Atomic Model Research Articles

Acoustic Loss in LiNb1−xTaxO3at Temperatures up to 900 °C

Lithium niobate‐lithium tantalate solid solutions are new piezoelectric crystals that enable to combine the advantages of their edge compounds with respect to the high thermal stability of lithium tantalate and the high Curie temperature of lithium niobate. This study aims to determine of the acoustic losses of bulk resonators with varying Nb/Ta ratios and their correlation with charge transport at temperatures up to 900 °C and at reduced oxygen partial pressures. Techniques such as resonant piezoelectric spectroscopy and contactless resonant ringdown spectroscopy are used to determine the acoustic losses. Further, the electrical conductivity is determined by impedance spectroscopy. A one‐dimensional physical model for vibrating plates is fitted to the data to extract key parameters such as piezoelectric coefficients and elastic modulus as a function of temperature. Noncontacting determination of loss excludes the impact of metal electrodes and reveals up to 300 °C values in the order of Akhiezer‐type losses. Resonators operated at 2 MHz show a rapid loss increase above about 450 °C, which is attributed to the piezoelectric/carrier relaxation. The latter follows from atomistic models using the key parameters mentioned and the electrical conductivity. The modeling includes variation of the resonance frequency and suggests higher resonance frequencies to lower the acoustic loss.

An atomistic model of myosin interacting heads motif dynamics and their modification by 2'-deoxy-ADP.

The contraction of striated muscle is driven by cycling myosin motor proteins embedded within the thick filaments of sarcomeres. In addition to cross-bridge cycling with actin, these myosin proteins can enter an inactive, sequestered state in which the globular S1 heads rest along the thick filament surface and are unable to perform motor activities. Structurally, this state is called the interacting heads motif (IHM) and is a critical conformational state of myosin that regulates muscle contractility and energy expenditure. Structural perturbation of the sequestered state via missense mutations can pathologically disrupt the mechanical performance of muscle tissue. Thus, the IHM state has become a target for therapeutic intervention. An ATP analogue called 2'-deoxy-ATP (dATP) is a potent myosin activator which destabilizes the IHM. Here we use molecular dynamics simulations to study the molecular mechanisms by which dATP modifies the structure and dynamics of myosin in a sequestered state. Simulations with IHM containing ADP.Pi in both nucleotide binding pockets revealed residual dynamics in an otherwise 'inactive' and 'sequestered' state of a motor protein. Replacement of ADP.Pi by dADP.Pi triggered a series of structural changes that modify the protein-protein interface that stabilizes the sequestered state, and changes to this interface were accompanied by allosteric changes in remote regions of the protein complex. A comparative analysis of these dynamics predicted new structural sites that may affect IHM stability.

Atomistic simulation of temperature dependence of tensile properties and estimation of DBTT of Cu–Ag core–shell nanowires

An atomistic model of Cu-Ag core–shell nanowire using molecular dynamics is proposed. The simulation model was utilized for the evolution of temperature dependent (in the range of 10–500 K) tensile behavior and the identification of ductile-to-brittle transition temperature (DBTT) of single-crystal Cu-Ag core–shell nanowire. The evolution of defects such as point defects, dislocations, and stacking faults, arising from tensile deformation in the mentioned temperature rage were analyzed. The Wigner-Seitz Defect analysis, Dislocation analysis, and Common Neighbor analysis methods were implemented in this study to estimate the various defects concentration in the nanowire. The study identified that Cu-Ag core–shell (core diameter = 4 nm and shell thickness = 1 nm nanowire) exhibits DBTT somewhere in the temperature between 25 K to 30 K. The modulus of elasticity found to be increasing from 19.7 TPa at 10 K to 23.7 TPa at 30 K (within brittle regime), followed by a steep fall to 14.9 TPa at 500 K where fracture seems to be in ductile mode. The observed mechanical properties of the nanowire are discussed in the article in view of the dislocation and stacking faults generation in the core–shell nanostructures.

Atomistic modeling of electric field poling of PMMA-based polymer material with guest quinoxaline chromophores

The effect of applied electric field strength on the chromophore alignment in composite PMMA-based material is studied by atomistic modeling. Polymer material of real density (1.07 g/cm3), established in the course of modeling using NPT protocol, is considered along with model materials with reduced density (0.6 and 0.9 g/cm3), applied fields ranging from 100 to 1000 V/μm. Glass transition temperature, at which materials simulation was performed, was estimated in the course of multistage simulation. Simulation was performed with OPLS3e force field. Both centric, 〈P2〉, and acentric, 〈cos3Θ〉, chromophores order parameters were estimated. For the polymer material with high density, ρ = 1.07 g/cm3, the value of the order parameter 〈cos3Θ〉 grows from 0.25 to 0.30 for field strength varying from 300 to 1000 V/μm; the values of 〈P2〉 for chromophores are in agreement with the results of measurements by UV–vis spectroscopy. The obtained values of order parameters (both 〈P2(ch)〉 and 〈cos3Θ〉 for model materials with decreased density (0.6 and 0.9 g/cm3) are quite close to each other and seem to be overestimated compared to the values for the material with high density; this observation is in agreement with calculated values of free volume in the composite. The applied approach may provide guidelines for the elaboration of optimal poling protocols used at the development of composite polymer materials with quadratic nonlinear optical properties, containing quinoxaline chromophores-guests possessing high dipole moments (more than 20 D).

Probing the microstructure and deformation mechanism of an FeCoCrNiAl0.5 high entropy alloy during nanoscratching: a combined atomistic and physical model study.

High entropy alloys (HEAs) exhibit superior mechanical properties. However, the nanoscratching properties and deformation behaviour of FeCoCrNiAl0.5 HEAs remain unknown at the nanoscale. Here, we investigate the effect of scratching depth on the microstructural and tribological characteristics of an FeCoCrNiAl0.5 HEA using molecular dynamics simulations combined with a physical model. The scratching force increases significantly as the scratching depth increases. In the lower part of the scratching region, there is a clear atomic movement process, with the load generated in the normal direction causing the atoms to shift downwards. Noticeable shear bands are formed in the subsurface area, and they are both small and narrow compared with the pure Ni. The plastic deformation mechanism of the compressed surface is mainly governed by the formation and expansion of stacking faults during the subsurface evolution process. The evolution process of screw dislocations is similar to that of edge dislocations. In addition, the high strength and deformation resistance of FeCoCrNiAl0.5 HEAs are further evaluated by establishing a microstructure-based physical model. The combined effect of the lattice distortion strengthening and dislocation strengthening promotes the high strength of the FeCoCrNiAl0.5 HEA, which is significantly better than the single strengthening mechanism of pure metals. These results accelerate the understanding of the mechanical properties and deformation mechanisms of HEAs.

Atomic structure, electron-impact excitation and collisional-radiative modelling for Ar II

The spectra from singly ionized argon Ar II has significant diagnostic capability in the characterization and modelling of both magnetically-confined fusion and astrophysical plasmas. The literature has several pre-existing data sets for Ar+ but this paper presents the results from 3 new atomic structure and electron-impact scattering models in order to better constrain the differences in atomic data and how they impact well-known plasma diagnostics. Several independent atomic structure methodologies are employed to calculate the energy levels and transition probabilities for each model. The first approach employs a relativistic Dirac–Coulomb Hamiltonian model, the second approach uses a semi-relativistic Breit–Pauli Hamiltonian with the mass-velocity, Darwin and spin–orbit corrections, and in a third case an ICFT approach. Three atomic structure models provide a foundation for Dirac R-matrix, a semi-relativistic ICFT (Intermediate Coupling Frame Transformation) and a Breit–Pauli R-Matrix with Pseudostates (BPRMPS) calculation. Synthetic spectra utilizing these three data sets are compared against measurements taken at the Compact Toroidal Hybrid (CTH) stellarator, and the total radiative power loss is also benchmarked against previous calculations.

Development of Mass-Conserving Atomistic Mathematical Model for Batch Anaerobic Digestion: Framework and Limitations

A variety of mathematical models have been developed to simulate the biochemical and physico-chemical aspects of the anaerobic digestion (AD) process to treat organic wastes and generate biogas. However, all these models, including the most widely accepted and implemented Anaerobic Digestion Model No.1, remain incapable of adequately representing the material balance of AD and are therefore inherently incapable of material conservation. The absence of robust mass conservation constrains reliable estimates of any kinetic parameters being estimated by regression of empirical data. To address this issue, the present work involved the development of a “framework” for a mass-conserving atomistic mathematical model which is capable of mass conservation, with a relative error in the range of machine precision value and an atom balance with a relative error of ±0.02% whilst obeying the Henry’s law and electroneutrality principle. Implementing the model in an Excel spreadsheet, the study calibrated the model using the empirical data derived from batch studies. Although the model shows high fidelity as assessed via inspection, considering several constraints including the drawbacks of the model and implementation platform, the study also provides a non-exhaustive list of limitations and further scope for development.

Latent-to-sensible heat conversion kinetics during nanoparticle coalescence.

Coagulational growth in an aerosol is a multistep process; first particles collide, and then they coalesce with one another. Coalescence kinetics have been investigated in numerous prior studies, largely through atomistic simulations of nanoclusters (102-104 atoms). However, with a few exceptions, they have either assumed the process is completely isothermal or is a constant energy process. During coalescence, there is the formation of new bonds, decreasing potential energy, and correspondingly increasing internal kinetic (thermal) energy. Internal kinetic energy evolution is dependent not only on coalescence kinetics but also on heat transfer to the surrounding gas. Here, we develop and test a model of internal kinetic energy evolution in collisionally formed nanoclusters in the presence of a background gas. We find that internal kinetic energy dynamics hinge upon a power law relationship describing latent-to-sensible heat release as well as a modified thermal accommodation coefficient. The model is tested against atomistic models of 1.5-3.0nm embedded-atom gold nanocluster sintering in argon and helium environments. The model results are in excellent agreement with the simulation results for all tested conditions. Results show that nanocluster effective temperatures can increase by hundreds of Kelvin due to coalescence, but that the rise and re-equilibration of the internal kinetic energy is strongly dependent on the background gas environment. Interestingly, internal kinetic energy change kinetics are also found to be distinct from surface area change kinetics, suggesting that modeling coalescence heat release solely due to surface area change is inaccurate.

Time-dependent Kohn-Sham electron dynamics coupled with nonequilibrium plasmonic response via atomistic electromagnetic model.

Computational modeling of plasmon-mediated molecular photophysical and photochemical behaviors can help us better understand and tune the bound molecular properties and reactivity and make better decisions to design and control nanostructures. However, computational investigations of coupled plasmon-molecule systems are challenging due to the lack of accurate and efficient protocols to simulate these systems. Here, we present a hybrid scheme by combining the real-time time-dependent density functional theory (RT-TDDFT) approach with the time-domain frequency dependent fluctuating charge (TD-ωFQ) model. At first, we transform ωFQ in the frequency-domain, an atomistic electromagnetic model for the plasmonic response of plasmonic metal nanoparticles (PMNPs), into the time-domain and derive its equation-of-motion formulation. The TD-ωFQ introduces the nonequilibrium plasmonic response of PMNPs and atomistic interactions to the electronic excitation of the quantum mechanical (QM) region. Then, we combine TD-ωFQ with RT-TDDFT. The derived RT-TDDFT/TD-ωFQ scheme allows us to effectively simulate the plasmon-mediated "real-time" electronic dynamics and even the coupled electron-nuclear dynamics by combining them with the nuclear dynamics approaches. As a first application of the RT-TDDFT/TD-ωFQ method, we study the nonradiative decay rate and plasmon-enhanced absorption spectra of two small molecules in the proximity of sodium MNPs. Thanks to the atomistic nature of the ωFQ model, the edge effect of MNP on absorption enhancement has also been investigated and unveiled.

Study of Solid-State Diffusion Impedance in Li-Ion Batteries Using Parallel-Diffusion Warburg Model

Anomalous diffusion impedance due to the solid-state Li+ diffusion in Li-ion batteries is often troublesome for the analysis. In this work, we propose a novel analytical Parallel-diffusion Warburg (PDW) model and couple it with the conventional equivalent electrical circuit model (EECM) analysis to tackle this long-standing challenge. The analytical expression of the PDW is derived from the classical Fickian diffusion framework, introducing non-unified diffusion coefficients that originate from the diverse crystalline conditions of Li+ diffusion paths, as theoretically demonstrated in the atomistic modeling results. The proposed approach (EECM + PDW) is successfully employed to study the diffusion impedance of thin-film LiNi0.5Mn1.5O4 (LNMO) electrodes and porous LiNi0.80Co0.15Al0.05O2 (NCA) electrodes, demonstrating the applicability and robustness of this method.

Exploring Multicomponent Phase Space to Discover New Materials

Multicomponent phase space has been shown to consist of an enormous number of materials with different compositions, the vast majority of which have never been made or investigated, with great potential, therefore, for the discovery of exciting new materials with valuable properties. At the same time, however, the enormous size of multicomponent phase space makes it far from straightforward to identify suitable strategies for exploring the plethora of potential material compositions and difficult, therefore, to be successful in discovering desirable new materials. Unfortunately, all our knowhow and understanding has been developed for materials with relatively few components in relatively limited proportions, with most of our scientific theories relying essentially on linear assumptions of component dilution and independence that no longer apply in concentrated multicomponent materials. Trial and error, controlled substitution, parameterisation, thermodynamic modelling, atomistic modelling and machine learning techniques have all been employed as methods of exploring multicomponent phase space, with varying levels of success, but ultimately none of these techniques has proved capable of delivering consistent or guaranteed results. This paper provides an overview of the different techniques that have been used to explore multicomponent phase space, indicates their main advantages and disadvantages, and describes some of their successes and failures.

Ansatz optimization of the variational quantum eigensolver tested on the atomic Anderson model

We present a detailed analysis and optimization of the variational quantum algorithms required to find the ground state of a correlated electron model, using several types of variational ansatz. Specifically, we apply our approach to the atomic limit of the Anderson model, which is widely studied in condensed matter physics since it can simulate fundamental physical phenomena, ranging from magnetism to superconductivity. The method is developed by presenting efficient state preparation circuits that exhibit total spin, spin projection, particle number and time-reversal symmetries. These states contain the minimal number of variational parameters needed to fully span the appropriate symmetry subspace allowing to avoid irrelevant sectors of Hilbert space. Then, we show how to construct quantum circuits, providing explicit decomposition and gate count in terms of standard gate sets. We test these quantum algorithms looking at ideal quantum computer simulations as well as implementing quantum noisy simulations. We finally perform an accurate comparative analysis among the approaches implemented, highlighting their merits and shortcomings.

Elucidating optimal nanohole structures for suppressing phonon transport in nanomeshes

Nanomeshes, often referred to as phononic crystals, have been extensively explored for their unique properties, including phonon coherence and ultralow thermal conductivity (κ). However, experimental demonstrations of phonon coherence are rare and indirect, often relying on comparison with numerical modeling. Notably, a significant aspect of phonon coherence, namely the disorder-induced reduction in κ observed in superlattices, has yet to be experimentally demonstrated. In this study, through atomistic modeling and spectral analysis, we systematically investigate and compare phonon transport behaviors in graphene nanomeshes, characterized by 1D line-like hole boundaries, and silicon nanomeshes, featuring 2D surface-like hole boundaries, while considering various forms of hole boundary roughness. Our findings highlight that to demonstrate a disorder-induced reduction in κ of nanomeshes, optimal conditions include low temperature, smooth and planar hole boundaries, and the utilization of thick films composed of 3D materials.

Effect of Repetitive High-Density Current Pulses on Plastic Deformation of Copper Wires under Stepwise Loading

High-density electric current pulses increase the plasticity and reduce the yield stress of metals with negligible heat generation. This effect has great potential for the development of energy-saving technologies for processing hard-to-deform metallic materials. Despite the long history of the study of electroplasticity, there is still no consensus on the physical nature of this effect. In this paper, the effect of repetitive pulses applied at the same or gradually increasing tensile stress on the plastic deformation of copper wire is investigated using a home-made experimental setup. The electroplasticity of the wire in the delivery state and after annealing is compared. It is shown that for a constant tensile stress, the incremental plastic deformation of the wire decreases with each successive pulse. This effect is stronger for annealed wires because they have a lower dislocation density and therefore a lower plasticity resource. The Joule heat release in the specimen and the heating due to plastic deformation are evaluated. The results obtained will be used to fit the parameters of the atomistic model being developed to describe the interaction of electron flow with dislocations.

Front Cover: Surface Engineering of the Mechanical Properties of Molecular Crystals via an Atomistic Model for Computing the Facet Stress Response of Solids (Chem. Eur. J. 38/2024)

Front Cover: Surface Engineering of the Mechanical Properties of Molecular Crystals via an Atomistic Model for Computing the Facet Stress Response of Solids (Chem. Eur. J. 38/2024)

Modeling Chromatography Binding through Molecular Dynamics Simulations with Resin Fragments.

Accurate atomistic modeling of the interactions of a chromatography resin with a solute can inform the selection of purification conditions for a product, an important problem in the biotech and pharmaceutical industries. We present a molecular dynamics simulation-based approach for the qualitative prediction of interaction sites (specificity) and retention times (affinity) of a protein for a given chromatography resin. We mimicked the resin with an unrestrained ligand composed of the resin headgroup coupled with successively larger fragments of the agarose backbone. The interactions of the ligand with the protein are simulated in an explicit solvent using the Replica Exchange Molecular Dynamics enhanced sampling approach in conjunction with Hydrogen Mass Repartitioning (REMD-HMR). We computed the ligand interaction surface from the simulation trajectories and correlated the features of the interaction surface with experimentally determined retention times. The simulation and analysis protocol were first applied to a series of ubiquitin mutants for which retention times on Capto MMC resin are available. The ubiquitin simulations helped identify the optimal ligand that was used in subsequent simulations on six proteins for which Capto MMC elution times are available. For each of the six proteins, we computed the interaction surface and characterized it in terms of a range of simulation-averaged residue-level physicochemical descriptors. Modeling of the salt concentrations required for elution with respect to the descriptors resulted in a linear fit in terms of aromaphilicity and Kyte-Doolittle hydrophobicity that was robust to outliers, showed high correlation, and correctly ranked the protein elution order. The physics-based model building approach described here does not require a large experimental data set and can be readily applied to different resins and diverse biomolecules.

Atomic-Scale Description of the Magnetic TiN|FeCo Multilayers.

Motivated by the experimental findings of Wolff et al., we investigated the TiN|FeCo multilayers at the atomic scale. Four different models were employed to investigate the interface, considering both Fe and Co surface terminations of the FeCo compounds. The interface formation energy formalism was employed to study the thermodynamic stability of these models. The results show that an interface mediated by Co atoms is most likely to appear in the experiment. Also, the Fe surface termination is more viable than a Co surface termination. The magnetic moments of Co at the interface are 1.48 μB/atom, which denotes a decay compared to bulk (1.76 μB/atom). Besides, Ti acquires a very small induced magnetization of -0.05 μB/atom. Our proposed atomistic model of the TiN|FeCo multilayer system fits perfectly with the structure obtained in experiments, and it is a step forward in the theoretical-experimental design of wear-resistant coatings with outstanding magnetic and mechanical properties.

Amorphous MoS2 from a machine learning inter-atomic potential.

Amorphous molybdenum disulfide has shown potential as a hydrogen evolution catalyst, but the origin of its high activity is unclear, as is its atomic structure. Here, we have developed a classical inter-atomic potential using the charge equilibration neural network method, and we have employed it to generate atomic models of amorphous MoS2 by melting and quenching processes. The amorphous phase contains an abundance of molybdenum and sulfur atoms in low coordination. Besides the 6-coordinated molybdenum typical of the crystalline phases, a substantial fraction displays coordinations 4 and 5. The amorphous phase is also characterized by the appearance of direct S-S bonds. Density functional theory shows that the amorphous phase is metallic, with a considerable contribution of the 4-coordinated molybdenum to the density of states at the Fermi level. S-S bonds are related to the reduction of sulfur, with the excess electrons spread over several molybdenum atoms. Moreover, S-S bond formation is associated with a distinctive broadening of the 3s states, which could be exploited for experimental characterization of the amorphous phases. The large variety of local environments and the high density of electronic states at the Fermi level may play a positive role in increasing the electrocatalytic activity of this compound.

Elasticity of self-organized frustrated disordered spring networks.

There have been some interesting recent advances in understanding the notion of mechanical disorder in structural glasses and the statistical mechanics of these systems' low-energy excitations. Here we contribute to these advances by studying a minimal model for structural glasses' elasticity in which the degree of mechanical disorder-as characterized by recently introduced dimensionless quantifiers-is readily tunable over a very large range. We comprehensively investigate a number of scaling laws observed for various macro, meso and microscopic elastic properties, and rationalize them using scaling arguments. Interestingly, we demonstrate that the model features the universal quartic glassy vibrational density of states as seen in many atomistic and molecular models of structural glasses formed by cooling a melt. The emergence of this universal glassy spectrum highlights the role of self-organization (toward mechanical equilibrium) in its formation, and elucidates why models featuring structural frustration alone do not feature the same universal glassy spectrum. Finally, we discuss relations to existing work in the context of strain stiffening of elastic networks and of low-energy excitations in structural glasses, in addition to future research directions.

Surface Engineering of the Mechanical Properties of Molecular Crystals via an Atomistic Model for Computing the Facet Stress Response of Solids.

Dynamic molecular crystals are an emerging class of crystalline materials that can respond to mechanical stress by dissipating internal strain in a number of ways. Given the serendipitous nature of the discovery of such crystals, progress in the field requires advances in computational methods for the accurate and high-throughput computation of the nanomechanical properties of crystals on specific facets which are exposed to mechanical stress. Here, we develop and apply a new atomistic model for computing the surface elastic moduli of crystals on any set of facets of interest using dispersion-corrected density functional theory (DFT-D) methods. The model was benchmarked against a total of 24 reported nanoindentation measurements from a diverse set of molecular crystals and was found to be generally reliable. Using only the experimental crystal structure of the dietary supplement, L-aspartic acid, the model was subsequently applied under blind test conditions, to correctly predict the growth morphology, facet and nanomechanical properties of L-aspartic acid to within the accuracy of the measured elastic stiffness of the crystal, 24.53±0.56 GPa. This work paves the way for the computational design and experimental realization of other functional molecular crystals with tailor-made mechanical properties.