title: Numerical investigation of molecular nano-array in potential-energy profile for a single dsDNA.
abstract: A Rigorous numerical investigation on dsDNA translocation in quasi-2-dimensional nano-array filter is performed using Molecular Dynamics (MD) method. Various dsDNA molecules with different sizes are chosen in order to model Ogston sieving in a nano-array filter. The radius of gyration of dsDNA molecule is less than the characteristic length of the shallow region in nano-array. The dsDNA molecule is assumed to be in the 0.05M NaCl electrolyte. MD shows acceptable results for potential-energy profile for nano-array filter. According to the MD outcomes, the dsDNA electrophoretic mobility decreases almost linearly with dsDNA size and show the same trend as Ogston sieving for gel electrophoresis. In addition, different shapes for nano-array filter are studied for a unique dsDNA molecule. It is concluded that steeping the nano-array wall can cause the retardation of dsDNA translocation and decreases dsDNA electrophoretic mobility.
authors.affiliation: School of Mechanical Engineering, Shiraz University, Shiraz, Iran.
authors.forename: Marzieh
authors.initials: M
authors.lastname: Alishahi
authors.affiliation: School of Mechanical Engineering, Shiraz University, Shiraz, Iran. rkamali@shirazu.ac.ir.
authors.forename: Reza
authors.initials: R
authors.lastname: Kamali
authors.affiliation: School of Mechanical Engineering, Shiraz University, Shiraz, Iran.
authors.forename: Omid
authors.initials: O
authors.lastname: Abouali
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000302:isolation & purification*; D004586:Electrophoresis / Q000295:instrumentation*; D056004:Molecular Dynamics Simulation; D036103:Nanotechnology / Q000295:instrumentation*; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA
keywords: Flowing Matter: Liquids and Complex Fluids