Far-infrared vibrational modes of DNA components studied by terahertz time-domain spectroscopy

A High-Power Broadband Terahertz Source Enabled by Three-Dimensional Light Confinement in a Plasmonic Nanocavity

The scope and potential uses of time-domain terahertz imaging and spectroscopy are mainly limited by the low optical-to-terahertz conversion efficiency of photoconductive terahertz sources. State-of-the-art photoconductive sources utilize short-carrier-lifetime semiconductors to recombine carriers that cannot contribute to efficient terahertz generation and cause additional thermal dissipation. Here, we present a novel photoconductive terahertz source that offers a significantly higher efficiency compared with terahertz sources fabricated on short-carrier-lifetime substrates. The key innovative feature of this source is the tight three-dimensional confinement of the optical pump beam around the terahertz nanoantennas that are used as radiating elements. This is achieved by means of a nanocavity formed by plasmonic structures and a distributed Bragg reflector. Consequently, almost all of the photo-generated carriers can be routed to the terahertz nanoantennas within a sub-picosecond time-scale. This results in a very strong, ultrafast current that drives the nanoantennas to produce broadband terahertz radiation. We experimentally demonstrate that this terahertz source can generate 4 mW pulsed terahertz radiation under an optical pump power of 720 mW over the 0.1–4 THz frequency range. This is the highest reported power level for terahertz radiation from a photoconductive terahertz source, representing more than an order of magnitude of enhancement in the optical-to-terahertz conversion efficiency compared with state-of-the-art photoconductive terahertz sources fabricated on short-carrier-lifetime substrates.

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.

Structural changes of Bombyx mori fibroin from silk gland to fiber as evidenced by Terahertz spectroscopy and other methods

Here we investigated the structural changes of silk fibroin during Bombyx mori silkworm spinning and reconstitution process. X-ray diffraction, Fourier transform infrared spectroscopy, polarized optical microscopy, and terahertz (THz) spectroscopy were applied to monitor the structural features of silk fibroin from posterior, middle silk glands, to cocoons, and then to reconstituted silk. Results show that from silk gland to cocoon, fibroin experiences a significant transformation in crystal structure from a typical silk I, to a silk I-rich mixed structure, and finally to a typical silk II state, accompanied with a change in secondary structure from α-helix and random coil structures to preferential orientation β-sheets. Compared with natural silk fibroins, the reconstituted silk fibroin lacks β-sheet conformation and orientation crystallization. Terahertz spectroscopy readily follows these silk fibroin structural changes. Two characteristic peaks for silk fibroin is observed in 2-10 THz. Their strength ratio is strongly correlated with the β-sheet conformation. The absorbance properties in 0.2-2.0THz also significantly change as a function of changing their crystal structures caused by diverse sources. All of these observations will help in the study of overall structure in silk fibroin to understand more completely the fibroin assembly process in natural spinning and reconstitution process.

Research on the Terahertz Absorption Spectra of Histidine Enantiomer (L) and its Racemic Compound (DL)

Terahertz time-domain spectroscopy (THz-TDS) is used to investigate the absorption spectra of polycrystalline L- and DL-histidine in the frequency range of 10-100 cm^-1. The spectra exhibit distinct differences in peak frequencies between the enantiomer (L-histidine) and racemic compound (DL-histidine). The observed spectral differences are attributed to the intermolecular interactions. With the density function theory (DFT) method, the frequencies of vibrational modes of L-histidine and DL-histidine in the THz range are calculated and well assigned according to the measured spectra. The origin of the observed vibrational modes is found to be non-localized and of a collective (phonon-like) nature, which points to the lattice and skeleton vibrations mediated by the hydrogen bond. Furthermore, we propose and demonstrate a method for determining the composition ratio of histidine mixtures based on the THz absorption spectra.

Aligned copper nanorod arrays for highly efficient generation of intense ultra-broadband THz pulses

We demonstrate an intense broadband terahertz (THz) source based on the interaction of relativistic-intensity femtosecond lasers with aligned copper nanorod array targets. For copper nanorod targets with a length of 5 μm, a maximum 13.8 times enhancement in the THz pulse energy (in ≤20 THz spectral range) is measured as compared to that with a thick plane copper target under the same laser conditions. A further increase in the nanorod length leads to a decrease in the THz pulse energy at medium frequencies (≤20 THz) and increase of the electromagnetic pulse energy in the high-frequency range (from 20–200 THz). For the latter, we measure a maximum energy enhancement of 28 times for the nanorod targets with a length of 60 μm. Particle-in-cell simulations reveal that THz pulses are mostly generated by coherent transition radiation of laser produced hot electrons, which are efficiently enhanced with the use of nanorod targets. Good agreement is found between the simulation and experimental results.

Far infrared spectroscopy of hydrogen bonding collective motions in complex molecular systems

Far infrared spectroscopy as a tool for the study of inter and intramolecular interactions in complex molecular structures.

Resolving the Origins of Crystalline Anharmonicity Using Terahertz Time-Domain Spectroscopy and ab Initio Simulations

Anharmonicity has been shown to be an important piece of the fundamental framework that dictates numerous observable phenomena. In particular, anharmonicity is the driving force of vibrational relaxation processes, mechanisms that are integral to the proper function of numerous chemical processes. However, elucidating its origins has proven difficult due to experimental and theoretical challenges, specifically related to separating the anharmonic contributions from other unrelated effects. While no one technique is particularly suited for providing a complete picture of anharmonicity, by combining multiple complementary methods such a characterization can be made. In this study the role of individual atomic interactions on the anharmonic properties of crystalline purine, the building block of many DNA and RNA nucleobases, is studied by experimental terahertz time-domain spectroscopy and first-principles density functional theory (DFT) and ab initio molecular dynamics simulations (AIMD). In particular, the detailed vibrational information provided by the DFT calculations is used to interpret the atomic origins of anharmonic-related effects as determined by the AIMD calculations, which are in good agreement with the experimental data. The results highlight that anharmonicity is especially pronounced in the intermolecular interactions, particularly along the amine hydrogen bond coordinate, and yields valuable insight into what is similarly observed complex biosystems and crystalline solids.

Terahertz molecular resonance of cancer DNA

Carcinogenesis involves the chemical and structural alteration of biomolecules in cells. Aberrant methylation of DNA is a well-known carcinogenic mechanism and a common chemical modification of DNA. Terahertz waves can directly observe changes in DNA because the characteristic energies lie in the same frequency region. In addition, terahertz energy levels are not high enough to damage DNA by ionization. Here, we present terahertz molecular resonance fingerprints of DNA methylation in cancer DNA. Methylated cytidine, a nucleoside, has terahertz characteristic energies that give rise to the molecular resonance of methylation in DNA. Molecular resonance is monitored in aqueous solutions of genomic DNA from cancer cell lines using a terahertz time-domain spectroscopic technique. Resonance signals can be quantified to identify the types of cancer cells with a certain degree of DNA methylation. These measurements reveal the existence of molecular resonance fingerprints of cancer DNAs in the terahertz region, which can be utilized for the early diagnosis of cancer cells at the molecular level.

Terahertz broadband modulation in a biased BiFeO3/Si heterojunction

A new terahertz (THz) modulator based on bias-driven carrier conductivity change in a heterojunction was proposed. BiFeO₃ film and silicon were selected as building blocks for fabricating the THz modulator. THz nonlinear transmission as a function of bias voltage was studied systematically. THz peak transmission as a function of bias shows a similar tendency as the current-voltage response of the heterojunction: the forward bias leads to the exponential enhancement of THz transmission, and in contrast, the reverse bias shows no observable changes in THz transmission. The modulation depth and modulation bandwidth of THz pulse can reach up to 42% and 1.0 THz with forward bias of 4.8 V, respectively. The observed bias dependent THz transmission in the BFO/Si heterojunction is well-interpreted by the proposed model: the diffused carriers across the heterojunction are localized in BFO thin film with applied forward bias. Our finding provides great potential for applications in designing all electrical broadband THz modulators.

Plasmon-Enhanced below Bandgap Photoconductive Terahertz Generation and Detection

We use plasmon enhancement to achieve terahertz (THz) photoconductive switches that combine the benefits of low-temperature grown GaAs with mature 1.5 μm femtosecond lasers operating below the bandgap. These below bandgap plasmon-enhanced photoconductive receivers and sources significantly outperform commercial devices based on InGaAs, both in terms of bandwidth and power, even though they operate well below saturation. This paves the way for high-performance low-cost portable systems to enable emerging THz applications in spectroscopy, security, medical imaging, and communication.

Focus: Phase-resolved nonlinear terahertz spectroscopy--From charge dynamics in solids to molecular excitations in liquids

Intense terahertz (THz) electric field transients with amplitudes up to several megavolts/centimeter and novel multidimensional techniques are the key ingredients of nonlinear THz spectroscopy, a new area of basic research. Both nonlinear light-matter interactions including the non-perturbative regime and THz driven charge transport give new insight into the character and dynamics of low-energy excitations of condensed matter and into quantum kinetic phenomena. This article provides an overview of recent progress in this field, combining an account of technological developments with selected prototype results for liquids and solids. The potential of nonlinear THz methods for future studies of low-frequency excitations of condensed-phase molecular systems is discussed as well.

Extraordinary sensitivity enhancement by metasurfaces in terahertz detection of antibiotics

We have detected trace amounts of molecules of antibiotics (kanamycin sulfate) dispersed on metasurfaces with terahertz (THz) spectroscopy. Utilizing the extraordinary optical transmission resonance of an array of square-shaped slits on a silicon substrate at ~0.3 THz, we were able to monitor varying concentrations of kanamycin sulfate as low as ~100 picogram/L. In contrast, the lowest detectable concentration of kanamycin sulfate on silicon without any metallic structure was ~1 gram/L. This dramatic ~10(10) times enhancement of sensitivity is due to the near-field enhancement of THz electric fields by the metamaterial structure. This result thus demonstrates the power and usefulness of metamaterial-assisted THz spectroscopy in trace molecular detection for biological and chemical sensing as well as for food product quality and safety inspection and control.

Concentration-dependent effects on fully hydrated DNA at terahertz frequencies

Using terahertz time-domain spectroscopy (THz-TDS), the frequency-dependent dielectric constant of deoxyribonucleic acid (DNA) in solution was measured. The response of the buffer solution is dominated by two Debye modes in this frequency range, and, from an analysis of the concentration dependence, the presence of the DNA increases the main relaxation time and dielectric constant. This reflects the fact that the water in the hydration layer is more tightly bound under the influence of the DNA molecule in comparison to bulk water. This dynamical slowing down with increasing DNA concentration is similar to what is observed with purine nucleotides, but opposite to the behavior of pyrimidine nucleotides. In addition, a suspension model was used with the concentration-dependent data to isolate the dielectric response of the hydrated DNA molecule. The data for the hydrated DNA molecule is still dominated by a Debye response. It is also possible to determine the thickness of the hydration layer, and the DNA molecule influences the surrounding water out to 16 or 17 Å, which corresponds to about six effective hydration layers.

Terahertz spectroscopy of oligonucleotides in aqueous solutions

A terahertz (THz) spectroscopic study is carried out to analyze DNA mutations in a label-free manner. Three newly designed liquid sample cells are considered and the best is selected as the sample carrier for THz transmission spectroscopic analyses. Discrimination based on spectral signatures of single-base mutations on single-stranded 20 nt oligonucleotides has been shown possible experimentally. The results clearly attest the ability of this promising approach for label-free analyses of single-base mutations of DNA molecules. This study has demonstrated that the THz spectroscopic technology can be considered as a potential diagnostic tool for investigating molecular reactions, such as DNA mutations.

Nanoplasmonics enhanced terahertz sources

Arrayed hexagonal metal nanostructures are used to maximize the local current density while providing effective thermal management at the nanoscale, thereby allowing for increased emission from photoconductive terahertz (THz) sources. The THz emission field amplitude was increased by 60% above that of a commercial THz photoconductive antenna, even though the hexagonal nanostructured device had 75% of the bias voltage. The arrayed hexagonal outperforms our previously investigated strip array nanoplasmonic structure by providing stronger localization of the current density near the metal surface with an operating bandwidth of 2.6 THz. This approach is promising to achieve efficient THz sources.

Molecular recognition and interaction between uracil and urea in solid-state studied by terahertz time-domain spectroscopy

Using terahertz time-domain spectroscopy characterization, we observe that urea is able to recognize and interact with uracil efficiently even in the solid phase without involving water or solvents. A cocrystal configuration linked by a pair of hydrogen bonds between uracil and urea was formed. The terahertz absorption spectrum of the cocrystal shows a distinct new absorption at 0.8 THz (26.7 cm(-1)), which originates from the intermolecular hydrogen bonding. Both mechanical milling and heating can accelerate the reaction efficiently. Density functional theory was adopted to simulate the vibrational modes of the cocrystal, and the results agree well with the experimental observation. Multiple techniques, including powder X-ray diffraction, scanning electron microscopy, and Fourier transform infrared spectroscopy, were performed to investigate the reaction process, and they presented supportive evidence. This work enables in-depth understanding of recognition and interaction of urea with nucleobases and comprehension of the denaturation related to RNA. We also demonstrate that terahertz spectroscopy is an effective and alternative tool for online measurement and quality control in pharmaceutical and chemical industries.

Experimental detection of long-distance interactions between biomolecules through their diffusion behavior: numerical study

The dynamical properties and diffusive behavior of a collection of mutually interacting particles are numerically investigated for two types of long-range interparticle interactions: Coulomb-electrostatic and dipole-electrodynamic. It is shown that when the particles are uniformly distributed throughout the accessible space, the self-diffusion coefficient is always lowered by the considered interparticle interactions, irrespective of their attractive or repulsive character. This fact is also confirmed by a simple model to compute the correction to the Brownian diffusion coefficient due to the interactions among the particles. These interactions are also responsible for the onset of dynamical chaos and an associated chaotic diffusion which still follows an Einstein-Fick-like law for the mean-square displacement as a function of time. Transitional phenomena are observed for Coulomb-electrostatic (repulsive) and dipole-electrodynamic (attractive) interactions considered both separately and in competition. The outcomes reported in this paper clearly indicate a feasible experimental method to probe the activation of resonant electrodynamic interactions among biomolecules.

Analytical model for THz emissions induced by laser-gas interaction

We develop a one-dimensional model of THz emissions induced by laser-driven, time-asymmetric ionization and current oscillations in a hydrogen gas. Our model highlights complex scalings of the THz fields with respect to the laser and gas parameters, in particular, a non-monotonic behavior against the laser parameters. Analytical expressions of the transmitted and reflected fields are presented, explaining the THz spectra observed in particle-in-cell and forward-pulse propagation codes. The backward-propagating THz wave is mainly driven by the electron current oscillations at the plasma frequency, and its resulting spectrum operates below the plasma frequency. The transmitted THz wave is emitted from both plasma current oscillations and photo-ionization. Their respective signal presents a contribution below and around the plasma frequency, plus a contribution at higher frequencies associated to the photo-induced current. The interplay between these two mechanisms relies on the ratio between the propagation length and the plasma skin depth.

Spectral investigation of hot spot and cavity resonance effects on the terahertz radiation from high-T(c) superconducting Bi2Sr2CaCu2O(8+δ) mesas

Terahertz (THz) electromagnetic radiation emitted from single and series-connected rectangular mesa devices of high-Tc superconducting Bi2Sr2CaCu2O8+δ is investigated spectroscopically during simultaneous temperature distribution observations using a microcrystalline SiC photoluminescence technique. In single mesas, a hot-spot region with its temperature T locally exceeding Tc was observed to jump suddenly in position under small current I-bias changes. Although these hot-spot position jumps cause large changes in the output power with small changes in I, as long as the voltage V per junction number N is kept constant, they do not affect the output frequency f, which is given by the ac Josephson frequency fJ. f can lock onto that of a particular mesa cavity resonance frequency fc, which enhances the emission power and serves as the primary mechanism for the synchronization of the emissions from each of the intrinsic Josephson junctions in the mesa.

Intense THz pulses down-regulate genes associated with skin cancer and psoriasis: a new therapeutic avenue?

Terahertz (THz) radiation lies between the infrared and microwave regions of the electromagnetic spectrum and is non-ionizing. We show that exposure of artificial human skin tissue to intense, picosecond-duration THz pulses affects expression levels of numerous genes associated with non-melanoma skin cancers, psoriasis and atopic dermatitis. Genes affected by intense THz pulses include nearly half of the epidermal differentiation complex (EDC) members. EDC genes, which are mapped to the chromosomal human region 1q21, encode for proteins that partake in epidermal differentiation and are often overexpressed in conditions such as psoriasis and skin cancer. In nearly all the genes differentially expressed by exposure to intense THz pulses, the induced changes in transcription levels are opposite to disease-related changes. The ability of intense THz pulses to cause concerted favorable changes in the expression of multiple genes implicated in inflammatory skin diseases and skin cancers suggests potential therapeutic applications of intense THz pulses.

Concentration-based measurement studies of L-tryptophan using terahertz time-domain spectroscopy (THz-TDS)

L-Tryptophan is an extremely important amino acid for a variety of biological functions in living organisms. In this study we were able to measure changes in the concentration of L-tryptophan when incorporated into pellets with polyethylene as a host. The changes were measured both through the characteristic absorption bands of the C11 and C12 bonds in the low terahertz frequency range and using changes in the refractive index where pellets with higher concentrations of L-tryptophan showed higher refractive indices. The volumetric concentration of L-tryptophan in the polyethylene pellet was accurately determined with a simple model that explains the contribution to the complex refractive index for the resultant sample due to the two constituent materials. These measurements show that terahertz time-domain techniques can be applied to detect variation in concentration of certain amino acids rapidly by examining the relative phase delay and amplitude change of the terahertz transients.

Intense THz pulses cause H2AX phosphorylation and activate DNA damage response in human skin tissue

Recent emergence and growing use of terahertz (THz) radiation for medical imaging and public security screening raise questions on reasonable levels of exposure and health consequences of this form of electromagnetic radiation. In particular, picosecond-duration THz pulses have shown promise for novel diagnostic imaging techniques. However, the effects of THz pulses on human cells and tissues thus far remain largely unknown. We report on the investigation of the biological effects of pulsed THz radiation on artificial human skin tissues. We observe that exposure to intense THz pulses for ten minutes leads to a significant induction of H2AX phosphorylation, indicating that THz pulse irradiation may cause DNA damage in exposed skin tissue. At the same time, we find a THz-pulse-induced increase in the levels of several proteins responsible for cell-cycle regulation and tumor suppression, suggesting that DNA damage repair mechanisms are quickly activated. Furthermore, we find that the cellular response to pulsed THz radiation is significantly different from that induced by exposure to UVA (400 nm).

Modeling the interaction of DNA with alternating fields

We study the influence of a terahertz field on thermal properties of DNA molecules. A Peyrard-Bishop-Dauxois model with the inclusion of a solvent interaction term is considered. The terahertz field is included as a sinusoidal driven force in the equation of motion. We show how under certain field and system parameters, the melting transition and bubble formation are modified.

Specificity and heterogeneity of terahertz radiation effect on gene expression in mouse mesenchymal stem cells

We report that terahertz (THz) irradiation of mouse mesenchymal stem cells (mMSCs) with a single-frequency (SF) 2.52 THz laser or pulsed broadband (centered at 10 THz) source results in irradiation specific heterogenic changes in gene expression. The THz effect depends on irradiation parameters such as the duration and type of THz source, and on the degree of stem cell differentiation. Our microarray survey and RT-PCR experiments demonstrate that prolonged broadband THz irradiation drives mMSCs toward differentiation, while 2-hour irradiation (regardless of THz sources) affects genes transcriptionally active in pluripotent stem cells. The strictly controlled experimental environment indicates minimal temperature changes and the absence of any discernable response to heat shock and cellular stress genes imply a non-thermal response. Computer simulations of the core promoters of two pluripotency markers reveal association between gene upregulation and propensity for DNA breathing. We propose that THz radiation has potential for non-contact control of cellular gene expression.

Terahertz time-domain spectroscopic ellipsometry: instrumentation and calibration

We present a new instrumentation and calibration procedure for terahertz time-domain spectroscopic ellipsometry (THz-TDSE) that is a newly established characterization technique. The experimental setup is capable of providing arbitrary angle of incidence in the range of 15°-85° in the reflection geometry, and with no need for realignment. The setup is also configurable easily into transmission geometry. For this setup, we successfully used hollow core photonic band gap fiber with no pre-chirping in order to deliver a femtosecond laser into a THz photoconductive antenna detector, which is the first demonstration of this kind. The proposed calibration scheme can compensate for the non-ideality of the polarization response of the THz photoconductive antenna detector as well as that of wire grid polarizers used in the setup. In the calibration scheme, the ellipsometric parameters are obtained through a regression algorithm which we have adapted from the conventional regression calibration method developed for rotating element optical ellipsometers, and used here for the first time for THz-TDSE. As a proof-of-principle demonstration, results are presented for a high resistivity silicon substrate as well as an opaque Si substrate with a high phosphorus concentration. We also demonstrate the capacity to measure a few micron thick grown thermal oxide on top of Si. Each sample was characterized by THz-TDSE in reflection geometry with different angle of incidence.

Long-range guided THz radiation by thin layers of water

We propose a novel method to guide THz radiation with low losses along thin layers of water. This approach is based on the coupling of evanescent surface fields at the opposite sides of the thin water layer surrounded by a dielectric material, which leads to a maximum field amplitude at the interfaces and a reduction of the energy density inside the water film. In spite of the strong absorption of water in this frequency range, calculations show that the field distribution can lead to propagation lengths of several centimeters. By means of attenuated total reflection measurements we demonstrate the coupling of incident THz radiation to the long-range surface guided modes across a layer of water with a thickness of 24 μm. This first demonstration paves the way for THz sensing in aqueous environments.

Terahertz time-domain spectroscopy for monitoring the curing of dental composites

We apply terahertz (THz) time-domain spectroscopy for monitoring the curing process of three different light-curing dental composites. Exact knowledge of the sample thickness is required for a precise determination of the THz dielectric parameters, as the materials exhibit shrinkage when they are cured. We find very small but significant changes of the THz refractive index and absorption coefficient during stepwise light exposure. The changes in the refractive index are correlated with changes in the density of the materials. Furthermore, the refractive index and the sample thickness are found to give the most reliable result for monitoring the curing process of the dental composites.

Experimental assessment of the contribution of electrodynamic interactions to long-distance recruitment of biomolecular partners: Theoretical basis

Highly specific spatiotemporal interactions between cognate molecular partners essentially sustain all biochemical transactions in living matter. That such an exquisite level of accuracy may result from encountering forces solely driven by thermal diffusive processes is unlikely. Here we propose a yet unexplored strategy to experimentally tackle the long-standing question of a possibly active recruitment at a distance of cognate partners of biomolecular reactions via the action of resonant electrodynamic interactions. We considered two simplified models for a preliminary feasibility investigation of the devised methodology. By taking advantage of advanced experimental techniques nowadays available, we propose to measure the characteristic encounter time scales of dually interacting biopartners and to compare them with theoretical predictions worked out in both the presence and absence of putative long-range electromagnetic forces.

Metamaterials application in sensing

Metamaterials are artificial media structured on a size scale smaller than wavelength of external stimuli, and they can exhibit a strong localization and enhancement of fields, which may provide novel tools to significantly enhance the sensitivity and resolution of sensors, and open new degrees of freedom in sensing design aspect. This paper mainly presents the recent progress concerning metamaterials-based sensing, and detailedly reviews the principle, detecting process and sensitivity of three distinct types of sensors based on metamaterials, as well as their challenges and prospects. Moreover, the design guidelines for each sensor and its performance are compared and summarized.

Evaluation of coupling terms between intra- and intermolecular vibrations in coarse-grained normal-mode analysis: does a stronger acid make a stiffer hydrogen bond?

Using theory of harmonic normal-mode vibration analysis, we developed a procedure for evaluating the anisotropic stiffness of intermolecular forces. Our scheme for coarse-graining of molecular motions is modified so as to account for intramolecular vibrations in addition to relative translational/rotational displacement. We applied this new analytical scheme to four carboxylic acid dimers, for which coupling between intra- and intermolecular vibrations is crucial for determining the apparent stiffness of the intermolecular double hydrogen bond. The apparent stiffness constant was analyzed on the basis of a conjunct spring model, which defines contributions from true intermolecular stiffness and molecular internal stiffness. Consequently, the true intermolecular stiffness was in the range of 43-48 N m(-1) for all carboxylic acids studied, regardless of the molecules' acidity. We concluded that the difference in the apparent stiffness can be attributed to differences in the internal stiffness of the respective molecules.

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.

Noncovalent interactions between modified cytosine and guanine DNA base pair mimics investigated by terahertz spectroscopy and solid-state density functional theory

Modified cytosine and guanine nucleobases cocrystallize in a hydrogen bonding configuration similar to that observed in native DNA. The noncovalent interactions binding these base pairs in the crystalline solid were investigated using terahertz (THz) spectroscopy and solid-state density functional theory (DFT). While stronger hydrogen bonding interactions are responsible for the general molecular orientations in the crystalline state, it is the weaker dipole-dipole and dispersion forces that determine the overall packing arrangement. The inclusion of dispersion interactions in the DFT calculations was found to be necessary to accurately simulate the unit cell structure and THz vibrational spectrum. Using properly modeled intermolecular potentials, the lattice vibrational motions of the cytosine and guanine derivatives were calculated. The vibrational characters of the modes exhibited by the DNA base pair mimic in the THz region were primarily rotational motions and are indicative of the energies and the nature of vibrations that would likely be observed between similar base pairs in DNA molecules.

Coherent optical phonon generation in Bi3Ge4O12

Time-domain spectroscopy of coherent optical phonons in bismuth germinate (Bi4Ge3O12) is presented. Utilizing both impulsive stimulated Raman scattering and time-domain terahertz spectroscopy, more than 12 unique vibrational states ranging in frequency from 2 to 11 THz are identified, each with coherent lifetimes ranging from 1 to 20 ps. These modes are highly sensitive to crystal orientation and demonstrate frequency shifts on picosecond timescales consistent with an anharmonic lattice potential.

Non-thermal effects of terahertz radiation on gene expression in mouse stem cells

In recent years, terahertz radiation sources are increasingly being exploited in military and civil applications. However, only a few studies have so far been conducted to examine the biological effects associated with terahertz radiation. In this study, we evaluated the cellular response of mesenchymal mouse stem cells exposed to THz radiation. We apply low-power radiation from both a pulsed broad-band (centered at 10 THz) source and from a CW laser (2.52 THz) source. Modeling, empirical characterization, and monitoring techniques were applied to minimize the impact of radiation-induced increases in temperature. qRT-PCR was used to evaluate changes in the transcriptional activity of selected hyperthermic genes. We found that temperature increases were minimal, and that the differential expression of the investigated heat shock proteins (HSP105, HSP90, and CPR) was unaffected, while the expression of certain other genes (Adiponectin, GLUT4, and PPARG) showed clear effects of the THz irradiation after prolonged, broad-band exposure.

THz Medical Imaging: in vivo Hydration Sensing

The application of THz to medical imaging is experiencing a surge in both interest and federal funding. A brief overview of the field is provided along with promising and emerging applications and ongoing research. THz imaging phenomenology is discussed and tradeoffs are identified. A THz medical imaging system, operating at ~525 GHz center frequency with ~125 GHz of response normalized bandwidth is introduced and details regarding principles of operation are provided. Two promising medical applications of THz imaging are presented: skin burns and cornea. For burns, images of second degree, partial thickness burns were obtained in rat models in vivo over an 8 hour period. These images clearly show the formation and progression of edema in and around the burn wound area. For cornea, experimental data measuring the hydration of ex vivo porcine cornea under drying is presented demonstrating utility in ophthalmologic applications.