Results Of Molecular Dynamics Simulations Research Articles

Detailed kinetic mechanism of polyoxymethylene dimethyl ether 3 (PODE3). Part I: Ab initio thermochemistry and kinetic predictions for key reactions

In recent years, polyoxymethylene dimethyl ether 3 (PODE3) has emerged as a promising fuel additive to mitigate soot emissions in diesel engines, garnering significant research attention. Several detailed kinetic mechanisms of PODE3 have been developed to investigate its reaction pathways and to simulate its combustion process. Typically, these mechanisms employ analogy methods based on rate constants derived primarily from PODE1 sub-mechanisms. However, in this study, we present, for the first time, high-level ab initio quantum chemical calculations directly on PODE3 itself. (1) The bond dissociation energies (BDEs) of all CH and CO bonds in dimethyl ether (DME) and PODEn (n = 1–5) were calculated using combined compound methods (CBS-APNO/G3/G4). (2) The obtained BDE results were then utilized to investigate the unimolecular decomposition reactions of PODE3, demonstrating good agreement with previous Molecular Dynamics simulation results. (3) The rate constants of hydrogen abstraction reactions of PODE3 by H˙,C˙H3,CH3O˙,O˙H,HO˙2,O2 were calculated with all possible pre-reaction or post-reaction complexes identified. The rate constants of the H-atom abstraction reactions were found to primarily depend on the energy barriers following the order: O˙H>CH3O˙>H˙>C˙H3>HO˙2>O2. However, the abstraction by H˙ can dominate as temperature increases. (4) The rate constants of β-scission and isomerization reactions of PODE3 radicals were also computed. The calculated β-scission reaction rates supported the suitability of the rate analogy for PODEn, employing the long-chain PODE3. The energy barriers of the isomerization reactions with long chain transition states were comparable to the energy barrier of the β-scission reactions and are much lower than that in the case of PODE1 radicals. (5) The thermochemistry properties of all involved species, including PODE4–5 and their radicals, were calculated with the combined compound methods (CBS-APNO/G3/G4) for further combustion modeling. Considering PODE3′s nature as a long-chain PODEn, the rate constants computed for PODE3 can serve as a solid foundation for developing detailed mechanisms for PODE4–5.

The mechanism by which Naru 3 pill protects against intervertebral disc cartilage endplate degeneration based on network pharmacology and experimental verification

ContextNaru 3 pill is a traditional Mongolian medicine for the treatment of intervertebral disc degeneration (IDD), but the mechanism is not yet clear.ObjectiveThis study investigated the mechanism of Naru 3 pill in the treatment of IDD.Materials and methodsActive ingredients and related targets of Naru 3 pill, as well as IDD-related genes, were collected from public databases. The analysis was performed by protein‒protein interaction network analysis, gene ontology and Kyoto Gene and Genome Encyclopedia (KEGG) functional enrichment analysis, molecular docking and molecular dynamics simulations. Finally, the network pharmacology results were validated by in vitro experiments.ResultsNetwork analysis showed that sesamin, piperine and ellagic acid were potential key components and CASP3, BAX and BCL2 were key targets. KEGG analysis indicated the apoptotic pathway as a potential pathway. Molecular docking showed that sesamin interacted better with the targets than the other components. The results of molecular dynamics simulations indicated that the three systems BAX-sesamin, BCL2-sesamin and CASP3-sesamin were stable and reasonable during the simulation. In vitro experiments showed that sesamin had the least effect on cell growth and the most pronounced proliferation-promoting effect, and so sesamin was considered the key component. The experiments confirmed that sesamin had antiapoptotic effects and reversed the expression of CASP3, BAX and BCL2 in degeneration models, which was consistent with the network pharmacology results. Furthermore, sesamin alleviated extracellular matrix (ECM) degeneration and promoted cell proliferation in the IDD model.ConclusionThe present study suggested that Naru 3 pill might exert its therapeutic and antiapoptotic effects on IDD by delaying ECM degradation and promoting cell proliferation, which provides a new strategy for the treatment of IDD.

Tribological performance and lubrication mechanism of carbon nitride nanosheets as novel and high-efficiency additives for water lubrication

Recently, water-based nano-additives have attracted more attention with the resurrection of water lubrication owing to the increasing awareness of environmental protection and energy-saving. Highly water-dispersible carbon nitride nanosheets (C3N4 nanosheets), obtained via a high-yield and low-cost hydrothermal approach, were first used as a novel and environmentally-friendly nano-additive for water-based lubrication. The tribotest results exhibited that the tribological performances of C3N4 nanosheets in the water-based lubricant are highly sensitive to their adding concentrations. It was found that a C3N4 nanosheet concentration of 0.2 wt% could decrease the friction and wear in steel-steel contacts by 49.0% and 54.2%, respectively. The lubrication performances of C3N4 nanosheets as additives were much better than those of C3N4, attributed to their regular shape, good water dispersibility, and high reactivity. In addition, C3N4 nanosheets as additives exhibited a long service life even under harsh lubrication conditions. In addition, the molecular dynamics (MD) simulation technique was first employed to study the lubrication performances and lubrication regimes of C3N4 nanosheets. By combining the results of MD simulations and wear track surface analyses, the formation of water-based lubricating film and tribochemical film (mainly composed of organic compounds, metal nitrides, iron oxides, metal carbonates, and C3N4 nanosheets) coupled with the interlayer sliding and polishing effects of C3N4 nanosheets were primarily responsible for the excellent tribological performances of C3N4 nanosheets.

Tunable properties of poly(vinylidene fluoride)-derived polymers for advancing battery performance and enabling diverse applications

This study uses molecular dynamics (MD) simulations to examine the thermal, structural, mechanical, and dynamic characteristics of poly(vinylidene fluoride) (PVDF) and its copolymers. We constructed and simulated three copolymers by replacing 0 to 50 mol% of PVDF monomers with trifluoroethylene (TrFE), hexafluoropropylene (HFP), and chlorotrifluoroethylene (CTFE) in order to investigate their properties. Additionally, we conducted a simulation of a polyelectrolyte model using the copolymers we constructed, along with LiFSI salt and FEC solvent, in order to evaluate the ionic conductivity. The calculated properties, such as melting temperature, thermal conductivity, Young’s modulus, and ionic conductivity, were found to be dependent on the molar fraction of substituted monomers. We observed specific peaks in the ionic conductivity calculated at room temperature, with maximum values of 3.32 × 10−5 S/cm for P(VDF-3 mol% HFP) and 2.56 × 10−5 S/cm for P(VDF-10 mol% TrFE). The molecular dynamics simulation results were consistent with experimental findings and provided insights into the adjustable atomistic details of fluorinated polymers derived from PVDF.

Study on the Remediation of Pyrene-Contaminated Soil with Surfactants and their Mechanisms

Soil is the main aggregation site of polycyclic aromatic hydrocarbons and an important pathway of migration to other media. In this paper, the adsorption behavior of pyrene and seven different types of surfactants on kaolinite surfaces was studied by molecular dynamics simulation and desorption testing. The molecular dynamics simulation results showed that pyrene was more easily adsorbed on the 001 (-) side of kaolinite. SDBS, SDS, TW80, and TX-100 had strong interactions with pyrene, encapsulating pyrene molecules in aggregates. However, when the concentration of surfactant was too high, the desorption of pyrene molecules on a kaolinite surface will be inhibited. The desorption of pyrene molecules will be inhibited in the presence of BS-12, TW80, and TX-100, while the desorption process can be promoted by using CTAC, DDBAC, SDBS, and SDS as soil remediation agents. The removal rate of pyrene gradually increased with the increase of SDS dosage, while for SDBS, the removal rate showed a trend of first increasing and then decreasing. When the concentration of SDS was 0.014 mol/L, the elution rate of pyrene reached 72.86%. The molecular dynamics simulation results were similar to the desorption test results, verifying the reliability of molecular dynamics simulation. The research results provide theoretical support for the selection of surfactants in the remediation process of pyrene-contaminated soil.

Molecular dynamics simulations guided the preparation of nano-silica/polyimide/cellulose composite insulating paper

Following the surge in power loads and continuous improvement in the voltage level, insulating papers' mechanical and electrical properties face new challenges. However, traditional inefficient “tentative” trial and error experiments are formidable to rapidly and efficiently prepare cellulose composite insulating paper because the direct scientific theory or simulation guidance is insufficient. To solve this problem, the nano-silica(nano-SiO2)/polyimide(PI)/cellulose composite models were designed and their mechanical, and dielectric properties were predicted by molecular dynamics (MD) simulation. The preparation of corresponding nano-SiO2/PI/cellulose insulating paper was guided by the MD simulation results and their surface morphology, mechanical properties, and electrical properties were investigated. The experimental results are in good agreement with the MD simulation results and confirmed that P3 insulating paper possesses the best comprehensive performance, and its tensile strength, relative permittivity, dielectric loss, volume resistivity, and breakdown strength are 71.44 MPa, 2.39, 0.2%, 5.16 × 1015 Ω∙m, and 75.8 kV∙mm−1, respectively. This work proves the feasibility and effectiveness of using MD simulation to guide the development of new insulating papers, and compared with the existing traditional preparation methods, this method is expected to be applied to study various new materials in the future and promote the vigorous development of new materials.

Multi-scale analysis on the aggregation mechanism of oxygen-rich coal-derived asphaltene molecules

Significant differences exist in the structural features between coal-derived asphaltene and petroleum asphaltene (e.g., the degree of alkylation, aromatic nuclei size, heteroatom content, as well as morphology characteristics). The self-aggregation behavior exhibited by coal tar asphaltene for coal tar processing should be investigated in accordance with the structural characteristics of coal tar asphaltene. In this study, the focus was placed on the effect exerted by oxygen structure format, location and content on the aggregation behavior of asphaltene. The electrostatic potential (ESP) maps, theoretical reactivity parameters, molecular orbitals, dimerization interaction energies, and weak interactions of coal tar asphaltene were determined based on quantum chemistry. The self-aggregation behavior exhibited by coal-derived asphaltene was explored through molecular dynamics simulations. As indicated by the results of this study, the π-π interactions among asphaltenes were enhanced by the heteroatoms embedded in polycyclic aromatic hydrocarbons (PAHs). In the identical oxygen content, the π-π stacking of asphaltenes with five-membered heterocyclic structures turned out to be more intense. The carboxyl and hydroxyl were more likely to form hydrogen bonds, such that the stability of asphaltene aggregates was increased. Furthermore, as indicated by the molecular dynamics simulation results, the oxygen-containing structures far from PAHs exhibited small steric resistance and a higher probability of the formation of hydrogen bonds.

Molecular dynamics coupled with experimental study of the effects of polyethylene glycol on the structure and antifouling properties of polyethersulfone membranes

AbstractPolyethylene glycol (PEG), as a hydrophilic molecule, exerts a significant influence on the morphology and performance of membranes. However, the mechanism by which PEG influences polyethersulfone (PES) membranes remains unclear. In this work, the addition of varying concentrations (4, 12, 24 wt%) and molecular weights (200, 400, and 600 Da) of PEG on the PES membrane was investigated by molecular dynamics (MD) simulation and experimental study. Compared to the concentration of PEG (4, 12, and 24 wt%), the molecular weight of PEG (PEG200, PEG400, and PEG600) had little effect on the membrane pore size. The radial distribution function and fractional free volume results of MD simulation both proved that. Additionally, both the experimental adsorption capacity (QHA) and the calculated adsorption energy (Eads) revealed that the adsorption of humic acid (HA) on the PES membrane with 4 wt% PEG was higher than that on the pure PES membrane, which meant that PEG was not beneficial to the anti‐fouling property but improved the water flux of PES membranes. The results of this study not only provide theoretical predictions and a scientific basis for the formulation of PES membranes but also promotes an approach for exploring the mechanism by which additives affect polymer membranes.

Self-diffusion of aromatic compounds in the carbon tetrachloride – acetone binary system. NMR experiment and MD simulation

In this work, we studied the influence of the structure of molecules of aromatic compounds (methylparaben (MP), propylparaben (PP), syringic acid (SA), gallic acid (GA), protocatechualdehide (PAL), p-coumaric acid (p-CA), and caffeic acid (CA)) on their molecular association and self-diffusion in the binary carbon tetrachloride – acetone solvent. The self-diffusion coefficients of PAL, SA, and GA in the binary carbon tetrachloride – acetone‑d6 solvent were measured by the pulsed gradient spin-echo nuclear magnetic resonance (PGSE NMR) method at temperatures of 288, 298, and 308 K. The data obtained at 298 K were also compared with the data on the self-diffusion coefficients of MP, PP, CFA, and p-CA in the binary solvent available in the literature. According to the presented data, the self-diffusion coefficients of all the substances under consideration become greater with an increase in the acetone‑d6 concentration and decrease in the MP > PAL > PP > p-CA > SA > CA > GA series of compounds. Quantitative assessment of the degree of influence of molecular association on solute self-diffusion was carried out within the framework of a method based on the ratio of the self-diffusion coefficient of a solute to the self-diffusion coefficient of its monomers. The study shows that the degree of influence of molecular association of the solute on its self-diffusion is determined by the number and type of active functional groups in the structure of the solute molecules (MP < PP < PAL < SA < p-CA < CA < GA), but does not depend on the composition of the binary solvent. According to the results of molecular dynamics (MD) simulation, this effect correlates with the increase in the degree of self-association of solutes and decrease in the degree of solute – acetone heteroassociation observed when the carbon tetrachloride concentration becomes higher. This effect is also responsible for the similar concentration dependencies of the self-diffusion coefficients of active and inert compounds.

Development of novel natural gas hydrate inhibitor and the synergistic inhibition mechanism with NaCl: Experiments and molecular dynamics simulation

Drilling fluid systems with exceptional performance serve as a foundation for commercial hydrate extraction. However, most hydrate reservoirs are located at relatively deep water depths and have shallow burial depths. As a result, there are high demands on the density of a hydrate drilling fluid system. Thus, the traditional hydrate drilling fluid system no longer meet the drilling needs in deep water shallow hydrate reservoirs. In this paper, a copolymer SYZ-2 was synthesized based on N-Vinyl-ε-caprolactam and N, N-dimethyl acrylamide. The effects of SYZ-2 and its NaCl system on methane hydrate were first tested by a constant rate cooling method, and the inhibition mechanisms of the system on hydrate nucleation and formation were investigated by molecular simulations. Meanwhile, the formulation and properties of a low-density hydrate drilling fluid system (1.06 g/cm3) based on SYZ-2 were also described in detail. The experimental results show that the hydrate formation temperature with the influence of SYZ-2 decreases from 10.6 °C to 2.7 °C, which can even be significantly reduced to −3.1 °C in the presence of 7 % NaCl. The molecular dynamic simulation results show that SYZ-2 inhibits the nucleation of hydrates by decreasing the solubility of methane molecules, primarily by promoting the agglomeration of methane molecules. Additionally, SYZ-2 can also adsorb to the surface of hydrates and prevent the hydrate cage structure from capturing methane molecules. In contrast, NaCl inhibits hydrates formation by restricting the movement of water molecules. These results provide valuable insights into a better understanding of the gas hydrate inhibition mechanisms, the rational development of high-performance hydrate inhibitors for drilling fluids, as well as the construction of drilling fluid systems.

First-principles study on two-dimensional Mo2B for its potential application in gas sensing

Through first principles, we first demonstrated the structural and thermal stability of monolayer Mo2B by analyzing the results of phonon spectrum and ab initio molecular dynamics simulations. In addition, the adsorption energies for four kinds common noxious molecules NO, NO2, CO, CO2 are calculated with values of −2.978 eV, −2.838 eV, −1.914 eV and −0.586 eV, respectively. The relatively low adsorption energy for NO, NO2 means that Mo2B has a high selectivity for these molecules. The charge transfer number of NO, NO2, CO, and CO2 on monolayer Mo2B are 0.855 e, 1.189 e, 0.658 e, and 0.926 e. The CO2/Mo2B system has smallest adsorption energy and a relatively large charge transfer value, which suggests Mo2B may be used as a highly reversible and sensitive detector for CO2. More importantly, the recovery time for CO2/Mo2B system is only 10−4 s. The recovery time for the other three molecules is calculated to exceed 1010 s at room temperature which indicates irreversible detection of these molecules. These results could provide guidance for the achievement of high-performance gas sensitive materials.

Multifunctional composite membranes for interfacial solar steam and electricity generation

Emerging water purification technology, known as interfacial solar steam generation (ISSG), has been rapidly developing in recent years. ISSG offers a promising solution to address both freshwater shortage and energy demand by simultaneously producing freshwater and electricity. This is achieved through the combination of microporous films and highly efficient photothermal materials. In this study, we have developed a composite film using a 2D material, reduced graphene oxide (rGO), and a combination of 1D materials, chitin fiber@multi-walled carbon nanotube (Chiber@CNT). Through a hybrid dimensional design, these materials’ advantages are integrated, resulting in a composite film with a distinct laminar porous structure and excellent broadband absorption. Notably, under 1 kW·m−2 sunlight irradiation, the composite film achieves a water evaporation flux of 2.10 kg·m−2·h−1 with a photothermal conversion efficiency of 75.79%. In addition, by utilizing an energy-harvesting strategy based on natural water evaporation in porous nanomaterials for power generation, the composite film successfully enables the simultaneous production of freshwater and electricity. Its output voltage reaches 0.39 V in a 3.5 wt% NaCl solution. Furthermore, the film’s output voltage varies with the concentration of NaCl, increasing from 0.26 V (in deionized water) to 0.45 V (in the saturated NaCl solution). Molecular dynamic simulation results indicate that the enhanced power generation can be attributed to the difference in interatomic interaction strength between ions and hydrophilic functional groups in chitin fiber (Chiber). This finding provides a deep physical mechanism and opens up possibilities for the film’s application in highly concentrated salt solutions.

Nanobubble-Induced Aggregation of Ultrafine Particles: A Molecular Dynamics Study.

Nanobubble-induced aggregation (NBIA) of fine and ultrafine particles in liquid is a promising method for enhancing floatation rates in mineral processing, cleaning contaminants from water, and reviving marine ecosystems. Although the current experimental techniques can measure the nanobubble capillary force between two surfaces with controlled approach speed, they are not capable of imaging NBIA dynamics of fine/ultrafine particles by real-time observation with nanoscale spatial resolution. In this work, we use molecular dynamics (MD) simulations to study dynamics of NBIA of Ag particles in a Lennard-Jones fluid system. The molecular-level modeling allows us to study microscopic details of NBIA dynamics that are inaccessible by current experimental means. Using MD simulations, we investigated the effects of NB size, surface wettability, surface roughness, and contact line pinning on NBIA dynamics. Our modeling results show that both concave NB bridges between two hydrophobic surfaces and convex NB bridges between two hydrophilic surfaces can result in an attractive nanobubble capillary force (NBCF) that causes the aggregation of Ag particles in liquids. The equilibrium separation between two fully aggregated particles can be well predicted by the improved capillary force model. We also observe that the change of contact angle after the contact line pinning occurs at the sharp edge of a particle, which slows the aggregation process. Our thermodynamics analysis shows that there is a critical contact angle below which the merged surface NBs will detach from the surface instead of causing aggregation. The prediction of the critical contact angle is corroborated by our MD simulation results.

Grain size and scratching depth dependent tribological characteristics of CrCoNi medium-entropy alloy coatings: A molecular dynamics simulation study

In this work, we have investigated the impact of grain size and scratching depth on the tribological behavior of nanocrystalline CrCoNi medium-entropy alloy (MEA) coatings during scratching by molecular dynamics (MD) simulations. Regardless of the grain size, a monotonically increase in both friction coefficient and wear rate with increasing the scratching depth was observed in the nanocrystalline CrCoNi MEA coating. When its microstructure becomes coarser, the friction coefficient becomes lower. As a function of grain size, the evolutions of friction coefficient and wear rate can be divided into three regions, namely high friction coefficient (or wear rate) region in a grain size range of below 6 nm, relatively stable friction coefficient (or wear rate) region in a grain size range of 6–12 nm, and a relatively low friction coefficient (or wear rate) region in a grain size range of larger than 12 nm. According to the MD simulation results, the higher wear rate for a finer CrCoNi MEA coating can be explained by its lower hardness. In contrast, the reduction of friction force was mainly attributed to the scratching induced grain boundary (GB) sliding and dislocation emissions from GBs. Moreover, the scratching induced phase transformation from crystalline to amorphization and plastic deformation mode transitions also affect its tribological properties.

Cellulose dissolution in mixtures of ionic liquids and molecular solvents: The fruitful synergism of experiment and theory

We investigated the dependence of dissolution of microcrystalline cellulose (MCC) in binary solvent mixtures of ionic liquids (ILs) and the molecular solvents (MSs) N,N-dimethylacetamide (DMAc) and dimethyl sulfoxide (DMSO). The ILs we used are based on 1-(n-butyl)-3-methylimidazolium cation, BuMeIm+, with acetate (AcO−) and chloride (Cl−) anions. As experimental variables, we changed the mole fraction of the MS (χDMAc or χDMSO) and the temperature (T). MCC dissolution was determined using an optical microscope and expressed on the mass fraction scale (m%). The order of maximum m% was BuMeImAcO-DMSO > BuMeImAcO-DMAc ≫ BuMeImCl-DMSO. To rationalize this dependence, we used molecular dynamics (MD) simulations employing, as a model for cellulose, a crystallite of eight chains, each containing ten anhydroglucose units (AGUs). We calculated the root-mean-square-deviation (RMSD) and the radial distribution function, g(r). Values of RMSD showed that the separation of decamer-chains follows the same order as the maximum m%; more chain separation was taken to indicate greater crystallite dissolution. Additionally, the maximum values and the sharpness of the g(r) peaks followed the same order of dissolution, due to a combination of hydrogen bonding between the hydroxyl groups of the AGU and ions of the IL. We also recorded the turbidity of MCC-IL-DMSO solutions and the conductance of cellobiose-IL-MS solutions; the results of both experiments corroborated our interpretations of the MD simulation results. Our study suggests that MD simulations can be fruitfully employed to predict the best candidates among a series of solvents, e.g., IL-MS. This screening saves labor and material in the search for optimal solvents for cellulose dissolution.

DFT, FMO, ESP, Molecular Docking and Molecular Dynamics Simulations of Bis-2-(2-Phenethyl)Chromone as a Potential PPAR Agonist

Abstract: Globally, chronic diseases are becoming the leading cause of death. Because of the large number of patients, high medical cost, long duration of illness and the great demand for services. Diabetes is one of them and the prevalence is still rising, causing a serious physical burden to patients; it also affects a great economic burden on society. Therefore, the development of more effective antidiabetic medication is of great importance. To screen the rare chromone dimer compounds and study their inhibitory effects on type 2 diabetes mellitus. The structure was geometrically optimized and its thermodynamic properties were analyzed by DFT B3LYP-D3(BJ)/6-31G(d,p); molecular docking and molecular dynamics simulation were used to investigate the interaction of PPARγ with their ligands. In addition, its ESP and FMO were analyzed. The bis-2-(2-phenethyl)chromone derivatives have high molecular docking fractions and stable molecular dynamics simulation results, indicating that the extracts from Agarwood species bi-2-(2-phenethyl)chromone derivatives have good interactions with PPARγ. This implies that bis- 2-(2-phenethyl)chromone derivatives have good interactions with PPARγ. It is suggested that BPEC may be a natural agonist of PPARγ, which is expected to exert a more efficient hypoglycemic effect and avoid more drug side effects, laying a foundation for the research and development of anti-type 2 diabetes drugs.

Deep neural network-based reduced-order modeling of ion–surface interactions combined with molecular dynamics simulation

With the advent of complex and sophisticated architectures in semiconductor device manufacturing, atomic-resolution accuracy and precision are commonly required for industrial plasma processing. This demands a comprehensive understanding of the plasma–material interactions—particularly for forming fine high-aspect ratio (HAR) feature patterns with sufficiently high yield in wafer-level processes. In particular, because the shape distortion in HAR pattern etching is attributed to the deviation of the energetic ion trajectory, the detailed ion–surface interactions need to be thoroughly investigated. In this study, molecular dynamics (MD) simulations were utilized to obtain a fundamental understanding of the collisional nature of accelerated Ar ions on the fluorinated Si surface that may appear on the sidewall of the HAR etched hole. High-fidelity data for ion–surface interaction features representing the energy and angle distributions (EADs) of sputtered atoms for varying degrees of surface F coverage and ion incident angles were obtained via extensive MD simulations. A deep learning-based reduced-order modeling (DL-ROM) framework was developed for efficiently predicting the characteristics of the ion–surface interactions. In the ROM framework, a conditional variational autoencoder (AE) was implemented to obtain regularized latent representations of the distributional data with the condition of the governing factors of the physical system. The proposed ROM framework accurately reproduced the MD simulation results and significantly outperformed various DL-ROMs, such as AE, sparse AE, contractive AE, denoising AE, and variational AE. From the inferred features of the sputtering yield and EADs of sputtered/scattered species, significant insights can be obtained regarding the ion interactions with the fluorinated surface. As the ion incident angle deviated from the glancing-angle range (incident angle >80°), diffuse reflection behavior was observed, which can substantially affect the ion transport in the HAR patterns. Moreover, it was hypothesized that a shift in sputtering characteristics occurs as the surface F coverage varies, based on the inferred EADs. This conjecture was confirmed through detailed MD simulations that demonstrated the fundamental relationship between surface atomic conformations and their sputtering behavior. Combined with additional atomistic-scale investigations, this framework can provide an efficient way to reveal various fundamental plasma–material interactions which are highly demanded for the future development of semiconductor device manufacturing.

A molecular dynamics study of sintering of micro injection moulded alumina nano particles

ABSTRACT In this study, a comprehensive molecular dynamics (MD) study on the structural evolution of alumina nanoparticles during sintering has been performed using two-sphere model. The effect of variation in particle size and heating rate are investigated. A power-law equation is proposed to explain the increase of dimensionless neck radius, with the increasing sintering time. Two important parameters are extracted from the equation: a characteristic time related to the initiation of neck formation and an exponent related to the rate of neck growth. The variation of shrinkage and density of particles are also used to characterise the sintering of alumina nanoparticles. One of the novel findings is that instead of temporal variation of dimensionless neck radius, its variation with shrinkage can be used to correlate simulation and experimental results. From the results of the variation of heating rate, it is revealed that a lower heating rate initiates neck formation at a lower temperature. The sintering temperature has been successfully estimated for micron-sized particles from the results of molecular dynamics simulation using Herring’s scaling law. Moreover, it is evident from experimental validation that the developed MD model can successfully predict the average dimensionless neck size value of micro injection moulded alumina, at sintered state, and thereby can be effectively used as a process control tool.

Adsorption behaviors of dibutyl dithiophosphate and sodium-diisobutyl dithiophosphinate (3418A) on chalcopyrite: A combined experimental and theoretical study

Sodium-diisobutyl dithiophosphinate (3418A) is a new collector with good selectivity for lead and copper ore, even better than dibutyl dithiophosphate (DTP). However, there still exists a lack of research on a mechanism for the interaction between chalcopyrite and 3418A. In this study, micflotation, microcalorimetric, cyclic voltammetry, adsorption measurement, density functional theory (DFT) calculations, and molecular dynamics (MD) were carried out to investigate the adsorption behaviors and differences of DTP and 3418A on the chalcopyrite surface. The flotation results show that 3418A has higher chalcopyrite recoveries than DTP, and microcalorimetric and adsorption measurements indicate that the adsorption quantity and adsorption heat of 3418A on the chalcopyrite surface is higher than that of DTP. In addition, DFT calculations suggest that the chemical adsorption of 3418A on the chalcopyrite surface is stronger than that of DTP. MD simulation results suggest that the hydrophobicity of the chalcopyrite surface after 3418A adsorption is stronger than that of DTP. Hence, our results presented that the 3418A is more favorable to the flotation of chalcopyrite than DTP. Based on coordination chemistry theory, the orbital interaction between chalcopyrite and reagent molecules is analyzed. It is suggested that the interaction between DTP and chalcopyrite is positive σ action, as well as 3418A, while the π back-bonding has not occurred. In addition, the energy of the highest occupied molecular orbital (HOMO) of 3418A is higher than that of DTP. Therefore, the interaction of chalcopyrite with 3418A is stronger than with DTP.

Enantioselective effects of paclobutrazol and its enantiomers on glycolipid metabolism in zebrafish (Danio rerio)

Paclobutrazol is a plant growth inhibitor widely used in agricultural production. However, toxicology studies of paclobutrazol enantiomers towards aquatic organisms are limited. Herein, effects of paclobutrazol and its two enantiomers (2R, 3R; 2S, 3S) on glycolipid metabolism of zebrafish have been systemically explored at the concentration of 10 mg/L through biochemical analyses, LC-MS/MS, molecular dynamics simulation, and gene expression. In all treatments, the contents of glucose, citric acid and lactate significantly were increased while the glycogen and pyruvate contents were decreased, in which (2R, 3R)-paclobutrazol exhibited a greater effect than the (2S, 3S)-enantiomer (P < 0.05). Then, activities of hexokinase and lactate dehydrogenase in (2R, 3R)-paclobutrazol treatment were 0.74- and 1.18-fold higher than (2S, 3S)-enantiomer treatment, respectively (P < 0.001), and the results of molecular dynamics simulation revealed that the binding free energy of hexokinase 1 to (2R, 3R)-paclobutrazol was higher than that to the antipode. Moreover, lipids including triglycerides, total cholesterol, fatty acids, bile acids and glycerophospholipids in zebrafish were strikingly affected after paclobutrazol exposure. The (2R, 3R)-paclobutrazol-treated group showed the most obvious changes, indicating that it possessed much stronger disruption ability on the lipid metabolism of zebrafish. Furthermore, qRT-PCR analysis results revealed that (2R, 3R)-enantiomer significantly impacted expressions of glycolipid metabolism-related genes (hk1, g6pc, pck1, pk, aco, cebpa, cyp51, fasn and ppara) in zebrafish than (2S, 3S)-enantiomer (P < 0.05). Briefly, this study provides new evidences for the toxicity of paclobutrazol to aquatic organisms and the potential risk to human health at the chiral level.