DNA self-assembly has been proposed as a promising "bottomup" manufacturing technique to supersede photolithography at nanometer scale. This paper discusses the application of DNA self-assembly for manufacturing templates of QCA circuits. Using a synthesis algorithm, a tile set of reduced cardinality is utilized for growing multiple patterns of the same QCA circuit on a two-dimensional template. Errors in the DNA self-assembly process are then considered; their implications on the operation of faulty QCA circuits following the deposition of QCA cells, are discussed. The errors are mostly clustered and along facets; a detailed treatment with respect to manufacturing yield, circuit functionality, error tolerance and growth speed is pursued. As a general conclusion, it is shown that errors are pattern dependent, hence the faults occurring in the assembled QCA circuits are physically and logically different.

Quantum-dot Cellular Automata is an emerging technology that offers significant improvements over CMOS. Recently QCA has been advocated as a technology for implementing reversible computing. However, existing tools for QCA design and evaluation have limited capabilities. This paper presents a new mechanical-based model for computing in QCA. By avoiding a full quantum-thermodynamical calculation, it offers a classical view of the principles of QCA operation and can be used in evaluating energy dissipation for reversible computing. The proposed model is mechanically based and is applicable to six-dot (neutrally charged) QCA cells for molecular implementation. The mechanical model consists of a sleeve of changing shape; four electrically charged balls are connected by a stick that rotates around an axle in the sleeve. The sleeve acts as a clocking unit, while the angular position of the stick within the changing shape of the sleeve, identifies the phase for quasi-adiabatic switching. A thermodynamic analysis of the proposed model is presented. The behaviors of various QCA basic devices and circuits are analyzed using the proposed model. It is shown that the proposed model is capable of evaluating the energy consumption for reversible computing at device and circuit levels for molecular QCA implementation. As applicable to QCA, two clocking schemes are also analyzed for energy dissipation and performance (in terms of number of clocking zones).

This paper addresses the issues revolving around the synthesis of tile sets for DNA self-assembly as a promising approach for IC manufacturing in the nanoscale. As for a finite pattern, synthesis for minimizing tile or bond types is equivalent to a minimum graph coloring problem, two greedy algorithms that reduce the number of tiles (PATS_Tile) or bonds (PATS_Bond) in synthesized tile sets are proposed and evaluated. Both algorithms are O(l4) for a square pattern of dimension l. It is shown by simulation that PATS_Tile has a better average performance if both types of reduction must be accomplished.

Self-assembly by DNA tiles has been advocated as a possible technique for bottom-up manufacturing of scaffolds in the nanoscale region. However, self-assembly is severely affected by facet roughening errors. A particularly effective error tolerant method utilizes snake tile sets with a square block of even dimension (i.e. 2 k times 2 k) of tiles. Snake tile sets of odd dimension (i.e. (2 k - 1) x (2k - 1)) have also been proposed. To analyze error tolerant mechanism of snake tile sets, this paper presents an analytical Markov model for facet roughening errors. A generalized model is proposed and used to analyze snake tile sets for the realistic cases of k = 2 and 3. Closed form solutions are attained in the analysis. Simulation results are presented to confirm that snake tile sets of odd dimension are more tolerant to facet errors than other tile sets for self-assembly.

As a possible technology for bottom-up manufacturing, DNA self-assembly requires tolerance to different errors. Among the methods for reducing the error rate, snake tile sets utilize a square block of even dimension of tiles (i.e., 2ktimes2k). In this paper, an odd-sized square block (i.e., (2k-1)times(2k-1)) is proposed as basis for snake tile sets. In comparison with all other tile sets, the proposed snake tile sets achieve a considerable reduction in error rate for growth and facet roughening errors. Simulation results are provided.