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Molecular Physics
An International Journal at the Interface Between Chemistry and Physics
Volume 118, 2020 - Issue 19-20: Special Issue of Molecular Physics in Honour of Jürgen Gauss
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Research Articles

Automated determination of hybrid particle-field parameters by machine learning

Morten LedumDepartment of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, NorwayORCID Iconhttps://orcid.org/0000-0003-4244-4876View further author information
ORCID Icon,
Sigbjørn Løland BoreDepartment of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, NorwayORCID Iconhttps://orcid.org/0000-0002-8620-4885View further author information
ORCID Icon &
Michele CascellaDepartment of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, NorwayCorrespondence[email protected]
ORCID Iconhttps://orcid.org/0000-0003-2266-5399View further author information
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Article: e1785571 | Received 04 Apr 2020, Accepted 16 Jun 2020, Published online: 02 Jul 2020

References

  • K.C. Daoulas and M. Müller, J. Chem. Phys. 125 (18), 184904 (2006).
  • M. Müller, J. Stat. Phys. 145 (4), 967–1016 (2011).
  • G. Milano and T. Kawakatsu, J. Chem. Phys. 130 (21), 214106 (2009).
  • G.G. Vogiatzis, G. Megariotis and D.N. Theodorou, Macromolecules 50 (7), 3004–3029 (2017).
  • F. Schmid, J. Phys.: Condens. Matter 10 (37), 8105 (1998).
  • T. Kawakatsu, Statistical Physics of Polymers: An Introduction (Springer Science & Business Media, Berlin, 2013).
  • G. Fredrickson, The Equilibrium Theory of Inhomogeneous Polymers, Vol. 134 (Oxford University Press, Oxford, 2006).
  • Y. Zhao, A. De Nicola, T. Kawakatsu and G. Milano, J. Comput. Chem. 33 (8), 868–880 (2012).
  • L. Schneider and M. Müller, Comput. Phys. Commun. 235, 463–476 (2019).
  • Y.L. Zhu, H. Liu, Z.W. Li, H.J. Qian, G. Milano and Z.Y. Lu, J. Comput. Chem. 34 (25), 2197–2211 (2013).
  • G. Milano, T. Kawakatsu and A. De Nicola, Phys. Biol. 10 (4), 045007 (2013).
  • T.A. Soares, S. Vanni, G. Milano and M. Cascella, J. Phys. Chem. Lett. 8 (15), 3586–3594 (2017).
  • M. Cascella and S. Vanni, in Chemical Modelling: Applications and Theory, edited by Michael Springborg and Jan-Ole Joswig (Royal Society of Chemistry, London, 2015), Vol. 12, Chap. 1, pp. 1–52.
  • S.J. Marrink, V. Corradi, P.C.T. Souza, H.I. Ingólfsson, D.P. Tieleman and M.S.P. Sansom, Chem. Rev. 119 (9), 6184–6226 (2019).
  • S.L. Bore, G. Milano and M. Cascella, J. Chem. Theory Comput. 14 (2), 1120–1130 (2018).
  • A. De Nicola, T. Kawakatsu, F. Müller-Plathe and G. Milano, Eur. Phys. J. Spec. Top. 225 (8-9), 1817–1841 (2016).
  • Y. Zhao, M. Byshkin, Y. Cong, T. Kawakatsu, L. Guadagno, A. De Nicola, N. Yu, G. Milano and B. Dong, Nanoscale 8 (34), 15538–15552 (2016).
  • G. Munaò, A. Pizzirusso, A. Kalogirou, A. De Nicola, T. Kawakatsu, F. Müller-Plathe and G. Milano, Nanoscale 10 (46), 21656–21670 (2018).
  • G. Munaò, A. De Nicola, F. Müller-Plathe, T. Kawakatsu, A. Kalogirou and G. Milano, Macromolecules 52 (22), 8826–8839 (2019).
  • A. De Nicola, Y. Zhao, T. Kawakatsu, D. Roccatano and G. Milano, Theor. Chem. Acc. 131 (3), 1167 (2012).
  • A. De Nicola, Y. Zhao, T. Kawakatsu, D. Roccatano and G. Milano, J. Chem. Theory Comput. 7 (9), 2947–2962 (2011).
  • Y.L. Zhu, Z.Y. Lu, G. Milano, A.C. Shi and Z.Y. Sun, Phys. Chem. Chem. Phys. 18 (14), 9799–9808 (2016).
  • H.B. Kolli, A. De Nicola, S.L. Bore, K. Schäfer, G. Diezemann, J. Gauss, T. Kawakatsu, Z.Y. Lu, Y.L. Zhu, G. Milano and M. Cascella, J. Chem. Theory Comput. 14 (9), 4928–4937 (2018).
  • S.L. Bore, H.B. Kolli, T. Kawakatsu, G. Milano and M. Cascella, J. Chem. Theory Comput. 15 (3), 2033–2041 (2019).
  • A. De Nicola, T.A. Soares, D.E.S. Santos, S.L. Bore, G.J.A. Sevink, M. Cascella and G. Milano, Biochim. Biophys. Acta 0, 129570 (2020).
  • J. Brandrup, E.H. Immergut, E.A. Grulke, A. Abe and D.R. Bloch, Polymer Handbook, Vol. 7 (John Wiley & Sons, New York, 1989).
  • T. Lindvig, M.L. Michelsen and G.M. Kontogeorgis, Fluid Ph. Equilibria 203 (1-2), 247–260 (2002).
  • S. Venkatram, C. Kim, A. Chandrasekaran and R. Ramprasad, J. Chem. Inf. Model. 59 (10), 4188–4194 (2019).
  • A.P. Sgouros, A.T. Lakkas, G. Megariotis and D.N. Theodorou, Macromolecules 51 (23), 9798–9815 (2018).
  • S.L. Bore, H.B. Kolli, A. De Nicola, M. Byshkin, T. Kawakatsu, G. Milano and M. Cascella, J. Chem. Phys. 152 (18), 184908 (2020).
  • S. Izvekov and G.A. Voth, J. Phys. Chem. B 109 (7), 2469–2473 (2005).
  • D. Reith, M. Pütz and F. Müller-Plathe, J. Comput. Chem. 24 (13), 1624–1636 (2003).
  • A.P. Lyubartsev, in Coarse-Grained Modeling of Biomolecules, edited by Garegin A. Papoian (CRC Press, Boca Raton, 2017), Chap. 1, pp. 29–54.
  • S. Amaran, N.V. Sahinidis, B. Sharda and S.J. Bury, Ann. Oper. Res. 240 (1), 351–380 (2016).
  • R.H. Myers, D.C. Montgomery and C.M. Anderson-Cook, Response Surface Methodology: Process and Product Optimization Using Designed Experiments (John Wiley & Sons, New York, 2016).
  • S.A. Piyavskii, USSR Comput. Math. & Math. Phys. 12 (4), 57–67 (1972).
  • B.O. Shubert, SIAM J. Numer. Anal. 9 (3), 379–388 (1972).
  • K.H. Chang, L.J. Hong and H. Wan, Informs. J. Comput. 25 (2), 230–243 (2013).
  • J. Mockus, V. Tiesis and A. Zilinskas, The Application of Bayesian Methods for Seeking the Extremum, Vol. 2 (North-Holand, Amsterdam, 1978), pp. 117–129.
  • H.J. Kushner, J. Math. Anal. Appl 5 (1), 150–167 (1962).
  • M. Pelikan, D.E. Goldberg and E. Cantú-Paz, Proceedings of the 1st Annual Conference on Genetic and Evolutionary Computation, Vol. 1 (Morgan Kaufmann Publishers Inc., Burlington, 1999), pp. 525–532.
  • D. Whitley, Stat. Comput. 4 (2), 65–85 (1994).
  • C.R. Reeves, INFORMS J. Comput. 9 (3), 231–250 (1997).
  • S. Kirkpatrick, C.D. Gelatt and M.P. Vecchi, Science 220 (4598), 671–680 (1983).
  • D. Bertsimas and J. Tsitsiklis, Stat. Sci. 8 (1), 10–15 (1993).
  • T.M. Alkhamis, M.A. Ahmed and V.K. Tuan, Eur. J. Oper. Res. 116 (3), 530–544 (1999).
  • M.D. McKay, R.J. Beckman and W.J. Conover, Technometrics 21 (2), 239–245 (1979).
  • J. Snoek, H. Larochelle and R.P. Adams, in Advances in Neural Information Processing Systems 25, edited by F. Pereira, C.J.C. Burges, L. Bottou and K.Q. Weinberger (Curran Associates, Inc., Red Hook, 2012), pp. 2951–2959.
  • D.R. Jones, J. Global Optim. 21 (4), 345–383 (2001).
  • J. Azimi, A. Jalali and X. Fern, preprint, arXiv:1202.5597 (2012)..
  • J.S. Bergstra, R. Bardenet, Y. Bengio and B. Kégl, in Advances in Neural Information Processing Systems 24, edited by J. Shawe-Taylor, R.S. Zemel, P.L. Bartlett, F. Pereira and K.Q. Weinberger (Curran Associates, Inc., Red Hook, 2011), pp. 2546–2554.
  • K. Swersky, J. Snoek and R.P. Adams, in Advances in Neural Information Processing Systems 26, edited by C.J.C. Burges, L. Bottou, M. Welling, Z. Ghahramani and K.Q. Weinberger (Curran Associates, Inc., Red Hook, 2013), pp. 2004–2012.
  • N. Srinivas, A. Krause, S.M. Kakade and M. Seeger, preprint, arXiv:0912.3995 (2009).
  • B. Shahriari, K. Swersky, Z. Wang, R.P. Adams and N. de Freitas, Proc. IEEE 104 (1), 148–175 (2015).
  • T.A. Wassenaar, H.I. Ingólfsson, R.A. Böckmann, D.P. Tieleman and S.J. Marrink, J. Chem. Theory Comput. 11 (5), 2144–2155 (2015).
  • B. Matérn, Spatial Variation, Vol. 36 (Springer Science & Business Media, Berlin, 2013).
  • M.L. Stein, Interpolation of Spatial Data: Some Theory for Kriging (Springer Science & Business Media, Berlin, 2012).
  • H.I. Petrache, S.W. Dodd and M.F. Brown, Biophys. J. 79 (6), 3172–3192 (2000).
  • Q. Waheed and O. Edholm, Biophys. J. 97 (10), 2754–2760 (2009).
  • J.F. Nagle and S. Tristram-Nagle, Biochim. Biophys. Acta, Biomembr. 1469 (3), 159–195 (2000).
  • E. Lindahl and O. Edholm, J. Chem. Phys. 113 (9), 3882–3893 (2000).
  • Z.A. Levine, R.M. Venable, M.C. Watson, M.G. Lerner, J.E. Shea, R.W. Pastor and F.L. Brown, J. Am. Chem. Soc. 136 (39), 13582–13585 (2014).
  • S.J. Marrink, A.H. de Vries and A.E. Mark, J. Phys. Chem. B 108 (2), 750–760 (2004).
  • S.J. Marrink, H.J. Risselada, S. Yefimov, D.P. Tieleman and A.H. de Vries, J. Phys. Chem. B 111 (27), 7812–7824 (2007).
  • C.E. Shannon, Bell Syst. Tech. J. 27 (3), 379–423 (1948).
  • B. Frénay, G. Doquire and M. Verleysen, Neural Netw. 48, 1–7 (2013).
  • R.R. Griffiths and J.M. Hernández-Lobato, preprint, arXiv:1709.05501 (2017).
  • E. Brochu, V.M. Cora and N. De Freitas, preprint, arXiv:1012.2599 (2010).
  • R. Calandra, A. Seyfarth, J. Peters and M.P. Deisenroth, Ann. Math. Artif. Intel. 76 (1-2), 5–23 (2016).
  • D.J. Lizotte, T. Wang, M.H. Bowling and D. Schuurmans, in IJCAI, Vol. 7 (Institute of Electrical and Electronics Engineers, Piscataway, 2007), pp. 944–949.
  • A. Klein, S. Falkner, S. Bartels, P. Hennig and F. Hutter, Electron. J. Stat. 11 (2), 4945–4968 (2017).
  • C.I. Bayly, P. Cieplak, W. Cornell and P.A. Kollman, J. Phys. Chem. 97 (40), 10269–10280 (1993).

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