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287
31. Mpourmpakis G, Froudakis GE, Lithoxoos GP, Samios J (2006) SiC nanotubes: a novel
material for hydrogen storage. Nano Lett 6:1581–1583. https://doi.org/10.1021/nl0603911
32. Lithoxoos GP, Samios J, Carissan Y (2008) Investigation of silicon model nanotubes
as potential candidate nanomaterials for efficient hydrogen storage: a combined ab initio/grand canonical Monte Carlo simulation study. J Phys Chem C 112:16725–16728.
https://doi.org/10.1021/jp805559a
33. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L,
Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26:1781–1802.
https://doi.org/10.1002/jcc.20289
34. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph
Model 14:33–38. https://doi.org/10.1016/0263-7855(96)00018-5
35. Casciola M, Bonhenry D, Liberti M, Apollonio F, Tarek M (2014) A molecular dynamic study
of cholesterol rich lipid membranes: comparison of electroporation protocols. Bioelectrochemistry 100:11–17. https://doi.org/10.1016/j.bioelechem.2014.03.009
36. Dufourc EJ, Parish EJ, Chitrakorn S, Smith ICP (1984) Structural and dynamical details of
cholesterol-lipid interaction as revealed by deuterium NMR. Biochemistry (Mosc) 23:6062–
6071. https://doi.org/10.1021/bi00320a025
37. Raczynski P, Dawid A, Dendzik Z, Gburski Z (2005) Dielectric relaxation in watercholesterol mixture cluster: molecular dynamics simulation. J Mol Struct 750:18–21.
https://doi.org/10.1016/j.molstruc.2005.03.036
38. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926.
https://doi.org/10.1063/1.445869
39. MacKerell ADJ, Banavali N, Foloppe N (2000) Development and current
status of the CHARMM force field for nucleic acids. Biopolymers 56.
https://doi.org/10.1002/1097-0282(2000)56:4<257::AID-BIP10029>3.0.CO;2-W
40. Guo CY, Montgomery Pettitt B, Wheeler LT (2006) Force field comparisons of the heat capacity of carbon nanotubes. Mol Simul 32:839–848. https://doi.org/10.1080/08927020600962956
41. Alexiadis A, Kassinos S (2008) Molecular simulation of water in carbon nanotubes. Chem Rev
108:5014–5034. https://doi.org/10.1021/cr078140f
42. Shi B, Zuo G, Xiu P, Zhou R (2013) Binding preference of carbon nanotube over pro linerich motif ligand on SH3-domain: a comparison with different force fields. J Phys Chem B
117:3541–3547. https://doi.org/10.1021/jp312423y
43. Moradi Garakani F, Kalantarinejad R (2012) A molecular dynamics simulation of water
transport through C and SiC nanotubes: application for desalination. Int J Nano Dimens 2:151–
157
44. Henin J, Chipot C (2006) Hydrogen-bonding patterns of cholesterol in lipid membranes. Chem
Phys Lett 425:329–335. https://doi.org/10.1016/j.cplett.2006.04.115
45. Schlenkrich M, Brickmann J, MacKerell AD, Karplus M (1996) An empirical potential energy
function for phospholipids: criteria for parameter optimization and applications. In: Merz
KM, Roux B (eds) Biological membranes: a molecular perspective from computation and
experiment. Birkhäuser Boston, Boston, pp 31–81
46. Feller SE, Yin D, Pastor RW, MacKerell AD (1997) Molecular dynamics simulation of
unsaturated lipid bilayers at low hydration: parameterization and comparison with diffraction
studies. Biophys J 73:2269–2279. https://doi.org/10.1016/S0006-3495(97)78259-6
287
31. Mpourmpakis G, Froudakis GE, Lithoxoos GP, Samios J (2006) SiC nanotubes: a novel
material for hydrogen storage. Nano Lett 6:1581–1583. https://doi.org/10.1021/nl0603911
32. Lithoxoos GP, Samios J, Carissan Y (2008) Investigation of silicon model nanotubes
as potential candidate nanomaterials for efficient hydrogen storage: a combined ab initio/grand canonical Monte Carlo simulation study. J Phys Chem C 112:16725–16728.
https://doi.org/10.1021/jp805559a
33. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L,
Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26:1781–1802.
https://doi.org/10.1002/jcc.20289
34. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph
Model 14:33–38. https://doi.org/10.1016/0263-7855(96)00018-5
35. Casciola M, Bonhenry D, Liberti M, Apollonio F, Tarek M (2014) A molecular dynamic study
of cholesterol rich lipid membranes: comparison of electroporation protocols. Bioelectrochemistry 100:11–17. https://doi.org/10.1016/j.bioelechem.2014.03.009
36. Dufourc EJ, Parish EJ, Chitrakorn S, Smith ICP (1984) Structural and dynamical details of
cholesterol-lipid interaction as revealed by deuterium NMR. Biochemistry (Mosc) 23:6062–
6071. https://doi.org/10.1021/bi00320a025
37. Raczynski P, Dawid A, Dendzik Z, Gburski Z (2005) Dielectric relaxation in watercholesterol mixture cluster: molecular dynamics simulation. J Mol Struct 750:18–21.
https://doi.org/10.1016/j.molstruc.2005.03.036
38. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926.
https://doi.org/10.1063/1.445869
39. MacKerell ADJ, Banavali N, Foloppe N (2000) Development and current
status of the CHARMM force field for nucleic acids. Biopolymers 56.
https://doi.org/10.1002/1097-0282(2000)56:4<257::AID-BIP10029>3.0.CO;2-W
40. Guo CY, Montgomery Pettitt B, Wheeler LT (2006) Force field comparisons of the heat capacity of carbon nanotubes. Mol Simul 32:839–848. https://doi.org/10.1080/08927020600962956
41. Alexiadis A, Kassinos S (2008) Molecular simulation of water in carbon nanotubes. Chem Rev
108:5014–5034. https://doi.org/10.1021/cr078140f
42. Shi B, Zuo G, Xiu P, Zhou R (2013) Binding preference of carbon nanotube over pro linerich motif ligand on SH3-domain: a comparison with different force fields. J Phys Chem B
117:3541–3547. https://doi.org/10.1021/jp312423y
43. Moradi Garakani F, Kalantarinejad R (2012) A molecular dynamics simulation of water
transport through C and SiC nanotubes: application for desalination. Int J Nano Dimens 2:151–
157
44. Henin J, Chipot C (2006) Hydrogen-bonding patterns of cholesterol in lipid membranes. Chem
Phys Lett 425:329–335. https://doi.org/10.1016/j.cplett.2006.04.115
45. Schlenkrich M, Brickmann J, MacKerell AD, Karplus M (1996) An empirical potential energy
function for phospholipids: criteria for parameter optimization and applications. In: Merz
KM, Roux B (eds) Biological membranes: a molecular perspective from computation and
experiment. Birkhäuser Boston, Boston, pp 31–81
46. Feller SE, Yin D, Pastor RW, MacKerell AD (1997) Molecular dynamics simulation of
unsaturated lipid bilayers at low hydration: parameterization and comparison with diffraction
studies. Biophys J 73:2269–2279. https://doi.org/10.1016/S0006-3495(97)78259-6