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Jin J, Pak AJ, Durumeric AEP, Loose TD, Voth GA. Bottom-up Coarse-Graining: Principles and Perspectives. J Chem Theory Comput 2022; 18:5759-5791. [PMID: 36070494 PMCID: PMC9558379 DOI: 10.1021/acs.jctc.2c00643] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Indexed: 01/14/2023]
Abstract
Large-scale computational molecular models provide scientists a means to investigate the effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship between variations on the molecular scale and macroscopic observable properties facilitates an understanding of the molecular interactions driving the properties of real world materials and complex systems (e.g., those found in biology, chemistry, and materials science). As a result, discovering an explicit, systematic connection between microscopic nature and emergent mesoscopic behavior is a fundamental goal for this type of investigation. The molecular forces critical to driving the behavior of complex heterogeneous systems are often unclear. More problematically, simulations of representative model systems are often prohibitively expensive from both spatial and temporal perspectives, impeding straightforward investigations over possible hypotheses characterizing molecular behavior. While the reduction in resolution of a study, such as moving from an atomistic simulation to that of the resolution of large coarse-grained (CG) groups of atoms, can partially ameliorate the cost of individual simulations, the relationship between the proposed microscopic details and this intermediate resolution is nontrivial and presents new obstacles to study. Small portions of these complex systems can be realistically simulated. Alone, these smaller simulations likely do not provide insight into collectively emergent behavior. However, by proposing that the driving forces in both smaller and larger systems (containing many related copies of the smaller system) have an explicit connection, systematic bottom-up CG techniques can be used to transfer CG hypotheses discovered using a smaller scale system to a larger system of primary interest. The proposed connection between different CG systems is prescribed by (i) the CG representation (mapping) and (ii) the functional form and parameters used to represent the CG energetics, which approximate potentials of mean force (PMFs). As a result, the design of CG methods that facilitate a variety of physically relevant representations, approximations, and force fields is critical to moving the frontier of systematic CG forward. Crucially, the proposed connection between the system used for parametrization and the system of interest is orthogonal to the optimization used to approximate the potential of mean force present in all systematic CG methods. The empirical efficacy of machine learning techniques on a variety of tasks provides strong motivation to consider these approaches for approximating the PMF and analyzing these approximations.
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Affiliation(s)
- Jaehyeok Jin
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, Institute for Biophysical
Dynamics, and James Franck Institute, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Alexander J. Pak
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, Institute for Biophysical
Dynamics, and James Franck Institute, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Aleksander E. P. Durumeric
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, Institute for Biophysical
Dynamics, and James Franck Institute, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Timothy D. Loose
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, Institute for Biophysical
Dynamics, and James Franck Institute, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, Institute for Biophysical
Dynamics, and James Franck Institute, The
University of Chicago, Chicago, Illinois 60637, United States
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2
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Wang J, in ’t Veld PJ, Robbins MO, Ge T. Effects of Coarse-Graining on Molecular Simulation of Craze Formation in Polymer Glass. Macromolecules 2022. [DOI: 10.1021/acs.macromol.1c01969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiuling Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | | | - Mark O. Robbins
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ting Ge
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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3
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Rissanou A, Chazirakis A, Polinska P, Burkhart C, Doxastakis M, Harmandaris V. Polybutadiene Copolymers via Atomistic and Systematic Coarse-Grained Simulations. Macromolecules 2022. [DOI: 10.1021/acs.macromol.1c01939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anastassia Rissanou
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas, (FORTH), IACM/FORTH, GR-71110 Heraklion, Greece
- Department of Mathematics and Applied Mathematics, University of Crete, GR-71409 Heraklion, Crete, Greece
| | - Antonis Chazirakis
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas, (FORTH), IACM/FORTH, GR-71110 Heraklion, Greece
- Department of Mathematics and Applied Mathematics, University of Crete, GR-71409 Heraklion, Crete, Greece
| | | | - Craig Burkhart
- The Goodyear Tire and Rubber Company, 142 Goodyear Blvd., 44305 Akron, Ohio, United States
| | - Manolis Doxastakis
- Department of Chemical and Biomolecular Engineering, University of Tennessee, 37996 Knoxville, Tennessee, United States
| | - Vagelis Harmandaris
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas, (FORTH), IACM/FORTH, GR-71110 Heraklion, Greece
- Department of Mathematics and Applied Mathematics, University of Crete, GR-71409 Heraklion, Crete, Greece
- Computation-Based Science and Technology Research Center, The Cyprus Institute, 2121 Nicosia, Cyprus
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4
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Dhamankar S, Webb MA. Chemically specific coarse‐graining of polymers: Methods and prospects. JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1002/pol.20210555] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Satyen Dhamankar
- Department of Chemical and Biological Engineering Princeton University Princeton New Jersey USA
| | - Michael A. Webb
- Department of Chemical and Biological Engineering Princeton University Princeton New Jersey USA
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5
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Iwai Y, Nishiyama K. Molecular Dynamics Simulation of the Diffusion Coefficients of Anthraquinone in Poly(Methyl Methacrylate) Swollen by Supercritical Carbon Dioxide. JOURNAL OF CHEMICAL ENGINEERING OF JAPAN 2021. [DOI: 10.1252/jcej.21we023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yoshio Iwai
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University
| | - Kai Nishiyama
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University
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6
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Klippenstein V, Tripathy M, Jung G, Schmid F, van der Vegt NFA. Introducing Memory in Coarse-Grained Molecular Simulations. J Phys Chem B 2021; 125:4931-4954. [PMID: 33982567 PMCID: PMC8154603 DOI: 10.1021/acs.jpcb.1c01120] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Preserving the correct dynamics at the coarse-grained (CG) level is a pressing problem in the development of systematic CG models in soft matter simulation. Starting from the seminal idea of simple time-scale mapping, there have been many efforts over the years toward establishing a meticulous connection between the CG and fine-grained (FG) dynamics based on fundamental statistical mechanics approaches. One of the most successful attempts in this context has been the development of CG models based on the Mori-Zwanzig (MZ) theory, where the resulting equation of motion has the form of a generalized Langevin equation (GLE) and closely preserves the underlying FG dynamics. In this Review, we describe some of the recent studies in this regard. We focus on the construction and simulation of dynamically consistent systematic CG models based on the GLE, both in the simple Markovian limit and the non-Markovian case. Some recent studies of physical effects of memory are also discussed. The Review is aimed at summarizing recent developments in the field while highlighting the major challenges and possible future directions.
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Affiliation(s)
- Viktor Klippenstein
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Madhusmita Tripathy
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Gerhard Jung
- Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 21 A, A-6020 Innsbruck, Austria
| | - Friederike Schmid
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 9, 55128 Mainz, Germany
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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7
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Ge T, Wang J, Robbins MO. Effects of Coarse-Graining on Molecular Simulations of Mechanical Properties of Glassy Polymers. Macromolecules 2021. [DOI: 10.1021/acs.macromol.0c02467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ting Ge
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Jiuling Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Mark O. Robbins
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland 21218, United States
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Kritikos G, Rissanou AN, Harmandaris V, Karatasos K. Bound Layer Polymer Behavior on Graphene and Graphene Oxide Nanosheets. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c01040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Georgios Kritikos
- Laboratory of Physical Chemistry, Department of Chemical Engineering, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Anastassia N. Rissanou
- Institute of Applied and Computational Mathematics, Foundation for Research and Technology - Hellas, Heraklion GR-71110, Greece
| | - Vagelis Harmandaris
- Institute of Applied and Computational Mathematics, Foundation for Research and Technology - Hellas, Heraklion GR-71110, Greece
- Department of Mathematics and Applied Mathematics, University of Crete, Heraklion GR-71110, Greece
- Computation-based Science and Technology Research Center, The Cyprus Institute, Nicosia 2121, Cyprus
| | - Kostas Karatasos
- Laboratory of Physical Chemistry, Department of Chemical Engineering, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
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Shahidi N, Chazirakis A, Harmandaris V, Doxastakis M. Coarse-graining of polyisoprene melts using inverse Monte Carlo and local density potentials. J Chem Phys 2020; 152:124902. [PMID: 32241142 DOI: 10.1063/1.5143245] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Bottom-up coarse-graining of polymers is commonly performed by matching structural order parameters such as distribution of bond lengths, bending and dihedral angles, and pair distribution functions. In this study, we introduce the distribution of nearest-neighbors as an additional order parameter in the concept of local density potentials. We describe how the inverse-Monte Carlo method provides a framework for forcefield development that is capable of overcoming challenges associated with the parameterization of interaction terms in polymer systems. The technique is applied on polyisoprene melts as a prototype system. We demonstrate that while different forcefields can be developed that perform equally in terms of matching target distributions, the inclusion of nearest-neighbors provides a straightforward route to match both thermodynamic and conformational properties. We find that several temperature state points can also be addressed, provided that the forcefield is refined accordingly. Finally, we examine both the single-particle and the collective dynamics of the coarse-grain models, demonstrating that all forcefields present a similar acceleration relative to the atomistic systems.
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Affiliation(s)
- Nobahar Shahidi
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Antonis Chazirakis
- Department of Mathematics and Applied Mathematics, University of Crete, Heraklion GR-71110, Greece
| | - Vagelis Harmandaris
- Department of Mathematics and Applied Mathematics, University of Crete, Heraklion GR-71110, Greece
| | - Manolis Doxastakis
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
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10
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Recent Progress towards Chemically-Specific Coarse-Grained Simulation Models with Consistent Dynamical Properties. COMPUTATION 2019. [DOI: 10.3390/computation7030042] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Coarse-grained (CG) models can provide computationally efficient and conceptually simple characterizations of soft matter systems. While generic models probe the underlying physics governing an entire family of free-energy landscapes, bottom-up CG models are systematically constructed from a higher-resolution model to retain a high level of chemical specificity. The removal of degrees of freedom from the system modifies the relationship between the relative time scales of distinct dynamical processes through both a loss of friction and a “smoothing” of the free-energy landscape. While these effects typically result in faster dynamics, decreasing the computational expense of the model, they also obscure the connection to the true dynamics of the system. The lack of consistent dynamics is a serious limitation for CG models, which not only prevents quantitatively accurate predictions of dynamical observables but can also lead to qualitatively incorrect descriptions of the characteristic dynamical processes. With many methods available for optimizing the structural and thermodynamic properties of chemically-specific CG models, recent years have seen a stark increase in investigations addressing the accurate description of dynamical properties generated from CG simulations. In this review, we present an overview of these efforts, ranging from bottom-up parameterizations of generalized Langevin equations to refinements of the CG force field based on a Markov state modeling framework. We aim to make connections between seemingly disparate approaches, while laying out some of the major challenges as well as potential directions for future efforts.
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11
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Vergadou N, Theodorou DN. Molecular Modeling Investigations of Sorption and Diffusion of Small Molecules in Glassy Polymers. MEMBRANES 2019; 9:E98. [PMID: 31398889 PMCID: PMC6723301 DOI: 10.3390/membranes9080098] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 11/16/2022]
Abstract
With a wide range of applications, from energy and environmental engineering, such as in gas separations and water purification, to biomedical engineering and packaging, glassy polymeric materials remain in the core of novel membrane and state-of the art barrier technologies. This review focuses on molecular simulation methodologies implemented for the study of sorption and diffusion of small molecules in dense glassy polymeric systems. Basic concepts are introduced and systematic methods for the generation of realistic polymer configurations are briefly presented. Challenges related to the long length and time scale phenomena that govern the permeation process in the glassy polymer matrix are described and molecular simulation approaches developed to address the multiscale problem at hand are discussed.
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Affiliation(s)
- Niki Vergadou
- Molecular Thermodynamics and Modelling of Materials Laboratory, Institute of Nanoscience and Nanotechnology, National Center for Scientific Research Demokritos, Aghia Paraskevi Attikis, GR-15310 Athens, Greece.
| | - Doros N Theodorou
- School of Chemical Engineering, National Technical University of Athens, GR 15780 Athens, Greece
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12
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Mukherjee B, Peter C, Kremer K. Single molecule translocation in smectics illustrates the challenge for time-mapping in simulations on multiple scales. J Chem Phys 2018; 147:114501. [PMID: 28938812 DOI: 10.1063/1.5001482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Understanding the connections between the characteristic dynamical time scales associated with a coarse-grained (CG) and a detailed representation is central to the applicability of the coarse-graining methods to understand molecular processes. The process of coarse graining leads to an accelerated dynamics, owing to the smoothening of the underlying free-energy landscapes. Often a single time-mapping factor is used to relate the time scales associated with the two representations. We critically examine this idea using a model system ideally suited for this purpose. Single molecular transport properties are studied via molecular dynamics simulations of the CG and atomistic representations of a liquid crystalline, azobenzene containing mesogen, simulated in the smectic and the isotropic phases. The out-of-plane dynamics in the smectic phase occurs via molecular hops from one smectic layer to the next. Hopping can occur via two mechanisms, with and without significant reorientation. The out-of-plane transport can be understood as a superposition of two (one associated with each mode of transport) independent continuous time random walks for which a single time-mapping factor would be rather inadequate. A comparison of the free-energy surfaces, relevant to the out-of-plane transport, qualitatively supports the above observations. Thus, this work underlines the need for building CG models that exhibit both structural and dynamical consistency to the underlying atomistic model.
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Affiliation(s)
| | - Christine Peter
- Department of Chemistry, University of Konstanz, 78547 Konstanz, Germany
| | - Kurt Kremer
- Max-Planck-Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany
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13
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Lin E, You X, Kriegel RM, Moffitt RD, Batra RC. Interdiffusion of small molecules into a glassy polymer film via coarse-grained molecular dynamics simulations. POLYMER 2017. [DOI: 10.1016/j.polymer.2017.03.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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14
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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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15
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Xiao Q, Guo H. Transferability of a coarse-grained atactic polystyrene model: the non-bonded potential effect. Phys Chem Chem Phys 2016; 18:29808-29824. [DOI: 10.1039/c6cp03753d] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, we construct an efficient and simple coarse grained (CG) model for atactic polystyrene (PS) by using a 1 : 1 mapping scheme at 463 K and 1 atm pressure and derive the corresponding bonded and non-bonded potentials in the CG force field (FF) via a direct Boltzmann inversion approach and a combined structure-based and thermodynamic quantities-based CG method, respectively.
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Affiliation(s)
- Qiang Xiao
- Beijing National Laboratory for Molecular Sciences
- Joint Laboratory of Polymer Sciences and Materials
- State Key Laboratory of Polymer Physics and Chemistry
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Hongxia Guo
- Beijing National Laboratory for Molecular Sciences
- Joint Laboratory of Polymer Sciences and Materials
- State Key Laboratory of Polymer Physics and Chemistry
- Institute of Chemistry
- Chinese Academy of Sciences
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16
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Chen T, Qian HJ, Zhu YL, Lu ZY. Structure and Dynamics Properties at Interphase Region in the Composite of Polystyrene and Cross-Linked Polystyrene Soft Nanoparticle. Macromolecules 2015. [DOI: 10.1021/ma502383n] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Tao Chen
- State
Key Laboratory of Supramolecular Structure and Materials, Institute
of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Hu-Jun Qian
- State
Key Laboratory of Supramolecular Structure and Materials, Institute
of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - You-Liang Zhu
- State
Key Laboratory of Polymer Physics and Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Zhong-Yuan Lu
- State
Key Laboratory of Supramolecular Structure and Materials, Institute
of Theoretical Chemistry, Jilin University, Changchun 130023, China
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17
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Forrey C, Saylor DM, Silverstein JS, Douglas JF, Davis EM, Elabd YA. Prediction and validation of diffusion coefficients in a model drug delivery system using microsecond atomistic molecular dynamics simulation and vapour sorption analysis. SOFT MATTER 2014; 10:7480-7494. [PMID: 25115846 DOI: 10.1039/c4sm01297f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Diffusion of small to medium sized molecules in polymeric medical device materials underlies a broad range of public health concerns related to unintended leaching from or uptake into implantable medical devices. However, obtaining accurate diffusion coefficients for such systems at physiological temperature represents a formidable challenge, both experimentally and computationally. While molecular dynamics simulation has been used to accurately predict the diffusion coefficients, D, of a handful of gases in various polymers, this success has not been extended to molecules larger than gases, e.g., condensable vapours, liquids, and drugs. We present atomistic molecular dynamics simulation predictions of diffusion in a model drug eluting system that represent a dramatic improvement in accuracy compared to previous simulation predictions for comparable systems. We find that, for simulations of insufficient duration, sub-diffusive dynamics can lead to dramatic over-prediction of D. We present useful metrics for monitoring the extent of sub-diffusive dynamics and explore how these metrics correlate to error in D. We also identify a relationship between diffusion and fast dynamics in our system, which may serve as a means to more rapidly predict diffusion in slowly diffusing systems. Our work provides important precedent and essential insights for utilizing atomistic molecular dynamics simulations to predict diffusion coefficients of small to medium sized molecules in condensed soft matter systems.
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Affiliation(s)
- Christopher Forrey
- Division of Chemistry and Materials Science, Center for Devices and Radiological Health, US Food and Drug Administration, USA.
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19
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Poudyal I, Adhikari NP. Temperature dependence of diffusion coefficient of carbon monoxide in water: A molecular dynamics study. J Mol Liq 2014. [DOI: 10.1016/j.molliq.2014.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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20
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Harmandaris V, Doxastakis M. Molecular dynamics of polyisoprene/polystyrene oligomer blends: The role of self-concentration and fluctuations on blend dynamics. J Chem Phys 2013; 139:034904. [DOI: 10.1063/1.4813019] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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22
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Chakrabarti R, Kesselheim S, Košovan P, Holm C. Tracer diffusion in a crowded cylindrical channel. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:062709. [PMID: 23848717 DOI: 10.1103/physreve.87.062709] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Indexed: 06/02/2023]
Abstract
Based on a coarse-grained model, we carry out molecular dynamics simulations to analyze the diffusion of a small tracer particle inside a cylindrical channel whose inner wall is covered with randomly grafted short polymeric chains. We observe an interesting transient subdiffusive behavior along the cylindrical axis at high attraction between the tracer and the chains, however, the long-time diffusion is always normal. This process is found to be enhanced for the case that we immobilize the grafted chains, i.e., the subdiffusive behavior sets in at an earlier time and spans over a longer time period before becoming diffusive. Even if the grafted chains are replaced with a frozen sea of repulsive, nonconnected particles in the background, a transient subdiffusion is observed. The intermediate subdiffusive behavior only disappears when the grafted chains are replaced with a mobile background sea of mutually repulsive particles. Overall, the long-time diffusion coefficient of the tracer along the cylinder axis decreases with an increase in system volume fraction, the strength of the attraction between the tracer and the background, and also on freezing the background.
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Affiliation(s)
- Rajarshi Chakrabarti
- Institut für Computerphysik, Universität Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
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Harmandaris VA, Kremer K, Floudas G. Dynamic heterogeneity in fully miscible blends of polystyrene with oligostyrene. PHYSICAL REVIEW LETTERS 2013; 110:165701. [PMID: 23679622 DOI: 10.1103/physrevlett.110.165701] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Indexed: 05/09/2023]
Abstract
Binary blends of polystyrene with oligostyrene are perfectly miscible (χ=0) yet dynamically heterogeneous. This is evidenced by independent probing of the dipole relaxation perpendicular to the backbone by dielectric spectroscopy and molecular dynamics. The self-concentration model with a single intramolecular length scale qualitatively describes the slower segmental dynamics. A quantitative comparison based on MD, however, requires a composition-dependent length scale. The pertinent dynamic length scale that best describes the slow segmental dynamics in miscible blends relates to both intra- and intermolecular contributions.
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Affiliation(s)
- Vagelis A Harmandaris
- Department of Applied Mathematics, University of Crete, and IACM FORTH GR-71110 Heraklion, Greece.
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Xi L, Shah M, Trout BL. Hopping of Water in a Glassy Polymer Studied via Transition Path Sampling and Likelihood Maximization. J Phys Chem B 2013; 117:3634-47. [DOI: 10.1021/jp3099973] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Li Xi
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
| | - Manas Shah
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
| | - Bernhardt L. Trout
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
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25
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Liao LQ, Fu YZ, Liang XY, Mei LY, Liu YQ. Diffusion of CO2Molecules in Polyethylene Terephthalate/Polylactide Blends Estimated by Molecular Dynamics Simulations. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.3.753] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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26
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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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27
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Dahal U, Adhikari NP. Molecular dynamics study of diffusion of heavy water in normal water at different temperatures. J Mol Liq 2012. [DOI: 10.1016/j.molliq.2011.12.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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28
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29
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Adhikari NP, Straube E. Phase separation in mixtures of flexible and semiflexible polymers. Polym J 2011. [DOI: 10.1038/pj.2011.29] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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30
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Molecular simulation of structure, thermodynamic and transport properties of polyacrylonitrile, polystyrene and their alternating copolymers in high temperatures. Eur Polym J 2011. [DOI: 10.1016/j.eurpolymj.2010.09.041] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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31
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Fritz D, Koschke K, Harmandaris VA, van der Vegt NFA, Kremer K. Multiscale modeling of soft matter: scaling of dynamics. Phys Chem Chem Phys 2011; 13:10412-20. [DOI: 10.1039/c1cp20247b] [Citation(s) in RCA: 145] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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32
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Coarse-Grained Modeling for Macromolecular Chemistry. MULTISCALE MOLECULAR METHODS IN APPLIED CHEMISTRY 2011; 307:295-321. [DOI: 10.1007/128_2010_122] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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33
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Harmandaris VA, Floudas G, Kremer K. Temperature and Pressure Dependence of Polystyrene Dynamics through Molecular Dynamics Simulations and Experiments. Macromolecules 2010. [DOI: 10.1021/ma102179b] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vagelis A. Harmandaris
- Department of Applied Mathematics, University of Crete, GR-71110 Heraklion, Greece
- IACM FORTH, GR-71110 Heraklion, Greece
- Max Planck Institute for Polymer Research, D-55128 Mainz, Germany
| | - George Floudas
- Department of Physics, University of Ioannina, GR-45110, Ioannina, Greece
- Foundation for Research and Technology-Biomedical Research Institute, Ioannina, Greece
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, D-55128 Mainz, Germany
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34
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Hernandez HF, Tauer K. Radical Desorption Kinetics in Emulsion Polymerization, 2 - Brownian Dynamics Simulation of Radical Desorption in Non-Homogeneous Particles. MACROMOL THEOR SIMUL 2010. [DOI: 10.1002/mats.200900089] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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35
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36
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Hernández HF, Tauer K. Modeling of Molecular Transfer in Heterophase Polymerization. MACROMOL REACT ENG 2009. [DOI: 10.1002/mren.200900016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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37
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Lee WB, Kremer K. Entangled Polymer Melts: Relation between Plateau Modulus and Stress Autocorrelation Function. Macromolecules 2009. [DOI: 10.1021/ma9008498] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Won Bo Lee
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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38
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Cherdhirankorn T, Harmandaris V, Juhari A, Voudouris P, Fytas G, Kremer K, Koynov K. Fluorescence Correlation Spectroscopy Study of Molecular Probe Diffusion in Polymer Melts. Macromolecules 2009. [DOI: 10.1021/ma900605z] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - V. Harmandaris
- Max-Planck-Institute of Polymer Research, D-55128 Mainz, Germany
- Department of Applied Mathematics, University of Crete, 71110 Heraklion, Greece
| | - A. Juhari
- Max-Planck-Institute of Polymer Research, D-55128 Mainz, Germany
| | - P. Voudouris
- Departments of Chemistry and Materials Science and Technology, University of Crete and FORTH, 71110 Heraklion, Greece
| | - G. Fytas
- Max-Planck-Institute of Polymer Research, D-55128 Mainz, Germany
- Departments of Chemistry and Materials Science and Technology, University of Crete and FORTH, 71110 Heraklion, Greece
| | - K. Kremer
- Max-Planck-Institute of Polymer Research, D-55128 Mainz, Germany
| | - K. Koynov
- Max-Planck-Institute of Polymer Research, D-55128 Mainz, Germany
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39
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Deserno M. Mesoscopic Membrane Physics: Concepts, Simulations, and Selected Applications. Macromol Rapid Commun 2009; 30:752-71. [DOI: 10.1002/marc.200900090] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 03/03/2009] [Indexed: 12/24/2022]
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40
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Qian HJ, Carbone P, Chen X, Karimi-Varzaneh HA, Liew CC, Müller-Plathe F. Temperature-Transferable Coarse-Grained Potentials for Ethylbenzene, Polystyrene, and Their Mixtures. Macromolecules 2008. [DOI: 10.1021/ma801910r] [Citation(s) in RCA: 184] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Hu-Jun Qian
- Eduard-Zintl-Institut für Anorganische and Physikalische Chemie, Technische Universität Darmstadt, Petersenstrasse 20, D-64287 Darmstadt, Germany, Polymer Research, BASF SE, D-67056 Ludwigshafen, Germany, and School of Chemical Engineering and Analytical Science, University of Manchester, P.O. Box 88, Sackville Street, Manchester M60 1QD, U.K
| | - Paola Carbone
- Eduard-Zintl-Institut für Anorganische and Physikalische Chemie, Technische Universität Darmstadt, Petersenstrasse 20, D-64287 Darmstadt, Germany, Polymer Research, BASF SE, D-67056 Ludwigshafen, Germany, and School of Chemical Engineering and Analytical Science, University of Manchester, P.O. Box 88, Sackville Street, Manchester M60 1QD, U.K
| | - Xiaoyu Chen
- Eduard-Zintl-Institut für Anorganische and Physikalische Chemie, Technische Universität Darmstadt, Petersenstrasse 20, D-64287 Darmstadt, Germany, Polymer Research, BASF SE, D-67056 Ludwigshafen, Germany, and School of Chemical Engineering and Analytical Science, University of Manchester, P.O. Box 88, Sackville Street, Manchester M60 1QD, U.K
| | - Hossein Ali Karimi-Varzaneh
- Eduard-Zintl-Institut für Anorganische and Physikalische Chemie, Technische Universität Darmstadt, Petersenstrasse 20, D-64287 Darmstadt, Germany, Polymer Research, BASF SE, D-67056 Ludwigshafen, Germany, and School of Chemical Engineering and Analytical Science, University of Manchester, P.O. Box 88, Sackville Street, Manchester M60 1QD, U.K
| | - Chee Chin Liew
- Eduard-Zintl-Institut für Anorganische and Physikalische Chemie, Technische Universität Darmstadt, Petersenstrasse 20, D-64287 Darmstadt, Germany, Polymer Research, BASF SE, D-67056 Ludwigshafen, Germany, and School of Chemical Engineering and Analytical Science, University of Manchester, P.O. Box 88, Sackville Street, Manchester M60 1QD, U.K
| | - Florian Müller-Plathe
- Eduard-Zintl-Institut für Anorganische and Physikalische Chemie, Technische Universität Darmstadt, Petersenstrasse 20, D-64287 Darmstadt, Germany, Polymer Research, BASF SE, D-67056 Ludwigshafen, Germany, and School of Chemical Engineering and Analytical Science, University of Manchester, P.O. Box 88, Sackville Street, Manchester M60 1QD, U.K
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41
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Hernandez HF, Tauer K. Radical Desorption Kinetics in Emulsion Polymerization. 1. Theory and Simulation. Ind Eng Chem Res 2008. [DOI: 10.1021/ie800304t] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hugo F. Hernandez
- Max Planck Institute of Colloids and Interfaces, Colloid Chemistry Department, Research Campus Golm, Am Mühlenberg 1, 14476 Golm, Germany
| | - Klaus Tauer
- Max Planck Institute of Colloids and Interfaces, Colloid Chemistry Department, Research Campus Golm, Am Mühlenberg 1, 14476 Golm, Germany
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42
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Illya G, Deserno M. Coarse-grained simulation studies of peptide-induced pore formation. Biophys J 2008; 95:4163-73. [PMID: 18641080 PMCID: PMC2567957 DOI: 10.1529/biophysj.108.131300] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2008] [Accepted: 07/11/2008] [Indexed: 11/18/2022] Open
Abstract
We investigate the interactions between lipid bilayers and amphiphilic peptides using a solvent-free coarse-grained simulation technique. In our model, each lipid is represented by one hydrophilic and three hydrophobic beads. The amphiphilic peptide is modeled as a hydrophobic-hydrophilic cylinder with hydrophilic caps. We find that with increasing peptide-lipid attraction the preferred state of the peptide changes from desorbed, to adsorbed, to inserted. A single peptide with weak attraction binds on the bilayer surface, while one with strong attraction spontaneously inserts into the bilayer. We show how several peptides, which individually bind only to the bilayer surface, cooperatively insert. Furthermore, hydrophilic strips along the peptide cylinder induce the formation of multipeptide pores, whose size and morphology depend on the peptides' overall hydrophilicity, the distribution of hydrophilic residues, and the peptide-peptide interactions. Strongly hydrophilic peptides insert less readily, but prove to be more destructive to bilayer integrity.
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Affiliation(s)
- Gregoria Illya
- Max-Planck-Institute for Polymer Research, Mainz, Germany
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43
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Mulder T, Harmandaris VA, Lyulin AV, van der Vegt NFA, Michels MAJ. Molecular Simulation Via Connectivity-altering Monte Carlo and Scale-jumping Methods: Application to Amorphous Polystyrene. MACROMOL THEOR SIMUL 2008. [DOI: 10.1002/mats.200800024] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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44
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Hernandez HF, Tauer K. Stochastic Simulation of Imperfect Mixing in Free Radical Polymerization. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/masy.200851107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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45
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Makrodimitri ZA, Economou IG. Atomistic Simulation of Poly(dimethylsiloxane) Permeability Properties to Gases and n-Alkanes. Macromolecules 2008. [DOI: 10.1021/ma800650u] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zoi A. Makrodimitri
- Molecular Thermodynamics and Modeling of Materials Laboratory, Institute of Physical Chemistry, National Center for Scientific Research “Demokritos”, GR - 153 10 Aghia Paraskevi, Attikis, Greece
| | - Ioannis G. Economou
- Molecular Thermodynamics and Modeling of Materials Laboratory, Institute of Physical Chemistry, National Center for Scientific Research “Demokritos”, GR - 153 10 Aghia Paraskevi, Attikis, Greece
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