles. Combining a surface acoustic wave (SAW) based microfluidic reactor with an atomic force microscope (AFM) we were able to study the relaxation of stretched VWF bundles formed by hydrodynamic stress. We found that the dynamical response of the network is well characterized by stretched exponentials, indicating that the relaxation process proceeds through hopping events between a multitude of minima. This finding is in accordance with current ideas of VWF self-association. The longest relaxation time does not show a clear dependence on the length of the bundle, and is dominated by the internal conformations and effective friction within the bundle.
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Affiliation(s)
- D M Steppich
- University of Augsburg, Experimental Physics I, Biological Physics Group, Universitaetstr. 1, D-86159 Augsburg, Germany
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Sabeur SA, Hamdache F, Schmid F. Kinetically driven helix formation during the homopolymer collapse process. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 77:020802. [PMID: 18351979 DOI: 10.1103/physreve.77.020802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Indexed: 05/26/2023]
Abstract
Using Langevin simulations, we find that simple "generic" bead-and-spring homopolymer chains in a sufficiently bad solvent spontaneously develop helical order during the process of collapsing from an initially stretched conformation. The helix formation is initiated by the unstable modes of the straight chain, which drive the system towards a long-lived metastable transient state. The effect is most pronounced if hydrodynamic interactions are screened.
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Affiliation(s)
- Sid Ahmed Sabeur
- Département de Physique, Faculté des Sciences, USTO, Oran, Algeria
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Mansfield ML. Development of knotting during the collapse transition of polymers. J Chem Phys 2007; 127:244902. [DOI: 10.1063/1.2806929] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Reddy G, Yethiraj A. Implicit and Explicit Solvent Models for the Simulation of Dilute Polymer Solutions. Macromolecules 2006. [DOI: 10.1021/ma061176+] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Marenduzzo D, Maritan A, Rosa A, Seno F. Stepwise unfolding of collapsed polymers. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2004; 15:83-93. [PMID: 15480919 DOI: 10.1140/epje/i2004-10039-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Motivated by recent experimental data on DNA stretching in presence of polyvalent counterions, we study the force-induced unfolding of a homopolymer on and off lattice. In the fixed force ensemble the globule unravels via a series of steps due to surface effects which play an important role for finite-size chains. This holds both for flexible and stiff polymers. We discuss in a qualitative way how this result may impact on the interpretation of DNA stretching experiments showing peaks in the characteristic curves, by extracting from the raw data the corresponding elongation- versus-force characteristic curves. Furthermore, approximate analytical and numerical calculations, valid in a quasi-equilibrium fixed stretch ensemble, and if the initial low-temperature state is ordered in a spool, show that the average force versus elongation displays peaks related to the geometry of the initial configuration. We finally argue how the proposed mechanisms identified for the arising of peaks may couple in the experiments, and comment on the role of dynamic effects.
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Affiliation(s)
- D Marenduzzo
- Department of Physics, Theoretical Physics, University of Oxford, 1 Keble Road, Oxford, OX1 3NP, England, UK.
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Celestini F, Frisch T, Oyharcabal X. Stretching an adsorbed polymer globule. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2004; 70:012801. [PMID: 15324102 DOI: 10.1103/physreve.70.012801] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2003] [Revised: 03/17/2004] [Indexed: 05/24/2023]
Abstract
Using molecular dynamic simulation, we study the stretching of an adsorbed homopolymer in a poor solvent with one end held at a distance ze from the substrate. We measure the vertical force f on the end of the chain as a function of the extension ze and the substrate interaction energy w. The force reaches a plateau value at large extensions. In the strong adsorption limit, we show that the plateau value increases linearly in w in good agreement with a theoretical model. In the weak adsorption limit, a polymer globule with a layered structure is formed and elastically deformed when stretched. In both cases a simple theoretical model permits us to predict the relation between the necessary force to fully detach the polymer and its critical extension.
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Affiliation(s)
- Franck Celestini
- Laboratoire de Physique de la Matière Condensée, UMR 6622, CNRS, Université de Nice Sophia-Antipolis, Parc Valrose, 06108 Nice Cedex 2, France
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