Submit to Polymers Review for Polymers Propose a Special Issue

Journal Menu

Journal Browser

► Journal Browser

Coarse-Grained Models for Polymers

Print Special Issue Flyer
Special Issue Editors
Special Issue Information
Keywords
Benefits of Publishing in a Special Issue
Published Papers

A special issue of Polymers (ISSN 2073-4360). This special issue belongs to the section "Polymer Physics and Theory".

Deadline for manuscript submissions: closed (30 November 2022) | Viewed by 29031

Share This Special Issue

Special Issue Editors

Prof. Dr. Vlasis Mavrantzas

E-Mail Website1 Website2
Guest Editor

1. Department of Chemical Engineering, University of Patras & FORTH-ICE/HT, GR 26504 Patras, Greece
2. Particle Technology Laboratory, Department of Mechanical and Process Engineering, ETH-Z, CH-8093 Zürich, Switzerland
Interests: polymer physics; polymer rheology; molecular simulations; statistical mechanics; nonequilibrium thermodynamics; constitutive modelling; dissipative quantum field theory
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Doros Theodorou

E-Mail Website
Guest Editor

School of Chemical Engineering, National Technical University of Athens (NTUA), GR-15780 Athens, Greece
Interests: computer modelling of matter; application of statistical mechanics, thermodynamics, and transport phenomena for the elucidation of structure-property-processing-performance relations in materials; polymer science and engineering; separation and catalytic properties of zeolites

Special Issue Information

Dear Colleagues,

To cope with the large spectrum of characteristic length and time scales characterizing structure and dynamics in polymers, an approach that is often invoked is coarse-graining. In coarse-graining, collections of atoms are lumped into a new type of entities, referred to as super-atoms or particles or beads or even blobs (implying a cruder representation). Coarse-graining is accompanied by a significant reduction in the number of degrees of freedom, and can be realized by a variety of schemes for mapping atoms or repeat units to larger groups, depending on the properties of interest. Recognizing the importance of coarse-graining in polymer science, this Special Issue of Polymers invites contributions highlighting several recent developments and applications of the method in addressing a variety of systems: entangled polymers, polymers with nonlinear architectures, polymer blends and copolymers, semiconducting conjugated polymers, polymer networks, polymer hydrogels, polymer nanocomposites, ring polymers, polymers for biological or medical applications, and many others.

Prof. Dr. Vlasis Mavrantzas
Prof. Dr. Doros Theodorou
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Polymers is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

polymers
coarse-grained models
simulation
beads
effective potentials

Benefits of Publishing in a Special Issue

Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue polices can be found here.

Published Papers (11 papers)

Download All Papers

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

Research

28 pages, 10324 KiB

Open AccessArticle

Constraint Release Rouse Mechanisms in Bidisperse Linear Polymers: Investigation of the Release Time of a Short-Long Entanglement

by Céline Hannecart, Christian Clasen and Evelyne van Ruymbeke

Polymers 2023, 15(6), 1569; https://doi.org/10.3390/polym15061569 - 21 Mar 2023

Cited by 2 | Viewed by 1677

Abstract

Despite a wide set of experimental data and a large number of studies, the quantitative description of the relaxation mechanisms involved in the disorientation process of bidisperse blends is still under discussion. In particular, while it has been shown that the relaxation of self-unentangled long chains diluted in a short chain matrix is well approximated by a Constraint Release Rouse (CRR) mechanism, there is no consensus on the value of the average release time of their entanglements,

τ_{o b s}

, which fixes the timescale of the CRR relaxation. Therefore, the first objective of the present work is to discuss the different approaches proposed to determine this time and compare them to a large set of experimental viscoelastic data, either newly measured (poly(methyl-)methacrylate and 1,4-polybutadiene blends) or coming from the literature (polystyrene and polyisoprene blends). Based on this large set of data, it is found that with respect to the molar mass of the short chain matrix,

τ_{o b s}

follows a power law with an exponent close to 2.5, rather than 3 as previously proposed. While this slight change in the power law exponent does not strongly affect the values of the constraint release times, the results obtained suggest the universality of the CRR process. Finally, we propose a new description of

τ_{o b s}

, which is implemented in a tube-based model. The accurate description of the experimental data obtained provides a good starting point to extend this approach to self-entangled binary blends. Full article

(This article belongs to the Special Issue Coarse-Grained Models for Polymers)

► Show Figures

Figure 1

22 pages, 528 KiB

Open AccessArticle

Simulating Stress–Strain Behavior by Using Individual Chains: Uniaxial Deformation of Amorphous Cis- and Trans-1,4-Polybutadiene

by Suvrajyoti Kar, Julie L. Cuddigan and Michael L. Greenfield

Polymers 2023, 15(6), 1441; https://doi.org/10.3390/polym15061441 - 14 Mar 2023

Viewed by 1747

Abstract

This work develops a probability-based numerical method for quantifying mechanical properties of non-Gaussian chains subject to uniaxial deformation, with the intention of being able to incorporate polymer–polymer and polymer–filler interactions. The numerical method arises from a probabilistic approach for evaluating the elastic free energy change of chain end-to-end vectors under deformation. The elastic free energy change, force, and stress computed by applying the numerical method to uniaxial deformation of an ensemble of Gaussian chains were in excellent agreement with analytical solutions that were obtained with a Gaussian chain model. Next, the method was applied to configurations of cis- and trans-1,4-polybutadiene chains of various molecular weights that were generated under unperturbed conditions over a range of temperatures with a Rotational Isomeric State (RIS) approach in previous work (Polymer 2015, 62, 129–138). Forces and stresses increased with deformation, and further dependences on chain molecular weight and temperature were confirmed. Compression forces normal to the imposed deformation were much larger than tension forces on chains. Smaller molecular weight chains represent the equivalent of a much more tightly cross-linked network, resulting in greater moduli than larger chains. Young’s moduli computed from the coarse-grained numerical model were in good agreement with experimental results. Full article

(This article belongs to the Special Issue Coarse-Grained Models for Polymers)

► Show Figures

Figure 1

24 pages, 6522 KiB

Open AccessArticle

Expansion of Single Chains Released from a Spherical Cavity

by Chia-Cheng Chu and Pai-Yi Hsiao

Polymers 2023, 15(1), 198; https://doi.org/10.3390/polym15010198 - 30 Dec 2022

Cited by 1 | Viewed by 1656

Abstract

A two-stage model is developed to explain the phenomena of chain expansion, released from a confining cavity. In the first stage, the chain is assumed to expand as a sphere, while in the second stage it expands like a coil. The kinetic equations for the variation of chain size are derived in the two stages by balancing the rate of the free energy change with the rate of the energy dissipation. Langevin dynamics simulations are then performed to examine the theory. We find that the expansion process is dominated by the second stage and the evolution of chain size follows, mainly, the predicted curve for coil expansion, which depends on the chain length and is not sensitive to the confining volume fraction. It permits to define the expansion time for the process. Further study reveals that the chain does undergo a spherical expansion in the first stage with the characteristic time much shorter than the one for the second stage. As a consequence, the first-stage variation of chain size can be regarded as an add-on to the principal curve of expansion designated by the second stage. The scaling behaviors and the associated scaling exponents are analyzed in details. The simulation results well support the theory. Full article

(This article belongs to the Special Issue Coarse-Grained Models for Polymers)

► Show Figures

Figure 1

16 pages, 1324 KiB

Open AccessArticle

The Local Topological Free Energy of the SARS-CoV-2 Spike Protein

by Quenisha Baldwin, Bobby Sumpter and Eleni Panagiotou

Polymers 2022, 14(15), 3014; https://doi.org/10.3390/polym14153014 - 26 Jul 2022

Cited by 4 | Viewed by 2883

Abstract

The novel coronavirus SARS-CoV-2 infects human cells using a mechanism that involves binding and structural rearrangement of its Spike protein. Understanding protein rearrangement and identifying specific amino acids where mutations affect protein rearrangement has attracted much attention for drug development. In this manuscript, we use a mathematical method to characterize the local topology/geometry of the SARS-CoV-2 Spike protein backbone. Our results show that local conformational changes in the FP, HR1, and CH domains are associated with global conformational changes in the RBD domain. The SARS-CoV-2 variants analyzed in this manuscript (alpha, beta, gamma, delta Mink, G614, N501) show differences in the local conformations of the FP, HR1, and CH domains as well. Finally, most mutations of concern are either in or in the vicinity of high local topological free energy conformations, suggesting that high local topological free energy conformations could be targets for mutations with significant impact of protein function. Namely, the residues 484, 570, 614, 796, and 969, which are present in variants of concern and are targeted as important in protein function, are predicted as such from our model. Full article

(This article belongs to the Special Issue Coarse-Grained Models for Polymers)

► Show Figures

Figure 1

24 pages, 2442 KiB

Open AccessArticle

Large Scale Hydrodynamically Coupled Brownian Dynamics Simulations of Polymer Solutions Flowing through Porous Media

by Vishal Raju Ahuja, Jasper van der Gucht and Wim Briels

Polymers 2022, 14(7), 1422; https://doi.org/10.3390/polym14071422 - 31 Mar 2022

Cited by 1 | Viewed by 2885

Abstract

Large scale simulations of polymer flow through porous media provide an important tool for solving problems in enhanced oil recovery, polymer processing and biological applications. In order to include the effects of a wide range of velocity and density fluctuations, we base our work on a coarse-grain particle-based model consisting of polymers following Brownian dynamics coupled to a background fluid flow through momentum conserving interactions. The polymers are represented as Finitely Extensible Non-Linear Elastic (FENE) dumbbells with interactions including slowly decaying transient forces to properly describe dynamic effects of the eliminated degrees of freedom. Model porous media are constructed from arrays of parallel solid beams with circular or square cross-sections, arranged periodically in the plane perpendicular to their axis. No-slip boundary conditions at the solid–fluid interfaces are imposed through interactions with artificial particles embedded within the solid part of the system. We compare the results of our simulations with those of standard Smoothed Particle Hydrodynamics simulations for Newtonian flow through the same porous media. We observe that in all cases the concentration of polymers at steady state is not uniform even though we start the simulations with a uniform polymer concentration, which is indicative of shear-induced cross-flow migration. Furthermore, we see the characteristic flattening of the velocity profile experimentally observed for shear-thinning polymer solutions flowing through channels as opposed to the parabolic Poiseuille flow profile for Newtonian fluids. Full article

(This article belongs to the Special Issue Coarse-Grained Models for Polymers)

► Show Figures

Graphical abstract

12 pages, 3316 KiB

Open AccessArticle

Analysis of Elongational Viscosity of Entangled Poly (Propylene Carbonate) Melts by Primitive Chain Network Simulations

by Yuichi Masubuchi, Lixin Yang, Takashi Uneyama and Yuya Doi

Polymers 2022, 14(4), 741; https://doi.org/10.3390/polym14040741 - 14 Feb 2022

Cited by 4 | Viewed by 2883

Abstract

It has been established that the elongational rheology of polymers depends on their chemistry. However, the analysis of experimental data has been reported for only a few polymers. In this study, we analyzed the elongational viscosity of poly (propylene carbonate) (PPC) melts in terms of monomeric friction via primitive chain network simulations. By incorporating a small polydispersity of materials, the linear viscoelastic response was semi-quantitatively reproduced. Owing to this agreement, we determined units of time and modulus to carry out elongational simulations. The simulation with constant monomeric friction overestimated elongational viscosity, whereas it nicely captured the experimental data if friction decreased with increasing segment orientation. To see the effect of chemistry, we also conducted the simulation for a polystyrene (PS) melt, which has a similar entanglement number per chain and a polydispersity index. The results imply that PPC and PS behave similarly in terms of the reduction of friction under fast deformations. Full article

(This article belongs to the Special Issue Coarse-Grained Models for Polymers)

► Show Figures

Figure 1

19 pages, 6300 KiB

Open AccessArticle

Coarse Grained Modeling of Multiphase Flows with Surfactants

by Thao X. D. Nguyen, Tuan V. Vu, Sepideh Razavi and Dimitrios V. Papavassiliou

Polymers 2022, 14(3), 543; https://doi.org/10.3390/polym14030543 - 28 Jan 2022

Cited by 6 | Viewed by 2986

Abstract

Coarse-grained modeling methods allow simulations at larger scales than molecular dynamics, making it feasible to simulate multifluid systems. It is, however, critical to use model parameters that represent the fluid properties with fidelity under both equilibrium and dynamic conditions. In this work, dissipative particle dynamics (DPD) methods were used to simulate the flow of oil and water in a narrow slit under Poiseuille and Couette flow conditions. Large surfactant molecules were also included in the computations. A systematic methodology is presented to determine the DPD parameters necessary for ensuring that the boundary conditions were obeyed, that the oil and water viscosities were represented correctly, and that the velocity profile for the multifluid system agreed with the theoretical expectations. Surfactant molecules were introduced at the oil–water interface (sodium dodecylsulfate and octaethylene glycol monododecyl ether) to determine the effects of surface-active molecules on the two-phase flow. A critical shear rate was found for Poiseuille flow, beyond which the surfactants desorbed to form the interface forming micelles and destabilize the interface, and the surfactant-covered interface remained stable under Couette flow even at high shear rates. Full article

(This article belongs to the Special Issue Coarse-Grained Models for Polymers)

► Show Figures

Graphical abstract

19 pages, 9764 KiB

Open AccessArticle

Investigation of Crystallization and Relaxation Effects in Coarse-Grained Polyethylene Systems after Uniaxial Stretching

by Dirk Grommes, Martin R. Schenk, Olaf Bruch and Dirk Reith

Polymers 2021, 13(24), 4466; https://doi.org/10.3390/polym13244466 - 20 Dec 2021

Cited by 5 | Viewed by 2852

Abstract

In this study, we investigate the thermo-mechanical relaxation and crystallization behavior of polyethylene using mesoscale molecular dynamics simulations. Our models specifically mimic constraints that occur in real-life polymer processing: After strong uniaxial stretching of the melt, we quench and release the polymer chains at different loading conditions. These conditions allow for free or hindered shrinkage, respectively. We present the shrinkage and swelling behavior as well as the crystallization kinetics over up to 600 ns simulation time. We are able to precisely evaluate how the interplay of chain length, temperature, local entanglements and orientation of chain segments influences crystallization and relaxation behavior. From our models, we determine the temperature dependent crystallization rate of polyethylene, including crystallization onset temperature. Full article

(This article belongs to the Special Issue Coarse-Grained Models for Polymers)

► Show Figures

Figure 1

17 pages, 5948 KiB

Open AccessArticle

Polymerization and Structure of Opposing Polymer Brushes Studied by Computer Simulations

by Krzysztof Halagan, Michal Banaszak, Jaroslaw Jung, Piotr Polanowski and Andrzej Sikorski

Polymers 2021, 13(24), 4294; https://doi.org/10.3390/polym13244294 - 8 Dec 2021

Cited by 9 | Viewed by 2813

Abstract

A model of the polymerization process during the formation of a pair of polymer brushes was designed and investigated. The obtained system consisted of two impenetrable parallel surfaces with the same number of chains grafted on both surfaces. Coarse-grained chains embedded in nodes of a face-centered cubic lattice with excluded volume interactions were obtained by a ‘grafted from’ procedure. The structure of synthesized macromolecular systems was also studied. Monte Carlo simulations using the dynamic lattice liquid model were employed using dedicated parallel machine ARUZ in a large size and time scale. The parameters of the polymerization process were found to be crucial for the proper structure of the brush. It was found that for high grafting densities, chains were increasingly compressed, and there is surprisingly little interpenetration of chains from opposite surfaces. It was predicted and confirmed that in a polydisperse sample, the longer chains have unique configurations consisting of a stretched stem and a coiled crown. Full article

(This article belongs to the Special Issue Coarse-Grained Models for Polymers)

► Show Figures

Graphical abstract

20 pages, 4148 KiB

Open AccessArticle

Ionic Polymer Nanocomposites Subjected to Uniaxial Extension: A Nonequilibrium Molecular Dynamics Study

by Ahmad Moghimikheirabadi, Argyrios V. Karatrantos and Martin Kröger

Polymers 2021, 13(22), 4001; https://doi.org/10.3390/polym13224001 - 19 Nov 2021

Cited by 12 | Viewed by 2257

Abstract

We explore the behavior of coarse-grained ionic polymer nanocomposites (IPNCs) under uniaxial extension up to 800% strain by means of nonequilibrium molecular dynamics simulations. We observe a simultaneous increase of stiffness and toughness of the IPNCs upon increasing the engineering strain rate, in agreement with experimental observations. We reveal that the excellent toughness of the IPNCs originates from the electrostatic interaction between polymers and nanoparticles, and that it is not due to the mobility of the nanoparticles or the presence of polymer–polymer entanglements. During the extension, and depending on the nanoparticle volume fraction, polymer–nanoparticle ionic crosslinks are suppressed with the increase of strain rate and electrostatic strength, while the mean pore radius increases with strain rate and is altered by the nanoparticle volume fraction and electrostatic strength. At relatively low strain rates, IPNCs containing an entangled matrix exhibit self-strengthening behavior. We provide microscopic insight into the structural, conformational properties and crosslinks of IPNCs, also referred to as polymer nanocomposite electrolytes, accompanying their unusual mechanical behavior. Full article

(This article belongs to the Special Issue Coarse-Grained Models for Polymers)

► Show Figures

Graphical abstract

18 pages, 4706 KiB

Open AccessArticle

Dynamics of Opposing Polymer Brushes: A Computer Simulation Study

by Krzysztof Hałagan, Michał Banaszak, Jarosław Jung, Piotr Polanowski and Andrzej Sikorski

Polymers 2021, 13(16), 2758; https://doi.org/10.3390/polym13162758 - 17 Aug 2021

Cited by 11 | Viewed by 2351

Abstract

Opposing polymer brush systems were synthesized and investigated by molecular modeling. Chains were restricted to a face-centered cubic lattice with the excluded volume interactions only. The system was confined between two parallel impenetrable walls, with the same number of chains grafted to each surface. The dynamic properties of such systems were studied by Monte Carlo simulations based on the dynamic lattice liquid model and using a highly efficient parallel machine ARUZ, which enabled the study of large systems and long timescales. The influence of the surface density and mean polymer length on the system dynamic was discussed. The self-diffusion coefficient of the solvent depended strongly on the degree of polymerization and on the polymer concentration. It was also shown that it is possible to capture changes in solvent mobility that can be attributed to the regions of different polymer densities. Full article

(This article belongs to the Special Issue Coarse-Grained Models for Polymers)

► Show Figures

Journal Menu

Journal Browser

Coarse-Grained Models for Polymers

Share This Special Issue

Special Issue Editors

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Published Papers (11 papers)

Research

Further Information

Guidelines

MDPI Initiatives

Follow MDPI