THz time domain spectroscopy of biomolecular conformational modes

Characteristic fingerprint spectrum of α-synuclein mutants on terahertz time-domain spectroscopy

α-Synuclein, a presynaptic neuronal protein encoded by the SNCA gene, is involved in the pathogenesis of Parkinson's disease. Point mutations and multiplications of α-synuclein (A30P and A53T) are correlated with early-onset Parkinson's disease characterized by rapid progression and poor prognosis. Currently, the clinical identification of SNCA variants, especially disease-related A30P and A53T mutants, remains challenging and also time consuming. This study aimed to develop a novel label-free detection method for distinguishing the SNCA mutants using transmission terahertz (THz) time-domain spectroscopy. The protein was spin-coated onto the quartz to form a thin film, which was measured using THz time-domain spectroscopy. The spectral characteristics of THz broadband pulse waves of α-synuclein protein variants (SNCA wild type, A30P, and A53T) at different frequencies were analyzed via Fourier transform. The amplitude A intensity (AWT, AA30P, and AA53T) and peak occurrence time in THz time-domain spectroscopy sensitively distinguished the three protein variants. The phase φ difference in THz frequency domain followed the trend of φWT > φA30P > φA53T. There was a significant difference in THz frequency amplitude A' corresponding to the frequency ranging from 0.4 to 0.66 THz (A'A53T > A'A30P > A'WT). At a frequency of 0.4-0.6 THz, the transmission T of THz waves distinguished three variants (TA53T > TA30P > TWT), whereas there was no difference in the transmission T at 0.66 THz. The SNCA wild-type protein and two mutant variants (A30P and A53T) had distinct characteristic fingerprint spectra on THz time-domain spectroscopy. This novel label-free detection method has great potential for the differential diagnosis of Parkinson's disease subtypes.

Breaking the limitations with sparse inputs by variational frameworks (BLIss) in terahertz super-resolution 3D reconstruction

Data acquisition, image processing, and image quality are the long-lasting issues for terahertz (THz) 3D reconstructed imaging. Existing methods are primarily designed for 2D scenarios, given the challenges associated with obtaining super-resolution (SR) data and the absence of an efficient SR 3D reconstruction framework in conventional computed tomography (CT). Here, we demonstrate BLIss, a new approach for THz SR 3D reconstruction with sparse 2D data input. BLIss seamlessly integrates conventional CT techniques and variational framework with the core of the adapted Euler-Elastica-based model. The quantitative 3D image evaluation metrics, including the standard deviation of Gaussian, mean curvatures, and the multi-scale structural similarity index measure (MS-SSIM), validate the superior smoothness and fidelity achieved with our variational framework approach compared with conventional THz CT modal. Beyond its contributions to advancing THz SR 3D reconstruction, BLIss demonstrates potential applicability in other imaging modalities, such as X-ray and MRI. This suggests extensive impacts on the broader field of imaging applications.

Harmonic and anharmonic studies on THz spectra of two vanillin polymorphs

Polymorphism commonly exists in organic molecular crystals. The fingerprint features in low-frequency vibrational range are important information reflecting different intermolecular interactions of polymorphs. Interpreting these features is very helpful to understand vibrational property of polymorphs and reveal the thermodynamic stability. In this work, the low-frequency vibrations of form I and II of vanillin are investigated using terahertz time-domain spectroscopy. Static DFT calculation and ab initio molecular dynamics (AIMD) are employed to interpret their low-frequency vibrations of both forms in harmonic and anharmonic ways, respectively. Their low-frequency vibration characteristics in harmonic calculations are discussed, and anharmonic mode couplings between OH bond stretch and the stretching and bending motion of hydrogen bonds are uncovered. Moreover, the thermodynamic energies including electronic potential energy and vibrational/kinetic energy arising from nuclear motions are calculated. The result reveals that the stability order of the two forms is mainly dependent on their electric potential energy difference.

Study of low-frequency spectroscopic characteristics of γ-aminobutyric acid with THz and low-wavenumber Raman spectroscopy

γ-aminobutyric (GABA) is the most important inhibitory neurotransmitier in vertebrate central nervous systems. The content level of GABA is related to the different degree of malignancy gliomas. Thus, it can be considered a promising glioma biomarker. In this paper, the spectroscopic properties of GABA have been characterized by combining the THz spectroscopy with low-wavenumber Raman spectroscopy. The experimental results showed that, GABA exhibited three absorption peaks and three refractive index peaks in the range of 0.6-2.1 THz. The limit of detection can reach up to 0.428 % based on the absorption coefficient at the peak of 2.04 THz. Moreover, the low-wavenumber Raman spectrum of GABA showed seven characteristic peaks at 41.0, 50.8, 58.8, 77.2, 98.8, 115.6, 141.2 cm-1 in 0-150 cm-1 region. Moreover, the THz and low-wavenumber theoretical spectra of GABA were simulated with solid-state density function theory, respectively. The calculated results were in good agreement with the experimental observations. On the basis of calculated result, the vibrational motions of each THz and Raman characteristic modes were quantitatively decomposed by analytical mode-decoupling method, where the contribution percentages of external translation, external librations and intramolecular vibration of each vibration modes were analyzed Furthermore, the low-frequency characteristics of GABA was analyzed by combining the THz and low-wavenumber Raman spectroscopy. It is beneficial for the structural information analysis and quantitative identification of biomarker GABA in early stage diagnosis of glioma.

Sub-THz acoustic excitation of protein motion

The application of terahertz radiation has been shown to affect both protein structure and cellular function. As the key to such structural changes lies in the dynamic response of a protein, we focus on the susceptibility of the protein's internal dynamics to mechanical stress induced by acoustic pressure waves. We use the open-boundary molecular dynamics method, which allows us to simulate the protein exposed to acoustic waves. By analyzing the dynamic fluctuations of the protein subunits, we demonstrate that the protein is highly susceptible to acoustic waves with frequencies corresponding to those of the internal protein vibrations. This is confirmed by changes in the compactness of the protein structure. As the amplitude of the pressure wave increases, even larger deviations from average positions and larger changes in protein compactness are observed. Furthermore, performing the mode-projection analysis, we show that the breathing-like character of collective modes is enhanced at frequencies corresponding to those used to excite the protein.

Prediction of IDH mutation status of glioma based on terahertz spectral data

Gliomas are the most common type of primary tumor in the central nervous system in adults. Isocitrate dehydrogenase (IDH) mutation status is an important molecular biomarker for adult diffuse gliomas. In this study, we were aiming to predict IDH mutation status based on terahertz time-domain spectroscopy technology. Ninety-two frozen sections of glioma tissue from nine patients were included, and terahertz spectroscopy data were obtained. Through Least Absolute Shrinkage and Selection Operator (LASSO), Principal component analysis (PCA), and Random forest (RF) algorithms, a predictive model for predicting IDH mutation status in gliomas was established based on the terahertz spectroscopy dataset with an AUC of 0.844. These results indicate that gliomas with different IDH mutation status have different terahertz spectral features, and the use of terahertz spectroscopy can establish a predictive model of IDH mutation status, providing a new way for glioma research.

Specific detection of n-propanol gas via terahertz metasurface sensor modified by molecularly imprinted polymer

As an organic substance, n-propanol gas has been paid attention to in environmental monitoring and exhalation of lung cancer patient. In this paper a rapid detection method for n-propanol gas is developed based on molecularly imprinted polymers (MIP) and terahertz (THz) metasurface sensors. We first prepared a MIP suitable for detecting the n-propanol gas. And then the n-propanol MIP was modified to the THz metasurface sensor for detecting the n-propanol gas. Since the MIP adsorbed with n-propanol changes the dielectric environment of the sensor, the resonance frequency of the sensor also change. So we based on the n-propanol concentration was analyzed according to the change in resonance frequency. The experimental results showed that the sensor can effectively detect the n-propanol concentration in the range of 50-500 ppm (parts per million). In addition, we also verified the specificity and repeatability of the sensor. This work provides a new idea and method for the sensitive and specific detection of n-propanol gas.

Frequency-domain terahertz spectroscopy using long-carrier-lifetime photoconductive antennas

We present a telecommunication-compatible frequency-domain terahertz spectroscopy system realized by novel photoconductive antennas without using short-carrier-lifetime photoconductors. Built on a high-mobility InGaAs photoactive layer, these photoconductive antennas are designed with plasmonics-enhanced contact electrodes to achieve highly confined optical generation near the metal/semiconductor surface, which offers ultrafast photocarrier transport and, hence, efficient continuous-wave terahertz operation including both generation and detection. Consequently, using two plasmonic photoconductive antennas as a terahertz source and a terahertz detector, we successfully demonstrate frequency-domain spectroscopy with a dynamic range more than 95 dB and an operation bandwidth of 2.5 THz. Moreover, this novel approach to terahertz antenna design opens up a wide range of new possibilities for many different semiconductors and optical excitation wavelengths to be utilized, therefore bypassing short-carrier-lifetime photoconductors with limited availability.

Incoherent Neutron Scattering and Terahertz Time-Domain Spectroscopy on Protein and Hydration Water

Incoherent inelastic and quasi-elastic neutron scattering (INS) and terahertz time-domain spectroscopy (THz-TDS) are spectroscopy methods that directly detect molecular dynamics, with an overlap in the measured energy regions of each method. Due to the different characteristics of their probes (i.e., neutron and light), the information obtained and the sample conditions suitable for each method differ. In this review, we introduce the differences in the quantum beam properties of the two methods and their associated advantages and disadvantages in molecular spectroscopy. Neutrons are scattered via interaction with nuclei; one characteristic of neutron scattering is a large incoherent scattering cross-section of a hydrogen atom. INS records the auto-correlation functions of atomic positions. By using the difference in neutron scattering cross-sections of isotopes in multi-component systems, some molecules can be selectively observed. In contrast, THz-TDS observes the cross-correlation function of dipole moments. In water-containing biomolecular samples, the absorption of water molecules is particularly large. While INS requires large-scale experimental facilities, such as accelerators and nuclear reactors, THz-TDS can be performed at the laboratory level. In the analysis of water molecule dynamics, INS is primarily sensitive to translational diffusion motion, while THz-TDS observes rotational motion in the spectrum. The two techniques are complementary in many respects, and a combination of the two is very useful in analyzing the dynamics of biomolecules and hydration water.

Biomedical applications of terahertz spectra in clinical and molecular pathology of human glioma

Gliomas are the most common type of primary tumor originating in the central nervous system of adults. Tumor histological type, pathological grade, and molecular pathology are significant prognosis and predictive factors. In this study, we were aiming to predict histological type and molecular pathological features based on terahertz time-domain spectroscopy technology. Nine gliomas with different grades, one meningioma, and one lymphoma were enrolled. There were significant differences in terahertz absorption coefficient between normal brain tissue, tumoral-periphery, and tumoral-center tissue in specific frequency bands (0.2-1.4 THz). Histological type, pathological grade, and glioma-specific biomarkers were closely related to the terahertz absorption coefficient in both tumoral-periphery and tumoral-center tissues. Interestingly, tumoral-periphery showed more obvious differences than tumoral-center tissues in almost all aspects. All the results show that the terahertz technology has potential application value in the intraoperative real-time glioma recognition and diagnosis of glioma histological and molecular pathological features.

Quantitative Measurements of DP in Cellulose Paper Based on Terahertz Spectroscopy

The power transformer is vital to the reliability of the power grid which is most commonly insulated with Kraft paper and immersed in mineral oil, among which the aged state of the paper is mainly correlated to the operating life of the transformer. Degree of polymerization (DP) is a direct parameter to assess the aged condition of insulating paper, but existing DP measurement by viscosity methods are destructive and complicated. In this paper, terahertz time-domain spectroscopy (THz-TDS) was introduced to reach rapid, non-destructive detection of the DP of insulating paper. The absorption spectra of insulating paper show that characteristic peak regions at 1.8 and 2.23 THz both exhibit a log-linear quantitative relationship with DP, and their universalities are confirmed by conducting the above relationship on different types of insulating paper. Fourier transform infrared spectroscopy (FTIR) analysis and molecular dynamics modeling further revealed that 1.8 and 2.23 THz were favorably associated with the growth of water-cellulose hydrogen bond strength and amorphous cellulose, respectively. This paper demonstrates the viability of applying THz-TDS to the non-destructive detection of DP in insulating paper and assigned the vibration modes of the characteristic absorption peaks.

Terahertz Spectroscopy and Ab-Initio Vibrational Analysis of Two Crystalline Forms of 5,5-Diethylbarbituric Acid

Terahertz (THz) absorption spectra of the two crystalline forms of 5,5-diethylbarbituric acid (barbital) were measured with THz time-domain spectroscopy (THz-TDS). The spectra exhibited the dissimilarity between the two forms. Identification of the polymorphs and quantitative analysis of the two forms are possible by THz-TDS. Further, we performed ab-initio calculations of the vibrational modes considering the crystal structures of the two forms, and the results were in good agreement with the experimental data. We discuss the difference between the THz absorption spectra of the two forms.

Photoactive terahertz metasurfaces for ultrafast switchable sensing of colorectal cells

Metasurfaces with a strongly enhanced local field are envisioned as a powerful platform for ultrasensitive optical sensors to significantly amplify imperceptible differences between compatible bioanalytes. Through the use of phototunable silicon-based terahertz (THz) metasurfaces, we experimentally demonstrate ultrafast switchable sensing functions. It is found that the THz responses of the coupled-resonances in the metasurfaces shift from Lorentz-lattice mode to electromagnetism-induced transparency (EIT) mode under optical pumping within an ultrashort time of 32 ps, enabling an ultrafast sensitive sensor. For the Lorentz-lattice mode, the THz time-domain signal directly shows a highly sensitive response to detect tiny analytes without extra Fourier transformation as the mismatch between the two modes increases. Once the metasurfaces are switched to the EIT mode, the silicon-metal hybrid structure supports frequency-domain sensing ability due to strong field confinement with a sensitivity of 118.4 GHz/RIU. Both of the sensing configurations contribute to more subtle information and guarantee the accuracy of the sensor performance. Combined with the aforementioned advantages, the proposed metasurfaces have successfully identified colorectal cells between normal, adenoma, and cancer states in experiments. This work furnishes a new paradigm of constructing reliable and flexible metasurface sensors and can be extended to other optics applications.

Calibration-free, high-precision, and robust terahertz ultrafast metasurfaces for monitoring gastric cancers

Optical sensors, with great potential to convert invisible bioanalytical response into readable information, have been envisioned as a powerful platform for biological analysis and early diagnosis of diseases. However, the current extraction of sensing data is basically processed via a series of complicated and time-consuming calibrations between samples and reference, which inevitably introduce extra measurement errors and potentially annihilate small intrinsic responses. Here, we have proposed and experimentally demonstrated a calibration-free sensor for achieving high-precision biosensing detection, based on an optically controlled terahertz (THz) ultrafast metasurface. Photoexcitation of the silicon bridge enables the resonant frequency shifting from 1.385 to 0.825 THz and reaches the maximal phase variation up to 50° at 1.11 THz. The typical environmental measurement errors are completely eliminated in theory by normalizing the Fourier-transformed transmission spectra between ultrashort time delays of 37 ps, resulting in an extremely robust sensing device for monitoring the cancerous process of gastric cells. We believe that our calibration-free sensors with high precision and robust advantages can extend their implementation to study ultrafast biological dynamics and may inspire considerable innovations in the field of medical devices with nondestructive detection.

Terahertz polarization sensing for protein concentration and a crystallization process on a reflective metasurface

Terahertz (THz) waves have attracted much attention in the field of biosensing due to advantages including non-destructiveness, being label-free, and high-sensitivity detection. Here we have experimentally demonstrated a THz polarization sensing method based on reflective metasurface sensors for detecting concentrations of protein solutions and their crystallization process. The protein with varying concentrations has been detected by five different polarization parameters, which show different spectral responses and sensing sensitivities. The sensing accuracy can reach the order of ng/mm². Furthermore, the crystallization process of the protein sample from the dissolved state to the crystalline has been dynamically measured by polarization sensing, of which the highest sensitivity can reach 0.67 °/%. Therefore, this new sensing platform can have broad development prospects in the trace matter detection of the biological sample.

Terahertz Spectroscopic Analysis in Protein Dynamics: Current Status

Proteins play a key role in living organisms. The study of proteins and their dynamics provides information about their functionality, catalysis and potential alterations towards pathological diseases. Several techniques are used for studying protein dynamics, e.g., magnetic resonance, fluorescence imaging techniques, mid-infrared spectroscopy and biochemical assays. Spectroscopic analysis, based on the use of terahertz (THz) radiation with frequencies between 0.1 and 15 THz (3–500 cm−1), was underestimated by the biochemical community. In recent years, however, the potential of THz spectroscopy in the analysis of both simple structures, such as polypeptide molecules, and complex structures, such as protein complexes, has been demonstrated. The THz absorption spectrum provides some information on proteins: for small molecules the THz spectrum is dominated by individual modes related to the presence of hydrogen bonds. For peptides, the spectral information concerns their secondary structure, while for complex proteins such as globular proteins and viral glycoproteins, spectra also provide information on collective modes. In this short review, we discuss the results obtained by THz spectroscopy in the protein dynamics investigations. In particular, we will illustrate advantages and applications of THz spectroscopy, pointing out the complementary information it may provide.

Terahertz circular polarization sensing for protein denaturation based on a twisted dual-layer metasurface

Protein denaturation has very important research value in nutrition, biomedicine, and the food industry, which is caused by the changes in the molecular structure of the protein. Since the collective vibrational and torsional modes of protein molecules are within the terahertz (THz) frequency range, THz spectroscopy can characterize the protein denaturation with several advantages of non-contact, label-free, real-time, and non-destructive. Therefore, we proposed a reflective THz time-domain polarization spectroscopy sensing method, and use a flexible twisted dual-layer metasurface film as a sensor to realize the thermal denaturation sensing, concentration sensing, and types identification of protein aqueous solutions. The experiment tested three proteins (bovine serum albumin, whey protein, and ovalbumin), and the results show that: for the thermal denaturation sensing, its detection sensitivity can reach 6.30 dB/% and the detection accuracy is 0.77%; for the concentration sensing, the detection sensitivity and detection accuracy reach 52.9 dB·mL/g and 3.6·10^-5 g/mL, respectively; in addition, different protein types can be distinguished by the difference of the circular polarization spectra.

A Review of Feasible Applications of THz Waves in Medical Diagnostics and Treatments

Introduction: Terahertz (THz) waves with frequencies in the range of 0.1 to 10 THz are electromagnetic radiation with growing applications in various fields of science and technology. Attractive features of this radiation have brought out many novel possibilities for medical diagnostics and treatments with considerable advantages compared to other conventional methods. Methods: In this paper, we present a review of more recent reports on practical applications of THz radiation for diagnostic, biosensing and clinical treatments. The review includes the diagnosis of breast, skin, mouth, cervical, lungs, small intestine, prostate, colon, and stomach cancers, the evaluation of biomolecules, the detection of genetic mutations, the determination of burn depth, the diagnosis of tooth decay, diabetes, and emotional-psychological states, the evaluation of corneal water to diagnose visual diseases, and wound healing monitoring. Further, it embraces the use of THz therapy in reducing the size of the tumor, treating skin cancer, and healing burn wounds, cardiovascular disease, corneal epithelium, angina, and THz heating. Results: This review has emphasized the capabilities of THz waves as a novel tool for future clinical diagnostics and treatments. Conclusion: The paper provides a comprehensive understanding of the feasible potential application of THz waves for clinical purposes and its advantages in comparison with other conventional tools.

Optically Controlled Ultrafast Terahertz Metadevices with Ultralow Pump Threshold

Arming metasurface with active materials furnishes a feasible solution to dynamically control over terahertz (THz) waves, which is extremely significant for the realization of upcoming sixth generation telecommunications. However, the present active materials are mainly limited to single external driving field, hindering the capability of metasurface for flexible manipulation of THz waves. Besides, less attention has been paid to the energy question how to significantly reduce the pump threshold for achieving the desired function. Here, a germanium (Ge) hybrid Fano metasurface under dual-stimulus control is experimentally demonstrated. Photoexcitation of Ge thin film enables 100% modulation depth of Fano resonance and ultrafast switching time within 10 ps. By adding current-bias, the pump threshold to modulate the metasurface is greatly reduced from 1600 to 200 µJ cm^-2 . Different from the optical modulation independent of film thickness, it is found that the current function is in proportion with the thickness of Ge thin film. Moreover, it is demonstrated that compared to the single optical-stimulus, the THz amplitude modulation is increased by 56.3% under dual-stimulus function. This work naturally improves the flexibility and practicality of Ge-based metadevice and inspires more innovations to boost the development of switchable sensing, lasing spacer, and nonlinear systems.

Low-Frequency Harmonic Perturbations Drive Protein Conformational Changes

Protein dynamics has been investigated since almost half a century, as it is believed to constitute the fundamental connection between structure and function. Elastic network models (ENMs) have been widely used to predict protein dynamics, flexibility and the biological mechanism, from which remarkable results have been found regarding the prediction of protein conformational changes. Starting from the knowledge of the reference structure only, these conformational changes have been usually predicted either by looking at the individual mode shapes of vibrations (i.e., by considering the free vibrations of the ENM) or by applying static perturbations to the protein network (i.e., by considering a linear response theory). In this paper, we put together the two previous approaches and evaluate the complete protein response under the application of dynamic perturbations. Harmonic forces with random directions are applied to the protein ENM, which are meant to simulate the single frequency-dependent components of the collisions of the surrounding particles, and the protein response is computed by solving the dynamic equations in the underdamped regime, where mass, viscous damping and elastic stiffness contributions are explicitly taken into account. The obtained motion is investigated both in the coordinate space and in the sub-space of principal components (PCs). The results show that the application of perturbations in the low-frequency range is able to drive the protein conformational change, leading to remarkably high values of direction similarity. Eventually, this suggests that protein conformational change might be triggered by external collisions and favored by the inherent low-frequency dynamics of the protein structure.

Hydration Shells of DPPC Liposomes from the Point of View of Terahertz Time-Domain Spectroscopy

Analysis of structural and dynamic properties of water in suspensions of liposomes composed from 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) in three phase states (gel, rippled gel, liquid crystalline phase) by means of terahertz time-domain spectroscopy in 0.3-3.3 THz range was conducted in the current work. Fraction of free water molecules in DPPC liposome suspension was shown to decrease with temperature (compared to the analogous aqueous solution without liposomes), and intermolecular water binding was enhanced. The most crucial changes occur during gel-rippled gel phase transition (pretransition): at temperatures below pretransition point, liposomes alleviate water binding degree, while at temperatures above the transition point, they enhance water binding. This study has demonstrated the high information content of the terahertz time-domain spectroscopy method for exploring the hydration properties of phospholipids in water.

Experimental measurement of the wake field in a plasma filament created by a single-color ultrafast laser pulse

A laser plasma wake field in a single-color femtosecond laser filament determines the acceleration of ionized electrons, which affects the intensity and bandwidth of the emitted terahertz wave and is important for understanding the fundamental nonlinear process of THz generation. Since the THz wave generated by a laser wake field is extremely small and easily hidden by other THz generation mechanisms, no method exists to measure this wake field directly. In this paper, a simple and stable method for determining the amplitude of the laser plasma wake field is presented. Based on the cancellation of a positive laser plasma wake field and an external negative electric field, the "zero point" of the intensity of the generated THz wave at some frequency can be used to determine the exact amplitude of the corresponding laser plasma wake field. This finding opens an avenue toward the clarification of ultrafast electronic dynamic processes in laser-induced plasmas.

Kinetic coherence underlies the dynamics of disordered proteins

The dynamics of two proteins of similar size, the globular lysozyme and the intrinsically disordered Huntingtin interacting protein, has been simulated in three states resembling a globule, a pre-molten globule, and a molten globule. A coherence time τ has been defined, measuring the delay in the display of a stochastic behaviour after a perturbation of the system. This time has been computed for two sets of collective variables: the projection of the phase point onto the positions and momenta subspaces (τ_r and τ_p), and the principal components (PCs) of positions q and momenta π produced by a covariance analysis in these subspaces (τ_q and τ_π). In all states τ_p ≈ 3.5τ_r, and τ_π ≈ 3.5τ_q. The coherence times of individual PCs, τ^(l)_q and τ^(l)_π, have also been computed, and τ^(l)_π > τ^(l)_q in all states. The prevalence of τ_p over τ_r, or of τ_π over τ_q, drives the dynamics of the protein over a time range of ≈1–2 ps; moreover, a hidden synchronism appears to raise the momenta subspace's coherence above that of its individual PCs. In the transition of lysozyme to the molten globule the τ^(l)_q decrease but, unexpectedly, the τ^(l)_π increase; after this transition τ_p ≈ 5τ_r and τ_π ≈ 5τ_q. A gain of kinetic coherence accompanies thus the loss of structural coherence caused by the denaturation of the protein in the transition from globule to molten globule. The increase of the τ^(l)_π does not take place in the analogous transition of the Huntingtin protein. These results are compared with those of a similar analysis performed on three pseudo-proteins designed by scrambling the primary sequence of the Huntingtin interacting protein, and on two oligopeptides. The hidden synchronism appears to be a generic property of these polypeptides. The τ^(l)_π spectrum is similar in denaturated and in intrinsically disordered biomolecules; but the gain of kinetic coherence as a result of denaturation seems to be a specific property of the biologically functional lysozyme.

In the phase space of a globular or intrinsically disordered protein, the momenta's dynamics is less chaotic than the coordinates' dynamics. When a protein is denaturated, a gain in kinetic coherence accompanies the loss of structural coherence.

Nanoantenna enhanced terahertz interaction of biomolecules

Terahertz time-domain spectroscopy (THz-TDS) is a non-invasive, non-contact and label-free technique for biological and chemical sensing as THz-spectra are less energetic and lie in the characteristic vibration frequency regime of proteins and DNA molecules. However, THz-TDS is less sensitive for the detection of micro-organisms of size equal to or less than λ/100 (where, λ is the wavelength of the incident THz wave), and molecules in extremely low concentration solutions (like, a few femtomolar). After successful high-throughput fabrication of nanostructures, nanoantennas were found to be indispensable in enhancing the sensitivity of conventional THz-TDS. These nanostructures lead to strong THz field enhancement when in resonance with the absorption spectrum of absorptive molecules, causing significant changes in the magnitude of the transmission spectrum, therefore, enhancing the sensitivity and allowing the detection of molecules and biomaterials in extremely low concentration solutions. Herein, we review the recent developments in ultra-sensitive and selective nanogap biosensors. We have also provided an in-depth review of various high-throughput nanofabrication techniques. We also discussed the physics behind the field enhancements in the sub-skin depth as well as sub-nanometer sized nanogaps. We introduce finite-difference time-domain (FDTD) and molecular dynamics (MD) simulation tools to study THz biomolecular interactions. Finally, we provide a comprehensive account of nanoantenna enhanced sensing of viruses (like, H1N1) and biomolecules such as artificial sweeteners which are addictive and carcinogenic.

Near-field THz micropolarimetry

We introduce a method for rapid determination of anisotropic terahertz absorption with sub micron resolution and high spectral integrity in the terahertz range. The method is ideal for microscopic and environmentally sensitive materials such as 2-D materials and protein crystals where the anisotropic absorption is critical to understanding underlying physics. We introduce the idea of using an iso-response relationship between the THz polarization and electro optic probe polarization to enable stationary sample polarization measurements covering a full 2π polarization dependence measurement.

Assessment of the VDW interaction converting DMAPS from the thermal-motion form to the hydrogen-bonded form

Assessment of van der Waals (VDW) interactions is fundamental to all of the central quest of structure that regulates the biological function. VDW interactions contributing to intramolecular weak hydrogen bonding are regarded as an important force to regulate the thermal stimuli-sensitive function of sulfobetaine methacrylate, DMAPS. We present here the conversion from the thermal-motion form at room temperature to the weak-hydrogen-bonded form against thermal motion as a terahertz spectral change with a definite isosbestic point from an absorption peak of one form to the other. Vibrational absorptions are used as a probe for assessing VDW interactions in conjunction with highly reliable and well-established density functional theory (DFT) calculations for analysis. Complicated spectral features and uncertain conformations of DMAPS in the amorphous state are clearly resolved under the polarizable continuum model and the dispersion correction for the pure DFT calculations.

Mitigating the effects of granular scattering using cepstrum analysis in terahertz time-domain spectral imaging

Terahertz (THz) imaging is a widely used technique in the study and detection of many chemicals and biomolecules in polycrystalline form because the spectral absorption signatures of these target materials often lie in the THz frequencies. When the size of dielectric grain boundaries are comparable to the THz wavelengths, spectral features can be obscured due to electromagnetic scattering. In this study, we first investigate this granular scattering effect in identification of chemicals with THz spectral absorption features. We then will propose a signal processing technique in the so-called "quefrency" domain to improve the ability to resolve these spectral features in the diffuse scattered THz images. We created a pellet with α-lactose monohydrate and riboflavin, two biologically significant materials with well-known vibrational spectral resonances, and buried the pellet in a highly scattering medium. THz transmission measurements were taken at all angles covering the half focal plane. We show that, while spectral features of lactose and riboflavin cannot be distinguished in the scattered image, application of cepstrum filtering can mitigate these scattering effects. By employing our quefrency-domain signal processing technique, we were able to unambiguously detect the dielectric resonance of lactose in the diffused scattering geometries. Finally we will discuss the limitation of the new proposed technique in spectral identification of chemicals.

Electric and Magnetic Hotspots via Hollow InSb Microspheres for Enhanced Terahertz Spectroscopy

We study electric and magnetic hotspots in the gap between hollow InSb microspheres forming dimers and trimers. The outer radius, core volume fraction, distance, and temperature of the microspheres can be chosen to achieve field enhancement at a certain frequency corresponding to the transition between energy levels of a molecule placed in the gap. For example, utilizing 80 μm radius spheres at a gap of 2 μm held at a temperature of 295 K, allow electric field intensity enhancements of 10-2880 and magnetic field intensity enhancements of 3-61 in the frequency window 0.35-1.50 THz. The core volume fraction and the ambient temperature affect the enhancements, particularly in the frequency window 1.5-2 THz. Electric and magnetic hotspots are promising for THz absorption and circular dichroism spectroscopy.

Calculated Terahertz Spectra of Glycine Oligopeptide Solutions Confined in Carbon Nanotubes

To reduce the intense terahertz (THz) wave absorption of water and increase the signal-to-noise ratio, the THz spectroscopy detection of biomolecules usually operates using the nanofluidic channel technologies in practice. The effects of confinement due to the existence of nanofluidic channels on the conformation and dynamics of biomolecules are well known. However, studies of confinement effects on the THz spectra of biomolecules are still not clear. In this work, extensive all-atom molecular dynamics simulations are performed to investigate the THz spectra of the glycine oligopeptide solutions in free and confined environments. THz spectra of the oligopeptide solutions confined in carbon nanotubes (CNTs) with different radii are calculated and compared. Results indicate that with the increase of the degree of confinement (the reverse of the radius of CNT), the THz absorption coefficient decreases monotonically. By analyzing the diffusion coefficient and dielectric relaxation dynamics, the hydrogen bond life, and the vibration density of the state of the water molecules in free solution and in CNTs, we conclude that the confinement effects on the THz spectra of biomolecule solutions are mainly to slow down the dynamics of water molecules and hence to reduce the THz absorption of the whole solution in confined environments.

A dual-port THz Time Domain Spectroscopy System optimized for recovery of a sample's Jones matrix

We describe the design, build and characterization of a novel two-output port configuration for a THz-Time Domain Spectroscopy (TDS) system. By introducing a tilted THz ultra-broadband polarizer, we split the THz beam in two orthogonal polarization detector branches. The probe laser is similarly split (with an optical polarizer) replicating the detection chain to obtain two independent orthogonal polarization detection units. We describe the system's performance highlighting some of the advantages of this system in one of its two modes of operation: optimized polarimetry for Jones matrix measurements. A bi-refringent sapphire standard was measured to confirm its capabilities and assess the performance of the system showing good agreement with existing literature data.

Metasurfaces for Advanced Sensing and Diagnostics

Interest in sensors and their applications is rapidly evolving, mainly driven by the huge demand of technologies whose ultimate purpose is to improve and enhance health and safety. Different electromagnetic technologies have been recently used and achieved good performances. Despite the plethora of literature, limitations are still present: limited response control, narrow bandwidth, and large dimensions. MetaSurfaces, artificial 2D materials with peculiar electromagnetic properties, can help to overcome such issues. In this paper, a generic tool to model, design, and manufacture MetaSurface sensors is developed. First, their properties are evaluated in terms of impedance and constitutive parameters. Then, they are linked to the structure physical dimensions. Finally, the proposed method is applied to realize devices for advanced sensing and medical diagnostic applications: glucose measurements, cancer stage detection, water content recognition, and blood oxygen level analysis. The proposed method paves a new way to realize sensors and control their properties at will. Most importantly, it has great potential to be used for many other practical applications, beyond sensing and diagnostics.

Broadband terahertz recognizing conformational characteristics of a significant neurotransmitter γ-aminobutyric acid

γ-Aminobutyric acid (GABA) is the chief inhibitory neurotransmitter in the central nervous system, its conformational behavior is critical for selective biological functions and the process of signal transmission. Although this neuroactive molecule has been extensively studied, its vibrational properties related to the conformation and intermolecular interactions in the terahertz (THz) band have not been identified experimentally yet. In this study, we applied a broadband THz time-domain spectroscopy (THz-TDS) system from 0.5 to 18 THz to characterize a unique THz fingerprint of GABA. The density functional theory calculation results agree well with the THz experimental spectrum. The study shows that the vibrational modes of GABA at 1.15 and 1.39 THz originate from distinct collective vibrations. The absorptions at the higher THz frequencies also carry part of collective vibrations, but more reflect the specific and local vibrational information, including the skeleton deformation and the rocking of the functional groups, which are closely associated with the conformation and flexibility of GABA. This study may help to understand the conformational transitions of neurotransmitter molecules and the resonant response to THz waves.

γ-Aminobutyric acid (GABA) is the chief inhibitory neurotransmitter in the central nervous system, its conformational behavior is critical for selective biological functions and the process of signal transmission.

Anticancer drug impact on DNA – a study by neutron spectroscopy coupled with synchrotron-based FTIR and EXAFS

Complementary information on drug–DNA interplay has been achieved for Pt/Pd anticancer agents, by a combined QENS, SR-FTIR-ATR and EXAFS approach.

Nanostructure-Enhanced Photoconductive Terahertz Emission and Detection

Photoconductive antennas are commonly used for terahertz wave generation and detection. However, their relatively low radiation power and detection sensitivity often place limitations on the signal-to-noise ratio and operation bandwidth of terahertz imaging and spectroscopy systems. Several different techniques are attempted to address these limitations. The most promising ones take advantage of the unique tools provided by nanotechnology. In this review, the recent nanotechnology-enabled advances in photoconductive antennas, which use nanostructures, such as optical nanoantennas, plasmonic structures, and optical nanocavities, to increase the interaction of the optical pump beam with the photoconductive semiconductor, are discussed. All of these techniques are experimentally demonstrated to be efficient tools for enhancing the performance of photoconductive antennas for terahertz wave generation and detection.

Terahertz-infrared spectroscopy of Shewanella oneidensis MR-1 extracellular matrix

Employing optical spectroscopy we have performed a comparative study of the dielectric response of extracellular matrix and filaments of electrogenic bacteria Shewanella oneidensis MR-1, cytochrome c, and bovine serum albumin. Combining infrared transmission measurements on thin layers with data of the terahertz spectra, we obtain the dielectric permittivity and AC conductivity spectra of the materials in a broad frequency band from a few cm-1 up to 7000 cm-1 in the temperature range from 5 to 300 K. Strong absorption bands are observed in the three materials that cover the range from 10 to 300 cm-1 and mainly determine the terahertz absorption. When cooled down to liquid helium temperatures, the bands in Shewanella oneidensis MR-1 and cytochrome c reveal a distinct fine structure. In all three materials, we identify the presence of liquid bound water in the form of librational and translational absorption bands at ≈ 200 and ≈ 600 cm-1, respectively. The sharp excitations seen above 1000 cm-1 are assigned to intramolecular vibrations.

High-Precision Megahertz-to-Terahertz Dielectric Spectroscopy of Protein Collective Motions and Hydration Dynamics

The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus crucial to uncover the mystery of the hydration structure and dynamics as well as their coupling to collective motions of proteins in aqueous solutions. Here, we report dielectric properties of aqueous bovine serum albumin protein solutions as a model system using an extremely sensitive dielectric spectrometer with frequencies spanning from megahertz to terahertz. The dielectric relaxation spectra reveal several polarization mechanisms at the molecular level with different time constants and dielectric strengths, reflecting the complexity of protein-water interactions. Combining the effective-medium approximation and molecular dynamics simulations, we have determined collective vibrational modes at terahertz frequencies and the number of water molecules in the tightly bound and loosely bound hydration layers. High-precision measurements of the number of hydration water molecules indicate that the dynamical influence of proteins extends beyond the first solvation layer, to around 7 Å distance from the protein surface, with the largest slowdown arising from water molecules directly hydrogen-bonded to the protein. Our results reveal critical information of protein dynamics and protein-water interfaces, which determine biochemical functions and reactivity of proteins.

Design Considerations for Integration of Terahertz Time-Domain Spectroscopy in Microfluidic Platforms

Microfluidic platforms have received much attention in recent years. In particular, there is interest in combining spectroscopy with microfluidic platforms. This work investigates the integration of microfluidic platforms and terahertz time-domain spectroscopy (THz-TDS) systems. A semiclassical computational model is used to simulate the emission of THz radiation from a GaAs photoconductive THz emitter. This model incorporates white noise with increasing noise amplitude (corresponding to decreasing dynamic range values). White noise is selected over other noise due to its contributions in THz-TDS systems. The results from this semiclassical computational model, in combination with defined sample thicknesses, can provide the maximum measurable absorption coefficient for a microfluidic-based THz-TDS system. The maximum measurable frequencies for such systems can be extracted through the relationship between the maximum measurable absorption coefficient and the absorption coefficient for representative biofluids. The sample thickness of the microfluidic platform and the dynamic range of the THz-TDS system play a role in defining the maximum measurable frequency for microfluidic-based THz-TDS systems. The results of this work serve as a design tool for the development of such systems.

High Sensitivity of T-Ray for Thrombus Sensing

Atherosclerotic plaque rupture or erosion and subsequent development of platelet-containing thrombus formation is the fundamental cause of cardiovascular disease, which is the most common cause of death and disability worldwide. Here we show the high sensitivity of 200-270 GHz T-ray to distinguish thrombus formation at its early stage from uncoagulated blood. A clinical observational study was conducted to longitudinally monitor the T-ray absorption constant of ex-vivo human blood during the thrombus formation from 29 subjects. Compared with the control group (28 subjects) with uncoagulated blood samples, our analysis indicates the high sensitivity of 200-270 GHz T-Ray to detect thrombus with a low p-value < 10-5. Further analysis supports the significant role of platelet-activated thrombotic cascade, which modified the solvation dynamics of blood and occurred during the early coagulation stage, on the measured T-Ray absorption change. The ability to sense the thrombus formation at its early stage would hold promise for timely identification of patients at risk of various atherothrombotic disorders and save billions of lives.

Mechanisms and applications of terahertz metamaterial sensing: a review

Terahertz (THz) technology has attracted great worldwide interest and novel high-intensity THz sources and plasmonics are two of the most active fields of recent research. Being situated between infrared light and microwave radiation, the absorption of THz rays in molecular and biomolecular systems is dominated by the excitation of intramolecular and intermolecular vibrations. This indicates that THz technology is an effective tool for sensing applications. However, the low sensitivity of free-space THz detection limits the sensing applications, which gives a great opportunity to metamaterials. Metamaterials are periodic artificial electromagnetic media structured with a size scale smaller than the wavelength of external stimuli. They present localized electric field enhancement and large values of quality factor (Q factor) and show high sensitivity to minor environment changes. In the present work, the mechanism of THz metamaterial sensing and dry sample and microfluidic sensing applications based on metamaterials are introduced. Moreover, new directions of THz metamaterial sensing advancement and introduction of two-dimensional materials and nanoparticles for future THz applications are summarized and discussed.

Hydrogen Bond Network of Water around Protein Investigated with Terahertz and Infrared Spectroscopy

The dynamical and structural properties of water at protein interfaces were characterized on the basis of the broadband complex dielectric constant (0.25 to 400 THz) of albumin aqueous solutions. Our analysis of the dielectric responses between 0.25 and 12 THz first revealed hydration water with retarded reorientational dynamics extending ∼8.5 Å (corresponding to three to four layers) out from the albumin surface. Second, the number of nonhydrogen-bonded water was decreased in the presence of the albumin solute, indicating protein inhibits the fragmentation of the water hydrogen-bond network. Finally, water molecules at the albumin interface were found to form a distorted hydrogen-bond structure due to topological and energetic disorder of the protein surface. In addition, the intramolecular O-H stretching vibration of water (∼100 THz), which is sensitive to hydrogen-bond environment, pointed to a trend that hydration water has a larger population of strongly hydrogen-bonded water molecules compared with that of bulk water. From these experimental results, we concluded that the "strengthened" water hydrogen bonds at the protein interface dynamically slow down the reorientational motion of water and form the less-defective hydrogen-bond network by inhibiting the fragmentation of water-water hydrogen bonds. Nevertheless, such a strengthened water hydrogen-bond network is composed of heterogeneous hydrogen-bond distances and angles, and thus characterized as structurally "distorted."

New Method to Study the Vibrational Modes of Biomolecules in the Terahertz Range Based on a Single-Stage Raman Spectrometer

The low-frequency vibrational (LFV) modes of biomolecules reflect specific intramolecular and intermolecular thermally induced fluctuations that are driven by external perturbations, such as ligand binding, protein interaction, electron transfer, and enzymatic activity. Large efforts have been invested over the years to develop methods to access the LFV modes due to their importance in the studies of the mechanisms and biological functions of biomolecules. Here, we present a method to measure the LFV modes of biomolecules based on Raman spectroscopy that combines volume holographic filters with a single-stage spectrometer, to obtain high signal-to-noise-ratio spectra in short acquisition times. We show that this method enables LFV mode characterization of biomolecules even in a hydrated environment. The measured spectra exhibit distinct features originating from intra- and/or intermolecular collective motion and lattice modes. The observed modes are highly sensitive to the overall structure, size, long-range order, and configuration of the molecules, as well as to their environment. Thus, the LFV Raman spectrum acts as a fingerprint of the molecular structure and conformational state of a biomolecule. The comprehensive method we present here is widely applicable, thus enabling high-throughput study of LFV modes of biomolecules.

Terahertz Frequency Spectroscopy to Determine Cold Shock Protein Stability upon Solvation and Evaporation - A Molecular Dynamics Study

Infrared (IR) and Terahertz (THz) spectroscopy simulations were carried out using CHARMM35b2 to determine protein stability. The stabilities of three bacterial cold shock proteins (Csps) originating from mesophiles, thermophiles and hyper- thermophiles respectively were investigated in this study. The three different Csps were investigated by Normal-Mode analysis and Molecular Dynamics simulation of THz spectra using the Hessian matrix for solvated systems, interpreted in the harmonic approximation at optimum near-melting temperatures of each homologue, by incorporating differences in the hydrous and anhydrous states of the Csps. The results show slight variations in the large scale protein motion. However, the IR spectra of Csps observed at the low frequency saddle surface region, clearly distinguishes the thermophilic and mesophilic proteins based on their stability. Further studies on protein stability employing low-frequency collective modes have the potential to reveal functionally important conformational changes that are biologically significant.

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.

Fingerprints of Conformational States of Human Hsp70 at Sub-THz Frequencies

Large multidomain proteins occur in different conformational states to function. Detection and monitoring of these different structural states are of crucial interest for understanding the mechanics of proteins. Using computational methods, we show that different protein conformational states of the two-domain 70 kDa human Heat-shock protein (hHsp70), with similar vibrational density of states, lead to remarkably different far-IR spectra at acoustical frequencies (ν < 300 GHz). We found that the slow damped motions of the positively charged residues of hHsp70 contribute the most to collective IR active modes at low frequencies (ν < 300 GHz). We predicted that different structural states and functional modes of large proteins, such as hHsp70, might be detected in the sub-THz frequency range by single-molecule spectroscopy similar to the recent extraordinary acoustic Raman spectroscopy (Wheaton S.; Nat. Photonics2015, 9, 68-72).

Theoretical Insights into Sub-Terahertz Acoustic Vibrations of Proteins Measured in Single-Molecule Experiments

Proteins are an important class of nanobioparticles with acoustical modes in the sub-THz frequency range. There is considerable interest to measure and establish the role of these acoustical vibrations for biological function. So far, the technique providing the most detailed information about the acoustical modes of proteins is the very recent Extraordinary Acoustic Raman (EAR) spectroscopy. In this technique, proteins are trapped in nanoholes and excited by two optical lasers of slightly different wavelengths producing an electric field at low frequency (<100 GHz). We demonstrate that the acoustical modes of proteins studied by EAR spectroscopy are both infrared- and Raman-active modes, and we provided interpretation of the spectroscopic fingerprints measured at the single-molecule level. A combination of the present calculations with techniques based on the excitation of a single nanobioparticle by an electric field, such as EAR spectroscopy, should provide a wealth of information on the role of molecular dynamics for biological function.