Abstract
The availability of user-friendly software and affordable multi-processor computers opens the door to the world of simulations to experimentalists, for “advanced data analysis”. Neutron scattering (NS), which explores length and time scales and probes the relative positions and motions of atoms as in simulations, constitutes the ideal partner for atomistic simulations. On the experimental side, the ever-increasing complexity of samples and therefore data requires more elaborate and realistic models. This chapter therefore describes, in practical terms, the simulation methods that can be used to interpret quasielastic and inelastic NS data, namely molecular dynamics and lattice dynamics. Both of these methods are based on the knowledge of inter-atomic interactions and total energy for which density functional theory and classical, force field-based methods are presented as the most viable.
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References
Allen MP, Tildesley DJ (1987) Computer simulation of liquids. Clarendon, Oxford
Frenkel D, Smit B (2002) Understanding molecular simulation. Academic, San Diego
Cramer CJ (2004) Essentials of computational chemistry, theories and models. Wiley Ed, New York
Springborg M (2000) Methods of electronic structure calculations. Wiley, New York
Sutmann G (2002) Classical molecular dynamics in quantum simulations of complex many-body systems: from theory to algorithms, lecture notes. In: Grotendorst J, Marx D, Muramatsu A (eds) John von Neumann Institute for Computing, Julich, NIC Series, vol 10. ISBN 3-00-009057-6, pp 211–254
Allen MP (2004) Introduction to molecular dynamics simulation in computational soft matter: from synthetic polymers to proteins, lecture notes. In: Norbert Attig, Kurt Binder, Helmut Grubmuller, Kurt Kremer (eds) John von Neumann Institute for Computing, Julich, NIC Series, vol 23. ISBN 3-00-012641-4, pp 1–28
Parlinski K (1999) Calculation of phonon dispersion curves by the direct method. Am Instr Phys Conf Proc 479:121–126
Merzel F, Fontaine-Vive F, Johnson MR (2007) NMscatt: a program for calculating inelastic scattering from large biomolecular systems using classical force field simulations. Comput Phys Commun 177:530–538
Meinhold L, Merzel F, Smith JC (2007) Lattice dynamics of a protein crystal. Phys Rev Lett 99:138101
Plazanet M, Fontaine-Vive F, Gardner KH, Forsyth TV, Ivanov A, Ramirez-Cuesta AJ, Johnson MR (2005) Neutron vibrational spectroscopy gives new insight into the structure of poly (p-phenylene terephthalamide). J Am Chem Soc 127:6672
Plazanet M, Fukushima N, Johnson MR, Horsewill AJ, Trommsdorff HP (2001) The vibrational spectrum of crystalline benzoic acid: inelastic neutron scattering and density functional theory calculations. J Chem Phys 115:3241
Zbiri M, Johnson MR, Mutka H, Payen C, Schober H (2010) Phonon control of magnetic relaxation in the pyrochlore slab SCGO through rocking motion of the Kagome-plane triangles. Phys Rev B81:104414
Johnson MR, Koza MM, Capogna L, Mutka H (2009) Probing coupling between ‘rattling’ and extended lattice modes using time-of-flight neutron scatteringcombinedwith ab-initio calculations—introducing the PALD method. Nucl Instr Meth A 600:226–228
Koza MM, Johnson MR, Viennois R, Mutka H, Girard L, Ravot D (2008) Breakdown of phonon glass paradigm in La- and Ce-filled skutterudites. Nat Mater 7:805–810
Merzel F, Fontaine-Vive F, Johnson MR, Kearley GJ (2007) Atomistic model of DNA: phonons and base-pair opening. Phys Rev E 76:31917–31921
Rog T, Murzyn K, Hinsen K, Kneller GR (2003) nMoldyn: a program package for neutron scattering oriented analysis of molecular dynamics simulations. J Comp Chem 24:657–667. http://dirac.cnrs-orleans.fr/plone/software/nmoldyn/ (Accessed 14 December 2011)
Kneller GR, Calligari P (2006) Efficient characterization of protein secondary structure in terms of screw motions. Acta Cryst D62:302–311
Brooks BR, Janezic D, Karplus M (1994) Harmonic analysis of large systems. I. Methodology. J Comp Chem 16:1522
Sniechowski M, Djurado D, Bee M, Gonzalez MA, Johnson MR, Rannou P, Dufour B, Luzny W (2005) Force field based molecular dynamics simulations in highly conducting compounds of poly(aniline). A comparison with quasi-elastic neutron scattering measurements. Chem Phys 317:289–297
Sun H (1998) COMPASS: an ab initio force field optimised for condensed phase application – overview with detail on alkane and benzene compounds. J Phys Chem B 102:7338
Fouquet P, Johnson MR, Hedgeland H, Jardine AP, Ellis J, Allison W (2009) Molecular dynamics simulations of the diffusion of benzene sub-monolayer films on graphite basal plane surfaces. Carbon 47:2627
Hedgeland H, Fouquet P, Jardine AP, Alexandrowicz G, Allison W, Ellis J (2009) Measurement of single-molecule frictional dissipation in a prototypical nanoscale system. Nat Phys 5:561
Fontaine-Vive F, Johnson MR, Kearley GJ, Cowan J, Howard JAK, Parker SF (2006) Phonon driven proton transfer in crystals with short strong hydrogen bonds. J Chem Phys 124:234503
Cleland WW, Kreevoy MM (1994) Low barrier hydrogen bonds and enzymic catalysis. Science 264:1887–1890
Trylska J, Grochowski P, McGammon JA (2004) The role of hydrogen bonding in enzymatic reaction catalysed by HIV-1 protease. Protein Sci 13:513–528
CASTEP. http://www.castep.org/
ABINIT. http://www.abinit.org/
Gaussian. http://www.gaussian.com/
CHARMM. http://www.charmm.org/
AMBER. http://ambermd.org/
Kohn W (1996) Density functional and density matrix method scaling linearly with the number of atoms. Phys Rev Lett 76:3168–3171
Siesta. http://www.xmarks.com/site/www.uam.es/departamentos/ciencias/fismateriac/siesta/
Hine NDM, Haynes PD, Mostofi AA, Skylaris C-K, Payne MC (2009) Linear-scaling density-functional theory with tens of thousands of atoms: expanding the scope and scale of calculations with ONETEP. Comput Phys Commun 180:1041. http://www2.tcm.phy.cam.ac.uk/onetep/ (Accessed on 3 December 2011)
Fontaine-Vive F, Merzel F, Johnson MR, Kearley GJ (2009) Collagen and component polypeptides: low frequency and amide vibrations. Chem Phys 355:141–148
McStas. http://neutron.risoe.dk/
Farhi E, Hugouvieux V, Johnson MR, Kob W (2009) Virtual experiments: combining realistic neutron scattering instrument and sample simulations. J Comp Phys 228:5251–5261
Hartree DR (1928) The wave mechanics of an atom with a non-coulomb central field. Part I. Theory and Methods. Proc Cambridge Phil Soc 24:89–110
Fock V (1930) Z Physik 61:126
Middendorf HD, Hayward RL, Parker SF, Bradshaw J, Miller A (1995) Vibrational neutron spectroscopy of collagen and model polypeptides. Biophys J 69:660–673
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Johnson, M.R., González, M.A., Zbiri, M., Pellegrini, E. (2012). Computational Tools to Understand Inelastic and Quasielastic Neutron Scattering Data. In: García Sakai, V., Alba-Simionesco, C., Chen, SH. (eds) Dynamics of Soft Matter. Neutron Scattering Applications and Techniques. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-0727-0_2
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DOI: https://doi.org/10.1007/978-1-4614-0727-0_2
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