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OnderzoekZernike (ZIAM)

Refereed academic publications of 2002

Molecular Dynamics
  1. Amadei, A., Apol, M.E.F., Brancato, G. & Di Nola, A. Theoretical equations of state for temperature and electromagnetic field dependence of fluid systems, based on the quasi-Gaussian entropy theory. Journal of Chemical Physics 116 (11) 4437-4449 (2002)

  2. Apol, M.E.F., Amadei, A. & Di Nola, A. Statistical mechanics and thermodynamics of magnetic and dielectric systems based on magnetization and polarization fluctuations: Application of the quasi-Gaussian entropy theory. Journal of Chemical Physics 116 (11) 4426-4436 (2002)

  3. Colombo, G., Roccatano, D. & Mark, A.E. Folding and stability of the three-stranded beta-sheet peptide betanova: Insights from molecular dynamics simulations. Proteins-Structure Function and Genetics 46 (4) 380-392 (2002)

  4. Feenstra, K.A., Peter, C., Scheek, R.M., Gunsteren, W.F.v. & Mark, A.E. A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides. Journal of Biomolecular Nmr 23 (3) 181-194 (2002)

  5. Flohil, J.A., Vriend, G. & Berendsen, H.J.C. Completion and refinement of 3-D homology models with restricted molecular dynamics: Application to targets 47, 58, and 111 in the CASP modeling competition and posterior analysis. Proteins-Structure Function and Genetics 48 (4) 593-604 (2002)

  6. Groenhof, G., Lensink, M.F., Berendsen, H.J.C., Snijders, J.G. & Mark, A.E. Signal transduction in the photoactive yellow protein. I. Photon absorption and the isomerization of the chromophore. Proteins-Structure Function and Genetics 48 (2) 202-211 (2002)

  7. Groenhof, G., Lensink, M.F., Berendsen, H.J.C. & Mark, A.E. Signal transduction in the photoactive yellow protein. II. Proton transfer initiates conformational changes. Proteins-Structure Function and Genetics 48 (2) 212-219 (2002)

  8. Gunsteren, W.F.v., Daura, X. & Mark, A.E. Computation of free energy. Helvetica Chimica Acta 85 (10) 3113-3129 (2002)

  9. Hess, B. Convergence of sampling in protein simulations. Physical Review E 65 (3) art-031910 (2002)

  10. Hess, B. Determining the shear viscosity of model liquids from molecular dynamics simulations. Journal of Chemical Physics 116 (1) 209-217 (2002)

  11. Hess, B., Saint-Martin, H. & Berendsen, H.J.C. Flexible constraints: An adiabatic treatment of quantum degrees of freedom, with application to the flexible and polarizable mobile charge densities in harmonic oscillators model for water. Journal of Chemical Physics 116 (22) 9602-9610 (2002)

  12. Marrink, S.J. & Mark, A.E. Molecular dynamics simulations of mixed micelles modeling human bile. Biochemistry 41 (17) 5375-5382 (2002)

  13. Marrink, S.J. & Tieleman, D.P. Molecular dynamics simulation of spontaneous membrane fusion during a cubic-hexagonal phase transition. Biophysical Journal 83 (5) 2386-2392 (2002)

  14. Odaert, B., Landrieu, I., Dijkstra, K., Schuurman-Wolters, G.K., Casteels, P., Wieruszeski, J.M., Inze, D., Scheek, R.M. & Lippens, G. Solution NMR study of the monomeric form of p13(suc1) protein sheds light on the hinge region determining the affinity for a phosphorylated substrate. Journal of Biological Chemistry 277 (14) 12375-12381 (2002)

  15. Pikkemaat, M.G., Linssen, A.B.M., Berendsen, H.J.C. & Janssen, D.B. Molecular dynamics simulations as a tool for improving protein stability. Protein Engineering 15 (3) 185-192 (2002)

  16. Roccatano, D., Colombo, G., Fioroni, M. & Mark, A.E. Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: A molecular dynamics study. Proceedings of the National Academy of Sciences of the United States of America 99 (19) 12179-12184 (2002)

  17. Schafer, H., Smith, L.J., Mark, A.E. & Gunsteren, W.F.v. Entropy calculations on the molten globule state of a protein: Side-chain entropies of alpha-lactalbumin. Proteins-Structure Function and Genetics 46 (2) 215-224 (2002)

  18. Soto, P. & Mark, A.E. The effect of the neglect of electronic polarization in peptide folding simulations. Journal of Physical Chemistry B 106 (49) 12830-12833 (2002)

  19. van den Berg, P.A.W., Feenstra, K.A., Mark, A.E., Berendsen, H.J.C. & Visser, A.J.W.G. Dynamic conformations of flavin adenine dinucleotide: Simulated molecular dynamics of the flavin cofactor related to the time- resolved fluorescence characteristics. Journal of Physical Chemistry B 106 (34) 8858-8869 (2002)

  20. van Eijk, M.C.P., Bergsma, M. & Marrink, S.J. Association behaviour of glucitol amine gemini surfactants - Self-consistent-field theory and molecular-dynamics simulations. European Physical Journal E 7 (4) 317-324 (2002)

  21. van Lune, F., Manning, L., Dijkstra, K., Berendsen, H.J.C. & Scheek, R.M. Order-parameter tensor description of HPr in a medium of oriented bicelles. Journal of Biomolecular Nmr 23 (3) 169-179 (2002)

  22. Villa, A. & Mark, A.E. Calculation of the free energy of solvation for neutral analogs of amino acid side chains. Journal of Computational Chemistry 23 (5) 548-553 (2002)

  23. Zangi, R., de Vocht, M.L., Robillard, G.T. & Mark, A.E. Molecular dynamics study of the folding of hydrophobin SC3 at a hydrophilic/hydrophobic interface. Biophysical Journal 83 (1) 112-124 (2002)

Laatst gewijzigd:22 oktober 2012 14:29