1. A method for improving a nucleic acid-based molecular computing system, comprising (A) identifying a computing system comprised of (i) a nucleic acid structure that comprises an incompletely base-paired duplex domain, (ii) at least one polynucleotide displacement molecule that can bind with said nucleic acid structure under hybridizing conditions, such that said nucleic acid structure undergoes a transition in energy state due to a branch migration reaction involving said duplex domain, and (iii) a clashing polynucleotide molecule that competes with said polynucleotide displacement molecule for binding said nucleic acid structure under said conditions but that cannot produce a branch migration reaction involving said duplex domain; then (B) reconfiguring at least one of said displacement molecule and said nucleic acid structure, respectively, to incorporate a chemical modification relative to a first reference molecule that comprises natural nucleosides and has the same sequence content as said displacement molecule or said nucleic acid structure, as the case may be, wherein said modification causes binding of said displacement molecule and said nucleic acid structure to have a hybridization free energy, differing from that of a first reference binding between said displacement molecule or said nucleic acid structure and said first reference molecule, such that said branch migration reaction is facilitated relative to said first reference binding; and/or (C) reconfiguring at least one of said clashing molecule and said nucleic acid structure, respectively, to incorporate a chemical modification relative to a second reference molecule that comprises natural nucleosides and has the same sequence content as said clashing molecule or said nucleic acid structure, as the case may be, wherein said modification causes binding of said clashing molecule and said nucleic acid structure to have a hybridization free energy, differing from that of a second reference binding between said clashing molecule or said nucleic acid structure and said second reference molecule, such that binding of said clashing molecule is impeded relative to said second reference binding.