Molecular-dynamics study

Straub J E, Borkovec M and Berne B J 1988 Molecular dynamics study of an isomerizing diatomic Lennard-Jones fluid J. Chem. Phys. 89 4833... 

Jesson B J, Foley M and Madden P A 1997 Thermal properties of the self-interstitlal In aluminum an ab initio molecular-dynamics study Pbys. Rev. B 55 4941-6... 

AokI M I and Tsumuraya K 1997 Ab initio molecular-dynamics study of pressure-induced glass-to-crystal transitions In the sodium system Pbys. Rev. B 56 2962-8... 

Parrinello M and Rahman A 1980 Crystal structure and pair potentials a molecular dynamics study Phys. Rev.L 45 1196-9... 

Lutsko J F ef a/1989 Molecular-dynamic study of lattice-defect-nucleated melting in metals using an embedded-atom-method potential Phys. Rev. B 40 2841... 

Rahman, A., Stillinger, F.H. Molecular dynamics study of liquid water. J. Chem. Phys. 55 (1971) 3336-3359. 

Tieleman, D.P., Berendsen, H.J.C. A molecular dynamics study of the pores formed by E. coli OmpF porin in a fully hydrated POPE bilayer. Biophys. J., in print (1998). 

Meier, R.J., Van Doremaele, H.J., larlori, S., Buda, F. Ab-initio molecular dynamics study of metallocene-catalysed ethylene polymerization. J. Amer. Chem. Soc. 116 (1994) 7274-7281. 

Mavri, J., Berendsen, H.J.C., Van Gunsteren, W.F. Influence of solvent on intramolecular proton transfer in hydrogen malonate. Molecular dynamics study of tunneling by density matrix evolution and nonequilibrium solvation. J. Phys. Chem. 97 (1993) 13469-13476. 

Izrailev et al., 1997] Izrailev, S., Stepaniants, S., Balsera, M., Oono, Y., and Schulten, K. Molecular dynamics study of unbinding of the avidin-biotin complex. Biophys. J. 72 (1997) 1568-1581... 

In molecular mechanics and molecular dynamics studies of proteins, assig-ment of standard, non-dynamical ionization states of protein titratable groups is a common practice. This assumption seems to be well justified because proton exchange times between protein and solution usually far exceed the time range of the MD simulations. We investigated to what extent the assumed protonation state of a protein influences its molecular dynamics trajectory, and how often our titration algorithm predicted ionization states identical to those imposed on the groups, when applied to a set of structures derived from a molecular dynamics trajectory [34]. As a model we took the bovine... 

Figiue 7.12 from Guillot B 1991. A Molecular Dynamics Study of the Infrared Spectrum of Water. The Journal of Chemical Physics 95 1543-1551. 

Fig. 7.12 Experimental and calculated infrared spectra for liquid water. The black dots are the experimental values. The thick curve is the classical profile produced by the molecular dynamics simulation. The thin curve is obtained by applying quantum corrections. (Figure redrawn from Guilbt B 1991. A Molecular Dynamics Study of the Infrared Spectrum of Water. Journal of Chemical Physics 95 1543-1551.)...

Leach A R and T E Klein 1995. A Molecular Dynamics Study of the Inhibitors of Dihydrofola Reductase by a Phenyl Triazine. Journal of Computational Chemistry 16 1378-1393. 

Catlow C R A1994. Molecular Dynamics Studies of Defects in Solids. In NATO ASI Series C 418 (Defects and Disorder in Crystalline and Amorphous Solids), pp. 357-373. 

Zhaiig X and C R A Callow 1992. Molecular Dynamics Study of Oxygen Diffusion in YBa2Cu306]9. Physical Review B46 457-462. 

Molecular dynamics studies are best done with a force field designed for that purpose. 

Both molecular dynamics studies and femtosecond laser spectroscopy results show that molecules with a sufficient amount of energy to react often vibrate until the nuclei follow a path that leads to the reaction coordinate. Dynamical calculations, called trajectory calculations, are an application of the molecular dynamics method that can be performed at semiempirical or ah initio levels of theory. See Chapter 19 for further details. 

Molecular dynamics studies can be done to examine how the path and orientation of approaching reactants lead to a chemical reaction. These studies require an accurate potential energy surface, which is most often an analytic... 

RM Fine, H Wang, PS Shenkm, DL Yarmush, C Levmthal. Predicting antibody hypervariable loop conformations. II Minimization and molecular dynamics studies of MCP603 from many randomly generated loop conformations. Proteins 1 342-362, 1986. 

Once the model of a ligand-receptor complex is built, its stability should be evaluated. Simple molecular mechanics optimization of the putative ligand-receptor complex leads only to the identification of the closest local minimum. However, molecular mechanics optimization of molecules lacks two crucial properties of real molecular systems temperature and, consequently, motion. Molecular dynamics studies the time-dependent evolution of coordinates of complex multimolecular systems as a function of inter- and intramolecular interactions (see Chapter 3). Because simulations are usually performed at nonnal temperature (—300 K), relatively low energy barriers, on the order of kT (0.6 kcal), can... 

Despite their simplicity, certainly compared to the all-atom potentials used in molecular dynamics studies, these contact energy functions enable the exploration of different interaction scenarios. This diversity is achieved by changing the heterogeneity of the sequence, by altering the number N of different types of residues that are being used. The most elementary lattice model involves only two types of monomers hydrophobic... 

A Caflisch, M Karplus. Molecular dynamics studies of protein and peptide folding and unfolding. In K Merz Jr, S Le Grand, eds. The Protein Eoldmg Problem and Tertiary Structure Prediction. Boston Birkhauser, 1994, pp 193-230. 

RB Yelle, BW Beck, JB Koerner, CA Sacksteder, T Ichiye. Influence of the metal site on the structure and solvation of nibredoxm and its analogs A molecular dynamics study. Proteins accepted. 

WE van Gunsteren. Molecular dynamics studies of proteins. Curr Opinion Struct Biol 3 277-281, 1993. 

J. Stadler, R. Mikulla, H.-R. Trebin. IMD a software package for molecular dynamics studies on parallel computers. Int J Mod Phys C 5 1131, 1997. 

Molecular Dynamics Study of Liquid Water Aneesur Rahman and Frank H. Stillinger The Journal of Chemical Physics 55 (1972) 3336-3359... 

THE MARTENSITIC TRANSFORMATION IN IRON-NICKEL ALLOYS A MOLECULAR DYNAMICS STUDY... 

R. Meyer and P. Entel, Molecular dynamics study of iron-nickel alloys. 

In the synthesis of l,3-dithiolan-2-ones from spirocyclic intermediates, via episulfides, substituted tetrathiacyclododecane and the related pentathiacyclopentadecane were isolated in good yields <96JCS(P1)289>. Preparation and molecular dynamics studies of 2,5,8,17,20,23-hexathia[9.9]-p-cyclophane have been reported <96P4203>. The syntheses and properties of thiocrowned l,3-dithiole-2-thiones and their conversion to tetrathiafiilvenes via treatment with triethylphosphine have been described <96LA551>. 

Wang, H. and Hu, Y. Z., Molecular Dynamics Study on Interfacial Slip Phenomenon of Ultra-thin Lubricating Films," presented 2XITC2000, Nagasaki, Japan, Oct. 2000. 

Glosli, J. N. and McClelland, G., "Molecular Dynamics Study of Sliding Friction of Ordered Organic Monolayers, Phys. Rev. Lett., Vol. 70,1993, pp. 1960-1963. 

Rousseau, R., Schreiner, E., Kohbneyer, A., and Marx, D., Ternperamre-dependent conformational transitions and hydrogen-bond d3mamics of the elastin-bke octapeptide GVG(VPGVG) A molecular-dynamics study, Biophys. J., 86, 1393-1407, 2004. 

Molecular Dynamics Studies of Crystal Growth and Thin Films... 

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