paper.bib

@article{Buyl:2014,
  title={H5MD: A structured, efficient, and portable file format for molecular data},
  author={de Buyl, Pierre and Colberg, Peter H and H{\"o}fling, Felix},
  journal={Comput. Phys. Commun.},
  volume={185},
  number={6},
  pages={1546--1553},
  year={2014},
  publisher={Elsevier},
  doi={10.1016/j.cpc.2014.01.018},
}

@software{Feng:2017,
  author       = {Yu Feng and Nick Hand and Biwei Dai},
  title        = {rainwoodman/pmesh 0.1.33},
  month        = nov,
  year         = 2017,
  publisher    = {Zenodo},
  version      = {0.1.33},
  doi          = {10.5281/zenodo.1051254},
}

@article{Pippig:2013,
  title={PFFT: An extension of FFTW to massively parallel architectures},
  author={Pippig, Michael},
  journal={SIAM J. Sci. Comput.},
  volume={35},
  number={3},
  pages={C213--C236},
  year={2013},
  publisher={SIAM},
  doi={10.1137/120885887},
}

@Article{Alemani:2010,
  author  = {Alemani, Davide and Collu, Francesca and Cascella, Michele and Dal Peraro, Matteo},
  journal = {J. Chem. Theory Comput.},
  title   = {A Nonradial Coarse-Grained Potential for Proteins Produces Naturally Stable Secondary Structure Elements},
  year    = {2010},
  number  = {1},
  pages   = {315--324},
  volume  = {6},
  doi     = {10.1021/ct900457z},
}

@Article{Cascella:2008,
  author  = {Cascella, Michele and Neri, Marilisa A. and Carloni, Paolo and Dal Peraro, Matteo},
  journal = {J. Chem. Theory Comput.},
  title   = {Topologically Based Multipolar Reconstruction of Electrostatic Interactions in Multiscale Simulations of Proteins},
  year    = {2008},
  number  = {8},
  pages   = {1378--1385},
  volume  = {4},
  doi     = {10.1021/ct800122x},
}

@article{Bore:2020:2,
  title={Hamiltonian and alias-free hybrid particle--field molecular dynamics},
  author={Bore, Sigbj{\o}rn L{\o}land and Cascella, Michele},
  journal={J. Chem. Phys.},
  volume={153},
  number={9},
  pages={094106},
  year={2020},
  publisher={AIP Publishing LLC},
  doi={10.1063/5.0020733},
}

@article{Zhu:2013,
    author = {Zhu, You-Liang and Liu, Hong and Li, Zhan-Wei and Qian, Hu-Jun and Milano, Giuseppe and Lu, Zhong-Yuan},
    title = {GALAMOST: GPU-accelerated large-scale molecular simulation toolkit},
    journal = {J. Comput. Chem.},
    volume = {34},
    number = {25},
    pages = {2197-2211},
    keywords = {polymers • MD • GPU • anisotropic particles • polymerization},
    doi = {10.1002/jcc.23365},
    year = {2013}
}

@Article{Zhao:2012,
  author       = {Zhao, Ying and De Nicola, Antonio and Kawakatsu, Toshihiro and Milano, Giuseppe},
  title        = {Hybrid particle-field molecular dynamics simulations: Parallelization and benchmarks},
  volume       = {33},
  number       = {8},
  pages        = {868--880},
  year         = {2012},
  journal      = {J. Comput. Chem.},
  publisher    = {Wiley Online Library},
  doi          = {10.1002/jcc.22883},
}

@Article{Bore:2018,
  author    = {Bore, Sigbj{\o}rn L{\o}land and Milano, Giuseppe and Cascella, Michele},
  title     = {Hybrid Particle-Field Model for Conformational Dynamics of Peptide Chains},
  journal   = {J. Chem. Theory Comput.},
  year      = {2018},
  volume    = {14},
  number    = {2},
  pages     = {1120--1130},
  doi       = {10.1021/acs.jctc.7b01160},
  publisher = {ACS Publications},
}

@Article{Schafer:2020,
  author  = {K. Sch{\"{a}}fer and H. B. Kolli and M.K. Christensen and S. L. Bore and G. Diezemann and J. Gauss and G. Milano and R. Lund and M. Cascella},
  title   = {Beyond the Molecular Packing Model: Understanding Morphological Transitions of Charged Surfactant Micelles},
  journal = {Angew. Chem. Int. Ed.},
  year    = {2020},
  volume  = {59},
  pages   = {18591--18598},
  doi     = {10.1002/anie.202004522},
}

@Article{Kolli:2018,
  author    = {Kolli, Hima Bindu and De Nicola, Antonio and Bore, Sigbj{\o}rn L{\o}land and Sch{\"{a}}fer, Ken and Diezemann, Gregor and Gauss, J{\"{u}}rgen and Kawakatsu, Toshihiro and Lu, Zhong-Yuan and Zhu, You-Liang and Milano, Giuseppe and Michele Cascella},
  title     = {Hybrid Particle-Field Molecular Dynamics Simulations of Charged Amphiphiles in an Aqueous Environment},
  journal   = {J. Chem. Theory Comput.},
  year      = {2018},
  volume    = {14},
  number    = {9},
  pages     = {4928--4937},
  doi       = {10.26434/chemrxiv.6264644.v1},
  publisher = {ACS Publications},
}

@article{Ledum:2020,
  author = { Morten   Ledum  and  Sigbjørn   Løland Bore  and  Michele   Cascella },
  title = {Automated determination of hybrid particle-field parameters by machine learning},
  journal = {Mol. Phys.},
  volume = {118},
  number = {19-20},
  pages = {e1785571},
  year  = {2020},
  doi = {10.1080/00268976.2020.1785571},
}

@Article{Bore:2019,
  author       = {Bore, Sigbj{\o}rn L{\o}land and Kolli, Hima Bindu and Kawakatsu, Toshihiro and Milano, Giuseppe and Cascella, Michele},
  title        = {Mesoscale Electrostatics Driving Particle Dynamics in Nonhomogeneous Dielectrics},
  volume       = {15},
  number       = {3},
  pages        = {2033--2041},
  year         = {2019},
  doi          = {10.26434/chemrxiv.7398719},
  journal      = {J. Chem. Theory Comput.},
  publisher    = {ACS Publications},
}

@Article{Nicola:2020,
  author       = {Antonio {De~Nicola} and Thereza A. Soares and Denys E. S. Santos and Sigbj{\o}rn L{\o}land Bore and G. J. Agur Sevink and Michele Cascella and Giuseppe Milano},
  title        = {Aggregation of Lipid A variants: A hybrid particle-field model},
  pages        = {129570},
  year         = {2021},
  volume       = {1865},
  doi          = {10.1016/j.bbagen.2020.129570},
  journal      = {Biochim. Biophys. Acta},
}

@Article{Bore:2020:1,
  author    = {Bore, Sigbj{\o}rn L{\o}land and Kolli, Hima Bindu and De Nicola, Antonio and Byshkin, Maksym and Kawakatsu, Toshihiro and Milano, Giuseppe and Cascella, Michele},
  title     = {Hybrid particle-field molecular dynamics under constant pressure},
  journal   = {J. Chem. Phys},
  year      = {2020},
  volume    = {152},
  number    = {18},
  pages     = {184908},
  doi       = {10.1063/5.0007445},
  publisher = {AIP Publishing LLC},
}

@article{Nicola:2015,
  title={Self-Assembly of triton X-100 in water solutions: A multiscale simulation study linking mesoscale to atomistic models},
  author={De~Nicola, Antonio and Kawakatsu, Toshihiro and Rosano, Camillo and Celino, Massimo and Rocco, Mattia and Milano, Giuseppe},
  journal={J. Chem. Theory Comput.},
  volume={11},
  number={10},
  pages={4959--4971},
  year={2015},
  publisher={ACS Publications},
  doi={10.1021/acs.jctc.5b00485},
}

@Article{Carrer:2020,
  author  = {Manuel Carrer and Tatjana Skrbic and Sigbj{\o}rn L{\o}land Bore and Giuseppe Milano and Michele Cascella and Achille Giacometti},
  title   = {Can Polarity-Inverted Surfactants Self-Assemble in Nonpolar Solvents?},
  journal = {J. Phys. Chem. B},
  year    = {2020},
  month   = jun,
  doi     = {10.26434/chemrxiv.12388772.v1},
}

@article{Wu:2021,
  title={Knotting behaviour of polymer chains in the melt state for soft-core models with and without slip-springs},
  author={Wu, Zhenghao and Alberti, Simon AN and Schneider, Jurek and M{\"u}ller-Plathe, Florian},
  journal={J. Phys-Condens. Mat.},
  volume={33},
  number={24},
  pages={244001},
  year={2021},
  publisher={IOP Publishing},
  doi={10.1088/1361-648X/abef25},
}

@article{Wu:2020,
  title={Combination of hybrid particle-field molecular dynamics and slip-springs for the efficient simulation of coarse-grained polymer models: Static and dynamic properties of polystyrene melts},
  author={Wu, Zhenghao and Milano, Giuseppe and M{\"u}ller-Plathe, Florian},
  journal={J. Chem. Theory Comput.},
  volume={17},
  number={1},
  pages={474--487},
  year={2020},
  publisher={ACS Publications},
  doi={10.1021/acs.jctc.0c00954},
}

@book{Frenkel:2001,
  title={Understanding molecular simulation: from algorithms to applications},
  author={Frenkel, Daan and Smit, Berend},
  volume={1},
  year={2001},
  publisher={Elsevier},
  doi={10.1063/1.881812},
}

@Article{Milano:2009,
  author       = {Milano, Giuseppe and Kawakatsu, Toshihiro},
  title        = {Hybrid particle-field molecular dynamics simulations for dense polymer systems},
  volume       = {130},
  number       = {21},
  pages        = {214106},
  year         = {2009},
  doi          = {10.1063/1.3142103},
  journal      = {J. Chem. Phys.},
  publisher    = {AIP},
}

@article{Milano:2013,
  title={A hybrid particle--field molecular dynamics approach: a route toward efficient coarse-grained models for biomembranes},
  author={Milano, Giuseppe and Kawakatsu, Toshihiro and De Nicola, Antonio},
  journal={Phys. Biol.},
  volume={10},
  number={4},
  pages={045007},
  year={2013},
  publisher={IOP Publishing},
  doi={10.1088/1478-3975/10/4/045007},
}