Collective Vibrational Modes Research Articles

Hunting the Cell Cycle Snark.

In this very personal hunt for the meaning of the bacterial cell cycle, the snark, I briefly revisit and update some of the mechanisms we and many others have proposed to regulate the bacterial cell cycle. These mechanisms, which include the dynamics of calcium, membranes, hyperstructures, and networks, are based on physical and physico-chemical concepts such as ion condensation, phase transition, crowding, liquid crystal immiscibility, collective vibrational modes, reptation, and water availability. I draw on ideas from subjects such as the 'prebiotic ecology' and phenotypic diversity to help with the hunt. Given the fundamental nature of the snark, I would expect that its capture would make sense of other parts of biology. The route, therefore, followed by the hunt has involved trying to answer questions like "why do cells replicate their DNA?", "why is DNA replication semi-conservative?", "why is DNA a double helix?", "why do cells divide?", "is cell division a spandrel?", and "how are catabolism and anabolism balanced?". Here, I propose some relatively unexplored, experimental approaches to testing snark-related hypotheses and, finally, I propose some possibly original ideas about DNA packing, about phase separations, and about computing with populations of virtual bacteria.

Theory and experiment on the terahertz vibrational spectrum of ferulic acid

Ferulic acid (FA, C10H10O4), a type of hydroxycinnamic acid derivative, has beneficial pharmacological effects and biological activities and is known for its high application value in medicine, health care, and cosmetic products. The vibration spectrum of FA ranging from 0.3 THz to 2.0 THz has been investigated by terahertz time-domain spectroscopy. The characteristic absorption peaks located at 0.937, 1.159, 1.464, 1.694, and 1.910 THz are obtained experimentally. To understand the origin of the characteristic absorption peaks of FA, density functional theory calculations based on isolated molecule and crystalline structure are separately performed to differentiate the intramolecular and intermolecular vibrational modes. Combined analysis of the experimental and theoretical results informs that the characteristic absorption peak at 1.464 THz comes from intramolecular interaction, and the ones at 0.937, 1.159, 1.694, and 1.910 THz originate from intermolecular collective vibrational modes.

Higgs response and pair condensation energy in superfluid nuclei

Abstract The pairing correlation in nuclei causes a characteristic excitation, known as the pair vibration, which is populated by the pair transfer reactions. Here we introduce a new method of characterizing the pair vibration by employing an analogy to the Higgs mode, which emerges in infinite superconducting/superfluid systems as a collective vibrational mode associated with the amplitude oscillation of the Cooper pair condensate. The idea is formulated by defining a pair-transfer probe, the Higgs operator, and then describing the linear response and the strength function to this probe. We will show that the pair condensation energy in nuclei can be extracted with use of the strength sum and the static polarizability of the Higgs response. In order to demonstrate and validate the method, we perform numerical analysis for Sn isotopes based on the quasi-particle random phase approximation to the Skyrme–Hartree–Fock–Bogoliubov model. We discuss the possibility of applying this new scheme to pair-transfer experiments.

Pressure effect of the charge density wave transition on Raman spectra and transport properties of 2H−NbSe2

Charge density wave (CDW) order is widely existing and fundamentally important in solid-state physics. However, several critical issues regarding the vibrational and electronic subsystems and their coupling still need to be better understood. Here, we tune the electrical transport and collective vibrational excitation, i.e., phonon and amplitude mode, by pressure in a prototype charge density wave material, $2H\text{\ensuremath{-}}{\mathrm{NbSe}}_{2}$. A complete pressure-temperature phase diagram is revisited. The anomaly in Hall and magnetoresistivity at CDW critical temperature, ${T}_{\mathrm{CDW}}$, was suppressed by the pressure. In the Raman spectroscopy measurements, the appearance of CDW amplitude mode is accompanied by the freezing of the two-phonon mode. The frequency of CDW amplitude mode under pressure follows modified mean-field theory with power-law scaling $(\ensuremath{\beta}=0.18)$. The renormalization of the Raman phonon across the CDW transition and the mean-field temperature dependence of CDW amplitude mode emphasized the importance of electron-phonon coupling in the formation of CDW state in $2H\text{\ensuremath{-}}{\mathrm{NbSe}}_{2}$. Our work clarifies the complex vibrational and electronic subsystems and sheds light on the mechanism of the charge density state in $2H\text{\ensuremath{-}}{\mathrm{NbSe}}_{2}$.

Laser-free method for creation of two-mode squeezed state and beam-splitter transformation with trapped ions

We propose a laser-free method for creation of a phonon two-mode squeezed state and a beam-splitter transformation, using time-varying electric fields and non-linear couplings between the normal modes in a linear ion crystal. Such non-linear Coulomb-mediated interactions between the collective vibrational modes arise under specific trap-frequency conditions in an ion trap. We study the quantum metrological capability for parameter estimation of the two quantum states and show that a Heisenberg limit of precision can be achieved when the initial state with n phonons evolves under the action of the beam-splitter transformation. Furthermore, we show that the phonon non-linearity and the spin-dependent force can be used for creation of a three-qubit Fredkin gate.

Molecular Optomechanics Induced Hybrid Properties in Soft Materials Filled Plasmonic Nanocavities.

The optomechanical interaction between nanocavity plasmons and molecular vibrations can result in interfacial phenomena that can be tailored for sensing and photocatalytic applications. Here, we report for the first time that plasmon-vibration interaction can induce laser-plasmon detuning dependent plasmon resonance linewidth broadening, indicating energy transfer from the plasmon field to collective vibrational modes. The linewidth broadening accompanied by the large enhancement of the Raman scattering signal is observed as the laser-plasmon blue-detuning approaches the CH vibrational frequency of the molecular systems integrated in gold nanorod-on-mirror nanocavities. The experimental observations can be explained based on the molecular optomechanics theory that predicts dynamical backaction amplification of the vibrational modes and high sensitivity of Raman scattering when the plasmon resonance overlaps with the Raman emission frequency. The results presented here suggest that molecular optomechanics coupling may be manipulated for creating hybrid properties based on interactions between molecular oscillators and nanocavity electromagnetic optical modes.

Scalable and programmable phononic network with trapped ions

Controllable bosonic systems can provide post-classical computational power with sub-universal quantum computational capability. A network that consists of a number of bosons evolving through beam-splitters and phase-shifters between different modes, has been proposed and applied to demonstrate quantum advantages. While the network has been implemented mostly in optical systems with photons, recently alternative realizations have been explored, where major limitations in photonic systems such as photon loss, and probabilistic manipulation can be addressed. Phonons, the quantized excitations of vibrational modes, of trapped ions can be a promising candidate to realize the bosonic network. Here, we experimentally demonstrate a minimal-loss phononic network that can be programmed and in which any phononic states are deterministically prepared and detected. We realize the network with up to four collective-vibrational modes, which can be straightforwardly extended to reveal quantum advantage. We benchmark the performance of the network with an exemplary algorithm of tomography for arbitrary multi-mode states with a fixed total phonon number. We obtain reconstruction fidelities of 94.5 $\pm$ 1.95 % and 93.4 $\pm$ 3.15 % for single-phonon and two-phonon states, respectively. Our experiment demonstrates a clear and novel pathway to scale up a phononic network for various quantum information processing beyond the limitations of classical and other quantum systems.

Anharmonic potential energy landscapes of thermally excited protein vibrations.

At room temperature, low frequency vibrations below 6 THz are thermally excited and are not restricted to the vibrational ground state. Therefore, low frequency vibrations are also not restricted to harmonic fluctuations around a potential energy minimum. On short timescales, such low-frequency vibrations in proteins are responsible for the exploration of the potential energy surface and enable slower stochastic dynamics responsible for functional dynamics and conformational changes. However, current methods that describe and identify collective vibrational modes in proteins either rely on harmonic approximations or lack atomistic detail.

The collective vibrational modes of dihydropyridine in nifedipine studied by terahertz spectroscopy

Cardiovascular pharmaceuticals have drawn huge attention in drug development. Nifedipine (NFD) is an important member of calcium channel blockers (CCB) with the structural characteristic of dihydropyridine (DHP), but the binding mechanism to its target remains an open question. Even though several analytical techniques have been used for structural characterizations, the information of collective vibrational behavior is still lacking. In this work, we use terahertz (THz) spectroscopy to investigate the spectral fingerprints of NFD, and quantitatively evaluate the temperature-induced frequency shifts. Combined with quantum chemical calculations, each THz fingerprint is attributed to specific collective vibrational modes. The collective vibrations of DHP are mainly distributed below 2.5 THz, which provides complementary information to understand the behavior of rigid DHP ring. The rotation of methyl group and the wagging of nitrophenyl group are widely distributed in the range of 1.0–4.0 THz, which is helpful for the conformational recognition between NFD and target molecule. THz spectroscopy is demonstrated to be suitable for characterizing the collective vibrational modes of DHP and elucidating the drug-target binding behavior from the perspective of noncovalent interactions. It has the potential to become a non-invasive technology for conformational analysis and pharmaceutical development.

Quantum traps for coupling of fluorofullerene molecules

The interaction of fluorine atoms with Cu(111) surface has been analyzed by means of scanning tunneling microscopy and x-ray photoelectron spectroscopy (XPS). A submonolayer coverage of fluorinated fullerene C60F18 has been chosen to provide a well controllable arrival of fluorine atoms on copper surface. The appearance of F-induced surface structures on the Cu(111) surface caused by defluorination of C60F18 molecules adsorbed on the surface was shown. XPS measurements unambiguously indicate the existence of chemical state of fluorine not typical for CuF2 formation. Superstructure of well ordered metastable clusters consisting of fluorofullerene molecules are formed on the Cu(111) surface as a result of the balance of two interactions: the dipole-dipole interaction between fluorofullerene molecules and the interaction of C60F18 molecules with the two-dimensional gas phase, emerging above the copper surface. Regular surface structure formed by fullerene molecules interacting through collective vibrational mode can be used for entanglement formation between two qubits each associated with ground and excited electronic states of the molecule by applying two coherent laser pulses.

Description of Nuclear Properties for 114-128Cd Isotopes

In this paper, the energy levels of the ground-state band (GSB) and other states for 114−128Cd isotopes have been determined using the Interacting Boson Model (IBM-1) with a New Empirical Equation (NEE). The GSB results showed that the IBM-1, NEE, and available experimental data were all in fairly consistent. The NEE and IBM-1 calculations for the high states above 6+ state are slightly overestimated compared to the experimental data, with the exception of the 114Cd and 118Cd nuclei. Furthermore, the reduced transition probabilities B(E2) extracted from the IBM-1 model agree well with the available experimental data. The potential energy surface (EPS) was also examined with the IBM-1. The EPS contour results for Cd isotopes demonstrate that the Cd isotopes under investigation represent a smooth transition behavior from light Cd nuclei toward a more collective vibrational mode as the neutron number increases.

Adsorption of croconic acid anions at silver electrodes in sodium fluoride solutions. Interplay of DFT calculations and in situ ATR-SEIRAS measurements for the interpretation of experimental spectra of adsorbed species

The adsorption of species coming from the disodium salt of croconic acid (4,5-dihydroxy-4-cyclopentene-1,2,3-trione, H2C5O5) at chemically deposited silver electrodes was studied in aqueous sodium fluoride solutions by combining in situ ATR-SEIRAS (Surface-Enhanced Infrared Reflection Absorption Spectroscopy experiments under Attenuated Total Reflection conditions) and Density Functional Theory (DFT) calculations. Voltammetric experiments suggest the existence of reversible adsorption processes in the potential range between −0.55 and −0.20 V vs Ag/AgCl (KCl 1 M), whereas irreversible reduction is observed for potentials below-0.55 V. ATR-SEIRA spectra show potential-dependent adsorbate bands in the potential range for reversible adsorption, that were assigned according to DFT calculations. Calculated optimized geometry of adsorbed croconate and bicroconate correspond to bonding to the silver surface in a bidentate configuration through two oxygen atoms with the molecular plane perpendicular to the metal surface. The broadening and splitting at high electrode potentials of the CO stretching bands for adsorbates coming from croconic acid can be explained by invoking the existence of collective vibrational modes appearing at high coverage. In overall, the ATR-SEIRA spectra obtained with Ag thin layer electrodes resembles that reported for Au thin layers. As a difference, higher adsorbate coverage seems to be obtained in the case of silver. Moreover, a strong feature at ca. 1580 cm−1 is experimentally observed, that was much weaker on gold samples. The calculated frequencies for adsorbed croconate and bicroconate do not change significantly with the adsorption bonding sites for the optimized geometries. Taking into account the calculated frequencies of both types of species, a better agreement with the experimental behavior (including the splitting/shifting caused by dipole–dipole coupling in high-coverage collective modes) is obtained in the case of bicroconate. The coexistence with some adsorbed croconate species cannot be ruled out.

Dissipative Preparation of Generalized Bell States with the Sørensen-Mølmer Setting

Quantum entanglement is an important resource in quantum information processing tasks, such as quantum cryptography, quantum teleportation, and quantum computation. The main obstacle to faithful and reliable preparation of entangled states is environment-induced decoherence. Dissipative transition of a general quantum state to an entangled steady state provides an effective strategy to protect entanglement from decoherence, where the decoherence converts into an essential resource. In this paper, we put forward a scheme to prepare generalized Bell states based on trapped ions, in which unitary dynamics and spontaneous emission are combined to drive an arbitrary quantum state in the ground-state space to a unique steady state. The scheme is realized by using the renowned S\o{}rensen-M\o{}lmer setting and is therefore compatible with current experimental technology. Moreover, the vibrational degree of freedom is decoupled from the unitary dynamics so that the scheme does not need to cool the collective vibrational mode to its ground state and thus it works for thermally excited states. Besides, our scheme is demonstrated to be insensitive to variations of some parameters with the aid of numerical simulation.

Probing Adaptation of Hydration and Protein Dynamics to Temperature.

Protein dynamics is strongly influenced by the surrounding environment and physiological conditions. Here we employ broadband megahertz-to-terahertz spectroscopy to explore the dynamics of water and myoglobin protein on an extended time scale from femto- to nanosecond. The dielectric spectra reveal several relaxations corresponding to the orientational polarization mechanism, including the dynamics of loosely bound, tightly bound, and bulk water, as well as collective vibrational modes of protein in an aqueous environment. The dynamics of loosely bound and bulk water follow non-Arrhenius behavior; however, the dynamics of water molecules in the tightly bound layer obeys the Arrhenius-type relation. Combining molecular simulations and effective-medium approximation, we have determined the number of water molecules in the tightly bound hydration layer and studied the dynamics of protein as a function of temperature. The results provide the important impact of water on the biochemical functions of proteins.

The fingerprints of nifedipine/isonicotinamide cocrystal polymorph studied by terahertz time-domain spectroscopy

Cocrystal is constructed to improve physicochemical properties of active pharmaceutical ingredient and prevent polymorphism via intermolecular interactions. However, recent examples on cocrystal polymorphs display significantly different properties. Even though some analytical techniques have been used to characterize the cocrystal polymorphic system, it remains unclear how intermolecular interactions drive and stabilize the structure. In this work, we study the cocrystal polymorphs of nifedipine (NFD) and isonicotinamide (INA) using terahertz (THz) spectroscopy. Form I and form II of NFD-INA cocrystals show spectral fingerprints in THz region. Temperature-dependent THz spectra display distinguished frequency shifts of each fingerprint. Combined with solid-state density functional theory (DFT) calculations, the experimental fingerprints and their distinct responses to temperature are elucidated by specific collective vibrational modes. The vibrations of hydrogen bonding between dihydropyridine ring of NFD and INA are generally distributed below 1.5 THz, which play important roles in stabilizing cocrystal and preventing the oxidation of NFD. The rotations of methyl group in NFD are widely distributed in the range of 1.5–4.0 THz, which helps the steric recognition. The results demonstrate that THz spectroscopy is a sensitive tool to discriminate cocrystal polymorphs. It has the potential to be used as a non-invasive technique for pharmaceutical screening.

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.

Long-range DNA-water interactions

DNA functions only in aqueous environments and adopts different conformations depending on the hydration level. The dynamics of hydration water and hydrated DNA leads to rotating and oscillating dipoles that, in turn, give rise to a strong megahertz to terahertz absorption. Investigating the impact of hydration on DNA dynamics and the spectral features of water molecules influenced by DNA, however, is extremely challenging because of the strong absorption of water in the megahertz to terahertz frequency range. In response, we have employed a high-precision megahertz to terahertz dielectric spectrometer, assisted by molecular dynamics simulations, to investigate the dynamics of water molecules within the hydration shells of DNA as well as the collective vibrational motions of hydrated DNA, which are vital to DNA conformation and functionality. Our results reveal that the dynamics of water molecules in a DNA solution is heterogeneous, exhibiting a hierarchy of four distinct relaxation times ranging from ∼8 ps to 1 ns, and the hydration structure of a DNA chain can extend to as far as ∼18 Å from its surface. The low-frequency collective vibrational modes of hydrated DNA have been identified and found to be sensitive to environmental conditions including temperature and hydration level. The results reveal critical information on hydrated DNA dynamics and DNA-water interfaces, which impact the biochemical functions and reactivity of DNA.

Spectroelectrochemical and DFT approaches to the study of croconic acid adsorption at gold electrodes in acidic solutions

• Croconate anions adsorb at Au electrodes in croconic acid-containing solutions. • Croconate species bons in a bidentate configuration with O atoms on top positions. • Adsorption occurs with the molecular plane (quasi) normal to the metal surface. • Adsorption causes significant changes on the geometry and symmetry of croconate. • Collective vibrations broaden and split croconate bands at high coverage. The adsorption of species coming from croconic acid (4,5-dihydroxy-4-cyclopentene-1,2,3-trione, H 2 C 5 O 5 , CA) at gold electrodes was studied spectroelectrochemically in aqueous perchloric acid solutions. Voltammetric experiments suggest the existence of reversible adsorption processes in the potential range between 0.30 and 0.80 V vs RHE. Surface-Enhanced Infrared Reflection Absorption Spectroscopy experiments under Attenuated Total Reflection conditions (ATR-SEIRA) show potential-dependent adsorbate bands in the latter potential range that, according to Density Functional Theory calculations, can be assigned to adsorbed croconate. Calculated optimized geometry corresponds to bonding of croconate species to the gold surfaces involving two oxygen atoms in a bidentate configuration, with the molecular plane perpendicular to the metal surface for low and high crocoanate coverage. For intermediate coverage, lateral repulsions between neighbor croconate adsorbates give rise to the tilting of the molecular plane. The broadening and splitting at high electrode potentials of the C O stretching bands for adsorbed croconate can be explained by invoking the existence of collective vibrational modes appearing at high coverage. The cyclic voltammograms recorded in the CA-containing solutions also show the existence of reversible redox processes at potentials below 0.30 V involving adsorbed species, which are detected in the collected ATR-SEIRA spectra.

Phonon gas model for thermal conductivity of dense, strongly interacting liquids

Developing predictive thermal property models for liquids based on microscopic principles has been elusive. The difficulty is that liquids have gas-like and solid-like attributes that are at odds when considering the frameworks of microscopic models: Models for gases are simple due to randomness and low density, whereas models for crystalline solids rely on symmetry and long-range order for easier calculation. The short-range order in liquids does, however, provide structure to neighboring molecules similar to amorphous solids, and there have been recent advances indicating that collective vibrational modes store heat in liquids. Models combining Debye approximations from solid-state physics and Frenkel’s theory of liquids can accurately predict the heat capacity of liquids. Phonon-like dispersions in liquids have also been widely observed in neutron scattering experiments. These developments motivate us to propose a model where high-frequency vibrational modes, which travel at the speed of sound and have a mean free path on the order of the average intermolecular distance, conduct heat in liquids. We use this liquid phonon gas model to calculate the thermal conductivity of liquids with varying intermolecular interaction energies from strongest to weakest—Coulomb, hydrogen-bonding, Keesom, and London dispersion energy. Generally, the model is more accurate as the intermolecular interaction energy and density of liquids increase. The calculated thermal conductivity of Coulombic-bound molten sodium nitrate and hydrogen-bonded water is within 1.46% and 2.98% of the experimentally measured values, respectively, across their entire temperature ranges. Further modal analysis of the velocity and the mean free path of collective vibrations could establish the liquid phonon gas model as an accurate model for weakly interacting liquids as well.

Infrared surface phonon nanospectroscopy of an interacting dielectric-particle–dielectric-substrate dimer using fast electrons

Refinements in energy monochromation and aberration correction in state-of-the-art scanning transmission electron microscopes has opened access to the far infrared regime for spectroscopic characterization at the nanoscale. At these low energies, the dielectric environment, such as a dielectric slab adjacent to the target specimen, may no longer play a passive role in the spectrum. Instead, the environment may itself host resonances that mix with those of the target and complicate interpretation of its spectral responses. This paper explores a theoretical description of the coupling between the collective vibrational surface modes of a dielectric particle and dielectric slab of varying thickness for the purpose of elucidating the interacting phononic excitations in dielectric materials typical of inelastic electron scattering measurements in the infrared. Dynamical coordinates and a governing Hamiltonian are rigorously defined in the quasistatic limit to account for phonon mode mixing and forcing by an aloof electron probe, which travels along a grazing trajectory, parallel to the dielectric slab. As the spectral window of interrogation by fast electron probes has been extended down to thermal energies with unprecedented meV energy resolution, theoretical models like that presented herein are crucial for accurate interpretation of experimental data.