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SPICA: Surface Property fItting Coarse grAined model

Publication

Publication: SPICA force field

SPICA force field

[1] S. Seo and W. Shinoda, "SPICA force field for lipid membranes: Domain formation induced by cholesterol " J. Chem. Theory Comput. 15, 762-774 (2019). DOI: 10.1021/acs.jctc.8b00987.

[2] H. O. S. Yadav, S. Harada, A. Kuo, S. Urata, W. Shinoda, "Hemimicelle formation of semi-fluorocarbon chains at air-water interface: coarse-grained molecular dynamics study with an extension of the SPICA force field." Mol. Phys. 119, e1910355 (2021). DOI: 10.1080/00268976.2021.1910355

[3] S. Kawamoto, H. Liu, Y. Miyazaki, S. Seo, M. Dixit, R. DeVane, C. MacDarmaid, G. Fiorin, M. L. Klein, and W. Shinoda, "The SPICA force field for proteins and peptides" J. Chem. Theory Comput. 18, 3204-3218 (2022). DOI:10.1021/acs.jctc.1c01207.

pSPICA force field

[1] Y. Miyazaki, S. Okazaki, and W. Shinoda, "pSPICA: A coarse-grained force field for lipid membranes based on a polar water model." J. Chem. Theory Comput. 16, 782-793 (2020). DOI: 10.1021/acs.jctc.9b00946.

[2] Y. Miyazaki and W. Shinoda, " Cooperative Antimicrobial Action of Melittin on Lipid Membranes: A Coarse Grained Molecular Dynamics Study" BBA-Biomembranes, 1864, 183955 (2022). DOI: 10.1016/j.bbamem.2022.183955

tSPICA force field

[1] M. Z. Griffiths and W. Shinoda, " tSPICA: Temperature- and Pressure-dependent Coarse-Grained Force Field for Organic Molecules", J. Chem. Info. Model. 58, 3829-3838 (2019). DOI: 10.1021/acs.jcim.9b00480.

Recent related publication

[1] K. Hall, T. Sirk, M. L. Klein, and W. Shinoda, "A Coarse-Grain Model for Entangled Polyethylene Melts and Polyethylene Crystallization", J. Chem. Phys. 150, 244901 (2019). DOI: 10.1063/1.5092229

[2] K. W. Hall, T. W. Srik, S. Percec, M. L. Klein, and W. Shinoda, "Divining the Shape of Nascent Polymer Crystal Nuclei." J. Chem. Phys. 151, 144901 (2019). DOI: 10.1063/1.5123983

[3] S. Seo, M. Murata, and W. Shinoda, "Pivital Role of Interdigitation in Leaflets Interactions: Implication from Molecular Dynamics Simulations." J. Phys. Chem. Lett. 11, 5171-5176 (2020). DOI: 10.1021/acs.jpclett.0c01317

[4] V. Zoni, R. Khaddaj, I. Lukmantara, W. Shinoda, H. Yang, R. Schneiter, S. Vanni, "Seipin accumulates and traps diacylglycerols and triglycerides in its ring-like structure." Proc. Natl. Acad. Sci. U.S.A. 118, e2017205118 (2021). DOI: 10.1073/pnas.2017205118

[5] M. Z. Griffiths and W. Shinoda, "Analyzing the Role of Surfactants in the Colloidal Stability of Nanoparticles in Oil through Coarse-Grained Molecular Dynamics Simulations." J. Phys. Chem. B 125, 6315–6321 (2021).DOI: 10.1021/acs.jpcb.1c01148

Previous publication

Shinoda-DeVane-Klein (SDK) model

[1] W. Shinoda, R. DeVane, M. L. Klein, "Multi-property Fitting and Parameterization of a Coarse Grained Model for Aqueous Surfactants", Mol. Simul. 33 27(2007). DOI: 10.1080/08927020601054050

[2] W. Shinoda, R. DeVane, M. L. Klein, "Coarse-grained molecular modeling of nonionic surfactant self-assembly" Soft Matter, 4, 2454 (2008). DOI: 10.1039/B808701F

[3] W. Shinoda, R. DeVane, M. L. Klein, "Self-assembly of Surfactants in Bulk Phases and at Interfaces using Coarse-grain Models", Chapter 22 of the book "Coarse-Graining of Condensed Phase and Biomolecular Systems", G. A. Voth Ed., CRC Press, 2008. 

[4] W. Shinoda, R. DeVane, M. L. Klein, "Zwitterionic lipid assemblies: Molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field." J. Phys. Chem. B, 114, 6836 (2010). DOI: 10.1021/jp9107206

[5] W. Shinoda, R. DeVane, M. L. Klein, "Coarse-Grained Force Field for Ionic Surfactants." Soft Matter, 7, 6178 (2011). DOI: 10.1039/C1SM05173C

[6] R. DeVane, W. Shinoda, P. B. Moore, M. L. Klein, "Transferable Coarse Grain Nonbonded Interaction Model for Amino Acids" J. Chem. Theory Comput. 5, 2115 (2009).DOI: 10.1021/ct800441u

SDK (& SPICA) compatible CG model

(triglycerides model)
[1] A. Bacle, R. Gautier, C. L. Jackson, P. F. J. Fuchs, S. Vanni, "Interdigitation between Triglycerides and Lipids Modulates Surface Properties of Lipid Droplets", Biophys. J. 112, 1417-1430 (2017). DOI: 10.1016/j.bpj.2017.02.032

Reviews

[1] M. L. Klein and W. Shinoda, "Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems" Science, 321, 798 (2008). DOI: 10.1126/science.1157834

[2] W. Shinoda, R. DeVane, M. L. Klein, "Computer Simulation Studies of Self-Assembling Macromolecules" Curr. Opin. Struct. Biol. 22, 175-186 (2012).DOI: 10.1016/j.sbi.2012.01.011

[3] G. Fiorin, M. L. Klein, R. DeVane, and W. Shinoda, "Computer Simulation of Self-Assembling Macromolecules" Adv. Polym. Sci. 262, 93 (2013).

Extension and Application of the SDK model

[1] X. He, W. Shinoda, R. DeVane, K. Andersen, M. L. Klein, "Paramaterization of a Coarse-Grained Model for Linear Alkylbenzene Sulfonate Surfactants and Molecular Dynamics Studies of Their Self-assembly in Aqueous Solution" Chem. Phys. Lett. 487, 71(2010). DOI: 10.1016/j.cplett.2010.01.029

[2] X. He, W. Shinoda, R. DeVane, M. L. Klein, "Exploring the utility of coarse-grained water models for computational studies of interfacial systems" Mol. Phys. 108, 2007 (2010).DOI: 10.1080/00268976.2010.503197

[3] R. DeVane, C. C. Chiu, S. O. Nielsen, W. Shinoda, P. B. Moore, and M. L. Klein, "Coarse Grained Molecular Dynamics of Phenyl Based Molecules: I. Parametrization" J. Phys. Chem. B, 114, 6386 (2010). DOI: 10.1021/jp9117369

[4] C. C. Chiu, R. DeVane, M. L. Klein, W. Shinoda, P. B. Moore, and S. O. Nielsen, "Coarse Grained Molecular Dynamics of Phenyl Based Molecules: II. Application to Fullerenes" J. Phys. Chem. B, 114, 6394 (2010). DOI: 10.1021/jp9117375

[5] R. DeVane, A. Jusufi, W. Shinoda, C. C. Chiu, S. O. Nielsen, P. B. Moore, M. L. Klein, "Parameterization and application of a coarse grained forcefield for benzene/fullerene interactions with lipids" J. Phys. Chem. B, 114, 16364 (2010). DOI: 10.1021/jp1070264

[6] A. Jusufi, R. DeVane, W. Shinoda, M. L. Klein, "Nanoscale Carbon Particles and the Stability of Lipid Bilayers", Soft Matter, 7, 1139 (2011). DOI: 10.1039/C0SM00963F

[7] W. Shinoda, T. Nakamura, and S. O. Nielsen, "Free Energy Analysis of Vesicle-to-Bicelle Transformation", Soft Matter, 7, 9012-9020 (2011). DOI:10.1039/C1SM05404J

[8] B. Levine, D. LeBard, R. DeVane, W. Shinoda, A. Kohlmeyer, M. L. Klein, "Micellization studied by GPU-accelerated coarse-grained molecular dynamics", J. Chem. Theory Comput. 7, 4135 (2011). DOI: 10.1021/ct2005193

[9] D. LeBard, B. Levine, R. DeVane, W. Shinoda, M. L. Klein, "Premicelles In Aqueous Surfactant Solutions Above and Below the Critical Micelle Concentration" Chem. Phys. Lett. 552, 38 (2012). DOI: 10.1016/j.cplett.2011.11.075

[10] C. -C. Chiu, W. Shinoda, R. DeVane, S. O. Nielsen, "Effects of spherical fullerene nanoparticles on a dipalmitoyl phosphatidylcholine lipid monolayer: a coarse grain molecular dynamics approach.", Soft Matter, 8, 9610 (2012). DOI: 10.1039/C2SM26357B

[11] S. Kawamoto, T. Nakamura, S. O. Nielsen, and W. Shinoda, "A Guiding Potential Method for Evaluating the Bending Rigidity of Tensionless Lipid Membranes from Molecular Simulation" J. Chem. Phys. 139, 034108 (2013). DOI: 10.1063/1.4811677

[12] T. Nakamura and W. Shinoda, "Method of evaluating curvature-dependent elastic parameters for small unilamellar vesicles using molecular dynamics trajectory", J. Chem. Phys. 138, 124903 (2013). DOI: 10.1063/1.4795579

[13] W. Shinoda, D. Discher, M. Klein, S. Loverde, "Probing the Structure of PEGylated-lipid Assemblies by Coarse-grained Molecular Dynamics" Soft Matter, 9, 11549 (2013). DOI: 10.1039/C3SM52290C

[14] W. Shinoda and M. L. Klein, "Effective Interaction Between Small Unilamellar Vesicles as Probed by Coarse-Grained Molecular Dynamic Simulations" Pure Appl. Chem., 86, 215-222, (2014). DOI: 10.1515/pac-2014-5023

[15] S. Kawamoto and W. Shinoda, "Free energy analysis along the stalk mechanism of membrane fusion" Soft Matter, 10, 3048 (2014). DOI: 10.1039/C3SM52344F

[16] S. Kawamoto, M. L. Klein, W. Shinoda, "Coarse-Grained Molecular Dynamics Study of Membrane Fusion: Curvature Effects on Free Energy Barrieres along the Stalk Mechanism" J. Chem. Phys. 143, 243112 (2015). DOI: 10.1063/1.4933087

[17] C. M. MacDermaid, H. K. Kashyap, R. DeVane, W. Shinoda, J. B. Klauda, M. L. Klein, and G. Fiorin, "Molecular Dynamics Simulations of Cholesterol-Rich Membranes Using a Coarse-Grained Force Field for Cyclic Alkanes." J. Chem. Phys. 143, 243144 (2015). DOI: 10.1063/1.4937153

[18] A. Bacle, R. Gautier, C. L. Jackson, P. F. J. Fuchs, S. Vanni, "Interdigitation between triglycerides and lipids modulates surface properties of lipid droplets." Biophys. J. 112, 1417-1430 (2017). DOI: 10.1016/j.bpj.2017.02.032

SPICA Force Field

Okayama University