Anharmonic surface interactions for biomolecular screening and characterization.

The acoustic response of conventional mechanical oscillators, such as a piezoelectric crystal, is predominantly harmonic at modest amplitudes. However, here, we observe from the electrical response that significant motional anharmonicity is introduced in the presence of attached analyte. Experiments were conducted with streptavidin-coated polystyrene microbeads of various sizes attached to a quartz crystal resonator via specific and nonspecific molecular tethers in liquid. Quantitative analysis reveals that the deviation of odd Fourier harmonics of the response caused by introduction of microbeads as a function of oscillation amplitude presents a unique signature of the molecular tether. Hence, the described anharmonic detection technique (ADT) based on this function allows screening of biomolecules and provides an additional level of selectivity in receptor-based detection that is often associated with nonspecific interactions. We also propose methods to extract mechanical force-extension characteristics of the molecular tether and activation energy using this technique.

Independent component analysis of microarray data in the study of endometrial cancer.

Gene microarray technology is highly effective in screening for differential gene expression and has hence become a popular tool in the molecular investigation of cancer. When applied to tumours, molecular characteristics may be correlated with clinical features such as response to chemotherapy. Exploitation of the huge amount of data generated by microarrays is difficult, however, and constitutes a major challenge in the advancement of this methodology. Independent component analysis (ICA), a modern statistical method, allows us to better understand data in such complex and noisy measurement environments. The technique has the potential to significantly increase the quality of the resulting data and improve the biological validity of subsequent analysis. We performed microarray experiments on 31 postmenopausal endometrial biopsies, comprising 11 benign and 20 malignant samples. We compared ICA to the established methods of principal component analysis (PCA), Cyber-T, and SAM. We show that ICA generated patterns that clearly characterized the malignant samples studied, in contrast to PCA. Moreover, ICA improved the biological validity of the genes identified as differentially expressed in endometrial carcinoma, compared to those found by Cyber-T and SAM. In particular, several genes involved in lipid metabolism that are differentially expressed in endometrial carcinoma were only found using this method. This report highlights the potential of ICA in the analysis of microarray data.

Analysis of the ellipsometric spectra of amorphous carbon thin films for evaluation of the sp3-bonded carbon content

Using spcctroscopic ellipsometry (SE), we have measured the optical properties and optical gaps of a series of amorphous carbon (a-C) films ∼ 100-300 Å thick, prepared using a filtered beam of C+ ions from a cathodic arc. Such films exhibit a wide range of sp3-bonded carbon contents from 20 to 76 at.%, as measured by electron energy loss spectroscopy (EELS). The Taue optical gaps of the a-C films increase monotonically from 0.65 eV for 20 at.% sp3 C to 2.25 eV for 76 at.% sp3 C. Spectra in the ellipsometric angles (1.5-5 eV) have been analyzed using different effective medium theories (EMTs) applying a simplified optical model for the dielectric function of a-C, assuming a composite material with sp2 C and sp3 C components. The most widely used EMT, namely that of Bruggeman (with three-dimensionally isotropic screening), yields atomic fractions of sp3 C that correlate monotonically with those obtained from EELS. The results of the SE analysis, however, range from 10 to 25 at.% higher than those from EELS. In fact, we have found that the volume percent sp3 C from SE using the Bruggeman EMT shows good numerical agreement with the atomic percent sp3 C from EELS. The SE-EELS discrepancy has been reduced by using an optical model in which the dielectric function of the a-C is determined as a volume-fraction-weighted average of the dielectric functions of the sp2 C and sp3 C components. © 1998 Elsevier Science S.A.

Analysis of amorphous carbon thin films by spectroscopic ellipsometry

Using spectroscopic ellipsometry (SE), we have measured the optical properties of amorphous carbon (a-C) films ∼ 10-30 nm thick prepared using a filtered beam of C+ ions from a cathodic arc. Such films exhibit a wide range of sp3-bonded carbon contents from 20 to 76 at.% as measured by electron energy loss spectroscopy (EELS), and a range of optical gaps from 0.65 eV (20 at.% sp3 C) to 2.25 eV (76 at.% sp3 C) as measured by SE. SE data from 1.5 to 5 eV have been analyzed by applying the most widely used effective medium theory (EMT) namely that of Bruggeman with isotropic screening, assuming a model of the material as a composite with sp2 C and sp3 C components. Although the atomic fractions of sp3 C deduced by SE with the Bruggeman EMT correlate monotonically with those obtained by EELS, the SE results range from 10 to 25 at.% higher. The possible origins of this discrepancy are discussed within the framework of an optical composite. Improved agreement between SE and EELS is obtained by employing a simple form for the EMT, in which the effective dielectric function is determined as a volume-fraction-weighted average of the dielectric functions of the two components. © 1998 Elsevier Science B.V. All rights reserved.