Publications

@article{MM.pezzella.jpcb:2020,

title = {Water Dynamics Around Proteins: T- and R-States of Hemoglobin and Melittin},

author = {M. Pezzella and K. El Hage and M. J. M. Niesen and S. Shin and A. P. Willard and M. Meuwly and M. Karplus},

year  = {2020},

date = {2020-01-01},

journal = {J. Phys. Chem. B},

volume = {124},

pages = {6540-6554},

keywords = {Hemoglobin, Molecular Dynamics, Solvation},

pubstate = {published},

tppubtype = {article}

}

@article{MM.salehi.jpcb:2020,

title = {The Dynamics and Infrared Spectrocopy of Monomeric and Dimeric Wild Type and Mutant Insulin},

author = {S. M. Salehi and D. Koner and M. Meuwly},

year  = {2020},

date = {2020-01-01},

journal = {J. Phys. Chem. B},

volume = {in print},

keywords = {Computational Vibrational Spectroscopy, Insulin, Molecular Dynamics},

pubstate = {published},

tppubtype = {article}

}

@article{MM.hemoglobin:2018,

title = {Valid Molecular Dynamics Simulations of Human Hemoglobin Require a Surprisingly Large Box Size},

author = {K. El Hage and F. Hedin and P. K. Gupta and M. Meuwly and M. Karplus},

year  = {2018},

date = {2018-01-01},

journal = {eLife},

volume = {7},

pages = {e35560},

keywords = {Hemoglobin, Molecular Dynamics, Molecular Simulations},

pubstate = {published},

tppubtype = {article}

}

@article{MM.weiss.bj:2017,

title = {Non-Standard Protein Engineering at the Boundary of Molecular Mechanics and Quantum Chemistry:  Halogen-Based Design of Insulin Analogs},

author = {M. A. Weiss and N. F. Phillips and F. Ismail-Beigi and V. Pandyarajan and Y. Yang and Y-S Chen and N.Wickramasinghe and B. Smith and J. G. Menting and M. C. Lawrence and K. El Hage and M. Meuwly},

year  = {2017},

date = {2017-01-01},

journal = {Biophys. J.},

volume = {112},

pages = {53A},

keywords = {Halogenation, Halogens, Insulin, Molecular Dynamics, Protein Engineering, Quantum Chemistry},

pubstate = {published},

tppubtype = {article}

}

@article{MM.greif.sd:2016,

title = {Following the Molecular Motion of Near-Resonant Excited CO on Pt(111): a Simulated X-Ray Photoelectron Diffraction Study Based on Molecular Dynamics Calculations},

author = {M. Greif and T. Nagy and M. Soloviov and L. Castiglioni and M. Hengsberger and M. Meuwly and J. Osterwalder},

year  = {2016},

date = {2016-01-01},

journal = {Struc. Dyn.},

volume = {3},

pages = {059901},

keywords = {CO, Molecular Dynamics, Molecular Motion, X-Ray Photoelectron Diffraction},

pubstate = {published},

tppubtype = {article}

}

@article{MM.jin.jpcb:2016,

title = {Copper Oxidation/Reduction in Water and Protein: Studies with DFTB3/MM and VALBOND Molecular Dynamics Simulations},

author = {H. Jin and P. Gojal and A. K. Das and M. Gaus and M. Meuwly and Q. Cui},

year  = {2016},

date = {2016-01-01},

journal = {J. Phys. Chem. B},

volume = {120},

pages = {1894},

keywords = {Copper, DFTB3, Molecular Dynamics, Molecular Mechanics, VALBOND},

pubstate = {published},

tppubtype = {article}

}

@article{MM.greif.sd:2015,

title = {Following the Molecular Motion of Near-Resonant Excited CO on Pt(111): a Simulated X-Ray Photoelectron Diffraction Study Based on Molecular Dynamics Calculations},

author = {M. Greif and T. Nagy and M. Soloviov and L. Castiglioni and M. Hengsberger and M. Meuwly and J. Osterwalder},

year  = {2015},

date = {2015-01-01},

journal = {Struc. Dyn.},

volume = {1},

pages = {035102},

keywords = {CO, Molecular Dynamics, Molecular Motion, X-Ray Photoelectron Diffraction},

pubstate = {published},

tppubtype = {article}

}

@article{MM.dudev.jcc:2015,

title = {Quantum-Chemistry Based Calibration of the Alkali Metal Cation Series (Li(+) to Cs(+)) for Large-Scale Polarizable Molecular Mechanics/Dynamics Simulations},

author = {T. Dudev and M. Devereux and M. Meuwly and C. Lim and J.-P. Piquemal and N. Gresh},

year  = {2015},

date = {2015-01-01},

journal = {J. Comp. Chem.},

volume = {36},

pages = {285-302},

keywords = {Alkali Metal Cation, Molecular Dynamics, Molecular Mechanics, Quantum Chemistry},

pubstate = {published},

tppubtype = {article}

}

@article{MM.devereux.jctc:2014,

title = {A Novel, Computationally Efficient Multipolar Model Employing Distributed Charges for Molecular Dynamics Simulation},

author = {M. Devereux and S. Raghunathan and D. G. Fedorov and M. Meuwly},

year  = {2014},

date = {2014-01-01},

journal = {J. Chem. Theo. Comput.},

volume = {10},

pages = {4229-4241},

keywords = {Distributed Charge Model, Molecular Dynamics, Molecular Simulation, Multipolar Model},

pubstate = {published},

tppubtype = {article}

}

@article{MM.bereau.jctc:2013,

title = {Leveraging Symmetries of Static Atomic Multipole Electrostatics in Molecular Dynamics Simulations},

author = {T. Bereau and C. Kramer and M. Meuwly},

year  = {2013},

date = {2013-01-01},

journal = {J. Chem. Theo. Comput.},

volume = {9},

pages = {5450},

keywords = {Electrostatics, Molecular Dynamics, Static Atomic Multipoles},

pubstate = {published},

tppubtype = {article}

}

@article{MM.lee.pccp:2013,

title = {Hydration Free Energies of Cyanide and Hydroxide Ions from Molecular Dynamics Simulations with Accurate Force Fields},

author = {M. W. Lee and M. Meuwly},

year  = {2013},

date = {2013-01-01},

journal = {PCCP},

volume = {15},

pages = {20303},

keywords = {Cyanide, Force fields, Hydroxide, Molecular Dynamics},

pubstate = {published},

tppubtype = {article}

}

@article{MM.lee.jcp:2013,

title = {2D IR Spectra of Cyanide in Water Investigated by Molecular Dynamics Simulations},

author = {M. W. Lee and J. K. Carr and M. Goellner and P. Hamm and M. Meuwly},

year  = {2013},

date = {2013-01-01},

journal = {J. Chem. Phys.},

volume = {139},

pages = {054506},

keywords = {2D IR, Cyanide, Molecular Dynamics},

pubstate = {published},

tppubtype = {article}

}

@article{MM.lee.jpcb:2012,

title = {Molecular Dynamics Simulation of Nitric Oxide in Myoglobin},

author = {M. W. Lee and M. Meuwly},

year  = {2012},

date = {2012-01-01},

journal = {J. Phys. Chem. B},

volume = {116},

pages = {4154},

keywords = {Molecular Dynamics, Molecular Simulation, Myoglobin, Nitric Oxide},

pubstate = {published},

tppubtype = {article}

}

@article{MM.meuwly.cmse:2009,

title = {Studying Chemical Reactions with Molecular Mechanics},

author = {M. Meuwly},

year  = {2009},

date = {2009-01-01},

journal = {Comp. Meth. Sci. Eng.},

volume = {1108},

pages = {138},

note = {Conference Information: International Conference on Computational Methods in Science and Engineering, SEP 25-30, 2008 Hersonissos, Greece

Comp. Meth. Sci. Eng., Vol 1 - Adv. Comp. Sci., AIP Conference Proceedings},

keywords = {Chemical Reactions, Molecular Dynamics},

pubstate = {published},

tppubtype = {article}

}