1
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Wu C. Temperature-Transferable Coarse-Grained Models for Volumetric Properties of Poly(lactic Acid). J Phys Chem B 2024; 128:358-370. [PMID: 38153413 DOI: 10.1021/acs.jpcb.3c07026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
A new coarse-grained (CG) model, for which each monomer is mapped as one bead at its center of mass, was developed for simulating the volumetric properties of the polylactide (PLA) bulk. The three bonded CG potentials are first parametrized against the strain energies of the dimer, trimer, and tetramer, and the nonbonded CG potentials are then optimized to match the melt densities of the decamer. With the derived CG potentials, molecular dynamics (MD) simulations are found to reproduce thermal expansion and glass transition. By rescaling the dihedral and nonbonded potentials with temperature-independent factors, the glass transition temperature (Tg) is also satisfactorily restored with little modifications on the volumetric expansive coefficients at both rubbery and glassy states. Therefore, the finally optimized CG potentials exhibit excellent temperature transferability, as rationalized by the Simha-Boyer relation. Furthermore, it is confirmed that the dihedral torsions and nonbonded interactions play key roles in glass transition. Also, the simulated bulk moduli and conformational properties in a wide temperature range compare well with the referenced data. The proposed multiscale scheme has great potential in simulating thermo-mechanical properties of PLA and other polymers.
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Affiliation(s)
- Chaofu Wu
- Hunan Provincial Key Laboratory of Fine Ceramics and Powder Materials, School of Materials and Environmental Engineering, Hunan University of Humanities, Science and Technology, Loudi 417000, Hunan, P. R. China
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2
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Wu C. Critical Thicknesses of Free-Standing Thin Films of Molten Polymers: A Multiscale Simulation Study. J Phys Chem B 2022; 126:6500-6510. [PMID: 35979674 DOI: 10.1021/acs.jpcb.2c02627] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The free-standing thin films of melted poly(ethylene oxide) have been extensively simulated by the chemically specific coarse-grained (CG) molecular dynamics (MD) method. It is revealed that if the polymer thin film becomes thinner than some critical value, it would initially turn into a fiber, accompanied by an increase in the free surface area and a decrease in surface tension. A simple but efficient scheme is proposed to determine the critical interfacial thickness and the film thickness from the non-intrinsic density and pressure profiles, and the ratio of the two thicknesses is defined as the interfacial fraction. The critical film thickness is found to increase with the number of chains or equivalently the transverse area. With increasing temperature, the critical interfacial thickness increases a bit whereas the critical film thickness slightly decreases, highlighting the important role of the interfacial fraction. For both of the "critical" and "thick" films, the outermost surface layers are confirmed to undergo the greatest movements. The "critical" film exhibits the intrinsic interfacial thickness and bulk density almost identical to those of the "thick" film, dictating the thickness independence of the surface tension. Therefore, the phase stability of the film is essentially determined from the intrinsic thickness of the bulk layer, and the identified temperature dependence of the critical film thickness can be mainly explained by the surface tension.
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Affiliation(s)
- Chaofu Wu
- Hunan Provincial Key Laboratory of Fine Ceramics and Powder Materials, School of Materials and Environmental Engineering, Hunan University of Humanities, Science and Technology, Loudi 417000, Hunan, P. R. China
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3
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Molecular Modeling in Anion Exchange Membrane Research: A Brief Review of Recent Applications. Molecules 2022; 27:molecules27113574. [PMID: 35684512 PMCID: PMC9182285 DOI: 10.3390/molecules27113574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/24/2022] [Accepted: 05/30/2022] [Indexed: 12/04/2022] Open
Abstract
Anion Exchange Membrane (AEM) fuel cells have attracted growing interest, due to their encouraging advantages, including high power density and relatively low cost. AEM is a polymer matrix, which conducts hydroxide (OH−) ions, prevents physical contact of electrodes, and has positively charged head groups (mainly quaternary ammonium (QA) groups), covalently bound to the polymer backbone. The chemical instability of the quaternary ammonium (QA)-based head groups, at alkaline pH and elevated temperature, is a significant threshold in AEMFC technology. This review work aims to introduce recent studies on the chemical stability of various QA-based head groups and transportation of OH− ions in AEMFC, via modeling and simulation techniques, at different scales. It starts by introducing the fundamental theories behind AEM-based fuel-cell technology. In the main body of this review, we present selected computational studies that deal with the effects of various parameters on AEMs, via a variety of multi-length and multi-time-scale modeling and simulation methods. Such methods include electronic structure calculations via the quantum Density Functional Theory (DFT), ab initio, classical all-atom Molecular Dynamics (MD) simulations, and coarse-grained MD simulations. The explored processing and structural parameters include temperature, hydration levels, several QA-based head groups, various types of QA-based head groups and backbones, etc. Nowadays, many methods and software packages for molecular and materials modeling are available. Applications of such methods may help to understand the transportation mechanisms of OH− ions, the chemical stability of functional head groups, and many other relevant properties, leading to a performance-based molecular and structure design as well as, ultimately, improved AEM-based fuel cell performances. This contribution aims to introduce those molecular modeling methods and their recent applications to the AEM-based fuel cells research community.
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4
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Wu C, Li K, Ning X, Zhang L. An Enhanced Scheme for Multiscale Modeling of Thermomechanical Properties of Polymer Bulks. J Phys Chem B 2021; 125:8612-8626. [PMID: 34291641 DOI: 10.1021/acs.jpcb.1c02663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While multiscale modeling significantly enhances the capability of molecular simulations of polymer systems, it is well realized that the systematically derived coarse-grained (CG) models generally underestimate the thermomechanical properties. In this work, a charge-based mapping scheme has been adopted to include explicit electrostatic interactions and benchmarked against two typical polymers, atactic poly(methyl methacrylate) (PMMA) and polystyrene (PS). The CG potentials are parameterized against the oligomer bulks of nine monomers per chain to match the essential structural features and the two basic pressure-volume-temperature (PVT) properties, which are obtained from the all-atomistic (AA) molecular dynamics (MD) simulations at a single elevated temperature. The so-parameterized CG potentials are extended with the MD method to simulate the two polymer bulks of one hundred monomers per chain over a wide temperature range. Without any scaling, all the simulated results, including mass densities and bulk moduli at room temperature, thermal expansion coefficients at rubbery and glassy states, and glass transition temperatures (Tg), compare well with the corresponding experimental data. The proposed scheme not only contributes to realistically simulating various thermomechanical properties of both apolar and polar polymers but also allows for directly simulating their electrical properties.
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Affiliation(s)
- Chaofu Wu
- Hunan Provincial Key Laboratory of Fine Ceramics and Powder Materials, School of Materials and Environmental Engineering, Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, P. R. China
| | - Kewen Li
- Hunan Provincial Key Laboratory of Fine Ceramics and Powder Materials, School of Materials and Environmental Engineering, Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, P. R. China
| | - Xutao Ning
- Hunan Provincial Key Laboratory of Fine Ceramics and Powder Materials, School of Materials and Environmental Engineering, Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, P. R. China
| | - Lei Zhang
- Hunan Provincial Key Laboratory of Fine Ceramics and Powder Materials, School of Materials and Environmental Engineering, Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, P. R. China
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5
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Wu C. Tacticity Effects on the Bulk Modulus of Poly(methyl methacrylate) Explored by Coarse-Grained Simulations. J Phys Chem B 2020; 124:10811-10821. [DOI: 10.1021/acs.jpcb.0c06596] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chaofu Wu
- Hunan Provincial Key Laboratory of Fine Ceramics and Powder Materials, School of Materials and Environmental Engineering, Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, China
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6
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Joshi SY, Deshmukh SA. A review of advancements in coarse-grained molecular dynamics simulations. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1828583] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Soumil Y. Joshi
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
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7
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Wu C. Molecular-weight dependence of simulated glass transition temperature for isolated poly(ethylene oxide) chain. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1763986] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Chaofu Wu
- Hunan Provincial Key Laboratory of Fine Ceramics and Powder Materials, School of Materials and Environmental Engineering, Hunan University of Humanities, Science and Technology, Loudi, People’s Republic of China
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8
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Mantha S, Qi S, Schmid F. Bottom-up Construction of Dynamic Density Functional Theories for Inhomogeneous Polymer Systems from Microscopic Simulations. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00130] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Sriteja Mantha
- Institut für Physik, Johannes Gutenberg Universität Mainz, Staudingerweg 9, 55128 Mainz, Germany
| | - Shuanhu Qi
- Key Laboratory of Bio-inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry, Beihang University, Beijing 100191, China
| | - Friederike Schmid
- Institut für Physik, Johannes Gutenberg Universität Mainz, Staudingerweg 9, 55128 Mainz, Germany
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9
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Wörner SJ, Bereau T, Kremer K, Rudzinski JF. Direct route to reproducing pair distribution functions with coarse-grained models via transformed atomistic cross correlations. J Chem Phys 2020; 151:244110. [PMID: 31893905 DOI: 10.1063/1.5131105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Coarse-grained (CG) models are often parameterized to reproduce one-dimensional structural correlation functions of an atomically detailed model along the degrees of freedom governing each interaction potential. While cross correlations between these degrees of freedom inform the optimal set of interaction parameters, the correlations generated from the higher-resolution simulations are often too complex to act as an accurate proxy for the CG correlations. Instead, the most popular methods determine the interaction parameters iteratively while assuming that individual interactions are uncorrelated. While these iterative methods have been validated for a wide range of systems, they also have disadvantages when parameterizing models for multicomponent systems or when refining previously established models to better reproduce particular structural features. In this work, we propose two distinct approaches for the direct (i.e., noniterative) parameterization of a CG model by adjusting the high-resolution cross correlations of an atomistic model in order to more accurately reflect correlations that will be generated by the resulting CG model. The derived models more accurately describe the low-order structural features of the underlying AA model while necessarily generating inherently distinct cross correlations compared with the atomically detailed reference model. We demonstrate the proposed methods for a one-site-per-molecule representation of liquid water, where pairwise interactions are incapable of reproducing the true tetrahedral solvation structure. We then investigate the precise role that distinct cross-correlation features play in determining the correct pair correlation functions, evaluating the importance of the placement of correlation features as well as the balance between features appearing in different solvation shells.
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Affiliation(s)
- Svenja J Wörner
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
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10
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A multiscale scheme for simulating polymer Tg. J Mol Model 2018; 24:335. [DOI: 10.1007/s00894-018-3867-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/18/2018] [Indexed: 10/27/2022]
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11
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Computational modelling of drug delivery to solid tumour: Understanding the interplay between chemotherapeutics and biological system for optimised delivery systems. Adv Drug Deliv Rev 2018; 132:81-103. [PMID: 30059703 DOI: 10.1016/j.addr.2018.07.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 01/10/2023]
Abstract
Drug delivery to solid tumour involves multiple physiological, biochemical and biophysical processes taking place across a wide range of length and time scales. The therapeutic efficacy of anticancer drugs is influenced by the complex interplays among the intrinsic properties of tumours, biophysical aspects of drug transport and cellular uptake. Mathematical and computational modelling allows for a well-controlled study on the individual and combined effects of a wide range of parameters on drug transport and therapeutic efficacy, which would not be possible or economically viable through experimental means. A wide spectrum of mathematical models has been developed for the simulation of drug transport and delivery in solid tumours, including PK/PD-based compartmental models, microscopic and macroscopic transport models, and molecular dynamics drug loading and release models. These models have been used as a tool to identify the limiting factors and for optimal design of efficient drug delivery systems. This article gives an overview of the currently available computational models for drug transport in solid tumours, together with their applications to novel drug delivery systems, such as nanoparticle-mediated drug delivery and convection-enhanced delivery.
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12
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Vanduyfhuys L, Vandenbrande S, Wieme J, Waroquier M, Verstraelen T, Van Speybroeck V. Extension of the QuickFF force field protocol for an improved accuracy of structural, vibrational, mechanical and thermal properties of metal-organic frameworks. J Comput Chem 2018; 39:999-1011. [PMID: 29396847 PMCID: PMC5947575 DOI: 10.1002/jcc.25173] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 01/16/2023]
Abstract
QuickFF was originally launched in 2015 to derive accurate force fields for isolated and complex molecular systems in a quick and easy way. Apart from the general applicability, the functionality was especially tested for metal-organic frameworks (MOFs), a class of hybrid materials consisting of organic and inorganic building blocks. Herein, we launch a new release of the QuickFF protocol which includes new major features to predict structural, vibrational, mechanical and thermal properties with greater accuracy, without compromising its robustness and transparent workflow. First, the ab initio data necessary for the fitting procedure may now also be derived from periodic models for the molecular system, as opposed to the earlier cluster-based models. This is essential for an accurate description of MOFs with one-dimensional metal-oxide chains. Second, cross terms that couple internal coordinates (ICs) and anharmonic contributions for bond and bend terms are implemented. These features are essential for a proper description of vibrational and thermal properties. Third, the fitting scheme was modified to improve robustness and accuracy. The new features are tested on MIL-53(Al), MOF-5, CAU-13 and NOTT-300. As expected, periodic input data are proven to be essential for a correct description of structural, vibrational and thermodynamic properties of MIL-53(Al). Bulk moduli and thermal expansion coefficients of MOF-5 are very accurately reproduced by static and dynamic simulations using the newly derived force fields which include cross terms and anharmonic corrections. For the flexible materials CAU-13 and NOTT-300, the transition pressure is accurately predicted provided cross terms are taken into account. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Louis Vanduyfhuys
- Center for Molecular Modeling (CMM), Ghent UniversityTechnologiepark903, 9052ZwijnaardeBelgium
| | - Steven Vandenbrande
- Center for Molecular Modeling (CMM), Ghent UniversityTechnologiepark903, 9052ZwijnaardeBelgium
| | - Jelle Wieme
- Center for Molecular Modeling (CMM), Ghent UniversityTechnologiepark903, 9052ZwijnaardeBelgium
| | - Michel Waroquier
- Center for Molecular Modeling (CMM), Ghent UniversityTechnologiepark903, 9052ZwijnaardeBelgium
| | - Toon Verstraelen
- Center for Molecular Modeling (CMM), Ghent UniversityTechnologiepark903, 9052ZwijnaardeBelgium
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13
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Multiscale modeling of glass transition in polymeric films: Application to stereoregular poly(methyl methacrylate)s. POLYMER 2018. [DOI: 10.1016/j.polymer.2018.05.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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14
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Sabater i Serra R, Torregrosa Cabanilles C, Meseguer Dueñas JM, Gómez Ribelles JL, Molina-Mateo J. Conformational Changes and Dynamics during Adsorption of Macromolecules with Different Degree of Polymerization Studied by Monte Carlo Simulations. MACROMOL THEOR SIMUL 2018. [DOI: 10.1002/mats.201800012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Roser Sabater i Serra
- Centre for Biomaterials and Tissue Engineering; Universitat Politècnica de València; 46022 València Spain
- CIBER-BBN; Biomedical Research Networking Centre in Bioengineering; Biomaterials and Nanomedicine; Valencia Spain
| | | | - José María Meseguer Dueñas
- Centre for Biomaterials and Tissue Engineering; Universitat Politècnica de València; 46022 València Spain
- CIBER-BBN; Biomedical Research Networking Centre in Bioengineering; Biomaterials and Nanomedicine; Valencia Spain
| | - José Luis Gómez Ribelles
- Centre for Biomaterials and Tissue Engineering; Universitat Politècnica de València; 46022 València Spain
- CIBER-BBN; Biomedical Research Networking Centre in Bioengineering; Biomaterials and Nanomedicine; Valencia Spain
| | - José Molina-Mateo
- Centre for Biomaterials and Tissue Engineering; Universitat Politècnica de València; 46022 València Spain
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15
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D'Adamo G, Pelissetto A. Polymer models with optimal good-solvent behavior. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:435104. [PMID: 28737167 DOI: 10.1088/1361-648x/aa8191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We consider three different continuum polymer models, which all depend on a tunable parameter r that determines the strength of the excluded-volume interactions. In the first model, chains are obtained by concatenating hard spherocylinders of height b and diameter rb (we call them thick self-avoiding chains). The other two models are generalizations of the tangent hard-sphere and of the Kremer-Grest models. We show that for a specific value [Formula: see text], all models show optimal behavior: asymptotic long-chain behavior is observed for relatively short chains. For [Formula: see text], instead, the behavior can be parametrized by using the two-parameter model, which also describes the thermal crossover close to the θ point. The bonds of the thick self-avoiding chains cannot cross each other, and therefore the model is suited for the investigation of topological properties and for dynamical studies. Such a model also provides a coarse-grained description of double-stranded DNA, so that we can use our results to discuss under which conditions DNA can be considered as a model good-solvent polymer.
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16
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Tripathy M, Kumar PBS, Deshpande AP. Molecular Structuring and Percolation Transition in Hydrated Sulfonated Poly(ether ether ketone) Membranes. J Phys Chem B 2017; 121:4873-4884. [PMID: 28430444 DOI: 10.1021/acs.jpcb.7b01045] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The extent of phase separation and water percolation in sulfonated membranes are the key to their performance in fuel cells. Toward this, the effect of hydration on the morphology and transport characteristics of sulfonated poly(ether ether ketone), sPEEK, membrane is investigated using atomistic molecular dynamics simulation at various hydration levels(λ: number of water molecules per sulfonate group). The evolution of local morphology is investigated using structural correlations and minimum pair distances. Transport properties are probed using mean squared displacements and diffusion coefficients. The water-sulfonate interaction in sPEEK is found to be stronger than that in Nafion, as observed in experiments. Analyses indicate the presence of narrow connected path of water and hydronium at λ = 4 and large domains, spanning half the simulation box, at λ = 15. The behavior of membrane water remains far from bulk as indicated by its diffusion coefficient. The persistence of small isolated water clusters demonstrates the extent of phase separation in sPEEK to be lesser than that in Nafion. Analyses at molecular and collective levels suggest the occurrence of a percolation transition between λ = 8 and 10, which leads to a connected network of water channels in the membrane, thereby boosting the hydronium mobility.
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Affiliation(s)
- Madhusmita Tripathy
- Department of Physics, Indian Institute of Technology Madras , Chennai, Tamil Nadu, 600036, India
| | - P B Sunil Kumar
- Department of Physics, Indian Institute of Technology Madras , Chennai, Tamil Nadu, 600036, India
| | - Abhijit P Deshpande
- Department of Chemical Engineering, Indian Institute of Technology Madras , Chennai, Tamil Nadu, 600036, India
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17
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Zubova EA, Strelnikov IA, Balabaev NK, Savin AV, Mazo MA, Manevich LI. Coarse-grained polyethylene: 1. The simplest model for the orthorhombic crystal. POLYMER SCIENCE SERIES A 2017. [DOI: 10.1134/s0965545x17010175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Abstract
More than 20 coarse-grained (CG) DNA models have been developed for simulating the behavior of this molecule under various conditions, including those required for nanotechnology. However, none of these models reproduces the DNA polymorphism associated with conformational changes in the ribose rings of the DNA backbone. These changes make an essential contribution to the DNA local deformability and provide the possibility of the transition of the DNA double helix from the B-form to the A-form during interactions with biological molecules. We propose a CG representation of the ribose conformational flexibility. We substantiate the choice of the CG sites (six per nucleotide) needed for the "sugar" GC DNA model, and obtain the potentials of the CG interactions between the sites by the "bottom-up" approach using the all-atom AMBER force field. We show that the representation of the ribose flexibility requires one non-harmonic and one three-particle potential, the forms of both the potentials being different from the ones generally used. The model also includes (i) explicit representation of ions (in an implicit solvent) and (ii) sequence dependence. With these features, the sugar CG DNA model reproduces (with the same parameters) both the B- and A- stable forms under corresponding conditions and demonstrates both the A to B and the B to A phase transitions. Graphical Abstract The proposed coarse-grained DNA model allows to reproduce both the B- and A- DNA forms and the transitions between them under corresponding conditions.
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19
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Xie Z, Chai D, Wang Y, Tan H. Directly Modifying the Nonbonded Potential Based on the Standard Iterative Boltzmann Inversion Method for Coarse-Grained Force Fields. J Phys Chem B 2016; 120:11834-11844. [PMID: 27766876 DOI: 10.1021/acs.jpcb.6b06457] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Effective potentials are of great importance for coarse-grained (CG) simulations, which can be obtained by the structure-based iterative Boltzmann inversion (IBI) method. However, the standard IBI method is incapable of maintaining the mechanical and thermodynamic properties of the CG model in agreement with those of the all-atom model. Unlike the existing techniques, such as introducing friction force as the dissipative force to reduce the superatom motion while keeping the conservative force arising from the CG potential intact, we directly modified the standard IBI nonbonded potential by adding an empirical function. According to an analysis of the dissipative particle dynamics, the additional function did compensate for the friction reduction of the standard IBI CG model. In this work, the thermal fluctuation information from the nonbonded radial distribution function was incorporated into the additional empirical function. As an illustration of the new CG force fields, we presented simulations of the stress-strain relation and thermodynamic properties in terms of cis-polyisoprene and compared the statistical structure information of the superatoms with those of the IBI CG model and the all-atom model. It should be emphasized that the additional empirical function contributed to compensating for the friction reduction, irrespective of the functional form it took. In this sense, the proposed method was easily operable.
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Affiliation(s)
- Zhimin Xie
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environment, Center for Composite Materials and Structures, Harbin Institute of Technology , Harbin 150001, People's Republic of China
| | - Dongliang Chai
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environment, Center for Composite Materials and Structures, Harbin Institute of Technology , Harbin 150001, People's Republic of China
| | - Youshan Wang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environment, Center for Composite Materials and Structures, Harbin Institute of Technology , Harbin 150001, People's Republic of China
| | - Huifeng Tan
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environment, Center for Composite Materials and Structures, Harbin Institute of Technology , Harbin 150001, People's Republic of China
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20
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Kreis K, Potestio R. The relative entropy is fundamental to adaptive resolution simulations. J Chem Phys 2016; 145:044104. [DOI: 10.1063/1.4959169] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Karsten Kreis
- Max-Planck-Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany
- Graduate School Materials Science in Mainz, Staudingerweg 9, 55128 Mainz, Germany
| | - Raffaello Potestio
- Max-Planck-Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany
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21
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D’Adamo G, Pelissetto A, Pierleoni C. Phase Diagram and Structure of Mixtures of Large Colloids and Linear Polymers under Good-Solvent Conditions. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b00600] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Andrea Pelissetto
- Dipartimento di Fisica, Sapienza Università di Roma and INFN, Sezione di Roma I, P.le Aldo Moro
2, I-00185 Rome, Italy
| | - Carlo Pierleoni
- Dipartimento di Scienze Fisiche
e Chimiche, Università dell’Aquila, V. Vetoio 10, Loc. Coppito, I-67100 L’Aquila, Italy
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22
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Melt-phase behavior of collapsed PMMA/PVC chains revealed by multiscale simulations. J Mol Model 2016; 22:99. [DOI: 10.1007/s00894-016-2963-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 03/14/2016] [Indexed: 12/20/2022]
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23
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Developing coarse-grained potentials for the prediction of multi-properties of trans-1,4-polybutadiene melt. POLYMER 2015. [DOI: 10.1016/j.polymer.2015.05.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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D’Adamo G, Pelissetto A, Pierleoni C. Accurate coarse-grained models for mixtures of colloids and linear polymers under good-solvent conditions. J Chem Phys 2014; 141:244905. [DOI: 10.1063/1.4904392] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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25
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De Nicola A, Kawakatsu T, Milano G. Generation of Well-Relaxed All-Atom Models of Large Molecular Weight Polymer Melts: A Hybrid Particle-Continuum Approach Based on Particle-Field Molecular Dynamics Simulations. J Chem Theory Comput 2014; 10:5651-67. [PMID: 26583248 DOI: 10.1021/ct500492h] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A procedure based on Molecular Dynamics (MD) simulations employing soft potentials derived from self-consistent field (SCF) theory (named MD-SCF) able to generate well-relaxed all-atom structures of polymer melts is proposed. All-atom structures having structural correlations indistinguishable from ones obtained by long MD relaxations have been obtained for poly(methyl methacrylate) (PMMA) and poly(ethylene oxide) (PEO) melts. The proposed procedure leads to computational costs mainly related on system size rather than to the chain length. Several advantages of the proposed procedure over current coarse-graining/reverse mapping strategies are apparent. No parametrization is needed to generate relaxed structures of different polymers at different scales or resolutions. There is no need for special algorithms or back-mapping schemes to change the resolution of the models. This characteristic makes the procedure general and its extension to other polymer architectures straightforward. A similar procedure can be easily extended to the generation of all-atom structures of block copolymer melts and polymer nanocomposites.
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Affiliation(s)
- Antonio De Nicola
- Dipartimento di Chimica e Biologia, Università degli Studi di Salerno , via Ponte don Melillo, Fisciano, Salerno I-84085, Italy.,IMAST Scarl-Technological District in Polymer and Composite Engineering, Piazza Bovio 22, Napoli, Napoli I-80133, Italy
| | - Toshihiro Kawakatsu
- Department of Physics, Tohoku University , Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Giuseppe Milano
- Dipartimento di Chimica e Biologia, Università degli Studi di Salerno , via Ponte don Melillo, Fisciano, Salerno I-84085, Italy.,IMAST Scarl-Technological District in Polymer and Composite Engineering, Piazza Bovio 22, Napoli, Napoli I-80133, Italy
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26
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Andrews CT, Elcock AH. COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids. J Chem Theory Comput 2014; 10:5178-5194. [PMID: 25400526 PMCID: PMC4230375 DOI: 10.1021/ct5006328] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Indexed: 02/06/2023]
Abstract
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We describe the derivation of a set
of bonded and nonbonded coarse-grained
(CG) potential functions for use in implicit-solvent Brownian dynamics
(BD) simulations of proteins derived from all-atom explicit-solvent
molecular dynamics (MD) simulations of amino acids. Bonded potential
functions were derived from 1 μs MD simulations of each of the
20 canonical amino acids, with histidine modeled in both its protonated
and neutral forms; nonbonded potential functions were derived from
1 μs MD simulations of every possible pairing of the amino acids
(231 different systems). The angle and dihedral probability distributions
and radial distribution functions sampled during MD were used to optimize
a set of CG potential functions through use of the iterative Boltzmann
inversion (IBI) method. The optimized set of potential functions—which
we term COFFDROP (COarse-grained Force Field for Dynamic Representation
Of Proteins)—quantitatively reproduced all of the “target”
MD distributions. In a first test of the force field, it was used
to predict the clustering behavior of concentrated amino acid solutions;
the predictions were directly compared with the results of corresponding
all-atom explicit-solvent MD simulations and found to be in excellent
agreement. In a second test, BD simulations of the small protein villin
headpiece were carried out at concentrations that have recently been
studied in all-atom explicit-solvent MD simulations by Petrov and
Zagrovic (PLoS Comput. Biol.2014, 5, e1003638). The anomalously strong intermolecular interactions
seen in the MD study were reproduced in the COFFDROP simulations;
a simple scaling of COFFDROP’s nonbonded parameters, however,
produced results in better accordance with experiment. Overall, our
results suggest that potential functions derived from simulations
of pairwise amino acid interactions might be of quite broad applicability,
with COFFDROP likely to be especially useful for modeling unfolded
or intrinsically disordered proteins.
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Affiliation(s)
- Casey T Andrews
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Adrian H Elcock
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
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27
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Wu C. Coarse-grained molecular dynamics simulations of stereoregular poly(methyl methacrylate)/poly(vinyl chloride) blends. ACTA ACUST UNITED AC 2014. [DOI: 10.1002/polb.23608] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Chaofu Wu
- Department of Chemistry and Materials Science; Hunan University of Humanities Science & Technology; Dixing Road 487, Louxing District Loudi 417000 Hunan Province People's Republic of China
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28
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Kobryn AE, Nikolić D, Lyubimova O, Gusarov S, Kovalenko A. Dissipative Particle Dynamics with an Effective Pair Potential from Integral Equation Theory of Molecular Liquids. J Phys Chem B 2014; 118:12034-49. [DOI: 10.1021/jp503981p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Alexander E. Kobryn
- National
Institute for Nanotechnology, National Research Council of Canada, 11421
Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
| | - Dragan Nikolić
- National
Institute for Nanotechnology, National Research Council of Canada, 11421
Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
- Department
of Mechanical Engineering, University of Alberta, Edmonton, Alberta T6G 2G8, Canada
| | - Olga Lyubimova
- National
Institute for Nanotechnology, National Research Council of Canada, 11421
Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
- Department
of Mechanical Engineering, University of Alberta, Edmonton, Alberta T6G 2G8, Canada
| | - Sergey Gusarov
- National
Institute for Nanotechnology, National Research Council of Canada, 11421
Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
| | - Andriy Kovalenko
- National
Institute for Nanotechnology, National Research Council of Canada, 11421
Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
- Department
of Mechanical Engineering, University of Alberta, Edmonton, Alberta T6G 2G8, Canada
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29
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Steinhauser MO, Schmidt M. Destruction of cancer cells by laser-induced shock waves: recent developments in experimental treatments and multiscale computer simulations. SOFT MATTER 2014; 10:4778-88. [PMID: 24818846 DOI: 10.1039/c4sm00407h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In this emerging area article we review recent progress in the mechanical destruction of cancer cells using laser-induced shock waves. The pure mechanical damaging and destruction of cancer cells associated with this technique possibly opens up a new route to tumor treatments and the corresponding therapies. At the same time progress in multiscale simulation techniques makes it possible to simulate mechanical properties of soft biological matter such as membranes, cytoskeletal networks and even whole cells and tissue. In this way an interdisciplinary approach to understanding key mechanisms in shock wave interactions with biological matter has become accessible. Mechanical properties of biological materials are also critical for many physiological processes and cover length scales ranging from the atomistic to the macroscopic scale. We argue that the latest developments and progress in experimentation enable the investigation of the shock wave interaction with cancer cells on multiple time- and length-scales. In this way the integrated use of experiment and simulation can address key challenges in this field. The exploration of the biological effects of laser-generated shock waves on a fundamental level constitutes an emerging multidisciplinary research area combining scientific methods from the areas of physics, biology, medicine and computer science.
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Affiliation(s)
- Martin Oliver Steinhauser
- Fraunhofer Research Group "Shock Waves in Soft Biological Matter", Ernst-Mach-Institut, EMI, Eckerstrasse 4, Freiburg, Germany.
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30
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Rudzinski JF, Noid WG. Investigation of coarse-grained mappings via an iterative generalized Yvon-Born-Green method. J Phys Chem B 2014; 118:8295-312. [PMID: 24684663 DOI: 10.1021/jp501694z] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Low resolution coarse-grained (CG) models enable highly efficient simulations of complex systems. The interactions in CG models are often iteratively refined over multiple simulations until they reproduce the one-dimensional (1-D) distribution functions, e.g., radial distribution functions (rdfs), of an all-atom (AA) model. In contrast, the multiscale coarse-graining (MS-CG) method employs a generalized Yvon-Born-Green (g-YBG) relation to determine CG potentials directly (i.e., without iteration) from the correlations observed for the AA model. However, MS-CG models do not necessarily reproduce the 1-D distribution functions of the AA model. Consequently, recent studies have incorporated the g-YBG equation into iterative methods for more accurately reproducing AA rdfs. In this work, we consider a theoretical framework for an iterative g-YBG method. We numerically demonstrate that the method robustly determines accurate models for both hexane and also a more complex molecule, 3-hexylthiophene. By examining the MS-CG and iterative g-YBG models for several distinct CG representations of both molecules, we investigate the approximations of the MS-CG method and their sensitivity to the CG mapping. More generally, we explicitly demonstrate that CG models often reproduce 1-D distribution functions of AA models at the expense of distorting the cross-correlations between the corresponding degrees of freedom. In particular, CG models that accurately reproduce intramolecular 1-D distribution functions may still provide a poor description of the molecular conformations sampled by the AA model. We demonstrate a simple and predictive analysis for determining CG mappings that promote an accurate description of these molecular conformations.
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Affiliation(s)
- Joseph F Rudzinski
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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31
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Abstract
By focusing on essential features, while averaging over less important details, coarse-grained (CG) models provide significant computational and conceptual advantages with respect to more detailed models. Consequently, despite dramatic advances in computational methodologies and resources, CG models enjoy surging popularity and are becoming increasingly equal partners to atomically detailed models. This perspective surveys the rapidly developing landscape of CG models for biomolecular systems. In particular, this review seeks to provide a balanced, coherent, and unified presentation of several distinct approaches for developing CG models, including top-down, network-based, native-centric, knowledge-based, and bottom-up modeling strategies. The review summarizes their basic philosophies, theoretical foundations, typical applications, and recent developments. Additionally, the review identifies fundamental inter-relationships among the diverse approaches and discusses outstanding challenges in the field. When carefully applied and assessed, current CG models provide highly efficient means for investigating the biological consequences of basic physicochemical principles. Moreover, rigorous bottom-up approaches hold great promise for further improving the accuracy and scope of CG models for biomolecular systems.
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Affiliation(s)
- W G Noid
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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32
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Muntean SA, Michels MAJ, Lyulin AV. Myoglobin Interactions with Polystyrene Surfaces of Different Hydrophobicity. MACROMOL THEOR SIMUL 2013. [DOI: 10.1002/mats.201300133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Stela-Andrea Muntean
- Theory of Polymers and Soft Matter (TPS), Department of Applied Physics; Technische Universiteit Eindhoven; P.O. Box 513, 5600 MB Eindhoven The Netherlands
- Dutch Polymer Institute; P.O. Box 902, 5600 AX Eindhoven The Netherlands
| | - Matthias A. J. Michels
- Theory of Polymers and Soft Matter (TPS), Department of Applied Physics; Technische Universiteit Eindhoven; P.O. Box 513, 5600 MB Eindhoven The Netherlands
| | - Alexey V. Lyulin
- Theory of Polymers and Soft Matter (TPS), Department of Applied Physics; Technische Universiteit Eindhoven; P.O. Box 513, 5600 MB Eindhoven The Netherlands
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33
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D'Adamo G, Pelissetto A, Pierleoni C. Consistent coarse-graining strategy for polymer solutions in the thermal crossover from good to θ solvent. J Chem Phys 2013; 139:034901. [DOI: 10.1063/1.4812691] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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34
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Wu C. A Combined Scheme for Systematically Coarse-Graining of Stereoregular Polymer Blends. Macromolecules 2013. [DOI: 10.1021/ma400572f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Chaofu Wu
- Department of Chemistry and Materials
Science, Hunan University of Humanities, Science and Technology, Loudi 417000, People’s Republic of
China
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35
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Molecular basis for the dissociation dynamics of protein A-immunoglobulin G1 complex. PLoS One 2013; 8:e66935. [PMID: 23776704 PMCID: PMC3680412 DOI: 10.1371/journal.pone.0066935] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 05/13/2013] [Indexed: 12/24/2022] Open
Abstract
Staphylococcus aureus protein A (SpA) is the most popular affinity ligand for immunoglobulin G1 (IgG1). However, the molecular basis for the dissociation dynamics of SpA-IgG1 complex is unclear. Herein, coarse-grained (CG) molecular dynamics (MD) simulations with the Martini force field were used to study the dissociation dynamics of the complex. The CG-MD simulations were first verified by the agreement in the structural and interactional properties of SpA and human IgG1 (hIgG1) in the association process between the CG-MD and all-atom MD at different NaCl concentrations. Then, the CG-MD simulation studies focused on the molecular insight into the dissociation dynamics of SpA-hIgG1 complex at pH 3.0. It is found that there are four steps in the dissociation process of the complex. First, there is a slight conformational adjustment of helix II in SpA. This is followed by the phenomena that the electrostatic interactions provided by the three hot spots (Glu143, Arg146 and Lys154) of helix II of SpA break up, leading to the dissociation of helix II from the binding site of hIgG1. Subsequently, breakup of the hydrophobic interactions between helix I (Phe132, Tyr133 and His137) in SpA and hIgG1 occurs, resulting in the disengagement of helix I from its binding site of hIgG1. Finally, the non-specific interactions between SpA and hIgG1 decrease slowly till disappearance, leading to the complete dissociation of the SpA-hIgG1 complex. This work has revealed that CG-MD coupled with the Martini force field is an effective method for studying the dissociation dynamics of protein-protein complex.
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36
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Mirzoev A, Lyubartsev AP. MagiC: Software Package for Multiscale Modeling. J Chem Theory Comput 2013; 9:1512-20. [PMID: 26587613 DOI: 10.1021/ct301019v] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We present software package MagiC, which is designed to perform systematic structure-based coarse graining of molecular models. The effective pairwise potentials between coarse-grained sites of low-resolution molecular models are constructed to reproduce structural distribution functions obtained from the modeling of the system in a high resolution (atomistic) description. The software supports coarse-grained tabulated intramolecular bond and angle interactions, as well as tabulated nonbonded interactions between different site types in the coarse-grained system, with the treatment of long-range electrostatic forces by the Ewald summation. Two methods of effective potential refinement are implemented: iterative Boltzmann inversion and inverse Monte Carlo, the latter accounting for cross-correlations between pair interactions. MagiC uses its own Metropolis Monte Carlo sampling engine, allowing parallel simulation of many copies of the system with subsequent averaging of the properties, which provides fast convergence of the method with nearly linear scaling at parallel execution.
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Affiliation(s)
- Alexander Mirzoev
- Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE-10691, Sweden
| | - Alexander P Lyubartsev
- Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE-10691, Sweden
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37
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Karimi-Varzaneh HA, van der Vegt NFA, Müller-Plathe F, Carbone P. How Good Are Coarse-Grained Polymer Models? A Comparison for Atactic Polystyrene. Chemphyschem 2012; 13:3428-39. [DOI: 10.1002/cphc.201200111] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 05/09/2012] [Indexed: 02/02/2023]
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38
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Ghanbari A, Ndoro TVM, Leroy F, Rahimi M, Böhm MC, Müller-Plathe F. Interphase Structure in Silica–Polystyrene Nanocomposites: A Coarse-Grained Molecular Dynamics Study. Macromolecules 2011. [DOI: 10.1021/ma202044e] [Citation(s) in RCA: 146] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Azadeh Ghanbari
- Eduard-Zintl-Institut für Anorganische und Physikalische
Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Petersenstrasse 20, D-64287 Darmstadt, Germany
| | - Tinashe V. M. Ndoro
- Eduard-Zintl-Institut für Anorganische und Physikalische
Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Petersenstrasse 20, D-64287 Darmstadt, Germany
| | - Frédéric Leroy
- Eduard-Zintl-Institut für Anorganische und Physikalische
Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Petersenstrasse 20, D-64287 Darmstadt, Germany
| | - Mohammad Rahimi
- Eduard-Zintl-Institut für Anorganische und Physikalische
Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Petersenstrasse 20, D-64287 Darmstadt, Germany
| | - Michael C. Böhm
- Eduard-Zintl-Institut für Anorganische und Physikalische
Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Petersenstrasse 20, D-64287 Darmstadt, Germany
| | - Florian Müller-Plathe
- Eduard-Zintl-Institut für Anorganische und Physikalische
Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Petersenstrasse 20, D-64287 Darmstadt, Germany
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