A rotary nano ion pump: a molecular dynamics study
Tóm tắt
The dynamics of a rotary nano ion pump, inspired by the F
0 part of the F0F1-ATP synthase biomolecular motor, were investigated. This nanopump is composed of a rotor, which is constructed of two carbon nanotubes with benzene rings, and a stator, which is made of six graphene sheets. The molecular dynamics (MD) method was used to simulate the dynamics of the ion nanopump. When the rotor of the nanopump rotates mechanically, an ion gradient will be generated between the two sides of the nanopump. It is shown that the ion gradient generated by the nanopump is dependant on parameters such as the rotary frequency of the rotor, temperature and the amounts and locations of the positive and negative charges of the stator part of the nanopump. Also, an electrical potential difference is generated between the two sides of the pump as a result of its operation.
Tài liệu tham khảo
Xing J, Wang H, Ballmoos CV, Dimroth P, Oster G (2004) Torque generation by the F0 motor of the sodium ATPase. Biophys J 87:21482163
Aksimentiev A, Balabin IA, Fillingame RH, Schulten K (2004) Insights into the molecular mechanism of rotation in the F0 sector of ATP synthase. Biophys J 86:1332–1344
Lohrasebi A, Jamali Y, Rafii-Tabar H (2008) Modeling the effect of external electric field and current on the stochastic dynamics of ATPase nano-biomolecular motors. Phys A 387:5466–5476
Barreiro A, Rurali R, Hernndez ER, Moser J, Pichler T, Forr L, Bachtold A (2008) Sub-nanometer motion of cargoes driven by thermal gradients along carbon nanotubes. Science 320:775–778
Rurali R, Hernandez ER (2010) Thermally induced directed motion of fullerene clusters encapsulated in carbon nanotubes. Chem Phys Lett 497:62–65
Schoen PAE, Walther JH, Arcidiacono S, Poulikakos D, Koumoutsakos P (2006) Nanoparticle traffic on helical tracks: Thermophoretic mass transport through carbon nanotubes. Nano Lett 6:1910–1917
Shiomi J, Maruyama S (2009) Water transport inside a single-walled carbon nanotube driven by a temperature gradient. Nanotechnology 20(055708):1–5
Wang BY, Kral P (2007) Chemically tunable nanoscale propellers of liquids. Phys Rev Lett 98(266102):1–4
Wang B, Vukovic L, Kral P (2008) Nanoscale rotary motors driven by electron tunneling. Phys Rev Lett 101:1868081–1868084
Lohrasebi A, Rafii-Tabar H (2008) Computational modeling of an ion-driven nanopump. J Mol Graph Model 29:1025–1029
Gong X, Ji L, Lu H, Wan R, Li J, Hu J, Fang H (2007) A charge-driven molecular water pump. Nature 2:709712
Lohrasebi A, Jamali Y (2011) Computational modeling of a rotary nanopump. J Mol Graph Model 27:116–123
Allen MP, Tildesley DJ (1987) Computer simulation of liquids. Clarendon, Oxford
Wang H (2003) Mathematical theory of molecular motors and a new approach for uncovering motor mechanism. IEE Proc Nanobiotechnol 150:127–133
Brenner DW (1990) Empirical potential for hydrocarbons for use in simulating the chemical vapor deposition of diamond films. Phys Rev B 42(9458):1–14
Crozier PS, Henderson D, Rowley RL, Busath DD (2001) Model channel ion currents in NaCl-SPC/E solution with applied-field molecular dynamics. Biophys J 81:3077–3089
Stan G, Bojan MJ, Curtarolo S, Gatica SM, Cole MW (2000) Uptake of gases in bundles of carbon nanotubes. Phys Rev B 62:2173–2180
Neumann M (1985) The dielectric constant of water. Computer simulations with the MCY potential. J Chem Phys 82:5663–5672
Tironi IG, Sperb R, Smith PE, van Gunsteren WF (1995) A generalized reaction field method for molecular dynamics simulations. J Chem Phys 102:5451–5459
Praprotnik M, Janezic D, Mavri J (2004) Temperature dependence of water vibrational spectrum: a molecular dynamics simulation study. J Phys Chem A 108:1105611062
Charron FM, Blanchard MG, Lapointe JY (2006) Intracellular hypertonicity is responsible for water flux associated with Na+/glucose cotransport. Biophys J 90:3546–3554