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Special Issue "Multiscale Simulations in Soft Matter"

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A special issue of Polymers (ISSN 2073-4360).

Deadline for manuscript submissions: closed (31 March 2013)

Special Issue Editor

Guest Editor
Prof. Dr. Martin Kröger (Website)

Polymer Physics, Department of Materials, ETH Zurich, Leopold-Ruzicka-Weg 4, CH-8093 Zurich, Switzerland
Interests: computational polymer physics; complex liquids; anisotropic liquids; coarse-graining issues; new simulation methods; nonequilibrium phenomena; polymer brushes, melts, solutions, gels, and networks; dendritic structures; scaling concepts; topology; pattern recognition; molecular dynamics

Special Issue Information

Dear Colleagues,

Multiscale modeling is interdisciplinary. Dynamics of complex, soft and biological materials typically exhibits large-scale, ultra-slow time evolution which can easily become several orders larger than typical microscopic length and time scales. Concepts and effective simulation methods bridging between different length and time scales are strongly desired. This issue aims to review the current state of the art in multi-scale simulations for bio- and soft materials and to highlight latest advances in applications and methodologies. The topical themes include computational methods for intermolecular forces, computational modelings for fluids, bio- and soft materials, coarse-graining methods, hybrid methods of micro/meso/macro simulations, non-equilibrium simulations, etc.

Prof. Dr. Martin Kröger
Guest Editor

Submission

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. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as 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 refereed through a 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 monthly 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 1400 CHF (Swiss Francs).

Published Papers (6 papers)

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Research

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Open AccessArticle Coarse-Grained Models for Protein-Cell Membrane Interactions
Polymers 2013, 5(3), 890-936; doi:10.3390/polym5030890
Received: 26 April 2013 / Revised: 20 June 2013 / Accepted: 20 June 2013 / Published: 2 July 2013
Cited by 10 | PDF Full-text (13847 KB) | HTML Full-text | XML Full-text
Abstract
The physiological properties of biological soft matter are the product of collective interactions, which span many time and length scales. Recent computational modeling efforts have helped illuminate experiments that characterize the ways in which proteins modulate membrane physics. Linking these models across [...] Read more.
The physiological properties of biological soft matter are the product of collective interactions, which span many time and length scales. Recent computational modeling efforts have helped illuminate experiments that characterize the ways in which proteins modulate membrane physics. Linking these models across time and length scales in a multiscale model explains how atomistic information propagates to larger scales. This paper reviews continuum modeling and coarse-grained molecular dynamics methods, which connect atomistic simulations and single-molecule experiments with the observed microscopic or mesoscale properties of soft-matter systems essential to our understanding of cells, particularly those involved in sculpting and remodeling cell membranes. Full article
(This article belongs to the Special Issue Multiscale Simulations in Soft Matter)
Open AccessArticle A Multiscale Mechanical Model for Plant Tissue Stiffness
Polymers 2013, 5(2), 730-750; doi:10.3390/polym5020730
Received: 1 April 2013 / Revised: 10 May 2013 / Accepted: 13 May 2013 / Published: 10 June 2013
Cited by 4 | PDF Full-text (23476 KB) | HTML Full-text | XML Full-text
Abstract
Plant petioles and stems are hierarchical cellular structures, displaying structuralfeatures defined at multiple length scales. The current work focuses on the multi-scalemodelling of plant tissue, considering two orders of structural hierarchy, cell wall and tissue.The stiffness of plant tissue is largely governed [...] Read more.
Plant petioles and stems are hierarchical cellular structures, displaying structuralfeatures defined at multiple length scales. The current work focuses on the multi-scalemodelling of plant tissue, considering two orders of structural hierarchy, cell wall and tissue.The stiffness of plant tissue is largely governed by the geometry of the tissue cells, thecomposition of the cell wall and the structural properties of its constituents. The cell wallis analogous to a fiber reinforced composite, where the cellulose microfibril (CMF) is theload bearing component. For multilayered cell wall, the microfibril angle (MFA) in themiddle layer of the secondary cell wall (S2 layer) largely affects the longitudinal stiffnessfor values up to 40o. The MFA in turn influences the overall wall stiffness. In this work,the effective stiffness of a model system based on collenchyma cell wall of a dicotyledonousplant, the Rheum rhabarbarum, is computed considering generic MFA and volume fractions.At the cellular level, a 2-D Finite Edge Centroidal Voronoi tessellation (FECVT) has beendeveloped and implemented to generate the non-periodic microstructure of the plant tissue.The effective elastic properties of the cellular tissue are obtained through finite elementanalysis (FEA) of the Voronoi model coupled with the cell wall properties. The stiffness ofthe hierarchically modeled tissue is critically important in determining the overall structuralproperties of plant petioles and stems. Full article
(This article belongs to the Special Issue Multiscale Simulations in Soft Matter)
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Open AccessArticle Fluctuating Entanglements in Single-Chain Mean-Field Models
Polymers 2013, 5(2), 643-678; doi:10.3390/polym5020643
Received: 22 March 2013 / Revised: 9 May 2013 / Accepted: 20 May 2013 / Published: 3 June 2013
Cited by 10 | PDF Full-text (489 KB) | HTML Full-text | XML Full-text
Abstract
We consider four criteria of acceptability for single-chain mean-field entangled polymer models: consistency with a multi-chain level of description, consistency with nonequilibrium thermodynamics, consistency with the stress-optic rule, and self-consistency between Green–Kubo predictions and linear viscoelastic predictions for infinitesimally driven systems. Each [...] Read more.
We consider four criteria of acceptability for single-chain mean-field entangled polymer models: consistency with a multi-chain level of description, consistency with nonequilibrium thermodynamics, consistency with the stress-optic rule, and self-consistency between Green–Kubo predictions and linear viscoelastic predictions for infinitesimally driven systems. Each of these topics has been considered independently elsewhere. However, we are aware of no molecular entanglement model that satisfies all four criteria simultaneously. Here we show that an idea from Ronca and Allegra, generalized to arbitrary flows, can be implemented in a slip-link model to create a model that does satisfy all four criteria. Aside from the direct benefits of agreement, the result modifies the relation between the initial relaxation modulus G(0) and the entanglement molecular weight Me. If this implementation is correct, current estimates for Me would require modification that brings their values more in line with estimates based on topological analysis of molecular dynamics simulations. Full article
(This article belongs to the Special Issue Multiscale Simulations in Soft Matter)
Open AccessArticle Energetic and Entropic Contributions to the Landau–de Gennes Potential for Gay–Berne Models of Liquid Crystals
Polymers 2013, 5(2), 328-343; doi:10.3390/polym5020328
Received: 15 February 2013 / Revised: 15 March 2013 / Accepted: 19 March 2013 / Published: 27 March 2013
Cited by 5 | PDF Full-text (312 KB) | HTML Full-text | XML Full-text
Abstract
The Landau–de Gennes theory provides a successful macroscopic description of nematics. Cornerstone of this theory is a phenomenological expression for the effective free energy as a function of the orientational order parameter. Here, we show how such a macroscopic Landau–de Gennes free [...] Read more.
The Landau–de Gennes theory provides a successful macroscopic description of nematics. Cornerstone of this theory is a phenomenological expression for the effective free energy as a function of the orientational order parameter. Here, we show how such a macroscopic Landau–de Gennes free energy can systematically be constructed for a microscopic model of liquid crystals formed by interacting mesogens. For the specific example of the Gay–Berne model, we obtain an enhanced free energy that reduces to the familiar Landau–de Gennes expression in the limit of weak ordering. By carefully separating energetic and entropic contributions to the free energy, our approach reconciles the two traditional views on the isotropic–nematic transition of Maier–Saupe and Onsager, attributing the driving mechanism to attractive interactions and entropic effects, respectively. Full article
(This article belongs to the Special Issue Multiscale Simulations in Soft Matter)
Open AccessArticle Multiscale Modeling of Chemical Vapor Deposition (CVD) Apparatus: Simulations and Approximations
Polymers 2013, 5(1), 142-160; doi:10.3390/polym5010142
Received: 27 November 2012 / Revised: 16 January 2013 / Accepted: 22 January 2013 / Published: 5 February 2013
Cited by 4 | PDF Full-text (1819 KB) | HTML Full-text | XML Full-text
Abstract
We are motivated to compute delicate chemical vapor deposition (CVD) processes. Such processes are used to deposit thin films of metallic or ceramic materials, such as SiC or a mixture of SiC and TiC. For practical simulations and for studying the characteristics [...] Read more.
We are motivated to compute delicate chemical vapor deposition (CVD) processes. Such processes are used to deposit thin films of metallic or ceramic materials, such as SiC or a mixture of SiC and TiC. For practical simulations and for studying the characteristics in the deposition area, we have to deal with delicate multiscale models. We propose a multiscale model based on two different software packages. The large scales are simulated with computational fluid dynamics (CFD) software based on the transportreaction model (or macroscopic model), and the small scales are simulated with ordinary differential equations (ODE) software based on the reactive precursor gas model (or microscopic model). Our contribution is to upscale the correlation of the underlying microscale species to the macroscopic model and reformulate the fast reaction model. We obtain a computable model and apply a standard CFD software code without losing the information of the fast processes. For the multiscale model, we present numerical results of a real-life deposition process. Full article
(This article belongs to the Special Issue Multiscale Simulations in Soft Matter)

Review

Jump to: Research

Open AccessReview Challenges in Multiscale Modeling of Polymer Dynamics
Polymers 2013, 5(2), 751-832; doi:10.3390/polym5020751
Received: 3 April 2013 / Revised: 16 May 2013 / Accepted: 30 May 2013 / Published: 13 June 2013
Cited by 38 | PDF Full-text (3813 KB) | HTML Full-text | XML Full-text
Abstract
The mechanical and physical properties of polymeric materials originate from the interplay of phenomena at different spatial and temporal scales. As such, it is necessary to adopt multiscale techniques when modeling polymeric materials in order to account for all important mechanisms. Over [...] Read more.
The mechanical and physical properties of polymeric materials originate from the interplay of phenomena at different spatial and temporal scales. As such, it is necessary to adopt multiscale techniques when modeling polymeric materials in order to account for all important mechanisms. Over the past two decades, a number of different multiscale computational techniques have been developed that can be divided into three categories: (i) coarse-graining methods for generic polymers; (ii) systematic coarse-graining methods and (iii) multiple-scale-bridging methods. In this work, we discuss and compare eleven different multiscale computational techniques falling under these categories and assess them critically according to their ability to provide a rigorous link between polymer chemistry and rheological material properties. For each technique, the fundamental ideas and equations are introduced, and the most important results or predictions are shown and discussed. On the one hand, this review provides a comprehensive tutorial on multiscale computational techniques, which will be of interest to readers newly entering this field; on the other, it presents a critical discussion of the future opportunities and key challenges in the multiscale modeling of polymeric materials and how these methods can help us to optimize and design new polymeric materials. Full article
(This article belongs to the Special Issue Multiscale Simulations in Soft Matter)
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