Special Issue "Multiscale Simulations in Soft Matter"

Guest Editor
Prof. Dr. Martin Kröger
Polymer Physics, Department of Materials, Swiss Federal Institute of Technology, ETH Zurich, Wolfgang-Pauli-Str. 10, CH-8093 Zurich, Switzerland
Website: http://www.complexfluids.ethz.ch
E-Mail: mk@mat.ethz.ch
Phone: +41 44 632 66 22
Fax: +41 44 632 10 76
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

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 quarterly 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 500 CHF (Swiss Francs). English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.

Juergen Geiser Article: 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; in revised form: 16 January 2013 / Accepted: 22 January 2013 / Published: 5 February 2013 Show/Hide Abstract | Download PDF Full-text (1819 KB) 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 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.

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Bhaskar Gupta and Patrick Ilg Article: 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; in revised form: 15 March 2013 / Accepted: 19 March 2013 / Published: 27 March 2013 Show/Hide Abstract | Download PDF Full-text (312 KB) 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 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.

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Type of Paper: Article
Title: A Multi-Scale Mechanical Model to Determine the Stiffness Properties of Plant Tissue
Authors: Md Tanvir Faisal, Alejandro Rey and Damiano Pasini *
Affiliation: Mechanical Engineering Department, McGill University,817 Sherbrooke Street West, Room 372 Montreal, Quebec, H3A0C3, Canada; E-Mail: damiano.pasini@mcgill.ca
Abstract: The stiffness of plant tissue is largely governed by the cell wall composition and the structural properties of the constituents. The cell wall is analogous to a fiber reinforced composite, where the cellulose microfibril (CMF) is the load bearing component. In this work, experimentally determined wall composition and microfibril angle (MFA) are used to derive the wall stiffness at the subcellular level, using a novel composite micromechanics approach. At the cellular level, we resort to a 2-D Finite Edge Centroidal Voronoi tessellation (FECVT) to generate the non-periodic tissue microstructure. The effective elastic properties of the cellular tissue are obtained through finite element analysis (FEA) of the Voronoi model coupled with the cell wall properties; the results are compared with the experimentally measured stiffness of a Rheum rhabarbarum tissue. The stiffness of the hierarchically modeled tissue is critically important in determining the overall structural properties of plant petioles and stems, and it can serve as a biomimetic platform for the design of hierarchical functional and structural materials.

Type of Paper: Article
Title: A Coarse Grained Model for Nucleic Acids with Dipolar Contributions and Explicit Solvation
Authors: Christos Lamprakis and Michele Cascella
Affiliation: University of Bern, Department of Chemistry and Biochemistry Freiestrasse 3, 3012 Bern, Switzerland; E-Mail: michele.cascella@iac.unibe.ch
Abstract: Atomistic simulations are prohibitively expensive for large scale systems like biological polymers. Here, we propose a coarse grained model for DNA and RNA based on explicit definition of the electrostatic dipolar contributions of the corresponding all‐atom representations. Seven and six interaction sites represent the purine and pyrimidine bases, respectively. A genetic algorithm is ues to perform parameterization of the coarse‐grained model, by means of a force‐matching procedure. The performance is evaluated by comparison with all atom simulations of both the Drew‐Dickerson DNA dodecamer and of different RNA small molecules. Finally, the effect of explicit solvation with a polarisable water model and ionic strength is examined.

Type of Paper: Review
Title: Multiscale models for protein-cell membrane interaction
Authors： Ryan Bradley, N. Ramakrishnan, Richard Tourdot and Ravi Radhakrishnan *
Affiliation: Department of Bioengineering, Department of Chemical and Biomolecular Engineering, University of Pennsylvania, USA; E-Mail: rradhak@seas.upenn.edu (R.R.)
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 which 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 (mesoscale) properties of soft-matter systems essential to our understanding of cells, particularly those involved in sculpting and remodeling cell membranes.

Type of Paper: Review
Title: State of the Art and Remaining Challenges in Multiscale Modeling of Polymers: A Comparison of Eleven Methods
Authors: Ying Li, Brendan C. Abberton, Martin Kröger and Wing Kam Liu
Affiliation: Department of Mechanical Engineering, Northwestern University, Evanston, IL 60208, USA, and Polymer Physics, ETH Zurich, Switzerland
Abstract: The mechanical and physical properties of polymeric materials represent phenomena that originate from the interplay of different spatial and temporal scales. To account for all important mechanisms in the modeling of polymeric materials it is necessary to adopt multiscale modeling techniques. A number of different multiscale computational techniques have been developed during the last two decades, and especially in the last five years. We aim at reviewing these developments for polymeric materials 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. Eleven different multiscale computational techniques falling under these categories are discussed and compared with each other, and critically assessed according to their ability to provide the rigorous link between polymer chemistry and rheological material properties. For each multiscale computational technique, the fundamental ideas and equations are introduced, and illustrated by their most important results or predictions. This review attempts to provide, on one hand, a comprehensive tutorial for multiscale computational techniques of interest to readers newly entering this field. On the other, we present a critical discussion on the future opportunities and remaining challenges in the multiscale modeling of polymeric materials, and how these methods can help us to optimize and design new polymeric materials.