Polaris(MD)
Polarisation and Simulation (Molecular Dynamics)
Publications related to the POLARIS(MD) project.

[1] W. Jalby, D. Kuck, A. D. Malony, M. Masella, A. Mazouz, and M. Popov. The long and winding road toward efficient high-performance computing. Proceedings of the IEEE, 106(11):1985-2003, Nov 2018. [ DOI ]
[2] Celine Houriez, Michael Meot-Ner (Mautner), and Michel Masella. Solvation of the guanidinium ion in pure aqueous environments: A theoretical study from an “ab initio”-based polarizable force field. Journal of Physical Chemistry B, 121(50):11219-11228, Dec 21 2017. [ DOI ]
[3] Celine Houriez, Valerie Vallet, Florent Real, Michael Meot-Ner (Mautner), and Michel Masella. Organic ion association in aqueous phase and ab initio-based force fields: The case of carboxylate/ammonium salts. Journal of Chemical Physics, 147(16):161720, Oct 28 2017. [ DOI ]
[4] Stephan Mohr, Michel Masella, Laura E. Ratcliff, and Luigi Genovese. Complexity reduction in large quantum systems: Fragment identification and population analysis via a local optimized minimal basis. Journal of Chemical Theory and Computation, 13(9):4079-4088, Sep 2017. [ DOI ]
[5] Laura E. Ratcliff, Stephan Mohr, Georg Huhs, Thierry Deutsch, Michel Masella, and Luigi Genovese. Challenges in large scale quantum mechanical calculations. Wiley Interdisciplinary Reviews-Computational Molecular Science, 7(1), Jan-Feb 2017. [ DOI ]
[6] Jonathan P. Coles, Celine Houriez, Michael Meot-Ner (Mautner), and Michel Masella. Extrapolating single organic ion solvation thermochemistry from simulated water nanodroplets. Journal of Physical Chemistry B, 120(35):9402-9409, Sep 8 2016. [ DOI ]
[7] Florent Real, Andre Severo Pereira Gomes, Yansel Omar Guerrero Martinez, Tahra Ayed, Nicolas Galland, Michel Masella, and Valerie Vallet. Structural, dynamical, and transport properties of the hydrated halides: How do at- bulk properties compare with those of the other halides, from f- to i-? Journal of Chemical Physics, 144(12):124513, Mar 28 2016. [ DOI ]
[8] Celine Houriez, Michael Meot-Ner (Mautner), and Michel Masella. Simulated solvation of organic ions ii: Study of linear alkylated carboxylate ions in water nanodrops and in liquid water. propensity for air/water interface and convergence to bulk solvation properties. Journal of Physical Chemistry B, 119(36):12094-12107, Sep 10 2015. [ DOI ]
[9] Jonathan P. Coles and Michel Masella. The fast multipole method and point dipole moment polarizable force fields. Journal of Chemical Physics, 142(2):024109, Jan 14 2015. [ DOI ]
[10] Valerie Vallet and Michel Masella. Benchmark binding energies of ammonium and alkyl-ammonium ions interacting with water. are ammonium-water hydrogen bonds strong? Chemical Physics Letters, 618:168-173, Jan 2 2015. [ DOI ]
[11] Celine Houriez, Michael Meot-Ner (Mautner), and Michel Masella. Simulated solvation of organic ions: Protonated methylamines in water nanodroplets. convergence toward bulk properties and the absolute proton solvation enthalpy. Journal of Physical Chemistry B, 118(23):6222-6233, Jun 12 2014. [ DOI ]
[12] Michel Masella, Daniel Borgis, and Philippe Cuniasse. A multiscale coarse-grained polarizable solvent model for handling long tail bulk electrostatics. Journal of Computational Chemistry, 34(13):1112-1124, May 15 2013. [ DOI ]
[13] Florent Real, Valerie Vallet, Jean-Pierre Flament, and Michel Masella. Revisiting a many-body model for water based on a single polarizable site: From gas phase clusters to liquid and air/liquid water systems. Journal of Chemical Physics, 139(11):114502, Sep 21 2013. [ DOI ]
[14] Florent Real, Michael Trumm, Bernd Schimmelpfennig, Michel Masella, and Valerie Vallet. Further insights in the ability of classical nonadditive potentials to model actinide ionwater interactions. Journal of Computational Chemistry, 34(9):707-719, Apr 5 2013. [ DOI ]
[15] Celine Houriez, Nicolas Ferre, Didier Siri, Paul Tordo, and Michel Masella. Assessing the accuracy of a qm/mm//md combined protocol to compute spectromagnetic properties of polyfunctional nitroxides in solution. Theoretical Chemistry Accounts, 131(6):1240, Jun 2012. [ DOI ]
[16] Michael Trumm, Yansel Omar Guerrero Martinez, Florent Real, Michel Masella, Valerie Vallet, and Bernd Schimmelpfennig. Modeling the hydration of mono-atomic anions from the gas phase to the bulk phase: The case of the halide ions f-, cl-, and br-. Journal of Chemical Physics, 136(4):044509, Jan 28 2012. [ DOI ]
[17] Michel Masella, Daniel Borgis, and Philippe Cuniasse. Combining a polarizable force-field and a coarse-grained polarizable solvent model. ii. accounting for hydrophobic effects. Journal of Computational Chemistry, 32(12):2664-2678, Sep 2011. [ DOI ]
[18] Florent Real, Michael Trumm, Valerie Vallet, Bernd Schimmelpfennig, Michel Masella, and Jean-Pierre Flament. Quantum chemical and molecular dynamics study of the coordination of th(iv) in aqueous solvent. Journal of Physical Chemistry B, 114(48):15913-15924, Dec 9 2010. [ DOI ]
[19] Celine Houriez, Nicolas Ferre, Didier Siri, Paul Tordo, and Michel Masella. Structure and spectromagnetic properties of the superoxide radical adduct of the dmpo in water: Elucidation by theoretical investigations (114b, pg 11793, 2010). Journal of Physical Chemistry B, 114(42):13616, Oct 28 2010. [ DOI ]
[20] Celine Houriez, Michel Masella, and Nicolas Ferre. Structural and atoms-in-molecules analysis of hydrogen-bond network around nitroxides in liquid waters. Journal of Chemical Physics, 133(12):124508, Sep 28 2010. [ DOI ]
[21] Celine Houriez, Nicolas Ferre, Didier Siri, Paul Tordo, and Michel Masella. Structure and spectromagnetic properties of the superoxide radical adduct of dmpo in water: Elucidation by theoretical investigations. Journal of Physical Chemistry B, 114(36):11793-11803, Sep 16 2010. [ DOI ]
[22] Celine Houriez, Nicolas Ferre, Didier Siri, and Michel Masella. Further insights into the environmental effects on the computed hyperfine coupling constants of nitroxides in aqueous solution. Journal of Physical Chemistry B, 113(45):15047-15056, Nov 12 2009. [ DOI ]
[23] Celine Houriez, Nicolas Ferre, Michel Masella, and Didier Siri. Quantitative evaluation of the aqueous dihydronitroxide nitrogen hyperfine coupling constant from qm/mm//md computations. Journal of Molecular Structure-Theochem, 898(1-3):49-55, Mar 30 2009. [ DOI ]
[24] Michel Masella, Daniel Borgis, and Philippe Cuniasse. Combining a polarizable force-field and a coarse-grained polarizable solvent model: Application to long dynamics simulations of bovine pancreatic trypsin inhibitor. Journal of Computational Chemistry, 29(11):1707-1724, Aug 2008. [ DOI ]
[25] Celine Houriez, Nicolas Ferre, Michel Masella, and Didier Siri. Prediction of nitroxide hyperfine coupling constants in solution from combined nanosecond scale simulations and quantum computations. Journal of Chemical Physics, 128(24):244504, Jun 28 2008. [ DOI ]
[26] C. Houriez, N. Ferre, J. P. Flament, M. Masella, and D. Siri. Electronic basis of the comparable hydrogen bond properties of small h2co/(h2o)(n) and h2no/(h2o)n systems (n=1, 2). Journal of Physical Chemistry A, 111(45):11673-11682, Nov 15 2007. [ DOI ]
[27] P Llinas, M Masella, T Stigbrand, A Menez, EA Stura, and MH Le Du. Structural studies of human alkaline phosphatase in complex with strontium: Implication for its secondary effect in bones. Protein Science, 15(7):1691-1700, Jul 2006. [ DOI ]
[28] Michel Masella. The multiple time step r-respa procedure and polarizable potentials based on induced dipole moments. Molecular Physics, 104(3):415-428, Feb 10 2006. [ DOI ]
[29] Philippe Cuniasse and Michel Masella. A many-body model to study proteins. ii. incidence of many-body polarization effects on the interaction of the calmodulin protein with four ca2+ dications and with a target enzyme peptide. The Journal of Chemical Physics, 119(3):1874-1878, 2003. [ DOI ]
[30] M Masella and P Cuniasse. A many-body model to study proteins. i. applications to mlnm+ complexes, mm+=li+, na+, k+, mg2+, ca2+, and zn2+, l=h2o, ch3oh, hconh2, n=1-6, and to small hydrogen bonded systems. Journal of Chemical Physics, 119(3):1866-1873, Jul 15 2003. [ DOI ]
[31] P Vitorge and M Masella. A theoretical study of [be, (h2o)(n)](2+), [beoh, (h2o)(n-1)](+) and [be(oh)(2), (h2o)(n-2)] aggregates (n=1-6). incidence of the first hydration shells on the hydrolysis reactions of be2+ and beoh+ systems. Chemical Physics Letters, 332(3-4):367-374, Dec 22 2000. [ DOI ]
[32] M Masella and JP Flament. Influence of cooperativity on hydrogen bond networks. Molecular Simulation, 24(1-3):131-156, 2000. Virtual Conference on Applications and Methodology of Molecular Simulation in the Physical and Biological Sciences, Electr Network, Apr 19-May 04, 1999. [ DOI ]
[33] SB Nielsen, M Masella, and P Kebarle. Competitive gas-phase solvation of alkali metal ions by water and methanol. Journal of Physical Chemistry A, 103(48):9891-9898, Dec 2 1999. [ DOI ]
[34] M Masella and JP Flament. Hydrogen bond network fluctuations in small (h2o)(n) clusters (n=8-12-24). Journal of Chemical Physics, 111(11):5081-5090, Sep 15 1999. [ DOI ]
[35] G van der Rest and M Masella. Do cooperative effects influence the bending hoh vibrational spectra of small (h2o) (n) clusters (n=2-4)? Journal of Molecular Spectroscopy, 196(1):146-148, Jul 1999. [ DOI ]
[36] M Masella and JP Flament. A theoretical study of five water/ammonia/formaldehyde cyclic trimers: Influence of cooperative effects. Journal of Chemical Physics, 110(15):7245-7255, Apr 15 1999. [ DOI ]
[37] P Manivet and M Masella. An ab initio study of three (ethane-1,2 diol/water) complexes. Chemical Physics Letters, 288(5-6):642-646, May 29 1998. [ DOI ]
[38] M Masella and JP Flament. Relation between cooperative effects in cyclic water, methanol/water, and methanol trimers and hydrogen bonds in methanol/water, ethanol/water, and dimethylether/water heterodimers. Journal of Chemical Physics, 108(17):7141-7151, May 1 1998. [ DOI ]
[39] M Masella, N Gresh, and JP Flament. A theoretical study of nonadditive effects in four water tetramers. Journal of the Chemical Society-Faraday Transactions, 94(18):2745-2753, Sep 21 1998. [ DOI ]
[40] M Masella and JP Flament. A many-body model for alcohols: applications to the cyclic methanol/water hetero trimers, and to the (methanol)(n), (ethanol)(n) and (t-butanol)(n) cyclic clusters (n = 2-6). Molecular Physics, 95(1):97-106, Sep 1998. [ DOI ]
[41] M Masella. Cooperative effects in water tetramers. comparison between the empirical many-body model tcpe and ab initio calculations. Comptes Rendus de l Academie des Sciences Serie II Fascicule C-Chimie, 1(7):441-447, Jul 1998. [ DOI ]
[42] M Masella and JP Flament. Can the oh stretch vibrational spectra of (h2o)(n) cluster (n = 1-6) be estimated from an empirical many-body model and a polynomial oh stretch potential? Chemical Physics Letters, 286(1-2):177-182, Apr 3 1998. [ DOI ]
[43] M Masella and JP Flament. A pairwise and two many-body models for water: Influence of nonpairwise effects upon the stability and geometry of (h2o)(n) cyclic (n=3-6) and cagelike (n=6-20) clusters. Journal of Chemical Physics, 107(21):9105-9116, Dec 1 1997. [ DOI ]

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