Molecular Dynamics Simulation - Science topic

Dear Colleagues, Corrosion studies have attracted considerable interest in the areas of materials chemistry and industrial chemistry, as it affects the direct and indirect costs of industry, leading to huge economic setbacks due to the need for repair, maintenance, and even shutdowns due corrosion damage. This new volume is a comprehensive resource...

High Nb-containing TiAl alloys exhibit exceptional high-temperature strength and room-temperature ductility, making them widely used in hot-section components of automotive and aerospace engines. However, the lack of accurate interatomic interaction potential for large-scale modeling severely hampers a comprehensive understanding of the failure mec...

While the precipitation of α (hcp) from β (bcc) in various Ti alloys has been investigated in great detail, less is known about the precipitation of β from α. This study conducts a systematic investigation of structures and migrations of interfaces between β precipitates and α′ matrix in a Ti-2.6 wt% Mo alloy. Utilizing conventional and high-resolu...

The residual stress has significant effects on the microstructure and service performance of films. With good toughness and low stacking fault energy, high-entropy alloy (HEA) can act as dopant to reduce the residual stress of films via self-plastic deformation. Nevertheless, the microscopic mechanism buried deep under the surface is difficult to s...

Increasing the length of alkyl side chains is a typical way to improve the solubility of π-conjugated polymers designed for use in solution-processed devices. However, these modifications have also been reported to alter the film morphology. Given that the mechanism leading to improved solubility is not well documented yet and the nanoscale (local)...

Based on the bond energy model, we investigate the particle size and shape effects on the melting temperature, Debye temperature, and specific heat at constant pressure of Ni nanoparticles with carbon impurity. We have derived analytical expressions for these thermodynamic quantities as functions of the size and shape of nanoparticles. Numerical ca...

High temperature and ultrafast heating rate, the characteristics of ultrafast high‐temperature sintering (UHS) process, make it difficult to capture the evolution of sintering behavior and explore sintering mechanism of alumina ceramics. In this study, molecular dynamic simulations are adopted to describe the sintering behaviors of equal‐sized and...

Triboelectrification is of great importance for many classical (petroleum, pharmaceutical, polymers) and emerging (generators, sensors) technologies. For energy generation, the contact area between the materials experiencing tribocharging is a key parameter: in addition to the nature of the materials, tribocharging scales with contact area. In this...

We present a computational study of the structure and of the transport properties of electrolytes based on Li[(CF₃SO₂)₂N] solutions in mixtures of sulfoxides and sulfones solvents. The simulations of the liquid phases have been carried out using molecular dynamics with a suitably parametrized model of the intermolecular potential based on a polariz...

Molecular dynamics models combined with computational approaches can be used as advanced screening techniques for finding highly efficient material‐molecule interactions based on binding affinity, including in the development of gas sensors. However, most models are originally designed for liquid phase interactions, which do not align with gas sens...

Hematite is a well-known catalyst for the oxygen evolution reaction on photoanodes in photoelectrochemical water-splitting cells. However, the knowledge of hematite-water interfaces and water oxidation mechanisms is still lacking, which limits improvements in photoelectrochemical water-splitting performance. Herein, we use the Fe-terminated hematit...

Melting properties are critical for designing novel materials, especially for discovering high-performance, high-melting refractory materials. Experimental measurements of these properties are extremely challenging due to their high melting temperatures. Complementary theoretical predictions are, therefore, indispensable. One of the most accurate a...

Reaction-sintered silicon carbide (RS-SiC) is an ideal material for spacecraft reflectors due to its excellent mechanical properties. However, its high hardness, brittleness, and multiphase nature pose significant challenges to conventional polishing techniques. To address this, photocatalytic modification and vibration assistance have been employe...

A thermodynamic approach is proposed to model and simulate nanostructured porous carbon using all-atom molecular dynamics simulations. In this work, molecular dynamics models with a size of 800000 atoms have been developed and applied to analyze their mechanical structure−property relations. Models are generated for a wide range of densities (0.59−...

We present molecular dynamics simulations to study the thermodynamics of nanobubbles trapped at the mouth of narrow slit pores. Except when the slit dimensions are comparable to typical molecular sizes, the predictions of macroscopic thermodynamic theory are recovered by our simulations. Our simulations confirm that in this case, the internal press...

Through the decomposition of the pressure into the kinetic and the intermolecular contributions, we show that the pressure anisotropy in the fluid interface, which is the source of the interfacial tension, comes solely from the latter contribution. The pressure anisotropy due to the intermolecular force between the fluid particles in the same or th...

Recent advancements in protein structure determination are revolutionizing our understanding of proteins. Still, a significant gap remains in the availability of comprehensive datasets that focus on the dynamics of proteins, which are crucial for understanding protein function, folding, and interactions. To address this critical gap, we introduce m...

Molecular Dynamics (MD) simulations provide accurate descriptions of the motions of molecular systems, yet their computational demands pose significant challenges in applications in molecular biology and materials science. Given the success of deep learning methods in a wide range of fields, a timely question concerns whether these methods could be...

Aluminum-air batteries (AABs) are considered among highpower battery systems with various potential applications. However, the strong self-corrosion of Al in alkaline electrolytes negatively affects its Coulombic efficiency and significantly limits their large-scale application. This work presents the use of cetylpyridinium chloride (CPC) as an ine...

The crystal structure of the Kob–Andersen mixture has been probed by genetic algorithm calculations. The stable structures of the system with different molar fractions of the components have been identified, and their stability at finite temperatures has been verified. It has been found that the structures of composition ABn, where n = 2, 3, or 4,...

Understanding the oxygen‐redox reactions within Mn‐rich layered cathode materials is an important strategy to improve the capacity of sodium‐ion batteries (SIBs) while satisfying the demand for low cost and the use of abundant resources. Nonetheless, the P2‐type Nay[AxMn1‐x]O2 compositions (where A = electro‐inactive elements) exhibit poor capacity...

The base‐promoted Kemp elimination reaction has been used as a model system for enzyme design. Among the multiple computationally designed and evolved Kemp eliminases generated along the years, the HG3‐to‐HG3.17 evolutionary trajectory is particularly interesting due to the high catalytic efficiency of HG3.17 and the debated role of glutamine 50 (G...

Potassium channels encoded by human Ether-à-go-go-Related Gene (hERG) are inhibited by diverse cardiac and non-cardiac drugs. Disopyramide is a chiral Class Ia antiarrhythmic that inhibits hERG at clinical concentrations. This study evaluated effects of disopyramide enantiomers on hERG current (IhERG) from hERG expressing HEK 293 cells at 37 °C. S(...

The short-range order and intermediate-range order in GeO2 glass are investigated by molecular dynamics using machine-learning interatomic potential trained on ab initio calculation data and compared with the reverse Monte Carlo fitting of neutron diffraction data. To characterize the structural differences in each model, the total/partial structur...

The 10 kV switchgear is widely utilized in power systems due to its convenience and reliability. However, in high-humidity environments, switchgear is susceptible to condensation, which can severely damage its internal insulation components. To address this issue, this study modifies epoxy resin (EP) by incorporating nano-MgO to improve its hydroph...

Drug delivery plays a pivotal and essential role in modern medicine. This field encompasses a wide range of strategies and technologies designed to facilitate the safe transportation of therapeutic agents within living organisms. These systems serve a fundamental role in addressing various challenges in drug delivery, including reducing side effect...

The present study employs equilibrium molecular dynamics simulations to explore the potential mechanism for controlling friction by applying electrostatic fields in nanoconfined aqueous electrolytes. The slip friction coefficient demonstrates a gradual increase corresponding to the surface charge density for pure water and aqueous electrolytes, exh...

The bulk modulus is one of the most important properties of fullerenes. This parameter indicates the volumetric deformation under the influence of external pressure. Therefore, the strength of fullerene can be interpolated from its bulk modulus. The strength of fullerene is often measured indirectly through its vibration frequency (a non-destructiv...

Given the prominence of G protein coupled receptors (GPCRs) as drug targets, targeting their immediate downstream effectors, G proteins, could be of immense therapeutic value. The discovery that the natural product YM-254890 (YM) can arrest uveal melanoma by specifically inhibiting constitutively active Gq/11without impacting other G protein famili...

Plain Language Summary Geochemical and seismic observations suggest that subducted oceanic crust can accumulate at the core‐mantle boundary, but its effects on the seismic velocity of the D'' layer remain poorly constrained. In fact, the thermoelastic properties of seifertite, which is a major mineral in the deeply subducted oceanic crust at the lo...

The plasma hydrogenation technique is widely recognized as an efficient tool for modifying graphene’s physical and chemical properties. Therefore, a comprehensive understanding of the interaction between plasma and graphene at the atomic scale can provide valuable insights into the potential applications of graphene. Here, using MD (molecular dynam...

Experiments have shown that crystalline–amorphous nanolayered composites show a strong size dependence in strength and plasticity. However, the underlying mechanism remains unknown. Here, the layer thickness (h)-dependent compressive strength and plastic deformation of Nb/amorphous CuNb nanolayered composites with h ranging from 2.8 to 20 nm have b...

A model for studying displacement damage in irradiated HfO 2 ferroelectric thin films was developed using deep learning and a repulsive table, combining the accuracy of density functional theory with the efficiency of molecular dynamics. This model accurately predicts the properties of various HfO 2 phases, such as PO ( Pca 2 1 ), T ( P 4 2 / nmc )...

Dipeptidyl peptidase 8 (DPP8) and 9 (DPP9) are proteases gaining significant attention for their role in health and disease. Distinctive studies of these proteases are hampered by their close homology. Furthermore, designing selective compounds is a major challenge due to the highly conserved catalytic site. Here, we provide mechanistic insights un...

Fe–Ni nanowires (NWs) containing coherent twin boundaries (CTBs) have received widespread attention in recent years owing to their unique chemical properties. It is important to understand the influence of CTBs on the deformation mechanism of Fe–Ni alloy NWs to develop functional materials based on Fe–Ni alloy NWs. The deformation process of BCC Fe...

Xanthione is a sulfated polycyclic aromatic hydrocarbon which exhibits unique anti-Kasha properties and substantial sensitivity to its medium. Due to this sensitivity however, this makes xanthione-based systems very difficult to simulate. Further, xanthione’s is understood to be come more photostable in the presence of a highly polar medium, howeve...

A dynamical rearrangement in the electronic structure of a molecule can be driven by different phenomena, including nuclear motion, electronic coherence or electron correlation. Recording such electronic dynamics and identifying its fate in an aqueous solution has remained a challenge. Here, we reveal the electronic dynamics induced by electronic r...

Optimizing the liquid reaction phase holds significant potential for enhancing the efficiency of biocatalytic processes since it determines reaction equilibrium and kinetics. This study investigates the influence of the addition of deep eutectic solvents on the stability and activity of α‐chymotrypsin, a proteolytic enzyme with industrial relevance...

Unraveling the nature of adsorbed olefins in zeolites is crucial to understand numerous zeolite‐catalyzed processes. A well‐grounded theoretical description critically depends on both an accurate determination of the potential energy surface (PES) and a reliable account of entropic effects at operating conditions. Herein, we propose a transfer lear...

Cementitious material durability is affected by the transport and adsorption of water molecules and ions in the nanopore channels of cement hydration products. Hydrated calcium silicate (C-S-H) accounts for about 70% of the hydration product. It determines the mechanical properties of cementitious materials and their internal transport properties....

Hardness decreases as indentation depth increases at both the nano- and micro-meter scales. By incorporating interfacial contributions, the indentation size effect can provide valuable information on the deformation behaviors of Ni-based single-crystal superalloys. In this paper, through experimental studies and atomistic simulations, we examine th...

While the emergence of PM6 : Y6 active layer re‐energized the organic photovoltaic community, excessive aggregation of Y6 molecules induced by their strong intermolecular interactions has limited the performance of PM6 : Y6‐based organic solar cells (OSCs). Adding 3D multi‐arm small‐molecule acceptors is an effective strategy to inhibit such aggreg...

In Couette flow, the liquid atoms adjacent to a solid substrate may have a finite average tangential velocity relative to the substrate. This so-called slip has been observed frequently. However, the particular molecular-level mechanisms that give rise to liquid slip are poorly understood. It is often assumed that liquid slip occurs by surface diff...

Echelle gratings, a specialized type of diffraction grating, feature a periodic groove pattern that exhibits excellent light-splitting capabilities. These gratings are characterized by a low density of lines per millimeter and a significant blaze angle. The primary substrate for echelle gratings in mechanical scratching is an aluminum film with a l...

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is an ancient protein critical for CO2-fixation and global biogeochemistry. Form-I RuBisCO complexes uniquely harbor small subunits that form a hexadecameric complex together with their large subunits. The small subunit protein is thought to have significantly contributed to RuBisCO's respon...

In this study, we leveraged a sophisticated active learning model to enhance virtual screening for SQLE inhibitors. The model’s improved predictive accuracy identified compounds with significant advantages in binding affinity and thermodynamic stability. Detailed analyses, including molecular dynamics simulations and ADMET profiling, were conducted...

This study presents a comprehensive computational approach aimed at repurposing an FDA-approved drug, retrieved from DrugBank database, as a potential inhibitor of the SARS-CoV-2 main protease, a crucial target for antiviral drug development. Utilizing e-pharmacophore-based virtual screening, molecular docking, MM-GBSA calculations, and molecular d...

In this work, a novel series of fifteen pyrazole-linked hydrazide-hydrazone derivatives (4a-o) were designed, synthesized, characterized, and evaluated for their antihyperglycemic activity against α-amylase and α-glucosidase. In vitro results revealed that all synthesized compounds (4a-o) showed good to excellent antihyperglycemic activity with IC5...

The properties of La2Sn2O7 have been studied by employing density functional theory with the GGA-PBE exchange-correlation functional. This research mainly focused on the essential physical characteristics of the La2Sn2O7 under the application of hydrostatic pressure. Our findings indicate that La2Sn2O7 remains in its cubic phase under all the press...

Molecular dynamics simulation is used to investigate the interdiffusion across the interfaces of high-entropy alloys (HEAs), reactive nano-multilayer foils (NMFs), NMFs, and crystalline Al. This study reveals highly asymmetric interdiffusivity within adjacent reactive NMFs and HEAs, exhibiting strong temperature dependency. Abnormal interdiffusion...

Sodium-proton antiporter NhaA of Escherichia coli is a paradigm to investigate the mechanistic basis of the fundamental Na+/H+ exchange in cells. However, all existing crystal structures of NhaA are inward-facing (IF) and the putative outward-facing (OF) structures are still unsolved by experiment, limiting a complete understanding of the transport...

Consisting of more than 11,000 members distributed over five families, the tautomerase superfamily (TSF) is a large collection of proteins with diverse biological functions. While much attention has been given to individual TSF enzymes, a majority remain structurally and functionally uncharacterized. Given its large size, studying a representative...

Direct regeneration of electrode materials has been in the spotlight due to its potential resource recovery and environmental benefits, especially for LiNixCoyMnzO2 (NCM) cathode materials. Yet, prior studies have predominantly emphasized innovating regeneration methods, overlooking the intrinsic defects of spent NCM and their effects in the regene...

Water plays a fundamental role in the structure and function of proteins and other biomolecules. The thermodynamic profile of water molecules surrounding a protein are critical for ligand binding and recognition. Therefore, identifying the location and thermodynamic behavior of relevant water molecules is important for generating and optimizing lea...