title: Multiscale modeling of protein transport in silicon membrane nanochannels. Part 1. Derivation of molecular parameters from computer simulations.
abstract: We report in this account our efforts in the development of a novel multiscale simulation tool for integrated nanosystem design, analysis and optimization based on a three-tiered modeling approach consisting of (i) molecular models, (ii) atomistic molecular dynamics simulations, and (iii) dynamical models of protein transport at the continuum scale. In this work we used molecular simulations for the analysis of lysozyme adsorption on a pure silicon surface. The molecular modeling procedures adopted allowed (a) to elucidate the specific mechanisms of interaction between the biopolymer and the silicon surface, and (b) to derive molecular energetic and structural parameters to be employed in the formulation of a mathematical model of diffusion through silicon-based nanochannel membranes, thus filling the existing gap between the nano--and the macroscale.
authors.affiliation: Molecular Simulation Engineering (MOSE) Laboratory, Department of Chemical Engineering, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy. sabrina.pricl@dicamp.units.it
authors.forename: Sabrina
authors.initials: S
authors.lastname: Pricl
authors.forename: Marco
authors.initials: M
authors.lastname: Ferrone
authors.forename: Maurizio
authors.initials: M
authors.lastname: Fermeglia
authors.forename: Francesco
authors.initials: F
authors.lastname: Amato
authors.forename: Carlo
authors.initials: C
authors.lastname: Cosentino
authors.forename: Mark Ming-Cheng
authors.initials: MM
authors.lastname: Cheng
authors.forename: Robert
authors.initials: R
authors.lastname: Walczak
authors.forename: Mauro
authors.initials: M
authors.lastname: Ferrari
mesh_terms: D000327:Adsorption; D003198:Computer Simulation; D008567:Membranes, Artificial; D008954:Models, Biological; D008958:Models, Molecular; D009113:Muramidase / Q000737:chemistry / Q000378:metabolism; D017434:Protein Structure, Tertiary; D021381:Protein Transport / Q000502:physiology; D012825:Silicon / Q000737:chemistry
chemical_list: D008567:Membranes, Artificial; D009113:Muramidase; D012825:Silicon