Atomic Method Research Articles

Mechanical and Optical Properties of Cr2O3 Thin Films Grown by Atomic Layer Deposition Method Using Cr(thd)3 and Ozone.

Cr2O3 thin films were grown on a Si (1 0 0) substrate using Cr(thd)3 and O3 by atomic layer deposition (ALD) at substrate temperatures (TG) from 200 to 300 °C. X-ray amorphous films were deposited at a TG ≤ 225 °C, whereas at higher temperatures (TG ≥ 250 °C), the eskolaite phase was observed in the films. The growth rate of the films increased from 0.003 to 0.01 nm/cycle by increasing TG from 200 to 275 °C. The relatively low growth rate of Cr(thd)3-O3 makes it appropriate for the ALD of precisely controllable solid solution-type ternary-component thin films. The Ti-doped Cr2O3 film showed higher hardness (16.7 GPa) compared with that of the undoped film (12.8 GPa) with similar thickness. The band gap values of the pure Cr2O3 corresponding to the indirect transition model showed no dependence on TG; however, doping the Cr2O3 with Ti decreased its band gap energy value from 3.1 to 2.2 eV.

Atomic connectivity group contribution method for predicting the boiling and melting points of organic compounds

Boiling point (Tb) and melting point (Tm) are the fundamental physical properties in the petroleum-related and chemical industries. In this work, the Tb and Tm models are established by the atomic connectivity group contribution (ACGC) method. In the proposed methodology, shape factors (SFs) and atomic connectivity factors (ACFs) are employed to distinguish among isomers and improve the prediction accuracy. In addition, external and internal validations and Y-randomization tests are performed to analyze and evaluate the predictability and robustness of the ACGC models. The results indicate that the ACGC method could predict the Tb with high accuracy, with a squared correlation coefficient (R2) of 0.9767 and an absolute average relative error (AARE) of 1.70%. Moreover, the ACGC model for Tm achieves an R2 of 0.8423 and an AARE of 8.73%, demonstrating that the ACGC method can effectively predict the Tm.

CryoREAD: de novo structure modeling for nucleic acids in cryo-EM maps using deep learning.

DNA and RNA play fundamental roles in various cellular processes, where their three-dimensional structures provide information critical to understanding the molecular mechanisms of their functions. Although an increasing number of nucleic acid structures and their complexes with proteins are determined by cryogenic electron microscopy (cryo-EM), structure modeling for DNA and RNA remains challenging particularly when the map is determined at a resolution coarser than atomic level. Moreover, computational methods for nucleic acid structure modeling are relatively scarce. Here, we present CryoREAD, a fully automated de novo DNA/RNA atomic structure modeling method using deep learning. CryoREAD identifies phosphate, sugar and base positions in a cryo-EM map using deep learning, which are traced and modeled into a three-dimensional structure. When tested on cryo-EM maps determined at 2.0 to 5.0 Å resolution, CryoREAD built substantially more accurate models than existing methods. We also applied the method to cryo-EM maps of biomolecular complexes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Nanoscale mechanical and thermal properties of a multilayer polyethylene film with varying densities

Various atomic force microscopy methods for the imaging and measurement of the modulus of polyethylene (PE) layers in a five-layer multilayer film are described. The film includes linear low-density polyethylene (LLDPE) products with densities ranging from 0.940 to 0.912 gm/cm3. Conventional TappingMode AFM phase imaging can reveal the layers but is sensitive to measurement conditions. PeakForce Tapping AFM using quantitative nanomechanics (QNM) mode can resolve all five layers based on at least three different signals – stiffness mapping, penetration, and energy dissipation. In particular, the difference is statistically significant for the modulus and penetration data. This is remarkable considering that the method is sensitive to density differences of only 0.004 density units. Quasistatic AFM indentation was also done using the same probe and peak load. Here we see the effect of time dependence on the mechanical properties, where the slower interaction times yield estimated moduli much closer to the long-time moduli measured in bulk tensile experiments, compared to the value obtained at much higher frequency using PeakForce Tapping AFM. Nano-thermal analysis of the same five-layer film using heated tip technology can also discriminate the layers statistically, based on softening temperature, which shows excellent correlation with bulk properties.

The Influence of Crystal Anisotropy on the Characteristics of Solitary Waves in the Nonlinear Supratransmission Effect: Molecular Dynamic Modeling

This study examines the mechanism of nonlinear supratransmission (NST), which involves the transfer of disturbance to discrete media at frequencies not supported by the structure. We considered a model crystal with A3B stoichiometry. The investigation was carried out using atomistic modeling through molecular dynamics. The interatomic interaction was determined by a potential obtained through the embedded atom method, which approximates the properties of the Pt3Al crystal. The effect of NST is an important property of many discrete structures. Its existence requires the discreteness and nonlinearity of the medium, as well as the presence of a forbidden zone in its spectrum. This work focuses on the differences in the NST effect due to the anisotropy of crystallographic directions. Three planes along which the disturbance caused by NST propagated were considered: (100), (110), and (111). It was found that the intensity of the disturbance along the (100) plane is an order of magnitude lower than for more densely packed directions. Differences in the shape of solitary waves depending on the propagation direction were shown. Moreover, all waves can be described by a single equation, being a solution of the discrete variational equations of macroscopic and microscopic displacements, with different parameters, emphasizing the unified nature of the waves and the contribution of crystal anisotropy to their properties. Studying the NST phenomenon is essential due to numerous applications of the latter, such as implications in information transmission and signal processing. Understanding how disturbances propagate in discrete media could lead to advancements in communication technologies, data storage, and signal amplification where the earlier mentioned ability to describe it with analytical equations is of particular importance.

Design of spinning disk atomization equipment for synthesis of drug-loaded microparticles.

The synthesis of drug-loaded microparticles with precise control over size distribution and shape is crucial for achieving desired drug distribution in microparticles and tuning drug release profiles. Common large-scale production techniques produce microparticles with a broad particle size distribution and require challenging operating conditions. Recent methods employing microfluidics have enabled the production of microparticles with a uniform size distribution. Still, these methods are limited to low and moderate production rates and can handle fluids with a limited range of physicochemical properties. In this study, we couple the spinning disk atomization (SDA) technique for microdroplet production with a precipitation method to generate drug-loaded polymeric microparticles with a narrow size distribution. The design criteria and fabrication of equipment with a non-contact seal system that integrates spinning disk atomization and precipitation methods for conducting laboratory experiments involving volatile hydrocarbons while ensuring operational and personnel safety are discussed. The production of itraconazole drug-loaded microparticles using the SDA setup that considers the system's operation, maintenance, and safety aspects are discussed, and the system's efficiency is evaluated through material balance. This laboratory equipment is capable of producing drug-loaded microparticles with a narrow size distribution under moderate operating conditions and can be scaled up suitably to meet high production requirements. The applications of this equipment can be explored in various fields, such as the production of drug particles, conversion of waste polymers into microparticles, and microencapsulation of food ingredients.

Effect of Al2O3 insertion layer on ferroelectricity in HfO2/ZrO2 nanolaminates

Ferroelectric HfO2 with excellent scaling capability and good complementary-metal-oxide-semiconductor (CMOS) technology compatibility has triggered the interest in nonvolatile memories. Here, (HfO2−ZrO2)3/mAl2O3/ (HfO2−ZrO2)3 (m donate the Al2O3 (AO) thickness) nanolaminates with different AO thicknesses were fabricated using atomic layer deposition method. Ferroelectricity and reliability were investigated by varying AO thickness in the deposition process. The highest remnant polarization (Pr) of 23.87 μC/cm2 is obtained in (HZO)3/1AO/(HZO)3 nanolaminate with 1 nm-thick AO dielectric layer. The leakage current can be decreased by 2−3 orders of magnitude with the increase of AO thickness. The performance enhancement is ascribed to the interfacial polarization because of the dielectric mismatch between AO and HfO2−ZrO2 (HZO) and high breakdown strength of AO. The insertion of lower-permittivity AO can effectively modulate the distribution of electric field in nanolaminates and achieves a significant improvement in reliability. Improved ferroelectricity and reliability in ferroelectric/dielectric/ferroelectric structure pave a new way for the designation of HfO2-based ferroelectric memories with broader thickness range.

Analysis of the spatiotemporal fields of chemical soil pollution as a basic component of urban ecosystems

The soil is a depositing medium and an indicator of geochemical load. The fulfillment of important ecosystem functions by urban soils ensures the ecological safety of urban ecosystems as a whole. The purpose of the work is to forecast soil pollution as a basic component of the urban ecosystem with a high level of technogenic load. The calculation of the spatio-temporal fields of chemical pollution of soils in the city of Kolchugino, Vladimir region, was carried out using a balance model based on ecological and analytical data utilizing the results of area surveys of soils and snow cover. The content of heavy metals of hazard classes 1 and 2 in soil and snow samples (solid and liquid phases) was determined by atomic absorption method according to standard methods. The analysis of spatio-temporal fields of soil contamination for each heavy metal is performed on the basis of map diagrams constructed using the INTEGRO GIS software-technological complex. Taking into account aerotechnogenic intake, an assessment of the degree of accumulation of heavy metals in soils and their time to reach the critical level is given. In the soils of Kolchugino, an excess of sanitary and hygienic standards (gross forms) is revealed for all the metals studied. Analysis of the data of spatio-temporal fields of soil pollution with heavy metals in the city of Kolchugino showed that the established level of soil pollution exceeding the MPC is primarily associated with the past economic activity of non-ferrous metallurgy enterprises and will remain at the same level in the near future.

Serum levels of heavy metals in patients with Bell's palsy: a case-control study.

The exact etiology of Bell's palsy (BP) remains unknown, while its potential etiopathology includes neuritis and inflammation-related demyelination as in optic neuritis. It has been reported that disruption of heavy metal homeostasis may be associated with the inflammatory process of optic neuritis; therefore, heavy metals may be involved in the pathogenesis of facial nerve neuritis. In this study, we aimed to investigate serum levels of heavy metals including essential elements [iron (Fe), zinc (Zn), copper (Cu), cobalt (Co), and manganese (Mn)], and nonessential elements [lead (Pb) and cadmium (Cd)] in patients with BP. The study included 25 patients with BP and 31 healthy volunteers. For each participant, serum levels of essential and nonessential elements were measured using the atomic absorption spectrophotometer method. Serum levels of essential elements were significantly lower in the patient group compared to the control group (p < 0.001, for each). Serum levels of Pb increased in the patient group compared to the control group although no significant difference was achieved (p = 0.105). In contrast, serum Cd levels increased significantly in the patient group compared to the control group (p < 0.001). Our findings suggest that decreased essential and increased nonessential elements may be associated with BP and thus, serum concentrations of these elements should be taken into account in BP. Studies are warranted to determine the role of these elements in treatment of BP.

Mechanical Properties and Nanomotion of BT-20 and ZR-75 Breast Cancer Cells Studied by Atomic Force Microscopy and Optical Nanomotion Detection Method.

Cells of two molecular genetic types of breast cancer-hormone-dependent breast cancer (ZR-75 cell line) and triple-negative breast cancer (BT-20 cell line)-were studied using atomic force microscopy and an optical nanomotion detection method. Using the Peak Force QNM and Force Volume AFM modes, we revealed the unique patterns of the dependence of Young's modulus on the indentation depth for two cancer cell lines that correlate with the features of the spatial organization of the actin cytoskeleton. Within a 200-300 nm layer just under the cell membrane, BT-20 cells are stiffer than ZR-75 cells, whereas in deeper cell regions, Young's modulus of ZR-75 cells exceeds that of BT-20 cells. Two cancer cell lines also displayed a difference in cell nanomotion dynamics upon exposure to cytochalasin D, a potent actin polymerization inhibitor. The drug strongly modified the nanomotion pattern of BT-20 cells, whereas it had almost no effect on the ZR-75 cells. We are confident that nanomotion monitoring and measurement of the stiffness of cancer cells at various indentation depths deserve further studies to obtain effective predictive parameters for use in clinical practice.

Exploring structural transitions at grain boundaries in Nb using a generalized embedded atom interatomic potential

The advancement in experimental techniques, like the atom probe tomography and high resolution electron microscopy, is fueling interest in studying structural transformations of grain boundaries in metal and alloys to uncover correlations between mechanical properties and solute or impurity segregation to grain boundaries. Atomistic modeling is an important tool that can pinpoint the intricate dynamics of grain boundary phase transitions, but the lack of accurate interatomic potentials needed to simulate the complex dynamics of grain boundary structural transitions and identify different metastable phases has been the bottleneck. To this end, we use niobium as a model body centered cubic (BCC) metal and develop an interatomic potential to study grain boundary phase transitions. The potential for Nb is based on a generalization of the embedded atomic method potential and has sufficient flexibility to learn complex energy landscapes using a small set of training structures. We systematically test and validate the using data from ab initio density functional theory calculations and experiments. Using this potential, we calculate energies of multiple symmetric-tilt grain boundaries spanning a wide range of misorientation angles. Further, we explore different metastable structures of the Σ27(552) [11̄0] grain boundary and use molecular dynamic simulations to study the coexistence of metastable phases and grain boundary transitions at finite temperature.

Study of the deorbit sail damage under the combined effects of atomic oxygen erosion and material defects

In order to help control the spread of space debris and junk, deorbit sail devices have been used for deorbiting techniques; however, this approach is still considered risky due to potential failure or malfunction as it need to be exposed to the harsh space environment for a prolonged period of time, particularly in low-Earth orbit. China has made new strides forward in managing space junk, as it has successfully unfolded a 25-square-meter deorbit sail developed by the Shanghai Academy of Spacecraft Technology in-orbit for the payload capsule of a recently launched rocket. Accordingly in this paper, a full life-cycle modelling based on Monte Carlo method is developed to reveal the damage behavior of the 25-square-meter deorbit sail surface under the combined effects of atomic oxygen erosion and deorbit sail defects. The simulation results show that as the atomic oxygen fluence increases and the material defect width widens, the interaction effect of the two factors becomes more and more pronounced, which decisively influences the erosion rate of the sail surface. Morphological characterization of aluminized film PET material, activated silanisation modified material and plasma-polymerization coating material before and after atomic oxygen erosion combined defects is carried out and the atomic oxygen erosion of the deorbit sail surfaces is quantitatively assessed. The assessment results show that compared to the PET material and activation silanisation surface modification material, the plasma polymeric coated material showed much better flexibility, folding resistance and irradiation resistance to prevent geological fold and to shield from the atomic oxygen erosion in space. The atomic oxygen erosion combined defects assessment method studied in this paper provides valuable reference data for the subsequent serialisation of deorbit sail products and other typical lightweight film materials for space applications.

Development of an interatomic potential for the W–Ta system

A physics-inspired, data-driven interatomic potential framework for multi-element system is presented. This potential is based on the generalization of the embedded atom method potential and systematically incorporates two-, three- and many-body effects. Different atomic environments are described by atom-centered Gaussian basis sets which provides sufficient flexibility to capture diverse atomic environments and allows for easy optimization of the free parameters. An interatomic potential model for the tungsten–tantalum (W–Ta) system is developed using this framework by training on data from ab initio density functional theory (DFT) calculations. The potential is thoroughly tested at various compositions by comparing bulk and defect properties from experimental and DFT data. It is shown that the potential predicts the elastic constants, defect properties, such as vacancy and interstitial formation energies, core structures of dislocations, and melting points for both pure and tantalum and tungsten with an accuracy comparable to other single element machine learning based potentials. The potential model is used to investigate the formation energies of ordered alloys and vacancy formation energies for chemically random W–Ta alloys.

Investigating medium range order in Mg-Al binary metallic glasses: Molecular dynamics approach

In this work, we used molecular dynamics (MD) simulations in order to investigate the Medium-Range Order (MRO) in Mg-Al binary metallic glasses (MGs). The embedded atom method (EAM) has been adopted to accurately model the interatomic interactions. Various techniques such as radial distribution function (RDF), coordination number (CN) analyses and Gaussian fitting have been mobilized to comprehensively study the impact of cooling rate, composition and mechanical solicitations, on the structural properties at the MRO level. Our results reveal that the 1-atom connection mode is consistently dominant across all cooling rates. Moreover, as the cooling rate increases in the Mg25Al75 binary MG, the abundance of the 4-atom and 2-atom connection modes increases, while the percentage of the 3-atom mode experiences a slight decrease. Furthermore, we investigate the influence of composition on the properties of MgxAl100-x alloys, demonstrating that the RDF peaks and connection modes are highly sensitive to variations in the Al concentration. Additionally, we explore the relationship between mechanical properties and connection modes during tensile deformation. The 3-atom connection mode exhibits superior hardness and stability, while the 4-atom and 2-atom connection modes offer increased flexibility. These significant findings enhance our understanding of MGs structural evolution, stability and deformation behavior. Ultimately, this knowledge facilitates the design and optimization of tailored MGs for advanced applications.

A second nearest-neighbor modified embedded-atom method combined with a charge equilibration interatomic potential for the Al-O binary system

An interatomic potential for the Al-O binary system has been developed within the formalism of the second nearest-neighbor modified embedded atom method (2NNMEAM) potential integrated with a charge equilibrium model (Qeq). The characteristics of aluminum oxide (energetic, structural, elastic and thermal stability) reproduced by this potential are in good agreements with experimental and first-principle calculations. As a result of tensile strain molecular dynamics simulation using the developed potential, the amorphous aluminum oxide thin film showed a remarkable elongation of more than 80 %, consistent with experiments and other simulations. This highly reproducible potential of the Al-O binary system is expected to be applied in fields utilizing alumina nanofilms.

Dual‐single‐atoms of Pt–Co boost sulfur redox kinetics for ultrafast Li–S batteries

AbstractApplications of lithium–sulfur (Li–S) batteries are still limited by the sluggish conversion kinetics from polysulfide to Li2S. Although various single‐atom catalysts are available for improving the conversion kinetics, the sulfur redox kinetics for Li–S batteries is still not ultrafast. Herein, in this work, a catalyst with dual‐single‐atom Pt‐Co embedded in N‐doped carbon nanotubes (Pt&amp;Co@NCNT) was proposed by the atomic layer deposition method to suppress the shuttle effect and synergistically improve the interconversion kinetics from polysulfides to Li2S. The X‐ray absorption near edge curves indicated the reversible conversion of Li2Sx on the S/Pt&amp;Co@NCNT electrode. Meanwhile, density functional theory demonstrated that the Pt&amp;Co@NCNT promoted the free energy of the phase transition of sulfur species and reduced the oxidative decomposition energy of Li2S. As a result, the batteries assembled with S/Pt&amp;Co@NCNT electrodes exhibited a high capacity retention of 80% at 100 cycles at a current density of 1.3 mA cm−2 (S loading: 2.5 mg cm−2). More importantly, an excellent rate performance was achieved with a high capacity of 822.1 mAh g−1 at a high current density of 12.7 mA cm−2. This work opens a new direction to boost the sulfur redox kinetics for ultrafast Li–S batteries.

Electron Transport Layer Engineering Induced Carrier Dynamics Optimization for Efficient Cd-Free Sb2 Se3 Thin-Film Solar Cells.

Antimony selenide (Sb2 Se3 ) is a highly promising photovoltaic material thanks to its outstanding optoelectronic properties, as well as its cost-effective and eco-friendly merits. However, toxic CdS is widely used as an electron transport layer (ETL) in efficient Sb2 Se3 solar cells, which largely limit their development toward market commercialization. Herein, an effective green Cd-free ETL of SnOx is introduced and deposited by atomic layer deposition method. Additionally, an important post-annealing treatment is designed to further optimize the functional layers and the heterojunction interface properties. Such engineering strategy can optimize SnOx ETL with higher nano-crystallinity, higher carrier density, and less defect groups, modify Sb2 Se3 /SnOx heterojunction with better interface performance and much desirable "spike-like" band alignment, and also improve the Sb2 Se3 light absorber layer quality with passivated bulk defects and prolonged carrier lifetime, and therefore to enhance carrier separation and transport while suppressing non-radiative recombination. Finally, the as-fabricated Cd-free Mo/Sb2 Se3 /SnOx /ITO/Ag thin-film solar cell exhibits a stimulating efficiency of 7.39%, contributing a record value for Cd-free substrate structured Sb2 Se3 solar cells reported to date. This work provides a viable strategy for developing and broadening practical applications of environmental-friendly Sb2 Se3 photovoltaic devices.

The Bond Length of Intermetallic Ternary Phases of Al-Fe-Si Alloy Using Molecular Dynamics Simulation with the Application of [001] Compression

The research on tolerance stress in aluminum alloys is focused on examining the mechanical behavior of τ4-Al3FeSi2 and τ12-Al3Fe2Si phases during [001] compression and their structural evolution. The use of MD computational bond length measurements allows for a comparison to be made with previous studies on tensile deformation. The simulations were performed at a constant strain rate of 21×1010 s-1, using NPT conditions (isothermal-isobaric), with approximately 20,000 atoms, 1 atmosphere of pressure, and 300 K temperature, using a Nosé-Hoover thermostat. Under periodic boundary conditions, the Modified Embedded Atoms Method (MEAM) potential was applied to all 3D faces, and the average bond length behavior between Al, Fe, and Si was calculated. A comprehensive investigation is carried out to explore the properties of these phases, including a detailed structural analysis at the atomic scale. This paper presents a comprehensive analysis of how changes in compound concentration affect mechanical behavior during compression. The average bond length varies depending on the applied stress axis, and it demonstrates good agreement with literature data. The mechanical deformations alter the behavior of atomic phases, as discussed in detail in the conclusion.

Comparing interatomic potentials in calculating basic structural parameters and Peierls stress in tungsten-based random binary alloys

The field of machine learning-based interatomic potentials (ML-IAPs) has seen increasing development in recent years. In this work, we compare three widely used ML-IAPs–the moment tensor potential (MTP), the spectral neighbor analysis potential (SNAP), and the tabulated Gaussian approximation potential (tabGAP)with a conventional non-ML-IAP, the embedded atom method (EAM) potential. We evaluated these potentials on the basis of their accuracy and efficiency in determining basic structural parameters and Peierls stress under equivalent conditions. Three tungsten (W)-based alloys (Mo-W, Nb-W, and Ta-W) are considered, and their lattice parameter, formation energy, elastic tensor, and Peierls stress of edge dislocation are calculated. Compared with DFT results, MTP demonstrates the highest accuracy in predicting the lattice parameter and the best computational efficiency among the three ML-IAPs, while tabGAP accurately predicts two independent elastic constants, C 11 and C 12. Despite being the slowest, SNAP shows the highest accuracy in predicting the third independent elastic constant C 44 and its Peierls stress value is comparable to that based on MTP.

First-principles calculations to investigate structural, electronic, optical and elastic properties of α-Ca3N2

The optoelectronic industry, which has become a cornerstone, requires a semiconductor compound to function as a sustainable and green energy source. In this connection, the present study provides a systematic approach to examine the electronic and optical properties of α-Ca3N2 using the linear combination of atomic orbitals method. The xc-functional BECKE-PBE gives the best results for electronic properties by describing the band gap correctly. The dispersion curve shows that α-Ca3N2 is a semiconductor with an indirect band gap of 1.33 eV along the H-Γ direction. Effective masses of electrons and holes are calculated at the peak of the lowest conduction band and highest valence band, along the Γ- direction. Calculation for optical properties has been performed using coupled-perturbed Hartree-Fock scheme for static values and phonon spectrum calculations are performed for dynamic dielectric functions. Further, frequency dependent electron loss function and reflectivity are determined from the dielectric functions. The elastic constants are estimated and elastic moduli are determined. Bulk modulus of 80.6 GPa and Poisson’s ratio of 0.275 reveals that α-Ca3N2 is a hard and ductile material. The characteristic properties of α-Ca3N2 make it a suitable candidate for optoelectronic applications.