The influence of the gate voltage or base pair ratio modulation on the λ-DNA FET performance was examined. The result of the gate voltage modulation indicated that the captured electrons in the guanine base of the λ-DNA molecules greatly influenced the Id-Vd characteristics, and that of the base pair ratio modulation indicated that the tendency of the conductivity was partly clarified by considering the activation energy of holes and electrons and the length and numbers of the serial AT or GC sequences over which the holes or electrons jumped. In addition, the influence of the dimensionality of the DNA molecule on the conductivity was discussed theoretically.

This paper reports on the ambipolar conduction for the λ-Deoxyribonucleic Acid (DNA) field effect transistor (FET) with 450, 400 and 250 base pair experimentally and theoretically. It was found that the drain current of the p-type DNA/Si FET increased as the ratio of the guanine-cytosine (GC) pair increased and that of the n-type DNA/Si FET decreased as the ratio of the adenine-thymine (AT) pair decreased, and the ratio of the GC pair and AT pair was controlled by the total number of the base pair. In addition, it was found that the hole conduction mechanism of the 400 bp DNA/Si FET was polaron hopping and its activation energy was 0.13eV. By considering the electron affinity of the adenine, thymine, guanine, and cytosine, the ambipolar characteristics of the DNA/Si FET was understood. The holes are injected to the guanine base for the negative gate voltage, and the electrons are injected to the adenine, thymine, and cytosine for the positive gate voltage.

Hydrophobic DNA (H-DNA) nano-film was formed as the surface modifier on a thin glass plate working as a slab optical waveguide (SOWF). Cytochrom c (cytc) molecules were immobilized from aqueous solution with direct contacting to the H-DNA nano-film for 30 minutes. From SOWG absorption spectral changes during automated solution exchange (SE) processes, it was found that about 28.1% of cytc molecules was immobilized in the H-DNA nano-film with keeping their reduction functionality by reducing reagent.

Photophysical properties of water-soluble porphyrin were studied in aqueous solutions with/without DNA and in DNA solid films. Ultrathin films were prepared from aqueous DNA solutions by a spin-coating method on glass or on gold nanoparticles (AuNPs). Remarkable enhancement of phosphorescence was observed for porphyrin immobilized in DNA films spin-coated on AuNPs, which was attributed to the electric field enhancement and the increased radiative rate by localized surface plasmon resonance of AuNPs.

Hydrophobic DNA (H-DNA) nano-film was formed on a thin glass plate of 50μm thick working as a slab optical waveguide. Bromothymol blue (BTB) molecules were immobilized from aqueous solution with direct contacting to the H-DNA nano-film for 20 minutes. From changes in absorption spectra observed with slab optical wave guide (SOWG) during automated solution exchange (SE) processes for 100 times, it was found that about 95% of bromothymol blue (BTB) molecules was immobilized in the H-DNA nano-film with keeping their functionality of color change responsible to pH change in the solution.

To construct good DNA codes based on biologically motivated constraints, it is important that they have a large minimum Hamming distance and the number of GC-content is kept constant. Also, maximizing the number of codewords in a DNA code is required for given code length, minimum Hamming distance, and number of GC-content. In most previous works on the construction of DNA codes, quaternary constant weight codes were directly used because the alphabet of DNA strands is quaternary. In this paper, we propose new coding theoretic constructions of DNA codes based on the binary Hadamard matrix from a binary sequence with ideal autocorrelation. The proposed DNA codes have a greater number of codewords than or the equal number to existing DNA codes constructed from quaternary constant weight codes. In addition, it is numerically shown that for the case of codes with length 8 or 16, the number of codewords in the proposed DNA code sets is the largest with respect to the minimum reverse complementary Hamming distances, compared to all previously known results.

Microwave heating is expected to increase the yield of product, to decrease the reaction time, and to discover the new reaction system. The Rolling Circle Amplification (RCA) is an enzymatic synthesis method of deoxyribonucleic acid (DNA) strands with repeated sequence of a circulate template-DNA. In previous study, controlled microwave heating accelerated the maximum 4-fold compared with the conventional condition. Further, we indicated that the selectively heat of some buffer components by microwave irradiation induced the acceleration of RCA. The purpose of this research is to clarify the relationship between the microwave heating and buffer components. The understanding of role of ion-containing buffer components under microwave will be able to control the microwave-assisted enzymatic reaction. We studied the relation between the microwave power loss and RCA components via dielectric measurements, cavity resonator feature measurement, and electromagnetic simulation. Electromagnetic simulation of the TM010 cavity showed that the sample tube was heated only by an electric field. The buffer containing ions of the RCA components was selectively heated via microwave irradiation in the TM010 cavity resonator.

This paper presents an information hiding method for DNA steganography with which a massive amount of data can be hidden in a noncoding strand. Our method maps the encrypted data to the DNA sequence using a numerical mapping table, before concealing it in the noncoding sequence using a secret key comprising sector length and the random number generator's seed. Our encoding algorithm is sector-based and reference dependent. Using modular arithmetic, we created a unique binary-base translation for every sector. By conducting a simulation study, we showed that our method could preserve amino acid information, extract hidden data without reference to the host DNA sequence, and detect the position of mutation error. Experimental results verified that our method produced higher data capacity than conventional methods, with a bpn (bit-per-nucleotide) value that ranged from approximately 1-2, depending on the selected sector length. Additionally, our novel method detected the positions of mutation errors by the presence of a parity base in each sector.

This paper proposes a new algorithm for substring searching. Our algorithm is an improvement on the famous BM algorithm. When a mismatch happens while searching a substring (pattern), the BM algorithm will use two strategies to calculate shifting distances of the substring respectively and selects the larger one. In comparison, our algorithm uses each of the two strategies for their most suitable cases separately without a selection operation. Experimental results demonstrated that our algorithm is more efficient than the BM algorithm and the Quick Search algorithm, especially for binary strings and DNA strings.

We outline a number of high temperature superconducting Josephson junction-based devices including superconducting quantum interference devices (SQUIDs) developed for a wide range of applications including geophysical exploration, magnetic anomaly detection, terahertz (THz) imaging and microwave communications. All these devices are based on our patented technology for fabricating YBCO step-edge junction on MgO substrates. A key feature to the successful application of devices based on this technology is good stability, long term reliability, low noise and inherent flexibility of locating junctions anywhere on a substrate.

A charge-integration read scheme has been developed for a solid-nanopore DNA-sequencer that determines a genome by direct and electrical measurements of transverse tunneling current in single-stranded DNA. The magnitude of the current was simulated with a first-principles molecular dynamics method. It was found that the magnitude is as small as in the sub-pico ampere range, and signals from four bases represent wide distributions with overlaps between each base. The distribution is believed to originate with translational and rotational motion of DNA in a nanopore with a frequency of over 105 Hz. A sequence scheme is presented to distinguish the distributed signals. The scheme makes widely distributed signals time-integrated convergent by cumulating charge at the capacitance of a nanopore device and read circuits. We estimated that an integration time of 1.4 ms is sufficient to obtain a signal difference of over 10 mV for distinguishing between each DNA base. Moreover, the time is shortened if paired bases, such as A-T and C-G in double-stranded DNA, can be measured simultaneously with two nanopores. Circuit simulations, which included the capacitance of a nanopore calculated with a device simulator, successfully distinguished between DNA bases in less than 2.0 ms. The speed is roughly six orders faster than that of a conventional DNA sequencer. It is possible to determine the human genome in one day if 100-nanopores are operated in parallel.

We have investigated the effect of deoxyribonucleic acid (DNA) adsorption on a graphene field-effect-transistor (FET) device. We have used graphene which is grown on a Ni substrate by chemical vapour deposition. The Raman spectra of our graphene indicate its high quality, and also show that it consists of only a few layers. The current-voltage characteristics of our bare graphene strip FET show a hole conduction behavior, and the gate sensitivity of 0.0034 µA/V, which is reasonable with the size of the strip (510 µm2). After the adsorption of 30 base pairs single-stranded poly (dT) DNA molecules, the conductance and gate operation of the graphene FET exhibit almost 11% and 18% decrease from those of the bare graphene FET device. The observed change may suggest a large sensitivity for a small enough (nm size) graphene strip with larger semiconducting property.

Given a set of strings U = {T1, T2, ...,T}, the longest common repeat problem is to find the longest common substring that appears at least twice in each string, considering direct, inverted, and mirror repeats. We define the generalised longest common repeat problem and present a linear time solution.

In this paper, we propose a new method for detecting label-free T4-DNA molecules quantitatively using a surface plasmon resonance (SPR) technique on a gold thin film. We used a solution that dissolved T4-DNA molecules in pure water, and examined the relationship between DNA concentration change and SPR angle change in the solution. As a result, it was confirmed that the SPR angle change increased with increasing DNA concentration change. Therefore, it was feasible to detect the DNA concentration change using the SPR technique. Furthermore, to examine and detect a single or a few DNA molecule, we tried to fabricate an SPR chip in which SPR area is narrowed so that it has the same effect as focusing the beam. To narrow the SPR area, we decreased the area of gold thin film in this chip, and, to reflect light from only the area of gold thin film, the area without a gold thin film was micromachined to increase its unevenness for the reduction of light reflection. By the above-mentioned method, we examined the possibility of detecting a label-free DNA molecule using the SPR technique.

Watson-Crick automata were introduced as a new computer model and have been intensively investigated regarding their computational power. In this paper, aiming to establish the relations among language families defined by Watson-Crick automata and the family of context-free languages completely, we obtain the following results. (1) F1WK = FSWK = FWK, (2) FWK = AWK, (3) there exists a language which is not context-free but belongs to NWK, and (4) there exists a context-free language which does not belong to AWK.

In STS-based mapping, it is necessary to obtain the correct order of probes in a DNA sequence from a given set of fragments or an equivalently a hybridization matrix A. It is well-known that the problem is formulated as the combinatorial problem of obtaining a permutation of A's columns so that the resulting matrix has a consecutive-one property. If the data (the hybridization matrix) is error free and includes enough information, then the above column order uniquely determines the correct order of the probes. Unfortunately this does not hold if the data include errors, and this has been a popular research target in computational biology. Even if there is no error, ambiguities in the probe order may still remain. This in fact happens because of the lack of some information regarding the data, but almost no further investigation has previously been made. In this paper, we define a measure of such imperfectness of the data as the minimum amount of the additional fragments that are needed to uniquely fix the probe order. Polynomial-time algorithms to compute such additional fragments of the minimum cost are presented. A computer simulation using genes of human chromosome 20 is also noted.

An Insertion-Deletion system, first introduced in [1], is a theoretical computing model in the DNA computing framework based on insertion and deletion operations. When insertion and deletion operations work together, as expected, they are very powerful. In fact, it has been shown that even the very restricted Insertion-Deletion systems can characterize the class of recursively enumerable languages [1]-[4]. In this paper, we investigate the computational power of Insertion-Deletion systems and show that they preserve the computational universality without using contexts.

This paper shows how to use sticker to construct solution space of DNA for the library sequences in the set-packing problem and the clique problem. Then, with biological operations, we propose DNA-based algorithms to remove illegal solutions and to find legal solutions for the set-packing and clique problems from the solution space of sticker. Any NP-complete problem in Cook's Theorem can be reduced and solved by the proposed DNA-based computing approach if its size is equal to or less than that of the set-packing problem. Otherwise, Cook's Theorem is incorrect on DNA-based computing and a new DNA algorithm should be developed from the characteristics of the NP-complete problem. Finally, the result to DNA simulation is given.

DNA Sequence Design Problem is a crucial problem in information-based biotechnology such as DNA computing. In this paper, we introduce a powerful design strategy for DNA sequences by refining Random Generator. Random Generator is one of the design strategies and offers great advantages, but it is not a good algorithm for generating a large set of DNA sequences. We propose a Two-Step Search algorithm, then show that TSS can generate a larger set of DNA sequences than Random Generator by computer simulation.

Watson-Crick automata, recently introduced in, are new types of automata in the DNA computing framework, working on tapes which are double stranded sequences of symbols related by a complementarity relation, similar to a DNA molecule. The automata scan separately each of the two strands in a corelated mannar. Some restricted variants of them were also introduced and the relationship between the families of languages recognized by them were investigated in. In this paper, we clarify some relations between the families of languages recognized by the restricted variants of Watson-Crick finite automata and the families in the Chomsky hierarchy.