Atomic Geometry Research Articles

A Joint Experimental and Large Eddy Simulation Characterization of the Liquid Fuel Spray in a Swirl Injector

Abstract The quality of liquid fuel spray injection determines to a large extent the performance of aero-engine combustors. This investigation focuses on the detailed characterization of the liquid fuel spray in a test rig targeted at aero-engine applications. The liquid fuel is injected as a hollow cone by a simplex atomizer and the injector comprises a radial swirler. Two features of the droplet distribution are less commonly found. First, the distributions of droplet diameters exhibit nonaxisymmetric patterns, which are investigated for three types of swirlers. Second, it is found that the size-conditioned velocity distributions feature a single wide peak for small droplets and become bimodal for the largest droplets, with a first peak at low velocities, and a second one at higher velocities. Experiments are complemented with large eddy simulations and Lagrangian particle tracking. The spray interacts with the lateral injector surface and requires a droplet–wall interaction model for the liquid film. Simulations do not retrieve the lack of rotational symmetry that is found experimentally indicating that this feature is not linked to the nature of the flow. This is also consistent with further experiments with a different atomizer confirming that this is due to imperfections in the atomizer geometry. Another result is that certain swirler designs are more robust to atomizer imperfections. Simulations accounting for the liquid film yield a bimodal distribution for the droplets' axial velocity distribution which is not obtained without this model, indicating that it is important to represent the droplet–wall interaction.

Determining the atomic charge of calcium ion requires the information of its coordination geometry in an EF-hand motif.

It is challenging to parameterize the force field for calcium ions (Ca2+) in calcium-binding proteins because of their unique coordination chemistry that involves the surrounding atoms required for stability. In this work, we observed a wide variation in Ca2+ binding loop conformations of the Ca2+-binding protein calmodulin, which adopts the most populated ternary structures determined from the molecular dynamics simulations, followed by ab initio quantum mechanical (QM) calculations on all 12 amino acids in the loop that coordinate Ca2+ in aqueous solution. Ca2+ charges were derived by fitting to the electrostatic potential in the context of a classical or polarizable force field (PFF). We discovered that the atomic radius of Ca2+ in conventional force fields is too large for the QM calculation to capture the variation in the coordination geometry of Ca2+ in its ionic form, leading to unphysical charges. Specifically, we found that the fitted atomic charges of Ca2+ in the context of PFF depend on the coordinating geometry of electronegative atoms from the amino acids in the loop. Although nearby water molecules do not influence the atomic charge of Ca2+, they are crucial for compensating for the coordination of Ca2+ due to the conformational flexibility in the EF-hand loop. Our method advances the development of force fields for metal ions and protein binding sites in dynamic environments.

Conical Two-Phase Swirl Flow Atomizers—Numerical and Experimental Study

This paper presents the results of numerical simulations for the developed and discussed conical two-phase atomizers with swirl flow, differing in the ratio of the height of the swirl chamber to its diameter. Experiments were carried out for SAN-1 with HS/DS = 1 and SAN-2 with HS/DS = 4 atomizers. The study was conducted over a range of Reynolds number for liquid ReL = (1400; 5650) and for gas ReG = (2970; 9900). Numerical calculations were performed with the use of computational fluid dynamics (CFD), which were verified on the basis of experimental data. Based on the analysis of experimental studies and simulations results the influence of operational parameters and changes of the atomizer geometry on the generated spray was demonstrated. As the gas flow rate increased and the swirl chamber height decreased, the spray angle increased. Higher velocity values of the liquid and greater turbulence occur in the center of the spray. The flow inside the atomizer determines the nature of the spray obtained. The geometry of the swirl chamber influences the air core formed inside the atomizer, and this determines the atomization effect. The results of numerical simulations not only confirm the results of experimental studies, but also provide additional information on internal and external fluid flow.

Oxygen adsorption on (100) surfaces in Fe\u2013Cr alloys

The adsorption of oxygen on bcc Fe–Cr(100) surfaces with two different alloy concentrations is studied using ab initio density functional calculations. Atomic-scale analysis of oxygen–surface interactions is indispensable for obtaining a comprehensive understanding of macroscopic surface oxidation processes. Up to two chromium atoms are inserted into the first two surface layers. Atomic geometries, energies and electronic properties are investigated. A hollow site is found to be the preferred adsorption site over bridge and on-top sites. Chromium atoms in the surface and subsurface layers are found to significantly affect the adsorption properties of neighbouring iron atoms. Seventy-one different adsorption geometries are studied, and the corresponding adsorption energies are calculated. Estimates for the main diffusion barriers from the hollow adsorption site are given. Whether the change in the oxygen affinity of iron atoms can be related to the chromium-induced charge transfer between the surface atoms is discussed. The possibility to utilize the presented theoretical results in related experimental research and in developing semiclassical potentials for simulating the oxidation of Fe–Cr alloys is addressed.

Epitaxial growth of massively parallel germanium nanoribbons by segregation through Ag(1 1 0) thin films on Ge(1 1 0)

We investigate the epitaxial growth of low-dimensional nanostructures formed by surface segregation of germanium on single crystalline Ag(110) thin films supported by a Ge(110) template. Detailed studies of the atomic geometries have been carried out using scanning tunneling microscopy, low-energy electron diffraction, Auger electron spectroscopy, and high-resolution synchrotron radiation core-level spectroscopy. At very low Ge coverages the segregated Ge atoms form two kinds of commensurate and incommensurate quantum structures after annealing. With increasing Ge coverages, narrow stripes, 0.5 nm in width and with lengths ranging from 5 nm to 50 nm, are formed. With further increase of the Ge atoms’ segregation on the surface, the narrow stripes transform into massively parallel one-dimensional Ge nanostructures with specific widths. From a combined analysis, these fascinating quantum structures are proposed to be zig-zag germanene nanoribbons, potentially with very exciting electronic, spintronic, and topological properties.

AFLOW-XtalFinder: a reliable choice to identify crystalline prototypes

The accelerated growth rate of repository entries in crystallographic databases makes it arduous to identify and classify their prototype structures. The open-source AFLOW-XtalFinder package was developed to solve this problem. It symbolically maps structures into standard designations following the AFLOW Prototype Encyclopedia and calculates the internal degrees of freedom consistent with the International Tables for Crystallography. To ensure uniqueness, structures are analyzed and compared via symmetry, local atomic geometries, and crystal mapping techniques, simultaneously grouping them by similarity. The software (i) distinguishes distinct crystal prototypes and atom decorations, (ii) determines equivalent spin configurations, (iii) reveals compounds with similar properties, and (iv) guides the discovery of unexplored materials. The operations are accessible through a Python module ready for workflows, and through command line syntax. All the 4+ million compounds in the AFLOW.org repositories are mapped to their ideal prototype, allowing users to search database entries via symbolic structure-type. Furthermore, 15,000 unique structures — sorted by prevalence — are extracted from the AFLOW-ICSD catalog to serve as future prototypes in the Encyclopedia.

Computational structure characterization, nonlinear optical properties and antitumor activities of Nickel(II) complexes containing alkoxy-derived dicyandiamide ligands

[Ni(dcda-O-Me) 2 ] 2+ (1) , [Ni(dcda-O-Et) 2 ] 2+ (2) , [Ni(dcda-O-nPr) 2 ] 2+ (3) , and [Ni(dcda-O-nBu) 2 ] 2+ (4) complexes (dcda-O-R is dicyandiamide ligands with alkoxy-derived) have been optimized in the gas phase at B3LYP/LANL2DZ/6-31+G(d,p) level. Computational structure characterization has been performed from the structural parameters, IR spectra, 1 H-NMR, 13 C-NMR chemical shift values. It has been found that the central metal atom geometry in the complexes is a distorted square plane. Some electronic structure descriptors of the complexes are calculated in the gas phase and nonlinear optical properties are predicted. Complex 1 is found as the most suitable compound to produce optical material. The complexes are optimized at the same level in the aqueous phase to determine antitumor activity. Some electronic structure descriptors are calculated and molecular docking calculations are made against the 3WZE protein. According to the calculated electronic structure descriptors and molecular docking results, it is found that the complex 3 has the highest antitumor activity against the selected target protein.

Mechanical manipulation of electronic properties of SnO2 monolayer

A unique and novel SnO2 monolayer structure was introduced and studied by first-principles calculations based on the density functional theory (DFT). Bonding nature and band gap relation to elastic properties were obtained by fitting elastic energy as a function of Green-Lagrangian strain and calculating the elastic constants. The application of uniaxial strain produced a small in-plane stiffness with high Poisson’s ratio. These values revealed no lateral stress was resulted on bonds by the applied longitudinal strain. Area stiffness constant was defined for in-plane area expansion or compression. A higher area stiffness was found for biaxially placed strains, attributed to bending of the Sn-O-Sn bonds, which imposed a direct strain on the Sn-O bonds. Also, the electrons band gap varied from semiconductor energy at equilibrium atomic geometry to narrower gap with the application of biaxial strain. The variance was insignificant for the uniaxial strain case. We Show that the stability in the atomic bonding at strained conditions with fixed unit cell area gave controllability over the electronic state. Interlayer hybridization between O and Sn atoms made the band gap distinctly tunable with biaxial strain.

Fine control of lattice thermal conductivity in low-dimensional materials

Optimal regulation of lattice thermal conductivity in low-dimensional materials is fundamental to obtain highly efficient miniaturized devices. To this aim, we use quantum-mechanical based analyses to understand how atomic type and structural geometry determine electron density and lattice dynamic features ruling the thermal conduction. As a case study, we consider layered van der Waals transition metal dichalcogenides with a finite number of layers. We find that a large thermal conductivity is realized when the atomic bonds display highly covalent character, promoting fast motions of the cations in correspondence of the low-frequency phonon band. Such an effect is the result of the entangled electronic and phonon features, which are captured by the covalency and cophonicity metric. The investigation protocol that we present has general applicability and can be used to design novel thermal low-dimensional materials irrespective of the kind of atomic topology and chemical composition.

Molecular structure, FT-Raman, IR, NLO, NBO, HOMO—LUMO analysis, physicochemical descriptors, ADME parameters, and pharmacokinetic bioactivity of 2,3,5,6-tetrachloro-p-benzoquinone

Vibrational, NLO, NBO, FMO, NMR substance move, and an auxiliary investigation of 2,3,5,6-tetrachloro-p-benzoquinone, utilizing quantum computational figuring, are performed. Atomic geometry, Mulliken charges, and vibrational wavenumbers are resolved by Hartree—Fock (HF) and DFT calculations in the B3LYP framework with the 6-311++G(d,p) premise set and confirmed by the experimental information. The potential energy distribution (PED) generates the assignments of vibrational wavenumbers. An analysis of the electronic properties is carried out using the time-autonomous DFT technique, providing HOMO and LUMO energies. Molecular electrostatic potential (MEP), natural bond orbitals (NBO), and nonlinear optical (NLO) properties are also reported. 13C and 1H NMR synthetic movements are distinguished by the GIAO procedure and diverged from the test substance move. The TED commitment as a blended mode with different vibrations is around 75 %. Physicochemical descriptors, ADME boundaries, pharmacokinetics, pH significance, medicative and restorative nature are proces­sed for the title compound. These properties are computed utilizing a computer aided drug design to encourage the sedate disclosure.

Particle Modeling Based on Interatomic Potential and Crystal Structure: A Multi-Scale Simulation of Elastic-Plastic Deformation of Metallic Material

We formulate a macroscopic particle modeling analysis of metallic materials (aluminum and copper, etc.) based on theoretical energy and atomic geometries derivable from their interatomic potential. In fact, particles in this framework are presenting a large mass composed of huge collection of atoms and are interacting with each other. We can start from cohesive energy of metallic atoms and basic crystalline unit (e.g. face-centered cubic). Then, we can reach to interparticle (macroscopic) potential function which is presented by the analytical equation with terms of exponent of inter-particle distance, like a Lennard-Jones potential usually used in molecular dynamics simulation. Equation of motion for these macroscopic particles has dissipative term and fluctuation term, as well as the conservative term above, in order to express finite temperature condition. First, we determine the parameters needed in macroscopic potential function and check the reproduction of mechanical behavior in elastic regime. By using the present framework, we are able to carry out uniaxial loading simulation of aluminum rod. The method can also reproduce Young’s modulus and Poisson’s ratio as elastic behavior, though the result shows the dependency on division number of particles. Then, we proceed to try to include plasticity in this multi-scale framework. As a result, a realistic curve of stress-strain relation can be obtained for tensile and compressive loading and this new and simple framework of materials modeling has been confirmed to have certain effectiveness to be used in materials simulations. We also assess the effect of the order of loadings in opposite directions including yield and plastic states and find that an irreversible behavior depends on different response of the particle system between tensile and compressive loadings.

Lysine-arginine advanced glycation end-product cross-links and the effect on collagen structure: A molecular dynamics study.

The accumulation of advanced glycation end‐products is a fundamental process that is central to age‐related decline in musculoskeletal tissues and locomotor system function and other collagen‐rich tissues. However, although computational studies of advanced glycation end‐product cross‐links could be immensely valuable, this area remains largely unexplored given the limited availability of structural parameters for the derivation of force fields for Molecular Dynamics simulations. In this article, we present the bonded force constants, atomic partial charges and geometry of the arginine‐lysine cross‐links DOGDIC, GODIC, and MODIC. We have performed in vacuo Molecular Dynamics simulations to validate their implementation against quantum mechanical frequency calculations. A DOGDIC advanced glycation end‐product cross‐link was then inserted into a model collagen fibril to explore structural changes of collagen and dynamics in interstitial water. Unlike our previous studies of glucosepane, our findings suggest that intra‐collagen DOGDIC cross‐links furthers intra‐collagen peptide hydrogen‐bonding and does not promote the diffusion of water through the collagen triple helices.

Dynamics of formation of poly(vinyl alcohol) filaments with an energetically efficient micro-mixing mechanism

We present a pneumatic approach for massive production of poly(vinyl alcohol) (PVA) filaments based on a mixing mechanism at the micrometer scale using so-called Flow Blurring (FB) atomizers. This micro-mixing is triggered by a turbulent, bubbly motion generated by implosion of a gas current into a liquid feeding tube. The energy of the gas, the liquid viscosity, and the geometry of the atomizer play an active role in the size and shape of the ejecta. The shear viscosity of aqueous solutions of PVA of various molecular weights was investigated to assess their rheological nature using a dimensionless parameter based on the solutions’ concentration and the polymer’s molecular weight and its entanglement molecular weight. The solutions exhibited a shear thinning behavior at low shear rates and a Newtonian behavior at moderate rates. PVA solution with viscosity above the threshold value is prone to forming filaments during atomization with FB devices. Analyses of the dynamics of the atomization revealed two main types of ejections depending on the liquid flow rate and viscosity: either a bundle of filaments formed from within the atomizer or a more continuous single structure developed in the vicinity of the atomizer exit. Furthermore, based on Kolmogorov’s energy cascade, we propose a scaling law for the mean filament diameter as a function of liquid properties, atomizer geometry, and imposed pressure. The present work may have significant implications in the large-scale processing of liquids leading to useful materials.

Atomically resolved tomographic reconstruction of nanoparticles from single projection: Influence of amorphous carbon support

Nanoparticles have a wide range of applications due to their unique geometry and arrangement of atoms. For a precise structure-property correlation, information regarding atomically resolved 3D structures of nanoparticles is utmost beneficial. Though modern aberration-corrected transmission electron microscopes can resolve atoms with the sub-angstrom resolution, an atomic-scale 3D reconstruction of a nanoparticle using Scanning Transmission Electron Microscopy (STEM) based tomographic method faces hurdles due to high electron irradiation damage and “missing-wedge”. Instead, inline 3D holography based tomographic reconstructions from single projection registered at low electron doses is more suitable for defining atomic positions at nanostructures. Nanoparticles are generally supported on amorphous carbon film for Transmission Electron Microscopy (TEM) experiments. However, neglecting the influence of carbon film on the tomographic reconstruction of the nanoparticle may lead to ambiguity. To address this issue, the effect of amorphous carbon support was quantitatively studied using simulations and experiments and it was revealed that increasing thickness and/or density of carbon support increases distortion in tomograms.

A Geometric Definition of Short to Medium Range Hydrogen-Mediated Interactions in Proteins.

We present a method to rapidly identify hydrogen-mediated interactions in proteins (e.g., hydrogen bonds, hydrogen bonds, water-mediated hydrogen bonds, salt bridges, and aromatic π-hydrogen interactions) through heavy atom geometry alone, that is, without needing to explicitly determine hydrogen atom positions using either experimental or theoretical methods. By including specific real (or virtual) partner atoms as defined by the atom type of both the donor and acceptor heavy atoms, a set of unique angles can be rapidly calculated. By comparing the distance between the donor and the acceptor and these unique angles to the statistical preferences observed in the Protein Data Bank (PDB), we were able to identify a set of conserved geometries (15 for donor atoms and 7 for acceptor atoms) for hydrogen-mediated interactions in proteins. This set of identified interactions includes every polar atom type present in the Protein Data Bank except OE1 (glutamate/glutamine sidechain) and a clear geometric preference for the methionine sulfur atom (SD) to act as a hydrogen bond acceptor. This method could be readily applied to protein design efforts.

Propane Dehydrogenation on Single-Site [PtZn4] Intermetallic Catalysts

Summary Propane dehydrogenation (PDH) is a commercial propylene production technology that has received much attention, but high reaction temperatures result in a decrease of propylene selectivity and catalyst stability. This paper describes a single-site [PtZn4] catalyst by assembling atomically ordered intermetallic alloy (IMA) as a selective and ultrastable PDH catalyst. The catalyst enables more than 95% of propylene selectivity from 520°C to 620°C. No obvious deactivation is observed within the 160-h test, superior to PtSn/Al2O3 and state-of-the-art Pt-based catalysts. Based on in situ X-ray absorption fine structure, X-ray photoelectron spectroscopy measurements, and density functional theory calculations, we reveal that the surface [PtZn4] ensembles in PtZn IMAs serve as the key active site structures, wherein the geometry-isolated and electron-rich Pt1 site in [PtZn4] ensembles readily promotes the first and second C–H cleavage of propane but inhibits further dehydrogenation of surface-bounded propylene. This significantly improves the selectivity and stability by prohibiting coke side reactions.

Device architectures for low voltage and ultrafast graphene integrated phase modulators.

The atomic layer thin geometry and semi-metallic band diagram of graphene can be utilized for significantly improving the performance matrix of integrated photonic devices. Its semiconductor-like behavior of Fermi-level tunability allows graphene to serve as an active layer for electro-optic modulation. As a low loss metal layer, graphene can be placed much closer to active layer for low voltage operation. In this work, we investigate hybrid device architectures utilizing semiconductor and metallic properties of the graphene for ultrafast and energy efficient electro-optic phase modulators on semiconductor and dielectric platforms. (1) Directly contacted graphene-silicon heterojunctions. Without oxide layer, the carrier density of graphene can be modulated by the directly contact to silicon layer, while silicon intrinsic region stays mostly depleted. With doped silicon as electrodes, carrier can be quickly injected and depleted from the active region in graphene. The ultrafast carrier transit time and small RC constant promise ultrafast modulation speed (3dB bandwidth of 67 GHz) with an estimated Vπ·L of 1.19 V·mm. (2) Graphene integrated lithium niobite modulator. As a transparent electrode, graphene can be placed close to integrated lithium niobate waveguide for improving coupling coefficient between optical mode profile and electric field with minimal additional loss (4.6 dB/cm). Numerical simulation indicates 2.5× improvement of electro-optic field overlap coefficient, with estimated V π of 0.2 V.

Tuning the electronic structure and thermodynamic properties of hybrid graphene-hexagonal boron nitride monolayer

A hybrid system which comprises in-plane graphene and hexagonal boron nitride (h-BN) has sparked intense research due to its tailorable and promising physical properties. We have investigated by first-principle calculations the effect of graphene or h-BN domain size on the atomic geometries, electronic properties and thermodynamic properties of graphene/h-BN hybrid systems with a zigzag interface. Lattice dynamics calculations produced no imaginary frequencies suggesting that the structure is dynamically stable regardless of the graphene (h-BN) domain size. However, the band gap and the thermodynamic properties have been demonstrated to be sensitive to the graphene (h-BN) domain size. The band gap, tunable up to 1.01 eV, decreases with the graphene domain size. The Debye temperature responds differently: it increases with the size of the graphene domain. The thermodynamic properties of the hybrid system are bounded by the values for the graphene and h-BN and can be tuned to converge to either the value of graphene or h-BN depending on the size of graphene domain. Detailed chemical and physical insights revealed by this study can pave a way for a more rational design of future nano-devices with optimized electronic and thermal properties.

Atomically Asymmetric Inversion Scales up to Mesoscopic Single-Crystal Monolayer Flakes.

Symmetry is highly relevant with various quantities and phenomena in physics. While the translational symmetry breaks at the edges of two-dimensional hexagonal crystalline flakes, it is usually associated with the breaking of central inversion symmetry that is yet to be observed in terms of physical properties. Here, we report an experiment-theory joint study on in-plane compressed single-crystal monolayer WS2 flakes. Although the flakes show a hexagonal appearance with a C6 symmetry, our density functional theory calculations predict that their in-plane strain, geometric structure, work-function, energy bandgap, and mechanical modulus are nonequivalent among the triangular regions with different edge terminations at the atomic scale, and the flakes exhibit self-patterns with a C3 symmetry. Such nonequivalence of physical properties and concomitant self-patterns persist even in a 50 μm-sized monolayer WS2, observed using atomic force microscopy. This indicates that the symmetry arising from the atomic geometry could preserve up to tens of microns for both geometric and properties of the flake, regardless of its mesoscopic geometry, i.e., C6 here. Such a detectable mesoscopic scale and symmetric nano- to mesoscale patterns provide promising building blocks for 2D materials and devices and also allow edge terminations of 2D flakes to be directly distinguished.

Superconductivity in undoped BaFe2As2 by tetrahedral geometry design

Fe-based superconductors exhibit a diverse interplay between charge, orbital, and magnetic ordering. Variations in atomic geometry affect electron hopping between Fe atoms and the Fermi surface topology, influencing magnetic frustration and the pairing strength through changes of orbital overlap and occupancies. Here, we experimentally demonstrate a systematic approach to realize superconductivity without chemical doping in BaFe2As2, employing geometric design within an epitaxial heterostructure. We control both tetragonality and orthorhombicity in BaFe2As2 through superlattice engineering, which we experimentally find to induce superconductivity when the As-Fe-As bond angle approaches that in a regular tetrahedron. This approach to superlattice design could lead to insights into low-dimensional superconductivity in Fe-based superconductors.