Geodesic
Estimation of parameters of the large-grained model of lipids with quantum-chemical methods
Vestnik Ûžno-Uralʹskogo gosudarstvennogo universiteta. Seriâ, Matematika, mehanika, fizika, no. 6 (2012), pp. 89-96 Cet article a éte moissonné depuis la source Math-Net.Ru

Voir la notice de l'article

A large-grained model of a lipid bilayer is analyzed in the article. The parameters of the intramolecular potentials of coarse-grained dipalmitoilphosphatidilcholine (DpPC) molecule are determined by adjusting to its mechanical properties evaluated by quantum-chemical calculations from first principles. Physicochemical properties of the bilayer obtained by the offered model are in good agreement with the experimental results.
Keywords: lipids, quantum chemistry, molecular dynamics.
Mots-clés : lipid membranes 
@article{VYURM_2012_6_a13,
     author = {A. V. Ivanova and V. P. Beskachko},
     title = {Estimation of parameters of the large-grained model of lipids with quantum-chemical methods},
     journal = {Vestnik \^U\v{z}no-Uralʹskogo gosudarstvennogo universiteta. Seri\^a, Matematika, mehanika, fizika},
     pages = {89--96},
     year = {2012},
     number = {6},
     language = {ru},
     url = {http://geodesic.mathdoc.fr/item/VYURM_2012_6_a13/}
}
TY  - JOUR
AU  - A. V. Ivanova
AU  - V. P. Beskachko
TI  - Estimation of parameters of the large-grained model of lipids with quantum-chemical methods
JO  - Vestnik Ûžno-Uralʹskogo gosudarstvennogo universiteta. Seriâ, Matematika, mehanika, fizika
PY  - 2012
SP  - 89
EP  - 96
IS  - 6
UR  - http://geodesic.mathdoc.fr/item/VYURM_2012_6_a13/
LA  - ru
ID  - VYURM_2012_6_a13
ER  - 
%0 Journal Article
%A A. V. Ivanova
%A V. P. Beskachko
%T Estimation of parameters of the large-grained model of lipids with quantum-chemical methods
%J Vestnik Ûžno-Uralʹskogo gosudarstvennogo universiteta. Seriâ, Matematika, mehanika, fizika
%D 2012
%P 89-96
%N 6
%U http://geodesic.mathdoc.fr/item/VYURM_2012_6_a13/
%G ru
%F VYURM_2012_6_a13
A. V. Ivanova; V. P. Beskachko. Estimation of parameters of the large-grained model of lipids with quantum-chemical methods. Vestnik Ûžno-Uralʹskogo gosudarstvennogo universiteta. Seriâ, Matematika, mehanika, fizika, no. 6 (2012), pp. 89-96. http://geodesic.mathdoc.fr/item/VYURM_2012_6_a13/

[1] M. Venturoli, M. M. Sperotto, M. Kranenburg, B. Smit, “Mesoscopic models of biological membranes”, Physics Reports, 437:1–2 (2006), 1–54 | DOI

[2] G. Ayton, G. A. Voth, “Bridging microscopic and mesoscopic simulations of lipid bilayers”, Biophysical Journal, 83:6 (2002), 3357–3370 | DOI

[3] A. H. de Vries, A. E. Mark, S. J. Marrink, “Molecular dynamics simulation of the spontaneous formation of a small DPPC vesicle in water in atomistic detail”, Journal of the American Chemical Society, 126:14 (2004), 4488–4489 | DOI

[4] http://classic.chem.msu.su/gran/firefly/index.html

[5] M. W. Schmidt, K. K. Baldridge, J. A. Boatz, S. T. Elbert et al., “Advances in electronic structure theory: GAMESS a decade later”, Journal of Computational Chemistry, 14 (1993), 1347–1363 | DOI

[6] S. J. Marrink, A. H. de Vries, A. E. Mark, “Coarse grained model for semi-quantitative lipid simulations”, Journal of Physical Chemistry B, 108:2 (2004), 750–760 | DOI

[7] S. J. Marrink, H. J. Risselada, S. Yefimov et al., “The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations”, Journal of Physical Chemistry B, 111:27 (2007), 7812–7824 | DOI

[8] D. van der Spoel, E. Lindahl, B. Hess et al., “GROMACS: Fast, Flexible and Free”, Journal of Computational Chemistry, 26:16 (2005), 1701–1718 | DOI

[9] B. Hess, C. Kutzner, D. van der Spoel, E. Lindahl, “GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation”, Journal of Chemical Theory and Computation, 4:3, 435–447 | DOI | MR

[10] H. J. C. Berendsen, J. P. M. Postma, A. Di Nola, J. R. Haak, “Molecular dynamics with coupling to an external bath”, Journal of Chemical Physics, 81:8 (1984), 3684–3690 | DOI

[11] http://www.ks.uiuc.edu/Research/vmd/

[12] J. F. Nagle, S. Tristram-Nagle, “Structure of lipid bilayers”, Biochimica et Biophysica Acta, 1469:3 (2000), 159–195 | DOI

[13] E. Lindahl, O. Edholm, “Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations”, Biophysical journal, 79:1 (2000), 426–433 | DOI

[14] J. R. Sheats, H. M. McConnell, “A photochemical technique for measuring lateral diffusion of spin-labeled phospholipids in membranes”, PNAS, 75:10 (1978), 4661–4663 | DOI

[15] http://www.gromacs.org