Collective ion dynamics in liquid zinc: evidence for complex dynamics in a non-free-electron liquid metal

Intra-protein interacting collective modes in the terahertz frequency region

Understanding how proteins work requires a thorough understanding of their internal dynamics. Proteins support a wide range of motions, from the femtoseconds to seconds time scale, relevant to crucial biological functions. In this context, the term "protein collective dynamics" refers to the complex patterns of coordinated motions of numerous atoms throughout the protein in the sub-picosecond time scale (terahertz frequency region). It is hypothesized that these dynamics have a substantial impact on the regulation of functional dynamical mechanisms, including ligand binding and allosteric signalling, charge transport direction, and the regulation of thermodynamic and thermal transport properties. Using the theoretical framework of hydrodynamics, the collective dynamics of proteins had previously been described in a manner akin to that of simple liquids, i.e. in terms of a single acoustic-like excitation, related to intra-protein vibrational motions. Here, we employ an interacting-mode model to analyse the results from molecular dynamics simulations and we unveil that the vibrational landscape of proteins is populated by multiple acoustic-like and low-frequency optic-like modes, with mixed symmetry and interfering with each other. We propose an interpretation at the molecular level of the observed scenario that we relate to the side-chains and the hydrogen-bonded networks dynamics. The present insights provide a perspective for understanding the molecular mechanisms underlying the energy redistribution processes in the interior of proteins.

Does a Quark-Gluon Plasma Feature an Extended Hydrodynamic Regime?

We investigate the response of the near-equilibrium quark-gluon plasma (QGP) to perturbation at nonhydrodynamic gradients. We propose a conceivable scenario under which sound mode continues to dominate the medium response in this regime. Such a scenario has been observed experimentally for various liquids and liquid metals. We further show that this extended hydrodynamic regime (EHR) indeed exists for both the weakly coupled kinetic equation in the relaxation time approximation (RTA) and the strongly coupled N=4 supersymmetric Yang-Mills (SYM) theory. We construct a simple but nontrivial extension of Müller-Israel-Stewart (MIS) theory-namely MIS*-and demonstrate that it describes the EHR response for both the RTA and SYM theory. This indicates that MIS* equations can potentially be employed to search for QGP EHR via heavy-ion collisions.

Collective excitations in a melt of fast phase change material GeCu2Te3

Inelastic x-ray scattering measurements have been carried out to investigate atomic dynamics in a melt of fast phase change material GeCu₂Te₃. The dynamic structure factor was analysed using the model function with three damped harmonic oscillator components. By investigating the correlation between the excitation energy and the linewidth, and that between the excitation energy and the intensity on contour maps of a relative approximate probability distribution function proportional toexp(-χ2/N), we could judge the reliability of each inelastic excitation in the dynamic structure factor. The results indicate that there are two inelastic excitation modes besides the longitudinal acoustic one in the liquid. The lower energy excitation could be assigned to the transverse acoustic one whereas the higher energy one disperses like fast sound. The latter result may imply that the liquid ternary alloy exhibits a microscopic phase separation tendency.

Phonon dispersion curves in the type-I crystalline and molten clathrate compound Eu8Ga16Ge30

The dynamic structure factorS(Q,E), whereQandEare momentum and energy transfer, respectively, has been measured for liquid Eu₈Ga₁₆Ge₃₀(EGG), using inelastic x-ray scattering. The excitation energy of the longitudinal acoustic mode in the liquid was scaled to that in liquid Ba₈Ga₁₆Sn₃₀(BGS) with the effective mass. This result means that the local structure in both liquids are similar. The longitudinal acoustic excitation energy of type-I clathrate compound EGG disperses faster than that in the liquid, suggesting that the interatomic force is weakened on melting. The lower energy excitation was observed in both liquid EGG and liquid BGS. In comparison with the longitudinal phonon dispersion in crystalline clathrate compound EGG obtained by density functional theory-based calculations, the lower energy in the liquid was found to be near the optical mode energy. The result indicates that the lower energy mode arises from the relative motion between Eu and (Ga, Ge) atoms.

Onset of collective excitations in the transverse dynamics of simple fluids

A thorough analysis of the transverse current autocorrelation function obtained by molecular dynamics simulations of a dense Lennard-Jones fluid reveals that even such a simple system is characterized by a varied dynamical behavior with changing length scale. By using the exponential expansion theory, we provide a full account of the time correlation at wavevectors Q between the upper boundary of the hydrodynamic region and Q_{p}/2, with Q_{p} being the position of the main peak of the static structure factor. In the Q range studied, we identify and accurately locate the wavevector at which shear wave propagation starts to take place, and show clearly how this phenomenon may be represented by a damped harmonic oscillator changing, in a continuous way, from an overdamped to an underdamped condition. The decomposition into exponential modes allows one to convincingly establish not only the crossover related to the onset of transverse waves but, surprisingly, also the existence of a second pair of modes equivalent to another oscillator that undergoes, at higher Q values, a similarly smooth over to underdamped transition.

Low energy excitation in liquid Sb and liquid Bi observed in inelastic x-ray scattering spectra

The dynamic structure factorS(Q,E), whereQandEare momentum and energy transfer, respectively, has been measured for liquid Sb, using inelastic x-ray scattering. A modified damped harmonic oscillator model function was applied to analyseS(Q,E) of liquid Sb and also to that of liquid Bi by Inuiet al(2015Phys. Rev.B92, 054206). The obtained excitation energy was in fairly good agreement with that predicted byab initiomolecular dynamics simulations on these liquid semi-metals. The excitation energy of the longitudinal acoustic mode in liquid Sb and liquid Bi exhibits flat-toppedQdependence whereas the lower excitation energy below the longitudinal acoustic excitation showsQ-gap behaviour. From the viscosity estimated from theQ-gap experimentally obtained, it is inferred that the lower energy excitation arises from the transverse acoustic excitation in the liquids.

Searching for a second excitation in the inelastic neutron scattering spectrum of a liquid metal: a Bayesian analysis

When probed at nanometer and picosecond scales, the properties of a liquid present striking analogies with the ones of the corresponding solid, one of the most surprising is the ability of supporting shear wave propagation, as a rigid medium. Although this evidence is being reported by a growing number of terahertz scattering measurements, it remains an open question whether it is universal or rather typical of some liquids only. Furthermore, given its elusive signatures in the scattering signal, the detection of this effect appears as a typical case where an unintentional “bias of confirmation” can mislead experimentalists. We thus decided to use a Bayesian inference approach to achieve a probabilistically grounded and evidence-based lineshape modeling of the inelastic neutron scattering spectra from liquid silver, whose simulated density autocorrelations bear evidence of a shear mode propagation over very short distances. The result of our analysis indicates that the observation of any additional, non-longitudinal, acoustic modes in this simple system goes beyond the accuracy of the used scattering method.

Transverse acoustic phonon excitations in liquid metals

In this article, transverse acoustic (TA) phonon excitations in various liquid metals are reviewed. Low-frequency TA phonon excitations were investigated on liquid Ga, Sn, Fe, Cu, Zn, and Bi, by using high energy resolution inelastic X-ray scattering (IXS). The current correlation functions obtained from the IXS spectra were analyzed by using two Gaussians to evaluate the excitation energies and widths of the longitudinal acoustic and TA excitation modes, which are consistent with ab initio molecular dynamics simulations. The lifetimes and propagating lengths of the TA modes were determined, and may respectively correspond to the lifetimes and sizes of cages instantaneously formed in each liquid metal. The microscopic elastic constants were estimated and characteristic differences from macroscopic polycrystalline values were found in Poisson’s ratios. Future experimental and analytical problems to be solved in the near future are addressed.

Transverse acoustic phonon excitations in liquid metals

In this article, transverse acoustic (TA) phonon excitations in various liquid metals are reviewed. Low-frequency TA phonon excitations were investigated on liquid Ga, Sn, Fe, Cu, Zn, and Bi, by using high energy resolution inelastic X-ray scattering (IXS). The current correlation functions obtained from the IXS spectra were analyzed by using two Gaussians to evaluate the excitation energies and widths of the longitudinal acoustic and TA excitation modes, which are consistent with ab initio molecular dynamics simulations. The lifetimes and propagating lengths of the TA modes were determined, and may respectively correspond to the lifetimes and sizes of cages instantaneously formed in each liquid metal. The microscopic elastic constants were estimated and characteristic differences from macroscopic polycrystalline values were found in Poisson’s ratios. Future experimental and analytical problems to be solved in the near future are addressed.

First principles study of liquid uranium at temperatures up to 2050 K

Uranium compounds are used as fissile materials in nuclear reactors. In present day reactors the most used nuclear fuel is uranium dioxide, but in generation-IV reactors other compounds are also being considered, such as uranium carbide and uranium mononitride. Upon possible accidents where the coolant would not circulate or be lost the core of the reactor would reach very high temperatures, and therefore it is essential to understand the behaviour of the nuclear fuel under such conditions for proper risk assessment. We consider here molten metallic uranium at several temperatures ranging from 1455 to 2050 K. Even though metallic uranium is not a candidate for nuclear fuel it could nevertheless be produced due to the thermochemical instability of uranium nitride at high temperatures. We use first principles techniques to analyse the behaviour of this system and obtain basic structural and dynamic properties, as well as some thermodynamic and transport properties, including atomic diffusion and viscosity.

Interpreting the Terahertz Spectrum of Complex Materials: The Unique Contribution of the Bayesian Analysis

In the last few decades, experimental studies of the terahertz spectrum of density fluctuations have considerably improved our knowledge of the mesoscopic dynamics of disordered materials, which also have imposed new demands on the data modelling and interpretation. Indeed, lineshape analyses are no longer limited to the phenomenological observation of inelastic features, as in the pioneering stage of Neutron or X-ray spectroscopy, rather aiming at the extraction from their shape of physically relevant quantities, as sound velocity and damping, relaxation times, or other transport coefficients. In this effort, researchers need to face both inherent and practical obstacles, respectively stemming from the highly damped nature of terahertz modes and the limited energy resolution, accessible kinematic region and statistical accuracy of the typical experimental outcome. To properly address these challenges, a global reconsideration of the lineshape modelling and the enforcement of evidence-based probabilistic inference is becoming crucial. Particularly compelling is the possibility of implementing Bayesian inference methods, which we illustrated here through an in-depth discussion of some results recently obtained in the analysis of Neutron and X-ray scattering results.

Disentangling time-focusing from beam divergence: A novel approach for high-flux thermal neutron spectroscopy at continuous and long-pulse sources

We present the concept of a novel time-focusing technique for neutron spectrometers, which allows us to disentangle time-focusing from beam divergence. The core of this approach is a double rotating-crystal monochromator that can be used to extract a larger wavelength band from a white beam, thus providing a higher flux at the sample compared to standard time-of-flight instruments, yet preserving energy resolution and beam collimation. The performances of a spectrometer based on this approach are quantitatively discussed in terms of possible incident wavelengths, flux at the sample, and (Q, E)-resolution. Analytical estimates suggest flux gains of about one order of magnitude at comparable resolutions in comparison to conventional time-of-flight spectrometers. Moreover, the double monochromator configuration natively shifts the sample away from the source line-of-sight, thus significantly improving the signal-to-noise ratio. The latter, in combination with a system that does not increase the beam divergence, brings the further advantage of a cleaner access to the low-Q region, which is recognized to be of fundamental interest for magnetism and for disordered materials, from glasses to biological systems.

Static and dynamic structures of liquid Ba8Ga16Sn30: a melt of the thermoelectric clathrate compounds

X-ray diffraction and inelastic x-ray scattering measurements of liquid Ba₈Ga₁₆Sn₃₀ have been carried out to investigate local structure and atomic dynamics in the liquid. The pair distribution function shows shorter and longer interatomic distances in the first coordination shell. The dynamic structure factor exhibits the inelastic excitations on both sides of the quasielastic central peak. The inelastic excitations disperse with increasing the momentum transfer, suggesting the longitudinal acoustic mode. We found a low energy excitation in addition to the longitudinal acoustic excitation in the dynamic structure factor and it reminds us a strong relationship with a rattling motion of a guest (Ba) atom in the solid state. The temperature dependence of the pair distribution function and the longitudinal acoustic excitation energy is very weak in a range from 600 to 900 °C. The result suggests that Ba and other atoms in the melt are located around minimum positions of the effective pair potential approximated as a harmonic one.

Multiple Interacting Collective Modes and Phonon Gap in Phospholipid Membranes

We combine Brillouin neutron scattering measurements with recent inelastic X-ray scattering [ Zhernenkov et al. Nat. Commun. 2016 , 7 , 11575 ] to propose a model for the collective dynamics of phospholipid bilayers. Neutron and X-ray spectra were fitted by the model response function associated with the Hamiltonian of an interacting-phonon system. This approach allows for a comprehensive and unprecedented picture of the vibrational collective features of phospholipids. At low wavevectors Q, the dispersion relations can be interpreted in terms of two acoustic-like modes, one longitudinal and one transverse, plus a dispersionless optic-like mode. The transverse mode of the liquid phase shows a phonon gap that can be linked to a passive transport mechanism through membranes, an interpretation that was proposed in Zhernenkov et al. At higher Q values, the interaction of the longitudinal acoustic excitation with the dispersionless mode gives rise to a pattern that is consistent with avoided-crossing behavior. Evidence is found for a slow- to fast-sound transition, similar to bulk water and other biomolecules.

Switching off hydrogen-bond-driven excitation modes in liquid methanol

Hydrogen bonding plays an essential role on intermolecular forces, and consequently on the thermodynamics of materials defined by this elusive bonding character. It determines the property of a vital liquid as water as well as many processes crucial for life. The longstanding controversy on the nature of the hydrogen bond (HB) can be settled by looking at the effect of a vanishing HB interaction on the microscopic properties of a given hydrogen-bonded fluid. This task suits the capabilities of computer simulations techniques, which allow to easily switch off HB interactions. We then use molecular dynamics to study the microscopic properties of methanol, a prototypical HB liquid. Fundamental aspects of the dynamics of methanol at room temperature were contextualised only very recently and its rich dynamics was found to have striking analogies with that of water. The lower temperature (200 K) considered in the present study led us to observe that the molecular centre-of-mass dynamics is dominated by four modes. Most importantly, the computational ability to switch on and off hydrogen bonds permitted us to identify which, among these modes, have a pure HB-origin. This clarifies the role of hydrogen bonds in liquid dynamics, disclosing new research opportunities and unexplored interpretation schemes.

A high-flux upgrade for the BRISP spectrometer at ILL

To date, the BRISP spectrometer represents the state-of-the-art for every instrument aiming to perform Brillouin neutron scattering. Exploiting accurate ray-tracing McStas simulations, we investigate an improved configuration of the BRISP primary spectrometer to provide a higher flux at the sample position, while preserving all the present capabilities of the instrument. This configuration is based on a neutron guide system and is designed to fit the instrument platform with no modifications of the secondary spectrometer. These evaluations show that this setup can achieve a flux gain factor ranging from 3 to 6, depending on the wavelength. This can expand the experimental possibilities of BRISP towards smaller samples, possibly using also complex sample environments.

A search for manifestation of two types of collective excitations in dynamic structure of a liquid metal: Ab initio study of collective excitations in liquid Na

Using a combination of ab initio molecular dynamics and several fit models for dynamic structure of liquid metals, we explore an issue of possible manifestation of non-acoustic collective excitations in longitudinal dynamics having liquid Na as a case study. A model with two damped harmonic oscillators (DHOs) in time domain is used for analysis of the density-density time correlation functions. Another similar model with two propagating contributions and three lowest exact sum rules is considered, as well as an extended hydrodynamic model known as thermo-viscoelastic one which permits two types of propagating modes outside the hydrodynamic region to be used for comparison with ab initio obtained time correlation functions and calculations of dispersions of collective excitations. Our results do not support recent suggestions that, even in simple liquid metals, non-hydrodynamics transverse excitations contribute to the longitudinal collective dynamics and can be detected as a DHO-like spectral shape at their transverse frequency. We found that the thermo-viscoelastic dynamic model permits perfect description of the density-density and current-current time correlation functions of the liquid Na in a wide range of wave numbers, which implies that the origin of the non-hydrodynamic collective excitations contributing to longitudinal dynamics can be short-wavelength heat waves.

Density of states from mode expansion of the self-dynamic structure factor of a liquid metal

We show that by exploiting multi-Lorentzian fits of the self-dynamic structure factor at various wave vectors it is possible to carefully perform the Q→0 extrapolation required to determine the spectrum Z(ω) of the velocity autocorrelation function of a liquid. The smooth Q dependence of the fit parameters makes their extrapolation to Q=0 a simple procedure from which Z(ω) becomes computable, with the great advantage of solving the problems related to resolution broadening of either experimental or simulated self-spectra. Determination of a single-particle property like the spectrum of the velocity autocorrelation function turns out to be crucial to understanding the whole dynamics of the liquid. In fact, we demonstrate a clear link between the collective mode frequencies and the shape of the frequency distribution Z(ω). In the specific case considered in this work, i.e., liquid Au, analysis of Z(ω) revealed the presence, along with propagating sound waves, of lower frequency modes that were not observed before by means of dynamic structure factor measurements. By exploiting ab initio simulations for this liquid metal we could also calculate the transverse current-current correlation spectra and clearly identify the transverse nature of the above mentioned less energetic modes. Evidence of propagating transverse excitations has actually been reported in various works in the recent literature. However, in some cases, like the present one, these modes are difficult to detect in density fluctuation spectra. We show here that the analysis of the single-particle dynamics is able to unveil their presence in a very effective way. The properties here shown to characterize Z(ω), and the information in it contained therefore allow us to identify it with the density of states (DoS) of the liquid. We demonstrate that only nonhydrodynamic modes contribute to the DoS, thus establishing its purely microscopic origin. Finally, as a by-product of this work, we provide our estimate of the self-diffusion coefficient of liquid gold just above melting.

Density of states and dynamical crossover in a dense fluid revealed by exponential mode analysis of the velocity autocorrelation function

Extending a preceding study of the velocity autocorrelation function (VAF) in a simulated Lennard-Jones fluid [Phys. Rev. E 92, 042166 (2015)PLEEE81539-375510.1103/PhysRevE.92.042166] to cover higher-density and lower-temperature states, we show that the recently demonstrated multiexponential expansion method allows for a full account and understanding of the basic dynamical processes encompassed by a fundamental quantity as the VAF. In particular, besides obtaining evidence of a persisting long-time tail, we assign specific and unambiguous physical meanings to groups of exponential modes related to the longitudinal and transverse collective dynamics, respectively. We have made this possible by consistently introducing the interpretation of the VAF frequency spectrum as a global density of states in fluids, generalizing a solid-state concept, and by giving to specific spectral components, obtained through the VAF exponential expansion, the corresponding meaning of partial densities of states relative to specific dynamical processes. The clear identification of a high-frequency oscillation of the VAF with the near-top excitation frequency in the dispersion curve of acoustic waves is a neat example of the power of the method. As for the transverse mode contribution, its analysis turns out to be particularly important, because the multiexponential expansion reveals a transition marking the onset of propagating excitations when the density is increased beyond a threshold value. While this finding agrees with the recent literature debating the issue of dynamical crossover boundaries, such as the one identified with the Frenkel line, we can add detailed information on the modes involved in this specific process in the domains of both time and frequency. This will help obtain a still missing full account of transverse dynamics, in both its nonpropagating and propagating aspects which are linked through dynamical transitions depending on both the thermodynamic states and the excitation wave vectors.

Pressure-induced changes in structural and dynamic properties of liquid Fe close to the melting line. An ab initio study

The static and dynamic properties of liquid Fe at high pressure and temperature have been studied using an ab initio molecular dynamics method. We have focused on four thermodynamic states at pressures of 27, 42, 50 and 58 GPa for which x-ray scattering data are available. The calculated static structure shows very good agreement with the available experimental data, including an asymmetric second peak which becomes more marked with increasing pressure. The dynamical structure reveals the existence of propagating density fluctuations and the associated dispersion relation has also been determined. The relaxation mechanisms for the density fluctuations have been analyzed in terms of a model with two decay channels (fast and slow, respectively). We found that the thermal relaxation proceeds along the slow decaying channel whereas the fast one is that of the viscoelastic relaxation. The possible coupling between longitudinal and transverse excitation modes has been investigated by looking at specific signatures in two wavevector regions: the first one is located around the position of the main peak of the structure factor, qp, as suggested by the recently reported appearance of high frequency transverse waves in liquid Li under high pressures; the second region is around qp/2, as suggested by the recent finding of transverse acoustic modes in inelastic x-ray scattering intensities of liquid Fe at ambient pressure. Finally, results are also reported for several transport coefficients.