IEEE Transactions on NanoBioscience (IEEE T NANOBIOSCI )

Publisher: IEEE Engineering in Medicine and Biology Society, Institute of Electrical and Electronics Engineers


This transaction reports on original, innovative and interdisciplinary work on all aspects of molecular systems, cellular systems, and tissues - including molecular electronics.

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    IEEE transactions on nanobioscience
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Institute of Electrical and Electronics Engineers

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Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: We analyzed tubulin proteins using Resonant Recognition Model to predict possible electromagnetic resonances in tubulin and microtubules. These electromagnetic resonances are proposed to be caused by charge transfer through protein molecule. The frequencies of these electromagnetic resonances depend on charge velocity. Using different velocities of charge transfer, we predicted resonant frequencies in different frequency ranges from KHz to THz. We also proposed that these resonant frequencies could be relevant for taxol binding as well as to possible role of microtubules as macromolecular computer.
    IEEE Transactions on NanoBioscience 12/2014;
  • [Show abstract] [Hide abstract]
    ABSTRACT: Molecular Communication is an emerging and promising communication paradigm for several multidisciplinary domains like bio-medical, industry and military. Differently to the traditional communication paradigm, the information is encoded on the molecules, that are then used as carriers of information. Novel approaches related to this new communication paradigm have been proposed, mainly focusing on architectural aspects and categorization of potential applications. So far, security and privacy aspects related to the molecular communication systems have not been investigated at all and represent an open question that need to be addressed. The main motivation of this paper lies on providing some first insights about security and privacy aspects of molecular communication systems, by highlighting the open issues and challenges and above all by outlining some specific directions of potential solutions. We start with a general presentation of attacks in traditional telecommunication systems, and then we describe the main features of the molecular communication paradigm. This structure will allow to highlight that the existing cryptographic methods and security approaches are not suitable at all for these new communication systems. Specific issues and challenges will be considered that need ad-hoc solutions. We will discuss directions in terms of potential solutions by trying to highlight the main advantages and potential drawbacks for each direction considered. We will try to answer to the main questions: 1) why this solution can be exploited in the molecular communication field to safeguard the system and its reliability; 2) which are the main issues related to the specific approach.
    IEEE Transactions on NanoBioscience 09/2014; 13(3):167-168.
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    ABSTRACT: This paper investigates the exponential stability problem of switched stochastic genetic regulatory networks (GRNs) with time-varying delays. Two types of switched systems are studied respectively: one is the stochastic switched delayed GRNs with only stable subsystems and the other is the stochastic switched delayed GRNs with both stable and unstable subsystems. By using switching analysis techniques and the modified Halanay differential inequality, new criteria are developed for the exponential stability of switched stochastic GRNs with time-varying delays. Finally, an example is given to illustrate the main results.
    IEEE Transactions on NanoBioscience 09/2014; 13(3):336-342.
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    ABSTRACT: To coordinate their behavior and virulence and to synchronize attacks against their hosts, bacteria communicate by continuously producing signaling molecules (called autoinducers) and continuously monitoring the concentration of these molecules. This communication is controlled by biological circuits called quorum sensing (QS) circuits. Recently QS circuits and have been recognized as an alternative target for controlling bacterial virulence and infections without the use of antibiotics. Pseudomonas aeruginosa is a Gram-negative bacterium that infects insects, plants, animals and humans and can cause acute infections. This bacterium has three interconnected QS circuits that form a very complex and versatile QS system, the operation of which is still under investigation. Here we use Boolean networks to model the complete QS system of Pseudomonas aeruginosa and we simulate and analyze its operation in both synchronous and asynchronous modes. The state space of the QS system is constructed and it turned out to be very large, hierarchical, modular and scale-free. Furthermore, we developed a simulation tool that can simulate gene knock-outs and study their effect on the regulons controlled by the three QS circuits. The model and tools we developed will give to life scientists a deeper insight to this complex QS system.
    IEEE Transactions on NanoBioscience 08/2014; 13(3):1-7.
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    ABSTRACT: We report the extracellular biosynthesis of gold nanoparticles (AuNPs) using a fungus Fusarium acuminatum. Mycosynthesis of Au-NPs was carried out by challenging the fungal cells filtrate with HAuCl4 solution (1mM), as nanoparticles synthesizing enzyme secrete extracellularly by the fungi. The AuNPs were characterized with the help of UV-Visible spectrophotometer, Fourier Transform Infrared spectroscopy, Zeta Potential, X-ray diffraction (XRD) and Transmission electron microscopy (TEM). We observed absorbance peak in between 520 nm-550 nm corresponding to the surface plasmon absorbance of the gold nanoparticles. The nanoparticles synthesised in the present investigation were found to be capped by proteins. XRD results showed that the distinctive formation of crystalline gold nanoparticles in the solution. The spherical and polydispersed AuNPs in the range 8 to 28 nm with average size of 17 nm were observed by TEM analysis. We also standardised the parameters like the effect of pH, temperature and salt concentration on the biosynthesis of gold nanoparticles. It was found that acidic pH, 1mM salt concentration and 370C temperature were found to be optimum for the synthesis of Au-NPs. Therefore, the present study introduces the easy, better and cheaper method for biosynthesis of AuNPs.
    IEEE Transactions on NanoBioscience 08/2014;
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    ABSTRACT: Adsorption of target molecules on the immobilised microcantilever surface produced beam displacement due to the differential surface stress generated between the immobilised and non-immobilised surface. Surface stress is caused by the intermolecular forces between the molecules. Van der Waals, electrostatic forces, hydrogen bonding, hydrophobic effect and steric hindrance are some of the intermolecular forces involved. A theoretical framework describing the adsorption-induced microcantilever displacement is derived in this paper. Experimental displacement of thrombin aptamer-thrombin interactions was carried out. The relation between the electrostatic interactions involved between adsorbates (thrombin) as well as adsorbates and substrates (thrombin aptamer) and the microcantilever beam displacement utilising the proposed mathematical model was quantified and compared to the experimental value. This exercise is important to aid the designers in microcantilever sensing performance optimisation.
    IEEE Transactions on NanoBioscience 08/2014;
  • [Show abstract] [Hide abstract]
    ABSTRACT: Nanoscale communication based on F¨orster Resonance Energy Transfer (FRET) enables nanoscale single molecular devices to communicate with each other utilizing excitons generated on fluorescent molecules as information carriers. Based on the point-to-point single-exciton FRET-based nanocommunication model, we investigate the multiple-exciton case for pointto- point and broadcast communications following an information theoretical approach and conducting simulations through Monte Carlo approach. We demonstrate that the multi-exciton transmission significantly improves the channel reliability and the range of the communication up to tens of nanometers for immobile nanonodes providing high data transmission rates. Furthermore, our analyses indicate that multi-exciton transmission enables broadcasting of information from a transmitter nanonode to many receiver nanonodes pointing out the potential of FRETbased communication to extend over nanonetworks. In this study, we also propose electrically and chemically controllable routing mechanisms exploiting the strong dependence of FRET rate on spectral and spatial characteristics of fluorescent molecules. We show that the proposed routing mechanisms enable the remote control of information flow in FRET-based nanonetworks. The high transmission rates obtained by multi-exciton scheme for point-to-point and broadcast communications, as well as the routing opportunities make FRET-based communication promising for future molecular computers.
    IEEE Transactions on NanoBioscience 07/2014;
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    ABSTRACT: This paper describes a mobile bionanosensor network designed for target tracking. The mobile bionanosensor network is composed of bacterium-based autonomous biosensors that coordinate their movement through the use of two types of signaling molecules, repellents and attractants. In search of a target, the bacterium-based autonomous biosensors release repellents to quickly spread over the environment, while, upon detecting a target, they release attractants to recruit other biosensors in the environment toward the location around the target. A mobility model of bacterium-based autonomous biosensors is first developed based on the rotational diffusion model of bacterial chemotaxis, and from this their collective movement to track a moving target is demonstrated. In simulation experiments, the mobile bionanosensor network is evaluated based on the mean tracking time. Simulation results show a set of parameter values that can optimize the mean tracking time, providing an insight into how bacterium-based autonomous biosensors may be designed and engineered for target tracking.
    IEEE Transactions on NanoBioscience 07/2014;
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    ABSTRACT: In this paper, we propose a symbol interval optimization algorithm in molecular communication with drift. Proper symbol intervals are important in practical communication systems since information needs to be sent as fast as possible with low error rates. There is a trade-off, however, between symbol intervals and inter-symbol interference (ISI) from Brownian motion. Thus, we find proper symbol interval values considering the ISI inside two kinds of blood vessels, and also suggest no ISI system for strong drift models. Finally, an isomer-based molecule shift keying (IMoSK) is applied to calculate achievable data transmission rates (achievable rates, hereafter). Normalized achievable rates are also obtained and compared in one-symbol ISI and no ISI systems.
    IEEE Transactions on NanoBioscience 07/2014;
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    ABSTRACT: The purpose of this study was to investigate the uptake and cytotoxic effects of magnetic poly lactic-co-glycolic acid (PLGA)-coated iron oxide nanoparticles as a carrier of 5-fluorouracil (5-FU) and X-ray on the level of proliferation capacity of DU145 prostate carcinoma cell line in monolayer culture. Following monolayer culture, DU 145 cells were treated with different concentrations of 5-FU or 5-FU loaded nanoparticles for 24 h and 2Gy X-ray (6 Mega-voltage (MV)). The rate of nanoparticles penetration was then measured using atomic adsorption spectroscopy (AAS). The cytotoxicity effect of these nanoparticles with/ without X-ray radiation was evaluated using colony formation assay. Spectroscopy results showed that iron content and therefore the cellular uptake of 5-FU loaded nanoparticles increased with increasing nanoparticle concentrations. Further, the proliferation capacity of the cells decreased with the increase of 5-FU and 5- FU loaded nanoparticle concentrations in combination with X-ray radiation. However the extent of reduction in colony number following treatment with 5-FU-loaded nanoparticles in combination with 2Gy of megavoltage X-ray radiation was significantly more than for free 5-FU. Thus, drug-loaded nanoparticles could deliver 5-FU more efficiently into the cells. PLGA coated iron oxide nanoparticles are therefore effective drug delivery vehicles for 5-FU. PLGA coated iron oxide nanoparticles are biocompatible and this coating is an appropriate surface that can penetrate into the cells.
    IEEE Transactions on NanoBioscience 07/2014;
  • [Show abstract] [Hide abstract]
    ABSTRACT: The reliable and accurate identification of cancer categories is crucial to a successful diagnosis and a proper treatment of the disease. In most existing work, samples of gene expression data are treated as one-dimensional signals, and are analyzed by means of some statistical signal processing techniques or intelligent computation algorithms. In this paper, from an image-processing viewpoint, a spectralfeature- based Tikhonov-regularized least-squares (TLS) ensemble algorithm is proposed for cancer classification using gene expression data. In the TLS model, a test sample is represented as a linear combination of the atoms of a dictionary. Two types of dictionaries, namely singular value decomposition (SVD)-based eigenassays and independent component analysis (ICA)-based eigenassays, are proposed for the TLS model, and both are extracted via a two-stage approach. The proposed algorithm is inspired by our finding that, among these eigenassays, the categories of some of the testing samples can be assigned correctly by using the TLS models formed from some of the spectral features, but not for those formed from the original samples only. In order to retain the positive characteristics of these spectral features in making correct category assignments, a strategy of classifier committee learning (CCL) is designed to combine the results obtained from the different spectral features. Experimental results on standard databases demonstrate the feasibility and effectiveness of the proposed method.
    IEEE Transactions on NanoBioscience 06/2014;
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    ABSTRACT: Nanonetworks refer to a group of nano-sized machines with very basic operational capabilities communicating to each other in order to accomplish more complex tasks such as in-body drug delivery, or chemical defense. Realizing reliable and high-rate communication between these nanomachines is a fundamental problem for the practicality of these nanonetworks. Recently, we have proposed a molecular communication method based on F¨orster Resonance Energy Transfer (FRET) which is a nonradiative excited state energy transfer phenomenon observed among fluorescent molecules, i.e., fluorophores. We have modeled the FRET-based communication channel considering the fluorophores as single-molecular immobile nanomachines, and shown its reliability at high rates, and practicality at the current stage of nanotechnology. In this study, for the first time in the literature, we investigate the network of mobile nanomachines communicating through FRET. We introduce two novel mobile molecular nanonetworks: FRET-based mobile molecular sensor/actor nanonetwork (FRET-MSAN) which is a distributed system of mobile fluorophores acting as sensor or actor node; and FRET-based mobile ad hoc molecular nanonetwork (FRETMAMNET) which consists of fluorophore-based nanotransmitter, nanoreceivers and nanorelays. We model the single message propagation based on birth-death processes with continuous time Markov chains. We evaluate the performance of FRETMSAN and FRET-MAMNET in terms of successful transmission probability and mean extinction time of the messages, system throughput, channel capacity and achievable communication rates.
    IEEE Transactions on NanoBioscience 06/2014;