Atomic Dynamics Research Articles

Vibrational properties of YbAs2S4 and YbAs2Se4 compounds: by infrared spectroscopy

The atomic dynamics and vibrational properties of YbAs2S4 and YbAs2Se4 compounds has been studied. The studies were carried out by infrared spectroscopy at room temperature in the frequency range ν = 400–2000 cm−1. When analyzing the obtained spectra, 8 main maxima were observed. As a result of the analysis, it was found that these maxima correspond to the vibrations of the metal (As) – chalcogen (S,Se) bonds. The differences in the infrared spectra of the YbAs2S4 and YbAs2Se4 compounds are explained by the difference in the ionic radii of the sulfur and selenium atoms in the divalent state.

The DREAM Endstation at the Linac Coherent Light Source

Free-electron lasers (FEL), with their ultrashort pulses, ultrahigh intensities, and high repetition rates at short wavelength, have provided new approaches to Atomic and Molecular Optical Science. One such approach is following the birth of a photo electron to observe ion dynamics on an ultrafast timescale. Such an approach presents the opportunity to decipher the photon-initiated structural dynamics of an isolated atomic and molecular species. It is a fundamental step towards understanding single- and non-linear multi-photon processes and coherent electron dynamics in atoms and molecules, ultimately leading to coherent control following FEL research breakthroughs in pulse shaping and polarization control. A key aspect for exploring photoinduced quantum phenomena is visualizing the collective motion of electrons and nuclei in a single reaction process, as dynamics in atoms/ions proceed at femtosecond (10−15 s) timescales while electronic dynamics take place in the attosecond timescale (10−18 s). Here, we report on the design of a Dynamic Reaction Microscope (DREAM) endstation located at the second interaction point of the Time-Resolved Molecular and Optical (TMO) instrument at the Linac Coherent Light Source (LCLS) capable of following the photon–matter interactions by detecting ions and electrons in coincidence. The DREAM endstation takes advantage of the pulse properties and high repetition rate of LCLS-II to perform gas-phase soft X-ray experiments in a wide spectrum of scientific domains. With its design ability to detect multi-ions and electrons in coincidence while operating in step with the high repetition rate of LCLS-II, the DREAM endstation takes advantage of the inherent momentum conservation of reaction product ions with participating electrons to reconstruct the original X-ray photon–matter interactions. In this report, we outline in detail the design of the DREAM endstation and its functionality, with scientific opportunities enabled by this state-of-the-art instrument.

On Atomic Lifetimes and Environmental Density

Atomic lifetime measurements span a wide range, from attoseconds to years. The frontier of exploratory lifetime measurements, presently, is in the long part of the above time range, with an eye on astrophysical problems. In a combination of review paper, tutorial, and Editorial, the physical environments and experiments are discussed, in which the results of such lifetime measurements matter. Although accurate lifetime measurement results are important for our understanding of atomic structure and dynamics, and for the diagnostics of various plasma environments, the order of magnitude is often precise enough to see why time resolution may be of interest in an experiment, from laser-produced plasmas of high densities to planetary nebulae of very low densities.

Direct visualization of cooperative adsorption of a string-like molecule onto a solid.

Natural systems, composite materials, and thin-film devices adsorb macromolecules in different phases onto their surfaces. In general, polymer chains form interfacial layers where their aggregation states and thermal molecular motions differ from the bulk. Here, we visualize well-defined double-stranded DNAs (dsDNAs) using atomic force microscopy and molecular dynamics simulations to clarify the adsorption mechanism of polymer chains onto solid surfaces. Initially, short and long dsDNAs are individually and cooperatively adsorbed, respectively. Cooperative adsorption involves intertwining of multiple chains. The dependence of adsorption on the chain affects the formation of the interfacial layer, realizing different mechanical properties of DNA/filler bulk composites. These findings will contribute to the development of light and durable polymer composites and films for various industrial, biomedical, and environmental applications.

Molecular insights on the crystalline cellulose-water interfaces via three-dimensional atomic force microscopy.

Cellulose, a renewable structural biopolymer, is ubiquitous in nature and is the basic reinforcement component of the natural hierarchical structures of living plants, bacteria, and tunicates. However, a detailed picture of the crystalline cellulose surface at the molecular level is still unavailable. Here, using atomic force microscopy (AFM) and molecular dynamics (MD) simulations, we revealed the molecular details of the cellulose chain arrangements on the surfaces of individual cellulose nanocrystals (CNCs) in water. Furthermore, we visualized the three-dimensional (3D) local arrangement of water molecules near the CNC surface using 3D AFM. AFM experiments and MD simulations showed anisotropic water structuring, as determined by the surface topologies and exposed chemical moieties. These findings provide important insights into our understanding of the interfacial interactions between CNCs and water at the molecular level. This may allow the establishment of the structure-property relationship of CNCs extracted from various biomass sources.

Anharmonic lattice dynamics from vibrational dynamical mean-field theory

We present a vibrational dynamical mean-field theory (VDMFT) of the dynamics of atoms in solids with anharmonic interactions. Like other flavors of DMFT, VDMFT maps the dynamics of a periodic anharmonic lattice of atoms onto those of a self-consistently defined impurity problem with local anharmonicity and coupling to a bath of harmonic oscillators. VDMFT is exact in the harmonic and molecular limits, nonperturbative systematically improvable through its cluster extensions, usable with classical or quantum impurity solvers (depending on the importance of nuclear quantum effects) and can be combined with existing low-level diagrammatic theories of anharmonicity. When tested on models of anharmonic optical and acoustic phonons; we find that classical VDMFT gives good agreement with classical molecular dynamics, including the temperature dependence of phonon frequencies and lifetimes. Using a quantum impurity solver, signatures of nuclear quantum effects are observed at low temperatures. We test the description of nonlocal anharmonicity via cellular VDMFT and the combination with self-consistent phonon (SCPH) theory, yielding the powerful SCPH $+$ VDMFT approach.

In Situ TEM Observation of the Atomic Transport Process during the Coalescence of Au Nanoparticles.

In practical applications, the coalescence of metal nanoparticles (NPs) is a major factor affecting their physical chemistry properties. Currently, due to a lack of understanding of the atomic-level mechanisms during the nucleation and growth stages of coalescence, the correlation between the different dynamic factors in the different stages of NP coalescence is unclear. In this study, we used advanced in situ characterization techniques to observe the formation of atomic material transport channels (Au chains) during the initiation of coalescence nucleation. We focused on the movement and migration states of Au atoms and discovered an atomic ordered arrangement growth mechanism that occurs after the completion of nucleation. Simultaneously, we used density functional theory to reveal the formation principle of Au chains. These findings improve our understanding of the atomic-scale coalescence process, which can provide a new perspective for further research on coalescence atomic dynamics.

Spectral approaches in momentum space for dynamics of atoms in strong laser fields: application to long pulses and low-frequency regime

In this work, we present in detail a novel approach to solve the time-dependent Schrödinger equation in the momentum space (TDSE-). It is based on the expansion of the electron wavepacket and the nonlocal interacting Coulomb potential in a Coulomb Sturmian basis. It allows a spectral treatment of the TDSE- from which another formulation of our previous model potential is proposed. This latter enables us to go easily beyond the 1s + 2sp states, and accordingly, may help to have more insight on the role of the Coulomb potential or the atomic structure in the ionization process. In order to bring out the improvement of this approximation and as an illustration, the case of 3spd states supported by the Coulomb potential is derived analytically, leaving the other cases for later investigations. Physical observables such as oscillator strengths, bound states populations, ionization probabilities, energy spectra, momentum and energy-angle distributions, are described in detail and their formulas employed in our ab initio computations are given in compact matrix forms The calculations can be done either by using the ionized wave function or by projecting the wavepacket onto the incoming Coulomb wave function. For illustrative purpose, we apply these theories in the dipole approximation to two one-electron atomic targets initially prepared in the ground and excited electronic states, and driven by intense low-frequency electromagnetic fields. We consider several laser parameters for long pulses recently reported in the literature. Our results compare remarkably well with reference data of atomic structure, and their agreement with the atomic dynamics outcome of previous treatments is quite satisfactory.

On the development of relativistic distorted wave approximation for the energies and collision dynamics of atoms or ions subjected to the outside plasma

In this manuscript, we present the development of a relativistic distorted wave method for determining the energies and collision dynamics of plasma-immersed atoms or ions. The methodology is based on the Dirac–Coulomb Hamiltonian, in which contributions from relativity and higher order effects, such as quantum electrodynamics and Breit interaction, are incorporated. The key element in this method is that a modified Debye–Hückel approximation is employed to represent the effect of plasma screening. In order to correctly describe the (bound and continuous state) wave functions, a self-consistent field calculation incorporating the shielding potential is performed within the fully relativistic framework. The particle interaction within the scattering matrix element of the excitation process is described by the shielded Coulomb interaction. The present technique is illustrated by calculations of energy, line shift, transition probability, electron-impact excitation/ionization cross section, and photoionization cross section of a few-electron system confined in plasma environments. The present model is tested and validated against a number of known cases (simulations are made for the He-like Al11+ ion) in the literatures. Numerical results demonstrate that the modifications to the Coulomb potential proposed in the spatial and temporal criteria of the Debye–Hückel approximation allow us to improve the theoretical description of the plasma shielding and thus the dynamical processes in dense plasmas. Comparisons of our computational predictions and the recent experimental measurements are performed. The current work not only has far-reaching implications for our understanding of the dense plasma screening, but also has potential applications in fusion, laboratory astrophysics, and related disciplines.

Strain-Induced asymmetry and on-site dynamics of silicon defects in graphene

• DFT calculations predict two distinct isomers for Si defects in strained graphene. • STEM images capture transitions between distinct Si structures with the same bonding. • Anisotropic strain can be generated and also exposed by Si defects in graphene. In the last decade, the atomically-focused electron beams utilized in scanning transmission electron microscopes (STEMs) have been shown to induce a broad set of local structural transformations in materials, opening pathways for directing material synthesis and modification atom-by-atom. The mechanisms underlying these transformations remain largely unknown, due to the intractability of modeling the myriad of reaction pathways that can be accessed through high-energy electron scattering. The information on materials’ structure and dynamics that can be extracted from STEM images is similarly left underexplored. Here, we report the observation of anomalous on-site dynamics of individual silicon impurity atoms in graphene during STEM imaging. Density functional theory-based structural optimizations of anisotropically-strained molecular nanographenes reveal two distinct (but nearly degenerate) stable structures for four-fold coordinated silicon impurities, where interconversion between the two structures manifests slight changes of the silicon position within the lattice site. Implications for defect-based strain engineering in graphene are discussed.

Effect of modifier on Low-Temperature reversible aging behavior of asphalt binder and its morphology analysis

• Rubber powder can alleviate the effect of reversible hardening on asphalt binders. • The addition of modifiers can reduce the reversible hardening degree of the asphalt binder. • Cone penetration test can be used to characterize the reversible hardening degree of the asphalt binder. • With the extension of conditioning time, the average area of asphalt binder “bee” structure increases gradually. Reversible aging of asphalt binders is one of the reasons for the premature failure of asphalt pavements. To better understand the effect of modifier types on the reversible aging in asphalt binder, styrene–butadienestyrene (SBS), styrene-butadiene rubber (SBR), crumb rubber (CR), and Nano-CaCO 3 were selected to prepare modified asphalt binder. Firstly, an extended bending beam rheometer (Ex-BBR) test and a cone penetration test (CPT) were carried out on base asphalt (BA) and modified asphalt binders under different conditions. Secondly, the reversible aging behavior of asphalt binders was characterized using a logistic regression model. Furthermore, the mechanisms of asphalt reversible aging were analyzed by atomic force microscopy (AFM) and molecular dynamics (MD) simulation. The results show that the addition of modifiers affects the reversible aging behavior of asphalt binders. Compared with SBS, SBR, and nano-CaCO 3 , CR can improve the mobility of asphalt molecules and mitigate the aggregation of asphalt molecules, thereby alleviating the impact of reversible aging on asphalt binder performance. After 72 h low-temperature conditioning, CR modified asphalt binder has the smallest grade loss of 1.7 °C. The low-temperature conditioning time can greatly affect the microstructure of the asphalt binder. With the increase of low-temperature conditioning time, the average area of the asphalt binder’s “bee” structures increases linearly. Furthermore, the reversible aging behavior of asphalt binders can be better understood using MD simulation.

Analysis of propagating wave structures of the cold bosonic atoms in a zig-zag optical lattice via comparison with two different analytical techniques.

The wave propagation has the significant role in the field of coastal engineering and ocean. In the geographical fields, waves are primary source of environmental process owed to energy conveyance on floating structure. This study aims to investigate the system of cold bosonic atoms in zig-zag optics lattices. The solitonic patterns of the considered model successfully surveyed by using two integrated analytical techniques new extended direct algebraic and frac{G'}{G^{2}} expansion method. The exact solutions are presented by rational, trigonometric, hyperbolic and exponential functions. On the basis of solitons, we need to show that which one is more integrated and robust scheme. These solutions will help to understood the dynamics of cold bosonic atoms in zig-zag optical lattices and the several other systems. Three dimensional as well as two dimensional comparison presented for a cold bosonic atoms model solutions which are revealed diagrammatically for appropriate parameters by using Mathematica. This study will help physicists to predict some new hypothesis and theories in the field of mathematical physics.

SPLA2 Wobbles on the Lipid Bilayer between Three Positions, Each Involved in the Hydrolysis Process.

Secreted phospholipases A2 (sPLA2s) are peripheral membrane enzymes that hydrolyze phospholipids in the sn-2 position. The action of sPLA2 is associated with the work of two active sites. One, the interface binding site (IBS), is needed to bind the enzyme to the membrane surface. The other one, the catalytic site, is needed to hydrolyze the substrate. The interplay between sites, how the substrate protrudes to, and how the hydrolysis products release from, the catalytic site remains in the focus of investigations. Here, we report that bee venom PLA2 has two additional interface binding modes and enzyme activity through constant switching between three different orientations (modes of binding), only one of which is responsible for substrate uptake from the bilayer. The finding was obtained independently using atomic force microscopy and molecular dynamics. Switching between modes has biological significance: modes are steps of the enzyme moving along the membrane, product release in biological milieu, and enzyme desorption from the bilayer surface.

Rotation of complex ions with ninefold hydrogen coordination studied by quasielastic neutron scattering and first-principles molecular dynamics calculations

Quasielastic neutron scattering (QENS) and neutron powder diffraction of the complex transition metal hydrides ${\mathrm{Li}}_{5}{\mathrm{MoH}}_{11}$ and ${\mathrm{Li}}_{6}{\mathrm{NbH}}_{11}$ were measured in a temperature range of 10--300 K to study their structures and dynamics, especially the dynamics of the hydrogen atoms. These hydrides contain unusual ninefold H-coordinated complex ions (${\mathrm{MoH}}_{9}^{3\ensuremath{-}}$ or ${\mathrm{NbH}}_{9}^{4\ensuremath{-}}$) and hydride ions $({\mathrm{H}}^{\ensuremath{-}})$. A QENS signal appeared >150 K due to the relaxation of H atoms. The intermediate scattering functions derived from the QENS spectra are well fitted by a stretched exponential function called the Kohlrausch-Williams-Watts functions with a small stretching exponent \ensuremath{\beta} \ensuremath{\approx} 0.3--0.4, suggesting a wide relaxation time distribution. The $Q$ dependence of the elastic incoherent structure factor is reproduced by the rotational diffusion of $M{\mathrm{H}}_{9}$ ($M=\mathrm{Mo}$ or Nb) anions. The results are well supported by a van Hove analysis for the motion of H atoms obtained using first-principles molecular dynamics calculations. We conclude that the wide relaxation time distribution of the $M{\mathrm{H}}_{9}$ rotation is due to the positional disorder of the surrounding Li ions and a unique rotation with $M{\mathrm{H}}_{9}$ anion deformation (pseudorotation).

Behavior of Citrate-Capped Ultrasmall Gold Nanoparticles on a Supported Lipid Bilayer Interface at Atomic Resolution.

Nanomaterials have the potential to transform biological and biomedical research, with applications ranging from drug delivery and diagnostics to targeted interference of specific biological processes. Most existing research is aimed at developing nanomaterials for specific tasks such as enhanced biocellular internalization. However, fundamental aspects of the interactions between nanomaterials and biological systems, in particular, membranes, remain poorly understood. In this study, we provide detailed insights into the molecular mechanisms governing the interaction and evolution of one of the most common synthetic nanomaterials in contact with model phospholipid membranes. Using a combination of atomic force microscopy (AFM) and molecular dynamics (MD) simulations, we elucidate the precise mechanisms by which citrate-capped 5 nm gold nanoparticles (AuNPs) interact with supported lipid bilayers (SLBs) of pure fluid (DOPC) and pure gel-phase (DPPC) phospholipids. On fluid-phase DOPC membranes, the AuNPs adsorb and are progressively internalized as the citrate capping of the NPs is displaced by the surrounding lipids. AuNPs also interact with gel-phase DPPC membranes where they partially embed into the outer leaflet, locally disturbing the lipid organization. In both systems, the AuNPs cause holistic perturbations throughout the bilayers. AFM shows that the lateral diffusion of the particles is several orders of magnitude smaller than that of the lipid molecules, which creates some temporary scarring of the membrane surface. Our results reveal how functionalized AuNPs interact with differing biological membranes with mechanisms that could also have implications for cooperative membrane effects with other molecules.

Photoinduced Ultrafast Transition of the Local Correlated Structure in Chalcogenide Phase-Change Materials.

Revealing the bonding and time-evolving atomic dynamics in functional materials with complex lattice structures can update the fundamental knowledge on rich physics therein, and also help to manipulate the material properties as desired. As the most prototypical chalcogenide phase change material, Ge_{2}Sb_{2}Te_{5} has been widely used in optical data storage and nonvolatile electric memory due to the fast switching speed and the low energy consumption. However, the basic understanding of the structural dynamics on the atomic scale is still not clear. Using femtosecond electron diffraction, structure factor calculation, and time-dependent density-functional theory molecular dynamic simulation, we reveal the photoinduced ultrafast transition of the local correlated structure in the averaged rocksalt phase of Ge_{2}Sb_{2}Te_{5}. The randomly oriented Peierls distortion among unit cells in the averaged rocksalt phase of Ge_{2}Sb_{2}Te_{5} is termed as local correlated structures. The ultrafast suppression of the local Peierls distortions in the individual unit cell gives rise to a local structure change from the rhombohedral to the cubic geometry within ∼0.3 ps. In addition, the impact of the carrier relaxation and the large number of vacancies to the ultrafast structural response is quantified and discussed. Our Letter provides new microscopic insights into contributions of the local correlated structure to the transient structural and optical responses in phase change materials. Moreover, we stress the significance of femtosecond electron diffraction in revealing the local correlated structure in the subunit cell and the link between the local correlated structure and physical properties in functional materials with complex microstructures.

Spatial variation in nanoscale wear behavior of chemical vapor deposited monolayer WS2

Two-dimensional (2D) materials are potential solid lubricants for a wide range of tribological applications. However, such atomically thin lubricants require detailed understanding of mechanisms underlying their tribological characteristics. In the present study, the nanoscale wear behavior of chemical vapor deposition (CVD) grown monolayer tungsten disulfide (WS2) was investigated using a combination of atomic force microscopy (AFM) and molecular dynamics (MD) simulations. The critical load to initiate wear in the interior region of the WS2 monolayer was found to be higher than the regions near the edge. Experimental findings also reveal significant variability in critical load values in both regions. The observed difference in wear behavior can be attributed to the presence of structural defects as elucidated from MD simulations. Our combined experimental and simulation study provides fundamental insights into the atomistic wear mechanism of monolayer WS2.

Development of a Multitimescale Time-Resolved Electron Diffraction Setup: Photoinduced Dynamics of Oxygen Radicals on Graphene Oxide.

We developed a multitimescale time-resolved electron diffraction setup by electrically synchronizing a nanosecond laser with our table-top picosecond time-resolved electron diffractometer. The setup covers the photoinduced structural dynamics of target materials at timescales ranging from picoseconds to submilliseconds. Using this setup, we sequentially observed the ultraviolet (UV) photoinduced bond dissociation, radical formation, and relaxation dynamics of the oxygen atoms in the epoxy functional group on the basal plane of graphene oxide (GO). The results show that oxygen radicals formed via UV photoexcitation on the basal plane of GO in several tens of picoseconds and then relaxed back to the initial state on the microsecond timescale. The results of first-principles calculations also support the formation of oxygen radicals in the excited state on an early timescale. These results are essential for the further discussion of the reactivities on the basal plane of GO, such as catalytic reactions and antibacterial and antiviral activities. The results also suggest that the multitimescale time-resolved electron diffraction system is a promising tool for laboratory-based molecular dynamics studies of materials and chemical systems.

Laser-induced fluorescence spectroscopy on xenon atoms and ions in the magnetic nozzle of a helicon plasma thruster

The dynamics of xenon atoms and ions expanding in the magnetic nozzle (MN) of a helicon plasma thruster is studied by means of near-infrared laser-induced fluorescence spectroscopy on resonant and metastable states. Fluorescence spectra are measured for several operating conditions inside and outside the thruster discharge chamber. In the near-field plume, the relatively intense magnetic field induces Zeeman effect on the probed optical transitions. Hence, modeling of the atomic lineshapes is addressed to accurately compute the Doppler shift and infer the velocity. The first direct measurements of the neutral flow in a MN reveal that atoms are accelerated to supersonic velocities behind the thruster exit. The ions acceleration region extends several centimeters downstream the exit plane. Larger axial ion speeds are attained when the thruster operates at lower mass flow rates and higher levels of input power.

Probing the Structural Details of Chitin Nanocrystal–Water Interfaces by Three‐Dimensional Atomic Force Microscopy (Small Methods 9/2022)

Chitin Nanocrystal Structure In article number 2200320, Yurtsever, Fukuma, and co-workers provided the molecular-scale structural details of chitin nanocrystals in water by combining 3D atomic force microscopy experiments and molecular dynamics simulations. The characterization of chitin nanocrystal surfaces at the molecular scale could pave the way for assessing the chemical and enzymatic activities on chitin nanocrystals, offering an understanding of the mechanisms of chitin degradation.