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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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Reisjalali M, Manurung R, Carbone P, Troisi A. Development of hybrid coarse-grained atomistic models for rapid assessment of local structuring of polymeric semiconductors. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2022; 7:294-305. [PMID: 35646391 PMCID: PMC9074845 DOI: 10.1039/d1me00165e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/06/2022] [Indexed: 05/05/2023]
Abstract
Decades of work in the field of computational study of semiconducting polymers using atomistic models illustrate the challenges of generating equilibrated models for this class of materials. While adopting a coarse-grained model can be helpful, the process of developing a suitable model is particularly non-trivial and time-consuming for semiconducting polymers due to a large number of different interactions with some having an anisotropic nature. This work introduces a procedure for the rapid generation of a hybrid model for semiconducting polymers where atoms of secondary importance (those in the alkyl side chains) are transformed into coarse-grained beads to reduce the computational cost of generating an equilibrated structure. The parameters are determined from easy-to-equilibrate simulations of very short oligomers and the model is constructed to enable a very simple back-mapping procedure to reconstruct geometries with atomistic resolution. The model is illustrated for three related polymers containing DPP (diketopyrrolopyrrole) to evaluate the transferability of the potential across different families of polymers. The accuracy of the model, determined by comparison with the results of fully equilibrated simulations of the same material before and after back-mapping, is fully satisfactory for two out of the three cases considered. We noticed that accuracy can be determined very early in the workflow so that it is easy to assess when the deployment of this method is advantageous. The hybrid representation can be used to evaluate directly the electronic properties of structures sampled by the simulations.
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Affiliation(s)
- Maryam Reisjalali
- Department of Chemistry, University of Liverpool Crown St L69 7ZD Liverpool UK
| | - Rex Manurung
- Department of Chemistry, University of Liverpool Crown St L69 7ZD Liverpool UK
| | - Paola Carbone
- Department of Chemical Engineering and Analytical Science Oxford Road M13 9PL Manchester UK
| | - Alessandro Troisi
- Department of Chemistry, University of Liverpool Crown St L69 7ZD Liverpool UK
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3
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Co NT, Li MS, Krupa P. Computational Models for the Study of Protein Aggregation. Methods Mol Biol 2022; 2340:51-78. [PMID: 35167070 DOI: 10.1007/978-1-0716-1546-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein aggregation has been studied by many groups around the world for many years because it can be the cause of a number of neurodegenerative diseases that have no effective treatment. Obtaining the structure of related fibrils and toxic oligomers, as well as describing the pathways and main factors that govern the self-organization process, is of paramount importance, but it is also very difficult. To solve this problem, experimental and computational methods are often combined to get the most out of each method. The effectiveness of the computational approach largely depends on the construction of a reasonable molecular model. Here we discussed different versions of the four most popular all-atom force fields AMBER, CHARMM, GROMOS, and OPLS, which have been developed for folded and intrinsically disordered proteins, or both. Continuous and discrete coarse-grained models, which were mainly used to study the kinetics of aggregation, are also summarized.
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Affiliation(s)
- Nguyen Truong Co
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
- Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam
| | - Pawel Krupa
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
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4
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Dhamankar S, Webb MA. Chemically specific coarse‐graining of polymers: Methods and prospects. JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1002/pol.20210555] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Satyen Dhamankar
- Department of Chemical and Biological Engineering Princeton University Princeton New Jersey USA
| | - Michael A. Webb
- Department of Chemical and Biological Engineering Princeton University Princeton New Jersey USA
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5
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Sadeghi M, Noé F. Hydrodynamic coupling for particle-based solvent-free membrane models. J Chem Phys 2021; 155:114108. [PMID: 34551532 DOI: 10.1063/5.0061623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The great challenge with biological membrane systems is the wide range of scales involved, from nanometers and picoseconds for individual lipids to the micrometers and beyond millisecond for cellular signaling processes. While solvent-free coarse-grained membrane models are convenient for large-scale simulations and promising to provide insight into slow processes involving membranes, these models usually have unrealistic kinetics. One major obstacle is the lack of an equally convenient way of introducing hydrodynamic coupling without significantly increasing the computational cost of the model. To address this, we introduce a framework based on anisotropic Langevin dynamics, for which major in-plane and out-of-plane hydrodynamic effects are modeled via friction and diffusion tensors from analytical or semi-analytical solutions to Stokes hydrodynamic equations. Using this framework, in conjunction with our recently developed membrane model, we obtain accurate dispersion relations for planar membrane patches, both free-standing and in the vicinity of a wall. We briefly discuss how non-equilibrium dynamics is affected by hydrodynamic interactions. We also measure the surface viscosity of the model membrane and discuss the affecting dissipative mechanisms.
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Affiliation(s)
- Mohsen Sadeghi
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
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6
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Yang XD, Chen W, Ren Y, Chu LY. Exploring the structural transition mechanisms of a pair of poly( N-isopropylacrylamide) chains in aqueous solution through coarse-grained molecular simulations coupled with metadynamics. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1881086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Xue-Dan Yang
- School of Chemical Engineering, Sichuan University, Chengdu, Sichuan, People's Republic of China
- State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, Sichuan, People's Republic of China
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Wei Chen
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, Liaoning, People's Republic of China
| | - Ying Ren
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
- Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Liang-Yin Chu
- School of Chemical Engineering, Sichuan University, Chengdu, Sichuan, People's Republic of China
- State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, Sichuan, People's Republic of China
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7
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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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8
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Li Q, Guo Y, Tong J, He H, Zhang X, Huo F. Development of a coarse-grained force field model of polymeric 1-vinyl-3-ethylimidazolium tetrafluoroborate ionic liquids. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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9
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Large-scale simulation of biomembranes incorporating realistic kinetics into coarse-grained models. Nat Commun 2020; 11:2951. [PMID: 32528158 PMCID: PMC7289815 DOI: 10.1038/s41467-020-16424-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 04/28/2020] [Indexed: 12/12/2022] Open
Abstract
Biomembranes are two-dimensional assemblies of phospholipids that are only a few nanometres thick, but form micrometre-sized structures vital to cellular function. Explicit molecular modelling of biologically relevant membrane systems is computationally expensive due to the large number of solvent particles and slow membrane kinetics. Coarse-grained solvent-free membrane models offer efficient sampling but sacrifice realistic kinetics, thereby limiting the ability to predict pathways and mechanisms of membrane processes. Here, we present a framework for integrating coarse-grained membrane models with continuum-based hydrodynamics. This framework facilitates efficient simulation of large biomembrane systems with large timesteps, while achieving realistic equilibrium and non-equilibrium kinetics. It helps to bridge between the nanometer/nanosecond spatiotemporal resolutions of coarse-grained models and biologically relevant time- and lengthscales. As a demonstration, we investigate fluctuations of red blood cells, with varying cytoplasmic viscosities, in 150-milliseconds-long trajectories, and compare kinetic properties against single-cell experimental observations.
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Ortiz de Solorzano I, Bejagam KK, An Y, Singh SK, Deshmukh SA. Solvation dynamics of N-substituted acrylamide polymers and the importance for phase transition behavior. SOFT MATTER 2020; 16:1582-1593. [PMID: 31951239 DOI: 10.1039/c9sm01798d] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Functional groups present in thermo-responsive polymers are known to play an important role in aqueous solutions by manifesting their coil-to-globule conformational transition in a specific temperature range. Understanding the role of these functional groups and their interactions with water is of great interest as it may allow us to control both the nature and temperature of this coil-to-globule transition. In this work, polyacrylamide (PAAm), poly(N-isopropylacrylamide) (PNIPAm), and poly(N-isopropylmethacrylamide) (PNIPMAm) solvated in water are studied with the goal of discovering the structure of the solvent and its interaction with these polymers in determining the polymer conformations. Specifically, all-atom molecular dynamics (MD) simulations were performed on polymer chains with 30 monomer units (30-mers) at 295 K, 310 K and 320 K, which is below and above the lower critical solution temperature (LCST) of PNIPAm (LCST = 305 K) and PNIPMAm (LCST = 315 K), respectively. The MD simulation trajectories suggest that changes in the functional groups in the backbone and side-chains alter the water solvation shell around the polymer. This results in a change in the residence time probability and hydrogen bond characteristics of water at simulated temperatures. Specifically, water molecules reside for longer times near PAAm (no LCST) and PNIPMAm (LCST = 315 K) chains as compared to PNIPAm. This might be one of the possible causes for the higher LCST of PNIPMAm as compared to that of PNIPAm. These results can guide experimentalists and theoreticians to design new polymer structures with tailor-made LCST transitions while controlling the water solvation shell around the functional group.
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Affiliation(s)
- Isabel Ortiz de Solorzano
- Department of Chemical Engineering, Aragon Institute of Nanoscience (INA), University of Zaragoza, Campus Río Ebro-Edificio I+D, C/Poeta Mariano Esquillor S/N, 50018-Zaragoza, Spain
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11
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Pérez-Ramírez HA, Odriozola G. A coil-to-globule transition capable coarse-grained model for poly(N-isopropylacrylamide). Phys Chem Chem Phys 2020; 22:17913-17921. [PMID: 32744283 DOI: 10.1039/d0cp03101a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We present a model for mesoscopic molecular dynamics simulations of poly(N-isopropyl-acrylamide) (pNIPAM).
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Affiliation(s)
- H. A. Pérez-Ramírez
- Área de Física de Procesos Irreversibles
- División de Ciencias Básicas e Ingeniería
- Universidad Autónoma Metropolitana-Azcapotzalco
- 02200 Ciudad de México
- Mexico
| | - G. Odriozola
- Área de Física de Procesos Irreversibles
- División de Ciencias Básicas e Ingeniería
- Universidad Autónoma Metropolitana-Azcapotzalco
- 02200 Ciudad de México
- Mexico
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12
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Bejagam KK, An Y, Singh S, Deshmukh SA. Machine-Learning Enabled New Insights into the Coil-to-Globule Transition of Thermosensitive Polymers Using a Coarse-Grained Model. J Phys Chem Lett 2018; 9:6480-6488. [PMID: 30372083 DOI: 10.1021/acs.jpclett.8b02956] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We present a computational framework that integrates coarse-grained (CG) molecular dynamics (MD) simulations and a data-driven machine-learning (ML) method to gain insights into the conformations of polymers in solutions. We employ this framework to study conformational transition of a model thermosensitive polymer, poly( N-isopropylacrylamide) (PNIPAM). Here, we have developed the first of its kind, a temperature-independent CG model of PNIPAM that can accurately predict its experimental lower critical solution temperature (LCST) while retaining the tacticity in the presence of an explicit water model. The CG model was extensively validated by performing CG MD simulations with different initial conformations, varying the radius of gyration of chain, the chain length, and the angle between the adjacent monomers of the initial configuration of PNIPAM (total simulation time = 90 μs). Moreover, for the first time, we utilize the nonmetric multidimensional scaling (NMDS) method, a data-driven ML approach, to gain further insights into the mechanisms and pathways of this coil-to-globule transition by analyzing CG MD simulation trajectories. NMDS analysis provides entirely new insights and shows multiple metastable states of PNIPAM during its coil-to-globule transition above the LCST.
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Affiliation(s)
- Karteek K Bejagam
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Yaxin An
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Samrendra Singh
- CNH Industrial , Burr Ridge , Illinois 60527 , United States
| | - Sanket A Deshmukh
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
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