271
Views
9
CrossRef citations to date
0
Altmetric
Research Article

Investigation of coarse-grained models across a glass transition

&
Pages 185-199 | Received 01 Nov 2019, Accepted 23 Dec 2019, Published online: 20 Jan 2020

References

  • Schlick, T.; Collepardo-Guevara, R.; Halvorsen, L. A.; Jung, S.; Xiao, X. Biomolecular Modeling and Simulation: A Field Coming of Age. Quart. Rev. Biophys. 2011, 44, 191–228. DOI: 10.1017/S0033583510000284.
  • Deserno, M.;. Mesoscopic Membrane Physics: Concepts, Simulations, and Selected Applications. Macromol. Rapid Comm. 2009, 30, 752–771. DOI: 10.1002/marc.200900090.
  • Murtola, T.; Bunker, A.; Vattulainen, I.; Deserno, M.; Karttunen, M. Multiscale Modeling of Emergent Materials: Biological and Soft Matter. Phys. Chem. Chem. Phys. 2009, 11, 1869–1892. DOI: 10.1039/b818051b.
  • Peter, C.; Kremer, K. Multiscale Simulation of Soft Matter Systems. Faraday Discuss. 2010, 144, 9–24. DOI: 10.1039/B919800H.
  • Riniker, S.; Allison, J. R.; van Gunsteren, W. F. On Developing Coarse-grained Models for Biomolecular Simulation: A Review. Phys. Chem. Chem. Phys. 2012, 14, 12423–12430. DOI: 10.1039/c2cp40934h.
  • Saunders, M. G.; Voth, G. A. Coarse-graining Methods for Computational Biology. Annu. Rev. Biophys. 2013, 42, 73–93. DOI: 10.1146/annurev-biophys-083012-130348.
  • Noid, W. G.;. Perspective: Coarse-grained Models for Biomolecular Systems. J. Chem. Phys. 2013, 139, 090901. DOI: 10.1063/1.4818908.
  • Brini, E.; Algaer, E. A.; Ganguly, P.; Li, C.; Rodríguez-Ropero, F.; van der Vegt, N. F. A. Systematic Coarse-graining Methods for Soft Matter Simulations - a Review. Soft Matter. 2013, 9, 2108–2119. DOI: 10.1039/C2SM27201F.
  • Noid, W. G.;. Systematic Methods for Structurally Consistent Coarse-grained Models. Methods Mol. Biol. 2013, 924, 487–531.
  • Likos, C. N.;. Effective Interactions in Soft Condensed Matter Physics. Phys. Rep. 2001, 348, 267–439. DOI: 10.1016/S0370-1573(00)00141-1.
  • Akkermans, R. L. C.; Briels, W. J. A Structure-based Coarse-grained Model for Polymer Melts. J. Chem. Phys. 2001, 114, 1020–1031. DOI: 10.1063/1.1330744.
  • Louis, A. A.;. Beware of Density Dependent Pair Potentials. J. Phys.: Condens. Matter. 2002, 14, 9187–9206.
  • Stillinger, F. H.; Sakai, H.; Torquato, S. Statistical Mechanical Models with Effective Potentials: Definitions, Applications, and Thermodynamic Consequences. J. Chem. Phys. 2002, 117, 288–296. DOI: 10.1063/1.1480863.
  • Wang, H.; Junghans, C.; Kremer, K. Comparative Atomistic and Coarse-grained Study of Water: What Do We Lose by Coarse-graining? Eur. Phys. J. E. 2009, 28, 221–229. DOI: 10.1140/epje/i2008-10413-5.
  • Lyubartsev, A.; Mirzoev, A.; Chen, L. J.; Laaksonen, A. Systematic Coarse-graining of Molecular Models by the Newton Inversion Method. Faraday Discuss. 2010, 144, 43–56. DOI: 10.1039/B901511F.
  • Clark, A. J.; McCarty, J.; Lyubimov, I. Y.; Guenza, M. G. Thermodynamic Consistency in Variable-level Coarse Graining of Polymeric Liquids. Phys. Rev. Lett. 2012, 109, 168301. DOI: 10.1103/PhysRevLett.109.168301.
  • McCarty, J.; Clark, A. J.; Lyubimov, I. Y.; Guenza, M. G. Thermodynamic Consistency between Analytic Integral Equation Theory and Coarse-grained Molecular Dynamics Simulations of Homopolymer Melts. Macromolecules. 2012, 45, 8482–8493. DOI: 10.1021/ma301502w.
  • D’Adamo, G.; Pelissetto, A.; Pierleoni, C. Predicting the Thermodynamics by Using State-dependent Interactions. J. Chem. Phys. 2013, 138, 234107. DOI: 10.1063/1.4810881.
  • Foley, T. T.; Shell, M. S.; Noid, W. G. The Impact of Resolution upon Entropy and Information in Coarse-grained Models. J. Chem. Phys. 2015, 143, 243104. DOI: 10.1063/1.4929836.
  • Wagner, J. W.; Dama, J. F.; Durumeric, A. E. P.; Voth, G. A. On the Representability Problem and the Physical Meaning of Coarse-grained Models. J. Chem. Phys. 2016, 145, 044108. DOI: 10.1063/1.4959168.
  • Dunn, N. J. H.; Foley, T. T.; Noid, W. G. Van Der Waals Perspective on Coarse-graining: Progress toward Solving Representability and Transferability Problems. Acc. Chem. Res. 2016, 49, 2832–2840. DOI: 10.1021/acs.accounts.6b00498.
  • Vettorel, T.; Meyer, H. Coarse Graining of Short Polyethylene Chains for Studying Polymer Crystallization. J. Chem. Theory Comput. 2006, 2, 616–629. DOI: 10.1021/ct0503264.
  • Wang, Y. T.; Izvekov, S.; Yan, T. Y.; Voth, G. A. Multiscale Coarse-graining of Ionic Liquids. J. Phys. Chem. B. 2006, 110, 3564–3575. DOI: 10.1021/jp0548220.
  • Johnson, M. E.; Head-Gordon, T.; Louis, A. A. Representability Problems for Coarse- Grained Water Potentials. J. Chem. Phys. 2007, 126, 144509. DOI: 10.1063/1.2715953.
  • Liwo, A.; Khalili, M.; Czaplewski, C.; Kalinowski, S.; O-ldziej, S.; Wachucik, K.; Scheraga, H. A. Modification and Optimization of the United-residue (UNRES) Potential Energy Function for Canonical Simulations. I. Temperature Dependence of the Effective Energy Function and Tests of the Optimization Method with Single Training Proteins. J. Phys. Chem. B. 2007, 111, 260–285. DOI: 10.1021/jp065380a.
  • Carbone, P.; Varzaneh, H. A. K.; Chen, X.; Müller-Plathe, F. Transferability of Coarse- Grained Force Fields: The Polymer Case. J. Chem. Phys. 2008, 128, 064904. DOI: 10.1063/1.2829409.
  • Qian, H.-J.; Carbone, P.; Chen, X.; Karimi-Varzaneh, H. A.; Liew, C. C.; Müller- Plathe, F. Temperature-transferable Coarse-grained Potentials for Ethylbenzene, Polystyrene and Their Mixtures. Macromolecules. 2008, 41, 9919–9929. DOI: 10.1021/ma801910r.
  • Krishna, V.; Noid, W. G.; Voth, G. A. The Multiscale Coarse-graining Method. Iv. Transferring Coarse-grained Potentials between Temperatures. J. Chem. Phys. 2009, 131, 024103. DOI: 10.1063/1.3167797.
  • Chaimovich, A.; Shell, M. S. Anomalous Waterlike Behavior in Spherically-symmetric Water Models Optimized with the Relative Entropy. Phys. Chem. Chem. Phys. 2009, 11, 1901–1915. DOI: 10.1039/b818512c.
  • Huang, D. M.; Faller, R.; Do, K.; Moule, A. J. Coarse-grained Computer Simulations of Polymer/fullerene Bulk Heterojunctions for Organic Photovoltaic Applications. J. Chem. Theory Comput. 2010, 6, 526–537. pMID: 26617308. DOI: 10.1021/ct900496t.
  • Lu, L.; Voth, G. A. The Multiscale Coarse-graining Method. VII. Free Energy Decomposition of Coarse-grained Effective Potentials. J. Chem. Phys. 2011, 134, 224107. DOI: 10.1063/1.3599049.
  • Izvekov, S.;. Towards an Understanding of Many-particle Effects in Hydrophobic Association in Methane Solutions. J. Chem. Phys. 2011, 134, 034104. DOI: 10.1063/1.3521480.
  • Dijkstra, M.; van Roij, R.; Evans, R. Direct Simulation of the Phase Behavior of Binary Hard-sphere Mixtures: Test of the Depletion Potential Description. Phys. Rev. Lett. 1999, 82, 117–120. DOI: 10.1103/PhysRevLett.82.117.
  • Louis, A. A.; Bolhuis, P. G.; Hansen, J. P.; Meijer, E. J. Can Polymer Coils Be Modeled as “Soft Colloids”? Phys. Rev. Lett. 2000, 85, 2522–2525. DOI: 10.1103/PhysRevLett.85.2522.
  • Silbermann, J.; Klapp, S. H. L.; Shoen, M.; Channamsetty, N.; Block, H.; Gubbins, K. E. Mesoscale Modeling of Complex Binary Fluid Mixtures: Towards an Atomistic Foundation of Effective Potentials. J. Chem. Phys. 2006, 124, 074105. DOI: 10.1063/1.2161207.
  • Fischer, J.; Paschek, D.; Gieger, A.; Sadowski, G. Modeling of Aqueous Poly(oxyethylene) Solutions. 2. Mesoscale Simulations. J. Phys. Chem. B. 2008, 112, 13561–13571. DOI: 10.1021/jp805770q.
  • Mirzoev, A.; Lyubartsev, A. P. Effective Solvent Mediated Potentials of Na+ and Cl− Ions in Aqueous Solution: Temperature Dependence. Phys. Chem. Chem. Phys. 2011, 13, 5722–5727. DOI: 10.1039/c0cp02397c.
  • Rudzinski, J. F.; Noid, W. G. Bottom-up Coarse-graining of Peptide Ensembles and Helix-coil Transitions. J. Chem. Theory Comput. 2015, 11, 1278–1291. DOI: 10.1021/ct5009922.
  • Rosenberger, D.; van der Vegt, N. F. A. Addressing the Temperature Transferability of Structure Based Coarse Graining Models. Phys. Chem. Chem. Phys. 2018, 20, 6617–6628. DOI: 10.1039/C7CP08246K.
  • Farah, K.; Fogarty, A. C.; Böhm, M. C.; Müller-Plathe, F. Temperature Dependence of Coarse-grained Potentials for Liquid Hexane. Phys. Chem. Chem. Phys. 2011, 13, 2894–2902. DOI: 10.1039/C0CP01333A.
  • Lebold, K. M.; Noid, W. G. Systematic Study of Temperature and Density Variations in Effective Potentials for Coarse-grained Models of Molecular Liquids. J. Chem. Phys. 2019, 150, 014104. DOI: 10.1063/1.5050509.
  • Lebold, K. M.; Noid, W. G. Dual Approach for Effective Potentials that Accurately Model Structure and Energetics. J. Chem. Phys. 2019, 150, 234107. DOI: 10.1063/1.5094330.
  • Lebold, K. M.; Noid, W. Dual-potential Approach for Coarse-grained Implicit Solvent Models with Accurate, Internally Consistent Energetics and Predictive Transferability. J. Chem. Phys. 2019, 151, 164113. DOI: 10.1063/1.5125246.
  • Mukherjee, B.; Delle Site, L.; Kremer, K.; Peter, C. Derivation of Coarse Grained Models for Multiscale Simulation of Liquid Crystalline Phase Transitions. J. Phys. Chem. B. 2012, 116, 8474–8484. DOI: 10.1021/jp212300d.
  • Brini, E.; Marcon, V.; van der Vegt, N. F. A. Conditional Reversible Work Method for Molecular Coarse Graining Applications. Phys. Chem. Chem. Phys. 2011, 13, 10468–10474. DOI: 10.1039/c0cp02888f.
  • Wang, Y. T.; Noid, W. G.; Liu, P.; Voth, G. A. Effective Force Coarse-graining. Phys. Chem. Chem. Phys. 2009, 11, 2002–2015. DOI: 10.1039/b819182d.
  • Ghosh, J.; Faller, R. State Point Dependence of Systematically Coarse-grained Potentials. Mol Simul. 2007, 33, 759–767. DOI: 10.1080/08927020701275050.
  • Müller-Plathe, F.;. Coarse-graining in Polymer Simulation: From the Atomistic to the Mesoscopic Scale and Back. ChemPhysChem. 2002, 3, 754–769. DOI: 10.1002/1439-7641(20020916)3:9<754::AID-CPHC754>3.0.CO;2-U.
  • Ediger, M. D.; Angell, C. A.; Nagel, S. R. Supercooled Liquids and Glasses. J. Chem. Phys. 1996, 100, 13200–13212. DOI: 10.1021/jp953538d.
  • Berthier, L.; Biroli, G. Theoretical Perspective on the Glass Transition and Amorphous Materials. Rev. Mod. Phys. 2011, 83, 587. DOI: 10.1103/RevModPhys.83.587.
  • Xia, W.; Song, J.; Jeong, C.; Hsu, D. D.; Phelan, J.; Frederick, R.; Douglas, J. F.; Keten, S. Energy-renormalization for Achieving Temperature Transferable Coarse-graining of Polymer Dynamics. Macromolecules. 2017, 50, 8787–8796. DOI: 10.1021/acs.macromol.7b01717.
  • Izvekov, S.; Voth, G. A. A Multiscale Coarse-graining Method for Biomolecular Sys- Tems. J. Phys. Chem. B. 2005, 109, 2469–2473. DOI: 10.1021/jp044629q.
  • Izvekov, S.; Voth, G. A. Multiscale Coarse Graining of Liquid-state Systems. J. Chem. Phys. 2005, 123, 134105. DOI: 10.1063/1.2038787.
  • Noid, W. G.; Chu, J.-W.; Ayton, G. S.; Krishna, V.; Izvekov, S.; Voth, G. A.; Das, A.; Andersen, H. C. The Multiscale Coarse-graining Method. I. A Rigorous Bridge between Atomistic and Coarse-grained Models. J. Chem. Phys. 2008, 128, 244114. DOI: 10.1063/1.2938860.
  • Noid, W. G.; Liu, P.; Wang, Y. T.; Chu, J.-W.; Ayton, G. S.; Izvekov, S.; Andersen, H. C.; Voth, G. A. The Multiscale Coarse-graining Method. II. Numerical Implementation for Molecular Coarse-grained Models. J. Chem. Phys. 2008, 128, 244115. DOI: 10.1063/1.2938857.
  • Lu, L.; Voth, G. A. The Multiscale Coarse-graining Method. Adv. Chem. Phys. 2012, 149, 47–81.
  • Das, A.; Andersen, H. C. The Multiscale Coarse-graining Method. V. Isothermal- Isobaric Ensemble. J. Chem. Phys. 2010, 132, 164106. DOI: 10.1063/1.3394862.
  • Dunn, N. J. H.; Noid, W. G. Bottom-up Coarse-grained Models that Accurately Describe the Structure, Pressure, and Compressibility of Molecular Liquids. J. Chem. Phys. 2015, 143, 243148. DOI: 10.1063/1.4937383.
  • Dunn, N. J. H.; Noid, W. G. Bottom-up Coarse-grained Models with Predictive Accuracy and Transferability for Both Structural and Thermodynamic Properties of Heptane-toluene Mixtures. J. Chem. Phys. 2016, 144, 204124. DOI: 10.1063/1.4952422.
  • Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. J. Am. Chem. Soc. 1996, 118, 11225–11236. DOI: 10.1021/ja9621760.
  • Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald: An N log(N) Method for Ewald Sums in Large Systems. J. Chem. Phys. 1993, 98, 10089–10092. DOI: 10.1063/1.464397.
  • Abraham, M. J.; Murtola, T.; Schulz, R.; Páll, S.; Smith, J. C.; Hess, B.; Lindahl, E. Gromacs: High Performance Molecular Simulations through Multi-level Parallelism from Laptops to Supercomputers. SoftwareX. 2015, 1–2, 19–25. DOI: 10.1016/j.softx.2015.06.001.
  • Bussi, G.; Donadio, D.; Parrinello, M. Canonical Sampling through Velocity Rescaling. J. Chem. Phys. 2007, 126, 014101. DOI: 10.1063/1.2408420.
  • Parrinello, M.; Rahman, A. Crystal Structure and Pair Potentials: A Molecular- Dynamics Study. Phys. Rev. Lett. 1980, 45, 1196–1199. DOI: 10.1103/PhysRevLett.45.1196.
  • Dunn, N. J. H.; Lebold, K. M.; DeLyser, M. R.; Rudzinski, J. F.; Noid, W. G. BOCS: Bottom-up Open-source Coarse-graining Software. J. Phys. Chem. B. 2018, 122, 3363–3377. DOI: 10.1021/acs.jpcb.7b09993.
  • Plimpton, S.;. Fast Parallel Algorithms for Short-range Molecular Dynamics. J. Comp. Phys. 1995, 117, 1–19. DOI: 10.1006/jcph.1995.1039.
  • Martyna, G. J.; Tobias, D. J.; Klein, M. L. Constant Pressure Molecular Dynamics Algorithms. J. Chem. Phys. 1994, 101, 4177–4189. DOI: 10.1063/1.467468.
  • Martyna, G. J.; Tuckerman, M. E.; Tobias, D. J.; Klein, M. L. Explicit Reversible Integrators for Extended Systems Dynamics. Mol. Phys. 1996, 87, 1117–1157. DOI: 10.1080/00268979600100761.
  • Martyna, G. J.; Klein, M. L.; Tuckerman, M. Nosé–Hoover Chains: The Canonical Ensemble via Continuous Dynamics. J. Chem. Phys. 1992, 97, 2635–2643. DOI: 10.1063/1.463940.
  • Naoki, M.; Koeda, S. Pressure-volume-temperature Relations of Liquid, Crystal, and Glass of O-terphenyl: Excess Amorphous Entropies, and Factors Determining Molecular Mobility. J. Chem. Phys. 1989, 93, 948–955. DOI: 10.1021/j100339a078.
  • Greet, R.; Turnbull, D. Glass Transition in O-terphenyl. J. Chem. Phys. 1967, 46, 1243–1251. DOI: 10.1063/1.1840842.
  • Kovacs, A. J.;. The Isothermal Contraction of the Volume of Amorphous Polymeric Materials. J. Polym. Sci. 1958, 30, 131–147. DOI: 10.1002/pol.1958.1203012111.
  • Izvekov, S.; Voth, G. A. Modeling Real Dynamics in the Coarse-grained Representation of Condensed Phase Systems. J. Chem. Phys. 2006, 125, 151101. DOI: 10.1063/1.2360580.
  • Hijon, C.; Espanol, P.; Vanden-Eijnden, E.; Delgado-Buscalioni, R. Mori-Zwanzig Formalism as a Practical Computational Tool. Faraday Discuss. 2010, 144, 301–322. DOI: 10.1039/B902479B.
  • Davtyan, A.; Dama, J. F.; Voth, G. A.; Andersen, H. C. Dynamic Force Matching: A Method for Constructing Dynamical Coarse-grained Models with Realistic Time Dependence. J. Chem. Phys. 2015, 142, 154104. DOI: 10.1063/1.4917454.
  • Li, Z.; Bian, X.; Li, X.; Karniadakis, G. E. Incorporation of Memory Effects in Coarse- Grained Modeling via the Mori - Zwanzig Formalism. J. Chem. Phys. 2015, 143, 243128. DOI: 10.1063/1.4935490.
  • Rudzinski, J. F.;. Recent Progress Towards Chemically-specific Coarse-grained Simulation Models with Consistent Dynamical Properties. Computation. 2019, 7, 42. DOI: 10.3390/computation7030042.
  • Mullinax, J. W.; Noid, W. G. A Generalized Yvon-Born-Green Theory for Molecular Systems. Phys. Rev. Lett. 2009, 103, 198104. DOI: 10.1103/PhysRevLett.103.198104.
  • Rudzinski, J. F.; Noid, W. G. The Role of Many-body Correlations in Determining Potentials for Coarse-grained Models of Equilibrium Structure. J. Phys. Chem. B. 2012, 116, 8621–8635. DOI: 10.1021/jp3002004.
  • Rudzinski, J. F.; Noid, W. G. A Generalized-yvon-born-green Method for Coarse- Grained Modeling. Eur. Phys. J. Spec. Top. 2015, 224, 2193–2216.
  • Towns, J.; Cockerill, T.; Dahan, M.; Foster, I.; Gaither, K.; Grimshaw, A.; Hazlewood, V.; Lathrop, S.; Lifka, D.; Peterson, G. D.; et al. Xsede: Accelerating Scientific Discovery. Comput. Sci. Eng. 2014, 16, 62–74. DOI: 10.1109/MCSE.2014.80.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.