Large-scale Molecular Dynamics Simulations Research Articles

Exceptional Microscale Plasticity in Amorphous Aluminum Oxide at Room Temperature.

Oxide glasses are an elementary group of materials in modern society, but brittleness limits their wider usability at room temperature. As an exception to the rule, amorphous aluminum oxide (a-Al2 O3 ) is a rare diatomic glassy material exhibiting significant nanoscale plasticity at room temperature. Here, it is shown experimentally that the room temperature plasticity of a-Al2 O3 extends to the microscale and high strain rates using in situ micropillar compression. All tested a-Al2 O3 micropillars deform without fracture at up to 50% strain via a combined mechanism of viscous creep and shear band slip propagation. Large-scale molecular dynamics simulations align with the main experimental observations and verify the plasticity mechanism at the atomic scale. The experimental strain rates reach magnitudes typical for impact loading scenarios, such as hammer forging, with strain rates up to the order of 1 000 s-1 , and the total a-Al2 O3 sample volume exhibiting significant low-temperature plasticity without fracture is expanded by 5 orders of magnitude from previous observations. The discovery is consistent with the theoretical prediction that the plasticity observed in a-Al2 O3 can extend to macroscopic bulk scale and suggests that amorphous oxides show significant potential to be used as light, high-strength, and damage-tolerant engineering materials.

High speed impact and solid-state deposition of alumina particles: A molecular dynamics study

This study provides an atomic-scale description of the high-velocity impact of α-Al2O3 particles onto an α-Al2O3 substrate, with a focus on unraveling the material behavior during Aerosol Deposition (AD). Large-scale Molecular Dynamics (MD) simulations were performed to model two defect-free single-crystal and one bicrystal particles, all with a diameter of 0.2 µm, impacting the substrate at different velocities using quasi-two-dimensional approach. The results suggest that the crystal orientation plays a crucial role in both plasticity and damage of the nanoparticles. As anticipated, we observed a direct correlation between impact velocity and both plasticity and fragmentation. However, the increase in adhesion efficiency remains marginal, suggesting that neither factor significantly impacts the deposition process. On the contrary, our MD results indicate that the crucial element lies in the substrate's surface alterations. These modifications arise from the fragments left on the substrate after impact and their subsequent interactions with incoming particles.

Effect of specimen size and crystallographic orientation on the nano/microscale mechanical properties and deformation behavior of CrCoNi medium-entropy alloy

CrCoNi medium-entropy alloy (MEA) shows an exceptional combination of macroscale mechanical properties, however, knowledge of its mechanical properties at nano/microscale is lacking. In this paper, nano/microscale single crystal MEA pillars with orientation of 〈116〉, 〈014〉, 〈102〉 were fabricated using focused ion beam milling, and the compressive strength was determined with micropillar compression testing using a flat-end tip in an indentation machine. Results showed that the yield and flow strength of these MEA pillars were orientation-dependent, i.e., the lower the Schmid factor, the higher the strength. At the same time the strength of the pillars was dependent on the pillar’s size, the strength increasing as the pillar diameter reduced. From the results of the micropillar compression testing, the bulk critical resolved shear stress (CRSS) was determined to be 92 MPa, which is the highest value of the group of CrCoNi-based medium and high-entropy alloys. Analysis of transmission electron microscope images and large-scale molecular dynamics simulations revealed a group of complimentary deformation mechanisms, including dislocation slides, dislocation annihilation, dislocation-slip band interaction, formation of nanoscale stacking-faulting networks, and deformation nanotwins.

Molecular docking and molecular dynamics simulations reveal the clinical resistance of the gatekeeper mutation V564F of FGFR2 against Infigratinib

Fibroblast growth factor receptor 2 (FGFR2), as a transmembrane receptor tyrosine kinase, is implicated in a plethora of human cancers, including intrahepatic cholangiocarcinomas, breast cancers, and non-small cell lung cancer. The clinically relevant V564F gatekeeper mutation conferred resistance to current FGFR2 drug − Infigratinib. In this study, the protein − ligand interactions between FGFR2 kinase domain (wild-type and V564F) and Infigratinib were compared through an integrated computational method. The multiple, large-scale molecular dynamics (MD) simulations, together with dynamic cross-correlation analysis and binding free energy calculations suggested that the resistant mutation may not trigger the conformational changes of the FGFR2 kinase domain. The simulation results also indicated that the driving force to decrease the binding affinity of Infigratinib to the FGFR2 V564F variant derived from the difference in the protein − ligand hydrogen bonding interactions. Moreover, the per-residue free energy decomposition analysis revealed that the reduced contributions from several residues in the ATP-binding site of FGFR2, especially Glu565 and Ala567 located at the kinase hinge domain, were the key residues responsible for the loss of binding affinity of Infigratinib to the V564F variant. This study may offer useful information for the design of novel selective kinase inhibitors targeting FGFR2.

Simultaneously enhancing the tensile strength and ductility of high entropy alloys by nanoscale precipitates/fillers

High entropy alloys (HEAs) in the solid solution (SS) phase have attracted much attention due to their novel strengthening mechanisms. Recent studies have shown that introducing nanoscale precipitates/fillers can further strengthen the SS HEAs. In this work, we performed large-scale molecular dynamics simulations of AlxCoCuFeNi HEAs filled with randomly distributed AlNi3 nanoparticles. The effects of AlNi3 particle size and volume fraction, the chemical composition of the HEA matrix, and temperature on the mechanical properties, deformation, and failure behavior of the composite are systematically investigated. Our simulations show that, remarkably, the AlNi3 nanoparticles can simultaneously enhance the ultimate tensile strength and ultimate tensile strain of the composite. The underlying mechanism is that the AlNi3 nanoparticles greatly suppressed the phase change and dislocation appearance in the HEA matrix, resulting in a delayed material failure during the deformation. We also find that Young’s modulus, ultimate tensile strength, and ultimate tensile strain follow the lower-bound of the rule of mixtures and further present the underlying reason for this lower-bound relation. The present work not only provides insights into the mechanical properties, deformation, and failure behavior of AlNi3 nanoparticle-reinforced AlxCoCuFeNi HEAs but is also useful for guiding the rational design of HEAs for engineering applications.

Effect of geometry of crystalline dendrite on the uniaxial tension behavior of metallic glass matrix composites based on molecular dynamics simulations

Introducing crystalline dendrites can effectively enhance the plasticity of metallic glass matrix composites. The geometry (e.g., shape and orientation) of the crystalline dendrites can significantly influence the mechanical properties of the material. In this study, we create numerical Cu-Zr glassy samples containing crystalline dendrites of realistic geometries and study their mechanical behaviors under uniaxial tension loading through large-scale molecular dynamics simulations. The results indicate that shear band formation is sensitive to the shape and orientation of the dendrites. The geometry of the dendrites significantly affects the behavior of shear bands in the materials and ultimately leads to different tensile plasticity. This work is aimed at providing guidelines for the design of metallic glass matrix composites with complex second phase dendritic structures.

Mapping microstructure to shock-induced temperature fields using deep learning

The response of materials to shock loading is important to planetary science, aerospace engineering, and energetic materials. Thermally activated processes, including chemical reactions and phase transitions, are significantly accelerated by energy localization into hotspots. These result from the interaction of the shockwave with the materials’ microstructure and are governed by complex, coupled processes, including the collapse of porosity, interfacial friction, and localized plastic deformation. These mechanisms are not fully understood and the lack of models limits our ability to predict shock to detonation transition from chemistry and microstructure alone. We demonstrate that deep learning can be used to predict the resulting shock-induced temperature fields in composite materials obtained from large-scale molecular dynamics simulations with the initial microstructure as the only input. The accuracy of the Microstructure-Informed Shock-induced Temperature net (MISTnet) model is higher than the current state of the art and its evaluation requires a fraction of the computation cost.

Nanoscale Prediction of the Thermal, Mechanical, and Transport Properties of Hydrated Clay on 106- and 1015-Fold Larger Length and Time Scales.

Coupled thermal, hydraulic, mechanical, and chemical (THMC) processes, such as desiccation-driven cracking or chemically driven fluid flow, significantly impact the performance of composite materials formed by fluid-mediated nanoparticle assembly, including energy storage materials, ordinary Portland cement, bioinorganic nanocomposites, liquid crystals, and engineered clay barriers used in the isolation of hazardous wastes. These couplings are particularly important in the isolation of high-level radioactive waste (HLRW), where heat generated by radioactive decay can drive the temperature up to at least 373 K in the engineered barrier. Here, we use large-scale all-atom molecular dynamics simulations of hydrated smectite clay nanoparticle assemblages to predict the fundamental THMC properties of hydrated compacted clay over a wide range of temperatures (up to 373 K) and dry densities relevant to HLRW management. Equilibrium simulations of clay-water mixtures at different hydration levels are analyzed to quantify material properties, including thermal conductivity, heat capacity, thermal expansion, suction, water and ion self-diffusivity, and hydraulic conductivity. Predictions are validated against experimental results for the properties of compacted bentonite clay. Our results demonstrate the feasibility of using atomistic-level simulations of assemblages of clay nanoparticles on scales of tens of nanometers and nanoseconds to infer the properties of compacted bentonite on scales of centimeters and days, a direct upscaling over 6 orders of magnitude in space and 15 orders of magnitude in time.

Viscosity Prediction of High-Concentration Antibody Solutions with Atomistic Simulations.

The computational prediction of the viscosity of dense protein solutions is highly desirable, for example, in the early development phase of high-concentration biopharmaceutical formulations where the material needed for experimental determination is typically limited. Here, we use large-scale atomistic molecular dynamics (MD) simulations with explicit solvation to de novo predict the dynamic viscosities of solutions of a monoclonal IgG1 antibody (mAb) from the pressure fluctuations using a Green-Kubo approach. The viscosities at simulated mAb concentrations of 200 and 250 mg/mL are compared to the experimental values, which we measured with rotational rheometry. The computational viscosity of 24 mPa·s at the mAb concentration of 250 mg/mL matches the experimental value of 23 mPa·s obtained at a concentration of 213 mg/mL, indicating slightly different effective concentrations (or activities) in the MD simulations and in the experiments. This difference is assigned to a slight underestimation of the effective mAb-mAb interactions in the simulations, leading to a too loose dynamic mAb network that governs the viscosity. Taken together, this study demonstrates the feasibility of all-atom MD simulations for predicting the properties of dense mAb solutions and provides detailed microscopic insights into the underlying molecular interactions. At the same time, it also shows that there is room for further improvements and highlights challenges, such as the massive sampling required for computing collective properties of dense biomolecular solutions in the high-viscosity regime with reasonable statistical precision.

Predicting the Fracture Propensity of Amorphous Silica Using Molecular Dynamics Simulations and Machine Learning

Amorphous silica (a-SiO2) is a widely used inorganic material. Interestingly, the relationship between the local atomic structures of a-SiO2 and their effects on ductility and fracture is seldom explored. Here, we combine large-scale molecular dynamics simulations and machine learning methods to examine the molecular deformations and fracture mechanisms of a-SiO2. By quenching at high pressures, we demonstrate that densifying a-SiO2 increases the ductility and toughness. Through theoretical analysis and simulation results, we find that changes in local bonding topologies greatly facilitate energy dissipation during plastic deformation, particularly if the coordination numbers decrease. The appearance of fracture can then be accurately located based on the spatial distribution of the atoms. We further observe that the static unstrained structure encodes the propensity for local atomic coordination to change during applied strain, hence a distinct connection can be made between the initial atomic configurations before loading and the final far-from-equilibrium atomic configurations upon fracture. These results are essential for understanding how atomic arrangements strongly influence the mechanical properties and structural features in amorphous solids and will be useful in atomistic design of functional materials.

Dynamic deformation behaviors and mechanisms of CoCrFeNi high-entropy alloys

Due to their unique microstructures and chemical compositions, high-entropy alloys (HEAs) exhibit remarkable mechanical properties, such as high strength, excellent ductility and good thermal stability. However, to date, there have been limited studies on the dynamic behaviors of HEAs. Here, we systemically investigated the mechanical behaviors and deformation mechanisms of CoCrFeNi HEAs and their connections under dynamic loading by combining mechanical tests and molecular dynamics simulations. Compressive testing on polycrystalline CoCrFeNi HEA samples at different strain rates showed that both yield and flow stresses increase with strain rate and exhibit a significant strain rate sensitivity due to solid solution strengthening and lattice distortion of the HEA. The strain rate sensitivity of the CoCrFeNi HEA transitions from 0.010 at low strain rates (5.0×10−5–2.5×103 s−1) to 0.333 at high strain rates (2.5×103–6.5×103 s−1). Large-scale molecular dynamics simulations further revealed that this transition is related to the plastic deformation mechanism transition from dislocation nucleation and slip at low strain rates to massive dislocation nucleation and drag at high strain rates. Furthermore, the CoCrFeNi HEA exhibited a remarkable strain-hardening capability at high strain rates, which originated from the formation of primary and secondary nanoscale twins and twin-twin and twin-dislocation interactions. Our current study sheds light on the plastic deformation mechanisms of HEAs under dynamic loading, providing guidance for the design and fabrication of HEAs with excellent dynamic mechanical properties.

An empirical potential for simulating hydrogen isotope retention in highly irradiated tungsten

We describe the parameterization of a tungsten-hydrogen empirical potential designed for use with large-scale molecular dynamics simulations of highly irradiated tungsten containing hydrogen isotope atoms, and report test results. Particular attention has been paid to getting good elastic properties, including the relaxation volumes of small defect clusters, and to the interaction energy between hydrogen isotopes and typical irradiation-induced defects in tungsten. We conclude that the energy ordering of defects changes with the ratio of H atoms to point defects, indicating that this potential is suitable for exploring mechanisms of trap mutation, including vacancy loop to plate-like void transformations.

Unraveling Anisotropy in Crystalline Orientation under Shock-Induced Dynamic Responses in High-Entropy Alloy Co25Ni25Fe25Al7.5Cu17.5.

Shock-induced plastic deformation and spall damage in the single-crystalline FCC Co25Ni25Fe25Al7.5Cu17.5 high-entropy alloy (HEA) under varying shock intensities were systematically investigated using large-scale molecular dynamics simulations. The study reveals the significant influence of crystalline orientation on the deformation mechanism and spall damage. Specifically, the shock wave velocities in the [110] and [111] directions are significantly higher than that in the [001] direction, resulting in a two-zone elastic-plastic shock wave structure observed in the [110] and [111] samples, while only a single-wave structure is found in the [001] sample. The plastic deformation is dominated by the FCC to BCC transformation following the Bain path and a small amount of stacking faults during the compression stage in the [001] sample, whereas it depends on the stacking faults induced by Shockley dislocation motion in the [110] and [111] samples. The stacking faults and phase transformation in the [001] sample exhibit high reversibility under release effects, while extensive dislocations are present in the [110] and [111] samples after release. Interestingly, tension-strain-induced FCC to BCC phase transformation is observed in the [001] sample during the release stage, resulting in increased spall strength compared to the [110] and [111] samples. The spall strength estimated from both bulk and free surface velocity history shows reasonable consistency. Additionally, the spall strength remains stable with increasing shock intensities. The study discusses in detail the shock wave propagation, microstructure change, and spall damage evolution. Overall, our comprehensive studies provide deep insights into the deformation and fracture mechanisms of Co25Ni25Fe25Al7.5Cu17.5 HEA under shock loading, contributing to a better understanding of dynamic deformation under extreme environments.

Large-scale machine-learning molecular dynamics simulation of primary radiation damage in tungsten

Large-scale machine-learning molecular dynamics simulation of primary radiation damage in tungsten

Phase Separation and Ion Diffusion in Ionic Liquid, Organic Solvent, and Lithium Salt Electrolyte Mixtures.

The highly desirable characteristics of ternary mixtures of ionic liquids, organic solvents, and metal salts make them a promising candidate for use in various electrothermal energy storage and conversion systems. In this study, using large-scale classical molecular dynamics simulations, we looked into 10 different ternary electrolyte mixtures using combinations of [EMIM]+, [BMIM]+, and [OMIM]+ cations with [NO3]-, [BF4]-, [PF6]-, [ClO4]-, [TFO]-, and [NTf2]- anions, tetraglyme, and Li salt to study the effect of ionic liquid composition on the phase behavior of ternary electrolyte mixtures. We uncovered that in these electrolytes, phase separation is mainly a function of pairwise binding energy of the constituents of the mixture. To corroborate this theory, several simulations are performed at various temperatures ranging from 260 to 500 K for each mixture, followed by calculating the binding energy of ionic liquid pairs using density functional theory. Our results verify that the transition temperature for the phase separation of each system is indeed a function of the pairwise binding energy of its ionic liquid pairs. It is also found that in some cases, the diffusion coefficient of the Li+ ions decreased even with the increase in the temperature, an effect that is attributed to the presence of condensed ionic domains in the electrolyte. This study provides a new insight for the design of multicomponent electrolyte mixtures for a wide range of energy applications.

High-temperature active oxidation of nanocrystalline silicon-carbide: A reactive force-field molecular dynamics study

Flexible woven SiC ceramics are prone to accelerated fiber embrittlement under high temperature oxidation in dynamic oxygen environments. The nanocrystalline structure of the constituent fibers impacts the reaction kinetics and phase transformations during active oxidation. However, fundamental understanding and quantification of grain boundary effects on oxidation behavior in nanocrystalline SiC remain elusive when temperatures exceed 1500 K. This study deploys large-scale molecular dynamics simulations with a reactive force-field to elucidate the complex roles of atomic oxygen reservoir conditions and grain size on oxidation kinetics and the nature of oxides produced in both monocrystalline and nanocrystalline 3C-SiC between 1100 K and 2000 K. The simulations with dynamically replenished oxygen provide good agreement with oxidation kinetics and activation energies for the monocrystalline Si(100) and C(100) orientations published in the available literature. This study reveals that, by contrast, nanocrystalline SiC samples exhibit two distinct oxidation kinetics with a transition point at 1500 K due to surface melting, which is supported by experimental evidence. The introduction of a grain-boundary network produces a two-fold decrease in oxidation activation energies compared to monocrystalline SiC below 1500 K. Above 1500 K, however, the activation energies rise substantially due to the formation of a liquid Si phase at the SiC/Si oxide interface. It is shown that the stability of the interfacial liquid phase is promoted by incoherent grain boundaries in the crystalline SiC. These findings are important for the deployment of nanocrystalline SiC fibers in advanced thermal protection systems for high-temperature applications.

Quinone Catalysis Modulates Proton Transfer Reactions in the Membrane Domain of Respiratory Complex I.

Complex I is a redox-driven proton pump that drives electron transport chains and powers oxidative phosphorylation across all domains of life. Yet, despite recently resolved structures from multiple organisms, it still remains unclear how the redox reactions in Complex I trigger proton pumping up to 200 Å away from the active site. Here, we show that the proton-coupled electron transfer reactions during quinone reduction drive long-range conformational changes of conserved loops and trans-membrane (TM) helices in the membrane domain of Complex I from Yarrowia lipolytica. We find that the conformational switching triggers a π → α transition in a TM helix (TM3ND6) and establishes a proton pathway between the quinone chamber and the antiporter-like subunits, responsible for proton pumping. Our large-scale (>20 μs) atomistic molecular dynamics (MD) simulations in combination with quantum/classical (QM/MM) free energy calculations show that the helix transition controls the barrier for proton transfer reactions by wetting transitions and electrostatic effects. The conformational switching is enabled by re-arrangements of ion pairs that propagate from the quinone binding site to the membrane domain via an extended network of conserved residues. We find that these redox-driven changes create a conserved coupling network within the Complex I superfamily, with point mutations leading to drastic activity changes and mitochondrial disorders. On a general level, our findings illustrate how catalysis controls large-scale protein conformational changes and enables ion transport across biological membranes.

Diameter-Optimum Spreading for the Impinging of Water Nanodroplets on Solid Surfaces.

The impinging of water nanodroplets on solid surfaces is crucial to many nanotechnologies. Through large-scale molecular dynamics simulations, the size effect on the spreading of water nanodroplets after impinging on hydrophilic, graphite, and hydrophobic surfaces under low impinging velocities has been systematically studied. The spreading rates of nanodroplets first increase and then decrease and gradually become constant with the increase of nanodroplet diameter. The nanodroplets with the diameters of 17-19 nm possess the highest spreading rates because of the combined effect of the strongest interfacial interaction and the strongest surface interaction within water molecules. The highest water molecule densities, hydrogen bond numbers, and dielectric constants of interface and surface layers mainly contribute to the lowest interface work of adhesion and surface tension values at optimal diameters. These results unveil the nonmonotonic characteristics of spreading velocity, interface work of adhesion and surface tension with nanodroplet diameter for nanodroplets on solid surfaces.

Effects of solvents on Li+ distribution and dynamics in PVDF/LiFSI solid polymer electrolytes: An all-atom molecular dynamics simulation study

Large-scale all-atom molecular dynamics simulations are used to investigate the structure and dynamics of a solid polymer electrolytes (SPE) model made up of polyvinylidene fluoride (PVDF) as the polymer matrix, lithium bis(fluorosulfonyl)imide salt (LiFSI), and six distinct solvent types in varying quantities. The influence of solvents on the physicochemical parameters of SPEs relevant to the Li-Battery sector is analysed. We prove that the presence of solvents containing oxygens atoms has different abilities to dissociate the LiFSI ions, form confined channels in the SPEs, and decrease the PVDF crystallinity. Besides, some solvents having a high affinity to the cations reduce the Li+ transport assembling in nano-domains, separated from the PVDF chains, when they present with a high amount, dramatically decreasing the Li+ transference number (tLi+). On the contrary, the ionic conductivity boosts preserving a good tLi+ for high dynamics solvents that form small Li+-solvent clusters. Our nanoscale investigations edify approaches for improving the ionic conductivity and controlling the arrangement of the ions in the SPE needed for proper battery operation by choosing a suitable solvent with a regulated amount.

Shock-induced deformation and spallation in CoCrFeMnNi high-entropy alloys at high strain-rates

Shock-induced deformation and fracture in single-crystalline and nanocrystalline CoCrFeMnNi high-entropy alloys (HEAs) under different shock intensities are investigated systematically using large-scale molecular dynamics simulations. The strong anisotropy in the single-crystalline HEA and how the reversibility of HCP-structured atoms influences the void nucleation and growth are revealed. Specifically, shock-induced FCC to HCP structural transformations are largely reversible in the case of the [001] loading direction, leading to homogeneous void nucleation; while they are largely irreversible in the cases of the [110] and [111] loading directions, resulting in void nucleation in the intersection of HCP layers. In nanocrystalline HEA, the deformations in the grain interior are similar to those in the single crystals, while the grain boundaries serve as void nucleation sites and thus weaken the spall strength. The SRO effects on the shock response in single-crystalline and nanocrystalline CoCrFeMnNi HEA are revealed, and the chemical heterogeneity is analyzed. Our results show that SRO can only slightly increase the shear stress and the spall strength, but it can cause a reduction of ductility during the spallation. The differences in SRO effects between single-crystalline and nanocrystalline models are attributed to the grain boundaries, where Cr and Mn are favorable, while Ni is favored inside the grains in the SRO model. Moreover, the comparison between CoCrFeMnNi HEA and its subsystem as well as single-element metal indicates Mn seems to be the most influential elements in CoCrFeMnNi HEA, resulting in significant changes in strength. A relation between the spall strength and strain rate is proposed to describe the simulation results and reported experimental data. Our comprehensive and systematical studies provide deep insights into the deformation and fracture in CoCrFeMnNi HEA subjected to shock loading, which deepens the understanding on the dynamic deformations of CoCrFeMnNi HEA and benefits the rational design of new HEAs/MEAs with enhanced performance.