Atomic Mechanisms Research Articles

Unveiling the intricacies of steel corrosion induced by chloride: Insights from reactive molecular dynamics simulation

Corrosion of reinforcing steels induced by chloride has long been a focal point of research, yet the atomic behavior and mechanism is not fully understood. In present study, we developed a reactive force field (ReaxFF) incorporating the Fe/Cl system based on Density Functional Theory calculations to elucidate atomic-scale behavior and mechanism underlying chloride-induced corrosion of reinforcing steel. Results from ReaxFF simulations employing this force field indicate that the initiation of steel corrosion is catalytically induced by chloride present in the outer layer, and the electron transfer between atoms is identified as a critical factor in corrosion. Specifically, Fe atoms become positively charged, detaching from the matrix surface and dissolving into the solution to form iron chloride compounds with surface Cl, while oxygen atoms turn negatively charged, progressively infiltrating the matrix and combining with Fe to create intricate iron oxide compounds. Furthermore, the entire dynamic process of corrosion oxidation on the surface of the ferritic matrix and the formation of product species has been fully captured. This ongoing corrosion process leads to significant matrix loss from metal surface and a reduction in structural integrity.

(Invited) Unveiling Fundamental Reaction Mechanisms at the Electrochemical Interface by Ab Initio Simulations

Direct experimental exploration of atomistic mechanisms governing electrocatalysis or wet corrosion at the solid-liquid interface is notoriously difficult. While fully parameter-free ab initio calculations have the potential to accurately elucidate such mechanisms, they encounter substantial conceptual challenges. Recent methodological breakthroughs, including the advent of efficient computational electrodes and the development of effective thermopotentiostats, overcame many of these limitations thus providing new research opportunities. This presentation outlines the fundamental concepts underlying these innovative methodologies and demonstrates their application in performing fully explicit calculations of structure and chemical reactions at electrified solid-water interfaces. The power of this approach in discovering new mechanisms will be demonstrated for fundamental electrochemical reactions such as metal dissolution and the hydrogen evolution reaction (HER). The identified mechanisms challenge existing understandings and empfasize the active involvement of water molecules in electrochemical reactions, challenging the perception that they are passive bystanders.

Evolution of liquid phase during homogenous non-equilibrium melting of Ta at superheating temperature.

Homogenous melting at superheating temperature is commonly described by classical nucleation theory (CNT), but the atomic mechanism of the formation and development of critical liquid nuclei is still unclear. Molecular dynamics simulations were conducted to analyze the melting process of Ta. It is found that the process of subcritical liquid clusters evolving into critical liquid nucleus occupies most of the melting time, and merging between neighboring liquid clusters is the main path for subcritical liquid clusters to grow in size. Total melting time is strongly affected by the distribution of formation sites of subcritical liquid clusters, which has been considered random in homogenous melting. This work depicts a clear picture of the formation and development of liquid phase during the homogeneous melting process at superheating temperature and suggests an internal factor of melting mechanism.

Impact of wrinkle orientation on the nanotribological properties of chemical vapor deposited TMD monolayers using AFM

Structural defects in two-dimensional (2D) materials are ubiquitous and can influence their physical and chemical properties. The presence of structural defects in single atom thick 2D materials such as graphene is detrimental to the tribological properties and is well documented; however, their effects on various other 2D materials such as transition metal dichalcogenides (TMDs) remain largely unexplored. Here, we report the role of wrinkles’ orientation on the nanoscale tribological behavior of the chemical vapor deposited (CVD) tungsten disulfide (WS2) monolayers. Our molecular dynamics (MD) simulations reveal the underlying atomistic mechanism which indicates the presence of wrinkles exhibiting various orientations, and maximum damage occurred when the tip moved at a 45-degree angle to the wrinkle. This underscores the significant influence of wrinkles’ orientation on the wear behavior of WS2 monolayers.

The formation process and mechanism of coaxial electrostatic atomization of nanofluid oil film droplets

Abstract In coaxial electrostatic atomization cutting, the atomization effect of nanofluid oil film droplets directly affects the cooling and lubrication performance. To further understand the formation process of tiny oil film water droplets in coaxial electrostatic atomization, this paper takes LB2000/water, LB2000/0.1 vol.% graphite water-based nanofluids, LB2000/0.3 vol.% graphite water-based nanofluids, LB2000/0.5 vol.% graphite water-based nanofluids as the research object. Coaxial electrostatic atomization simulation is carried out based on the determined common voltage of the conical jet (-6.5 kV). The formation process of nanofluid oil film water droplets was analyzed using electric field force, charge concentration, and volume force, and the droplet states under different fluid types were compared. The results show that when nanoparticles are added to the inner fluid, the charge concentration increases, the electric field force and volume increase, and the formation speed of the cone jet increases significantly.

Effect of interface type on deformation mechanisms of γ-TiAl alloy under different temperatures and strain rates by molecular dynamics simulation

Crystalline interface plays a significant role in strengthening lamellar γ-TiAl alloys through reconciling the strength and ductility. Herein, the effects of temperature and strain rate on the tensile deformation of three lamellar γ-TiAl interface models are investigated by molecular dynamics simulations. The three interfaces, pseudo twin (PT), rotational boundary (RB), and true twin (TT), exhibit different tensile responses due to the different interface effects: TT interface only acts as a barrier of dislocation traversing to facilitate crack extension; PT interface acts as both dislocation barrier and emission source and has a stronger release of strain energy than TT interface, retarding the crack extension; RB interface can retard and resist crack extension due to the blunting and deflection of the crack tip and the best interface geometry compatibility. The defect evolution indicates that the elevated temperature suppresses dislocation propagation at low strain rate, while the high strain rate causes small lamellar stacking faults and slit-shaped holes along tensile direction at low temperature. In addition, the dual conditions of high strain rate and low temperature induce the phase transition from FCC to BCC and then BCC to HCP. These findings provide a specific insight to understand the atomistic mechanism of interface-mediated deformation.

Numerical analysis of atomization characteristics of fuel-jet in crossflow

In order to study the breakup and atomization mechanisms of the fuel-jet in air crossflow and realize the accurate and controllable atomization effect of fuel, this paper proposes a method by coupling the large eddy simulation method and the VOF to DPM method. The results show that the breakup and atomization of the fuel-jet are mainly caused by the Rayleigh–Taylor (R–T) unstable surface wave and the Kelvin–Helmholtz (K–H) instability. The density of fuel-particles is higher near the central region of the fuel jet trajectory, decreasing as distance from the central region increases. As the momentum ratio increases, the penetration depth of the fuel-jet column also increases, resulting in a more concentrated spatial distribution of fuel particles. Conversely, with a lower momentum ratio, the spatial distribution of fuel particles becomes more uniform. For the spatial distribution of fuel particles, a new mathematical model is established to characterize the spatial distribution boundary of fuel particles. At the same momentum ratio, the higher the air velocity, the smaller the average particle diameter. At the same Weg number, the higher the fuel-jet velocity, the higher the average particle diameter. The relative error of the average particle diameter between the experiment and numerical simulation is very small, which is 6.4%.

In situ atomic-scale observation of deformation-induced reversible martensitic transformation in a CrMnFeCoNi high entropy alloy

High entropy alloys (HEAs) have attracted much attention for their excellent mechanical properties stemming from diverse deformation mechanisms. Particularly, face-centered cubic (FCC) to body-centered cubic (BCC) martensitic transformation is crucial for enhancing the strength and plasticity of HEAs, particularly at cryogenic temperatures. However, the fundamental atomic mechanism underlying martensitic transformation remains elusive, and the impact of martensitic transformation on the mechanical properties of HEAs at room temperature is unknown. Here, we report in situ atomic-scale observations of a reversible martensitic transformation from FCC to body-centered tetragonal (BCT) and ultimately back to FCC in nanostructured CrMnFeCoNi HEA at room temperature under deformation. This martensitic transformation is completed by the synergistic action of 90° partial dislocations slip on (111)FCC plane and atom shuffling, involving the periodic arrangement and slip of two 90° half Shockley partial dislocations a/12[1¯1¯2](111) and one 90° Shockley partial dislocation –a/6[1¯1¯2](111) on three successive (111)FCC atomic planes. Additionally, the reversible phase transformation induced by high stress dissipates strain energies and hinders crack propagation, thereby enhancing the fracture toughness of HEAs. Our findings contribute to a deeper comprehension of the martensitic transformation mechanisms in HEAs, offering valuable insights for improving their mechanical properties.

Subsurface oxygen at transition metal surfaces: Its direct atom-resolved imaging and role in metal oxidation

Clarifying how oxygen is incorporated into the subsurface region of metal surfaces is a crucial step towards a robust understanding of the initial oxidation of metals. Due to lack of direct atomic-resolution imaging of subsurface oxygen, the atomistic mechanisms of oxygen-metal interactions and the role of subsurface oxygen remain elusive. Here, by state-of-the-art transmission electron microscopy, we demonstrate a direct atom-resolved imaging of subsurface oxygen that is dissolved in the subsurface region of the Fe (001) and Ti (0001) surfaces. It is found that subsurface oxygen occupies the octahedral sites of the Fe and Ti lattices, rather than the tetrahedral sites. First-principles calculations reveal that the octahedral-site occupancy of subsurface oxygen is energetically more favorable compared to the tetrahedral-site occupancy and will facilitate the process of metal oxidation by reducing the formation energy of metal oxides. Our findings clarify the atomistic mechanism of how oxygen attacks metal surfaces for the initiation of oxidation that occurs everywhere in nature.

Effect of Kerosene Dual-Jet Spacing on the Mixing and Combustion Characteristics of a Scramjet Combustor.

As the core of a hypersonic propulsion system, the effective mixing efficiency of fuel and air in a supersonic combustor is crucial for its performance. This study focuses on a cold supersonic flow and employs computational fluid dynamics (CFD) techniques combined with Euler-Lagrange method's discrete-phase model (DPM) for multiphase flows, K-H and R-T (Kelvin-Helmholtz and Rayleigh-Taylor) mixing and atomization models, turbulence models, and surface evaporation models to investigate the injection, atomization, and mixing characteristics of kerosene in supersonic airflow. In order to enhance the mixing efficiency between kerosene and air while reducing flow losses, this study examines a staggered dual-jet injection scheme, with the dual jets arranged at the center of the cavity and having a dual-jet spacing of 10 and 20 mm, respectively. Starting from the interaction mechanism between jets, the impact of different staggered dual-jet spacings on the kerosene jet penetration height, span expansion area, angle of the shock wave, and Sauter mean diameter distribution was analyzed. The results show that a short dual-jet spacing (10 mm) leads to greater penetration height, wider span expansion, and a larger angle of the shock wave. When the dual-jet spacing is shorter, the interaction between the fuel jet and the cavity shear layer is stronger, resulting in an improved fuel mixing efficiency. The achievements of this study are consistent with previous experimental measurements and the literature, demonstrating a strong theoretical foundation for optimizing the design of hypersonic engines by deepening the understanding of the fundamental atomization mechanisms of kerosene jets in cold-state supersonic flows. Moreover, these results hold practical significance in improving the efficiency of kerosene combustion and enhancing the performance of flame stabilization devices.

Atomic oxygen erosion mechanism of polyimide via reactive molecular dynamics simulation and density functional theory calculation

Atomic oxygen (AO) causes serious oxidative degradation on polymeric materials in the space environment, yet understanding its reaction mechanism is a challenging task. Herein, we primarily investigate the reaction sites and reaction paths of pure polyimide material to AO erosion and propose a modification strategy involving electron-withdrawing groups to enhance the material's resistance to AO with density functional theory (DFT) and reactive force field molecular dynamics (ReaxFF MD). DFT calculations reveal that AO erosion is an electrophilic reaction, which preferentially interacts on the benzene ring with pronounced electron density distribution on the third part of the polyimide molecule. ReaxFF MD simulations validate this finding and provide additional reaction pathways that are divided into the early-stage reactions and later secondary reactions. In the early stage, only small number of AOs take part in the reactions that include the formation of CO bonds and ring opening processes. These reactions are relatively slow and majorly determine the AO resistance of the material. In the subsequent stage, AO predominantly reacts with reactive species and radicals generated from earlier reactions, leading to fast degradation. With these findings, we propose a strategy to enhance the AO resistance by introducing electron-withdrawing functional groups in the polyimides. As exemplified, the polyimide with -CF3 group shows 21.1% lower erosion yield than unmodified polymer. The present study gives a deep insight for the mechanism of AO erosion on polyimide by exploring its reaction sites and provides valuable theoretical guidance for improving the material's resistance to erosion.

Many-Body Function Corrected Neural Network with Atomic Attention (MBNN-att) for Molecular Property Prediction.

Recent years have seen a surge of machine learning (ML) in chemistry for predicting chemical properties, but a low-cost, general-purpose, and high-performance model, desirable to be accessible on central processing unit (CPU) devices, remains not available. For this purpose, here we introduce an atomic attention mechanism into many-body function corrected neural network (MBNN), namely, MBNN-att ML model, to predict both the extensive and intensive properties of molecules and materials. The MBNN-att uses explicit function descriptors as the inputs for the atom-based feed-forward neural network (NN). The output of the NN is designed to be a vector to implement the multihead self-attention mechanism. This vector is split into two parts: the atomic attention weight part and the many-body-function part. The final property is obtained by summing the products of each atomic attention weight and the corresponding many-body function. We show that MBNN-att performs well on all QM9 properties, i.e., errors on all properties, below chemical accuracy, and, in particular, achieves the top performance for the energy-related extensive properties. By systematically comparing with other explicit-function-type descriptor ML models and the graph representation ML models, we demonstrate that the many-body-function framework and atomic attention mechanism are key ingredients for the high performance and the good transferability of MBNN-att in molecular property prediction.

Advanced carbon nitride‐based single‐atom photocatalysts

AbstractSingle‐atom catalysts (SACs) have rapidly become a hot topic in photocatalytic research due to their unique physical and chemical properties, high activity, and high selectivity. Among many semiconductor carriers, the special structure of carbon nitride (C3N4) perfectly meets the substrate requirements for stabilizing SACs; they can also compensate for the photocatalytic defects of C3N4 materials by modifying energy bands and electronic structures. Therefore, developing advanced C3N4‐based SACs is of great significance. In this review, we focus on elucidating efficient preparation strategies and the burgeoning photocatalytic applications of C3N4‐based SACs. We also outline prospective strategies for enhancing the performance of SACs and C3N4‐based SACs in the future. A comprehensive array of methodologies is presented for identifying and characterizing C3N4‐based SACs. This includes an exploration of potential atomic catalytic mechanisms through the simulation and regulation of atomic catalytic behaviors and the synergistic effects of single or multiple sites. Subsequently, a forward‐looking perspective is adopted to contemplate the future prospects and challenges associated with C3N4‐based SACs. This encompasses considerations, such as atomic loading, regulatory design, and the integration of machine learning techniques. It is anticipated that this review will stimulate novel insights into the synthesis of high‐load and durable SACs, thereby providing theoretical groundwork for scalable and controllable applications in the field.

Quantum Tunneling Enhanced Hydrogen Desorption from Graphene Surface: Atomic versus Molecular Mechanism

Abstract We study the desorption mechanism of hydrogen isotopes from graphene surface using first-principles calculations, with focus on the effects of quantum tunneling. At low temperatures, quantum tunneling plays a dominant role in the desorption process of both hydrogen monomers and dimers. In the case of dimer desorption, two types of mechanisms, namely the traditional one-step desorption in the form of molecules (molecular mechanism), and the two-step desorption in the form of individual atoms (atomic mechanism) are studied and compared. For the ortho-dimers, the dominant desorption mechanism is found to switch from the molecular mechanism to the atomic mechanism above a critical temperature, which is respectively ~300 K and 200 K for H and D.

Reversible Crystalline‐Crystalline Transitions in Chalcogenide Phase‐Change Materials

AbstractPhase‐change random access memory (PCRAM) is one of the most technologically mature candidates for next‐generation non‐volatile memory and is currently at the forefront of artificial intelligence and neuromorphic computing. Traditional PCRAM exploits the typical phase transition and electrical/optical contrast between non‐crystalline and crystalline states of chalcogenide phase‐change materials (PCMs). Currently, traditional PCRAM faces challenges that vastly hinder further memory optimization, for example, the high‐power consumption, significant resistance drift, and the contradictory nature between crystallization speed and thermal stability, nearly all of them are related to the non‐crystalline state of PCMs. In this respect, a reversible crystalline‐to‐crystalline phase transition can solve the above problems. This review delves into the atomic structures and switching mechanisms of the emerging atypical crystalline‐to‐crystalline transitions, and the understanding of the thermodynamic and kinetic features. Ultimately, an outlook is provided on the future opportunities that atypical all‐crystalline phase transitions offer for the development of a novel PCRAM, along with the key challenges that remain to be addressed.

Revealing the atomic and electronic mechanism of human manganese superoxide dismutase product inhibition

Human manganese superoxide dismutase (MnSOD) is a crucial oxidoreductase that maintains the vitality of mitochondria by converting superoxide (O2●−) to molecular oxygen (O2) and hydrogen peroxide (H2O2) with proton-coupled electron transfers (PCETs). Human MnSOD has evolved to be highly product inhibited to limit the formation of H2O2, a freely diffusible oxidant and signaling molecule. The product-inhibited complex is thought to be composed of a peroxide (O22−) or hydroperoxide (HO2−) species bound to Mn ion and formed from an unknown PCET mechanism. PCET mechanisms of proteins are typically not known due to difficulties in detecting the protonation states of specific residues that coincide with the electronic state of the redox center. To shed light on the mechanism, we combine neutron diffraction and X-ray absorption spectroscopy of the product-bound, trivalent, and divalent states of the enzyme to reveal the positions of all the atoms, including hydrogen, and the electronic configuration of the metal ion. The data identifies the product-inhibited complex, and a PCET mechanism of inhibition is constructed.

Wild-Edible Allium Species from Highlands of Eastern Anatolia: Phytochemical Composition and In Vitro Biological Activities.

This study presents the phytochemical composition, antioxidant (hydrogen atom and single-atom transfer mechanisms), and digestive enzyme inhibitory (alpha-amylase, alpha-glucosidase, and pancreatic lipase) activities of ethanol-based extractions and traditional preparations (infusion) of the leaves of wild-edible Allium species (A. kharputense, A. affine, A. shirnakiense, and A. akaka) from the highlands of Eastern Anatolia. Among the eight extracts analyzed, ethanol extractions of the A. kharputense and A. akaka leaves exhibited better biotherapeutic activities and had the highest bioactive content. The dominant bioactive profile was composed of mainly allicin and phenolic compounds (chlorogenic acid, hesperidin, rutin, isoquercitrin, and quercetin) with small amounts of fatty acids. These data were similar to the biological activities and chemical composition of common Allium species and suggest the utilization of the extracts of wild-edible Allium species in the development of Allium-based biotherapeutics or nutraceuticals.

Spectroscopic and statistical physics elucidation for Cu(II) remediation using magnetic bio adsorbent based on Fe3O4-chitosan-graphene oxide

Efficient harnessing of heavy metal pollution is an urgent environmental task. Herein, magnetic bio adsorbent (MB) based on Fe3O4-chitosan-graphene oxide composite was fabricated via one step co-precipitation for adsorptive remediation of Cu(II). Remediation efficiency was evaluated by batch adsorption, meanwhile adsorption mechanism was elucidated by spectroscopic tests (XPS, UV–Vis absorption and fluorescent emission spectra), statistical physics formalism, isotherm and kinetic fittings. Results show, MB reaches adsorption percent and quantity of 87.61 % and 350.43 mg·g−1 for Cu(II) in 30 min. By virtue of paramagnetism, MB can be readily recovered with a permanent magnet for easy regeneration and cyclic use, thereby retaining adsorption quantity 279.99 mg·g−1 at the fifth cycle. The Freundlich and pseudo second order model satisfactorily describes the adsorption, designating chemical interaction as the rate limiting step. Statistical physics calculation suggests two points. (1) Multi-ionic adsorption mechanism with exothermic, spontaneous and energy lowering feature. (2) Density of adsorption sites increases with temperature, resulting in improved adsorption capacity. Spectroscopic analysis confirms the involvement of CO, CO, -NH2 in Cu(II) uptake via electron donation. These explorations contribute with novel theoretical illumination for understanding both the thermodynamic feature and atomic scale mechanism of common pollutants adsorption by bio adsorbent like Fe3O4-chitosan-graphene oxide.

Molecular dynamics study on tribological properties of AlCrFeCoNi HEA at different temperatures

The microscopically wear mechanism of AlCrFeCoNi HEA effected by high temperatures still remains unclear. In this work, the tribological properties of AlCrFeCoNi HEA and tungsten carbide (WC) at temperatures ranging from 250, 400, 550, 700, 850 °C was investigated using molecular dynamics methods. Additionally, the shear strain, contact stress, and energy change at different temperatures were analyzed to explore the atomic wear mechanism. The simulated results indicated that the coefficient of friction and wear rate decrease with the increasing temperature, since the dislocation types decrease and the kinetic energy and total system energy increase. And high temperature can inhibit the synergistic effect of strain accumulation and atomic wear on the surface of AlCrFeCoNi HEAs.

Two-metal ion mechanism of DNA cleavage by activated, filamentous SgrAI

Enzymes that form filamentous assemblies with modulated enzymatic activities have gained increasing attention in recent years. SgrAI is a sequence specific type II restriction endonuclease that forms polymeric filaments with accelerated DNA cleavage activity and expanded DNA sequence specificity. Prior studies have suggested a mechanistic model linking the structural changes accompanying SgrAI filamentation to its accelerated DNA cleavage activity. In this model, the conformational changes that are specific to filamentous SgrAI maximize contacts between different copies of the enzyme within the filament and create a second divalent cation binding site in each subunit, which in turn facilitates the DNA cleavage reaction. However, our understanding of the atomic mechanism of catalysis is incomplete. Herein, we present two new structures of filamentous SgrAI solved using cryo-electron microscopy (cryo-EM). The first structure, resolved to 3.3 Å, is of filamentous SgrAI containing an active site mutation that is designed to stall the DNA cleavage reaction, which reveals the enzymatic configuration prior to DNA cleavage. The second structure, resolved to 3.1 Å, is of WT filamentous SgrAI containing cleaved substrate DNA, which reveals the enzymatic configuration at the end of the enzymatic cleavage reaction. Both structures contain the phosphate moiety at the cleavage site and the biologically relevant divalent cation cofactor Mg2+ and define how the Mg2+ cation reconfigures during enzymatic catalysis. The data support a model for the activation mechanism that involves binding of a second Mg2+ in the SgrAI active site as a direct result of filamentation induced conformational changes.