1
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Zhang D, Wang Y, Safaripour M, Bellido-Aguilar DA, Van Donselaar KR, Webster DC, Croll AB, Xia W. Energy renormalization for temperature transferable coarse-graining of silicone polymer. Phys Chem Chem Phys 2024; 26:4541-4554. [PMID: 38241021 DOI: 10.1039/d3cp05969c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The bottom-up prediction of thermodynamic and mechanical behaviors of polymeric materials based on molecular dynamics (MD) simulation is of critical importance in polymer physics. Although the atomistically informed coarse-grained (CG) model can access greater spatiotemporal scales and retain essential chemical specificity, the temperature-transferable CG model is still a big challenge and hinders widespread application of this technique. Herein, we use a silicone polymer, i.e., polydimethylsiloxane (PDMS), having an incredibly low chain rigidity as a model system, combined with an energy-renormalization (ER) approach, to systematically develop a temperature-transferable CG model. Specifically, by introducing temperature-dependent ER factors to renormalize the effective distance and cohesive energy parameters, the developed CG model faithfully preserved the dynamics, mechanical and conformational behaviors compared with the target all-atomistic (AA) model from glassy to melt regimes, which was further validated by experimental data. With the developed CG model featuring tremendously improved computational efficiency, we systematically explored the influences of cohesive interaction strength and temperature on the dynamical heterogeneity and mechanical response of polymers, where we observed consistent trends with other linear polymers with varying chain rigidity and monomeric structures. This study serves as an extension of our proposed ER approach of developing temperature transferable CG models with diverse segmental structures, highlighting the critical role of cohesive interaction strength on CG modeling of polymer dynamics and thermomechanical behaviors.
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Affiliation(s)
- Dawei Zhang
- Department of Civil, Construction, and Environmental Engineering, North Dakota State University, Fargo, ND 58108, USA
| | - Yang Wang
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Maryam Safaripour
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND 58108, USA
| | - Daniel A Bellido-Aguilar
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND 58108, USA
| | | | - Dean C Webster
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND 58108, USA
| | - Andrew B Croll
- Department of Physics, North Dakota State University, Fargo, ND 58108, USA
| | - Wenjie Xia
- Department of Aerospace Engineering, Iowa State University, Ames, IA 50011, USA.
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2
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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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3
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Eghlidos O, Oswald J. Derived Coarse-Grained Potentials for Semicrystalline Polymers with a Blended Multistate Iterative Boltzmann Inversion Method. J Chem Theory Comput 2023; 19:9445-9456. [PMID: 38083860 DOI: 10.1021/acs.jctc.3c00935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
In this article, we employ the multistate iterative Boltzmann inversion (MS-IBI) method to develop coarse-grained potentials capable of representing molecular structure in both the amorphous and crystalline phases of semicrystalline polymers with improved accuracy while allowing for tunable control over the dynamics governing the α-relaxation process. A unique feature of this method is that the potentials are blended using the product of the target structural distributions, for example, the radial density function, for each phase and a weighting factor. To demonstrate this approach, a family of potentials for polyethylene is developed where the weighting factor of the crystalline phase ranges is varied from zero, incorporating information only from the amorphous phase, to unity, where the model is trained from only the crystalline phase. The most accurate representation of structural distributions was obtained when the crystalline phases is weighted at 50%. However, we show that when the crystalline phase is weighted at 90%, the model more accurately represents dynamics of the α-relaxation process, with realistic predicted values of activation energy and diffusion rates, with relatively minor impact on accuracy in structure.
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Affiliation(s)
- Omid Eghlidos
- School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
| | - Jay Oswald
- School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
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4
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Bryer AJ, Rey JS, Perilla JR. Performance efficient macromolecular mechanics via sub-nanometer shape based coarse graining. Nat Commun 2023; 14:2014. [PMID: 37037809 PMCID: PMC10086035 DOI: 10.1038/s41467-023-37801-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 03/30/2023] [Indexed: 04/12/2023] Open
Abstract
Dimensionality reduction via coarse grain modeling is a valuable tool in biomolecular research. For large assemblies, ultra coarse models are often knowledge-based, relying on a priori information to parameterize models thus hindering general predictive capability. Here, we present substantial advances to the shape based coarse graining (SBCG) method, which we refer to as SBCG2. SBCG2 utilizes a revitalized formulation of the topology representing network which makes high-granularity modeling possible, preserving atomistic details that maintain assembly characteristics. Further, we present a method of granularity selection based on charge density Fourier Shell Correlation and have additionally developed a refinement method to optimize, adjust and validate high-granularity models. We demonstrate our approach with the conical HIV-1 capsid and heteromultimeric cofilin-2 bound actin filaments. Our approach is available in the Visual Molecular Dynamics (VMD) software suite, and employs a CHARMM-compatible Hamiltonian that enables high-performance simulation in the GPU-resident NAMD3 molecular dynamics engine.
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Affiliation(s)
- Alexander J Bryer
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Juan S Rey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Juan R Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.
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5
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Zhang Y, Wang Y, Xia F, Cao Z, Xu X. Accurate and Efficient Estimation of Lennard-Jones Interactions for Coarse-Grained Particles via a Potential Matching Method. J Chem Theory Comput 2022; 18:4879-4890. [PMID: 35838523 DOI: 10.1021/acs.jctc.2c00513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Lennard-Jones (LJ) energy functions are commonly used to describe the nonbonded interactions in bulk coarse-grained (CG) models, which contribute significantly to the stabilization of a local binding configuration or a self-assembly system. In many cases, systematic development of the LJ interaction parameters in a CG model requires a comprehensive sampling of the objective molecules at the all-atom (AA) level, which is therefore extremely time-consuming for large systems. Inspired by the concept of electrostatic potential (ESP), we define the LJ static potential (LJSP), by which the embedding potential energy surface can be constructed analytically. A semianalytic approach, namely, the LJSP matching method, is developed here to derive the CG parameters by minimizing the LJSP difference between the AA and the CG models, which provides a universal way to derive the CG LJ parameters from the AA models without doing presampling. The LJSP matching method is successful not only in deriving the LJ interaction energy landscape in the CG models for proteins, lipids, and DNA but also in reproducing the critical properties such as intermediate structures and enthalpy contributions as exemplified in simulating the self-assembly process of the dipalmitoylphosphatidylcholine (DPPC) lipids.
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Affiliation(s)
- Yuwei Zhang
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Departments of Chemistry, Fudan University, Shanghai 200433, China
| | - Yunchu Wang
- LSEC, Institute of Computational Mathematics and Scientific/Engineering Computing, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
| | - Fei Xia
- School of Chemistry and Molecular Engineering, NYU-ECNU Center for Computational Chemistry at NYU Shanghai, East China Normal University, Shanghai 200062, China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemistry Engineering, Xiamen University, Xiamen 361005, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Departments of Chemistry, Fudan University, Shanghai 200433, China
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6
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Empereur-Mot C, Capelli R, Perrone M, Caruso C, Doni G, Pavan GM. Automatic multi-objective optimization of coarse-grained lipid force fields using SwarmCG. J Chem Phys 2022; 156:024801. [PMID: 35032979 DOI: 10.1063/5.0079044] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The development of coarse-grained (CG) molecular models typically requires a time-consuming iterative tuning of parameters in order to have the approximated CG models behave correctly and consistently with, e.g., available higher-resolution simulation data and/or experimental observables. Automatic data-driven approaches are increasingly used to develop accurate models for molecular dynamics simulations. However, the parameters obtained via such automatic methods often make use of specifically designed interaction potentials and are typically poorly transferable to molecular systems or conditions other than those used for training them. Using a multi-objective approach in combination with an automatic optimization engine (SwarmCG), here, we show that it is possible to optimize CG models that are also transferable, obtaining optimized CG force fields (FFs). As a proof of concept, here, we use lipids for which we can avail reference experimental data (area per lipid and bilayer thickness) and reliable atomistic simulations to guide the optimization. Once the resolution of the CG models (mapping) is set as an input, SwarmCG optimizes the parameters of the CG lipid models iteratively and simultaneously against higher-resolution simulations (bottom-up) and experimental data (top-down references). Including different types of lipid bilayers in the training set in a parallel optimization guarantees the transferability of the optimized lipid FF parameters. We demonstrate that SwarmCG can reach satisfactory agreement with experimental data for different resolution CG FFs. We also obtain stimulating insights into the precision-resolution balance of the FFs. The approach is general and can be effectively used to develop new FFs and to improve the existing ones.
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Affiliation(s)
- Charly Empereur-Mot
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano, Campus Est, Via la Santa 1, 6962 Lugano-Viganello, Switzerland
| | - Riccardo Capelli
- Politecnico di Torino, Department of Applied Science and Technology, Corso Duca degli Abruzzi 24, Torino 10129, Italy
| | - Mattia Perrone
- Politecnico di Torino, Department of Applied Science and Technology, Corso Duca degli Abruzzi 24, Torino 10129, Italy
| | - Cristina Caruso
- Politecnico di Torino, Department of Applied Science and Technology, Corso Duca degli Abruzzi 24, Torino 10129, Italy
| | - Giovanni Doni
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano, Campus Est, Via la Santa 1, 6962 Lugano-Viganello, Switzerland
| | - Giovanni M Pavan
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano, Campus Est, Via la Santa 1, 6962 Lugano-Viganello, Switzerland
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7
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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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8
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Fayaz‐Torshizi M, Müller EA. Coarse‐Grained Molecular Simulation of Polymers Supported by the Use of the SAFT‐γ$\gamma$ Mie Equation of State. MACROMOL THEOR SIMUL 2021. [DOI: 10.1002/mats.202100031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Erich A. Müller
- Department of Chemical Engineering Imperial College London London SW7 2AZ UK
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9
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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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10
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Upadhya R, Kosuri S, Tamasi M, Meyer TA, Atta S, Webb MA, Gormley AJ. Automation and data-driven design of polymer therapeutics. Adv Drug Deliv Rev 2021; 171:1-28. [PMID: 33242537 PMCID: PMC8127395 DOI: 10.1016/j.addr.2020.11.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 01/01/2023]
Abstract
Polymers are uniquely suited for drug delivery and biomaterial applications due to tunable structural parameters such as length, composition, architecture, and valency. To facilitate designs, researchers may explore combinatorial libraries in a high throughput fashion to correlate structure to function. However, traditional polymerization reactions including controlled living radical polymerization (CLRP) and ring-opening polymerization (ROP) require inert reaction conditions and extensive expertise to implement. With the advent of air-tolerance and automation, several polymerization techniques are now compatible with well plates and can be carried out at the benchtop, making high throughput synthesis and high throughput screening (HTS) possible. To avoid HTS pitfalls often described as "fishing expeditions," it is crucial to employ intelligent and big data approaches to maximize experimental efficiency. This is where the disruptive technologies of machine learning (ML) and artificial intelligence (AI) will likely play a role. In fact, ML and AI are already impacting small molecule drug discovery and showing signs of emerging in drug delivery. In this review, we present state-of-the-art research in drug delivery, gene delivery, antimicrobial polymers, and bioactive polymers alongside data-driven developments in drug design and organic synthesis. From this insight, important lessons are revealed for the polymer therapeutics community including the value of a closed loop design-build-test-learn workflow. This is an exciting time as researchers will gain the ability to fully explore the polymer structural landscape and establish quantitative structure-property relationships (QSPRs) with biological significance.
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Affiliation(s)
| | | | | | | | - Supriya Atta
- Rutgers, The State University of New Jersey, USA
| | - Michael A Webb
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540, USA
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11
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Berressem F, Nikoubashman A. BoltzmaNN: Predicting effective pair potentials and equations of state using neural networks. J Chem Phys 2021; 154:124123. [PMID: 33810691 DOI: 10.1063/5.0045441] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Neural networks (NNs) are employed to predict equations of state from a given isotropic pair potential using the virial expansion of the pressure. The NNs are trained with data from molecular dynamics simulations of monoatomic gases and liquids, sampled in the NVT ensemble at various densities. We find that the NNs provide much more accurate results compared to the analytic low-density limit estimate of the second virial coefficient and the Carnahan-Starling equation of state for hard sphere liquids. Furthermore, we design and train NNs for computing (effective) pair potentials from radial pair distribution functions, g(r), a task that is often performed for inverse design and coarse-graining. Providing the NNs with additional information on the forces greatly improves the accuracy of the predictions since more correlations are taken into account; the predicted potentials become smoother, are significantly closer to the target potentials, and are more transferable as a result.
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Affiliation(s)
- Fabian Berressem
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
| | - Arash Nikoubashman
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
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12
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Empereur-Mot C, Pesce L, Doni G, Bochicchio D, Capelli R, Perego C, Pavan GM. Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-Based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization. ACS OMEGA 2020; 5:32823-32843. [PMID: 33376921 PMCID: PMC7758974 DOI: 10.1021/acsomega.0c05469] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/26/2020] [Indexed: 05/23/2023]
Abstract
We present Swarm-CG, a versatile software for the automatic iterative parametrization of bonded parameters in coarse-grained (CG) models, ideal in combination with popular CG force fields such as MARTINI. By coupling fuzzy self-tuning particle swarm optimization to Boltzmann inversion, Swarm-CG performs accurate bottom-up parametrization of bonded terms in CG models composed of up to 200 pseudo atoms within 4-24 h on standard desktop machines, using default settings. The software benefits from a user-friendly interface and two different usage modes (default and advanced). We particularly expect Swarm-CG to support and facilitate the development of new CG models for the study of complex molecular systems interesting for bio- and nanotechnology. Excellent performances are demonstrated using a benchmark of 9 molecules of diverse nature, structural complexity, and size. Swarm-CG is available with all its dependencies via the Python Package Index (PIP package: swarm-cg). Demonstration data are available at: www.github.com/GMPavanLab/SwarmCG.
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Affiliation(s)
- Charly Empereur-Mot
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Galleria 2, Via Cantonale 2c, CH-6928 Manno, Switzerland
| | - Luca Pesce
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Galleria 2, Via Cantonale 2c, CH-6928 Manno, Switzerland
| | - Giovanni Doni
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Galleria 2, Via Cantonale 2c, CH-6928 Manno, Switzerland
| | - Davide Bochicchio
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Galleria 2, Via Cantonale 2c, CH-6928 Manno, Switzerland
| | - Riccardo Capelli
- Department of Applied Science and Techology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Claudio Perego
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Galleria 2, Via Cantonale 2c, CH-6928 Manno, Switzerland
| | - Giovanni M. Pavan
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Galleria 2, Via Cantonale 2c, CH-6928 Manno, Switzerland
- Department of Applied Science and Techology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
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13
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Kapoor U, Kulshreshtha A, Jayaraman A. Development of Coarse-Grained Models for Poly(4-vinylphenol) and Poly(2-vinylpyridine): Polymer Chemistries with Hydrogen Bonding. Polymers (Basel) 2020; 12:E2764. [PMID: 33238611 PMCID: PMC7709027 DOI: 10.3390/polym12112764] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 11/16/2022] Open
Abstract
In this paper, we identify the modifications needed in a recently developed generic coarse-grained (CG) model that captured directional interactions in polymers to specifically represent two exemplary hydrogen bonding polymer chemistries-poly(4-vinylphenol) and poly(2-vinylpyridine). We use atomistically observed monomer-level structures (e.g., bond, angle and torsion distribution) and chain structures (e.g., end-to-end distance distribution and persistence length) of poly(4-vinylphenol) and poly(2-vinylpyridine) in an explicitly represented good solvent (tetrahydrofuran) to identify the appropriate modifications in the generic CG model in implicit solvent. For both chemistries, the modified CG model is developed based on atomistic simulations of a single 24-mer chain. This modified CG model is then used to simulate longer (36-mer) and shorter (18-mer and 12-mer) chain lengths and compared against the corresponding atomistic simulation results. We find that with one to two simple modifications (e.g., incorporating intra-chain attraction, torsional constraint) to the generic CG model, we are able to reproduce atomistically observed bond, angle and torsion distributions, persistence length, and end-to-end distance distribution for chain lengths ranging from 12 to 36 monomers. We also show that this modified CG model, meant to reproduce atomistic structure, does not reproduce atomistically observed chain relaxation and hydrogen bond dynamics, as expected. Simulations with the modified CG model have significantly faster chain relaxation than atomistic simulations and slower decorrelation of formed hydrogen bonds than in atomistic simulations, with no apparent dependence on chain length.
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Affiliation(s)
- Utkarsh Kapoor
- Department of Chemical and Biomolecular Engineering, Colburn Laboratory, University of Delaware, 150 Academy Street, Newark, DE 19716, USA; (U.K.); (A.K.)
| | - Arjita Kulshreshtha
- Department of Chemical and Biomolecular Engineering, Colburn Laboratory, University of Delaware, 150 Academy Street, Newark, DE 19716, USA; (U.K.); (A.K.)
| | - Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, Colburn Laboratory, University of Delaware, 150 Academy Street, Newark, DE 19716, USA; (U.K.); (A.K.)
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA
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14
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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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15
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16
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Wu C. Tacticity Effects on Polymer Glass Transition Revisited by Coarse‐Grained Simulations. MACROMOL THEOR SIMUL 2020. [DOI: 10.1002/mats.202000001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Chaofu Wu
- Hunan Provincial Key Laboratory of Fine Ceramics and Powder MaterialsSchool of Materials and Environmental EngineeringHunan University of Humanities Science and Technology Loudi Hunan 417000 China
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17
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Kempfer K, Devémy J, Dequidt A, Couty M, Malfreyt P. Multi-scale modeling of the polymer-filler interaction. SOFT MATTER 2020; 16:1538-1547. [PMID: 31939976 DOI: 10.1039/c9sm01959f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We report mesoscopic simulations of the interaction between a silica nanoparticle and cis-1,4-polybutadiene chains with realistic coarse-(CG) grained models. The CG models are obtained with a bottom-up Bayesian method based on trajectory matching of atomistic configurations of the system. We then investigate the structural properties of the interfacial region as a function of the grafting density and polymer chain length. We take advantage of the realistic CG models to explore the dynamics of the nanoparticle over a period of 10 microseconds. We show that the dynamics of the nanoparticle is affected by the grafting density and the polymer chain length of the grafted chains.
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Affiliation(s)
- Kevin Kempfer
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France.
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18
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Walker CC, Genzer J, Santiso EE. Extending the fused-sphere SAFT-γ Mie force field parameterization approach to poly(vinyl butyral) copolymers. J Chem Phys 2020; 152:044903. [DOI: 10.1063/1.5126213] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Christopher C. Walker
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Jan Genzer
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Erik E. Santiso
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA
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19
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Bacle P, Jardat M, Marry V, Mériguet G, Batôt G, Dahirel V. Coarse-Grained Models of Aqueous Solutions of Polyelectrolytes: Significance of Explicit Charges. J Phys Chem B 2019; 124:288-301. [DOI: 10.1021/acs.jpcb.9b09725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Pauline Bacle
- CNRS, Physico-chimie des électrolytes et nano-systèmes interfaciaux, PHENIX, Sorbonne Université, F-75005 Paris, France
| | - Marie Jardat
- CNRS, Physico-chimie des électrolytes et nano-systèmes interfaciaux, PHENIX, Sorbonne Université, F-75005 Paris, France
| | - Virginie Marry
- CNRS, Physico-chimie des électrolytes et nano-systèmes interfaciaux, PHENIX, Sorbonne Université, F-75005 Paris, France
| | - Guillaume Mériguet
- CNRS, Physico-chimie des électrolytes et nano-systèmes interfaciaux, PHENIX, Sorbonne Université, F-75005 Paris, France
| | - Guillaume Batôt
- IFP Énergies Nouvelles, avenue de Bois Préau, 92852 Rueil-Malmaison Cedex, France
| | - Vincent Dahirel
- CNRS, Physico-chimie des électrolytes et nano-systèmes interfaciaux, PHENIX, Sorbonne Université, F-75005 Paris, France
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20
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Patrone PN, Dienstfrey A, McFadden GB. Model reduction of rigid-body molecular dynamics via generalized multipole potentials. Phys Rev E 2019; 100:063302. [PMID: 31962507 PMCID: PMC8020260 DOI: 10.1103/physreve.100.063302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Indexed: 06/10/2023]
Abstract
Motivated by the challenges of uncertainty quantification for coarse-grained (CG) molecular dynamics, we investigate the role of perturbation theory in model reduction of classical systems. In particular, we consider the task of coarse-graining rigid bodies in the context of generalized multipole potentials that have controllable levels of accuracy relative to their atomistic counterparts. We show how the multipole framework yields a hierarchy of models that systematically connects a CG "point molecule" approximation to the exact dynamics. We use these results to understand when and how the CG models fail to describe atomistic dynamics at the trajectory level and develop asymptotic error estimates for approximate molecular potential energies. Implications for other model-reduction strategies are also discussed. Key findings of this work are that (i) omitting rotational energy introduces significant error when coarse-graining and (ii) attention to symmetry can improve accuracy of "point-molecule" approximations. Analytical derivations and numerical results support these conclusions. Relevance to nonrigid bodies is also discussed.
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Affiliation(s)
- Paul N. Patrone
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Andrew Dienstfrey
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - G. B. McFadden
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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21
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Conformational Properties of Comb-shaped Polyelectrolytes with Negatively Charged Backbone and Neutral Side Chains Studied by a Generic Coarse-grained Bead-and-Spring Model. CHINESE JOURNAL OF POLYMER SCIENCE 2019. [DOI: 10.1007/s10118-020-2350-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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22
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Liu M, Oswald J. Coarse–grained molecular modeling of the microphase structure of polyurea elastomer. POLYMER 2019. [DOI: 10.1016/j.polymer.2019.04.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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23
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An Y, Singh S, Bejagam KK, Deshmukh SA. Development of an Accurate Coarse-Grained Model of Poly(acrylic acid) in Explicit Solvents. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b00615] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Yaxin An
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | | | - Karteek K. Bejagam
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Sanket A. Deshmukh
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
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24
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Li S, Wu B, Han W. Parametrization of MARTINI for Modeling Hinging Motions in Membrane Proteins. J Phys Chem B 2019; 123:2254-2269. [DOI: 10.1021/acs.jpcb.8b11244] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Shu Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Bohua Wu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Wei Han
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
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25
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Walker CC, Genzer J, Santiso EE. Development of a fused-sphere SAFT-γ Mie force field for poly(vinyl alcohol) and poly(ethylene). J Chem Phys 2019; 150:034901. [DOI: 10.1063/1.5078742] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Christopher C. Walker
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Jan Genzer
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Erik E. Santiso
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA
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26
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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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27
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Moore TC, Iacovella CR, Leonhard AC, Bunge AL, McCabe C. Molecular dynamics simulations of stratum corneum lipid mixtures: A multiscale perspective. Biochem Biophys Res Commun 2018; 498:313-318. [PMID: 28911866 PMCID: PMC5845828 DOI: 10.1016/j.bbrc.2017.09.040] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 09/04/2017] [Accepted: 09/08/2017] [Indexed: 10/18/2022]
Abstract
The lipid matrix of the stratum corneum (SC) layer of skin is essential for human survival; it acts as a barrier to prevent rapid dehydration while keeping potentially hazardous material outside the body. While the composition of the SC lipid matrix is known, the molecular-level details of its organization are difficult to infer experimentally, hindering the discovery of structure-property relationships. To this end, molecular dynamics simulations, which give molecular-level resolution, have begun to play an increasingly important role in understanding these relationships. However, most simulation studies of SC lipids have focused on preassembled bilayer configurations, which, owing to the slow dynamics of the lipids, may influence the final structure and hence the calculated properties. Self-assembled structures would avoid this dependence on the initial configuration, however, the size and length scales involved make self-assembly impractical to study with atomistic models. Here, we report on the development of coarse-grained models of SC lipids designed to study self-assembly. Building on previous work, we present the interactions between the headgroups of ceramide and free fatty acid developed using the multistate iterative Boltzmann inversion method. Validation of the new interactions is performed with simulations of preassembled bilayers and good agreement between the atomistic and coarse-grained models is found for structural properties. The self-assembly of mixtures of ceramide and free fatty acid is investigated and both bilayer and multilayer structures are found to form. This work therefore represents a necessary step in studying SC lipid systems on multiple time and length scales.
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Affiliation(s)
- Timothy C Moore
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, United States; Vanderbilt University Multiscale Modeling and Simulation Center, Nashville, TN 37235, United States
| | - Christopher R Iacovella
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, United States; Vanderbilt University Multiscale Modeling and Simulation Center, Nashville, TN 37235, United States
| | - Anne C Leonhard
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, United States; Vanderbilt University Multiscale Modeling and Simulation Center, Nashville, TN 37235, United States
| | - Annette L Bunge
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO 80401, United States
| | - Clare McCabe
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, United States; Vanderbilt University Multiscale Modeling and Simulation Center, Nashville, TN 37235, United States; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States.
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28
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Banerjee P, Roy S, Nair N. Coarse-Grained Molecular Dynamics Force-Field for Polyacrylamide in Infinite Dilution Derived from Iterative Boltzmann Inversion and MARTINI Force-Field. J Phys Chem B 2018; 122:1516-1524. [PMID: 29278334 DOI: 10.1021/acs.jpcb.7b09019] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a mesoscale model of aqueous polyacrylamide in the infinitely dilute concentration regime, by combining an extant coarse-grained (CG) force-field, MARTINI, and the Iterative Boltzmann Inversion protocol (IBI). MARTINI force-field was used to retain the thermodynamics of solvation of the polymer in water, whereas the structural properties and intrapolymer interactions were optimized by IBI. Atomistic molecular dynamics simulations of polymer in water were performed to benchmark the mesoscale simulations. Our results from the CG model show excellent agreement in structure with the atomistic system. We also studied the dynamical behavior of our CG system by computing the shear viscosity and compared it with the standard IBI model. The viscosity trends of our model were similar to the atomistic system, whereas the standard IBI model was highly dissimilar as expected. In summary, our hybrid CG model sufficiently mimics an infinitely dilute system, and is superior to both MARTINI and IBI in representing the structure and thermodynamics of the atomistic system, respectively. Our hybrid coarse-graining strategy promises applicability in large-scale simulations of polymeric/biological systems where the structure needs to be replicated accurately while preserving the thermodynamics of a smoother surrounding.
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Affiliation(s)
- Pallavi Banerjee
- Shell Technology Center , Bande Kodigehalli, Bengaluru, Karnataka 562149, India.,Department of Chemistry, Indian Institute of Science Education and Research , Pune, 411008 Maharashtra, India
| | - Sudip Roy
- Shell Technology Center , Bande Kodigehalli, Bengaluru, Karnataka 562149, India
| | - Nitish Nair
- Shell Technology Center , Bande Kodigehalli, Bengaluru, Karnataka 562149, India
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29
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Kovalenko A, Gusarov S. Multiscale methods framework: self-consistent coupling of molecular theory of solvation with quantum chemistry, molecular simulations, and dissipative particle dynamics. Phys Chem Chem Phys 2018; 20:2947-2969. [DOI: 10.1039/c7cp05585d] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In this work, we will address different aspects of self-consistent field coupling of computational chemistry methods at different time and length scales in modern materials and biomolecular science.
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Affiliation(s)
- Andriy Kovalenko
- National Institute for Nanotechnology
- National Research Council of Canada
- Edmonton
- Canada
- Department of Mechanical Engineering
| | - Sergey Gusarov
- National Institute for Nanotechnology
- National Research Council of Canada
- Edmonton
- Canada
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30
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Wu C. Multiscale Modeling Scheme for Simulating Polymeric Melts: Application to Poly(Ethylene Oxide). MACROMOL THEOR SIMUL 2017. [DOI: 10.1002/mats.201700066] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- C. Wu
- Hunan Provincial Key Laboratory of Fine Ceramics and Powder Materials; Hunan University of Humanities Science & Technology; Dixing Road 487, Louxing District Loudi 417000 Hunan Province P. R. China
- College of Materials and Environment Engineering; Hunan University of Humanities Science & Technology; Dixing Road 487, Louxing District Loudi 417000 Hunan Province P. R. China
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31
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Chudoba R, Heyda J, Dzubiella J. Temperature-Dependent Implicit-Solvent Model of Polyethylene Glycol in Aqueous Solution. J Chem Theory Comput 2017; 13:6317-6327. [DOI: 10.1021/acs.jctc.7b00560] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Richard Chudoba
- Institut
für Physik, Humboldt-Universität zu Berlin, Newtonstraße
15, D-12489 Berlin, Germany
- Institut
für Weiche Materie und Funktionale Materialen, Helmholtz-Zentrum Berlin, Hahn-Meitner-Platz 1, D-14109 Berlin, Germany
| | - Jan Heyda
- Department
of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, CZ-16628 Praha 6, Czech Republic
| | - Joachim Dzubiella
- Institut
für Physik, Humboldt-Universität zu Berlin, Newtonstraße
15, D-12489 Berlin, Germany
- Institut
für Weiche Materie und Funktionale Materialen, Helmholtz-Zentrum Berlin, Hahn-Meitner-Platz 1, D-14109 Berlin, Germany
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32
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Kuo AT, Okazaki S, Shinoda W. Transferable coarse-grained model for perfluorosulfonic acid polymer membranes. J Chem Phys 2017; 147:094904. [DOI: 10.1063/1.4986287] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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33
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Li B, Chen Q, Huang S, Liu H. Developing structure and thermodynamic properties-consistent coarse-grained model for random copolymer systems. POLYMER 2017. [DOI: 10.1016/j.polymer.2017.07.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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34
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Jiménez-Serratos G, Herdes C, Haslam AJ, Jackson G, Müller EA. Group Contribution Coarse-Grained Molecular Simulations of Polystyrene Melts and Polystyrene Solutions in Alkanes Using the SAFT-γ Force Field. Macromolecules 2017. [DOI: 10.1021/acs.macromol.6b02072] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Carmelo Herdes
- Department
of Chemical Engineering, University of Bath, Bath BA2 7AY, U.K
| | - Andrew J. Haslam
- Department
of Chemical Engineering, Imperial College London, London SW7 2AZ, U.K
| | - George Jackson
- Department
of Chemical Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Erich A. Müller
- Department
of Chemical Engineering, Imperial College London, London SW7 2AZ, U.K
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35
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Wang E, Escobedo F. Swelling and Tensile Properties of Tetra‐Polyethylene glycol via Coarse‐Grained Molecular Models. MACROMOL THEOR SIMUL 2017. [DOI: 10.1002/mats.201600098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Endian Wang
- School of Chemical and Biomolecular Engineering Cornell University Ithaca NY 14853 USA
| | - Fernando Escobedo
- School of Chemical and Biomolecular Engineering Cornell University Ithaca NY 14853 USA
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36
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Patrone PN, Rosch TW. Beyond histograms: efficiently estimating radial distribution functions via spectral Monte Carlo. J Chem Phys 2017; 146:094107. [PMID: 34234386 PMCID: PMC8260057 DOI: 10.1063/1.4977516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Despite more than 40 years of research in condensed-matter physics, state-of-the-art approaches for simulating the radial distribution function (RDF) g(r) still rely on binning pair-separations into a histogram. Such methods suffer from undesirable properties, including subjectivity, high uncertainty, and slow rates of convergence. Moreover, such problems go undetected by the metrics often used to assess RDFs. To address these issues, we propose (I) a spectral Monte Carlo (SMC) quadrature method that yields g(r) as an analytical series expansion; and (II) a Sobolev norm that assesses the quality of RDFs by quantifying their fluctuations. Using the latter, we show that, relative to histogram-based approaches, SMC reduces by orders of magnitude both the noise in g(r) and the number of pair separations needed for acceptable convergence. Moreover, SMC reduces subjectivity and yields simple, differentiable formulas for the RDF, which are useful for tasks such as coarse-grained force-field calibration via iterative Boltzmann inversion.
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Affiliation(s)
- Paul N. Patrone
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg MD 20899
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37
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Harrelson TF, Moulé AJ, Faller R. Modeling organic electronic materials: bridging length and time scales. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2016.1273526] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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38
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Patrone PN, Rosch TW, Phelan FR. Bayesian calibration of coarse-grained forces: Efficiently addressing transferability. J Chem Phys 2017; 144:154101. [PMID: 27389203 DOI: 10.1063/1.4945380] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Generating and calibrating forces that are transferable across a range of state-points remains a challenging task in coarse-grained (CG) molecular dynamics. In this work, we present a coarse-graining workflow, inspired by ideas from uncertainty quantification and numerical analysis, to address this problem. The key idea behind our approach is to introduce a Bayesian correction algorithm that uses functional derivatives of CG simulations to rapidly and inexpensively recalibrate initial estimates f0 of forces anchored by standard methods such as force-matching. Taking density-temperature relationships as a running example, we demonstrate that this algorithm, in concert with various interpolation schemes, can be used to efficiently compute physically reasonable force curves on a fine grid of state-points. Importantly, we show that our workflow is robust to several choices available to the modeler, including the interpolation schemes and tools used to construct f0. In a related vein, we also demonstrate that our approach can speed up coarse-graining by reducing the number of atomistic simulations needed as inputs to standard methods for generating CG forces.
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Affiliation(s)
- Paul N Patrone
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Thomas W Rosch
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Frederick R Phelan
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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39
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Gooneie A, Schuschnigg S, Holzer C. A Review of Multiscale Computational Methods in Polymeric Materials. Polymers (Basel) 2017; 9:E16. [PMID: 30970697 PMCID: PMC6432151 DOI: 10.3390/polym9010016] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/07/2016] [Accepted: 12/22/2016] [Indexed: 11/17/2022] Open
Abstract
Polymeric materials display distinguished characteristics which stem from the interplay of phenomena at various length and time scales. Further development of polymer systems critically relies on a comprehensive understanding of the fundamentals of their hierarchical structure and behaviors. As such, the inherent multiscale nature of polymer systems is only reflected by a multiscale analysis which accounts for all important mechanisms. Since multiscale modelling is a rapidly growing multidisciplinary field, the emerging possibilities and challenges can be of a truly diverse nature. The present review attempts to provide a rather comprehensive overview of the recent developments in the field of multiscale modelling and simulation of polymeric materials. In order to understand the characteristics of the building blocks of multiscale methods, first a brief review of some significant computational methods at individual length and time scales is provided. These methods cover quantum mechanical scale, atomistic domain (Monte Carlo and molecular dynamics), mesoscopic scale (Brownian dynamics, dissipative particle dynamics, and lattice Boltzmann method), and finally macroscopic realm (finite element and volume methods). Afterwards, different prescriptions to envelope these methods in a multiscale strategy are discussed in details. Sequential, concurrent, and adaptive resolution schemes are presented along with the latest updates and ongoing challenges in research. In sequential methods, various systematic coarse-graining and backmapping approaches are addressed. For the concurrent strategy, we aimed to introduce the fundamentals and significant methods including the handshaking concept, energy-based, and force-based coupling approaches. Although such methods are very popular in metals and carbon nanomaterials, their use in polymeric materials is still limited. We have illustrated their applications in polymer science by several examples hoping for raising attention towards the existing possibilities. The relatively new adaptive resolution schemes are then covered including their advantages and shortcomings. Finally, some novel ideas in order to extend the reaches of atomistic techniques are reviewed. We conclude the review by outlining the existing challenges and possibilities for future research.
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Affiliation(s)
- Ali Gooneie
- Chair of Polymer Processing, Montanuniversitaet Leoben, Otto Gloeckel-Strasse 2, 8700 Leoben, Austria.
| | - Stephan Schuschnigg
- Chair of Polymer Processing, Montanuniversitaet Leoben, Otto Gloeckel-Strasse 2, 8700 Leoben, Austria.
| | - Clemens Holzer
- Chair of Polymer Processing, Montanuniversitaet Leoben, Otto Gloeckel-Strasse 2, 8700 Leoben, Austria.
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40
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Moore TC, Iacovella CR, Hartkamp R, Bunge AL, McCabe C. A Coarse-Grained Model of Stratum Corneum Lipids: Free Fatty Acids and Ceramide NS. J Phys Chem B 2016; 120:9944-58. [PMID: 27564869 PMCID: PMC5287476 DOI: 10.1021/acs.jpcb.6b08046] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Ceramide (CER)-based biological membranes are used both experimentally and in simulations as simplified model systems of the skin barrier. Molecular dynamics studies have generally focused on simulating preassembled structures using atomistically detailed models of CERs, which limit the system sizes and time scales that can practically be probed, rendering them ineffective for studying particular phenomena, including self-assembly into bilayer and lamellar superstructures. Here, we report on the development of a coarse-grained (CG) model for CER NS, the most abundant CER in human stratum corneum. Multistate iterative Boltzmann inversion is used to derive the intermolecular pair potentials, resulting in a force field that is applicable over a range of state points and suitable for studying ceramide self-assembly. The chosen CG mapping, which includes explicit interaction sites for hydroxyl groups, captures the directional nature of hydrogen bonding and allows for accurate predictions of several key structural properties of CER NS bilayers. Simulated wetting experiments allow the hydrophobicity of CG beads to be accurately tuned to match atomistic wetting behavior, which affects the whole system, since inaccurate hydrophobic character is found to unphysically alter the lipid packing in hydrated lamellar states. We find that CER NS can self-assemble into multilamellar structures, enabling the study of lipid systems more representative of the multilamellar lipid structures present in the skin barrier. The coarse-grained force field derived herein represents an important step in using molecular dynamics to study the human skin barrier, which gives a resolution not available through experiment alone.
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Affiliation(s)
- Timothy C. Moore
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235
- Vanderbilt University Multiscale Modeling and Simulation (MuMS) Facility, Nashville, TN 37235
| | - Christopher R. Iacovella
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235
- Vanderbilt University Multiscale Modeling and Simulation (MuMS) Facility, Nashville, TN 37235
| | - Remco Hartkamp
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235
- Vanderbilt University Multiscale Modeling and Simulation (MuMS) Facility, Nashville, TN 37235
| | - Annette L. Bunge
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO 80401
| | - Clare McCabe
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235
- Vanderbilt University Multiscale Modeling and Simulation (MuMS) Facility, Nashville, TN 37235
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235
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41
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Agrawal V, Peralta P, Li Y, Oswald J. A pressure-transferable coarse-grained potential for modeling the shock Hugoniot of polyethylene. J Chem Phys 2016; 145:104903. [DOI: 10.1063/1.4962255] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Vipin Agrawal
- School for the Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, USA
| | - Pedro Peralta
- School for the Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, USA
| | - Yiyang Li
- School for the Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, USA
| | - Jay Oswald
- School for the Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, USA
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42
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Moore TC, Iacovella CR, McCabe C. Development of a coarse-grained water forcefield via multistate iterative Boltzmann inversion. FOUNDATIONS OF MOLECULAR MODELING AND SIMULATION : SELECT PAPERS FROM FOMMS 2015. INTERNATIONAL CONFERENCE ON FOUNDATIONS OF MOLECULAR MODELING AND SIMULATION (6TH : 2015 : MOUNT HOOD, OR.) 2016; 2016:37-52. [PMID: 32483559 PMCID: PMC7262820 DOI: 10.1007/978-981-10-1128-3_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A coarse-grained water model is developed using multistate iterative Boltzmann inversion. Following previous work, the k-means algorithm is used to dynamically map multiple water molecules to a single coarse-grained bead, allowing the use of structure-based coarse-graining methods. The model is derived to match the bulk and interfacial properties of liquid water and improves upon previous work that used single state iterative Boltzmann inversion. The model accurately reproduces the density and structural correlations of water at 305 K and 1.0 atm, stability of a liquid droplet at 305 K, and shows little tendency to crystallize at physiological conditions. This work also illustrates several advantages of using multistate iterative Boltzmann inversion for deriving generally applicable coarse-grained forcefields.
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Affiliation(s)
- Timothy C. Moore
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235
- Vanderbilt University Center for Multiscale Modeling and Simulation (MuMS), Nashville, TN 37235
| | - Christopher R. Iacovella
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235
- Vanderbilt University Center for Multiscale Modeling and Simulation (MuMS), Nashville, TN 37235
| | - Clare McCabe
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235
- Vanderbilt University Center for Multiscale Modeling and Simulation (MuMS), Nashville, TN 37235
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235
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Choudhury CK, Carbone P, Roy S. Scalability of Coarse-Grained Potentials Generated from Iterative Boltzmann Inversion for Polymers: Case Study on Polycarbonates. MACROMOL THEOR SIMUL 2016. [DOI: 10.1002/mats.201500079] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Paola Carbone
- School of Chemical Engineering and Analytical Science; The University of Manchester; Manchester UK
| | - Sudip Roy
- Physical Chemistry Division; National Chemical Laboratory; Pune India
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44
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Huang W, Ramesh R, Jha PK, Larson RG. A Systematic Coarse-Grained Model for Methylcellulose Polymers: Spontaneous Ring Formation at Elevated Temperature. Macromolecules 2016. [DOI: 10.1021/acs.macromol.5b02373] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Wenjun Huang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109-2136, United States
| | - Rahul Ramesh
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109-2136, United States
| | - Prateek K. Jha
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109-2136, United States
| | - Ronald G. Larson
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109-2136, United States
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45
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Gao P, Guo H. Transferability of the coarse-grained potentials for trans-1,4-polybutadiene. Phys Chem Chem Phys 2015; 17:31693-706. [DOI: 10.1039/c5cp05017k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The CG torsion potential has a dual effect on the reproduction of crystallization of trans-1,4-polybutadiene in CG simulation.
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Affiliation(s)
- Peiyuan Gao
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory of Polymer Physics and Chemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Hongxia Guo
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory of Polymer Physics and Chemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
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46
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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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47
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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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48
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Wu C. Multiscale simulations of the structure and dynamics of stereoregular poly(methyl methacrylate)s. J Mol Model 2014; 20:2377. [DOI: 10.1007/s00894-014-2377-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 07/07/2014] [Indexed: 10/25/2022]
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49
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Moore TC, Iacovella CR, McCabe C. Derivation of coarse-grained potentials via multistate iterative Boltzmann inversion. J Chem Phys 2014; 140:224104. [PMID: 24929371 PMCID: PMC4187284 DOI: 10.1063/1.4880555] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 05/19/2014] [Indexed: 11/15/2022] Open
Abstract
In this work, an extension is proposed to the standard iterative Boltzmann inversion (IBI) method used to derive coarse-grained potentials. It is shown that the inclusion of target data from multiple states yields a less state-dependent potential, and is thus better suited to simulate systems over a range of thermodynamic states than the standard IBI method. The inclusion of target data from multiple states forces the algorithm to sample regions of potential phase space that match the radial distribution function at multiple state points, thus producing a derived potential that is more representative of the underlying interactions. It is shown that the algorithm is able to converge to the true potential for a system where the underlying potential is known. It is also shown that potentials derived via the proposed method better predict the behavior of n-alkane chains than those derived via the standard IBI method. Additionally, through the examination of alkane monolayers, it is shown that the relative weight given to each state in the fitting procedure can impact bulk system properties, allowing the potentials to be further tuned in order to match the properties of reference atomistic and/or experimental systems.
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Affiliation(s)
- Timothy C Moore
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Christopher R Iacovella
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Clare McCabe
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA
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50
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Agrawal A, Aryal D, Perahia D, Ge T, Grest GS. Coarse-Graining Atactic Polystyrene and Its Analogues. Macromolecules 2014. [DOI: 10.1021/ma500319v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anupriya Agrawal
- Department
of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Dipak Aryal
- Department
of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Dvora Perahia
- Department
of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Ting Ge
- Department
of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Gary S. Grest
- Sandia
National Laboratories, Albuquerque, New Mexico 87185, United States
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