Atomic Motion Research Articles

New pathways to control the evolution of the atomic motion in metallic glasses

Metallic glass formers are a relatively new entry in glass physics, which has attracted large interest in both physics and materials science communities due to the unique mechanical and structural properties of these materials. Physical aging is however one of the main obstacle to their widespread use as it affects their properties at all length scales. The knowledge of the microscopic mechanisms inducing aging and relaxation is therefore extremely important for both fundamental and applied sciences. In this article we present a review of the recent advances made with the X-ray photon correlation spectroscopy technique on the study of the collective particle motion and physical aging in metallic glasses at the atomic level. We show that a careful tuning of the sample preparation or the application of specific thermal protocols have the potential to drive the glass into more aged or rejuvenated microscopic configurations with different stabilities.

In Situ TEM Tracking of Disconnection Motion and Atomic Cooperative Reorientation in the Oriented Attachment of Pt Nanoparticles.

The oriented attachment (OA) of nanoparticles (NPs) is an important crystal growth mechanism in many materials. However, a comprehensive understanding of the atomic-scale alignment and attachment processes is still lacking. We conducted in situ atomic resolution studies using high-resolution transmission electron microscopy to reveal how two Pt NPs coalesce into a single particle via OA, which involves the formation of atomic-scale links and a grain boundary (GB) between the NPs, as well as GB migration. Density functional theory calculations showed that the system energy changes as a function of the number of disconnections during the coalescence process. Additionally, the formation and annihilation processes of disconnection are always accompanied by the cooperative reorientation motion of atoms. These results further elucidate the growth mechanism of OA at the atomic scale, providing microscopic insights into OA dynamics and a framework for the development of processing strategies for nanocrystalline materials.

Sampling Real-Time Atomic Dynamics in Metal Nanoparticles by Combining Experiments, Simulations, and Machine Learning.

Even at low temperatures, metal nanoparticles (NPs) possess atomic dynamics that are key for their properties but challenging to elucidate. Recent experimental advances allow obtaining atomic-resolution snapshots of the NPs in realistic regimes, but data acquisition limitations hinder the experimental reconstruction of the atomic dynamics present within them. Molecular simulations have the advantage that these allow directly tracking the motion of atoms over time. However, these typically start from ideal/perfect NP structures and, suffering from sampling limits, provide results that are often dependent on the initial/putative structure and remain purely indicative. Here, by combining state-of-the-art experimental and computational approaches, how it is possible to tackle the limitations of both approaches and resolve the atomistic dynamics present in metal NPs in realistic conditions is demonstrated. Annular dark-field scanning transmission electron microscopy enables the acquisition of ten high-resolution images of an Au NP at intervals of 0.6 s. These are used to reconstruct atomistic 3D models of the real NP used to run ten independent molecular dynamics simulations. Machine learning analyses of the simulation trajectories allow resolving the real-time atomic dynamics present within the NP. This provides a robust combined experimental/computational approach to characterize the structural dynamics of metal NPs in realistic conditions.

The effect of temperature on the mechanisms of Cu nanoparticle sintering: A molecular dynamic study

Surface diffusion is considered the primary mechanism for low temperature sintering properties of Cu nano-solders. However, how surface diffusion affects the sintering quality and couples with the structure evolution mechanism is still unclear. We conduct an amount of randomized molecular dynamics simulations and reveal a temperature-dependent nanoparticle sintering mechanism. The results exclude the influence of non-major factors such as different sizes and contact angles. The atomic fast dynamic motions appear mainly at the sintering neck at 600 K and induce structure evolutions. It contributes to an abnormal mechanical performance increase, which could be further enhanced by pressure. Further investigations show that the phenomenological evaluations could hardly predict the sintering quality, as the internal structure strongly influences the tension strength. This comprehensive investigation provides a clear view of the coupled influence of temperature and pressure from the perspective of atomic motions, showing insights into the behavior of nanoparticles during the sintering process.

A unified theory of tunneling times promoted by Ramsey clocks.

What time does a clock tell after quantum tunneling? Predictions and indirect measurements range from superluminal or instantaneous tunneling to finite durations, depending on the specific experiment and the precise definition of the elapsed time. Proposals and implementations use the atomic motion to define this delay, although the inherent quantum nature of atoms implies a delocalization and is in sharp contrast to classical trajectories. Here, we rely on an operational approach: We prepare atoms in a coherent superposition of internal states and study the time read-off via a Ramsey sequence after the tunneling process without the notion of classical trajectories or velocities. Our operational framework (i) unifies definitions of tunneling delay within one approach, (ii) connects the time to a frequency standard given by a conventional atomic clock that can be boosted by differential light shifts, and (iii) highlights that there exists no superluminal or instantaneous tunneling.

Low temperature (210 °C) fabrication of Ge MOS capacitor and controllability of its flatband voltage

Germanium (Ge) and germanium tin (GeSn) are strong candidate materials for novel electronic device such as spin MOS field-effect transistor (FET) or flexible devices. A high-quality insulating layer on Ge(Sn) should be formed at low temperatures to realize these applications. In this study, we fabricated a Ge MOS capacitor (CAP) and n-MOSFET with a SiO2/GeO2 gate dielectric using an electron cyclotron resonance plasma process and subsequent post-deposition annealing at a low temperature of 210 °C. The MOSCAPs show the typical electrical characteristics without significant degradation compared with the samples fabricated at a higher temperature of 450 °C. The n-MOSFET shows distinct output characteristics with clear saturation behavior and high current drivability. From the flatband voltage comparison among different annealing temperatures, high-temperature annealing induces the interface dipole formation in the gate insulator, significantly shifting flatband voltage to a negative direction. X-ray photoelectron spectroscopy analysis suggests that the origin of the interface dipole is oxygen atom movement at a SiO2/GeO2 interface. This information will be an important guideline for fabricating a high-quality insulator on Ge(Sn) at low temperatures.

Advances in the Dynamics of Adsorbate Diffusion on Metal Surfaces: Focus on Hydrogen and Oxygen.

Adsorbates on metal surfaces are typically formed from the dissociative chemisorption of molecules occurring at gas-solid interfaces. These adsorbed species exhibit unique diffusion behaviors on metal surfaces, which are influenced by their translational energy. They play crucial roles in various fields, including heterogeneous catalysis and corrosion. This review examines recent theoretical advancements in understanding the diffusion dynamics of adsorbates on metal surfaces, with a specific emphasis on hydrogen and oxygen atoms. The diffusion processes of adsorbates on metal surfaces involve two energy transfer mechanisms: surface phonons and electron-hole pair excitations. This review also surveys new theoretical methods, including the characterization of the electron-hole pair excitation within electronic friction models, the acceleration of quantum chemistry calculations through machine learning, and the treatment of atomic nuclear motion from both quantum mechanical and classical perspectives. Furthermore, this review offers valuable insights into how energy transfer, nuclear quantum effects, supercell sizes, and the topography of potential energy surfaces impact the diffusion behavior of hydrogen and oxygen species on metal surfaces. Lastly, some preliminary research proposals are presented.

Surface Alloyed-Zn promotes stability of Cu-Au catalysts toward electrochemical CO2 reduction reaction

The electrochemical reduction of carbon dioxide (CO2RR) is a subject of great economic and social relevance, as it represents a promising solution for the storage of renewable energy in the form of valuable chemical compounds and fuels. Bimetallic Cu-Au catalysts show great promise in efficient CO2-to-CO electrochemical conversion, particularly within a less Au content. However, the stability issue of Cu-Au catalysts always places obstacles on the long-term CO2RR application due to the metal dissolution issue. Here, we report a trimetallic Cu-Au-Zn catalyst in which a few amounts of Zn are incorporated into the CuAu alloy shell to promote the stability of Cu-Au catalysts for electrochemical CO2RR. The incorporation of a low concentration of Zn not only modifies the CO binding affinity but also alters the catalytic properties of nearby CuAu through geometric and electronic effects. A few amounts of Zn play a vital role in suppressing the surface pits and potentially preventing preferential corrosion at specific sites during electrochemical reaction conditions, thus, the catalyst surface is stabilized. The as-synthesized Cu-Au-Zn catalyst (Zn = 3 at. % and Au < 20 at. %) exhibits a high CO2-to-CO activity, holding a CO faradaic efficiency of 82 % in 0.1 M KHCO3 saturated with CO2 at −0.8 V, and also shows superior stability with no obvious current and selectivity degradation in 10 h, as compared to the Cu-Au counterparts. It is revealed that the surface alloyed Zn significantly alleviates the movement of metal atoms, offers dissolution resistance, and improves both structural and performance stability while retaining excellent CO2-to-CO conversion. These important findings provide a strategy to strengthen the promising Cu-Au CO2RR catalysts with a high noble-metal utilization. More importantly, the addition of few amounts of metals and alloying can promote the stability of functional materials under reaction conditions.

Dark resonance spectra of trapped ions under the influence of micromotion

We study the influence of micromotion on the spectrum of trapped ions with a lambda-type level scheme, leading to dark resonances due to coherent population trapping. We work with calcium ions trapped in a ring-shaped Paul trap, in which one can compensate excess micromotion for only one ion of the crystal. We observe that micromotion affects the shapes of the dark resonances and causes the appearance of “echoes” separated by intervals given by the drive frequency. We present a theoretical model that provides good fits to the measurements and can be used to estimate the amplitude of the micromotion modulation of the atomic motion. We estimate an effective temperature of the ions from the spectra and observe clear micromotion heating as well as impaired cooling for sufficiently large excess micromotion.

Dynamic three-dimensional structures of a metal–organic framework captured with femtosecond serial crystallography

Crystalline systems consisting of small-molecule building blocks have emerged as promising materials with diverse applications. It is of great importance to characterize not only their static structures but also the conversion of their structures in response to external stimuli. Femtosecond time-resolved crystallography has the potential to probe the real-time dynamics of structural transitions, but, thus far, this has not been realized for chemical reactions in non-biological crystals. In this study, we applied time-resolved serial femtosecond crystallography (TR-SFX), a powerful technique for visualizing protein structural dynamics, to a metal–organic framework, consisting of Fe porphyrins and hexazirconium nodes, and elucidated its structural dynamics. The time-resolved electron density maps derived from the TR-SFX data unveil trifurcating structural pathways: coherent oscillatory movements of Zr and Fe atoms, a transient structure with the Fe porphyrins and Zr6 nodes undergoing doming and disordering movements, respectively, and a vibrationally hot structure with isotropic structural disorder. These findings demonstrate the feasibility of using TR-SFX to study chemical systems.

A closer examination of the nature of atomic motion in the interfacial region of crystals upon approaching melting.

Although crystalline materials are often conceptualized as involving a static lattice configuration of particles, it has recently become appreciated that string-like collective particle exchange motion is a ubiquitous and physically important phenomenon in both the melting and interfacial dynamics of crystals. This type of collective motion has been evidenced in melting since early simulations of hard disc melting by Alder et al. [Phys. Rev. Lett. 11(6), 241-243 (1963)], but a general understanding of its origin, along with its impact on melting and the dynamics of crystalline materials, has been rather slow to develop. We explore this phenomenon further by focusing on the interfacial dynamics of a model crystalline Cu material using molecular dynamics simulations where we emphasize the geometrical nature and spatial extent of the atomic trajectories over the timescale that they are caged, and we also quantify string-like collective motion on the timescale of the fast β-relaxation time, τf, i.e., "stringlets." Direct visualization of the atomic trajectories in their cages over the timescale over which the cage persists indicates that they become progressively more anisotropic upon approaching the melting temperature Tm. The stringlets, dominating the large amplitude atomic motion in the fast dynamics regime, are largely localized to the crystal interfacial region and correspond to "excess" modes in the density of states that give rise to a "boson peak." Moreover, interstitial point defects occur in direct association with the stringlets, demonstrating a link between classical defect models of melting and more recent studies of melting emphasizing the role of this kind of collective motion.

Capturing interference variations of atomic motion in vibrational modes by non-resonant Raman images

Non-resonant Raman imaging associated with vibrational modes provides an optical means to structure and function characterisation for a single molecule, where the interference between atomic motions in a vibrational mode plays an important role. Taking the [18]annulene as a proof-of-the-concept molecule, we present here a comprehensive study on the dependence of non-resonant Raman images on interference variations involving the phase and amplitude of atomic displacements in vibrational modes. Calculations demonstrate that constructive and destructive phase interferences contribute to the characteristic merging and repulsion of Raman patterns, respectively, which should be attributed to the same/opposite signs of Raman polarisability. In addition, the imaging characteristic by constructive and destructive interferences become more significant with the increase of plasmonic size. Moreover, Raman images are highly sensitive to the subtle variations of interference induced by molecular symmetry and element substitution, highlighting the importance of amplitude variations of interference in modes for Raman images to monitor molecular structure changes. Our findings propose the capability of Raman images toward capturing interference variations in modes, serving as good references for Raman imaging to characterise various molecules and their corresponding structure changes by analysing interference effects in vibrational modes.

Differentiating Three-Dimensional Molecular Structures Using Laser-Induced Coulomb Explosion Imaging.

Coulomb explosion imaging (CEI) with x-ray free electron lasers has recently been shown to be a powerful method for obtaining detailed structural information of gas-phase planar ring molecules [R. Boll et al., X-ray multiphoton-induced Coulomb explosion images complex single molecules, Nat. Phys. 18, 423 (2022).NPAHAX1745-247310.1038/s41567-022-01507-0]. In this Letter, we investigate the potential of CEI driven by a tabletop laser and extend this approach to differentiating three-dimensional structures. We study the static CEI patterns of planar and nonplanar organic molecules that resemble the structures of typical products formed in ring-opening reactions. Our results reveal that each molecule exhibits a well-localized and distinctive pattern in three-dimensional fragment-ion momentum space. We find that these patterns yield direct information about the molecular structures and can be qualitatively reproduced using a classical Coulomb explosion simulation. Our findings suggest that laser-induced CEI can serve as a robust method for differentiating molecular structures of organic ring and chain molecules. As such, it holds great promise as a method for following ultrafast structural changes, e.g., during ring-opening reactions, by tracking the motion of individual atoms in pump-probe experiments.

Decoding Electrochemical Processes of Lithium‐Ion Batteries by Classical Molecular Dynamics Simulations

AbstractLithium‐ion batteries (LIBs) have played an essential role in the energy storage industry and dominated the power sources for consumer electronics and electric vehicles. Understanding the electrochemistry of LIBs at the molecular scale is significant for improving their performance, stability, lifetime, and safety. Classical molecular dynamics (MD) simulations could directly capture the atomic and molecular motions and thus provide dynamic insights into the electrochemical processes and ion transport in LIBs during charging and discharging that are usually challenging to observe experimentally, which is momentous in developing LIBs with superb performance. This review discusses developments in MD approaches using non‐reactive force fields, reactive force fields, and machine learning potential for modeling chemical reactions and transport of reactants in the electrodes, electrolytes, and electrode‐electrolyte interfaces. It also comprehensively discusses how molecular interactions, structures, transport, and reaction processes affect electrode stability, energy capacity, and interfacial properties. Finally, the remaining challenges and envisioned future routes are commented on for high‐fidelity, effective simulation methods to decode the invisible interactions and chemical reactions in LIBs.

Unraveling motion in proteins by combining NMR relaxometry and molecular dynamics simulations: A case study on ubiquitin.

Nuclear magnetic resonance (NMR) relaxation experiments shine light onto the dynamics of molecular systems in the picosecond to millisecond timescales. As these methods cannot provide an atomically resolved view of the motion of atoms, functional groups, or domains giving rise to such signals, relaxation techniques have been combined with molecular dynamics (MD) simulations to obtain mechanistic descriptions and gain insights into the functional role of side chain or domain motion. In this work, we present a comparison of five computational methods that permit the joint analysis of MD simulations and NMR relaxation experiments. We discuss their relative strengths and areas of applicability and demonstrate how they may be utilized to interpret the dynamics in MD simulations with the small protein ubiquitin as a test system. We focus on the aliphatic side chains given the rigidity of the backbone of this protein. We find encouraging agreement between experiment, Markov state models built in the χ1/χ2 rotamer space of isoleucine residues, explicit rotamer jump models, and a decomposition of the motion using ROMANCE. These methods allow us to ascribe the dynamics to specific rotamer jumps. Simulations with eight different combinations of force field and water model highlight how the different metrics may be employed to pinpoint force field deficiencies. Furthermore, the presented comparison offers a perspective on the utility of NMR relaxation to serve as validation data for the prediction of kinetics by state-of-the-art biomolecular force fields.

Coverage-Dependent Site-Specific Placement and Correlated Diffusion of Atomic Oxygen on Moiré-Patterned Graphene on Ru(0001).

Nano-periodic arrays of atomic oxygen are visualized on epitaxial graphene on Ru(0001) via STM following supersonic beam exposure to non-equilibrium fluxes of atomic oxygen. Self-organization of atomic oxygen on graphene is directed by the intrinsic moiré pattern of the ruthenium-graphene interface. Atom-resolved STM imaging reveals the richness of multiparticle interactions, leading to correlated atomic diffusion and placement. Pair-distribution functions demonstrate that repulsive oxygen-oxygen interactions play an increasingly important role in the site specificity and diffusivity of atomic oxygen on the moiré lattice with increasing coverage. Atomic visualization shows the number of oxygen atoms in a local region changes overall diffusion rates and promotes the correlated motion of oxygen atoms. Understanding the site specificity of oxygen adsorption and diffusive behavior of atomic oxygen on epitaxial graphene on Ru(0001) provides insight for both the synthesis and stability of moiré-templated two-dimensional materials which show promise as platforms for next-generation quantum materials and catalysts.

Compact quartz tuning fork-atomic force microscope with a low thermal drift at room temperature

A quartz tuning fork-atomic force microscope (QTF-AFM) is one of the useful research instruments for studying atomic or molecular-level dynamics in an ultra-high vacuum and low-temperature environment. In such conditions, movement of atoms or molecules is minimized, eliminating concerns about thermal drift. However, if it is possible to accurately measure atomic or molecular-level dynamics at room temperature, valuable information about atomic or molecular motion in real-life scenarios can be obtained. Nonetheless, the biggest obstacle in observing molecular-level motion at room temperature is the difficulty in precisely determining the position due to thermal drift. In this study, to address this issue, glass material was used instead of conventional metal materials as a system body, and the size was significantly reduced to create a compact QTF-AFM system. The aim was to minimize the system's thermal drift (∼2 p.m./s), thereby compensating for the challenge of accurately confirming positions affected by thermal drift.

Understanding layered compounds under high pressure

This Tutorial focuses on the physics of layered compounds under high pressure. We have chosen h-BN and III–VI layered materials as representative materials. h-BN layers are strictly two-dimensional. Layers in III–VI compounds are more complex, and subtle details in their structural behavior play an important role in the evolution of high pressure properties. They are also interesting because they contain a different number of layers in their primitive unit cell and/or have a different ionic character. We begin describing the structural evolution. We discuss the experimental challenges encountered as well as the main findings related to intra- and interlayer compressibility, polytype influence, and geometrical modifications induced by pressure inside the layers. We then describe lattice vibrations. The origin of the modes is reviewed, paying attention to the relationships between atom motions in different layers. We discuss the convenience of redefining the Grüneisen parameter and describe the behavior of rigid layer modes, soft modes, and Davidov pairs. The last section is devoted to the electronic properties. We show that the changes observed when passing from a single layer to a three-dimensional BN are qualitatively similar to those induced by high pressure. The pressure behavior of electronic transitions in III–VI layered compounds is very rich, revealing the subtle balance between intra- and inter-layer interactions. Finally, we take advantage of high pressure studies to explain the formation of the Mexican hat type of valence band at ambient conditions in single layers of InSe and GaSe, but not in three-dimensional compounds.

Unravelling the potential of Triflusal as an anti-TB repurposed drug by targeting replication protein DciA

The increasing prevalence of drug-resistant Tuberculosis (TB) is imposing extreme difficulties in controlling the TB infection rate globally, making treatment critically challenging. To combat the prevailing situation, it is crucial to explore new anti-TB drugs with a novel mechanism of action and high efficacy. The Mycobacterium tuberculosis (M.tb)DciA is an essential protein involved in bacterial replication and regulates its growth. DciA interacts with DNA and provides critical help in binding other replication machinery proteins to the DNA. Moreover, the lack of any structural homology of M.tb DciA with human proteins makes it an appropriate target for drug development. In this study, FDA-approved drugs were virtually screened against M.tb DciA to identify potential inhibitors. Four drugs namely Lanreotide, Risedronate, Triflusal, and Zoledronic acid showed higher molecular docking scores. Further, molecular dynamics simulations analysis of DciA-drugs complexes reported stable interaction, more compactness, and reduced atomic motion. The anti-TB activity of drugs was further evaluated under in vitro and ex vivo conditions where Triflusal was observed to have the best possible activity with the MIC of 25 μg/ml. Our findings present novel DciA inhibitors and anti-TB activity of Triflusal. Further investigations on the use of Triflusal may lead to the discovery of a new anti-TB drug.

Effect of Cross Nanowall Surface on the Onset Time of Explosive Boiling: A Molecular Dynamics Study

Explosive boiling is a fast-phase transition from an ultra-thin liquid film to vapor under an extremely high heat flux, which typically has been studied using the molecular dynamics simulation (MDS) method. The present MDS study investigated the explosive boiling of a liquid argon nanofilm over different solid copper surfaces with different nanowall patterns, including parallel and cross nanowalls. For each surface, atomic motion trajectories, the number of liquid and vapor argon atoms, heat flux, and, mainly, the onset time of explosive boiling were investigated. The simulation results indicated that explosive boiling occurs earlier on parallel and cross nanowall surfaces than on an ideally smooth surface, regardless of the topology and configuration of the nanowalls. Moreover, the results revealed that by using the cross nanowall surfaces, the onset time of explosive boiling decreased by 0.7–4% compared to the parallel nanowall surfaces. In addition, it was found that the onset time of explosive boiling strongly depends on the potential energy barrier and the movement space between nanowalls for both parallel and cross nanowall surfaces. Furthermore, the simulation findings showed that even though increasing the height of cross nanowalls increases the heat flux and temperature of the fluid argon domain, it does not necessarily result in a shorter onset time for explosive boiling. These findings demonstrate the capability of cross nanowall surfaces for explosive boiling, thereby being utilized in future surface design for thermal management applications.