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NanoBioscience, IEEE Transactions on

Issue 1 • Date March 2006

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Displaying Results 1 - 15 of 15
  • Table of contents

    Publication Year: 2006 , Page(s): c1
    Cited by:  Papers (1)
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  • IEEE Transactions on NanoBioscience publication information

    Publication Year: 2006 , Page(s): c2
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  • Dielectrophoresis of DNA: time- and frequency-dependent collections on microelectrodes

    Publication Year: 2006 , Page(s): 1 - 8
    Cited by:  Papers (15)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (1181 KB)  

    This paper reports measurements that characterize the collection of DNA onto interdigitated microelectrodes by high-frequency dielectrophoresis. Measurements of time-dependent collection of 12 kilobase pair plasmid DNA onto microelectrodes by dielectrophoresis show significant reduction in the response as the frequency increases from 100 kHz to 20 MHz. Collection time profiles are quantitatively measured using fluorescence microscopy over the range 100 kHz to 5 MHz and are represented in terms of two parameters: the initial dielectrophoretic collection rate, and the initial to steady-state collection transition. Measured values for both parameters are consistent with trends in the frequency-dependent real part of the effective polarizability measured for the same plasmid DNA using dielectric spectroscopy. The experimentally measured parameters are qualitatively compared with trends predicted by theory that takes into account dielectrophoretic particle movement and diffusion. The differences between experiment and theory are discussed with suggested improvements to theoretical models, for example, including the effects of electrohydrodynamically driven fluid motion View full abstract»

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  • Nanofabrication of polymer surfaces utilizing colloidal lithography and ion etching

    Publication Year: 2006 , Page(s): 9 - 14
    Cited by:  Papers (7)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (2096 KB) |  | HTML iconHTML  

    In this paper, we utilize colloidal lithography based on electrostatic self-assembly of polystyrene colloidal particles onto a polymer surface as a nanoscale mask. The pattern is then transferred to the surface by ion beam etching. Each particle acts as an individual mask, resulting in an array of identical structure. Ion beam exposure etches away the unmasked surface between the particles, so the particle mask pattern can be transferred into the polymer surface. This method allows to nanofabricate bulk polymeric surfaces with systematic variation in relief, structure sizes, and aspect ratios. It is a fast, simple, and reliable method to fabricated different polymeric surfaces even on large area samples (>1 cm2). The structural variation is achieved by use of different conditions during the self-assembly of the mask (e.g., different particles sizes) or different ion etching conditions during the pattern transfer (e.g., ion energy, ion flux, ion incident angle, etching time, gas environment) View full abstract»

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  • Peptide-directed binding of quantum dots to integrins in human fibroblast

    Publication Year: 2006 , Page(s): 15 - 19
    Cited by:  Papers (2)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (1959 KB) |  | HTML iconHTML  

    There is currently a major international effort aimed at integrating semiconductor nanostructures with biological structures. This paper reports the use of peptide sequences with certain motifs like artinine-glycine-aspartic acid (RGD) and leucine-aspartic acid-valine (LDV) to functionalize zinc sulfide (ZnS)-capped cadmiun selenide (CdSe) quantum dots, so that the quantum dot-peptide complexes selectively bind to integrins on HT1080 human fibrosarcoma cells membrane. In this way, an interface between semiconductor nanocrystals and subcellular components was achieved, and the distribution pattern of RGD and LDV receptors on HT1080 cell membranes is revealed. These findings point the way to using a wide class of peptide-functionalized semiconductor quantum dots for the study of cellular processes involving integrins View full abstract»

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  • The effects of colloidal nanotopography on initial fibroblast adhesion and morphology

    Publication Year: 2006 , Page(s): 20 - 31
    Cited by:  Papers (14)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (3761 KB) |  | HTML iconHTML  

    Colloidal lithography offers a simple, inexpensive method of producing irregular nanotopographies, a pattern not easily attainable utilizing conventional serial writing processes. Colloids with 20- or 50-nm diameter were utilized to produce such an irregular topography and were characterized by calculating the percentage area coverage of particles. Interparticle and nearest neighbor spacing were also assessed for the individual colloids in the pattern. Two-way analysis of variance (ANOVA) indicated significant differences between the number of fibroblasts adhering to planar, 20-, and 50-nm-diameter colloidal topographies, the number of fibroblasts adhering to the substrates at the time intervals studied, namely 20 min, 1 h, and 3 h and significant interaction between time and topography on fibroblast adhesion (P<0.01). Tukey tests were utilized for sensitive identification of the differences between the sample means and compounded ANOVA results. Cytoskeletal and general cell morphology were investigated on planar and colloidal substrates, and indicated cells in contact with irregular nanotopographies exhibit many peripheral protrusions while such protrusions are absent in cells on planar control surfaces. These protrusions are rich in microtubules on 20-nm-diameter colloidal surfaces while microfilaments are prevalent on 50-nm-diameter surfaces. Moreover, by 3 h, cells on the colloidal substrates initiate cell-cell adhesions, also absent in controls View full abstract»

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  • A mathematical formulation of DNA computation

    Publication Year: 2006 , Page(s): 32 - 40
    Cited by:  Papers (10)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (335 KB) |  | HTML iconHTML  

    DNA computation is to use DNA molecules for information storing and processing. The task is accomplished by encoding and interpreting DNA molecules in suspended solutions before and after the complementary binding reactions. DNA computation is attractive, due to its fast parallel information processing, remarkable energy efficiency, and high storing capacity. Challenges currently faced by DNA computation are: 1) lack of theoretical computational models for applications and 2) high error rate for implementation. This paper attempts to address these problems from mathematical modeling and genetic coding aspects. The first part of this paper presents a mathematical formulation of DNA computation. The model may serve as a theoretical framework for DNA computation. In the second part, a genetic code based DNA computation approach is presented to reduce error rate for implementation, which has been a major concern for DNA computation. The method provides a promising alternative to reduce error rate for DNA computation View full abstract»

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  • Computational modeling of a new fluorescent biosensor for caspase proteolytic activity improves dynamic range

    Publication Year: 2006 , Page(s): 41 - 45
    Cited by:  Papers (3)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (596 KB)  

    The class of fluorescence resonance energy transfer (FRET) protein biosensors that are useful for measuring protease activity is composed of a tandem fusion of yellow fluorescent protein (YFP), a cleavage recognition sequence, and cyan fluorescent protein (CFP). The dynamic range of these FRET-based protein biosensors is often weak, but applications such as high throughput drug screening require stronger dynamic ranges. Using the biosensor for the caspase-3 protease as an example, here we showed a computational approach to improve the FRET dynamic range based on the atomic structure of caspase-3 bound to its inhibitor. This result was verified from our experiments where the FRET dynamic range improved by at least 60% on average in both in vitro and in vivo contexts. In concept, the same strategy can be applied to improve dynamic range of other FRET-based protein biosensors for protease activity where there exist solved atomic structures for protein complexes View full abstract»

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  • Rule generation for protein secondary structure prediction with support vector machines and decision tree

    Publication Year: 2006 , Page(s): 46 - 53
    Cited by:  Papers (7)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (575 KB) |  | HTML iconHTML  

    Support vector machines (SVMs) have shown strong generalization ability in a number of application areas, including protein structure prediction. However, the poor comprehensibility hinders the success of the SVM for protein structure prediction. The explanation of how a decision made is important for accepting the machine learning technology, especially for applications such as bioinformatics. The reasonable interpretation is not only useful to guide the "wet experiments," but also the extracted rules are helpful to integrate computational intelligence with symbolic AI systems for advanced deduction. On the other hand, a decision tree has good comprehensibility. In this paper, a novel approach to rule generation for protein secondary structure prediction by integrating merits of both the SVM and decision tree is presented. This approach combines the SVM with decision tree into a new algorithm called SVM_DT, which proceeds in three steps. This algorithm first trains an SVM. Then, a new training set is generated through careful selection from the output of the SVM. Finally, the obtained training set is used to train a decision tree learning system and to extract the corresponding rule sets. The results of the experiments of protein secondary structure prediction on RS126 data set show that the comprehensibility of SVM_DT is much better than that of the SVM. Moreover, the generalization ability of SVM_DT is better than that of C4.5 decision trees and is similar to that of the SVM. Hence, SVM_DT can be used not only for prediction, but also for guiding biological experiments View full abstract»

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  • The state of the art of nanobioscience in Japan

    Publication Year: 2006 , Page(s): 54 - 65
    Cited by:  Papers (2)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (3079 KB) |  | HTML iconHTML  

    This paper reviews a part of the state of the art of nanobioscience in Japan. The importance of combination and integration of interdisciplinary principles is emphasized for the development of nanobioscience. Biomagnetics, biomechanics, nanomachining, self-replicating cell model, neuronal network, drug delivery system, and tissue engineering are discussed View full abstract»

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  • Special issue on colloidal quantum dots for biomedical applications

    Publication Year: 2006 , Page(s): 66
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  • 28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering Revolution in BioMedicine

    Publication Year: 2006 , Page(s): 67
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  • 7th IEEE EMBS International Summer School on Biomedical Imaging

    Publication Year: 2006 , Page(s): 68
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  • IEEE Transactions on NanoBioscience statement of editorial policy

    Publication Year: 2006 , Page(s): c3
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  • Blank page [back cover]

    Publication Year: 2006 , Page(s): c4
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Aims & Scope

The IEEE Transactions on NanoBioscience publishes basic and applied papers dealing both with engineering, physics, chemistry, modeling and computer science and with biology and medicine with respect to molecules, cells, tissues. The content of acceptable papers ranges from practical/clinical/environmental applications to formalized mathematical theory.

Full Aims & Scope

Meet Our Editors

Editor-in-Chief
Henry Hess
Department of Biomedical Engineering
Columbia University