While the unique spectral information associated with chemical and biological molecules within the terahertz frequency
regime (~ 3.0-3.0 millimeters) motivates its use for practical sensing applications, limiting factors at the macroscale
(weak spectral absorption, broad line widths and masking geometrical effects introduced by the samples) provides
motivation for man-engineered sensing materials that allow for the transduction of the spectral information about target
molecules from the nanoscale. This brief letter will overview work being performed by our research group to define
molecular-level functionality that will be useful for realizing "THz/IR-sensitive" materials. Here the goal is to define
switchable molecular components that when incorporated into larger DNA-based nanoscaffolds lead to THz and/or IR
regime electronic and/or photonic material properties that are dictated in a predictable manner by novel functionality
paradigms. In particular, theoretical modeling and design studies are being performed to engineer organic and biological
switches that can be incorporated into DNA-based architectures that enable the precise extraction of nanoscale
information (e.g., composition, dynamics, conformation) through electronic/photonic transformations to the macroscale.
Hence, these studies seek to define new spectral-based sensing modalities useful for characterizing bio-molecules
In this work we present the results on combined experimental and computational study of sub-THz spectra of
liquid water. The important new result is the detection of hydrogen bonds in liquid water. The experimental
study was performed by employing Fourier Transform terahertz (THz) spectroscopy with spectral resolution of
0.25 cm<sup>-1</sup>. Resonance features in transmission spectra of water layers between thin film substrates are
demonstrated in the sub-THz range. The theoretical approach for computer simulation of THz absorption
spectra from liquid water is also discussed. The molecular dynamical (MD) simulations of water were
performed using Amber 8 and the TIP3P, SPCE (Extended Single Point Charge) and TIP4P water models.
Several examples of modeling results are presented. The experimental spectra are compared with the
theoretical predictions. The SPCE model better correlates with experimental spectra compare to two other
The development of an effective biological (bio) agent detection capability based upon terahertz (THz) frequency absorption spectra will require insight into how the constituent cellular components contribute to the overall THz signature. In this work, the specific contribution of ribonucleic acid (RNA) to THz spectra is analyzed in detail. Previously, it has only been possible to simulate partial fragments of the RNA (or DNA) structures due to the excessive computational demands. For the first time, the molecular structure of the entire transfer RNA (tRNA) molecule of <i>E. coli</i> was simulated and the associated THz signature was derived theoretically. The tRNA that binds amino acid tyrosine (tRNAtyr) was studied. Here, the molecular structure was optimized using the potential energy minimization and molecular dynamical (MD) simulations. Solvation effects (water molecules) were also included explicitly in the MD simulations. To verify that realistic molecular signatures were simulated, a parallel experimental study of tRNAs of <i>E. coli </i>was also conducted. Two very similar molecules, valine and tyrosine tRNA were investigated experimentally. Samples were prepared in the form of water solutions with the concentrations in the range 0.01-1 mg/ml. A strong correlation of the measured THz signatures associated with valine tRNA and tyrosine tRNA was observed. These findings are consistent with the structural similarity of the two tRNAs. The calculated THz signature of the tyrosine tRNA of <i>E. coli</i> reproduces many features of our measured spectra, and, therefore, provides valuable new insights into
The development of efficient biological agent detection techniques requires in-depth understanding of THz absorption spectral features of different cell components. Chromosomal DNA, RNAs, proteins, bacterial cell wall, proteinaceous coat might be essential for bacterial cells and spores THz signature. As a first step, the DNA's contribution into entire cell THz spectra was analyzed.
The experimental study of cells and DNAs of <i>E. coli</i> and cells/spores and DNA of <i>Bacillus subtilis</i> was conducted. Samples were prepared in the form of water solutions (suspension) with the concentrations in the range 0.01-1 mg/ml. The measurable difference in the THz transmission spectra of <i>E. coli</i> and <i>Bacillus subtilis</i> DNAs was observed. The correlation between chromosomal DNA signature and a corresponding entire spore/cell signature was observed. This correlation was especially pronounced for spores of <i>Bacillus subtilis</i> and their DNA. These experimental results justify our approach to develop a model for THz signatures of biological simulants and agents. In parallel with the experimental study, for the first time, the computer modeling and simulation of chromosome DNAs of <i>E. coli</i> and <i>Bacillus subtilis</i> was performed and their THz signatures were calculated. The DNA structures were optimized using the Amber software package. Also, we developed the initial model of the DNA fragment poly(dAT)-poly(dTA) solvated in water to be used in the simulations of genetic material (DNA and RNA) of spores and cells. Molecular dynamical simulations were conducted using explicit solvent (3-point TIP3P water) and implicit solvent (generalized Born) models. The calculated THz signatures of <i>E. coli</i> and <i>Bacillus subtilis</i> DNAs and poly(dAT)-poly(dTA) reproduce many features of our measured spectra. The results of this study demonstrate that THz Fourier transform infrared spectroscopy is a promising tool in generating spectral data for complex biological objects such as bacterial cells and spores.