Science and Technology of Biological and Chemical Sensing at Terahertz Frequencies

1. Science and Technology of Biological and Chemical Sensing at Terahertz Frequencies 2001 MURI Program Terahertz Research at the University of Virginia An Overview Thomas Jefferson National Accelerator Facility – April 10, 2002 Novel and Emerging Technologies for the Science and Technology of Biological and Chemical Sensing at Terahertz Frequencies By Thomas W. Crowe

2. Sub-Millimeter Wave Absorption Spectra of Artificial RNA Molecules Tatiana Globus a, Maria Bykhovskaia b, Dwight Woolard c , Boris Gelmont a a Dept. of Electrical and Computer Engineering, UVA, VA 22904-4743 b Dept. of Molecular physiology and Biol. Physics, UVA c U.S. Army Research Laboratory, ARO, Research Triangle Park, NC 27709. Globus, 2002

3. Science and Technology of Biological and Chemical Sensing at Terahertz Frequencies 2001 MURI Program THE SCIENCE AND TECHNOLOGY OF BIOLOGICAL AND CHEMICAL SENSING AT TERAHERTZ FREQUENCIES Primary Objective To discover and understand the fundamental physical principles governing the interaction of biological molecules and chemical agents with electromagnetic energy in the terahertz region of the spectrum. Secondary Objective To develop the technology needed to study these interactions and build a foundation for future instruments to detect and identify biological and chemical warfare agents

4. Terahertz Technology “the most scientifically rich, yet underutilized region of the electromagnetic spectrum” Challenges: • Atmospheric Attenuation • The transition from electronics to optics • The lack of convenient and reliable solid-state sources such as LEDs, lasers or electronic amplifiers

5. Terahertz Applications Compact Range Radar Remote Sensing • Radio Astronomy • Atmospheric Chemistry • Chemical Spectroscopy • Plasma and Accelerator Diagnostics • Collision Avoidance Radar • Detection of Chem./Bio. Hazards • Ultra Wideband & Secure Communications • Medical Diagnostics

6. Diode Process Evolution Whiskered Diodes Integrated Diode Circuits Planar Diodes

7. Terahertz Technology Computer Aided Design and Simulation An electromagnetic field simulation of one of our frequency multiplier circuits. The left image is a two-dimensional slice and the right image is a three dimensional rendition Benefits: • Accurate designs, the fist time, without the need for scale models. • E&M simulations give a “physical feel” for how the circuit behaves and how to optimize performance. • More complicated circuit designs can now be attempted, yielding improved performance and bandwidth.

8. Advanced Fabrication Technologies: * GaAs-on-Quartz integration * Air-bridge contacts * Novel device structures

9. Design Evolution Planar Balanced Doublers: N. Erickson, "High Efficiency Submillimeter Frequency Multipliers," 1990 IEEE MTT-S Intl. Microwave Symp. Dig., Dallas, TX, pp. 1301-1304, May 1990. N.R. Erickson, J. Tuovinen, B.J. Rizzi, and T.W. Crowe, "A Balanced Doubler Using a Planar Diode Array for 270 GHz," Fifth Intl. Space THz Tech. Symp., Ann Arbor, MI, pp. 409-413, May 1994.

10. Design Evolution: Planar Balanced Doublers D.W. Porterfield, T.W. Crowe, R.F. Bradley, N.R. Erickson, “A High-Power, Fixed-Tuned, Millimeter-Wave Balanced Frequency Doubler,” IEEE Trans., Vol. MTT-47, No. 4, pp. 419-425, April 1999.

11. Integrated Balanced Doublers Ideal Performance: This result assumes practical diode and circuit parameters, but with ideal packaging! - Exceptional heat sinking. - Enough anodes to handle the input power.

12. Integrated Balanced Doublers Direct integration on high thermal conductivity substrates. Integrated & cascaded doublers.

13. Terahertz Technology Broadband Circuit Designs A present day commercial frequency multiplier with mechanical tuners versus a broadband tripler to 200-400 GHz with integrated diode technology and an advanced circuit design. Benefits: • Full waveguide band frequency agility is achieved. • Tuners are eliminated. • Components have better performance and are more compact, more reliable and less expensive.

17. Science and Technology of Biological and Chemical Sensing at THz Frequencies Terahertz Wave Interaction with Biological Macromolecules Tatiana Globus, Boris Gelmont, Ludmila Dolmatova-Verbos GOALS: • To confirm the fundamental character of the observed resonant spectra in submillimeter wave range. • To demonstrate the feasibility of long-wavelength vibration spectroscopy as an approach for identification of DNA signatures. PREVIOUS RESULTS: • Highly resolved and reproducible spectra of DNA macromolecules have been received in spectral range from 10 cm-1 to 500 cm-1 . • The results demonstrate experimental evidence of multiple resonances-phonon modes in submillimeter wave transmission spectra. • Preliminary results indicate Neural Network Modeling can distinguish the FTIR spectra of Fish Genetic Material from two species with a high degree of confidence. • This work establishes an initial foundation for the future use of submillimeter-wave spectroscopy in the identification and characterization of DNA macromolecules. Theory predicts that far-infrared spectra possess features that might be used for the detection and identification of microorganisms and other living matter. Experimental spectra of herring and salmon DNA samples

18. What is Different in our Approach? 1) We used a resolution of 0.2cm–1and discovered features that are small on the frequency scale.

19. What is Different in our Approach? 2) Sample Preparation is Critical!!! • Films were prepared by dissolving herring and salmon DNA sodium salts from Sigma Chemical Co. using glass-distilled water with a concentration ratio between 5:1 and 10:1. • Material formed a gel that was brought to the desired thickness by placing the gel inside an arbor shim between two teflon films or polycarbonate membranes. The gel was left to dry at room temperature in air or under vacuum. The samples were then separated from the entire mold and all far IR results were obtained from free-standing films.

20. Various spectra of DNA Samples Calf thymus (CT) DNA Herring (H) and Salmon (S) DNA Bacillus subtillis [BG] with different amount of material.

21. What is Different in our Approach? 3) We are striving to “see beyond” the poor reproducibility of large scale features. Sample thickness affects the large scale standing wave pattern. Moisture content affects the sample thickness.

22. Differential transmission averaged over 20 spectra for herring and salmon DNA samples measured at identical orientation. Differential transmission of salmon DNA films with different thickness. • The quality of experimental data and their sensitivity to many factors determined the choice of submillimeter differential transmission spectra as input data for analysis.

23. What is different in our approach? Sensitivity ResolutionReproducibility Better resolution and higher sensitivity In earlier works, the resolution normally was 2 cm–1andonly structures large in wavenumbers (i.e. > 10 cm-1) could be detected. We use a resolution not worse than 0.2cm–1, and we discovered features that are small on the frequency scale. Transmission spectra of herring DNA with the resolution 0.2 cm-1. Reproducibility of background spectrum(100% line) is also shown. Two independent measurement resultsReproducible results over the entire spectral range. Spectrum of radiation. A significant reduction of power on both ends of the frequency domain.

24. What is Different in our Approach? 4) Reasons for poor reproducibility merit further study. Change in transmission spectra with sample rotation. • Optical characteristics are dependent on the orientation of aligned DNA fibers of the film samples in electromagnetic field of radiation. • Sample rotation changes the fine spectral structure probably because of coupling change between the electromagnetic field of radiation and the dipole moment of the DNA oscillators.

25. Image of the Poly[C]-Poly[G] sample in polarizing microscope. Film thicknessabout 6 mm. Gel concentration 1:26. RNA, as a rod-like polymer, spontaneously forms ordered liquid crystalline phases in aqueous solution 46with the long molecular axis preferentially aligned in one direction. The long axes of the molecules lie in pseudo-planes that are slightly twisted with respect to each other. In drying process, DNA solution undergoes a series of transitions and film samples are characterized by their microscopic textures with periodic variations in refractive index and fringe patterns observed in polarizing microscope. The film texture depends on the concentration of molecules in solution and on drying conditions.

26. PREDICTION OF THz SPECTRA FOR DNA DOUBLE HELIXMaria Bykhovskaia and Boris Gelmont Sequence Structure (energy minimum) Phonon modes AGTACGTATGC TCATGCATACG

27. Theoretical studies - calculation of RNA vibrational modes Recently we suggested a method for the prediction of far-IR absorption spectra of biomolecules.6,7 Here we applied this method. • RNA IR active modes have been calculated directly from the base pair sequence and topology of a molecule. • We employed the methods of molecular mechanics and normal mode analysis, which enables rigorous calculations of biopolymer structure and dynamics [ reviewed in10]. • Further, we coupled the molecular modeling with theoretical spectroscopy by calculations of oscillator strengths for the normal modes. Globus, 2002

28. Simulation results Calculation absorption spectra are presented for two values of oscillator decay g =0.5 cm -1 and g =1 cm –1, and for electric fieldEperpendicular to the long axes of a molecule (ax+y) and parallel to the long axes (az). The maximum absorption corresponds to the electric field perpendicular to the long molecular axis z. Globus, 2002

29. Absorption coefficient An interference spectroscopy technique (IST) for properly modeling of the multiple reflection behavior.8,9 The chemical structure of the backbones is similar for these homopolymers, therefore we would expect similar vibration and rotational modes. A similarity of resonance features thus indicating that most of the phonons in this spectral range are dependent on the backbone structure.

30. Comparison of experiment with theoretical prediction The quality of experimental data depends in high degree on the film thickness and as a rule much better resonance structure is observed in the thin films which are more difficult to fabricate with areas of sufficient size. Absorption spectrum of PolyC-PolyG (d=30 µm) and modeling results. Absorption spectrum of PolyC-PolyG (thick sample,d=75 µm) and modeling results with g =1 cm-1 and scaled absorption amplitude.

31. The intensity of resonance mode in the thickest samples does not directly correlate with oscillator dissipations g , but more probably with broadening of spectral lines in nonuniform material. The best resonance structure is observed in thin films The absorption spectrum of the most thin sample d=6.6 mm indicates that the typical oscillator dissipation is about 0.5 cm -1 Some calculated absorption peaks are absent in experimental spectra (for example, peaks at 16.5 cm -1 and 19.9 cm -1 ). Possible explanation is a very high sensitivity of peak intensity to the actual value of oscillator dissipation

32. CONCLUSIONS • We have measured absorption spectra of oligonucleotides with known base-pair sequences in the submillimeter-wave range. • Normal modes were calculated and the absorption spectra was derived for the 12 base pair RNA fragment PolyG-PolyC. • These studies indicate that there is a close correlation between calculated and experimentally observed spectra of RNA homopolymers. • These results confirm the fundamental physical nature of the observed resonance structure which is caused by the internal vibration modes in macromolecules. • Furthermore, experimental results may be combined with theoretical modeling to directly assign vibrational modes to specific structural features and topology of the macromolecules. • In the future, this research will be extended to the study of the absorption characteristics of Poly [A]-Poly [U] RNA.

33. Some Concluding Remarks • The University of Virginia has a long term commitment to developing technology for the terahertz frequency band. • ARO has funded a MURI to explore the potential of using terahertz science and technology to detect and/or monitor biological materials. • The research team includes participants from UVa, UofM, UCLA, Stevens and UNCG. The program began on June 1st, 2001 – we making good progress! • Previous work at UVa has indicated that biomacromolecules interact with terahertz radiation, leading to the conclusion that useful detection schemes may be possible. • Much work remains to be done with regards to all aspects of the problem – - Understanding the physical mechanism for this interaction • Establishing controllable and reproducible sample handling and measurement techniques. • Understanding the effect of environment on the Terahertz interaction. • Etc……