Диссертация (1149183), страница 13

Просмтор этого файла доступен только зарегистрированным пользователям. Но у нас супер быстрая регистрация: достаточно только электронной почты!

Текст из файла (страница 13)

et al. Molecular dynamics simulations of nucleic acids. Fromtetranucleotides to the ribosome //The journal of physical chemistry letters. – 2014. – Т. 5.– №. 10. – С. 1771-1782.92.Orozco M. Multiscale simulation of DNA Pablo D Dans, Ju rgen Walther, Hansel Gomez and //Current Opinion in Structural Biology. – 2016.

– Т. 37. – С. 29-45.93.Sim A. Y. L., Minary P., Levitt M. Modeling nucleic acids //Current opinion instructural biology. – 2012. – Т. 22. – №. 3. – С. 273-278.94.Lavery R. et al. A systematic molecular dynamics study of nearest-neighbor effectson base pair and base pair step conformations and fluctuations in B-DNA //Nucleic acidsresearch. – 2010. – Т. 38.

– №. 1. – С. 299-313.95.Olson W. K. et al. DNA sequence-dependent deformability deduced from protein–DNA crystal complexes //Proceedings of the National Academy of Sciences. – 1998. – Т.95. – №. 19. – С. 11163-11168.8296.Pérez A. et al. Towards a molecular dynamics consensus view of B-DNA flexibility//Nucleic acids research. – 2008.

– Т. 36. – №. 7. – С. 2379-2394.97.Lankaš F. et al. DNA basepair step deformability inferred from molecular dynamicssimulations //Biophysical journal. – 2003. – Т. 85. – №. 5. – С. 2872-2883.98.Lu X. J., Olson W. K. 3DNA: a software package for the analysis, rebuilding andvisualization of three‐dimensional nucleic acid structures //Nucleic acids research. – 2003.– Т. 31.

– №. 17. – С. 5108-5121.99.Lavery R. et al. Conformational analysis of nucleic acids revisited: Curves+//Nucleic acids research. – 2009. – Т. 37. – №. 17. – С. 5917-5929.100. Lavery R. et al. Analyzing ion distributions around DNA //Nucleic acids research. –2014. – Т. 42. – №. 12. – С. 8138-8149.101.

Kox A. J., Michels J. P. J., Wiegel F. W. Simulation of a lipid monolayer usingmolecular dynamics. – 1980.102. Van der Ploeg P., Berendsen H. J. C. Molecular dynamics simulation of a bilayermembrane //The Journal of Chemical Physics. – 1982.

– Т. 76. – №. 6. – С. 3271-3276.103. Lyubartsev A. P., Rabinovich A. L. Force Field Development for Lipid MembraneSimulations //Biochimica et Biophysica Acta (BBA)-Biomembranes. – 2016.104. Dickson C. J. et al. GAFFlipid: a General Amber Force Field for the accuratemolecular dynamics simulation of phospholipid //Soft Matter. – 2012. – Т. 8. – №. 37. – С.9617-9627.105. Jämbeck J. P. M., Lyubartsev A. P. An extension and further validation of an allatomistic force field for biological membranes //Journal of chemical theory andcomputation. – 2012.

– Т. 8. – №. 8. – С. 2938-2948.106. Boiko N. I. et al. Simulation of interactions between DNA and diglycerides //RussianChemical Bulletin. – 2008. – Т. 57. – №. 8. – С. 1775-1778.107. D'yachkov P. N. et al. DNA–phospholipid recognition: modulation by metal ion and83lipid nature. Complexes structure and stability calculated by molecular mechanics//Bioelectrochemistry. – 2002. – Т.

58. – №. 1. – С. 47-51.108. Bandyopadhyay S., Tarek M., Klein M. L. Molecular dynamics study of a lipid-DNAcomplex //The Journal of Physical Chemistry B. – 1999. – Т. 103. – №. 46. – С. 1007510080.109. Tarek M. Membrane electroporation: a molecular dynamics simulation //Biophysicaljournal. – 2005. – Т. 88. – №. 6. – С. 4045-4053.110. Khalid S. et al. DNA and lipid bilayers: self-assembly and insertion //Journal of TheRoyal Society Interface.

– 2008. – Т. 5. – №. Suppl 3. – С. 241-250.111. Hess B. et al. GROMACS 4: algorithms for highly efficient, load-balanced, andscalable molecular simulation //Journal of chemical theory and computation. – 2008. – Т.4. – №. 3. – С. 435-447.112. Jorgensen W. L. et al. Comparison of simple potential functions for simulating liquidwater //The Journal of chemical physics.

– 1983. – Т. 79. – №. 2. – С. 926-935.113. Bussi G., Donadio D., Parrinello M. Canonical sampling through velocity rescaling//The Journal of chemical physics. – 2007. – Т. 126. – №. 1. – С. 014101.114. Berendsen H. J. C. et al. Molecular dynamics with coupling to an external bath //TheJournal of chemical physics. – 1984. – Т. 81.

– №. 8. – С. 3684-3690.115. Essmann U. et al. A smooth particle mesh Ewald method //The Journal of chemicalphysics. – 1995. – Т. 103. – №. 19. – С. 8577-8593.116. Shields G. C., Laughton C. A., Orozco M. Molecular Dynamics Simulations of the d(TAT) Triple Helix //Journal of the American Chemical Society. – 1997. – Т. 119. – №.32. – С. 7463-7469.117.Analysis Implementation Including Robust Error and Autocorrelation Estimates //Journalof Chemical Theory and Computation. – 2010. – Т. 6. – №. 12.

– С. 3713-3720.84118. Gurtovenko A. A. Asymmetry of lipid bilayers induced by monovalent salt: atomistic molecular-dynamics study //The Journal of chemical physics. – 2005. – Т. 122. – №.24. – С. 244902.119. Humphrey W., Dalke A., Schulten K. VMD: visual molecular dynamics //Journal ofmolecular graphics. – 1996. – Т. 14. – №. 1. – С. 33-38.120.

Heikkilä E. et al. Atomistic simulations of anionic Au 144 (SR) 60 nanoparticlesinteracting with asymmetric model lipid membranes //Biochimica et Biophysica Acta(BBA)-Biomembranes. – 2014. – Т. 1838. – №. 11. – С. 2852-2860.121. Böckmann R. A., Grubmüller H. Multistep binding of divalent cations tophospholipid bilayers: a molecular dynamics study //Angewandte Chemie InternationalEdition. – 2004. – Т. 43. – №. 8. – С. 1021-1024.122. Böckmann R.

A. et al. Effect of sodium chloride on a lipid bilayer //BiophysicalJournal. – 2003. – Т. 85. – №. 3. – С. 1647-1655.123. Antipina A. Y., Gurtovenko A. A. Molecular Mechanism of Calcium-InducedAdsorption of DNA on Zwitterionic Phospholipid Membranes //The Journal of PhysicalChemistry B. – 2015. – Т. 119. – №. 22. – С. 6638-6645.124. Antipina A. Y., Gurtovenko A. A. Molecular-level insight into the interactions ofDNA with phospholipid bilayers: barriers and triggers //RSC Advances. – 2016. – Т. 6.

–№. 43. – С. 36425-36432..

Характеристики

Список файлов диссертации