1. A method for preparing an improved nucleic acid-based molecular computing system, comprising: (1) identifying a nucleic acid-based computing system that comprises (i) an input nucleic acid strand comprising a first fragment (A) and a second fragment (B); (ii) a target, incompletely base-paired nucleic acid duplex comprising a first strand and a second strand, wherein the first strand comprises a first fragment (B′) and a second fragment (A′), the second strand comprises a first fragment (B) and a second fragment (C), and the target duplex comprises a duplex region formed by base-pairing between B and B′ and two single-stranded regions, A′ and C, and wherein the input strand can bind with the first strand of the target duplex under hybridizing conditions to invoke a strand displacement reaction to produce an output duplex formed between the input strand (A-B) and the first strand of the target duplex (B′-A′), and (iii) a clashing, incompletely base-paired nucleic acid duplex comprising a first strand and a second strand, wherein the first strand comprises a first fragment (C′) and a second fragment (B′), the second strand comprises a first fragment (C) and a second fragment (D), and the clashing duplex comprises a duplex region formed by base-pairing between C and C′ and two single-stranded regions B′ and D, wherein the second strand of the target duplex can bind with the first strand of the clashing duplex under hybridizing conditions to invoke a strand displacement reaction to produce an output duplex formed between the second strand of the target duplex (B-C) and the first strand of the clashing duplex (C′-B′), and wherein the second fragment (B) of the input strand can bind with the single-stranded region B′ of the clashing duplex under hybridizing conditions; and then (2) synthesizing, in an aqueous solution, a variant of said nucleic acid-based molecular computing system that differs from the latter by (i) an incorporation into the first fragment (B) of the second strand of the target duplex a first chemical modification that causes binding with the second fragment (B′) of the first strand of the clashing duplex to have a decreased hybridization free energy, and/or (ii) an incorporation into the second fragment (B) of the input strand a second chemical modification that causes binding with the second fragment (B′) of the first strand of the clashing duplex to have an increased hybridization free energy, such that the first fragment (B) of the second strand of the target duplex, as compared to the second fragment (B) of the input strand, binds to the second fragment (B′) of the first strand of the clashing duplex to form a more stable duplex region, whereby the variant is improved over the nucleic acid-based molecular computing system in terms of a reduced incidence of hybridization between the input strand and the clashing duplex.