Rational surface design for molecular dynamics simulations of porous polymer adsorbent media

The construction and use of nonflat agarose surfaces in a simulation box, together with the employment of criteria for the immobilization of a set of dextran polymer chains on the nonflat agarose surfaces whose mathematical physics is compatible with that of the criteria used for the immobilization of the same set of dextran polymer chains on flat agarose surfaces, are shown to generate, through the use of molecular dynamics simulations whose simulation box has linear dimensions along the lateral directions that are the same when flat and nonflat agarose surfaces are used, dextran porous polymer structures whose pore sizes at the outermost surface and in the vicinity of the outermost surface of the porous medium can be controlled by an indirect manner through the variation of the parameters that characterize the nonflat surface. The use of a nonflat surface for the generation of desired large pores requires only a small or modest increase in the number of solvent molecules in the simulation box, while the use of a flat surface for the construction of the same desired large pores requires significant increases in the size of the linear dimensions of the flat surface. This increases so substantially the number of solvent molecules that the computational loads become intractable. The results in this work show that through the use of nonflat surfaces porous dextran polymer layers having pores of desired sizes can be effectively constructed, and this approach could be used for the design and construction of polymer-based porous adsorbent media that could effectively facilitate the transport and adsorption of an adsorbate biomolecule of interest that must be separated from a mixture of components. A useful definition about the properties that a porous polymer structure must have in order to become, for an adsorbate biomolecule of interest of known molecular size, a useful adsorbent medium, is presented and is used to (1) evaluate the porous polymer structures generated through the employment of different nonflat surface models and (2) determine and select the nonflat surface model from a set of nonflat surface models that is effective in producing promising porous structures. Then a procedure is presented by which a set of porous polymer media is generated through the use of the selected nonflat surface model, and the desired porous structure from this set is determined and could be considered to be used for the transport and immobilization of the selected affinity groups/ligands and the subsequent transport and adsorption of the desired to be separated adsorbate.