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Atomistic mechanisms of dynamics in a two-dimensional dodecagonal quasicrystal
Quasicrystals have been observed in a variety of materials ranging from metal alloys to block copolymers. However, their structural and dynamical properties cannot be readily described in terms of conventional solid-state models of liquids and solids. We may expect the dynamics of this specific class of quasicrystalline materials to be more like glass-forming liquids in the sense of exhibiting large fluctuations in the local mobility (“dynamic heterogeneity”) and non-Arrhenius temperature dependence of relaxation and diffusion. In this work, we investigate a model dodecagonal quasicrystal material in two dimensions (2D) using molecular dynamics simulations, with a focus on heterogeneous dynamics and non-Arrhenius relaxation and diffusion. As observed in glass-forming liquids and heated crystals, we observe a two-stage relaxation dynamics in the self-intermediate scattering function Fs(k, t) of our quasicrystal material. It involves a fast β-relaxation and α-relaxation process having a highly temperature dependent relaxation time whose activation energy varies in concert with the extent of string-like collective motion, a phenomenon recognized to occur in glass-forming liquids at low temperatures and crystalline materials at elevated temperatures. After examining the dynamics of our dodecagonal quasicrystalline material in great detail, we conclude that the dynamics of these materials more closely resembles observations on metallic glass-forming liquids than crystalline materials.
Data-driven assessment of optimal spatiotemporal resolutions for information extraction in noisy time series data
In general, comprehension of any type of complex system depends on the resolution used to examine the phenomena occurring within it. However, identifying a priori, for example, the best time frequencies/scales to study a certain system over time, or the spatial distances at which correlations, symmetries, and fluctuations are most often non-trivial. Here, we describe an unsupervised approach that, starting solely from the data of a system, allows learning the characteristic length scales of the dominant key events/processes and the optimal spatiotemporal resolutions to characterize them. We tested this approach on time series data obtained from the simulation or experimental trajectories of various example many-body complex systems ranging from the atomic to the macroscopic scale and having diverse internal dynamic complexities. Our method automatically analyzes the system data by analyzing correlations at all relevant inter-particle distances and at all possible inter-frame intervals in which their time series can be subdivided, namely, at all space and time resolutions. The optimal spatiotemporal resolution for studying a certain system thus maximizes information extraction and classification from the system’s data, which we prove to be related to the characteristic spatiotemporal length scales of the local/collective physical events dominating it. This approach is broadly applicable and can be used to optimize the study of different types of data (static distributions, time series, or signals). The concept of “optimal resolution” has a general character and provides a robust basis for characterizing any type of system based on its data, as well as to guide data analysis in general.
High pressure structural and lattice dynamics study of <i>α</i>-In2Se3
Layered α-In2Se3 has been studied using a combined in situ synchrotron angle-dispersive powder x-ray diffraction and Raman spectroscopy study in a diamond anvil cell up to 60+ GPa, at room temperature. Helium, which remains fairly hydrostatic up to the highest pressure in this study, was used as the pressure-transmitting medium. The results from both experimental methods reveal a pressure-induced structural phase transition from α-In2Se3 to a monoclinic β′-In2Se3 structure at ≈1 GPa, in agreement with previous studies. Based on our detailed measurements using both experimental techniques and the F–f formalism, the β′-In2Se3 structure remains stable up to 45 GPa, without a clear indication of a phase transition toward the previously reported β-In2Se3 phase. Above this pressure, In2Se3 adopts a disordered solid-solution-like orthorhombic structure, phase IV. The results are discussed in comparison with the relevant previous studies of α-In2Se3 under pressure.
Long timescale solvation dynamics and confinement: The case of non-ionic deep eutectic solvents of lauric acid and N-methylacetamide
Microscopic segregation and molecular heterogeneities in complex liquids are the result of the interplay between different intermolecular forces, all of which contribute to the energy landscape of the system. A consequence of the intricate energy landscape is the nontrivial effect on the solvation dynamics. Here, the impact of molecular heterogeneities on the solvation dynamics is studied using infrared spectroscopies and molecular dynamics simulations. In particular, this study focuses on the dynamical effect of nanoscopic heterogeneities present in deep eutectic solvents (DESs) composed of lauric acid (LA) and N-methylacetamide (NMA). To this end, a molecular probe containing a carbon triple bond is used as an infrared reporter. The results show that the vibrational probe is likely to be located in the NMA polar domains. Furthermore, the probe solvation dynamics derived from the 2DIR spectra presents a slowdown of its timescale with increasing LA concentration in the DES. Kubo modeling of the probe solvation dynamics shows a correlation between the amplitude of its long time component and the presence of molecular heterogeneities in the sample. Semiclassical modeling of the vibrational line shape of the triple bond stretch demonstrates that the heterogeneities affect the whole solvation dynamics of the system through the amplitudes of the frequency fluctuations. Molecular dynamics simulations confirm the experimental results and their interpretation by showing a slowdown of the solvation dynamics when the LA heterogeneities are present. Overall, the study presents a molecular framework to explain the effect of confinement created by nanoscopic LA heterogeneities on the solvation dynamics of the system.
Penetration of surface effects on structural relaxation and particle hops in glassy films
A free surface induces enhanced dynamics in glass formers. We study the dynamical enhancement of glassy films with a distinguishable-particle lattice model of glass free of elastic effects. We demonstrate that the thickness of the surface mobile layer depends on temperature differently under different definitions, although all are based on local structure relaxation rate. The rate can be fitted to a double exponential form with an exponential-of-power-law tail. Our approach and results exclude elasticity as the unique mechanism for the tail. Layer-resolved particle hopping rate, potentially a key measure for activated hopping, is also studied but it exhibits much shallower surface effects.
Continuum models for metal nanoparticles coupled to real-space real-time time-dependent DFT treatments of molecules
Plasmonic nanoparticle effects on nearby molecules can be treated within the Polarizable Continuum Model (PCM-NP). Numerically, PCM-NP relies on the Boundary Element Method (BEM), whereby nanoparticle polarization due to external electric fields is given in terms of point charges located on its meshed surface. Density Functional Theory (DFT) and time-dependent DFT descriptions for molecules can be performed using a real-space grid. However, combining the standard BEM of PCM-NP with a real-space quantum-mechanical treatment for molecules physisorbed on large nanoparticles (beyond ∼1 nm of radius) quickly faces memory bottlenecks for typical high performance computing architectures. In fact, the 3D spatial grid should be taken large enough to fit the entire NP, in order to interpolate the electrostatic potential at its surface. We propose a new BEM (dubbed dummy-surface BEM or ds-BEM, for short) to handle effectively PCM-NP calculations with a real-space grid and implement it in the widespread Octopus code. Our ds-BEM maps the electrostatic BEM problem from the actual physical interface at the nanoparticle surface to a compact surface around the molecule, which can be embedded in the small-sized real-space grid used in gas-phase calculations. To show the accuracy of ds-BEM results, we benchmark it against standard BEM for real-space and real-time nonequilibrium electronic dynamics of a prototypical system (namely, p-nitroaniline close to a small, gold nanoparticle) computed at the level of time-dependent density functional theory. Absorption and Raman spectra obtained from BEM and ds-BEM show remarkable agreement, opening up the extension of PCM-NP to all property simulations accessible via Octopus.
Dynamic buckling of Si tetramers on the Si(111)-7 × 7 surface
The atomic structure of Si tetramers that form on the Si(111)-7 × 7 surface during homoepitaxy is investigated by means of first-principles calculations with the currently available atomistic model as a starting point. It is demonstrated that the rectangular shape of the Si tetramer is unstable against buckling. The comparison of the calculated results with the available scanning tunneling microscopy (STM) data provides a new understanding of the problem, indicating that the recorded STM images are influenced by dynamic buckling.
Molecular dynamics study on hydrogen permeation behavior and mechanism in polyethylene type IV hydrogen storage cylinder liner
Polyethylene (PE) and other thermoplastic polymers are commonly used as liners for type IV hydrogen storage cylinders but are prone to hydrogen permeation in high-pressure environments, which can cause material degradation and safety risks, such as hydrogen leakage. In this study, the atomic structures of PE and H2 are modeled using molecular dynamics simulations and grand canonical Monte Carlo methods. This research investigates the free volume distribution in PE and the mechanisms of hydrogen dissolution and diffusion under different temperature and pressure conditions. Solubility and diffusion coefficients were calculated from adsorption isotherms and mean squared displacement curves, respectively. The results show that solubility, diffusion, and permeability coefficients of H2 in PE increase with temperature but decrease with pressure. Higher temperature increases molecular chain movement, generating more free volume, while higher pressure compresses the molecular chains, reducing free volume. Hydrogen density maps indicate that H2 dissolves mainly in the free volume of PE. The diffusion mechanism follows an “oscillating + hopping” model, as shown in the H2 trajectory graphs. This study provides a microscopic understanding of hydrogen permeation in polymers, offering valuable insights for optimizing and ensuring the safe use of liner materials in type IV hydrogen storage tanks.
An investigation of the dynamics of the ionization/dissociation in SF6 with femtosecond pulses
We systematically investigated the ionization and dissociation of SF6 in strong laser fields. The dependence of ion yield on laser intensity and the kinetic energy distributions and angular distributions of fragment ions were also measured. The observed sequence of fragment ions is consistent with the predictions of strong-field ionization theory. The kinetic energy distributions of the Fq+ (q = 1–3) fragment ions are presented. Using a point charge model, we propose that the structure-symmetric dissociation (SSD) explains the origin of the kinetic energy of Fq+ ions. Furthermore, we identify the relevant channels and the kinetic energies of the Fq+ fragment ions produced by these channels. These results are in excellent agreement with the experimental data. The angular distributions of the Fq+ and Sq+ (q = 3, 5) ions are all anisotropic and isotropic, respectively. This is the result of the SSD process of the parent ion. However, the anisotropic component in the angular distribution of SFn+ (n = 1–4), SFn2+ (n = 2, 4), and Sq+ (q = 1, 2) suggests that the molecular structure has undergone deformation by the presence of the laser field. A comparison of the time-of-flight (TOF) spectra of fragment ions under linearly polarized and circularly polarized laser fields reveals that the SF6 molecule exhibits negligible dynamic alignment in the laser field, with geometric alignment being the dominant mechanism. Furthermore, the rescattering process plays a significant role in the production of SFn2+ (n = 2, 4) ions. The dynamics of the ionization/dissociation mechanism are discussed in the context of the TOF mass spectra, kinetic energies, and angular distributions recorded for SF6.
Quantum transport in the presence of a chiral molecular potential
We investigate quantum transport in a two-dimensional electron system coupled to a chiral molecular potential, demonstrating how molecular chirality and orientation affect charge and spin transport properties. We propose a minimal model for realizing true chiral symmetry breaking on a magnetized surface, with a crucial role played by the tilt angle of the molecular dipole with respect to the surface. For non-zero tilting, we show that the Hall response exhibits clear signatures of chirality-induced effects, in both charge- and spin-resolved observables. Concerning the former, tilted enantiomers produce asymmetric Hall conductances and, even more remarkably, the persistence of this feature in the absence of spin–orbit coupling (SOC) signals how the enantiospecific charge response results from electron scattering off the molecular potential. Concerning spin-resolved observables where SOC plays a relevant role, we reveal that chiral symmetry breaking is crucial in enabling spin-flipping processes.
Can intramolecular rotors govern the thermal conductivity of molecular materials?
Controlling thermal transport at the nanoscale through phonon engineering remains a significant challenge in thermal management and nanodevice design. Molecular materials present a promising pathway for thermal control owing to their structural flexibility and dynamic behavior encompassing both intra- and intermolecular motions. However, the influence of these dynamics on thermal transport remains poorly understood. This study focuses on intramolecular rotation as a representative motion within molecular materials. These rotations are characterized by low-frequency spectra but fall outside the classification of standard normal modes. Through theoretical calculations, we assessed the thermal conductivity of self-assembled molecular multilayers, investigating the role of hindered and free rotations within these layers in influencing thermal transport. Our findings reveal that intramolecular rotation has minimal impact on thermal transport, even as rotational modes shift from cooperative hindered rotation to nearly free rotation through thermal activation. In contrast, intermolecular dynamics—particularly interlayer motions—play a dominant role in determining thermal conductivity. These motions drive the transition from ballistic to diffusive transport through thermal activation. These findings highlight intermolecular dynamics as the primary modes for thermal control, while interactions between intramolecular dynamics and thermal conduction pathways remain weak.
A time averaged semiclassical approach to the computation of nonadiabatic vibronic absorption spectra
In this work, we propose a method to compute semiclassical absorption spectra of nonadiabatic systems. We first report the working formula for the absorption cross section for diabatically coupled systems and review the main features of the Meyer–Miller–Stock–Thoss Hamiltonian and its semiclassical propagation. Then, by combining the mapped Hamiltonian and the initial value representation formalism, we introduce a time-averaged semiclassical method for the calculation of the absorption spectrum, which also accounts for nonadiabatic effects in vibronic spectroscopy. After improving an already existing symplectic algorithm for the symplectic phase space propagation, we consider a model system to benchmark our semiclassical approach against exact quantum mechanical calculations. Finally, we test our method on the four mode model of pyrazine—a fundamental benchmark in the field of nonadiabatic vibronic spectroscopy—for understanding the potentiality and limitations of our semiclassical approach.
Quantum alternating operator ansatz for the preparation and detection of long-lived singlet states in NMR
Designing efficient and robust quantum control strategies is vital for developing quantum technologies. One recent strategy is the Quantum Alternating Operator Ansatz (QAOA) sequence that alternatively propagates under two noncommuting Hamiltonians, whose control parameters can be optimized to generate a gate or prepare a state. Here, we describe the design of a QAOA sequence to prepare long-lived singlet states (LLSs) from the thermal state in NMR. With extraordinarily long lifetimes exceeding the spin–lattice relaxation time constant T1, LLSs have been of great interest for various applications, from spectroscopy to medical imaging. Accordingly, designing sequences for efficiently preparing LLS in a general spin system is crucial. Using numerical analysis, we study the efficiency and robustness of our QAOA sequence over a wide range of errors in the control parameters. Using a two-qubit NMR register, we conduct an experimental study to benchmark our QAOA sequence against other prominent methods of LLS preparation and observe superior performance, especially under noisy conditions. Finally, we numerically demonstrate the applicability of our QAOA sequence beyond two-qubit registers, specifically for polychromatic excitation of delocalized LLS in a six-proton system.
Vibrational dynamics of iron pentacarbonyl [Fe(CO)5] in liquid alkanes revisited
We explore the solvent-dependence of the vibrational dynamics of Fe(CO)5 (IPC) using a novel 2D-IR setup. A 320 pixel MCT camera allows us to achieve high spectral resolution within a large detection window, which can be matched in excitation by scanning coherence times of up to 250 ps. The dynamics of the IR active modes of IPC in the C≡O stretching range are probed in a series of alkanes of different chain lengths and viscosities. 2D-IR maps at short waiting times reveal the detailed anharmonic structure of the modes at play: we determined the cross-anharmonicity between the A2″ and E′ modes (δ = −0.8 ± 0.1 cm−1), and we are able to differentiate the diagonal anharmonicity of the doubly degenerate mode (ΔE ≃ 18 cm−1) from its non-diagonal anharmonicity (ΔEE ≃ 11 cm−1). Our analysis of the polarization dependence of the 2D-IR signals strongly confirms an exchange mechanism between the IR-active modes due to Berry pseudo-rotation, which shows very little dependence on solvent viscosity, in contrast to the anisotropy loss. The implications of our findings for the exchange mechanism are discussed.
Normalized topological indices discriminate between architectures of branched macromolecules
Branching architecture characterizes numerous systems, ranging from synthetic (hyper)branched polymers and biomolecules such as lignin, amylopectin, and nucleic acids to tracheal and neuronal networks. Its ubiquity reflects the many favorable properties that arise because of it. For instance, branched macromolecules are spatially compact and have a high surface functionality, which impacts their phase characteristics and self-assembly behavior, among others. The relationship between branching and physical properties has been studied by mapping macromolecules to mathematical trees whose architecture can be characterized using topological indices. These indices, however, do not allow for a comparison of macromolecules that map to trees of different sizes, be it due to different mapping procedures or differences in their molecular weight. To alleviate this, we introduce a novel normalization of topological indices using estimates of their probability density functions. We construct a phase space using two normalized topological indices, which enables a robust discrimination between different architectures of branched macromolecules. We demonstrate the necessity of such a phase space on two practical applications, one being ribonucleic acid molecules with various branching topologies and the other different methods of coarse-graining branched macromolecules. Our approach can be applied to any type of branched molecule and extended as needed to other topological indices, making it useful across a wide range of fields where branched molecules play an important role, including polymer physics, green chemistry, bioengineering, biotechnology, and medicine.
Osmolyte effects on water diffusion: Urea induces changes in the entropic barrier, TMAO in the energetic barrier
Osmolytes have attracted significant interest for their effects on protein structures. Prototypical examples are urea and trimethylamine N-oxide (TMAO), which destabilize and stabilize folded proteins, respectively. Whether the origin of these effects lies in direct osmolyte–protein interactions or indirect perturbations of the water solvent is still not fully clear. In this Communication, the details of the latter mechanism are investigated both theoretically and experimentally by examining how the two osmolytes influence water diffusion as a function of their concentration up to 8M. Addition of both urea and TMAO slow water diffusion, the latter more strongly. Importantly, the associated activation energies, characterized in detail here for the first time, show dramatically different driving forces underlying these behaviors: urea modestly lowers the water diffusion activation energy while TMAO strongly increases it.
Rotational quenching of monofluorides in a cryogenic helium bath
Buffer gas cooling, one of the most relevant direct cooling techniques for cooling molecules, relies on dissipating the energy of the molecule via collisions with a buffer gas. The cooling efficiency hinges on the molecule-atom scattering properties, concretely, on the transport properties. This work presents a global study on the interactions, collision dynamics, and transport properties of monofluoride molecules (X–F), with X being a metal, in the presence of a cold He buffer gas. The interactions are calculated using ab initio quantum chemistry methods, and the dynamics is treated fully quantal, assuming the monofluoride molecule is a rigid rotor. The resulting thermalization and rotational quenching rates are analyzed in light of the distorted-wave Born approximation, yielding an explanation based on the elemental physical properties of the molecule under consideration. Therefore, our findings contribute to understanding the rotational quenching of molecules in a cold buffer gas.
Improved algorithm for identifying partial saddle-points in polymer field theoretic simulations
Field-theoretic simulations that rely on a partial saddle-point approximation have become powerful tools for studying complex polymer materials. The computational cost of such simulations depends critically upon the efficiency of the iterative algorithm used to identify a partial saddle-point field configuration during each step of a stochastic simulation. We introduce a new algorithm for this purpose that relies on a physically motivated approximation in which the linear response of the density to a small change in a pressure-like field is approximated by the response of a hypothetical homogeneous system. The computational cost of the resulting algorithm is significantly less than that of the commonly used Anderson mixing algorithm.
Proposal of a reaction mechanism for the thermal carbonation of ethylene oxide by CO2 in ionic liquids
We revisit a possible mechanism for the thermal conversion of the title reaction, which appears to be driven by solvent effects by the ionic liquid (IL) dihydroxyethyldiethyl ammonium bromide Net2HE2Br. The effect of the solvent is discussed following two complementary models, namely, an explicit solvation approach, suggesting that the IL can be acting as a catalyst, and an implicit solvation model showing that stabilization/destabilization of the stationary points in the potential (free) energy, confirming that the epoxide ring opening is the rate determining step. The IL plays a key role in the activation of ethylene oxide, where the cation of the IL provides an efficient hydrogen bond to the epoxide moiety, together with a concerted approach of the Br− counterion. The activation step of the proposed mechanism is rationalized on the basis of a second order Fukui response function within the conceptual density functional theory. The proposed mechanism suggests a global third order reaction rate: order one in the cation and anion forming the IL structure and order one with respect to ethylene oxide.
Medium-range order and compositional correlation in metallic glasses
The compositional atomic ordering in metallic glasses was studied by simulation focusing on the medium-range order (MRO). Many metallic alloy liquids and glasses show MRO characterized by the oscillations in the atomic pair-distribution function (PDF) beyond the first peak, which decay exponentially with distance. To study the effects of the local chemical order on MRO, we examine the compositionally resolved PDF and its MRO for models of various binary metallic alloy glasses. We show that compositional ordering is limited mostly to the nearest-neighbor atoms and the MRO is largely independent of the compositional order. For some elements that strongly repel each other in the alloy, a second MRO periodicity is observed owing to the distinct correlations among them. These results are discussed in light of the idea that the MRO oscillations in the PDF describe the correlations in the atomic density fluctuations, rather than the detailed local atomic structure.