The physics and modeling of biological molecular components is discussed in the context of defining DNA-based biological molecule switches (BMSs) that will be useful for incorporating into larger DNA-based nanoscaffolds for the purposes of defining a novel class of smart materials for terahertz (THz) and/or very far-infrared (far-IR) based biological sensing. The chapter presents DNA-derivative architectures with new spectral-based sensing modalities that will be useful for long-wavelength bio-sensing applications. The exploration of bio-organic device functionality and sensing in the future will require interfacing to traditional electronic materials and/or structures. Resonant far-IR spectroscopy is a common technique for the characterization of biological (bio) molecules. If DNA-derivatives are used that allow for being light-induced into many different metastable states, then the large amount of resulting spectral signature information would allow for full identification and characterization of the associated genetic sequence information.

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 absorption edge of the complex calculated with TDDFT/MM was found to be virtually insensitive to the choice of the MM force field and strongly dependent on the type of embedding of the DFT partition. Both UV and terahertz light absorption spectra are predicted to be sensitive to the presence of biotin in the streptavidin tetramer.

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. Second, the atom-centered density matrix propagation molecular dynamics model that provides a good energy conservation was used to calculate the atomic trajectories, velocities, and a dipolemoment time history of biotin at lowand room temperatures. Predicted low-THz lines agree well with the experimental spectra. The influence of the polyethylene (PE) matrix embedment on the THz spectra of biotin at the nanoscale was studied using the developed hybrid DFT/molecular mechanical approach. While PE is almost transparent at THz frequencies, additional low-THz lines are predicted in the biotin/PE system, which reflects a dynamic interaction between biotin and a surrounding PE cavity.

Wavelength conversion (WC) imaging is a methodology that employs temperature sensitive detectors to convert photo-induced termperature into a detectable optical signal. One specific method is to use molecular detectors such as thermochromic liquid crystals (TLC), which exhibits thermochromism to observe the surface temperature of an area by observing the apparent color in the visible spectrum. Utilizing this methodology, an ultra-broadband room temperature imaging system was envisioned and realized using off the shelf thermochromic liquid crystals. The thermochromic properties of the sensor were characterized to show a thermochromic coefficient alpha = 10%/degrees K and a noise equivalent power (NEP) of 64 mu W. With the TLC camera, images of both pulsed and continuous wave (CW) sources spanning 0.6 mu m to 150 mu m wavelengths were captured to demonstrate its potential as a portable, low-cost, and ultra-broadband imaging tool.

A novel approach for the generation of THz radiation that utilizes "interband" transitions and tunneling processes occurring simultaneously within double-barrier (DB) GaSb/InAs/GaSb broken-gap (BG) resonant-tunneling-diodes (RTDs) is discussed. This paper focuses on the architectural and cavity designs for realizing TE polarized emission from single DB-BG-RTD devices and quantum-dot pillar arrays. Design techniques useful for mitigating CB drive current (& the associated thermal heating) while at the same time optimizing output power and power efficiency are discussed.

The U.S. Army has strong interests in nanoscale architectures that enable enhanced extraction and controllable multiplication of the THz/IR regime spectral signatures associated with specific bio-molecular targets. Emerging DNA-based nano-assemblies (i.e., either materials or structural devices) will be discussed that realize novel sensing paradigms through the incorporation of organic and/or biological molecules such that they effect highly predictable and controllable changes into the electro-optical properties of the resulting superstructures. Results will be given to illustrate the utility of functionalized DNA materials in biological (and chemical) sensing, and to demonstrate how the basic science can be leveraged to study and develop synthetic antibodies, reporters and vaccines for future medical applications.

: This final report discusses a completely novel approach for generating THz frequency radiation that utilizes interband transitions and tunneling processes which can be induced simultaneously within double-barrier (DB) GaSb/InAs/GaSb broken-gap (BG) resonant-tunneling-diodes (RTDs). This DB-BG-RTD device will utilizes two distinct innovations. First, ultra-fast heavy-hole (HH) interband tunneling is leveraged to depopulate a lower, valence-band (VB) well-state E1 which then allows electrons resonantly injected into an upper conduction-band (CB) well-state E2 (i.e., center region of the RTD) to serve as the electron source for the light-generating recombination at small photonic energy differences E2 - E1 lying within the THz regime. Second, the associated electrons and holes pairs are spatially-delocalized (SD) by the RTD heterostructures which leads to a significant suppression of all degrading nonradiative recombination processes. These effects allow for large population inversions and optical gains that may be used in single DB-BG-RTD microdisk laser structures operating at near room temperature ( 280 K) to produce 1-10 mW in the 1-3 THz gap region, which is a substantial improvement to the existing state-of-the-art solid-state THz source technology (i.e., 0.1 mW). Furthermore, it is expected that novel quantum-dot DB-BG-RTD nanopillar-array architectures can be used to further reduce drive-current heating effects to achieve additional multiplication of the output power.

This paper will illustrate the potential of InAs/GaSb broken-gap structures for providing a solution to the well-known and long-standing terahertz (THz) frequency gap in source technology. In a double-barrier GaSb/InAs/GaSb heterostructure, the ultrafast heavy-hole interband tunneling can be utilized to achieve electron depopulation of a quasi-bound, heavy-hole level located in the valence-band of the right GaSb barrier region. A population inversion is then created using electron injection into the conduction-band resonant state of the double-barrier structure. Degrading nonradiative processes such as acoustic phonon, optical phonon and Auger recombination are suppressed in this spatially separated two-level energy system. Hence, heavy-hole interband tunneling prevails over nonradative transition rates and establishes a population inversion at relatively high operating temperatures. Detailed simulations predict a significant optical (total) gain of similar to 0.001 which is comparable with GaAs/AlGaAs quantum well laser in spite of the small overlap of conduction band and heavy-hole wavefunctions. The TE emission allows for implementation of vertical surface emission in large area, for single or arrayed devices. Also, lateral quantum confinement of arrayed systems can be used to reduce the conduction band current density (and undesired thermal heating) and increase the quantum efficiency.

Modeling and simulation techniques are presented, which are both physically accurate and computationally efficient for treating complex organic structures that have relevance to sensing and characterization, including structures with covalent bonding to biological (i.e., DNA) molecules. The theoretical study of large and complex biological molecular systems is very challenging because ab initio quantum mechanical methods are usually too computationally demanding and alternative empirical approaches are often insufficient for describing the internal interactions and dynamics. The goal of this research is to provide detailed insight into the molecular interaction mechanisms (e.g., terahertz (THz) frequency spectral absorption), which can be used to define novel types of bioelectronic-sensing devices. Therefore, a mixed ab initio/molecular mechanical-modeling approach is implemented and applied to the study of stilbene-DNA conjugates that offer switchable spectral characteristics that may be useful for detection and identification purposes. In particular, results are generated for two conformations of a TGCGCA-DNA duplex with trimethoxystilbene carboxamide (TMS) end capping that are confirmed by experimental data. The model is also used to derive the influences of DNA sequence and/or TMS orientation on the conformation, electronic states, and atomic vibrations of single- and doubled-stranded variants of the TGCGCA-DNA duplex. These results, which include very distinct absorption spectra in the THz to UV range, demonstrate that hybrid methodologies can bridge the gap in understanding electronic and atomic structure, and light-induced interactions in complex bioorganic systems.

The paper is an editorial issue on enhancement algorithms, methodologies and technology for spectral sensing and serves as a valuable and useful reference for researchers and technologists interested in the evolving state-of-the-art and/or the emerging science and technology base associated with spectral-based sensing and monitoring problem. This issue is particularly relevant to those seeking new and improved solutions for detecting chemical, biological, radiological and explosive threats on the land, sea, and in the air.

The first principle study of hydrogen-terminated silicon (111) with deoxyguanosine (dG) residues chemically bonded to a silicon surface via carbon linkers is performed to reveal new insights into the spectral signatures of constrained DNA chains. Silicon surface structure models are generated to accommodate one or two dG residues. In particular, structural models for two dG residues bonded onto silicon nanodots and that formed a single strand of DNA in the lateral direction (along the surface) were developed. First principle simulations with valence electron basis and effective core potentials are conducted. These studies utilized all-atom geometric optimizations to determine the final conformations and normal mode analyses to derive the spectral absorption information. Stable dG conformations on silicon are obtained for varying types of DNA chain length and Nanodot size/shape. These results show that optically active modes lying within the terahertz spectrum typically arise out of joint coupling between the DNA's vibrational behavior and that of the substrate. However, the dominant absorption line below 6 THz is predicted to most strongly represent the DNA dynamics and effects of sodium, but it is only weakly influenced by the nanodot vibrations. In this study, the phonon-induced light absorption spectra of the DNA chains were analyzed in the context of nanodot influence (e.g., edge effects). These results suggest that DNA strands can be chemically bonded to arbitrary nanosized features on silicon surfaces without perturbing some of the key spectral signatures in the THz regime, and this suggests active THz illumination strategies for DNA identification and characterization.

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

A completely new type of solid-state laser device is presented that offers the potential for achieving significantly increased levels of terahertz (THz) frequency output power at relatively high operating temperatures. Specifically, a double-barrier GaSb/InAs/GaSb heterostructure device concept is introduced that simultaneously leverages resonant electron injection and interband tunneling electron depletion to realize electron-population inversion, while at the same time mitigating the scattering effects that degrade the lasing process. Here, the main innovations are the ability to spatially separate the upper and lower electron populations using the quantum confinement of the double-barrier conduction band well and the valence-band (VB) well (i.e., of the second barrier), respectively, and the depopulation of the VB well by heavy hole interband tunneling. A theoretical analysis of the radiative and nonradiative transition rates based upon a multiband Kane model formalism is used to confirm the large available optical gain and to estimate the lasing output power at very long wavelengths. Therefore, this study establishes the initial foundation for a solid-state THz laser that can provide significant levels of output power below 1 THz. Furthermore, the inherently high spectral purity and natural tunability offered by this novel laser technology will be instrumental in future spectroscopic analysis of nanoscale biological and/or organic systems that are well known to possess unique spectral signatures at very long wavelengths.

There is expanding interest in developing THz spectrum instruments for biochemical agent spectroscopy, environmental monitoring and medical imaging. This paper presents a brief review of recently published patents that target innovations for making improvements to THz radiation sources, which is one of the essential modules for building sensing and imaging systems. This analysis will summarize the novel physical aspects and/or innovative design methodology associated with each patent concept. The approaches presented include photonic crystal, ultrafast photoconductive switch, slow-wave structure, photo-mixing in piezoelectric material, stimulated Raman effect, multiquantum well multiplier, and Josephson Junction device. Keywords: Auston Switch, Josephson Effect, Photonic Crystal, Piezoelectric Material, Slow-Wave, Raman Effect, Terahertz.

The U.S. Army Research Office (ARO) and the U.S. Army Edgewood Chemical Biological Center (ECBC) jointly lead and support novel research programs that are advancing the state-of-the-art in nanoelectronic engineering in application areas that have relevance to national defense and security. One fundamental research area that is presently being emphasized by ARO and ECBC is the exploratory investigation of new bio-molecular architectural concepts that can be used to achieve rapid, reagent-less detection and discrimination of biological warfare (BW) agents, through the control of multi-photon and multi-wavelength processes at the nanoscale. This paper will overview an ARO/ECBC led multidisciplinary research program presently under the support of the U.S. Defense Threat Reduction Agency (DTRA) that seeks to develop new devices and nanoelectronic architectures that are effective for extracting THz signatures from target bio-molecules. Here, emphasis will be placed on the new nanosensor concepts and THz/Optical measurement methodologies for spectral-based sequencing/identification of genetic molecules.

Physical models are presented to describe magneto-transports within double-barrier structure with staggered-band lineups. Here, a special case, where the magnetic field is perpendicular to the heterolayers, is considered and the conduction-band electron current is calculated. In addition, the spatial charge transfer due to the heavyhole (HH) interband tunneling is also studied. The interband tunneling probability is related to the Landau index number, which characterizes the quantization of in-plane electron motions. As a consequence, the inversion of hole populations between Landau levels is shown to occur which is a new phenomenon that has relevance for millimeterwave amplification.

There is considerable interest in electrical sensing of biomolecular binding since it has the potential to be label free, to work easily in aqueous environments native to the biomolecules, and to be integrated with small, fast, and inexpensive microelectronoics as detection instrumentation. Although electrochemical methods have been used successfully in detections of DNA molecules with Ag labels at very high sensitivity (~ p ml), detection of DNA molecules in terms of label free techniques has a lower sensitivity (~ μ ml). Here, the surface attachment chemistry is critical towards the detection of ultra-low concentration of biomolecules. In this article, based on density functional theory, we have calculated and analyzed the electrical characteristics of the contact between aromatic molecules and silicon (100) − 2×1 surfaces. Design principles for silicon based electrodes of electrochemically biomolecular sensing instruments for label-free sensing of single or a few biomolecular molecules have also been discussed.

An In 1− x Ga x As / GaSb y As 1− y hetero-system with staggered band-lineups as solid-state platform for design of an interband resonant double-barrier tunneling diode (I-RTD) based optically-pulsed (OT) hybrid device for generating THz oscillations is theoretically investigated. It is demonstrated that this optical I-RTD hybrid is compatible with the robust state-of-art 1.55 micron laser technology Multi-band wave equations in the framework of six-band Kane's model are applied for understanding the carrier dynamics when strain-induced effects are present. Simulation results for practical circuit implementations clearly show the superiority of this new oscillator concept.

The so-called “mountain-pass” theorem allows for the finding of a critical point on the path between two points on a multidimensional contour where the maximal elevation is minimal. By implementing the “elastic string algorithm”, it is possible to not only find the critical point, but to compute the mountain-pass itself on a finite-dimensional contour. For a given molecule that sits between two probes making up a nanostructure device, we propose that the mountain-pass will be a likely path of electron transport through the molecule, the contour being the electronic potential of the molecule. This potential along this path will be used as the input potential for SETraNS, a 1D Wigner-Poisson electron transport solver in order to explore the current-bias characteristics of such the molecule in such a device. In order to calculate the mountain pass, the elastic string algorithm is used to set up a constrained non-linear optimization problem which is, in turn, solved via a Monte Carlo method. We will compute the mountain-pass for a well-known test contour in order to show the validity of this approach. The procedure developed here is to be combined with conformational analysis via the molecular modeling program AMBER and the quantum transport program SETraNS in order to predict molecular function. When achieved, this combined procedure will allow for the better design and implementation of nanoscale molecular devices for application such as sensing, switching and data processing.