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A reversible lithium-sulfur battery is considered one of the most promising high-energy-density energy storage systems. Organic sulfide cathodes have attracted widespread attention due to their fle...

Magnetic beads and magnetic Raman technology substrates have good magnetic response ability and surface-enhanced Raman technology (SERS) activity. Therefore, magnetic beads exhibit high sensitivity in SERS detection. In this paper, DNA cycle hybridization and magnetic bead models are combined to solve 0-1 integer programming problems. First, the model maps the variables to DNA strands with hairpin structures and weights them by the number of hairpin DNA strands. This result can be displayed by the specific binding of streptavidin and biotin. Second, the constraint condition of the 0-1 integer programming problem can be accomplished by detecting the signal intensity of the biological barcode to find the optimal solution. Finally, this model can be used to solve the general 0-1 integer programming problem and has more extensive applications than the previous DNA computing model.

Background: Molecular logic circuits have great potential applications. DNA logic circuit is an important research direction of DNA computing in nanotechnology. DNA self-assembly has become a powerful tool for building nanoscale structures. The combination of different self-assembly methods is an interesting topic. Aim: Two different self-assembly methods are combined to realize large-scale logic circuit. A basic logical unit is extended to complex logic circuits by self-assembly. Approach: The complex logic circuit is solved by combining nanoparticles. One DNA strand attached to nanoparticle maps to a logical unit. Just as the combination between logical units can form logic circuits, the combination between nanoparticles can be used to structure logic circuits. On a larger-scale logic circuits, this is done by attaching the assembled nanoparticles to an origami template. Different logical values are mapped into different DNA initiators. Results: After the reaction is over, the nanoparticles are dynamically separated from the DNA origami template, indicating that the result is true. The nanoparticles remain on the DNA origami template, indicating that the result is false. The simulation results show that this self-assembly model is highly feasible for complex logic circuits. Conclusions: The model combines two different self-assembly methods to realize large-scale logic circuits. Compared with previous models, this model implements a larger logic circuit on one origami template. This method can be used to construct more complex nanosystems and may have potential applications in molecular engineering.

DNA computing has the advantages of high parallelism and large storage. In this paper, DNA strand displacement techniques are applied to binary to decimal system. In the field of DNA calculation, binary numerical calculation is relatively mature, but it is difficult to implement decimal calculation. So it is very necessary to study the conversion of binary system to decimal system. In this paper, DNA strand displacement are used to construct a logic model that converts binary system into decimal system. The output strand is obtained through DNA strand displacement reaction in the logical device, and the decimal result is judged by the number of hairpin structures formed. The model has good operability, flexibility.

Given an undirected graph with weights on the vertices, the maximum weight clique problem requires finding the clique of the graph which has the maximum weight. The problem is a general form of the maximum clique problem. In this paper, we encode weight of vertex into a unique fixed length oligonucleotide segment and employ sticker model to solve the problem. The proposed method has two distinct characteristics. On one hand, we skip generating initial data pool that contains every possible solution to the problem of interest, the key point of which is constructing the solution instead of searching solution in the vast initial data pool according to logic constraints. On the other hand, oligonucleotide segments are treated like variables which store weights on vertices, no matter what kind of number the weights are, integer or real. Therefore, the proposed method can solve the problem with arbitrary weight values and be applied to solve the other weight-related problem. In addition, molecular beacon is also employed in order to overcome shortcomings of sticker model. Besides, we have analyzed the proposed algorithm’s feasibility.

A DNA algorithm by operating on plasmids was presented to solve a special integer programming, a typical hard computing problem. The DNA algorithm employed double-stranded molecules to encode variables of 0-1 programming problem, the encoded DNA molecules were inserted into circular plasmids as foreign DNA molecules. Followed by, a series of enzymatic treatments to plasmids were performed in order to find feasible solutions to the given problem. The final optimum was obtained by applying founded feasible solutions to object function. Compared with other DNA algorithms of integer programming problem, the proposed algorithm is simple, error-resistant, above all, feasible. Our work clearly showed the distinct advantages of plasmid DNA computing model when solving integer related programming problem.

American scientist Adelman first used DNA molecules to solve the NP-complete problem, thus creating a new research field. As an advanced interdisciplinary subject, it has attracted many scholars because of its high parallelism, great storage density and low energy consumption. DNA sequence design is critical in the field of DNA computing. The success of DNA computing depends on the quality of DNA sequence. In this paper, we proposed an improved gravitational search algorithm for DNA sequence design. We improved the gravitational coefficient and introduced chaotic system and Gaussian mutation to the position update of the particles. We compared the result from our improved algorithm with the result obtained by other algorithms. The result shows that our proposed algorithm can generate high quality DNA sequence for DNA computing.

Molecular logic gates play an important role in many fields and DNA-based logic gates are the basis of DNA computers. A dynamically NAND gate system on the DNA origami template is established in this paper. Naturally, the system is stable in solution without any reaction. Different logical values are mapped into different DNA input strands. When logical values are entered into the system, the corresponding DNA input strands undergo a directed hybridization chain reaction (HCR) at corresponding positions on the DNA origami template. The operation results are identified by disassembly between the nanogold particles (AuNPs) and DNA origami template. The nanogold particles remain on the DNA origami template, indicating that the result is true; The nanogold particles are dynamically separated from the DNA origami template, indicating that the result is false. The simulation of the system through Visual DSD shows that the reaction strictly followed the designed direction, and no error products are generated during the reaction. These simulation results show that the system has the advantages of feasibility, stability and intelligence.

It is difficult to find an effective algorithm for solving NP complete problems such as integer programming. The nanostructure constructed by DNA origami combines huge parallelism and massive storage capacity of DNA computing. In the calculation process, it can effectively avoid the number of experimental operations required by other DNA computing models. It greatly reduces the time consumption and the rate of misinterpretation, thus providing an effective way to efficiently solve integer programming. DNA tetrahedron is a nanostructure constructed by origami. It has stable structure, good toughness and compression resistance, simple production process, high yield, rich functional modification sites, good biocompatibility, but also resistance to a variety of specific or non-specific nuclease. Therefore it can reduce the misinterpretation rate of biochemical reactions using DNA tetrahedron and DNA single strand to construct probes, finding the true solution according to the constraint condition. And then it can improve the computational efficiency of the model.

DNA codes have a significant effect on the efficiency of DNA computing and other applications. Designing DNA codes is to obtain a certain sets of DNA codes with satisfying certain combinatorial constraints. Most works focus on algorithmic design for DNA codes. In this paper, Simulated Annealing and Clique Search are modified and combined into an iterated hybrid search to improve the lower bound for DNA codes set. Over 160 instances are considered, and the iterated hybrid search method is able to yield improvements for some lower bounds with n ≤ 16. Comparing with previous works, the proposed algorithm is more efficient for constructing DNA codes set.

The friction behavior of the harmonic drive (HD) at low speed is investigated in this paper. First, a dedicated experimental setup that integrates a pair of torque sensors is developed, and the friction torque of the HD is measured based on a torque transmission model. The results show that the friction torque of the HD has Stribeck effect at low speed. Further, a Coulomb-viscous-Stribeck friction model is established to replicate the friction behavior of the HD at low speed, and an exact match between the simulation and experimental results proves the validity of the model. Last, a parametric analysis is performed to investigate the dependence of the friction behavior of the HD on different model parameters. It is indicated that the Coulomb friction torque, the maximum static friction torque and the viscous friction coefficient affect the whole, ultra-low and high speed regions of the friction torque-rotating speed curve of the HD, respectively. Our research suggests that the friction loss of the HD can be reduced by applying surface coating and improving lubrication condition in teeth meshing and flexible bearing regions, and it also promotes further studies on friction mechanisms in these regions of the HD.

Scaffolded DNA origami, a long single-stranded DNA is folded into pre-designed pattern with the guidance of short staple strands, enables the fabrication of sophisticated nanodevice. Inspired by this nanotechnology, we presented searching the maximum clique in an undirected graph with six vertices and eleven edges. We initially folded a unique type of scaffolds into a pool of strands with $n$ hairpin-like structures, or hairpin for convenience, which corresponded to the total ensemble of six vertices cliques. Followed by, re-folded scaffolds by staples to perform a series of selection processes according to edges in the complementary graph. Scaffolds encoding correct cliques were selected via gel electrophoresis. When this selection processes terminated, all cliques were found. Scaffold with the maximum number of in-clique hairpins was selected by unfolding simultaneously all in-clique hairpins, followed by gel electrophoresis. Then a series of unfolding out-of-clique hairpins one by one via unfolding strands, each vertex in the given graph was decided whether it is in the maximum clique or not. When deciding processes terminated, the maximum clique in the given graph was eventually found. The proposed method employed relatively reliable biological operations. Gel electrophoresis guarantees the accuracy of each step of the proposed method. Therefore, the method proposed is reliable, error tolerant, and feasible. Our work demonstrates, with simple designs for scaffold, staples, and unfolding strands, NP-complete searching problem can be readily and reliably solved by using DNA origami. The work extends application fields of DNA origami a step further.

DNA strand displacement is a new molecular biological technology with strong operability and simple experimental conditions. In this paper, DNA strand displacement is applied to solve the 0–1 programming problem, and a model is constructed using the class closed-loop DNA structure (known as “circular DNA” in this paper). The model fixes the DNA strands which represent the variables on the circular DNA single strand in counterclockwise order. The DNA strand 5’ end is attached with the primers which are applied to the displacement of the DNA strand. The 3’ end is attached with the colored fluorophore. Taking the possible solutions as the input, the results are detected by different fluorescent colors resulting from the DNA strand displacement. The DNA computing model has better flexibility, realizability and applicability.

With the help of the special structure of the molecular beacon, a solution model of the Chinese postman problem is established by using the DNA strand displacement reaction principle. First, the problem is mapped into an undirected weighting graph. Then the vertex and arc of the graph are coded according to the coding principle. Secondly, structure probe, and make use of stand displacement to find solutions to satisfy the problem. Finally, the optimum solution was extracted by gel electrophoresis. The model has high sensitivity, specificity, and the lower error rate. The solution reaction can be carried out at normal temperature. The model calculation shows that the complexity of the problem can be reduced by using the molecular beacon strand displacement reaction to solve the Chinese postman problem.

One type of atmospheric plasma jet relay driven by a 40-kHz power supply and its representative characteristics have been proposed in this paper. The plasma jet relay succeeds in the same gas stem or inside another guided dielectric tube. The first plasma jet can be capable of dividing into many small plasma jets at the end of metal wires and the filial generations can easily merge together to form longer volume discharges. The experiment indicates that the filamentary discharge starts from the formation of one snake-like discharge passage first and the followed snakes give birth from the previous snake discharge body. Taking into account the advantage of easily production methods and available to extend its discharge volume, the proposed plasma jet relay device can be modulated for many potential applications.

Purpose – The bottleneck of current DNA computing paradigms based on brute‐force search strategy is that initial solution space grows exponentially with problem size, thus only trivial instances of NP‐complete problem can be solved. The purpose of this paper is to present a novel molecular program based on sticker models for solving dominating set problems.Design/methodology/approach – The authors do not synthesize the initial solution pool containing every possible candidate solution as previously reported algorithm. Instead, solutions DNA molecules to the problem of interest are constructed during the course of computation.Findings – It is shown that “exponential explosions” inherent in current DNA computing paradigms may be overcome in this way.Originality/value – The paper proposes an error‐resistant DNA algorithm based on sticker model for solving minimum dominating problems.

DNA computing aims at using nucleic acids for computing. Since micromolar DNA solutions can act as billions of parallel nanoprocessors, DNA computers can in theory solve optimization problems that require vast search spaces. However, the actual parallelism currently being achieved is at least a hundred million-fold lower than the number of DNA molecules used. This is due to the quantity of DNA molecules of one species that is required to produce a detectable output to the computations. In order to miniaturize the computation and considerably reduce the amount of DNA needed, we proposed that fluorescence labeling techniques can be applied to DNA computing. In the paper, we solved the simple 0-1 programming problem with fluorescence labeling techniques based on surface chemistry. It is attempt to apply DNA computing to programming problem.

Single-strand DNA can match with homologous double- stranded into a triple-stranded structure mediated by RecA protein.The paper provides a triple-stranded DNA computing model for minimum spanning tree problem. DNA fragments corresponding to edges are coded by double-stranded DNA, wrong hybridization does not take place and hairpin structure does not form. The single-strand DNA probe is bond with RecA protein, so the rate of wrong solution will reduce. And in this way, encoding complexity and the errors in computation will be decreased.

In the core of airport operation, aircraft stands assignment (ASA) is a typical kind of combinatorial optimization. In this paper, by analyzing the ASA problem, gate assignment problem is transferred to vertex coloring model. A DNA computing model for airport gate assignment is proposed. The simulation results show that the algorithm compared with other optimization is very easy and feasible.

Closed circle DNA algorithm of maximum weighted independent set problem is proposed upon closed circle DNA computing model and its biochemistry experiment. In the algorithm, first we get all independent sets though an appropriate encoding and delete experiments, and then we find the maximum weighted independent set using electrophoresis experiment and detect experiment. Only using delete experiment, the algorithm is simple and credible.

DNA self-assembly is a hierarchical build-up of complex assembly body; it is also a very important model in molecular computing. Cryptography problem not only has theoretical significance, but also has a very wide range of applications in national economy and other fields. We will use the way of self-assembly of DNA computing to solve the knapsack problem in the MH knapsack public key cryptosystem.

The design of DNA sequence is important in improving the reliability of DNA computing. Some appropriate constrained terms that DNA sequence should satisfy are selected, and then the evaluation formulas of each DNA individual corresponding to the selected constrained terms are proposed. The paper analyzes the objective and several constraints of DNA encoding, it builds a combinational optimization model. A Global Artificial Fish Swarm algorithm/Genetic Algorithm (GAFSA/GA) is proposed to produce DNA encoding sequences. The result shows that the DNA sequences produced by GAFSA/GA have better quality than that produce by the genetic algorithm.

Time-table problem is a classical NP-complete problem. Algorithm of DNA computing for time-table problem was obtained with introducing the technology of Acrydite TM gel separation. Each class period viewed as a graph vertex was mapped into DNA molecules chain. With the probe coding, the gel column was constructed to arrange the order of DNA chain through biological reaction. The problem was solved by gel column that performs the basic core processing and extraction that makes the result visible. The minimum number of cycles of arrangement was the minimum number of class hours. The simulation results show that the algorithm compared with others is very easy and feasible. DOI: http://dx.doi.org/10.11591/telkomnika.v10i5.1271

DNA computing is a novel method for solving a class of intractable computational problems, in which the computing can grow exponentially with the problem size. Up to now, many accomplishments have been achieved to improve its performance and increase its reliability. A Chinese Postman Problem has been solved by means of molecular biology techniques in the paper. A small graph was encoded in molecules of DNA, and the "operations" of the computation were performed with standard protocols and enzymes. This work represents further evidence for the ability of DNA computing to solve NP-complete search problems.

The technology of DNA self-assembly has played an important role in the field of DNA computing and nanotechnology. Many small-scaled NP complete problems can be solved by self-assembly model. In this paper, we based on the addition of two numbers, and proposed the addition of two matrices of DNA Tile self-assembly model. The algorithm can be applied to add two elements in the corresponding positions automatically, and then in top line of the assembly appears the final results. Theoretical analysis shows that the model can solve the matrix addition operation of any order.

Traveling salesman problem is the NP problem of graph theory. The superior solution for traveling salesman problem is the Hamilton ring that finds out to have minimum power in the graph. The triple-stranded DNA computing model has a low rate of wrong solutions. Because the pool of data generated, there are the double helix structure of DNA chain, and the stability of the double-stranded DNA than single strand of DNA stability. The use of triple-stranded DNA model, can be solved with plans to optimize the combination of some of the NP problem. In this paper we show that triple-stranded DNA structure model can be used for solving the traveling salesman problem.

This paper proposes a DNA algorithm based on biological technology for the maximal matching problem. Maximum matching problem is a typical combinatorial optimization problem. The main idea of the algorithm is draw the line graph to observe adjacent edges firstly, then use the direct proportional length-based DNA strands to encode the given weighted graph edges. All data pool generated in a test tube. Then the result comes out by a series of biological reaction and computation such as denaturation, anneal, Polymerase Chain Reaction, enzyme-cutting reaction, gel electrophoresis. The maximal matching of the graph will find. Finally this article discusses the feasibility of this algorithm and confirmed its effectiveness by an example.

Molecular beacons have the advantages of simple structure, high sensitivity and quick response etc. DNA computing is a new method of simulating bio-molecular structure and computing using molecule biology technology, and creates a precedent in using bio-chemical reaction as the calculating tools. It is a novel way to solve a class of problems that are difficult to calculate NP-complete problem. In this paper the corresponding DNA computing of implicit enumeration is given using the advantages of molecular beacons based on previous studies.

Given an undirected graph with weights on the vertices, the maximum weight clique problem requires to find the clique of the graph which has the maximum weight. The problem is a general form of the maximum clique problem. In this paper, we encoded weight of vertex into a unique fixed length oligonucleotide segment and employed sticker model to solve the problem. The proposed method has two distinct characteristics. On one hand, we skipped generating initial data pool that contained every possible solution to the problem of interest, the key point of which is constructing the solution instead of searching solution in the vast initial data pool according to logic constraints. On the other hand, oligonucleotide segments were treated as variables which stored weights on vertices, no matter what kind of number the weights are, integer or real. Therefore, the proposed method can solve the problem with arbitrary weight values and be applied to solve other weight-related problems. In addition, molecular beacons were also employed in order to overcome shortcomings of sticker model. And we analyzed the feasibility of the proposed algorithm as well.

DNA computing is a new approach to simulate the structure of biological molecules and compute using biotechnology, it creates a precedent of using biochemical reactions as the basis of calculation tools. This is a novel method for solving a class of intractable computational problem. Implicit enumeration is a method of solving integer programming problems, by which the optimal solution can be obtained without explicitly evaluating all of the possible solutions. Based on previous studies, we give the DNA computing model that corresponds to the implicit enumeration method using the fluorescent labeling strategy in the framework of surfacebased DNA computing. This method has the advantages of simple encoding, low supplies, short operation time, advanced technology etc..

We encoded weight of vertex into a unique fixed length oligonucleotide segment and employed sticker model to solve the problem. The proposed method has two distinct characteristics. On one hand, we skipped generating initial data pool that contained every possible solution to the problem of interest, the key point of which is constructing the solution instead of searching solution in the vast initial data pool according to logic constraints. On the other hand, oligonucleotide segments were treated like variables which stored weights on vertices, no matter what kind number the weights are, integer or real. Therefore, the proposed method can solve the problem with arbitrary weight values and be applied to solve other weight-related problem. In addition, two types of molecules, PNA and molecular beacon were also employed in order to overcome shortcomings of sticker model. And we analyzed the feasibility of the proposed algorithm as well.