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Meinel MK, Müller-Plathe F. Roughness Volumes: An Improved RoughMob Concept for Predicting the Increase of Molecular Mobility upon Coarse-Graining. J Phys Chem B 2022; 126:3737-3747. [PMID: 35559647 DOI: 10.1021/acs.jpcb.2c00944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reduced number of degrees of freedom in a coarse-grained molecular model compared to its parent atomistic model not only makes it possible to simulate larger systems for longer time scales but also results in an artificial mobility increase. The RoughMob method [Meinel, M. K. and Müller-Plathe, F. J. Chem. Theory Comput. 2020, 16, 1411.] linked the acceleration factor of the dynamics to the loss of geometric information upon coarse-graining. Our hypothesis is that coarse-graining a multiatom molecule or group into a single spherical bead smooths the molecular surface and, thus, leads to reduced intermolecular friction. A key parameter is the molecular roughness difference, which is calculated via a numerical comparison of the molecular surfaces of both the atomistic and coarse-grained models. Augmenting the RoughMob method, we add the concept of the region where the roughness acts. This information is contained in four so-called roughness volumes. For 17 systems of homogeneous hydrocarbon fluids, simple one-bead coarse-grained models are derived by the structure-based iterative Boltzmann inversion. They include 13 different homogeneous aliphatic and aromatic molecules and two different mapping schemes. We present a simple way to correlate the roughness volumes to the acceleration factor. The resulting relation is able to a priori predict the acceleration factors for an extended size and shape range of hydrocarbon molecules, with different mapping schemes and different densities.
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Affiliation(s)
- Melissa K Meinel
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Profile Area Thermofluids and Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Strasse 8, D-64287 Darmstadt, Germany
| | - Florian Müller-Plathe
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Profile Area Thermofluids and Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Strasse 8, D-64287 Darmstadt, Germany
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2
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Lickert B, Stock G. Modeling non-Markovian data using Markov state and Langevin models. J Chem Phys 2020; 153:244112. [DOI: 10.1063/5.0031979] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Benjamin Lickert
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
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Golmohammadi N, Boland-Hemmat M, Barahmand S, Eslami H. Coarse-grained molecular dynamics simulations of poly(ethylene terephthalate). J Chem Phys 2020; 152:114901. [PMID: 32199431 DOI: 10.1063/1.5145142] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We have constructed efficient coarse-grained (CG) models of poly(ethylene terephthalate) (PET), using three mapping schemes, in which a repeat unit is lumped into either three or four beads. The CG potentials are parameterized to reproduce target distributions of an underlying accurate atomistic model [H. Eslami and F. Müller-Plathe, Macromolecules 42, 8241-8250 (2009)]. The CG simulations allow equilibration of long PET chains at all length scales. The CG results on the density of PET in melt and glassy states, chain dimension, local packing, and structure factor are in good agreement with experiment. We have established a link between the glass transition temperature and the local movements including conformational transitions and mean-square displacements of chain segments. Temperature transferabilities of the three proposed models were studied by comparing CG results on the static and thermodynamic properties of a polymer with atomistic and experimental findings. One of the three CG models has a good degree of transferability, following all inter- and intra-structural rearrangements of the atomistic model, over a broad range of temperature. Furthermore, as a distinct point of strength of CG, over atomistic, simulations, we have examined the dynamics of PET long chains, consisting of 100 repeat units, over a regime where entanglements dominate the dynamics. Performing long-time (550 ns) CG simulations, we have noticed the signature of a crossover from Rouse to reptation dynamics. However, a clear separation between the Rouse and the reptation dynamics needs much longer time simulations, confirming the experimental findings that the crossover to full reptation dynamics is very protracted.
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Affiliation(s)
- Nazila Golmohammadi
- Department of Chemistry, College of Sciences, Persian Gulf University, Boushehr 75168, Iran
| | | | - Sanam Barahmand
- Department of Chemistry, College of Sciences, Persian Gulf University, Boushehr 75168, Iran
| | - Hossein Eslami
- Department of Chemistry, College of Sciences, Persian Gulf University, Boushehr 75168, Iran
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4
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Meinel MK, Müller-Plathe F. Loss of Molecular Roughness upon Coarse-Graining Predicts the Artificially Accelerated Mobility of Coarse-Grained Molecular Simulation Models. J Chem Theory Comput 2020; 16:1411-1419. [DOI: 10.1021/acs.jctc.9b00943] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Melissa K. Meinel
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Profile Area Thermofluids and Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Strasse 8, D-64287 Darmstadt, Germany
| | - Florian Müller-Plathe
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Profile Area Thermofluids and Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Strasse 8, D-64287 Darmstadt, Germany
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5
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Deichmann G, van der Vegt NFA. Bottom-up approach to represent dynamic properties in coarse-grained molecular simulations. J Chem Phys 2019; 149:244114. [PMID: 30599732 DOI: 10.1063/1.5064369] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Several molecular coarse-graining methods have been proposed in recent years to derive chemical- and state-point transferable force fields. While these force fields describe structural and thermodynamic properties in good agreement with fine-grained models and experiments, dynamic properties are usually overestimated. Herein, we examine if the long-time dynamic properties of molecular coarse-grained (CG) systems can be correctly represented by employing a dissipative particle dynamics (DPD) thermostat, which is "bottom-up informed" by means of a variant of the Markovian Mori-Zwanzig (MZ) DPD coarse-graining method. We report single-site and multiple-site CG models for a monomer, dimer, and 24mer based on 2,2-dimethyl propane as a chemical repeat unit and report data obtained from MZ-DPD simulations of liquids, polymer solutions, and polymer melts. We find that despite incomplete time scale separation of the molecular CG model, MZ-DPD achieves quantitative accuracy in predicting diffusive dynamics in single-component liquids and polymer solutions (24mers in a dimer solvent). We also find that MZ-DPD simulations of molecular penetrant diffusion in polymer networks do not reach quantitative agreement with the fine-grained model. Modeling diffusion governed by the activated barrier crossing of small molecular penetrants in these dense systems requires an accurate description of energy barriers, presumably combined with the treatment of memory effects. The use of a MZ-DPD thermostat extends the scope and applicability of molecular CG models for multicomponent systems where a correct description of the relative diffusion rates of the different components is important.
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Affiliation(s)
- Gregor Deichmann
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
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6
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Di Pasquale N, Hudson T, Icardi M. Systematic derivation of hybrid coarse-grained models. Phys Rev E 2019; 99:013303. [PMID: 30780282 DOI: 10.1103/physreve.99.013303] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Indexed: 06/09/2023]
Abstract
Molecular dynamics represents a key enabling technology for applications ranging from biology to the development of new materials. However, many real-world applications remain inaccessible to fully resolved simulations due to their unsustainable computational costs and must therefore rely on semiempirical coarse-grained models. Significant efforts have been devoted in the last decade towards improving the predictivity of these coarse-grained models and providing a rigorous justification of their use, through a combination of theoretical studies and data-driven approaches. One of the most promising research efforts is the (re)discovery of the Mori-Zwanzig projection as a generic, yet systematic, theoretical tool for deriving coarse-grained models. Despite its clean mathematical formulation and generality, there are still many open questions about its applicability and assumptions. In this work, we propose a detailed derivation of a hybrid multiscale system, generalizing and further investigating the approach developed in Español [Europhys. Lett. 88, 40008 (2009)10.1209/0295-5075/88/40008]. Issues such as the general coexistence of atoms (fully resolved degrees of freedom) and beads (larger coarse-grained units), the role of the fine-to-coarse mapping chosen, and the approximation of effective potentials are discussed. The theoretical discussion is supported by numerical simulations of a monodimensional nonlinear periodic benchmark system with an open-source parallel Julia code, easily extensible to arbitrary potential models and fine-to-coarse mapping functions. The results presented highlight the importance of introducing, in the macroscopic model, nonconstant fluctuating and dissipative terms, given by the Mori-Zwanzig approach, to correctly reproduce the reference fine-grained results, without requiring ad hoc calibration of interaction potentials and thermostats.
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Affiliation(s)
- Nicodemo Di Pasquale
- Department of Mathematics, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Thomas Hudson
- Warwick Mathematics Institute, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Matteo Icardi
- School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom
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7
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Ramos J, Vega J, Martínez-Salazar J. Predicting experimental results for polyethylene by computer simulation. Eur Polym J 2018. [DOI: 10.1016/j.eurpolymj.2017.12.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Takahashi KZ, Nishimura R, Yamato N, Yasuoka K, Masubuchi Y. Onset of static and dynamic universality among molecular models of polymers. Sci Rep 2017; 7:12379. [PMID: 28959052 PMCID: PMC5620073 DOI: 10.1038/s41598-017-08501-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/12/2017] [Indexed: 12/03/2022] Open
Abstract
A quantitatively accurate prediction of properties for entangled polymers is a long-standing challenge that must be addressed to enable efficient development of these materials. The complex nature of polymers is the fundamental origin of this challenge. Specifically, the chemistry, structure, and dynamics at the atomistic scale affect properties at the meso and macro scales. Therefore, quantitative predictions must start from atomistic molecular dynamics (AMD) simulations. Combined use of atomistic and coarse-grained (CG) models is a promising approach to estimate long-timescale behavior of entangled polymers. However, a systematic coarse-graining is still to be done for bridging the gap of length and time scales while retaining atomistic characteristics. Here we examine the gaps among models, using a generic mapping scheme based on power laws that are closely related to universality in polymer structure and dynamics. The scheme reveals the characteristic length and time for the onset of universality between the vastly different scales of an atomistic model of polyethylene and the bead-spring Kremer-Grest (KG) model. The mapping between CG model of polystyrene and the KG model demonstrates the fast onset of universality, and polymer dynamics up to the subsecond time scale are observed. Thus, quantitatively traceable timescales of polymer MD simulations can be significantly increased.
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Affiliation(s)
- Kazuaki Z Takahashi
- Multi-scale Soft-matter Simulation Team, Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8568, Japan.
- Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan.
| | - Ryuto Nishimura
- Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Nobuyoshi Yamato
- Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Kenji Yasuoka
- Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Yuichi Masubuchi
- National Composite Center, Nagoya University, Furocho, Chikusa, Nagoya, 464-8630, Japan
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Di Pasquale N, Carbone P. Local and global dynamics of multi-resolved polymer chains: Effects of the interactions atoms-beads on the dynamic of the chains. J Chem Phys 2017; 146:084905. [PMID: 28249431 DOI: 10.1063/1.4976645] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- N. Di Pasquale
- School of Chemistry, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - P. Carbone
- School of Chemical Engineering and Analytical Science, The University of Manchester, Manchester M13 9PL, United Kingdom
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10
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Xie Z, Chai D, Wang Y, Tan H. Directly Modifying the Nonbonded Potential Based on the Standard Iterative Boltzmann Inversion Method for Coarse-Grained Force Fields. J Phys Chem B 2016; 120:11834-11844. [PMID: 27766876 DOI: 10.1021/acs.jpcb.6b06457] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Effective potentials are of great importance for coarse-grained (CG) simulations, which can be obtained by the structure-based iterative Boltzmann inversion (IBI) method. However, the standard IBI method is incapable of maintaining the mechanical and thermodynamic properties of the CG model in agreement with those of the all-atom model. Unlike the existing techniques, such as introducing friction force as the dissipative force to reduce the superatom motion while keeping the conservative force arising from the CG potential intact, we directly modified the standard IBI nonbonded potential by adding an empirical function. According to an analysis of the dissipative particle dynamics, the additional function did compensate for the friction reduction of the standard IBI CG model. In this work, the thermal fluctuation information from the nonbonded radial distribution function was incorporated into the additional empirical function. As an illustration of the new CG force fields, we presented simulations of the stress-strain relation and thermodynamic properties in terms of cis-polyisoprene and compared the statistical structure information of the superatoms with those of the IBI CG model and the all-atom model. It should be emphasized that the additional empirical function contributed to compensating for the friction reduction, irrespective of the functional form it took. In this sense, the proposed method was easily operable.
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Affiliation(s)
- Zhimin Xie
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environment, Center for Composite Materials and Structures, Harbin Institute of Technology , Harbin 150001, People's Republic of China
| | - Dongliang Chai
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environment, Center for Composite Materials and Structures, Harbin Institute of Technology , Harbin 150001, People's Republic of China
| | - Youshan Wang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environment, Center for Composite Materials and Structures, Harbin Institute of Technology , Harbin 150001, People's Republic of China
| | - Huifeng Tan
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environment, Center for Composite Materials and Structures, Harbin Institute of Technology , Harbin 150001, People's Republic of China
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11
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Sridhar A, Kumar A, Dasmahapatra AK. Multi-scale molecular dynamics study of cholera pentamer binding to a GM1-phospholipid membrane. J Mol Graph Model 2016; 68:236-251. [PMID: 27474868 DOI: 10.1016/j.jmgm.2016.07.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/15/2016] [Accepted: 07/21/2016] [Indexed: 10/21/2022]
Abstract
The AB5 type toxin produced by the Vibrio cholerae bacterium is the causative agent of the cholera disease. The cholera toxin (CT) has been shown to bind specifically to GM1 glycolipids on the membrane surface. This binding of CT to the membrane is the initial step in its endocytosis and has been postulated to cause significant disruption to the membrane structure. In this work, we have carried out a combination of coarse-grain and atomistic simulations to study the binding of CT to a membrane modelled as an asymmetrical GM1-DPPC bilayer. Simulation results indicate that the toxin binds to the membrane through only three of its five B subunits, in effect resulting in a tilted bound configuration. Additionally, the binding of the CT can increase the area per lipid of GM1 leaflet, which in turn can cause the membrane regions interacting with the bound subunits to experience significant bilayer thinning and lipid tail disorder across both the leaflets.
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Affiliation(s)
- Akshay Sridhar
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati-781039, Assam, India
| | - Amit Kumar
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati-781039, Assam, India.
| | - Ashok Kumar Dasmahapatra
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati-781039, Assam, India.
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12
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Lu K, Maranas JK, Milner ST. Ion-mediated charge transport in ionomeric electrolytes. SOFT MATTER 2016; 12:3943-3954. [PMID: 27019986 DOI: 10.1039/c6sm00524a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Ionomers, or single-ion conductors, serve as a model system to study ion transport in polymeric systems. Conductivity is a system property that depends on the net charge transport in the system. The mechanism through which ions are transported can dramatically change the contribution of an ion's self-motion (i.e. diffusion coefficient) to the conductivity of the system. For example, positive and negative ions diffusing as a pair have no net contribution to conductivity. In a coarse-grained molecular dynamics simulation of sodium-neutralized poly(PEO-co-sulfoisophthalate), we show that ion transport is mediated through consecutive coordination with ion pairs and higher order clusters due to the high density of ions. This transport mechanism is highly efficient and shows evidence of cation relaying. We show that larger ion aggregates can serve as ion-conducting paths for positive charges, and demonstrate how a highly ordered ion aggregate network can improve conductivity by enhancing correlated ion transport.
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Affiliation(s)
- Keran Lu
- Pennsylvania State University, Department of Chemical Engineering, 120 Fenske Laboratory, University Park, PA 16802, USA.
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13
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Gowers RJ, Carbone P. A multiscale approach to model hydrogen bonding: The case of polyamide. J Chem Phys 2015; 142:224907. [PMID: 26071731 DOI: 10.1063/1.4922445] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We present a simple multiscale model for polymer chains in which it is possible to selectively remove degrees of freedom. The model integrates all-atom and coarse-grained potentials in a simple and systematic way and allows a fast sampling of the complex conformational energy surface typical of polymers whilst maintaining a realistic description of selected atomistic interactions. In particular, we show that it is possible to simultaneously reproduce the structure of highly directional non-bonded interactions such as hydrogen bonds and efficiently explore the large number of conformations accessible to the polymer chain. We apply the method to a melt of polyamide removing from the model only the degrees of freedom associated to the aliphatic segments and keeping at atomistic resolution the amide groups involved in the formation of the hydrogen bonds. The results show that the multiscale model produces structural properties that are comparable with the fully atomistic model despite being five times faster to simulate.
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Affiliation(s)
- Richard J Gowers
- School of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Paola Carbone
- School of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, United Kingdom
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14
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Sridhar A, Srikanth B, Kumar A, Dasmahapatra AK. Coarse-grain molecular dynamics study of fullerene transport across a cell membrane. J Chem Phys 2015; 143:024907. [DOI: 10.1063/1.4926668] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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15
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Aydin F, Ludford P, Dutt M. Phase segregation in bio-inspired multi-component vesicles encompassing double tail phospholipid species. SOFT MATTER 2014; 10:6096-6108. [PMID: 25008809 DOI: 10.1039/c4sm00998c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Our aim is to investigate the phase segregation and the structure of multi-component bio-inspired phospholipid vesicles via dissipative particle dynamics. The chemical distinction in the phospholipid species arises due to different head and tail group moieties, and molecular stiffness of the hydrocarbon tails. The individual amphiphilic phospholipid molecular species are represented by a hydrophilic head group and two hydrophobic tails. The distinct chemical nature of the moieties is modeled effectively via soft repulsive interaction parameters, and the molecular rigidity is tuned via suitable three-body potential constants. We demonstrate the formation of a stable hybrid vesicle through the self-assembly of the amphiphilic phospholipid molecules in the presence of a hydrophilic solvent. We investigate and characterize the phase segregation and the structure of the binary vesicles for different phospholipid mixtures. Our results demonstrate macroscopic phase separation for phospholipid mixtures composed of species with different hydrocarbon tail groups. We also investigate the relationship between the phase segregation and thermodynamic variables such as interfacial line tension and surface tension, and obtain correspondence between existing theory and experiments, and our simulation results. We report variations in the molecular chain stiffness to have negligible contributions to the phase segregation in the mixed bilayer, and to demonstrate shape transformations of the hybrid vesicle. Our results can be used to design novel bio-inspired hybrid vehicles for potential applications in biomedicine, sensing, imaging and sustainability.
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Affiliation(s)
- Fikret Aydin
- Department of Chemical Engineering, Rutgers The State University of New Jersey, Piscataway, NJ 08854, USA.
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16
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Abstract
By focusing on essential features, while averaging over less important details, coarse-grained (CG) models provide significant computational and conceptual advantages with respect to more detailed models. Consequently, despite dramatic advances in computational methodologies and resources, CG models enjoy surging popularity and are becoming increasingly equal partners to atomically detailed models. This perspective surveys the rapidly developing landscape of CG models for biomolecular systems. In particular, this review seeks to provide a balanced, coherent, and unified presentation of several distinct approaches for developing CG models, including top-down, network-based, native-centric, knowledge-based, and bottom-up modeling strategies. The review summarizes their basic philosophies, theoretical foundations, typical applications, and recent developments. Additionally, the review identifies fundamental inter-relationships among the diverse approaches and discusses outstanding challenges in the field. When carefully applied and assessed, current CG models provide highly efficient means for investigating the biological consequences of basic physicochemical principles. Moreover, rigorous bottom-up approaches hold great promise for further improving the accuracy and scope of CG models for biomolecular systems.
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Affiliation(s)
- W G Noid
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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17
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Lu K, Rudzinski JF, Noid WG, Milner ST, Maranas JK. Scaling behavior and local structure of ion aggregates in single-ion conductors. SOFT MATTER 2014; 10:978-989. [PMID: 24983107 DOI: 10.1039/c3sm52671b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Single-ion conductors are attractive electrolyte materials because of their inherent safety and ease of processing. Most ions in a sodium-neutralized PEO sulfonated-isophthalate ionomer electrolyte exist as one dimensional chains, restricted in dimensionality by the steric hindrance of the attached polymer. Because the ions are slow to reconfigure, atomistic MD simulations of this material are unable to adequately sample equilibrium ion structures. We apply a novel coarse-graining scheme using a generalized-YBG procedure in which the polymer backbone is completely removed and implicitly represented by the effective potentials of the remaining ions. The ion-only coarse-grained simulation allows for substantial sampling of equilibrium aggregate configurations. We extend the wormlike micelle theory to model ion chain equilibrium. Our aggregates are random walks which become more positively charged with increasing size. Defects occur on the string-like structure in the form of “dust” and “knots,” which form due to cation coordination with open sites along the string. The presence of these defects suggest that cation hopping along open third-coordination sites could be an important mechanism of charge transport using ion aggregates.
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18
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Milano G, Kawakatsu T, De Nicola A. A hybrid particle–field molecular dynamics approach: a route toward efficient coarse-grained models for biomembranes. Phys Biol 2013; 10:045007. [DOI: 10.1088/1478-3975/10/4/045007] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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19
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20
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Hong B, Chremos A, Panagiotopoulos AZ. Dynamics in coarse-grained models for oligomer-grafted silica nanoparticles. J Chem Phys 2012; 136:204904. [DOI: 10.1063/1.4719957] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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21
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Ohashi H, Tamaki T, Yamaguchi T. Physical Re-Examination of Parameters on a Molecular Collisions-Based Diffusion Model for Diffusivity Prediction in Polymers. J Phys Chem B 2011; 115:15181-7. [DOI: 10.1021/jp2068717] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hidenori Ohashi
- Chemical Resources Laboratory, Tokyo Institute of Technology, R1-17, 4259 Nagatsuta-cho, Midori-ku, Yokohama-city, Kanagawa 226-8503, Japan
| | - Takanori Tamaki
- Chemical Resources Laboratory, Tokyo Institute of Technology, R1-17, 4259 Nagatsuta-cho, Midori-ku, Yokohama-city, Kanagawa 226-8503, Japan
| | - Takeo Yamaguchi
- Chemical Resources Laboratory, Tokyo Institute of Technology, R1-17, 4259 Nagatsuta-cho, Midori-ku, Yokohama-city, Kanagawa 226-8503, Japan
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22
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Padding JT, Briels WJ. Systematic coarse-graining of the dynamics of entangled polymer melts: the road from chemistry to rheology. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2011; 23:233101. [PMID: 21613700 DOI: 10.1088/0953-8984/23/23/233101] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
For optimal processing and design of entangled polymeric materials it is important to establish a rigorous link between the detailed molecular composition of the polymer and the viscoelastic properties of the macroscopic melt. We review current and past computer simulation techniques and critically assess their ability to provide such a link between chemistry and rheology. We distinguish between two classes of coarse-graining levels, which we term coarse-grained molecular dynamics (CGMD) and coarse-grained stochastic dynamics (CGSD). In CGMD the coarse-grained beads are still relatively hard, thus automatically preventing bond crossing. This also implies an upper limit on the number of atoms that can be lumped together (up to five backbone carbon atoms) and therefore on the longest chain lengths that can be studied. To reach a higher degree of coarse-graining, in CGSD many more atoms are lumped together (more than ten backbone carbon atoms), leading to relatively soft beads. In that case friction and stochastic forces dominate the interactions, and action must be undertaken to prevent bond crossing. We also review alternative methods that make use of the tube model of polymer dynamics, by obtaining the entanglement characteristics through a primitive path analysis and by simulation of a primitive chain network. We finally review super-coarse-grained methods in which an entire polymer is represented by a single particle, and comment on ways to include memory effects and transient forces.
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Affiliation(s)
- J T Padding
- Institut de la Matière Condensée et des Nanosciences, Université Catholique de Louvain, Croix du Sud 1, B-1348 Louvain-la-Neuve, Belgium.
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Depa P, Chen C, Maranas JK. Why are coarse-grained force fields too fast? A look at dynamics of four coarse-grained polymers. J Chem Phys 2011; 134:014903. [PMID: 21219026 DOI: 10.1063/1.3513365] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Coarse-grained models decrease the number of force sites and thus reduce computational requirements for molecular simulation. While these models are successful in describing structural properties, dynamic evolution is faster than the corresponding atomistic simulations or experiments. We consider coarse-grained models for four polymers and one polymer mixture, where accurate dynamics are obtained by scaling to match the mean-squared displacements of the corresponding atomistic descriptions. We show that the required scaling is dictated by local friction and that this scaling is only valid after the onset of continuous motion.
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Affiliation(s)
- Praveen Depa
- Department of Chemical Engineering, 132C Fenske Laboratory, University Park, Pennsylvania 16802, USA
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Fritz D, Koschke K, Harmandaris VA, van der Vegt NFA, Kremer K. Multiscale modeling of soft matter: scaling of dynamics. Phys Chem Chem Phys 2011; 13:10412-20. [DOI: 10.1039/c1cp20247b] [Citation(s) in RCA: 145] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Hossain D, Tschopp M, Ward D, Bouvard J, Wang P, Horstemeyer M. Molecular dynamics simulations of deformation mechanisms of amorphous polyethylene. POLYMER 2010. [DOI: 10.1016/j.polymer.2010.10.009] [Citation(s) in RCA: 217] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Boland EK, Liu J, Maranas JK. A molecular picture of motion in polyolefins. J Chem Phys 2010; 132:144901. [DOI: 10.1063/1.3366660] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Pérez-Aparicio R, Colmenero J, Alvarez F, Padding JT, Briels WJ. Chain dynamics of poly(ethylene-alt-propylene) melts by means of coarse-grained simulations based on atomistic molecular dynamics. J Chem Phys 2010; 132:024904. [DOI: 10.1063/1.3280067] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Chen T, Hynninen AP, Prud'homme RK, Kevrekidis IG, Panagiotopoulos AZ. Coarse-grained simulations of rapid assembly kinetics for polystyrene-b-poly(ethylene oxide) copolymers in aqueous solutions. J Phys Chem B 2009; 112:16357-66. [PMID: 19367859 DOI: 10.1021/jp805826a] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a coarse-grained, implicit solvent model for polystyrene-b-poly(ethylene oxide) in aqueous solution and study its assembly kinetics using Brownian dynamics simulations. The polymer is modeled as a chain of freely jointed beads interacting through effective potentials. Coarse-grained force field parameters are determined by matching experimental thermodynamic quantities including radius of gyration, second virial coefficient, aggregation number, and critical micelle concentration. We investigate the influence of cooling rate (analogous to the rate of solvent quality change in rapid precipitations), polymer concentration, and friction coefficient on the assembly kinetics and compare simulation results to flash nanoprecipitation experiments. We find that assembly kinetics show a linear scaling relation with inverse friction coefficient when the friction coefficient is larger than 1. When the cooling time is less than the characteristic micellization time, stable kinetically arrested clusters are obtained; otherwise, close-to-equilibrium micelles are formed. The characteristic micellization time is estimated to be only 3-6 ms, in contrast to 30-40 ms previously determined in experiments. We suggest that previous experiments probed the formation of micellar clusters while simulations in this work studied the kinetics of a single micelle assembled from free polymer chains.
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Affiliation(s)
- Ting Chen
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544-5263, USA
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Coarse-Grained Intermolecular Potentials Derived From The Effective Fragment Potential: Application To Water, Benzene, And Carbon Tetrachloride. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/978-1-4020-9956-4_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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Abstract
The equilibrium properties of an isolated polyethylene ring chain are studied by using molecular dynamics (MD) simulations. The results of an 80-bond linear chain are also presented, which are in agreement with previous studies of square-well chains and Lennard-Jones (LJ) homopolymers. Mainly, we focus on the collapse of polyethylene ring chains. At high temperatures, a fully oblate structure is observed for the ring chains with different chain lengths. For such an oblate structure, a shape factor of delta(*)=0.25 and a rodlike scaling relation between the radius of gyration and chain lengths could be deduced easily in theory, and the same results are obtained by our MD simulations. Such an oblate structure can be obtained by Monte Carlo simulation only for sufficient stiff ring chains. When the temperature decreases, an internal energy barrier is observed. This induces a strong peak in the heat capacity, denoting a gas-liquid-like transition. This energy barrier comes mainly from the local monomer-monomer interactions, i.e., the bond-stretching, the bond-bending, and the torsion potentials. A low temperature peak is also observed in the same heat capacity curve, representing a liquid-solid-like transition. These numerical simulation results support a two-stage collapse of polyethylene ring chains; however, the nature should be different from the square-well and LJ ring chains.
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Affiliation(s)
- Jiaye Su
- Department of Physics, Zhejiang University, Hangzhou 310027, People's Republic of China
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Sacristan J, Chen C, Maranas JK. Role of Effective Composition on Dynamics of PEO−PMMA Blends. Macromolecules 2008. [DOI: 10.1021/ma8003373] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Javier Sacristan
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Chunxia Chen
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Janna K. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802
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