Results Of Molecular Dynamics Simulations Research Articles

Fabrication of beryllium oxide based fully ceramic microencapsulated nuclear fuels with dispersed TRISO particles by pressureless sintering method

In this research paper, two types of tristructural isotropic (TRISO) particles were dispersed within beryllium oxide (BeO) matrix using the pressureless sintering method to create fully ceramic microencapsulated (FCM) nuclear fuel. The findings indicated that TRISO particles with an outermost layer comprising silicon carbide (SiC) can establish interfacial bonding with BeO matrix, while those with an outermost layer comprising pyrocarbon (OPyC) and BeO matrix exhibit a noticeable gap after the sintering process. Results from transmission electron microscopy (TEM) revealed the presence of an amorphous phase transition zone between SiC and BeO. This zone, according to molecular dynamics (MD) simulation results, is an amorphous phase composed of Be, Si, and O atoms. Overall, TRISO particles with an outermost layer of SiC are more suitable for sintering with BeO matrix than those with an outermost layer of OPyC.

Capping Layer Determined Self-assembly of Au-Ag Bimetallic Janus Nanoparticles at An Oil/Water Interface by Molecular Dynamics Simulations.

Bimetallic Janus nanoparticles (BJNPs) have gained more attention due to their unique catalytic and optical properties. The self-assembly of BJNPs is expected as an effective way to fabricate metamaterials suitable for different potential applications. However, the self-assembly dynamic process of BJNPs, which is key to achieving a controllable synthesis, is limited in both experimental and theoretical investigations. Herein, all-atom molecular dynamics (MD) simulations were employed to investigate the self-assembly process of 1-dodecanethiol (DDT)-decorated Au-Ag BJNPs at an oil-water interface. We demonstrate that DDT's van der Waals (vdW) interaction dominates the self-assembly process. BJNPs form close-packed structures at both fast and slow evaporation rates. Au-Ag BJNPs exhibit relatively larger rotations at a low evaporation rate than those at a high evaporation rate, suggesting that the evaporation rate influences the orientation of the Au-Ag BJNPs. BJNPs tend to orient their electric dipole moments toward the external electric field, according to the ab initio MD simulation results. Based on the energy comparison and model analysis, it is found that the parallel array is more stable than the antiparallel one for the Au-Ag BJNP arrays. The dipole-dipole interaction difference between the parallel and antiparallel BJNP arrays obtained according to dipole moment obtained from ab initio calculation is qualitatively consistent with that obtained from MD simulations, indicating that the dipole plays a decisive role in determining the orientation of the BJNP array. This work uncovers the self-assembly dynamic process of BJNPs, paving the way for future applications.

In situ growth of nano-hydroxyapatite on multilayered Ti3C2Tx MXene as a drug carrier with superior-performance

Bone defects caused by tumor resection typically require bone repair materials to fill the defect sites. The development of multifunctional bone filling materials with integrated chemotherapy, photohermal therapy, and guided bone regeneration is very necessary and urgently needed. Herein, for the first time, the construction of novel multilayered Ti3C2Tx MXene (m-MXene)/nano-hydroxyaptite (nHAp) composites (m-MXene/nHAp) for bone repair is reported. The in situ growth of nHAp on multilayered Ti3C2Tx MXene is achieved through a facile hydrothermal method without using any organic additives. Due to the synergistic effects of nHAp and m-MXene, the m-MXene/nHAp composites show superior drug carrier performance with ultra-high drug loading capacity and ultra-long drug sustained release time. The molecular dynamics simulation results indicate that both Ti3C2Tx MXene and HAp show many adsorption sites and high binding energy with DOX. Moreover, the m-MXene/nHAp composites possess high photothermal conversion efficiency and excellent photothermal stability. The in situ growth of nano-HAp can significantly improve the biocompatibility of the m-MXene. The as-prepared multifunctional m-MXene/nHAp composites in this work can be used as bone filling powder and have great potential in bone defect reconstruction caused by bone tumor.

Unveiling the electrochemical characteristics of acetonitrile-catholyte-based Na-CO2 battery

The development of metal-CO2 batteries has attracted intense attention because of their unique electrochemical reaction for utilization of CO2 gas. However, unlike the alkali metal-based O2 batteries, a limited number of combinations of aprotic electrolytes have been employed for Li(Na)–CO2 batteries due to the sluggish reaction for the formation of the Li(Na)2CO3 discharge product. Here, we demonstrate an acetonitrile (MeCN)-based catholyte for use in a hybrid cell type Na-CO2 battery. The presence of a solid ceramic separator in our hybrid cell allows the stable operation of the MeCN catholyte-based Na-CO2 battery, resulting in improved electrochemical characteristics such as low overpotential, high energy density, and long cycle stability compared to the conventional TEGDME-based electrolyte. In particular, results of molecular dynamics simulations suggest that the improved performance is mainly due to the enhanced Na+ diffusion in the electrolyte. The calculated barrier for Na+ diffusion in MeCN is approximately four times lower than that in TEGDME. Thus, this work provides a promising electrolyte combination and reveals the mechanism for the improved performance of the MeCN-based electrolyte used in the hybrid cell structure, promoting the development of Na-CO2 batteries as practical secondary energy storage devices.

Comparison of the Molecular Motility of Tubulin Dimeric Isoforms: Molecular Dynamics Simulations and Diffracted X-ray Tracking Study.

Tubulin has been recently reported to form a large family consisting of various gene isoforms; however, the differences in the molecular features of tubulin dimers composed of a combination of these isoforms remain unknown. Therefore, we attempted to elucidate the physical differences in the molecular motility of these tubulin dimers using the method of measurable pico-meter-scale molecular motility, diffracted X-ray tracking (DXT) analysis, regarding characteristic tubulin dimers, including neuronal TUBB3 and ubiquitous TUBB5. We first conducted a DXT analysis of neuronal (TUBB3-TUBA1A) and ubiquitous (TUBB5-TUBA1B) tubulin dimers and found that the molecular motility around the vertical axis of the neuronal tubulin dimer was lower than that of the ubiquitous tubulin dimer. The results of molecular dynamics (MD) simulation suggest that the difference in motility between the neuronal and ubiquitous tubulin dimers was probably caused by a change in the major contact of Gln245 in the T7 loop of TUBB from Glu11 in TUBA to Val353 in TUBB. The present study is the first report of a novel phenomenon in which the pico-meter-scale molecular motility between neuronal and ubiquitous tubulin dimers is different.

Self-assembled WC@CN cage capture and anti-pitting effects synergize for integrated microwave absorption and corrosion protection

In the face of the current complex and changing electromagnetic environment, especially high humidity, high salt spray and other harsh environments in the ocean, the traditional microwave absorbing material (MAM) is difficult to meet its application needs, so the development of MAM adapted to the harsh marine environment is imminent. Here, we follow the concept of green synthesis and use self-assembly to prepare WC@CN (carbon nanosheets) composite material, integrated microwave absorption and corrosion protection, effective absorption bandwidth (EAB) of 5.07 GHz at an ultra-thin thickness of 1.59 mm, full band absorption from 2 to 18 GHz can be achieved by thickness regulation. The epoxy composite coating produced by blending 10 wt%WC@CN with epoxy resin has excellent corrosion resistance, which is attributed to the excellent resistance of WC to chloride ion pitting and the cage capture and barrier effects of CN, and the molecular dynamics simulations (MDs) results are also consistent with the experimental results. This work could provide new insights and strategies for high performance MAM with corrosion protection, with promising applications in the marine military equipment sector.

Review of Rydberg Spectral Line Formation in Plasmas

The present review is dedicated to the problem of an array of transitions between highly-excited atomic levels. Hydrogen atoms and hydrogen-like ions in plasmas are considered here. The presented methods focus on calculation of spectral line shapes. Fast and simple methods of universal ionic profile calculation for the Hnα (Δn=1) and Hnβ (Δn=2) spectral lines are demonstrated. The universal dipole matrix elements formulas for the Hnα and Hnβ transitions are presented. A fast method for spectral line shape calculations in the presence of an external magnetic field using the formulas for universal dipole matrix elements is proposed. This approach accounts for the Doppler and Stark–Zeeman broadening mechanisms. Ion dynamics effects are treated via the frequency fluctuation model. The accuracy of the presented model is discussed. A comparison of this approach with experimental data and the results of molecular dynamics simulation is demonstrated. The kinetics equation for the populations of highly-excited ionic states is solved in the parabolic representation. The population source associated with dielectronic recombination is considered.

Decoding the interaction mechanism between bis(2-methyl-3-furyl) disulfide and oral mucin

The interactions between mucin and aroma compounds have been shown to affect aroma perception. This study aimed to investigate the binding behavior between mucin and bis(2-methyl-3-furyl) disulfide and reveal the interaction mechanism at different pH levels. Based on our results, the binding percentages between mucin and bis(2-methyl-3-furyl) disulfide ranged from 37.03 % to 71.87 % at different contents. The complexes formation between mucin and bis(2-methyl-3-furyl) disulfide was confirmed by turbidity, particle size, zeta-potential, and surface hydrophobicity analyses. According to the results of multispectral techniques and molecular dynamic simulation, mucin could interact with bis(2-methyl-3-furyl) disulfide by hydrogen bonding, hydrophobic interactions, and van der Waals force. Furthermore, the binding constants of mucin to bis(2-methyl-3-furyl) disulfide were 1.26 × 103, 1.14 × 103, and 9.13 × 103 L mol−1 at pH 5.0, 7.0, and 8.5, respectively. These findings contribute to the comprehensive knowledge on the interaction mechanism between bis(2-methyl-3-furyl) disulfide and mucin, providing insights for flavor modulation in meat products.

Computational investigation of the structures, properties, and host‐guest chemistry of prism[n]arenes

AbstractThe discovery of new and functional macrocyclic host compounds is an important part of supramolecular chemistry. Since the experimental synthesis, prism[n]arenes (Pr[n]As), a class of naphthol‐based macrocyclic arenes, have attracted much attention. In this work, from the perspective of theoretical calculation and research, Pr[n]As (n = 4 ~ 7) were studied by density functional theory (DFT) calculations and molecular dynamics (MD) simulations. The prismatic configuration isomers, electronic structures, absorption spectra, and host‐guest chemistry were discussed thoroughly. DFT calculation results showed that 1,5‐, 3,7‐, and “hybrid” 15,37‐Pr[n]As were the most representative configurations with the rigid prismatic molecular skeleton. Based on time‐dependent density functional theory (TD‐DFT), the absorption spectra of Pr[n]As were all in the range of ultraviolet light which were mainly attributed to π‐π* transitions. The molecular cavities of Pr[n]As were electron‐rich and capable of accommodating a variety of cations or electron‐conjugated molecules. MD simulation results showed that a Pr[n]A molecule was able to capture the guest molecule into its molecular cavity and maintain in the state of equilibrium in solvents.

Electronic, magnetic, and electric properties of g-GaN monolayer adsorbing superhalogens

The electronic, magnetic, and electric behaviours of superhalogen molecules XY3 (X = Be, Mg, Ca; Y = F, Cl, Br) adsorbed on g-GaN monolayer (denoted as XY3@GaN) have been studied based on first-principles approaches. XY3@GaN are stable according to the binding energy and molecular dynamics simulation results. Because of the high electron affinities of the superhalogen molecules, the XY3 superhalogen molecule becomes a hole donor and the g-GaN monolayer becomes a hole acceptor, and p-doping is achieved. XY3@GaN are ferromagnetic half-metal with magnetic moment of 1 μB, which can be used in the field of spintronics device. In addition, XY3@GaN exhibit in-plane and out-of-plane piezoelectricity and negative differential resistance (NDR) behavior, which may open up new possibilities for g-GaN in the design of piezoelectric materials and switching devices.

Molecular dynamics and experiment on ultraviolet-thermal curing abrasive tools for polishing microstructures

To achieve efficient polishing of the microstructure array, a preparation method of the UV-thermal curing abrasive tools with diamond was proposed. The properties of the UV-thermal curing system were studied using molecular dynamics (MD) and experiments. The time, frequency, and pressure parameters of the UV-thermal curing abrasive tool were optimized by polishing the copper plate. MD simulation results show that increasing the temperature to 340 K can improve the blending compatibility. With the increase of the bisphenol A acrylate, the tensile property enhances from 16.38 MPa to 42.98 MPa, and the size shrinkage and mass loss weaken. The addition of diamond particles improves the anti-friction coefficient. Finally, the microstructure is polished twice under the polishing pressure of 300 N and 200 N, resulting in a roughness of Ra61nm on the upper surface and Ra105nm on the lower surface. This study can be used to guide the preparation and application of UV-thermal curing abrasive tools for polishing microstructure.

Glutamic Acid Enhances the Corrosion Inhibition of Polyaspartic Acid on Q235 Carbon Steel.

Currently, poly(aspartic acid) (PASP) is used with traditional toxic agents for corrosion inhibition, which greatly reduces the environmental significance of PASP as a green inhibitor. Amino acids, small-molecule compounds with amino and carboxyl groups, may react with PASP and act as chains to link PASP molecules, which might enhance the inhibition of PASP on metal corrosion. In this study, we selected glutamic acid (GLU) as a typical amino acid to explore the potential synergistic effect of the amino acid and PASP on corrosion inhibition via electrochemical experiments and molecular dynamics simulation. The corrosion inhibition of PASP was promoted by GLU with less weight loss and less pitting. The results of molecular dynamics simulation showed that GLU could bind with PASP at carboxyl groups and amino groups via donor-acceptor interactions and accelerate the diffusion of PASP to the carbon steel surface. Furthermore, the binding between PASP and the carbon steel surface can be enhanced by GLU, resulting in a dense and stable protective film. To the best of our knowledge, this is the first investigation into the mechanism of an amino acid as an enhancer to improve corrosion inhibition. This work provides a new strategy to enhance existing green inhibitors, which would significantly reduce the cost of cooling water treatment and its adverse environmental impacts.

Multiscale simulation of nanodrop over surfaces with varying hydrophilicity

Macroscale solvers primarily depend on empirical constitutive relations, which curbs their applicability and reliability. On the other hand, though the microscale solver is much more accurate, it cannot be used for engineering scale domains because of the high computational cost. As an alternative, in the present study, a new adiabatic two-phase multiscale solver has been developed by coupling Finite volume and molecular dynamics solvers with the help of the domain decomposition method. Due to the finiteness of the molecular subdomain, molecules near the boundary miss forces from the missing molecules. An effort has been made to develop a new boundary force model which mimics the effect of those missing molecules. The spreading of a drop has been simulated over surfaces with varying hydrophilicity using the solver and compared with the result of full molecular dynamics simulation. Further, the computational time has been compared with the full molecular dynamics simulation for different drop sizes to show the usefulness of the developed model. Drop translation over biphilic surfaces has also been simulated with the new solver.

Crystal–melt interfaces in Mg2SiO4 at high pressure: structural and energetics insights from first-principles simulations

The interplay between crystal–melt and grain boundary interfaces in partially melted polycrystalline aggregates controls many physical properties of mantle rocks. To understand this process at the fundamental level requires improved knowledge about the interfacial structures and energetics. Here, we report the results of first-principles molecular dynamics simulations of two grain boundaries of (0l1)/[100] type for tilt angles of 30.4° and 49.6° and the corresponding solid–liquid interfaces in Mg2SiO4 forsterite at the conditions of the upper mantle. Our analysis of the simulated position time series shows that structural distortions at the solid–liquid interfacial region are stronger than intergranular interfacial distortions. The calculated formation enthalpy of the solid–solid interfaces increases nearly linearly from 1.0 to 1.4 J/m2 for the 30.4° tilt and from 0.8 to 1.0 J/m2 for the 49.6° tilt with pressure from 0 to 16 GPa at 1500 K, being consistent with the experimental data. The solid–liquid interfacial enthalpy takes comparable values in the range 0.9 to 1.5 J/m2 over similar pressure interval. The dihedral angle of the forsterite–melt system estimated using these interfacial enthalpies takes values in the range of 67° to 146°, showing a decreasing trend with pressure. The predicted dihedral angle is found to be generally larger than the measured data for silicate systems, probably caused by compositional differences between the simulation and the measurements.

In Silico Screening, In Vitro Mpro Inhibitory, and Adjunctive Therapy Value of Minocycline for the Treatment of COVID-19

What Is Known and Objective. Novel coronavirus disease (COVID-19) is still ravaging globally since its first discovery in 2019. With the continuous emergence of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) mutant strains, therapeutic entities are still needed to be discovered. This study was to explore SARS-CoV-2 inhibitors and therapeutic entities for COVID-19. Methods. Based on Lipinski’s rule of 5, a small-scale “old” drug database (clinical drugs being used in Ordos Central Hospital) was established, and in silico screening of Mpro inhibitors was conducted. Binding affinity and interaction as well as structure-affinity relationship were analyzed. Furthermore, molecular dynamic (MD) simulation of the selected drugs was performed to understand the conformational changes in docked complex. In vitro Mpro inhibition tests were performed according to established methods. Finally, literature review of potential “old” drug for the treatment of COVID-19 was conducted. Results and Discussion. The antibiotic minocycline, an inhibitor of bacterial ribosomal RNA, was screened out which showed the highest binding affinity (−9.6 kcal/mol). Beside the hydrogen bond with Cys145 and hydrophobic interactions, minocycline formed a pi-cation with His41, which strongly supported minocycline as a Michael addition acceptor to bind with the catalytic site of Mpro. MD simulation results show that minocycline displayed less conformational changes. The structure-affinity relationship was summarized based on minocycline analogs, and minocycline showed in vitro Mpro inhibitory activity with IC50 of 5 mM. More importantly, the literature review found that minocycline had both in vitro and in vivo broad-spectrum antiviral as well as anti-inflammatory activities, and the levels of a broad spectrum of biological markers during minocycline administration were opposed to those of COVID-19 conditions (both severe and nonsevere). What is New and Conclusion. Minocycline deserves an adjunctive therapeutic option for COVID-19 condition (both severe and nonsevere). This study shed a new light on drug-repurposing strategy for the viral disease.

Effects of Hydrogen Bonds between Ethoxylated Alcohols and Sodium Oleate on Collecting Performance in Flotation of Quartz.

Hydrogen bonds play an important role in the interaction between surfactants. In this study, the effect of three different ethoxylated alcohols (OP-10, NP-10, AEO-9) on the collecting behavior of sodium oleate (NaOL) in the flotation of quartz was investigated. To explore the mechanism, the hydrogen bond between ethoxylated alcohols and NaOL was analyzed using molecular dynamics (MD) simulation. The results showed that ethoxylated alcohols promoted the collecting performance of NaOL and reduced the dosage of the activator CaO and the collector NaOL in the flotation of quartz. The Zeta potential measurement illustrated that ethoxylated alcohols promoted the adsorption of OL- on the activated quartz surface and the degree of promotion was in the order of OP-10 > NP-10 > AEO-9. The MD simulation results showed that a hydrogen bond presented between ethoxylated alcohols and OL-. Due to the hydrogen bond between the ethoxylated alcohols and OL-, the attraction force between OL- and the quartz surface increased with the addition of ethoxylated alcohols in the order of OP-10 > NP-10 > AEO-9 based on the MD simulation results. As the result, the addition of ethoxylated alcohols increased the adsorption density of OL- on the activated quartz surface, which explained the promotion of the collecting performance of OL- in the flotation of quartz.

QTY code designed antibodies for aggregation prevention: A structural bioinformatic and computational study.

Therapeutic monoclonal antibodies are the most rapidly growing class of molecular medicine, and they are beneficial to the treatment of a broad spectrum of human diseases. However, the aggregation of antibodies during the process of manufacture, distribution, and storage poses significant challenges, potentially compromising efficacy and inducing adverse immune responses. We previously conceived a QTY (glutamine, threonine, tyrosine) code, a simple tool for enhancing protein water-solubility by systematically pairwise replacing hydrophobic residues L (leucine), V (valine)/I (isoleucine), and F (phenylalanine). The QTY code offers a promising alternative to traditional methods of controlling aggregation in integral transmembrane proteins. In this study, we designed variants of four antibodies applying the QTY code, changing only the β-sheets. Through the structure-based aggregation analysis, we found that these QTY antibody variants demonstrated significantly decreased aggregation propensity compared to their wild-type counter parts. Our results of molecular dynamics simulations showed that the design by QTY code is capable of maintaining the antigen-binding affinity and structural stability. Our structural informatic and computational study suggests that the QTY code offers a significant potential in mitigating antibody aggregation.

In vitro, in vivo, and in silico evaluation of the glucocorticoid receptor antagonist activity of 3,6-dibromocarbazole.

3,6-Dibromocarbazole is a novel environmental contaminant which is currently detected in several environmental media worldwide. This work aims to investigate the anti-glucocorticoid potency and endocrine disrupting effects of 3,6-dibromocarbazole. In vitro experiments indicated that 3,6-dibromocarbazole possessed glucocorticoid receptor (GR) antagonistic activity and inhibited dexamethasone-induced GR nuclear translocation. 3,6-Dibromocarbazole reduced the expression levels of glucocorticoid responsive genes including glucose-6-phosphatase (G6Pase), phosphoenolpyruvate carboxykinase (PEPCK), fatty acid synthase (FAS), and tyrosine aminotransferase (TAT), and further disrupted the protein expression of two key enzymes PEPCK and FAS in gluconeogenesis. In vivo experiments showed that 3,6-dibromocarbazole induced abnormal development of zebrafish embryos and disrupted the major neurohormones involved in activation of hypothalamic-pituitary-adrenocortical (HPA) axis in zebrafish larvae. The results of molecular docking and molecular dynamics simulation contributed to explain the antagonistic effect of 3,6-dibromocarbazole. Taken together, this work identified 3,6-dibromocarbazole as a GR antagonist, which might exert endocrine disrupting effects by interfering the pathway of gluconeogenesis.

Comment on "Brownian motion with time-dependent friction and single-particle dynamics in liquids".

Recently, Lad, Patel, and Pratap [Phys. Rev. E 105, 064107 (2022)10.1103/PhysRevE.105.064107] revisited a microscopic theory of molecular motion in liquids, proposed by Glass and Rice [Phys. Rev. 176, 239 (1968)10.1103/PhysRev.176.239]. They argued that the friction coefficient for a Brownian particle in a liquid should exponentially depend on time and derived an equation of motion for the particle's velocity autocorrelation function (VAF). The equation was solved numerically and fitted to the results of molecular dynamics simulations on different liquids. We show that this solution, obtained under the condition of zero derivative of the VAF at time t=0, is physically incorrect at long times. This is evidenced by our exact analytical solution for the VAF, not found by Lad etal., and numerically, by using the same method as in the commented work.

Size effects on dislocation starvation in Cu nanopillars: a molecular dynamic simulations study

ABSTRACT Size plays an important role on the deformation mechanism of nanopillars. With decreasing size, many FCC nanopillars exhibit dislocation starvation which is responsible for their high strength. However, many details about the dislocation starvation like how often it occurs, and how much is its contribution to the total plastic strain, are still elusive. Similarly, the size below which the dislocation starvation occurs is not clearly established. In this context, atomistic simulations have been performed on the compression of <110> Cu nanopillars with size (d) ranging from 5 to 21.5 nm. Molecular dynamics (MD) simulation results indicate that the nanopillars deform by the slip of extended dislocations and exhibit dislocation starvation mainly at small sizes (<20 nm). The frequency of the occurrence of dislocation starvation is highest in small-sized nanowires and it decreases with increasing size. Above the size of 20 nm, no dislocation starvation has been observed. Furthermore, we define the dislocation starvation strain and based on this, it has been shown that the contribution of the dislocation starvation to the total plastic strain decreases from 70% in small-sized nanopillars to below 5% in large-sized pillars. The present results suggest that dislocation starvation is a dominant phenomenon in small-sized nanopillars.