DNA Computing Sequence Design Based on Bacterial Foraging Algorithm

The process of designing a set of good DNA sequences is an essential problem and one of the most practical and important research topics in DNA-based computing. In this field of research, a DNA sequence design problem is defined as a multi-objective problem, and it is evaluated using four objective functions, which are h-measure, similarity, continuity, and hairpin. In addition, two constraints, GC content and melting temperature, are used to maintain uniform chemical characteristics of the sequences. In the authors' previous research, ant colony system (ACS) was proposed to solve the DNA sequence design problem and the Watson-Crick base pair ÄGo37 was used as the distance between nodes in the computational model of DNA sequence design. In the current study, the use of other parameters, namely, unified near estneighbour thermodynamic parameters, are investigated and the result is compared with the previous work.

The process of designing a set of good DNA sequences is an essential problem and one of the most practical and important research topics in DNA-based computing. In this field of research, a DNA sequence design problem is defined as a multi-objective problem, and it is evaluated using four objective functions, which are h-measure, similarity, continuity, and hairpin. In addition, two constraints, GC content and melting temperature, are used to maintain uniform chemical characteristics of the sequences. In the authors' previous research, ant colony system (ACS) was proposed to solve the DNA sequence design problem and the Watson-Crick base pair ΔGo37 was used as the distance between nodes in the computational model of DNA sequence design. In the current study, the use of other parameters, namely, Breslauer nearest-neighbour thermodynamic parameters are investigated and the result is compared with the previous work.

Solid biofuels from energy crops are widely considered as an attractive alternative for power production in dedicated combustion or cofiring applications. The aim of this work is to present fuel and ash characterization along with thermogravimetric investigations of pyrolysis and combustion behavior for five crops (cardoon, Miscanthus, Paulownia, willow, and poplar) compared with Greek lignite. Devolatilization is well modeled by three independent parallel reactions and reaches higher rates than lignite; char reactivity of woody biomass and Miscanthus was high, whereas cardoon char resembled more closely that of lignite. High potassium concentration and low melting temperatures were found for all biomass ashes; therefore, a severe/high slagging or agglomeration potential is expected. Overall, cardoon appears to be the most problematic of the investigated biomass fuels, due to high ash content, low ash melting temperature, a slower char combustion rate, and risk of chlorine corrosion; cofiring with lignite appears to be a better option for this fuel. © 2011 American Chemical Society.

In this study we investigated lipolysis-triggered supersaturation and precipitation of a set of model compounds formulated in lipid-based formulations (LBFs). The purpose was to explore the relationship between precipitated solid form and inherent physicochemical properties of the drug. Eight drugs were studied after formulation in three LBFs, representing lipid-rich (extensively digestible) to surfactant-rich (less digestible) formulations. In vitro lipolysis of drug-loaded LBFs were conducted, and the amount of dissolved and precipitated drug was quantified. Solid form of the precipitated drug was characterized with polarized light microscopy (PLM) and Raman spectroscopy. A significant solubility increase for the weak bases in the presence of digestion products was observed, in contrast to the neutral and acidic compounds for which the solubility decreased. The fold-increase in solubility was linked to the degree of ionization of the weak bases and thus their attraction to free fatty acids. A high level of supersaturation was needed to cause precipitation. For the weak bases, the dose number indicated that precipitation would not occur during lipolysis; hence, these compounds were not included in further studies. The solid state analysis proved that danazol and griseofulvin precipitated in a crystalline form, while niclosamide precipitated as a hydrate. Felodipine and indomethacin crystals were visible in the PLM, whereas the Raman spectra showed presence of amorphous drug, indicating amorphous precipitation that quickly crystallized. The solid state analysis was combined with literature data to allow analysis of the relationship between solid form and the physicochemical properties of the drug. It was found that low molecular weight and high melting temperature increases the probability of crystalline precipitation, whereas precipitation in an amorphous form was favored by high molecular weight, low melting temperature, and positive charge.

DNA computing relies on biochemical reactions of DNA molecules and may result in incorrect or undesirable computations. Therefore, much work has focused on designing the DNA sequences to make the molecular computation more reliable. Sequence design involves with a number of heterogeneous and conflicting design criteria and traditional optimization methods may face difficulties. In this paper, we formulate the DNA sequence design as a multiobjective optimization problem and solve it using a constrained multiobjective evolutionary algorithm (EA). The method is implemented into the DNA sequence design system, NACST/Seq, with a suite of sequence-analysis tools to help choose the best solutions among many alternatives. The performance of NACST/Seq is compared with other sequence design methods, and analyzed on a traveling salesman problem solved by bio-lab experiments. Our experimental results show that the evolutionary sequence design by NACST/Seq outperforms in its reliability the existing sequence design techniques such as conventional EAs, simulated annealing, and specialized heuristic methods.

DNA computing is a new method that uses biological molecule DNA as computing medium and biochemical reaction as computing tools. The design of DNA sequence plays an important role in improving the reliability of DNA computation. The sequence design is an approach of the control, which aims to design of DNA sequences satisfying some constraints to avoid such unexpected molecular reactions .To deal these constraints ,we convert the design of DNA sequences into a multi-objective optimize problems, and then an example is illustrated to show the efficiency of our method given here.

DNA computing is a parallel computing model based on DNA molecules. High-quality DNA sequences can prevent unwanted hybridization errors in the computation process. The design of DNA molecules can be regarded as a multi-objective optimization problem, which needs to satisfy a variety of conflicting DNA encoding constraints and objectives. In this paper, a novel reference point based multi-objective optimization algorithm is proposed for designing reliable DNA sequences. In order to obtain balance Similarity and H-measure objective values, the reference point strategy is adapted to searching for idea solutions. Firstly, every individual should be assigned a rank value by the non-dominated sort algorithm. Secondly, the crowding distance is replaced by the distance to the reference point for each individual. Lastly, the proposed algorithm is compared with some state-of-the-art DNA sequence design algorithms. The experimental results show our algorithm can provide more reliability DNA sequences than existing sequence design techniques.

The design of DNA sequences is critical for many research fields such as DNA self-assembly, DNA hybridization arrays, DNA computing, and PCR-based applications. DNA secondary structure prediction is the key part for these DNA nanotechnologies. In this paper, we present a dynamic programming algorithm to predict the secondary structure of single-stranded DNA tiles. The algorithm calculates all possible maximum matches based on the nearest-neighbour model and global energy minimization. Experimental results show that the algorithm performers significantly to predict secondary str uctures for single-stranded DNA tiles.

Physical properties of extruded corn grits with corn fibre by CO2 injection extrusion

Molecular computing has proved its possibility to solve weighted graph problem such as Hamiltonian Path Problem (HPP), Traveling Salesman Problem (TSP) and the Shortest Path Problem (SPP). Normally, in molecular computation, the DNA sequences used for the computation should be critically designed in order to reduce error that could occur during computation. In the previous paper, we have proposed a readout method tailored specifically to HPP in DNA Computing using real-time PCR for output visualization. Six nodes of HPP was considered. Based on the example instance, the method requires 11 oligonucleotides, where 6 oligonucleotides are for the nodes and 5 oligonucleotides are for the edges. Three TaqMan probes and five primers are required as well. In this study, a procedure for DNA sequence design is presented in order to obtain good sequences for those nodes, primers, and probes. The experiment is done based on the generated DNA sequences and the Hamiltonian Path can be determined successfully.

Intracavity melting analysis of DNA methylation using laser emission

In DNA computing, the design of reliable DNA sequences is one of the most important tasks, because sequences used for that purpose have to fulfill several biochemical restrictions to avoid undesirable reactions. These reactions usually cause incorrect computations, so it is necessary to avoid this circumstance by generating robust and reliable sets of sequences. In this paper, we consider six different conflicting design criteria to solve the problem by using the multiobjective fast non dominated sorting genetic algorithm (NSGA-II). Our proposal is compared against other sequence design methods, and our results show that our version of NSGA-II outperforms in reliability other existing techniques published in the literature.

The melt temperature and a special polymeric nucleating agent [acrylonitrile–styrene copolymer (SAN)] were investigated to find an effective way for tailoring the crystalline structures of the water‐assisted injection‐molded polypropylene (WAIM PP) parts. The results showed that lowering the melt temperature led to the formation of a small amount of β‐form crystals in both outer and core layers of the WAIM PP parts. Nevertheless, the melt temperature had little effect on tailoring the crystalline structures of the WAIM PP parts. The addition of a low content (6 wt%) of the SAN was interestingly found to gradually influence the crystalline structures as lowering the melt temperature. WAIM PP/SAN blend parts with high contents of β‐form in both outer and core layers (30.7 and 18.4%, respectively), and high contents of transcrystals in the inner layer were molded at relatively low melt temperature (180°C), whereas the SAN had little influence on the crystalline structures at higher melt temperature (230°C). The formation of the transcrystals was ascribed to the in situ fibrillation of the SAN, which was resulted from high shear and cooling rates caused by high‐pressure water penetration during WAIM. POLYM. ENG. SCI., 2013. © 2013 Society of Plastics Engineers

In a DNA sequence, we have the celebrated Watson-Crick complement $\overline{T}=A, \overline{A}= {T}, \overline{C}= G$, and $\overline{G}= C$. The phenomenon of secondary structure refers to the tendency of a single stranded DNA sequence to fold back upon itself, and it is usually caused by the existence of two non-overlapping reverse complement consecutive subsequences, defined as follows. Given an integer $m \geq 2$, two non-overlapping consecutive subsequences of length m, denoted as $x=(x_{1}, x_{m})$ and $y=(y_{1}, y_{m})$, are called reverse complement if $x_{i}=\overline{y_{m-i+1}}$ for 1$\leq i \leq m$. The property of secondary structure avoidance (SSA) forbids a sequence to contain such reverse complement subsequences, and it is a key criterion in the design of single-stranded DNA sequences for DNA computing and storage. In this paper, we improve on a recent result of Nguyen et al., by introducing explicit constructions of secondary structure avoidance codes and analyzing the capacity for any given m. In particular, our constructions have optimal rate 1.1679bits/nt and 1.5515bits/nt when m = 2 and m + 3, respectively.

Development of lead-free solders with low melting temperature is important for substitution of Pb-based solders to reduce direct risks to human health and the environment. In the present work, Sn-Bi-In solders were studied for different ratios of Bi and Sn to obtain solders with low melting temperature. The microstructure, thermal properties, wettability, mechanical properties, and reliability of joints with Cu have been investigated. The results show that the microstructures of the Sn-Bi-In solders were composed of β-Sn, Bi, and InBi phases. The intermetallic compound (IMC) layer was mainly composed of Cu6Sn5, and its thickness increased slightly as the Bi content was increased. The melting temperature of the solders was around 100°C to 104°C. However, when the Sn content exceeded 50 wt.%, the melting range became larger and the wettability became worse. The tensile strength of the solder alloys and solder joints declined with increasing Bi content. Two fracture modes (IMC layer fracture and solder/IMC mixed fracture) were found in solder joints. The fracture mechanism of solder joints was brittle fracture. In addition, cleavage steps on the fracture surface and coarse grains in the fracture structure were comparatively apparent for higher Bi content, resulting in decreased elongation for both solder alloys and solder joints.