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Among the many challenges facing the development of a molecular-based nanotechnology, the directed assembly of discrete molecular objects, and their controlled integration into macroscopic structures, is fundamental. The selective self-assembly or self-organizing characteristic inherent to certain molecules, for example DNA, is a property that could be exploited to address these challenges. This integration problem can be separated into more fundamental tasks: attaching molecular anchors to the macroscopic structures with high spatial resolution; assembling the discrete molecular objects; and positioning and attaching the molecular objects onto the macroscopic structures.

Here, several aspects of these tasks will be discussed, for example using short DNA molecules as molecular anchors and their attachment to electrodes separated by a few ten nanometers; the generation of branched DNA complexes by molecular self-organization; and using AC electric fields for the manipulation, orientation, and positioning of DNA molecules.

Pathogen diseases cause considerable loses in production of food which impact human health from diverse bacterial/viral infections. Precise spotting and diagnosis of such infectious disease is significant to prevent it from further outbreak issues. Moreover, to detect this kind of diseases at an early stage with highly sensitive and selective basis is necessary to avoid the spread of invasive pathogens. The conventional methods such as ELISA, PCR techniques are currently in use to diagnose bacterial/viral disease with high throughput. Though these diagnostic techniques assist in detect and identify the diseases, there are few modern challenges to be meet in order to make this diagnostic more effective in recent days. In this paper, our designed device consists of Bionanosensor works on nucleic acid-based testing provides result with high specificity and selectivity which is vital for early stage identification in a rapid real-time effective manner

Biomolecules such as DNA and proteins exhibit a wealth of modes in the Terahertz (THz) range from the rotational, vibrational and stretching modes of biomolecules. Many materials such as drywall that are opaque to human eyes are transparent to THz. Therefore, it can be used as a powerful tool for biomolecular sensing, biomedical analysis and through-the-wall imaging. Experiments were carried out to study the absorption of various materials including DNA and see-through imaging of drywall using FTIR spectrometer and Time Domain Spectroscopy (TDS) system.

The convergence of terahertz spectroscopy and single molecule experimentation offers significant promise of enhancement in sensitivity and selectivity in molecular recognition, identification and quantitation germane to military and security applications. This paper provides a brief overview of the constraints set by single molecule recognition systems and reports the results of experiments which address fundamental barriers to the integration of large, patterned bio-compatible molecular opto-electronic systems with silicon based microelectronic systems. Central to this thrust is an approach involving sequential epitaxy on surface bound single stranded DNA one-dimensional substrates. The challenge of producing highly structured macromolecular substrates, which are necessary in order to implement molecular nanolithography, has been addressed experimentally by combining “designer” synthetic DNA with biosynthetically derived plasmid components. By design, these one dimensional templates are composed of domains which contain sites which are recognized, and therefore addressable by either complementary DNA sequences and/or selected enzymes. Such design is necessary in order to access the nominal 2 nm linewidth potential resolution of nanolithography on these one-dimensional substrates. The recognition and binding properties of DNA ensure that the lithographic process is intrinsically self-organizing, and therefore self-aligning, a necessity for assembly processes at the requisite resolution. Another requirement of this molecular epitaxy approach is that the substrate must be immobilized. The challenge of robust surface immobilization is being addressed via the production of the equivalent of molecular tube sockets. In this application, multi-valent core-shell fluorescent quantum dots provide a mechanism to prepare surface attachment sites with a pre-determined 1:1 attachment site : substrate (DNA) molecule ratio.

Terahertz signal transmission in DNA is simulated and analyzed using molecular dynamics and digital signal processing techniques to demonstrate that signals encoded in vibrational movements of hydrogen bonds can travel along the backbone of DNA and eventually be recovered and analyzed using digital signal processing techniques.

Nature offers an astonishing array of complex structures and functional devices. The most sophisticated examples of functional systems with multiple interconnected nano-scale components can be found in biology. Biology uses a limited number of building blocks to create complexity and to extend the size and the functional range of basic nano-scale structures to new domains. Three main groups of molecular tools used by biology include oligonucleotides (linear chains of nucleotides), proteins (folded chains of amino acids), and polysaccharides (chains of sugar molecules). Nature uses these tools to store information, to create structures, and to build nano-scale machines.

Recent advances in understanding the structure and function of these building blocks has enabled a number of novel uses for them outside the biological domain. Of particular interest to us is the use of these building blocks to self-assemble nano-scale electronic, photonics, or nanomechanical systems. In this chapter we will look at two groups of building blocks (oligonucleotides and proteins) and review how they have been used to self-assemble engineered structures and build functional devices in the nano-scale.

We will begin by a review of the basic structure and properties (both physical and chemical) of oligonucleotides and proteins. This section is meant to be used as a self-contained reference for the readers from the engineering community that may be less familiar with the symbols and jargon of biochemistry. The most salient properties of the biomolecules are emphasized and listed here to facilitate future research in the area. We continue by a review of recent advances in designing artificial nano-scale DNA structures that can be constructed entirely via engineered self-assembly. Rapid advances in the design and construction of self-assembled DNA structures has resulted in an impressive level of understanding and control over this type of nano-scale manufacturing. Polypeptides and proteins are decidedly less understood and their use in engineered self-assembly has been relatively limited. Nevertheless, as we discuss in the concluding sections of the chapter, both genetically engineered polypeptides and proteins can be used to guide self-assembly processes in nano-scale and help in interfacing nano-scale objects with micron-scale components and templates.

Biology now produces huge amount of data mainly in the form of symbolic sequences. These data are noisy and incomplete so that statistics is inevitable as a first step in any analysis. However, in order to reveal the biological regularities masked by billion years of random mutations and natural selection one must invoke more or less deterministic approaches. We will draw a few simple examples from our recent bioinformatics work that make use of Poisson distribution and Markov prediction in statistics, Goulden-Jackson cluster method in enumerative combinatorics, number of Eulerian loops in graph theory, and factorizable language in formal language theory.

Monolayers of thymine amphiphile containing azobenzene chromophore (Azo-Thy) were prepared on various aqueous oligonucleotide (dA₃₀, d(GA)₁₅, d(GGA)₁₀) subphases. Pressure–area isotherms and reflection absorption spectra of the monolayers on dA₃₀ or d(GA)₁₅ solution showed that the H-aggregate of the azobenzene units was formed at higher surface pressure than 25 mN/m. In contrast, the monolayer on an aqueous d(GGA)₁₀ solution did not form any aggregates of the azobenzene units even at high surface pressure. Base-pair formation between Azo-Thy and template d(GGA)₁₀ could give free volume to the azobenzene units in the monolayer to prevent the aggregation of the azobenzene units at the air–water interface.

In order to develop a new DNA sequencing method by using chemical force microscopy (CFM), we have investigated the interaction of the hydrogen bonding between surfaces of nucleobase self-assembled monolayers (SAMs) and AFM-tips modified with the nucleobases. The two different adhesion forces, the jump-in force and pull-off force, between the AFM-tip modified with cytosine-SAM and the surfaces of four kinds of nucleobase SAMs were measured in water (20°C) by CFM. The adsorption of poly (C) onto a nucleobase-SAM on a gold electrode of quartz crystal microbalance (QCM) was measured as resonance frequency changes. The relative relation among four bases showed similar tendency in the adhesion force measured by the cytosine AFM-tip and in the adsorption amount of poly (C) on the QCM electrode as well as in the theoretically calculated interaction energies between two nucleobases.

We propose a new method that double-stranded DNA molecules can be stretched and immobilized on the clean glass substrate by using a lipid monolayer at the air–water interface. This method is based on the substrate lifting of Langmuir–Blodgett method. We observed fluorescence images of polyion complex films with a scanning near-field optical microscope (SNOM). As a result, straight fluorescent lines aligned parallel to the lifting direction were observed and it was considered that isolated single DNA molecules were extended to align on the substrate. This method is applied to various DNA molecules.

A brief summary is provided of selected current activities in the field of nanoelectronics, which is taken here to mean the fabrication and integration of active microelectronic components with feature dimensions of tens of nanometers or less. Particular emphasis is placed upon the classes of nanoelectronic devices that were discussed at the 2002 WOFE Conference.

A novel nanoscale-engineering methodology is presented that has potential for the first-time development of a microscope-system capable of collecting terahertz (THz) frequency spectroscopic signatures from microscopic biological (bio) structures. This unique THz transmission microscopy approach is motivated by prior studies on bio-materials and bio-agents (e.g., DNA, RNA and bacterial spores) that have produced spectral features within the THz frequency regime (i.e., ∼ 300 GHz to 1000 GHz) that appear to be representative of the internal structure and characteristics of the constituent bio-molecules. The suggested THz transmission microscopy is a fundamentally new technological approach that seeks to avoid the limitations that exist in traditional experiments (i.e., that must average over large numbers of microscopic molecules) by prescribing a viable technique whereby the THz frequency signatures may be collected from individual bio-molecules and/or microscopic biological constructs. Specifically, it is possible to envision the development of a “nanoscale imaging array” that possesses the characteristics necessary (e.g., sub-wavelength resolution) for successfully performing “THz-frequency microscopy.”

Aligning or assembling an enormous amount of short reads is a core step for high throughput biological applications. Based on existing indexing and pattern matching technologies, several algorithms and software have been developed. Yet, there is still a strong need to further improve the speed. In this paper, a new revised, parallel algorithm for the Burrows-Wheeler transform is presented. This is used to construct the suffix arrray of large strings such as those produced by Next Generation Sequencing. The algorithm is designed for parallelism and can effectively exploit the combination of low capacity memory and Open MP. Furthermore, the implementation is up to 2 times faster than serial algorithms.

The team’s initial hypothesis states that the Mereon Matrix’s First Principles constitute a unitive template generally applicable as an information model. For verification of this premise, the knowledge domain of human molecular genetics was used in a study called ATCG. The Matrix’s seven functions and its fractal principle were applied using the latest (at the point of writing, i.e. up to the beginning of the year 2013) original scientific literature as the source of domain information. ATCG was elaborated through all seven functions with each further explored through its level of micro-functions. The Mereon Matrix was extremely useful in modelling as it constantly forced authors to pose specific questions with respect to the topics inherent at different micro-functions. This allowed searching for answers in the literature using an iterative and incremental modelling process. Upon completing the project it was concluded that the Mereon Matrix as a template for modelling human molecular genetics met and exceeded what was anticipated.

Genes influence the expression of each other through a complex, nonlinear, dynamical network of interactions. There are a number of interesting open questions about what kind of information can be determined about the structure and dynamics of this network from limited experimental data.

We employed biopolymer DNA as a template to form J-aggregates of pseudoisocyanine (PIC), and succeeded to optimize the conditions for their formation in solutions and solid films. The optical characteristics of J-aggregates were investigated by absorption, fluorescence and circular dichroic (CD) spectra. Polyvinylalcohol (PVA) introduced as a matrix for the films was proved to play a role to prevent the precipitation or recrystallization of the dyes in solutions and films. We investigated the dependence on concentrations of dye and DNA, and the ratio of these, and effects from counter ions for PIC. We also prepared the samples for more than 20 types of cyanine dyes, finding few dyes showing J-aggregate peak. These results show possibility of application of J-aggregate into novel optical devices requiring optical nonlinearity or superradiant behavior.

In this paper we look at links between biology and computer science, at how Turing machines may change our look of bacteria, at how colonies of bacteria could be classified and how hyperbolic cellular automata could be used to better understand the behaviour of colonies of bacteria.

In this paper, we demonstrate the applicability of the perturbation methods to different elastic models of DNA molecule. Two different kinds of perturbation methods are presented to find a first approximation for the force-extension characteristic of DNA in the anisotropic wormlike chain model, and the persistence length of DNA in the asymmetric elastic rod model. In both cases we show that it is meaningful to use the perturbation theory, and a first-order calculation is enough to find the result with an acceptable accuracy.

The principal criteria Cn (n = 1 to 23) and grammatical production rules are set out of a universal computational rewrite language spelling out a semantic description of an emergent, self-organizing architecture for the cosmos. These language productions already predicate: (1) Einstein’s conservation law of energy, momentum and mass and, subsequently, (2) with respect to gauge invariant relativistic space time (both Lorentz special & Einstein general); (3) Standard Model elementary particle physics; (4) the periodic table of the elements & chemical valence; and (5) the molecular biological basis of the DNA / RNA genetic code; so enabling the Cybernetic Machine specialist Groups Mission Statement premise;** (6) that natural semantic language thinking at the higher level of the self-organized emergent chemical molecular complexity of the human brain (only surpassed by that of the cosmos itself!) would be realized (7) by this same universal semantic language via (8) an architecture of a conscious human brain/mind and self which, it predicates consists of its neural / glia and microtubule substrates respectively, so as to endow it with; (9) the intelligent semantic capability to be able to specify, symbolize, spell out and understand the cosmos that conceived it; and (10) provide a quantum physical explanation of consciousness and of how (11) the dichotomy between first person subjectivity and third person objectivity or ‘hard problem’ is resolved.

The mechanism allowing a protein to search for a target sequence on DNA is currently described as an intermittent process made of 3D diffusion in bulk and 1D diffusion along the DNA molecule. Due to the relevant charge of protein and DNA, electrostatic interaction should play a crucial role during this search. In this paper, we explicitly derive the mean field theory allowing for a description of the protein-DNA electrostatics in solution. This approach leads to a unified model of the search process, where 1D and 3D diffusion appear as a natural consequence of the diffusion on an extended interaction energy profile.