Special Issue "Multiscale Simulations in Soft Matter"
A special issue of Polymers (ISSN 2073-4360).
Deadline for manuscript submissions: closed (31 March 2013)
Prof. Dr. Martin Kröger
Polymer Physics, Department of Materials, Swiss Federal Institute of Technology, ETH Zurich, Wolfgang-Pauli-Str. 10, CH-8093 Zurich, Switzerland
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
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
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.
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| Download PDF Full-text (1819 KB)
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| Download PDF Full-text (312 KB)
Polymers 2013, 5(2), 643-678; doi:10.3390/polym5020643
Received: 22 March 2013; in revised form: 9 May 2013 / Accepted: 20 May 2013 / Published: 3 June 2013| Download PDF Full-text (489 KB)
Polymers 2013, 5(2), 730-750; doi:10.3390/polym5020730
Received: 1 April 2013; in revised form: 10 May 2013 / Accepted: 13 May 2013 / Published: 10 June 2013| Download PDF Full-text (23476 KB)
Polymers 2013, 5(2), 751-832; doi:10.3390/polym5020751
Received: 3 April 2013; in revised form: 16 May 2013 / Accepted: 30 May 2013 / Published: 13 June 2013| Download PDF Full-text (3813 KB)
Polymers 2013, 5(3), 890-936; doi:10.3390/polym5030890
Received: 26 April 2013; in revised form: 20 June 2013 / Accepted: 20 June 2013 / Published: 2 July 2013| Download PDF Full-text (13847 KB)
The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.
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: email@example.com
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: firstname.lastname@example.org
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: email@example.com (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.
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.
Last update: 3 April 2013