Sub-terahertz vibrational spectroscopy of ovarian cancer and normal control tissue for molecular diagnostic technology.

We introduce here recently developed highly resolved Sub-Terahertz resonance spectroscopy of biological molecules and cells combined with molecular dynamics (MD) computational analysis as a new approach for optical visualization and quantification of the presence of microRNAs, particularly the mir-200 family, as potential biomarkers in samples from tissue of epithelial ovarian cancers for disease early detection, analysis, prognosis and treatment.METHOD: A set of samples for this study was prepared from anonymized archival formalin-fixed, paraffin-embedded ovarian epithelial tissue containing regions of invasive neoplastic cells from cases of high-histologic grade serous papillary ovarian carcinoma. Control samples were normal mucosa from fallopian tubes of patients with no known malignancy.

Terahertz spectra of biotin based on first principle, molecular mechanical, and hybrid simulations.

Terahertz (THz) absorption of biotin was simulated using the first principle and the density functional theory (DFT) both in the harmonic approximation and with corrections for the anharmonicity. Anharmonicity corrections were calculated using two different approaches. First, the perturbation theory-based first principle calculations were performed to include third- and fourth-order anharmonicity corrections in atomic displacements to harmonic vibrational states.

Analysis of electronic structure, binding, and vibrations in biotin-streptavidin complexes based on density functional theory and molecular mechanics.

In this work, the biotin-streptavidin complex was studied with density functional theory (DFT), molecular mechanical methods (MM), and a hybrid DFT/MM approach in order to obtain the theoretical predictions for electronic structures, binding, optical transitions, harmonic vibrations, and absorption spectra. It was demonstrated that biotin solvation in water can reduce the binding strength to streptavidin by more than half. All studied properties, including the biotin binding and the UV absorption of the biotin-streptavidin complex, are predicted to be protonation state dependent.

The influence of environment on terahertz spectra of biological molecules.

The variability of molecular vibrations and low terahertz spectra of biological molecules depending on the three-dimensional structure of molecular clusters, chemical bonding, and molecular concentration in the surrounding media is studied using computer simulations. The resonant terahertz spectra of biological molecules and their associations are described within the framework of molecular mechanics using an all-atom molecular mechanical force field for proteins and nucleic acids. Both the absolute values of absorption coefficients and their spectral properties are considered for murein-lipoprotein and thioredoxin of E.

Terahertz absorption of DNA decamer duplex.

This work combines experimental and theoretical approaches to investigate terahertz absorption spectra of the DNA formed by the sequence oligomer 5'-CCGGCGCCGG-3'. The three-dimensional structure of this self-complimentary DNA decamer has been well-studied, permitting us to perform direct identification of the low-frequency phonon modes associated with specific conformation and to conduct comprehensive computer simulations. Two modeling techniques, normal-mode analysis and nanosecond molecular dynamics with explicit solvent molecules, were employed to extract the low-frequency vibrational modes based on which the absorption spectra were calculated.

Enhanced coupling of subterahertz radiation with semiconductor periodic slot arrays.

In this work, a theoretical study of the coupling of TM polarized subterahertz (THz) radiation with periodic semiconductor rectangular slot arrays was conducted, using InSb as an example. Simulation results showed that the structure with 4-12 microm thickness provides over a 20-30-fold increase in the electric field at slot edges in a nanosize region ( approximately 500 nm). The enhancement of the THz electromagnetic field extends across the slots and reaches peak values at the edges due to discontinuity effects.