1
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Kunze T, Dreßler C, Lauer C, Paul W, Sebastiani D. Reverse Mapping of Coarse Grained Polyglutamine Conformations from PRIME20 Sampling. Chemphyschem 2024; 25:e202300521. [PMID: 38314956 DOI: 10.1002/cphc.202300521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/07/2024]
Abstract
An inverse coarse-graining protocol is presented for generating and validating atomistic structures of large (bio-) molecules from conformations obtained via a coarse-grained sampling method. Specifically, the protocol is implemented and tested based on the (coarse-grained) PRIME20 protein model (P20/SAMC), and the resulting all-atom conformations are simulated using conventional biomolecular force fields. The phase space sampling at the coarse-grained level is performed with a stochastical approximation Monte Carlo approach. The method is applied to a series of polypeptides, specifically dimers of polyglutamine with varying chain length in aqueous solution. The majority (>70 %) of the conformations obtained from the coarse-grained peptide model can successfully be mapped back to atomistic structures that remain conformationally stable during 10 ns of molecular dynamics simulations. This work can be seen as the first step towards the overarching goal of improving our understanding of protein aggregation phenomena through simulation methods.
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Affiliation(s)
- Thomas Kunze
- Faculty of Natural Sciences II, Martin-Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle, Germany
| | - Christian Dreßler
- Institut für Physik, Ilmenau University of Technology, Weimarer Straße 32, 98693, Ilmenau, Germany
| | - Christian Lauer
- Faculty of Natural Sciences II, Martin-Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle, Germany
| | - Wolfgang Paul
- Faculty of Natural Sciences II, Martin-Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle, Germany
| | - Daniel Sebastiani
- Faculty of Natural Sciences II, Martin-Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle, Germany
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2
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Nitta H, Ozawa T, Yasuoka K. Construction of full-atomistic polymer amorphous structures using reverse-mapping from Kremer-Grest models. J Chem Phys 2023; 159:194903. [PMID: 37982485 DOI: 10.1063/5.0159722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 10/30/2023] [Indexed: 11/21/2023] Open
Abstract
We propose a method to build full-atomistic (FA) amorphous polymer structures using reverse-mapping from coarse-grained (CG) models. In this method, three models with different resolutions are utilized, namely the CG1, CG2, and FA models. It is assumed that the CG1 model is more abstract than the CG2 model. The CG1 is utilized to equilibrate the system, and then sequential reverse-mapping procedures from the CG1 to the CG2 models and from the CG2 to the FA models are conducted. A mapping relation between the CG1 and the FA models is necessary to generate a polymer structure with a given density and radius of chains. Actually, we have used the Kremer-Grest (KG) model as the CG1 and the monomer-level CG model as the CG2 model. Utilizing the mapping relation, we have developed a scheme that constructs an FA polymer model from the KG model. In the scheme, the KG model, the monomer level CG model, and the FA model are successively constructed. The scheme is applied to polyethylene (PE), cis 1,4-polybutadiene (PB), and poly(methyl methacrylate) (PMMA). As a validation, the structures of PE and PB constructed by the scheme were carefully checked through comparison with those obtained using long-time FA molecular dynamics (MD) simulations. We found that both short- and long-range chain structures constructed by the scheme reproduced those obtained by the FA MD simulations. Then, as an interesting application, the scheme is applied to generate an entangled PMMA structure. The results showed that the scheme provides an efficient and easy way to construct amorphous structures of FA polymers.
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Affiliation(s)
- Hiroya Nitta
- JSOL Corporation, KUDAN-KAIKAN TERRACE 1-6-5, Kudanminami, Chiyoda-ku, Tokyo 102-0074, Japan
| | - Taku Ozawa
- JSOL Corporation, KUDAN-KAIKAN TERRACE 1-6-5, Kudanminami, Chiyoda-ku, Tokyo 102-0074, Japan
| | - Kenji Yasuoka
- Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
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3
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Jones MS, Shmilovich K, Ferguson AL. DiAMoNDBack: Diffusion-Denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces. J Chem Theory Comput 2023; 19:7908-7923. [PMID: 37906711 DOI: 10.1021/acs.jctc.3c00840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Coarse-grained molecular models of proteins permit access to length and time scales unattainable by all-atom models and the simulation of processes that occur on long time scales, such as aggregation and folding. The reduced resolution realizes computational accelerations, but an atomistic representation can be vital for a complete understanding of mechanistic details. Backmapping is the process of restoring all-atom resolution to coarse-grained molecular models. In this work, we report DiAMoNDBack (Diffusion-denoising Autoregressive Model for Non-Deterministic Backmapping) as an autoregressive denoising diffusion probability model to restore all-atom details to coarse-grained protein representations retaining only Cα coordinates. The autoregressive generation process proceeds from the protein N-terminus to C-terminus in a residue-by-residue fashion conditioned on the Cα trace and previously backmapped backbone and side-chain atoms within the local neighborhood. The local and autoregressive nature of our model makes it transferable between proteins. The stochastic nature of the denoising diffusion process means that the model generates a realistic ensemble of backbone and side-chain all-atom configurations consistent with the coarse-grained Cα trace. We train DiAMoNDBack over 65k+ structures from the Protein Data Bank (PDB) and validate it in applications to a hold-out PDB test set, intrinsically disordered protein structures from the Protein Ensemble Database (PED), molecular dynamics simulations of fast-folding mini-proteins from DE Shaw Research, and coarse-grained simulation data. We achieve state-of-the-art reconstruction performance in terms of correct bond formation, avoidance of side-chain clashes, and the diversity of the generated side-chain configurational states. We make the DiAMoNDBack model publicly available as a free and open-source Python package.
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Affiliation(s)
- Michael S Jones
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Kirill Shmilovich
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
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4
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Svaneborg C, Everaers R. Multiscale equilibration of highly entangled isotropic model polymer melts. J Chem Phys 2023; 158:054903. [PMID: 36754791 DOI: 10.1063/5.0123431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We present a computationally efficient multiscale method for preparing equilibrated, isotropic long-chain model polymer melts. As an application, we generate Kremer-Grest melts of 1000 chains with 200 entanglements and 25 000-2000 beads/chain, which cover the experimentally relevant bending rigidities up to and beyond the limit of the isotropic-nematic transition. In the first step, we employ Monte Carlo simulations of a lattice model to equilibrate the large-scale chain structure above the tube scale while ensuring a spatially homogeneous density distribution. We then use theoretical insight from a constrained mode tube model to introduce the bead degrees of freedom together with random walk conformational statistics all the way down to the Kuhn scale of the chains. This is followed by a sequence of simulations with carefully parameterized force-capped bead-spring models, which slowly introduce the local bead packing while reproducing the larger-scale chain statistics of the target Kremer-Grest system at all levels of force-capping. Finally, we can switch to the full Kremer-Grest model without perturbing the structure. The resulting chain statistics is in excellent agreement with literature results on all length scales accessible in brute-force simulations of shorter chains.
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Affiliation(s)
- Carsten Svaneborg
- University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Ralf Everaers
- ENSL, CNRS, Laboratoire de Physique and Centre Blaise Pascal de l'École Normale Supérieure de Lyon, F-69342 Lyon, France
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5
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Shmilovich K, Stieffenhofer M, Charron NE, Hoffmann M. Temporally Coherent Backmapping of Molecular Trajectories From Coarse-Grained to Atomistic Resolution. J Phys Chem A 2022; 126:9124-9139. [PMID: 36417670 PMCID: PMC9743211 DOI: 10.1021/acs.jpca.2c07716] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Coarse-graining offers a means to extend the achievable time and length scales of molecular dynamics simulations beyond what is practically possible in the atomistic regime. Sampling molecular configurations of interest can be done efficiently using coarse-grained simulations, from which meaningful physicochemical information can be inferred if the corresponding all-atom configurations are reconstructed. However, this procedure of backmapping to reintroduce the lost atomistic detail into coarse-grain structures has proven a challenging task due to the many feasible atomistic configurations that can be associated with one coarse-grain structure. Existing backmapping methods are strictly frame-based, relying on either heuristics to replace coarse-grain particles with atomic fragments and subsequent relaxation or parametrized models to propose atomic coordinates separately and independently for each coarse-grain structure. These approaches neglect information from previous trajectory frames that is critical to ensuring temporal coherence of the backmapped trajectory, while also offering information potentially helpful to producing higher-fidelity atomic reconstructions. In this work, we present a deep learning-enabled data-driven approach for temporally coherent backmapping that explicitly incorporates information from preceding trajectory structures. Our method trains a conditional variational autoencoder to nondeterministically reconstruct atomistic detail conditioned on both the target coarse-grain configuration and the previously reconstructed atomistic configuration. We demonstrate our backmapping approach on two exemplar biomolecular systems: alanine dipeptide and the miniprotein chignolin. We show that our backmapped trajectories accurately recover the structural, thermodynamic, and kinetic properties of the atomistic trajectory data.
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Affiliation(s)
- Kirill Shmilovich
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois60637, United States,E-mail:
| | | | - Nicholas E. Charron
- Weiss
School of Natural Sciences, Department of Physics and Astronomy, Rice University, Houston, Texas77005, United States,Department
of Physics, Freie Universität Berlin, Berlin14195, Germany
| | - Moritz Hoffmann
- Fachbereich
Mathematik und Informatik, Freie Universität
Berlin, Berlin14195, Germany
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6
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Abstract
Ion-containing polymers have continued to be an important research focus for several decades due to their use as an electrolyte in energy storage and conversion devices. Elucidation of connections between the mesoscopic structure and multiscale dynamics of the ions and solvent remains incompletely understood. Coarse-grained modeling provides an efficient approach for exploring the structural and dynamical properties of these soft materials. The unique physicochemical properties of such polymers are of broad interest. In this review, we summarize the current development and understanding of the structure-property relationship of ion-containing polymers and provide insights into the design of such materials determined from coarse-grained modeling and simulations accompanying significant advances in experimental strategies. We specifically concentrate on three types of ion-containing polymers: proton exchange membranes (PEMs), anion exchange membranes (AEMs), and polymerized ionic liquids (polyILs). We posit that insight into the similarities and differences in these materials will lead to guidance in the rational design of high-performance novel materials with improved properties for various power source technologies.
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Affiliation(s)
- Zhenghao Zhu
- Department of Chemical & Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Xubo Luo
- Department of Chemical & Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Stephen J Paddison
- Department of Chemical & Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
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7
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Vlachas PR, Zavadlav J, Praprotnik M, Koumoutsakos P. Accelerated Simulations of Molecular Systems through Learning of Effective Dynamics. J Chem Theory Comput 2021; 18:538-549. [PMID: 34890204 DOI: 10.1021/acs.jctc.1c00809] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Simulations are vital for understanding and predicting the evolution of complex molecular systems. However, despite advances in algorithms and special purpose hardware, accessing the time scales necessary to capture the structural evolution of biomolecules remains a daunting task. In this work, we present a novel framework to advance simulation time scales by up to 3 orders of magnitude by learning the effective dynamics (LED) of molecular systems. LED augments the equation-free methodology by employing a probabilistic mapping between coarse and fine scales using mixture density network (MDN) autoencoders and evolves the non-Markovian latent dynamics using long short-term memory MDNs. We demonstrate the effectiveness of LED in the Müller-Brown potential, the Trp cage protein, and the alanine dipeptide. LED identifies explainable reduced-order representations, i.e., collective variables, and can generate, at any instant, all-atom molecular trajectories consistent with the collective variables. We believe that the proposed framework provides a dramatic increase to simulation capabilities and opens new horizons for the effective modeling of complex molecular systems.
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Affiliation(s)
- Pantelis R Vlachas
- Computational Science and Engineering Laboratory, ETH Zurich, CH-8092, Switzerland
| | - Julija Zavadlav
- Professorship of Multiscale Modeling of Fluid Materials, TUM School of Engineering and Design, Technical University of Munich, 85748 Garching bei München, Germany.,Munich Data Science Institute, Technical University of Munich, 85748 Munich, Germany
| | - Matej Praprotnik
- Laboratory for Molecular Modeling, National Institute of Chemistry, SI-1001 Ljubljana, Slovenia.,Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Petros Koumoutsakos
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
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8
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Duong VT, Diessner EM, Grazioli G, Martin RW, Butts CT. Neural Upscaling from Residue-Level Protein Structure Networks to Atomistic Structures. Biomolecules 2021; 11:biom11121788. [PMID: 34944432 PMCID: PMC8698800 DOI: 10.3390/biom11121788] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/11/2021] [Accepted: 11/19/2021] [Indexed: 01/01/2023] Open
Abstract
Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a particularly useful way of obtaining highly compressed representations of molecular structures, and simulations operating via such representations can achieve substantial computational savings. A drawback of coarse-graining, however, is the loss of atomistic detail—an effect that is especially acute for topological representations such as protein structure networks (PSNs). Here, we introduce an approach based on a combination of machine learning and physically-guided refinement for inferring atomic coordinates from PSNs. This “neural upscaling” procedure exploits the constraints implied by PSNs on possible configurations, as well as differences in the likelihood of observing different configurations with the same PSN. Using a 1 μs atomistic molecular dynamics trajectory of Aβ1–40, we show that neural upscaling is able to effectively recapitulate detailed structural information for intrinsically disordered proteins, being particularly successful in recovering features such as transient secondary structure. These results suggest that scalable network-based models for protein structure and dynamics may be used in settings where atomistic detail is desired, with upscaling employed to impute atomic coordinates from PSNs.
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Affiliation(s)
- Vy T. Duong
- Department of Chemistry, University of California, Irvine, CA 92697, USA; (V.T.D.); (E.M.D.)
| | - Elizabeth M. Diessner
- Department of Chemistry, University of California, Irvine, CA 92697, USA; (V.T.D.); (E.M.D.)
| | - Gianmarc Grazioli
- Department of Chemistry, San Jose State University, San Jose, CA 95192, USA;
| | - Rachel W. Martin
- Department of Chemistry, University of California, Irvine, CA 92697, USA; (V.T.D.); (E.M.D.)
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA 92697, USA
- Correspondence: (R.W.M.); (C.T.B.)
| | - Carter T. Butts
- Departments of Sociology, Statistics and Electrical Engineering & Computer Science, University of California, Irvine, CA 92697, USA
- Correspondence: (R.W.M.); (C.T.B.)
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9
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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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10
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Kubincová A, Riniker S, Hünenberger PH. Solvent-scaling as an alternative to coarse-graining in adaptive-resolution simulations: The adaptive solvent-scaling (AdSoS) scheme. J Chem Phys 2021; 155:094107. [PMID: 34496576 DOI: 10.1063/5.0057384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A new approach termed Adaptive Solvent-Scaling (AdSoS) is introduced for performing simulations of a solute embedded in a fine-grained (FG) solvent region itself surrounded by a coarse-grained (CG) solvent region, with a continuous FG ↔ CG switching of the solvent resolution across a buffer layer. Instead of relying on a distinct CG solvent model, the AdSoS scheme is based on CG models defined by a dimensional scaling of the FG solvent by a factor s, accompanied by an s-dependent modulation of the atomic masses and interaction parameters. The latter changes are designed to achieve an isomorphism between the dynamics of the FG and CG models, and to preserve the dispersive and dielectric solvation properties of the solvent with respect to a solute at FG resolution. This scaling approach offers a number of advantages compared to traditional coarse-graining: (i) the CG parameters are immediately related to those of the FG model (no need to parameterize a distinct CG model); (ii) nearly ideal mixing is expected for CG variants with similar s-values (ideal mixing holding in the limit of identical s-values); (iii) the solvent relaxation timescales should be preserved (no dynamical acceleration typical for coarse-graining); (iv) the graining level NG (number of FG molecules represented by one CG molecule) can be chosen arbitrarily (in particular, NG = s3 is not necessarily an integer); and (v) in an adaptive-resolution scheme, this level can be varied continuously as a function of the position (without requiring a bundling mechanism), and this variation occurs at a constant number of particles per molecule (no occurrence of fractional degrees of freedom in the buffer layer). By construction, the AdSoS scheme minimizes the thermodynamic mismatch between the different regions of the adaptive-resolution system, leading to a nearly homogeneous scaled solvent density s3ρ. Residual density artifacts in and at the surface of the boundary layer can easily be corrected by means of a grid-based biasing potential constructed in a preliminary pure-solvent simulation. This article introduces the AdSoS scheme and provides an initial application to pure atomic liquids (no solute) with Lennard-Jones plus Coulomb interactions in a slab geometry.
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Affiliation(s)
- Alžbeta Kubincová
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Philippe H Hünenberger
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir Prelog-Weg 2, CH-8093 Zürich, Switzerland
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11
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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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12
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Stieffenhofer M, Wand M, Bereau T. Adversarial reverse mapping of equilibrated condensed-phase molecular structures. MACHINE LEARNING-SCIENCE AND TECHNOLOGY 2020. [DOI: 10.1088/2632-2153/abb6d4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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13
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Everaers R, Karimi-Varzaneh HA, Fleck F, Hojdis N, Svaneborg C. Kremer–Grest Models for Commodity Polymer Melts: Linking Theory, Experiment, and Simulation at the Kuhn Scale. Macromolecules 2020. [DOI: 10.1021/acs.macromol.9b02428] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ralf Everaers
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Physique and Centre Blaise Pascal de l’ENS de Lyon, F-69342 Lyon, France
| | | | - Frank Fleck
- Continental Reifen Deutschland GmbH, Jädekamp 30, D-30419 Hannover, Germany
| | - Nils Hojdis
- Institute of Applied Polymer Chemistry, Aachen University of Applied Sciences, Heinrich-Mussmann-Str.1, 52428 Jülich, Germany
| | - Carsten Svaneborg
- University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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14
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Glagolev MK, Vasilevskaya VV. Coarse-grained simulation of molecular ordering in polylactic blends under uniaxial strain. POLYMER 2020. [DOI: 10.1016/j.polymer.2020.122232] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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15
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Li M, Teng B, Lu W, Zhang JZ. Atomic-level reconstruction of biomolecules by a rigid-fragment- and local-frame-based (RF-LF) strategy. J Mol Model 2020; 26:31. [PMID: 31965325 DOI: 10.1007/s00894-020-4298-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 01/14/2020] [Indexed: 11/29/2022]
Abstract
Coarse-grained (CG) model has been a powerful tool in bridging the gap between theoretical studies and experimental phenomena in biological computing field. The reconstruction from a CG model to an atomic-detail structure is especially important in CG studies of biological systems. In this work, a rigid-fragment- and local-frame-based (RF-LF) backmapping method was proposed to achieve reverse mapping from CG models to atomic-level structures. The initial atomic-level structures were further refined to yield the final backmapping ones. With the popular Martini force field, the performance of the RF-LF method was extensively examined in the CG → AA (CG to AA) backmapping of protein/DNA/RNA systems. Besides, the RF-LF method was also extended to the backmapping of the TMFF model. Numerical results illustrate that the RF-LF backmapping method is generic and parameter-free and can provide a promising way to tackle atomic-level studies in CG models.
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Affiliation(s)
- Min Li
- College of Physics, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China.
| | - Bing Teng
- College of Physics, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China
| | - WenCai Lu
- College of Physics, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China
| | - John ZengHui Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, People's Republic of China.
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, People's Republic of China.
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16
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Kuo AT, Miyazaki Y, Jang C, Miyajima T, Urata S, Nielsen SO, Okazaki S, Shinoda W. Large-scale molecular dynamics simulation of perfluorosulfonic acid membranes: Remapping coarse-grained to all-atomistic simulations. POLYMER 2019. [DOI: 10.1016/j.polymer.2019.121766] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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17
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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: 38] [Impact Index Per Article: 7.6] [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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18
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Kubo A, Albina JM, Umeno Y. Construction of master yield stress curves for polycarbonate: A coarse-grained molecular dynamics study. POLYMER 2019. [DOI: 10.1016/j.polymer.2019.05.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Hall KW, Sirk TW, Klein ML, Shinoda W. A coarse-grain model for entangled polyethylene melts and polyethylene crystallization. J Chem Phys 2019; 150:244901. [PMID: 31255065 DOI: 10.1063/1.5092229] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The Shinoda-DeVane-Klein (SDK) model is herein demonstrated to be a viable coarse-grain model for performing molecular simulations of polyethylene (PE), affording new opportunities to advance molecular-level, scientific understanding of PE materials and processes. Both structural and dynamical properties of entangled PE melts are captured by the SDK model, which also recovers important aspects of PE crystallization phenomenology. Importantly, the SDK model can be used to represent a variety of materials beyond PE and has a simple functional form, making it unique among coarse-grain PE models. This study expands the suite of tools for studying PE in silico and paves the way for future work probing PE and PE-based composites at the molecular level.
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Affiliation(s)
- Kyle Wm Hall
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Timothy W Sirk
- U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, USA
| | - Michael L Klein
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Wataru Shinoda
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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20
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Peng J, Yuan C, Ma R, Zhang Z. Backmapping from Multiresolution Coarse-Grained Models to Atomic Structures of Large Biomolecules by Restrained Molecular Dynamics Simulations Using Bayesian Inference. J Chem Theory Comput 2019; 15:3344-3353. [PMID: 30908042 DOI: 10.1021/acs.jctc.9b00062] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Coarse-grained (CG) simulations have allowed access to larger length scales and longer time scales in the study of the dynamic processes of large biomolecules than all-atom (AA) molecular dynamics (MD) simulations. Backmapping from CG models to AA structures has long been studied because it enables us to gain detailed structure insights from CG simulations. Many methods first construct an AA structure from the CG model by fragments, random placement, or geometrical rules and subsequently optimize the solution via energy minimization, simulated annealing or position-restrained simulations. However, such methods may only work well on residue-level CG models and cannot consider the deviations of CG models. In this work, we describe, to the best of our knowledge, a new backmapping method based on Bayesian inference and restrained MD simulations. Restraints with log harmonic energy terms are defined according to the target CG model using the Bayesian inference in which the CG deviations can be estimated. From an initial AA structure obtained from either high-resolution experiments or homology modeling, a MD simulation with the aforementioned restraints is performed to obtain a final AA structure that is a backmapping of the target CG model. The method was validated using multiresolution CG models of the soluble extracellular region of the human epidermal growth factor receptor and was further applied to construct AA structures from CG simulations of the nucleosome core particle. The results demonstrate that our method can generate accurate AA structures of different types of biomolecules from multiple CG models with either residue-level resolution or much lower resolution than one-site-per-residue.
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Affiliation(s)
- Junhui Peng
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230026 , People's Republic of China
| | - Chuang Yuan
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230026 , People's Republic of China
| | - Rongsheng Ma
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230026 , People's Republic of China
| | - Zhiyong Zhang
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230026 , People's Republic of China
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21
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Xia W, Hansoge NK, Xu WS, Phelan FR, Keten S, Douglas JF. Energy renormalization for coarse-graining polymers having different segmental structures. SCIENCE ADVANCES 2019; 5:eaav4683. [PMID: 31016241 PMCID: PMC6474771 DOI: 10.1126/sciadv.aav4683] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 03/05/2019] [Indexed: 05/23/2023]
Abstract
Multiscale coarse-grained (CG) modeling of soft materials, such as polymers, is currently an art form because CG models normally have significantly altered dynamics and thermodynamic properties compared to their atomistic counterparts. We address this problem by exploiting concepts derived from the generalized entropy theory (GET), emphasizing the central role of configurational entropy s c in the dynamics of complex fluids. Our energy renormalization (ER) method involves varying the cohesive interaction strength in the CG models in such a way that dynamic properties related to s c are preserved. We test this ER method by applying it to coarse-graining polymer melts (i.e., polybutadiene, polystyrene, and polycarbonate), representing polymer materials having a relatively low, intermediate, and high degree of glass "fragility". We find that the ER method allows the dynamics of the atomistic polymer models to be faithfully described to a good approximation by CG models over a wide temperature range.
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Affiliation(s)
- Wenjie Xia
- Department of Civil and Environmental Engineering, North Dakota State University, Fargo, ND 58108, USA
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Nitin K. Hansoge
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Wen-Sheng Xu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
| | - Frederick R. Phelan
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Sinan Keten
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Jack F. Douglas
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
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22
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Hall KW, Percec S, Klein ML. Polymer nucleation under high-driving force, long-chain conditions: Heat release and the separation of time scales. J Chem Phys 2019; 150:114901. [PMID: 30902014 DOI: 10.1063/1.5084773] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
This study reveals important features of polymer crystal formation at high-driving forces in entangled polymer melts based on simulations of polyethylene. First and in contrast to small-molecule crystallization, the heat released during polymer crystallization does not appreciably influence structural details of early-stage, crystalline clusters (crystal nuclei). Second, early-stage polymer crystallization (crystal nucleation) can occur without substantial chain-level relaxation and conformational changes. This study's results indicate that local structures and environments guide crystal nucleation in entangled polymer melts under high-driving force conditions. Given that such conditions are often used to process polyethylene, local structures and the separation of time scales associated with crystallization and chain-level processes are anticipated to be of substantial importance to processing strategies. This study highlights new research directions for understanding polymer crystallization.
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Affiliation(s)
- Kyle Wm Hall
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Simona Percec
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Michael L Klein
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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23
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Zhang G, Chazirakis A, Harmandaris VA, Stuehn T, Daoulas KC, Kremer K. Hierarchical modelling of polystyrene melts: from soft blobs to atomistic resolution. SOFT MATTER 2019; 15:289-302. [PMID: 30543257 DOI: 10.1039/c8sm01830h] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We demonstrate that hierarchical backmapping strategies incorporating generic blob-based models can equilibrate melts of high-molecular-weight polymers, described with chemically specific, atomistic models. The central idea is first to represent polymers by chains of large soft blobs (spheres) and efficiently equilibrate the melt on large scales. Then, the degrees of freedom of more detailed models are reinserted step by step. The procedure terminates when the atomistic description is reached. Reinsertions are feasible computationally because the fine-grained melt must be re-equilibrated only locally. We consider polystyrene (PS) which is sufficiently complex to serve method development because of stereo-chemistry and bulky side groups. Our backmapping strategy bridges mesoscopic and atomistic scales by incorporating a blob-based, a moderately coarse-grained (CG), and a united-atom model of PS. We demonstrate that the generic blob-based model can be parameterised to reproduce the mesoscale properties of a specific polymer - here PS. The moderately CG model captures stereo-chemistry. To perform backmapping we improve and adjust several fine-graining techniques. We prove equilibration of backmapped PS melts by comparing their structural and conformational properties with reference data from smaller systems, equilibrated with less efficient methods.
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Affiliation(s)
- Guojie Zhang
- Institute for Systems Rheology, Advanced Institute of Engineering Science for Intelligent Manufacturing, Guangzhou University, 510006 Guangzhou, China.
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24
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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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25
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Abetz V, Kremer K, Müller M, Reiter G. Functional Macromolecular Systems: Kinetic Pathways to Obtain Tailored Structures. MACROMOL CHEM PHYS 2018. [DOI: 10.1002/macp.201800334] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Volker Abetz
- Institute of Polymer Research; Helmholtz-Zentrum Geesthacht Max-Planck-Straße 1 21502 Geesthacht Germany
- Institute of Physical Chemistry; University of Hamburg; Martin-Luther-King-Platz 6 20146 Hamburg Germany
| | - Kurt Kremer
- Polymer Theory; Max Planck Institute for Polymer Research; Ackermannweg 10 55128 Mainz Germany
| | - Marcus Müller
- Institute for Theoretical Physics; Georg-August University of Göttingen; Friedrich-Hund-Platz 1 37077 Göttingen Germany
| | - Günter Reiter
- Institute of Physics; Albert-Ludwigs-University of Freiburg; Hermann-Herder-Str. 3 79104 Freiburg Germany
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26
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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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27
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Kondratyuk ND, Norman GE, Stegailov VV. Microscopic mechanisms of diffusion of higher alkanes. POLYMER SCIENCE SERIES A 2018. [DOI: 10.1134/s0965545x16050072] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Effects and limitations of a nucleobase-driven backmapping procedure for nucleic acids using steered molecular dynamics. Biochem Biophys Res Commun 2018; 498:352-358. [DOI: 10.1016/j.bbrc.2017.12.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/13/2017] [Accepted: 12/11/2017] [Indexed: 11/19/2022]
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29
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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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30
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Zavadlav J, Bevc S, Praprotnik M. Adaptive resolution simulations of biomolecular systems. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 46:821-835. [PMID: 28905203 DOI: 10.1007/s00249-017-1248-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/12/2017] [Accepted: 08/15/2017] [Indexed: 10/18/2022]
Abstract
In this review article, we discuss and analyze some recently developed hybrid atomistic-mesoscopic solvent models for multiscale biomolecular simulations. We focus on the biomolecular applications of the adaptive resolution scheme (AdResS), which allows solvent molecules to change their resolution back and forth between atomistic and coarse-grained representations according to their positions in the system. First, we discuss coupling of atomistic and coarse-grained models of salt solution using a 1-to-1 molecular mapping-i.e., one coarse-grained bead represents one water molecule-for development of a multiscale salt solution model. In order to make use of coarse-grained molecular models that are compatible with the MARTINI force field, one has to resort to a supramolecular mapping, in particular to a 4-to-1 mapping, where four water molecules are represented with one coarse-grained bead. To this end, bundled atomistic water models are employed, i.e., the relative movement of water molecules that are mapped to the same coarse-grained bead is restricted by employing harmonic springs. Supramolecular coupling has recently also been extended to polarizable coarse-grained water models with explicit charges. Since these coarse-grained models consist of several interaction sites, orientational degrees of freedom of the atomistic and coarse-grained representations are coupled via a harmonic energy penalty term. The latter aligns the dipole moments of both representations. The reviewed multiscale solvent models are ready to be used in biomolecular simulations, as illustrated in a few examples.
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Affiliation(s)
- Julija Zavadlav
- Department of Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.,Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000, Ljubljana, Slovenia.,Chair of Computational Science, ETH Zurich, Clausiusstrasse 33, 8092, Zurich, Switzerland
| | - Staš Bevc
- Department of Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia
| | - Matej Praprotnik
- Department of Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia. .,Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000, Ljubljana, Slovenia.
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31
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Jones ML, Jankowski E. Computationally connecting organic photovoltaic performance to atomistic arrangements and bulk morphology. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1296958] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Matthew L. Jones
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID, USA
| | - Eric Jankowski
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID, USA
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32
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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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33
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Nanosecond-time-scale reversibility of dilation induced by carbon dioxide sorption in glassy polymer membranes. J Memb Sci 2016. [DOI: 10.1016/j.memsci.2016.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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34
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Zhang G, Stillinger FH, Torquato S. The Perfect Glass Paradigm: Disordered Hyperuniform Glasses Down to Absolute Zero. Sci Rep 2016; 6:36963. [PMID: 27892452 PMCID: PMC5125002 DOI: 10.1038/srep36963] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/24/2016] [Indexed: 01/06/2023] Open
Abstract
Rapid cooling of liquids below a certain temperature range can result in a transition to glassy states. The traditional understanding of glasses includes their thermodynamic metastability with respect to crystals. However, here we present specific examples of interactions that eliminate the possibilities of crystalline and quasicrystalline phases, while creating mechanically stable amorphous glasses down to absolute zero temperature. We show that this can be accomplished by introducing a new ideal state of matter called a "perfect glass". A perfect glass represents a soft-interaction analog of the maximally random jammed (MRJ) packings of hard particles. These latter states can be regarded as the epitome of a glass since they are out of equilibrium, maximally disordered, hyperuniform, mechanically rigid with infinite bulk and shear moduli, and can never crystallize due to configuration-space trapping. Our model perfect glass utilizes two-, three-, and four-body soft interactions while simultaneously retaining the salient attributes of the MRJ state. These models constitute a theoretical proof of concept for perfect glasses and broaden our fundamental understanding of glass physics. A novel feature of equilibrium systems of identical particles interacting with the perfect-glass potential at positive temperature is that they have a non-relativistic speed of sound that is infinite.
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Affiliation(s)
- G. Zhang
- Department of Chemistry, Princeton University, Princeton, 08540, USA
| | - F. H. Stillinger
- Department of Chemistry, Princeton University, Princeton, 08540, USA
| | - S. Torquato
- Department of Chemistry, Department of Physics, Princeton Institute for the Science and Technology of Materials, and Program in Applied and Computational Mathematics, Princeton University, Princeton, 08540, USA
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35
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Musiani F, Giorgetti A. Protein Aggregation and Molecular Crowding: Perspectives From Multiscale Simulations. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 329:49-77. [PMID: 28109331 DOI: 10.1016/bs.ircmb.2016.08.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Cells are extremely crowded environments, thus the use of diluted salted aqueous solutions containing a single protein is too simplistic to mimic the real situation. Macromolecular crowding might affect protein structure, folding, shape, conformational stability, binding of small molecules, enzymatic activity, interactions with cognate biomolecules, and pathological aggregation. The latter phenomenon typically leads to the formation of amyloid fibrils that are linked to several lethal neurodegenerative diseases, but that can also play a functional role in certain organisms. The majority of molecular simulations performed before the last few years were conducted in diluted solutions and were restricted both in the timescales and in the system dimensions by the available computational resources. In recent years, several computational solutions were developed to get close to physiological conditions. In this review we summarize the main computational techniques used to tackle the issue of protein aggregation both in a diluted and in a crowded environment.
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Affiliation(s)
- F Musiani
- Laboratory of Bioinorganic Chemistry, University of Bologna, Bologna, Italy.
| | - A Giorgetti
- Applied Bioinformatics Group, University of Verona, Verona, Italy.
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36
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Li X, Murthy NS, Becker ML, Latour RA. Multiscale approach for the construction of equilibrated all-atom models of a poly(ethylene glycol)-based hydrogel. Biointerphases 2016; 11:021002. [PMID: 27013229 PMCID: PMC4808066 DOI: 10.1116/1.4944829] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/09/2016] [Accepted: 03/15/2016] [Indexed: 11/17/2022] Open
Abstract
A multiscale modeling approach is presented for the efficient construction of an equilibrated all-atom model of a cross-linked poly(ethylene glycol) (PEG)-based hydrogel using the all-atom polymer consistent force field (PCFF). The final equilibrated all-atom model was built with a systematic simulation toolset consisting of three consecutive parts: (1) building a global cross-linked PEG-chain network at experimentally determined cross-link density using an on-lattice Monte Carlo method based on the bond fluctuation model, (2) recovering the local molecular structure of the network by transitioning from the lattice model to an off-lattice coarse-grained (CG) model parameterized from PCFF, followed by equilibration using high performance molecular dynamics methods, and (3) recovering the atomistic structure of the network by reverse mapping from the equilibrated CG structure, hydrating the structure with explicitly represented water, followed by final equilibration using PCFF parameterization. The developed three-stage modeling approach has application to a wide range of other complex macromolecular hydrogel systems, including the integration of peptide, protein, and/or drug molecules as side-chains within the hydrogel network for the incorporation of bioactivity for tissue engineering, regenerative medicine, and drug delivery applications.
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Affiliation(s)
- Xianfeng Li
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634
| | - N Sanjeeva Murthy
- New Jersey Center for Biomaterials, Rutgers University, Piscataway, New Jersey 08854
| | - Matthew L Becker
- Departments of Polymer Science and Biomedical Engineering, The University of Akron, Akron, Ohio 44325
| | - Robert A Latour
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634
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37
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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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38
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Salerno KM, Agrawal A, Perahia D, Grest GS. Resolving Dynamic Properties of Polymers through Coarse-Grained Computational Studies. PHYSICAL REVIEW LETTERS 2016; 116:058302. [PMID: 26894738 DOI: 10.1103/physrevlett.116.058302] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Indexed: 06/05/2023]
Abstract
Coupled length and time scales determine the dynamic behavior of polymers and underlie their unique viscoelastic properties. To resolve the long-time dynamics it is imperative to determine which time and length scales must be correctly modeled. Here we probe the degree of coarse graining required to simultaneously retain significant atomistic details and access large length and time scales. The degree of coarse graining in turn sets the minimum length scale instrumental in defining polymer properties and dynamics. Using linear polyethylene as a model system, we probe how the coarse-graining scale affects the measured dynamics. Iterative Boltzmann inversion is used to derive coarse-grained potentials with 2-6 methylene groups per coarse-grained bead from a fully atomistic melt simulation. We show that atomistic detail is critical to capturing large-scale dynamics. Using these models we simulate polyethylene melts for times over 500 μs to study the viscoelastic properties of well-entangled polymer melts.
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Affiliation(s)
| | - Anupriya Agrawal
- Department of Mechanical Engineering and Materials Science, Washington University, St. Louis, Missouri 63130, USA
- Department of Chemistry, Clemson University, Clemson, South Carolina 29634, USA
| | - Dvora Perahia
- Department of Chemistry, Clemson University, Clemson, South Carolina 29634, USA
| | - Gary S Grest
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
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39
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Heinz H, Ramezani-Dakhel H. Simulations of inorganic-bioorganic interfaces to discover new materials: insights, comparisons to experiment, challenges, and opportunities. Chem Soc Rev 2016; 45:412-48. [PMID: 26750724 DOI: 10.1039/c5cs00890e] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Natural and man-made materials often rely on functional interfaces between inorganic and organic compounds. Examples include skeletal tissues and biominerals, drug delivery systems, catalysts, sensors, separation media, energy conversion devices, and polymer nanocomposites. Current laboratory techniques are limited to monitor and manipulate assembly on the 1 to 100 nm scale, time-consuming, and costly. Computational methods have become increasingly reliable to understand materials assembly and performance. This review explores the merit of simulations in comparison to experiment at the 1 to 100 nm scale, including connections to smaller length scales of quantum mechanics and larger length scales of coarse-grain models. First, current simulation methods, advances in the understanding of chemical bonding, in the development of force fields, and in the development of chemically realistic models are described. Then, the recognition mechanisms of biomolecules on nanostructured metals, semimetals, oxides, phosphates, carbonates, sulfides, and other inorganic materials are explained, including extensive comparisons between modeling and laboratory measurements. Depending on the substrate, the role of soft epitaxial binding mechanisms, ion pairing, hydrogen bonds, hydrophobic interactions, and conformation effects is described. Applications of the knowledge from simulation to predict binding of ligands and drug molecules to the inorganic surfaces, crystal growth and shape development, catalyst performance, as well as electrical properties at interfaces are examined. The quality of estimates from molecular dynamics and Monte Carlo simulations is validated in comparison to measurements and design rules described where available. The review further describes applications of simulation methods to polymer composite materials, surface modification of nanofillers, and interfacial interactions in building materials. The complexity of functional multiphase materials creates opportunities to further develop accurate force fields, including reactive force fields, and chemically realistic surface models, to enable materials discovery at a million times lower computational cost compared to quantum mechanical methods. The impact of modeling and simulation could further be increased by the advancement of a uniform simulation platform for organic and inorganic compounds across the periodic table and new simulation methods to evaluate system performance in silico.
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Affiliation(s)
- Hendrik Heinz
- Department of Chemical and Biological Engineering, University of Colorado-Boulder, Boulder, CO 80309, USA.
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40
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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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41
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Szklarczyk OM, Bieler NS, Hünenberger PH, van Gunsteren WF. Flexible Boundaries for Multiresolution Solvation: An Algorithm for Spatial Multiscaling in Molecular Dynamics Simulations. J Chem Theory Comput 2015; 11:5447-63. [PMID: 26574333 DOI: 10.1021/acs.jctc.5b00406] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An algorithm is proposed for performing molecular dynamics (MD) simulations of a biomolecular solute represented at atomistic resolution surrounded by a surface layer of atomistic fine-grained (FG) solvent molecules within a bulk represented by coarse-grained (CG) solvent beads. The method, called flexible boundaries for multiresolution solvation (FBMS), is based on: (i) a three-region layering of the solvent around the solute, involving an FG layer surrounded by a mixed FG-CG buffer layer, itself surrounded by a bulk CG region; (ii) a definition of the layer boundary that relies on an effective distance to the solute surface and is thus adapted to the shape of the solute as well as adjusts to its conformational changes. The effective surface distance is defined by inverse-nth power averaging over the distances to all non-hydrogen solute atoms, and the layering is enforced by means of half-harmonic distance restraints, attractive for the FG molecules and repulsive for the CG beads. A restraint-free region at intermediate distances enables the formation of the buffer layer, where the FG and CG solvents can mix freely. The algorithm is tested and validated using the GROMOS force field and the associated FG (SPC) and CG (polarizable CGW) water models. The test systems include pure-water systems, where one FG molecule plays the role of a solute, and a deca-alanine peptide with two widely different solute shapes considered, α-helical and fully extended. In particular, as the peptide unfolds, the number of FG molecules required to fill its close-range solvation layer increases, with the additional molecules being provided by the buffer layer. Further validation involves simulations of four proteins in multiresolution FG/CG mixtures. The resulting structural, energetic, and solvation properties are found to be similar to those observed in corresponding pure FG simulations.
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Affiliation(s)
- Oliwia M Szklarczyk
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology ETH , 8093 Zürich, Switzerland
| | - Noah S Bieler
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology ETH , 8093 Zürich, Switzerland
| | - Philippe H Hünenberger
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology ETH , 8093 Zürich, Switzerland
| | - Wilfred F van Gunsteren
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology ETH , 8093 Zürich, Switzerland
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42
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Pluhackova K, Böckmann RA. Biomembranes in atomistic and coarse-grained simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015. [PMID: 26194872 DOI: 10.1088/0953-8984/27/32/323103] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The architecture of biological membranes is tightly coupled to the localization, organization, and function of membrane proteins. The organelle-specific distribution of lipids allows for the formation of functional microdomains (also called rafts) that facilitate the segregation and aggregation of membrane proteins and thus shape their function. Molecular dynamics simulations enable to directly access the formation, structure, and dynamics of membrane microdomains at the molecular scale and the specific interactions among lipids and proteins on timescales from picoseconds to microseconds. This review focuses on the latest developments of biomembrane force fields for both atomistic and coarse-grained molecular dynamics (MD) simulations, and the different levels of coarsening of biomolecular structures. It also briefly introduces scale-bridging methods applicable to biomembrane studies, and highlights selected recent applications.
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Affiliation(s)
- Kristyna Pluhackova
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
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43
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Naômé A, Laaksonen A, Vercauteren DP. A Coarse-Grained Simulation Study of the Structures, Energetics, and Dynamics of Linear and Circular DNA with Its Ions. J Chem Theory Comput 2015; 11:2813-26. [DOI: 10.1021/acs.jctc.5b00113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aymeric Naômé
- Laboratoire
de Physico-Chimie Informatique, Unité de Chimie Physique Théorique
et Structurale, University of Namur, 5000 Namur, Belgium
- Namur Medicine & Drug Innovation Center (NAMEDIC), University of Namur, 5000 Namur, Belgium
- Division
of Physical Chemistry, Department of Materials and Environmental Chemistry,
Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden
- Science for Life
Laboratory, 17121 Solna, Sweden
| | - Aatto Laaksonen
- Division
of Physical Chemistry, Department of Materials and Environmental Chemistry,
Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden
- Science for Life
Laboratory, 17121 Solna, Sweden
- Stellenbosch
Institute of Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, 7600 Stellenbosch, South Africa
| | - Daniel P. Vercauteren
- Laboratoire
de Physico-Chimie Informatique, Unité de Chimie Physique Théorique
et Structurale, University of Namur, 5000 Namur, Belgium
- Namur Medicine & Drug Innovation Center (NAMEDIC), University of Namur, 5000 Namur, Belgium
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Sethuraman V, Nguyen BH, Ganesan V. Coarse-graining in simulations of multicomponent polymer systems. J Chem Phys 2014; 141:244904. [DOI: 10.1063/1.4904390] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Bryan H. Nguyen
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
| | - Venkat Ganesan
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
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45
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Bevc S, Junghans C, Praprotnik M. STOCK: Structure mapper and online coarse-graining kit for molecular simulations. J Comput Chem 2014; 36:467-77. [DOI: 10.1002/jcc.23806] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 11/14/2014] [Accepted: 11/19/2014] [Indexed: 01/18/2023]
Affiliation(s)
- Staš Bevc
- Laboratory for Molecular Modeling; National Institute of Chemistry; Hajdrihova 19 Ljubljana SI-1001 Slovenia
| | - Christoph Junghans
- Computer, Computational, and Statistical Sciences Division; Los Alamos National Laboratory; Los Alamos New Mexico 87545
| | - Matej Praprotnik
- Laboratory for Molecular Modeling; National Institute of Chemistry; Hajdrihova 19 Ljubljana SI-1001 Slovenia
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46
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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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47
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Neyertz S, Brown D. The effect of structural isomerism on carbon dioxide sorption and plasticization at the interface of a glassy polymer membrane. J Memb Sci 2014. [DOI: 10.1016/j.memsci.2014.03.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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48
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Wassenaar TA, Pluhackova K, Böckmann RA, Marrink SJ, Tieleman DP. Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models. J Chem Theory Comput 2014; 10:676-90. [PMID: 26580045 DOI: 10.1021/ct400617g] [Citation(s) in RCA: 449] [Impact Index Per Article: 44.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The conversion of coarse-grained to atomistic models is an important step in obtaining insight about atomistic scale processes from coarse-grained simulations. For this process, called backmapping or reverse transformation, several tools are available, but these commonly require libraries of molecule fragments or they are linked to a specific software package. In addition, the methods are usually restricted to specific molecules and to a specific force field. Here, we present an alternative method, consisting of geometric projection and subsequent force-field based relaxation. This method is designed to be simple and flexible, and offers a generic solution for resolution transformation. For simple systems, the conversion only requires a list of particle correspondences on the two levels of resolution. For special cases, such as nondefault protonation states of amino acids and virtual sites, a target particle list can be specified. The mapping uses simple building blocks, which list the particles on the different levels of resolution. For conversion to higher resolution, the initial model is relaxed with several short cycles of energy minimization and position-restrained MD. The reconstruction of an atomistic backbone from a coarse-grained model is done using a new dedicated algorithm. The method is generic and can be used to map between any two particle based representations, provided that a mapping can be written. The focus of this work is on the coarse-grained MARTINI force field, for which mapping definitions are written to allow conversion to and from the higher-resolution force fields GROMOS, CHARMM, and AMBER, and to and from a simplified three-bead lipid model. Together, these offer the possibility to simulate mesoscopic membrane structures, to be transformed to MARTINI and subsequently to an atomistic model for investigation of detailed interactions. The method was tested on a set of systems ranging from a simple, single-component bilayer to a large protein-membrane-solvent complex. The results demonstrate the efficiency and the efficacy of the new approach.
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Affiliation(s)
- Tsjerk A Wassenaar
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW , Calgary, Alberta, Canada T2N 1N4.,Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands.,Computational Biology, Department of Biology, University of Erlangen-Nürnberg , Staudtstr. 5, 91058 Erlangen, Germany
| | - Kristyna Pluhackova
- Computational Biology, Department of Biology, University of Erlangen-Nürnberg , Staudtstr. 5, 91058 Erlangen, Germany
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, University of Erlangen-Nürnberg , Staudtstr. 5, 91058 Erlangen, Germany
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - D Peter Tieleman
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW , Calgary, Alberta, Canada T2N 1N4
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50
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Neyertz S, Brown D. Molecular Dynamics Study of Carbon Dioxide Sorption and Plasticization at the Interface of a Glassy Polymer Membrane. Macromolecules 2013. [DOI: 10.1021/ma302073u] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Sylvie Neyertz
- LEPMI (LMOPS), UMR 5279 CNRS, Grenoble
INP, University
of Savoie, University J. Fourier, Bât.
IUT, Savoie Technolac, 73376 Le Bourget du Lac Cedex, France
| | - David Brown
- LEPMI (LMOPS), UMR 5279 CNRS, Grenoble
INP, University
of Savoie, University J. Fourier, Bât.
IUT, Savoie Technolac, 73376 Le Bourget du Lac Cedex, France
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