Submillimeter-wave phonon modes in DNA macromolecules

Rapid sensing of hidden objects and defects using a single-pixel diffractive terahertz sensor

Terahertz waves offer advantages for nondestructive detection of hidden objects/defects in materials, as they can penetrate most optically-opaque materials. However, existing terahertz inspection systems face throughput and accuracy restrictions due to their limited imaging speed and resolution. Furthermore, machine-vision-based systems using large-pixel-count imaging encounter bottlenecks due to their data storage, transmission and processing requirements. Here, we report a diffractive sensor that rapidly detects hidden defects/objects within a 3D sample using a single-pixel terahertz detector, eliminating sample scanning or image formation/processing. Leveraging deep-learning-optimized diffractive layers, this diffractive sensor can all-optically probe the 3D structural information of samples by outputting a spectrum, directly indicating the presence/absence of hidden structures or defects. We experimentally validated this framework using a single-pixel terahertz time-domain spectroscopy set-up and 3D-printed diffractive layers, successfully detecting unknown hidden defects inside silicon samples. This technique is valuable for applications including security screening, biomedical sensing and industrial quality control.

Sub-THz spectroscopic characterization identification for pine wood nematode ribosomal DNA

This paper, we introduced Sub-terahertz (Sub-THz) technology to identify nematode DNA sequence. First, data mining technology and restriction enzyme digestion were used to cut out two corresponding sequences, each containing about 100 base pairs that could represent the characteristic fragments of Bursaphelenchus xylophilus (Bx) and Bursaphelenchus mucronatus (Bm) rDNA in internal transcribed spacer 1 (ITS1) region. Then, vibration spectra of the two enzyme-cut sequences were measured by Fourier transform infrared spectroscopy (FTIR). Meanwhile, the spectrum was analyzed by molecular dynamics method. It was found that the calculated and experimental spectra of the two enzyme-cut sequences were consistent, although the differences of the sequences could not be well reflected in the spectra. The vibration modes corresponding to diverse absorption peaks in the spectra were quite different, which were closely related to the internal bases sequencing. This can be used as an indicator for identifying Bx and Bm DNA. Moreover, the normal mode analysis (NMA) method was first adopted for spectral attribution analysis of DNA long sequences. Finally, the vibration spectra of shorter sequences predicted by second-order Markov chains and Monte Carlo method were studied. To some extent, the predicted short sequences can represent the complete sequence as the initial calculation structure.

THz spectra and corresponding vibrational modes of DNA base pair cocrystals and polynucleotides

The generalized energy-based fragmentation (GEBF) approach has been applied to study the THz spectra and vibrational modes of base pair cocrystals under periodic boundary conditions (denoted as PBC-GEBF). Results of vibrational mode reveal that hydrogen bonds play a pivotal role in the pairing process of base crystals, where most NH and CH bonds stretch to some extent. We also found that hydrogen bonds of a self-made A:T cocrystal completely break in a transition from liquid to the solid state, while self-made C:G cocrystal is different and easier to form a cocrystal, as confirmed by X-ray diffraction (XRD) and terahertz (THz) spectra. Furthermore, we have studied DNA polynucleotides (in both A and B forms) found that the vibrational modes changed a lot during the process of their forming double strand. Despite the key role played by hydrogen bonds, the key contribution originates from collective motions of the main skeleton. A comparative study of the spectra of some stranded fragments suggests that different sequences or forms have similar spectra in THz band. They distinguish from each other mainly in the low-frequency regions, especially below 1 THz. This study would make great contributions to the molecular dynamics model based DNA long-chain structure simulation in the future study.

Radiating pattern of surge-current-induced THz light in near-field and far-field zone

We generate the THz wave on the surface of an unbiased GaAs crystal by illuminating femtosecond laser pulses with a 45° incidence angle, and investigate its propagation properties comprehensively both in a near-field and in a far-field zone by performing a knife-edge scan measurement. In the near-field zone, i.e. 540 μm away from the generation point, we found that the beam simply takes a Gaussian shape of which width follows well a behavior predicted by a paraxial wave equation. In the far-field zone, on the other hand, it takes a highly anisotropic shape; whereas the beam profile maintains a Gaussian shape along the normal to the plane of incidence, it takes satellite peak structures along the direction in parallel to the plane of incidence. From the comparison with simulation results obtained by using a dipole radiation model, we demonstrated that this irregular beam pattern is attributed to the combined effect of the position-dependent phase retardation of the THz waves and the diffraction-limited size of the initial beam which lead to the interference of the waves in the far-field zone. Also, we found that this consideration accounting for a crossover of THz beam profile to the anisotropic non-Gaussian beam in the far-field zone can be applied for a comprehensive understanding of several other THz beam profiles obtained previously in different configurations.

Terahertz spectra of DNA nucleobase crystals: A joint experimental and computational study

Terahertz (THz) spectra of DNA nucleobase crystals were experimentally studied by terahertz time domain spectroscopy (THz-TDS), Fourier transform infrared spectroscopy (FTIR), and computationally studied by the generalized energy-based fragmentation approach under periodic boundary conditions (denoted as PBC-GEBF). We analyzed the vibrational spectra of solid-state DNA nucleobases and assigned the corresponding vibrational modes to the main peaks in the experimental spectra with the PBC-GEBF results. The computational results were verified to be in good accordance with the experimental data. Harmonic vibrational frequency results revealed that all the vibrational modes belong to collective vibrational modes, which involve complicated mixtures of inter- and intramolecular displacements, somewhere in the vicinity of 0.5-9THz.

How quantum entanglement in DNA synchronizes double-strand breakage by type II restriction endonucleases

Macroscopic quantum effects in living systems have been studied widely in pursuit of fundamental explanations for biological energy transport and sensing. While it is known that type II endonucleases, the largest class of restriction enzymes, induce DNA double-strand breaks by attacking phosphodiester bonds, the mechanism by which simultaneous cutting is coordinated between the catalytic centers remains unclear. We propose a quantum mechanical model for collective electronic behavior in the DNA helix, where dipole-dipole oscillations are quantized through boundary conditions imposed by the enzyme. Zero-point modes of coherent oscillations would provide the energy required for double-strand breakage. Such quanta may be preserved in the presence of thermal noise by the enzyme's displacement of water surrounding the DNA recognition sequence. The enzyme thus serves as a decoherence shield. Palindromic mirror symmetry of the enzyme-DNA complex should conserve parity, because symmetric bond-breaking ceases when the symmetry of the complex is violated or when physiological parameters are perturbed from optima. Persistent correlations in DNA across longer spatial separations-a possible signature of quantum entanglement-may be explained by such a mechanism.

Terahertz optical measurements of correlated motions with possible allosteric function

A suggested mechanism for allosteric response is the distortion of the energy landscape with agonist binding changing the protein structure's access to functional configurations. Intramolecular vibrations are indicative of the energy landscape and may have trajectories that enable functional conformational change. Here, we discuss the development of an optical method to measure the intramolecular vibrations in proteins, namely, crystal anisotropy terahertz microscopy, and the various approaches which can be used to identify the spectral data with specific structural motions.

Sub-wavelength terahertz beam profiling of a THz source via an all-optical knife-edge technique

Terahertz technologies recently emerged as outstanding candidates for a variety of applications in such sectors as security, biomedical, pharmaceutical, aero spatial, etc. Imaging the terahertz field, however, still remains a challenge, particularly when sub-wavelength resolutions are involved. Here we demonstrate an all-optical technique for the terahertz near-field imaging directly at the source plane. A thin layer (<100 nm-thickness) of photo carriers is induced on the surface of the terahertz generation crystal, which acts as an all-optical, virtual blade for terahertz near-field imaging via a knife-edge technique. Remarkably, and in spite of the fact that the proposed approach does not require any mechanical probe, such as tips or apertures, we are able to demonstrate the imaging of a terahertz source with deeply sub-wavelength features (<30 μm) directly in its emission plane.

Playing the notes of DNA with light: extremely high frequency nanomechanical oscillations

We use a double nanohole (DNH) optical tweezer with two trapping lasers beating to excite the vibrational modes of single-stranded DNA (ssDNA) fragments in the extremely high frequency range. We find the resonant vibration frequency of a 20 base ssDNA to be 40 GHz. We show that the change in the resonant frequency for different lengths of the DNA strand is in good agreement with one dimensional lattice vibration theory. Thus the DNH tweezer system could distinguish between different lengths of DNA strands with resolution down to a few bases. By varying the base sequence and length, it is possible to adjust the resonance frequency vibration spectrum. The technique shows the potential for use in sequencing applications if we can improve the resolution of the present system to detect changes in resonant frequency for a single base change in a given sequence. The technique is single-molecule and label-free as compared to the existing methods used for DNA characterization like gel electrophoresis.

Terahertz science and technology of carbon nanomaterials

The diverse applications of terahertz (THz) radiation and its importance to fundamental science makes finding ways to generate, manipulate and detect THz radiation one of the key areas of modern applied physics. One approach is to utilize carbon nanomaterials, in particular, single-wall carbon nanotubes and graphene. Their novel optical and electronic properties offer much promise to the field of THz science and technology. This article describes the past, current, and future of THz science and technology of carbon nanotubes and graphene. We will review fundamental studies such as THz dynamic conductivity, THz nonlinearities and ultrafast carrier dynamics as well as THz applications such as THz sources, detectors, modulators, antennas and polarizers.

THz-Spectroscopy of Biological Molecules

The terahertz frequency absorption spectraof DNA molecules reflect low-frequencyinternal helical vibrations involvingrigidly bound subgroups that are connectedby the weakest bonds, including thehydrogen bonds of the DNA base pairs,and/or non-bonded interactions. Althoughnumerous difficulties make the directidentification of terahertz phonon modes inbiological materials very challenging, ourresearch has shown that such measurementsare both possible and fruitful. Spectra ofdifferent DNA samples reveal a large numberof modes and a reasonable level ofsequence-specific uniqueness. In an attemptto show that the long wavelength absorptionfeatures are intrinsic properties ofbiological materials determined by phononmodes, a normal mode analysis has been usedto predict the absorption spectra ofpolynucleotide RNA Poly[G]-Poly[C]. Directcomparison demonstrated a correlationbetween calculated and experimentallyobserved spectra of the RNA polymers, thusconfirming that the fundamental physicalnature of the observed resonance structureis caused by the internal vibration modesin the macromolecules.In this work we demonstrate results fromFourier-Transform Infrared (FTIR)spectroscopy of DNA macromolecules andrelated biological materials in theterahertz frequency range. Carefulattention was paid to the possibility ofinterference or etalon effects in thesamples, and phenomena were clearlydifferentiated from the actual phononmodes. In addition, we studied thedependence of transmission spectra ofaligned DNA and polynucleotide film sampleson molecule orientation relative to theelectromagnetic field, showing the expectedchange in mode strength as a function ofsample orientation. Further, the absorptioncharacteristics were extracted from thetransmission data using the interferencespectroscopy technique, and a stronganisotropy of terahertz characteristics wasdemonstrated.

The potential of terahertz imaging for cancer diagnosis: A review of investigations to date

The terahertz region lies between the microwave and infrared regions of the electromagnetic spectrum such that it is strongly attenuated by water and very sensitive to water content. Terahertz radiation has very low photon energy and thus it does not pose any ionization hazard for biological tissues. Because of these characteristic properties, there has been an increasing interest in terahertz imaging and spectroscopy for biological applications within the last few years and more and more terahertz spectra are being reported, including spectroscopic studies of cancer. The presence of cancer often causes increased blood supply to affected tissues and a local increase in tissue water content may be observed: this acts as a natural contrast mechanism for terahertz imaging of cancer. Furthermore the structural changes that occur in affected tissues have also been shown to contribute to terahertz image contrast. This paper introduces terahertz technology and provides a short review of recent advances in terahertz imaging and spectroscopy techniques. In particular investigations relating to the potential of terahertz imaging and spectroscopy for cancer diagnosis will be highlighted.

Self-assembly of DNA on a gapped carbon nanotube

We perform molecular dynamics simulations to analyze the wrapping process of a single-stranded (ss) DNA around a gapped CNT immersed in a bath of water. We observe the formation of a stable molecular junction with the ssDNA adopting a helical or circular conformation around one CNT electrode and a linear conformation around the opposite electrode. We find that DNA undergoes several conformational changes during equilibration of the self-assembled molecular junction. This process would allow a higher yield of successful CNT-DNA interconnections, which constitutes a novel structure of interest in chemical and biological sensing at the single-molecule level.

THZ-FREQUENCY SPECTROSCOPIC SENSING OF DNA AND RELATED BIOLOGICAL MATERIALS

The terahertz frequency absorption spectra of DNA molecules reflect low-frequency internal helical vibrations involving rigidly bound subgroups that are connected by the weakest bonds, including the hydrogen bonds of the DNA base pairs, and/or non-bonded interactions. Although numerous difficulties make the direct identification of terahertz phonon modes in biological materials very challenging, recent studies have shown that such measurements are both possible and useful. Spectra of different DNA samples reveal a large number of modes and a reasonable level of sequence-specific uniqueness. This chapter utilizes computational methods for normal mode analysis and theoretical spectroscopy to predict the low-frequency vibrational absorption spectra of short artificial DNA and RNA. Here the experimental technique is described in detail, including the procedure for sample preparation. Careful attention was paid to the possibility of interference or etalon effects in the samples, and phenomena were clearly differentiated from the actual phonon modes. The results from Fourier-transform infrared spectroscopy of DNA macromolecules and related biological materials in the terahertz frequency range are presented. In addition, a strong anisotropy of terahertz characteristics is demonstrated. Detailed tests of the ability of normal mode analysis to reproduce RNA vibrational spectra are also conducted. A direct comparison demonstrates a correlation between calculated and experimentally observed spectra of the RNA polymers, thus confirming that the fundamental physical nature of the observed resonance structure is caused by the internal vibration modes in the macromolecules. Application of artificial neural network analysis for recognition and discrimination between different DNA molecules is discussed.

Disentangling time in a near-field approach to scanning probe microscopy

Microwave microscopy has recently attracted intensive effort, owing to its capability to provide quantitative information about the local composition and the electromagnetic response of a sample. Nonetheless, the interpretation of microwave images remains a challenge as the electromagnetic waves interact with the sample and the surrounding in a multitude of ways following different paths: microwave images are a convolution of all contributions. In this work we show that examining the time evolution of the electromagnetic waves allows us to disentangle each contribution, providing images with striking quality and unexplored scenarios for near-field microscopy.

A promising diagnostic method: Terahertz pulsed imaging and spectroscopy

The terahertz band lies between the microwave and infrared regions of the electromagnetic spectrum. This radiation has very low photon energy and thus it does not pose any ionization hazard for biological tissues. It is strongly attenuated by water and very sensitive to water content. Unique absorption spectra due to intermolecular vibrations in this region have been found in different biological materials. These unique features make terahertz imaging very attractive for medical applications in order to provide complimentary information to existing imaging techniques. There has been an increasing interest in terahertz imaging and spectroscopy of biologically related applications within the last few years and more and more terahertz spectra are being reported. This paper introduces terahertz technology and provides a short review of recent advances in terahertz imaging and spectroscopy techniques, and a number of applications such as molecular spectroscopy, tissue characterization and skin imaging are discussed.

Acoustic spectroscopy of DNA in the gigahertz range

We find a parametric resonance in the gigahertz range of DNA dynamics, generated by pumping hypersound. The resonance may be accompanied by the formation of localized phonon modes due to the random structure of elastic modulii of DNA.

Mammalian stem cells reprogramming in response to terahertz radiation

We report that extended exposure to broad-spectrum terahertz radiation results in specific changes in cellular functions that are closely related to DNA-directed gene transcription. Our gene chip survey of gene expression shows that whereas 89% of the protein coding genes in mouse stem cells do not respond to the applied terahertz radiation, certain genes are activated, while other are repressed. RT-PCR experiments with selected gene probes corresponding to transcripts in the three groups of genes detail the gene specific effect. The response was not only gene specific but also irradiation conditions dependent. Our findings suggest that the applied terahertz irradiation accelerates cell differentiation toward adipose phenotype by activating the transcription factor peroxisome proliferator-activated receptor gamma (PPARG). Finally, our molecular dynamics computer simulations indicate that the local breathing dynamics of the PPARG promoter DNA coincides with the gene specific response to the THz radiation. We propose that THz radiation is a potential tool for cellular reprogramming.

A dynamics study of the A-chain of ricin by terahertz vibrational calculation and normal modes analysis

We studied the terahertz (THz) spectroscopy and low frequency normal modes of both apo- and holo- (adenosine monophosphate (AMP)-bound) ricin-A-chain (RTA) as a means to understand the dynamical changes that RTA undergoes upon substrate binding. The calculated THz spectra of apo- and holo-RTAs demonstrated a general intensity suppression upon substrate binding, which is attributed to the reduced number of collective motion in THz region. In normal mode analysis of RTA we find a shearing motion that is shared by both the apo- and holo-RTAs, whereas a breathing motion, and an upward hinge rising and an alpha-G bending characteristic motion are dampened significantly upon AMP binding, suggesting these motions are involved in the necessary flexibility of the active site. In contrast, we find a normal mode motion that separates domains I and II of RTA at the interface that is more common in the holo-protein. We hypothesized that the flexibility of the entrance of RTA can facilitate the entry of rRNA and allow the substrate to adjust its conformation and orientation prior to depurination. This process suggests an rRNA binding pathway which is supplemental the current RTA depurination mechanism.

Low-frequency electrophoretic actuation of nanoscale optoentropic transduction mechanisms

Inherent bistabilities within DNA-assembled fluorescent resonant energy transfer systems demonstrated time-varying optical signals in response to an electrophoretic driving force. Frequency responses of electrophoretically driven FRET systems were shown to be sequence specific. Integration of these signals over time gave near single-molecule sensitivity within a high background of autofluorescence. This research suggests that externally driven nanoscale mechanical systems may help improve information flow within morphologically intact specimens.

Tunable terahertz waves generated by mixing two copropagating infrared beams in GaP

By mixing two copropagating coherent beams near 1 microm in a zinc blende GaP crystal, we have efficiently generated coherent terahertz (THz) waves. Such efficient conversion is made possible by use of a rest-strahlen band in the THz region to achieve phase matching in an isotropic crystal. A tuning range as wide as 71.1-2830 microm (0.106-4.22 THz) was achieved, whereas the highest output peak power reached 15.6 W at 173 microm. To obtain such a tuning range we continuously tuned the wavelength of one coherent infrared beam within a bandwidth of approximately 15.3 nm.

Torsional vibrational modes of tryptophan studied by terahertz time-domain spectroscopy

The low-frequency torsional modes, index of refraction, and absorption of a tryptophan film and pressed powders from 0.2 to 2.0 THz (6.6-66 cm(-1)) were measured by terahertz time-domain spectroscopy at room temperature. It was found that there were two dominated torsional vibrational modes at around 1.435 and 1.842 THz. The associated relaxation lifetimes ( approximately 1 ps) for these modes of the tryptophan molecule were measured. Using a density-functional calculation, the origins of the observed torsional vibrations were assigned to the chain and ring of the tryptophan molecule.

Terahertz sources and detectors and their application to biological sensing

Terahertz spectroscopy has long been used as an important measurement tool in fields such as radio astronomy, physical chemistry, atmospheric studies and plasma research. More recently terahertz technology has been used to develop an exciting new technique to investigate the properties of a wide range of biological materials. Although much research remains before a full understanding of the interaction between biomaterials and terahertz radiation is developed, these initial studies have created a compelling case for further scientific study. Also, the potential development of practical tools to detect and identify biological materials such as biological-warfare agents and food contaminants, or of medical diagnostic tools, is driving the need for improved terahertz technology. In particular, improved terahertz sources and detectors that can be used in practical spectroscopy systems are needed. This paper overviews some of the recent measurements of the terahertz spectra of biomaterials and the ongoing efforts to create an all-solid-state technology suitable not only for improved scientific experiments but also for military and commercial applications.

Terahertz circular dichroism spectroscopy: a potential approach to the in situ detection of life's metabolic and genetic machinery

We propose a terahertz (far-infrared) circular dichroism-based life-detection technology that may provide a universal and unequivocal spectroscopic signature of living systems regardless of their genesis. We argue that, irrespective of the specifics of their chemistry, all life forms will employ well-structured, chiral, stereochemically pure macromolecules (>500 atoms) as the catalysts with which they perform their metabolic and replicative functions. We also argue that nearly all such macromolecules will absorb strongly at terahertz frequencies and exhibit significant circular dichroism, and that this circular dichroism unambiguously distinguishes biological from abiological materials. Lastly, we describe several approaches to the fabrication of a terahertz circular dichroism spectrometer and provide preliminary experimental indications of their feasibility. Because terahertz circular dichroism signals arise from the molecular machinery necessary to carry out life's metabolic and genetic processes, this life-detection method differs fundamentally from more well-established approaches based on the detection of isotopic fractionation, "signature" carbon compounds, disequilibria, or other by-products of metabolism. Moreover, terahertz circular dichroism spectroscopy detects this machinery in a manner that makes few, if any, assumptions as to its chemical nature or the processes that it performs.