Synthesis Strategy of Reversible Circuits on DNA Computers

DNA computers and quantum computers are gaining attention as alternatives to classical digital computers. DNA is a biological material that can be reprogrammed to perform computing functions. Quantum computing performs reversible computations by nature based on the laws of quantum mechanics. In this paper, DNA computing and reversible computing are combined to propose novel theoretical methods to implement reversible gates and circuits in DNA computers based on strand displacement reactions, since the advantages of reversible logic gates can be exploited to improve the capabilities and functionalities of DNA computers. This paper also proposes a novel universal reversible gate library (URGL) for synthesizing n-bit reversible circuits using DNA to reduce the average length and cost of the constructed circuits when compared with previous methods. Each n-bit URGL contains building blocks to generate all possible permutations of a symmetric group of degree n. Our proposed group (URGL) in the paper is a permutation group. The proposed implementation methods will improve the efficiency of DNA computer computations as the results of DNA implementations are better in terms of quantum cost, DNA cost, and circuit length.

High-efficiency and integrable DNA arithmetic and logic system based on strand displacement synthesis

Powerful information processing and ubiquitous computing are crucial for all machines and living organisms. The Watson-Crick base-pairing principle endows DNA with excellent recognition and assembly abilities, which facilitates the design of DNA computers for achieving intelligent systems. However, current DNA computational systems are always constrained by poor integration efficiency, complicated device structures or limited computational functions. Here, we show a DNA arithmetic logic unit (ALU) consisting of elemental DNA logic gates using polymerase-mediated strand displacement. The use of an enzyme resulted in highly efficient logic gates suitable for multiple and cascaded computation. Based on our basic single-rail DNA configuration, additional combined logic gates (e.g., a full adder and a 4:1 multiplexer) have been constructed. Finally, we integrate the gates and assemble the crucial ALU. Our strategy provides a facile strategy for assembling a large-scale complex DNA computer system, highlighting the great potential for programming the molecular behaviors of complicated biosystems.

Secure Hash Algorithm-2 formed on DNA

We present a new version of the Secure Hash Algorithm-2 (SHA-2) formed on artificial sequences of deoxyribonucleic acid (DNA). This article is the first attempt to present the implementation of SHA-2 using DNA data processing. We called the new version DNSHA-2. We present new operations on an artificial DNA sequence, such as (1) $\bar {R}^{k}(\alpha)$ R ̄ k ( α ) and $\bar {L}^{k}(\alpha)$ L ̄ k ( α ) to mimic the right and left shift by k bits, respectively; (2) $\bar {S}^{k}(\alpha)$ S ̄ k ( α ) to mimic the right rotation by k bits; and (3) DNA-nucleotide addition (mod 264) to mimic word-wise addition (mod 264). We also show, in particular, how to carry out the different steps of SHA-512 on an artificial DNA sequence. At the same time, the proposed nucleotide operations can be used to mimic any hash algorithm of its bitwise operations similar to bitwise operations specified in SHA-2. The proposed hash has the following features: (1) it can be applied to all data, such as text, video, and image; (2) it has the same security level of SHA-2; and (3) it can be performed in a biological environment or on DNA computers.

Solving the 0/1 Knapsack Problem by a Biomolecular DNA Computer

Solving some mathematical problems such as NP-complete problems by conventional silicon-based computers is problematic and takes so long time. DNA computing is an alternative method of computing which uses DNA molecules for computing purposes. DNA computers have massive degrees of parallel processing capability. The massive parallel processing characteristic of DNA computers is of particular interest in solving NP-complete and hard combinatorial problems. NP-complete problems such as knapsack problem and other hard combinatorial problems can be easily solved by DNA computers in a very short period of time comparing to conventional silicon-based computers. Sticker-based DNA computing is one of the methods of DNA computing. In this paper, the sticker based DNA computing was used for solving the 0/1 knapsack problem. At first, a biomolecular solution space was constructed by using appropriate DNA memory complexes. Then, by the application of a sticker-based parallel algorithm using biological operations, knapsack problem was resolved in polynomial time.