Dense Spectrum Research Articles

Developments and applications of computational infrared spectroscopy in non-bonded systems: Quantal and classical systems

Infrared (IR) spectroscopy, responding to molecular vibrations, is one of the most important tools in understanding the behavior of molecules. For complex systems, because of the relatively dense spectra lines, it could be very difficult to assign IR spectra merely by experience, an instance of which is non-bonded system. For middle-size system, theory and computation, however, can handle part of this problem by construct the potential energy surfaces (PESs) of system following a nuclear motion calculation classic or quantum mechanically. For large-size non-bonded system, although it is hard to calculate the properties of the whole system directly, by decomposing the system into quasi-isolated parts, the spectra can be calculated from the first principle using some approximations, which belong to the toolchain of computational spectroscopy. In this review, we recall some of these methodology based on perturbation theory. (1) In the research of van der Waals complexes, intramolecular vibrations are separated from intermolecular motion via Born-Oppenheimer approximation and first order Rayleigh-Schrodinger perturbation theory. For the ground and first excited state of the chromophores, rigid body intermolecular PESs are build including the relative orientation of the rigid molecules. Based on the intermolecular PESs, rotation and intermolecular radial stretching are treated using Discrete Variable Representation/Finite Basis Representation (DVR/FBR) fully quantum mechanically. The rovibrational spectra are then obtained by the gap between energy levels and the transition dipole moments. (2) Spectroscopy of quantum clusters, where chromophores molecules are caged in helium or hydrogen molecules solvent, are another important topic where perturbation theory and quantum simulation get involved. As previous systems, accurate two-body intermolecular PESs are also needed. The potential of the system is then represented by the many-body expansion, often truncated at two-body term. Quantum effect of the rigid molecules is simulated by finite temperature Path Integral Monte Carlo (PIMC) method. Worm operator is used to take exchange phenomena of the boson into account. Rotation of the chromophore molecule and the boson exchange were found to be very important in the simulation of quantum clusters. By studying IR spectra of quantum cluster, microscopic superfluidity was discovered and confirmed. (3) In bulk system like solution and biological systems, computation of IR spectra remains a challenge. The birth of quantum vibrational perturbation (QVP) theory gives an opportunity of considering the quantum effect and the chemical environment in the same scheme. Regular molecular dynamics simulation (MD) is executed to deal with the solvent fluctuation, and then quantal molecular vibration of chromophore is calculated via DVR quantum solver based on low dimensional cut of intramolecular vibrational coordinate. At each MD step, the instantaneous vibration frequencies are computed by perturbation theory. This mixed quantum mechanical/classic mechanical, or quasi-classical MD simulation will generate the instantaneous frequencies as function of time. Using line shape theory for quasi-classical MD, the spectra line of such system can be obtained. All three situations rely on perturbation theory more or less, which can be very computationally efficient. Because the main part of the IR transition gap can be corrected by experimental data, these methods can focus on transition frequency shift without considering error canceling artifact. In the future, systems containing stronger secondary bond need more efforts in the development of calculation methodology. Kinetic coupling is also an interesting topic to be developed in the coming days. Besides, the new proceeding in electronic structure theory helps a lot in the computational IR spectroscopy.

Fast neutrino flavor conversion: Roles of dense matter and spectrum crossing

The flavor conversion of a neutrino usually occurs at densities $\lesssim G_F^{-1} \omega$, whether in the ordinary matter or the neutrino medium, and on time/distance scales of order $\omega^{-1}$, where $G_F$ is the Fermi weak coupling constant and $\omega$ is the vacuum oscillation frequency of the neutrino. In 2005 Sawyer and more recently both he and other groups have shown that neutrino flavor conversions can occur on scales much shorter than $\omega^{-1}$ in a very dense, anisotropic neutrino gas such as that in a core-collapse supernova or a binary neutron star merger. It has also been suggested that the fast neutrino flavor conversion require a crossing in the electron lepton number (ELN) angular distribution or spectrum. We study a few simple analytical models with which we elucidate the roles of the dense matter and the ELN spectrum crossing in neutrino fast flavor conversions. We show that a large matter density can induce fast neutrino flavor conversions in certain astrophysical scenarios such as at the early epoch of a core-collapse supernova.

Quantitative estimation of elemental composition employing a synthetic generated spectrum.

Composition of multielement samples is estimated by using a synthetic generated spectrum utilizing a nonlinear fitting routine. By fitting simultaneously a large number of emission lines, the error in the estimation is minimized. The procedure for synthetic spectrum generation includes self-absorption of emission lines by taking into account the number density of different species in the plasma. The Stark width of different emission lines is iteratively calculated based on the observed width and the degree of self-absorption in the individual lines. This procedure is found to be successful for achieving convergence of the retrieval algorithm even for dense spectra as well as for resolving merged lines with accuracy. This scheme was applied on a stainless steel and brass sample, and the laser-induced breakdown spectroscopy results match well with the reference value obtained from the electron probe microanalyzer measurement.

Accurate Sequence Analysis of a Monoclonal Antibody by Top-Down and Middle-Down Orbitrap Mass Spectrometry Applying Multiple Ion Activation Techniques.

Targeted top-down (TD) and middle-down (MD) mass spectrometry (MS) offer reduced sample manipulation during protein analysis, limiting the risk of introducing artifactual modifications to better capture sequence information on the proteoforms present. This provides some advantages when characterizing biotherapeutic molecules such as monoclonal antibodies, particularly for the class of biosimilars. Here, we describe the results obtained analyzing a monoclonal IgG1, either in its ∼150 kDa intact form or after highly specific digestions yielding ∼25 and ∼50 kDa subunits, using an Orbitrap mass spectrometer on a liquid chromatography (LC) time scale with fragmentation from ion-photon, ion-ion, and ion-neutral interactions. Ultraviolet photodissociation (UVPD) used a new 213 nm solid-state laser. Alternatively, we applied high-capacity electron-transfer dissociation (ETD HD), alone or in combination with higher energy collisional dissociation (EThcD). Notably, we verify the degree of complementarity of these ion activation methods, with the combination of 213 nm UVPD and ETD HD producing a new record sequence coverage of ∼40% for TD MS experiments. The addition of EThcD for the >25 kDa products from MD strategies generated up to 90% of complete sequence information in six LC runs. Importantly, we determined an optimal signal-to-noise threshold for fragment ion deconvolution to suppress false positives yet maximize sequence coverage and implemented a systematic validation of this process using the new software TDValidator. This rigorous data analysis should elevate confidence for assignment of dense MS2 spectra and represents a purposeful step toward the application of TD and MD MS for deep sequencing of monoclonal antibodies.

3-D Multilayer S-Bend Silicon Waveguide Optical Interconnect

A 3-D S-bend silicon waveguide optical interconnect on silicon on insulator is proposed to connect optical circuits in a multilayered photonic-integrated circuit (PIC). Critical parameters like bending loss, axial shift, and coupling loss are calculated for efficient implementation in the dense wavelength division multiplexing wavelength spectrum (1.46-1.62 μm). The critical parameters for tight bends are kept in control by optimizing geometrical parameters for application in miniaturized optical circuits in multilayered PIC. Possibility of fabrication of proposed complex interconnect is also explored.

Cavity Quantum Acoustic Device in the Multimode Strong Coupling Regime.

We demonstrate an acoustical analog of a circuit quantum electrodynamics system that leverages acoustic properties to enable strong multimode coupling in the dispersive regime while suppressing spontaneous emission to unconfined modes. Specifically, we fabricate and characterize a device that comprises a flux tunable transmon coupled to a 300 μm long surface acoustic wave resonator. For some modes, the qubit-cavity coupling reaches 6.5MHz, exceeding the cavity loss rate (200kHz), qubit linewidth (1.1MHz), and the cavity free spectral range (4.8MHz), placing the device in both the strong coupling and strong multimode regimes. With the qubit detuned from the confined modes of the cavity, we observe that the qubit linewidth strongly depends on its frequency, as expected for spontaneous emission of phonons, and we identify operating frequencies where this emission rate is suppressed.

A subband Steiglitz-McBride algorithm for automatic analysis of FID data.

Fast, accurate, and automatic extraction of parameters of nuclear magnetic resonance free induction decay (FID) signal for chemical spectroscopy is a challenging problem. Recently, the Steiglitz-McBride algorithm has been shown to exhibit superior performance in terms of speed, accuracy, and automation when applied to the extraction of T2 relaxation parameters for myelin water imaging of brain. Applying it to FID data reveals that it falls short of the second objective, the accuracy. Especially, it struggles with the issue of missed spectral peaks when applied to chemical samples with relatively dense frequency spectra. To overcome this issue, a preprocessing stage of subband decomposition is proposed before the application of Steiglitz-McBride algorithm to the FID signal. It is demonstrated that by doing so, a considerable improvement in accuracy is achieved. But this is not gained at the cost of the first objective, the speed. An adaptive subband decomposition is employed in conjunction with the Bayesian information criteria to carry out an efficient decomposition according to spectral content of the signal under investigation. Furthermore, adaptive subband decomposition and the Bayesian information criteria also serve to make the resulting algorithm independent of user input, which also fulfills the third objective, the automation. This makes the proposed algorithm favorable for fast, accurate, and automatic extraction of FID signal parameters.

Simplified approach to the mixed time-averaging semiclassical initial value representation for the calculation of dense vibrational spectra.

We present and test an approximate method for the semiclassical calculation of vibrational spectra. The approach is based on the mixed time-averaging semiclassical initial value representation method, which is simplified to a form that contains a filter to remove contributions from approximately harmonic environmental degrees of freedom. This filter comes at no additional numerical cost, and it has no negative effect on the accuracy of peaks from the anharmonic system of interest. The method is successfully tested for a model Hamiltonian and then applied to the study of the frequency shift of iodine in a krypton matrix. Using a hierarchic model with up to 108 normal modes included in the calculation, we show how the dynamical interaction between iodine and krypton yields results for the lowest excited iodine peaks that reproduce experimental findings to a high degree of accuracy.

Proposal for a Dual Spin Filter Based on [VO(C3S4O)2]2–

Polynuclear magnetic molecules often present dense electronic transmission spectra with many overlapping conduction spin channels. Single-metal complexes display a sparser density of states, which in the presence of a fixed external magnetic field makes them interesting candidates for spin filtering. Here we perform a DFT study of a family of bis- and tris-dithiolate vanadium complexes sandwiched between Au(111) electrodes and demonstrate that [VO(C3S4O)2]2– can behave as a dual spin filter. This means that an external electrical stimulus can switch between the selective transmission of spin-up and spin-down carriers. By using an electrostatic gate, we show that the onset for the spin-up conductance is at a voltage Vg = −0.51 V, but a small shift to Vg = −0.63 V is capable of switching to spin-down transport. For both cases, we estimate a large low-bias conductance (approximately 2 μS at Vbias 99.5%). We conclude by commenting on the general molecular requirement...

Nonlinear Stark--Wannier Equation

In this paper we consider stationary solutions to the nonlinear one-dimensional Schrödinger equation with a periodic potential and a Stark-type perturbation. In the limit of large periodic potential the Stark--Wannier ladders of the linear equation become a dense energy spectrum because a cascade of bifurcations of stationary solutions occurs when the ratio between the effective nonlinearity strength and the tilt of the external field increases.

Ionization potential depression and optical spectra in a Debye plasma model

We show how optical spectra in dense plasmas are determined by the shift of energy levels as well as by the broadening due to collisions with the plasma particles. In the lowest approximation, the interaction with the plasma particles is described by the random phase approximation (RPA) dielectric function, leading to the Debye shift of the continuum edge. The bound states remain nearly un‐shifted, and their broadening is calculated in the Born approximation. The roles of ionization potential depression as well as the Inglis–Teller effect are shown. The model calculations have to be improved going beyond the lowest (RPA) approximation when applying to warm dense matter spectra.

The 1943 K emission spectrum of H216O between 6600 and 7050 cm[formula omitted

An emission spectrum of H216O has been recorded, with Doppler-limited resolution, at 1943 K using Hot Gas Molecular Emission (HOTGAME) spectroscopy. The wavenumber range covered is 6600 to 7050 cm−1. This work reports the analysis and subsequent assignment of close to 3700 H216O transitions out of a total of more than 6700 measured peaks. The analysis is based on the Measured Active Rotational-Vibrational Energy Levels (MARVEL) energy levels of H216O determined in 2013 and emission line intensities obtained from accurate variational nuclear-motion computations. The analysis of the spectrum yields about 1300 transitions not measured previously and 23 experimentally previously unidentified rovibrational energy levels. The accuracy of the line positions and intensities used in the analysis was improved with the spectrum deconvolution software SyMath via creating a peak list corresponding to the dense emission spectrum. The extensive list of labeled transitions and the new experimental energy levels obtained are deposited in the Supplementary Material of this article as well as in the ReSpecTh (http://www.respecth.hu) information system.

Bifurcation trees of Stark-Wannier ladders for accelerated Bose-Einstein condensates in an optical lattice.

In this paper we show that in the semiclassical regime of periodic potential large enough, the Stark-Wannier ladders become a dense energy spectrum because of a cascade of bifurcations while increasing the ratio between the effective nonlinearity strength and the tilt of the external field; this fact is associated to a transition from regular to quantum chaotic dynamics. The sequence of bifurcation points is explicitly given.

Fast MinMax energy-based phase correction method for NMR spectra with linear phase distortion

This paper addresses the problem of phase correction of dense NMR spectra on the example of the etoxy derivative of the fused heterocyclic system 5,6,10b-triazaacephenanthrylene (TAAP-OEt). A new estimation method for the linear phase correction coefficients is proposed that successfully extends the min-max (minimization of maximum errors) approach of Siegel (1981). Distinctive to the Siegel method, the smallest values of the real part of the discrete Fourier transform (DFT) spectrum are maximized, not for the whole spectrum but only for DFT bins near the peaks selected by anew energy-based criterion. Additionally, the method makes use of two one-parameter optimizations for finding the phase correction line coefficients and not the single two-parameter search. The new method is demonstrated to be precise, fast and robust against additive noise. The method’s properties are verified in comparison with the state-of-the-art algorithms of Chen et al. (2002) and Bao et al. (2013) for laboratory recorded TAAP-OEt FID data and for simulated TAAP-OEt signal consisting of the sum of more than 100 complex damped exponentials. Extensive simulations were also conducted on the set of test signals derived from the TAAP-OEt signal by deterministic and pseudorandom manipulation of its content. The components of the signal model were identified by the Bertocco-Yoshida Interpolated DFT (IpDFT) algorithm with a spectral leakage correction. Simulated signals were embedded in the additive Gaussian noise, and the noise-robustness of all of the algorithms was evaluated. The obtained results demonstrate that the proposed method outperforms the Chen and the Bao algorithms, being more than 100 times faster than the Bao method (for a signal having 216 samples).

Electron recombination with tungsten ions with open f-shells

We calculate the electron recombination rates with target ions , q = 18–25, as functions of electron energy and electron temperature (i.e. the rates integrated over the Maxwellian velocity distribution). Comparison with available experimental data for , , and is used as a test of our calculations. Our predictions for , , , , and (where the experimental data are not available) may be used for plasma modeling in thermonuclear reactors. The results for the temperature-dependent rates for each ion are fitted with the standard analytical expressions to make them easy to use. All of these ions have an open electron f-shell and an extremely dense spectrum of chaotic many-electron compound resonances, which enhance the recombination rates by 2–3 orders of magnitude in comparison with the direct electron recombination. Conventional dielectronic recombination theory is not directly applicable in this case. Instead, we developed a statistical theory based on the properties of chaotic eigenstates. This theory describes a multi-electronic recombination (extension of the dielectronic recombination) via many-excited-electron compound resonances.

Cavity-Based Medium Resolution Spectroscopy (CBMRS) in the THz: A Bridge Between High- and Low-Resolution Techniques for Sensor and Spectroscopy Applications

System technologies and sensor applications in the THz largely bifurcate between high-resolution ( 1 GHz) methods. There is an extensive high-resolution literature and many approaches to low-resolution spectroscopy have been proposed and demonstrated. In this paper, we discuss and apply an approach, cavity-based medium resolution spectroscopy (CBMRS) that is applicable continuously across this intermediate resolution gap. CBMRS systems use high brightness and spectrally pure continuous wave electronic sources to determine absolute absorption coefficients by the measurement of 100–1000 mode widths of a high-finesse Fabry–Perot cavity. This eliminates the challenge of distinguishing broad spectral features from a complicated baseline that results from variations in source power, transmission efficiency, and detector response. CBMRS has many fewer data points than observed with high-resolution systems interrogating near Doppler-limited spectra. Thus, CBMRS sacrifices the “absolute” specificity of high resolution Doppler-limited systems, but still can retain excellent specificity. Indeed, this smaller sampling does not set the specificity limit, but rather it is set by whether or not the analyte has a specific THz signature. Results from pressure broadened (including atmospheric pressure) applications and molecules with dense and/or quasi-continuous spectra will be presented. Comparisons with related observations in the literature are discussed.

An efficient numerical algorithm for computing densely distributed positive interior transmission eigenvalues

We propose an efficient eigensolver for computing densely distributed spectra of the two-dimensional transmission eigenvalue problem (TEP), which is derived from Maxwell’s equations with Tellegen media and the transverse magnetic mode. The governing equations, when discretized by the standard piecewise linear finite element method, give rise to a large-scale quadratic eigenvalue problem (QEP). Our numerical simulation shows that half of the positive eigenvalues of the QEP are densely distributed in some interval near the origin. The quadratic Jacobi–Davidson method with a so-called non-equivalence deflation technique is proposed to compute the dense spectrum of the QEP. Extensive numerical simulations show that our proposed method processes the convergence efficiently, even when it needs to compute more than 5000 desired eigenpairs. Numerical results also illustrate that the computed eigenvalue curves can be approximated by nonlinear functions, which can be applied to estimate the denseness of the eigenvalues for the TEP.

Internal resonances in a transversally excited imperfect circular cylindrical shell

Cylindrical shells exhibit a dense frequency spectrum, especially near the lowest frequency range. In addition, due to the circumferential symmetry, frequencies occur in pairs. So, in the vicinity of the lowest natural frequencies, several equal or nearly equal frequencies may occur, leading to a complex dynamic behavior. The aim of the present work is to investigate the influence of several modal geometrical imperfections on the nonlinear vibration of simply supported transversally excited cylindrical shells with multiple equal or nearly equal natural frequencies. The shell is modelled using the Donnell nonlinear shallow shell theory and the discretized equations of motion are obtained by applying the Galerkin method. For this, a modal solution that takes into account the modal interaction among the relevant modes and the influence of their companion modes (modes with rotational symmetry), which satisfies the boundary and continuity conditions of the shell, is derived. Several numerical strategies are used to study the nonlinear behavior of the imperfect shell. Special attention is given to the shape and the magnitude of the initial geometric imperfection on the resonance curves and bifurcations of simply supported transversally excited cylindrical shells with 1:1:1:1 internal resonance (four interacting modes).

In vivo magnetic resonance spectroscopy for ovarian cancer diagnostics: quantification by the fast Pad\xe9 transform

Early-stage ovarian cancer has an excellent prognosis, but due mainly to late detection, ovarian cancer remains a major cause of cancer deaths among women. In vivo magnetic resonance spectroscopy (MRS) would be an excellent candidate for early ovarian cancer detection, being non-invasive, surpassing anatomic imaging to identify metabolic features of cancer, and free of ionizing radiation. However, the present meta-analysis of 13 studies indicates that with conventional Fourier-based processing, in vivo MRS insufficiently distinguished 134 cancerous from 114 benign ovarian lesions. The fast Padé transform (FPT), an advanced signal processor with high-resolution and parametric (quantification-equipped) capabilities is best qualified for MRS time signals from the ovary, as demonstrated in our earlier proof-of-concept studies. We now apply the FPT to MRS time signals encoded in vivo on a 3 T scanner, echo time of 30 ms, from a borderline serous cystic ovarian tumor. The FPT-produced total shape spectrum was better resolved than with Fourier processing. Spectra averaging through the FPT generated a denoised total shape spectrum. Subsequent parametric analysis reconstructed dense component spectra in the “usual” mode: absorption and dispersion components mixed and “ersatz” mode: reconstructed phases set to zero, thus eliminating interference effects. Numerous metabolites, including potential cancer biomarkers, were identified and quantified by the FPT, including isoleucine, valine, lipids, lactate, alanine, lysine, N-acetyl aspartate, N-acetylneuraminic acid, glutamine, choline, phosphocholine, myoinositol. Many of these are difficult or impossible to detect with Fourier plus fitting techniques for in vivo MRS of the ovary. These Padé-generated results are promising, overcoming major barriers hindering MRS from becoming a key method for non-invasively assessing ovarian lesions.

Determination of spectral reflectivity of spherically bent mica crystals applied for diagnostics of relativistic laser plasmas

Mica crystals are widely applied in x-ray spectroscopy diagnostics since their ability to effectively reflect the radiation in different orders covering a wide range of photon energy, including sub-keV range hardly accessible with other crystals. Particularly, spherically bent mica crystals are commonly used in high energy density plasma imaging spectrometry diagnostics. However, the detailed reflectivity properties of bent mica crystals are not known well. Here we propose and verify the way to calibrate mica crystal spectral reflectivity in the experiment with relativistic laser plasma. The approach is based on the comparison of dense laser plasma x-ray spectra measured by focusing spectrometers with spatial resolution equipped, with examined mica and pre-calibrated alpha-quartz bent crystals. As a result, the normalized reflectivity of spherically bent mica crystal operated in 2nd order of reflection was experimentally evaluated for the first time versus wavelength in the range of 6.7-8.7 Å. The obtained spectral calibration curve for bent mica crystal demonstrates remarkable difference to that one calculated for flat mica crystal and given in Henke tables and has to be applied further for a correct interpretation of the measured x-ray spectra.