Discrete Atoms Research Articles

Locally Varying Surface Binding Affinity on Pd-Au Nanocrystals Enhances Electrochemical Ethanol Oxidation Activity.

Noble metal nanocrystals face challenges in effectively catalyzing electrochemical ethanol oxidation reaction (EOR)-represented multistep, multielectron transfer processes due to the linear scaling relationship among binding energies of intermediates, impeding independent optimization of individual elemental steps. Herein, we develop noble metal nanocrystals with a range of local surface binding affinities in close proximity to overcome this challenge. Experimentally, this is demonstrated by applying tensile strain to a Pd surface and decorating it with discrete Au atoms, forming a diversity of binding sites with varying affinities in close proximity for guest molecules, as evidenced by CO probing and density functional theory calculations. Such a surface enables reaction intermediates to migrate between different binding sites as needed for each elemental step, thereby reducing the energy barrier for the overall EOR when compared to reactions at a single site. On these tailored surfaces, we attain specific and mass activities of 32.7 mA cm-2 and 47.8 A mgPd-1 in EOR, surpassing commercial Pd/C by 10.9 and 43.8 times, respectively, and outperforming state-of-the-art Pd-based catalysts. These results highlight the promise of this approach in improving a variety of multistep, multielectron transfer reactions, which are crucial for energy conversion applications.

Molecular dynamics analysis of the effect of temperature on the internal structure transformation of polycrystalline 3 C-SiC nanoindentation

To investigate the structure changes of polycrystalline 3 C-SiC nanoindentation process and the influence of temperature effect on its changes, the nanoindentation experiments of polycrystalline 3 C-SiC are constructed by molecular dynamics method. The initial nanoindentation model of polycrystalline 3 C-SiC and diamond indenter is constructed based on the characteristics of Voronoi method in constructing close-packed spatial lattice. The temperature conditions of 300 K, 500 K, 800 K and 1000 K are selected to analyze the dislocation structure, number and length, internal atomic structure, grain boundary structure and deformation degree of polycrystalline 3 C-SiC during nano-indentation process. The stress and deformation of diamond indenter are analyzed. The results show that the higher the temperature, the higher the degree of dislocation stacking. Temperature has an effect on the internal variation of polycrystalline silicon carbide, particularly on the transverse size of the structure. The central force of the diamond becomes weaker and the force on either side becomes stronger. The temperature effect can change the stacking degree of dislocations, reduce the internal structure transformation rate of polycrystalline 3 C-SiC, and transform fewer discrete atoms and increase the number of cubic lattice atoms.

KGDiff: towards explainable target-aware molecule generation with knowledge guidance.

Designing 3D molecules with high binding affinity for specific protein targets is crucial in drug design. One challenge is that the atomic interaction between molecules and proteins in 3D space has to be taken into account. However, the existing target-aware methods solely model the joint distribution between the molecules and proteins, disregarding the binding affinities between them, which leads to limited performance. In this paper, we propose an explainable diffusion model to generate molecules that can be bound to a given protein target with high affinity. Our method explicitly incorporates the chemical knowledge of protein-ligand binding affinity into the diffusion model, and uses the knowledge to guide the denoising process towards the direction of high binding affinity. Specifically, an SE(3)-invariant expert network is developed to fit the Vina scoring functions and jointly trained with the denoising network, while the domain knowledge is distilled and conveyed from Vina functions to the expert network. An effective guidance is proposed on both continuous atom coordinates and discrete atom types by taking advantages of the gradient of the expert network. Experiments on the benchmark CrossDocked2020 demonstrate the superiority of our method. Additionally, an atom-level explanation of the generated molecules is provided, and the connections with the domain knowledge are established.

Mean-Field Description of Cooperative Scattering by Atomic Clouds

We present analytic expressions for the scattering of light by an extended atomic cloud. We obtain the solution for the mean-field excitation of different atomic spherical distributions driven by a uniform laser, including the initial build up, the steady state and the decay after the laser is switched off. We show that the mean-field model does not describe subradiant scattering due to the negative interference of the photons scattered by N discrete atoms.

Molecular dynamics simulation of cutting mechanism of polycrystalline Fe-Cr-W alloy

In order to study the effect of cutting parameters on the machining mechanism of AISI M2 alloy tool steel during ultra-precision machining, the effects of cutting speed and depth of cut on crystal structure change, cutting force, cutting temperature, and transformation of amorphous atoms during turning are analyzed. The polycrystalline molecular dynamics model of alloy tool steel is established with three elements Fe, Cr, and W, and the molecular dynamics model of the tool is established with B and N two elements. Four potential energy functions of Tersoff, EAM, Morse, and L-J are used to characterize the interaction between atoms in the model. The following research results can be obtained by analyzing the microstructure changes of the material during the cutting process: (1) With the progress of cutting, some of the workpiece atoms accumulate on the rake face of the tool to form chips, and another part of the atoms flow to both sides of the tool to form surface peaks. (2) The shear extrusion effect of the tool on the material causes the reconfiguration and transformation of the grains inside the polycrystalline alloy. (3) The cutting temperature and cutting force of the molecular dynamics simulation system show an upward trend with the increase in cutting speed and cutting depth. Moreover, the cutting force fluctuates due to the existence of irregular grains, discrete atoms, and grain boundaries.

A novel algorithm for visualizing and quantifying vortices in complex 3D flows based on marching and converging vortex atoms

Numerous investigations aiming to reveal the underlying physics behind complex flows highlighted the important roles of vortices. This article proposes an integrative algorithm for visualizing and quantifying the vortices in three-dimensional flows. The algorithm not only extracts the vortex centerlines but also returns the vortex radii and circulations varying along the centerlines. The novel aspect of this algorithm is to represent the vortex field as a collection of discrete vortex atoms. By iteratively updating the positions of these vortex atoms, the algorithm manipulates them into marching toward the underlying vortex centerlines. The radii and circulations varying along the centerlines are estimated based on the vortex atoms converged on the vortex centerlines. The accuracy and robustness of the algorithm are first accessed by numerical tests based on a synthetic vortex ring. Subsequently, the algorithm is employed to investigate the complex vortices in a turbulent boundary layer, validating the scaling law of the vortices reported in the literature. At last, the algorithm is applied to the three-dimensional experimental data of the wake flow behind a wall-mounted hemisphere. It concludes that the algorithm can be used as an effective tool for analyzing vortices in complex flows.

Evaluation of Nanoscale Deformation Fields from Phase Field Crystal Simulations

Different methods for evaluation of displacement and strain fields based on phase field crystal (PFC) simulations are shown. Methods originally devised for molecular dynamics (MD) simulations or analysis of high-resolution microscopy images are adapted to a PFC setting, providing access to displacement and strain fields for systems of discrete atoms, such as in MD, as well as to continuous deformation fields. The latter being achieved by geometrical phase analysis. As part of the study, the application of prescribed non-affine deformations in a 3D structural PFC (XPFC) setting is demonstrated as well as an efficient numerical scheme for evaluation of PFC phase diagrams, such as, for example, those required to stabilize solid/liquid coexistence. The present study provides an expanded toolbox for using PFC simulations as a versatile numerical method in the analysis of material behavior at the atomic scale.

Crossing the Boundaries between Analogue and Digital

Given that they do not benefit from CMOS technology scaling, analogue integrated circuits are soon becoming a constraint in terms of the cost and performance of nanoscale integrated systems. This has led to some debate about whether analogue circuits are still useful in the era of digital technology. The usual reaction is that analogue circuitry will always be needed, if not everywhere, then at least in interface circuits that exchange data with physically analogue environments. The fact that matter is made up of discrete atoms and molecules, that basic physical quantities like electromagnetic radiation and electric charge are quantized, and even that information is transmitted as discrete pulses in biological systems all make the physical world less "intrinsically analog" than it first appears. In other words, it appears more and more plausible that the foundation for our regular analogue experiences is a distinct or digital one.

Atomic insights into effects of temperature and grain diameter on the micro-deformation mechanism, mechanical properties and sluggish diffusion of nanocrystalline high-entropy alloys

In this work, the effects of temperature and grain diameter on the micro- deformation mechanism, tensile properties, and sluggish diffusion of nanocrystalline Al0.1CoCrFeNi HEAs during uniaxial tension have been studied by molecular dynamics (MD) simulations. The Hall-Petch (H-P) relation and inverse Hall-Petch relation still exist in nanocrystalline HEAs. At the case of grain diameter over a critical size (e.g., DG>14.77 nm for 300 K), the deformation mechanism of HEAs is that the accumulation of dislocations at grain boundaries leads to the increase of HEAs strength, which conforms the H-P relation. At the case of grain diameter below a critical size (e.g., DG<14.77 nm for 300 K), the migration of grain boundaries, amorphization of atoms as well as the rotation and merging of grains becomes the main deformation mechanism of HEAs, which weaken the strength of HEAs and conform the reverse H-P relation. The increase of temperature has a negative influence on the mechanical properties including Young’s modulus, yield strength and flow stress of HEAs. The critical grain size that undergoes the H-P and reverse H-P relation transformation increases with the increase of temperature. An increase in grain boundary thickness and the appearance of a large number of discrete amorphous atoms in the grains can be observed at high temperatures. The shear strain of atoms at grain boundaries is larger than that of atoms in other regions, and high temperature promotes the increase of atomic shear strains in HEA, especially at grain boundaries. The lengths of all types of dislocation lines and dislocation densities tend to decrease with increasing temperature, and Shockley dislocations always dominate all other dislocations at 300–1200 K. The MSD results show that nanocrystalline HEA have good stability at 300–1200 K, and small-grained HEAs have higher MSD value and diffusion coefficient than those of large-grained HEAs at 1200 K. Moreover, at higher temperature (2500 K), the MSD values of HEAs with DG= 7.4–23.45 nm all increases significantly, and the time-dependent curves basically overlap, indicating that the influence of grain boundaries on atomic diffusion can be ignored.

Bio Imaging Applications of Noble Metal Nanoclusters

Metal nanoclusters are considered as the bridge between nanoparticle and discrete noble metal atoms. It comes typically in the size range of &lt;3 nm. They exhibit excellent photophysical properties. In the visible and near infra red (IR) range, they demonstrate fluorescence phenomena. Also, they are more stable in biological condition. Owing to these properties, the prospect of using noble metal nanoclusters for biomedical imaging has been exploited as the conventional fluorescent dues have limited use in cellular condition. In the current article, the synthesis and imaging application of noble metal nanoclusters have been discussed.

One bit compressive sensing with off-grid targets

The compressive sensing theory enables reconstruction of sparse or compressible signals at reduced sampling rate. Recent studies have shown that stable signal reconstruction is possible even if each measurement is quantized to one bit. In conventional compressive sensing framework, the signal can be sparsely represented by some discrete atoms. In many applications however, signals are sparse in a continuous parameter space, e.g., radar imaging. A commonly used method is to discretize the continuous parameter into grid points and build a dictionary to characterize the sparsity. However, the true targets may not coincide with the predefined grid points. This off-grid problem always leads to a mismatched basis matrix, which results in degradation of the performance. In this paper, a parameter perturbation method, based on 1-bit compressive sensing is proposed to deal with the off-grid problem. Especially for adjacent targets in the adjoining grids, a self-checking mechanism is proposed to further discriminate the adjacent targets located within the proximity of adjoining grids. In the proposed algorithm, the available grid points in the dictionary are adaptively updated to approach the true targets. The convergence of the algorithm can be theoretically guaranteed, and numerical experiments demonstrate that the proposed algorithm can be effectively applied to range profile and synthetic aperture radar imaging. Simulations indicate that the proposed algorithm outperforms the state-of-the-art techniques over a wide range of signal-to-noise ratio levels.

Highly exposed discrete Co atoms anchored in ultrathin porous N, P-codoped carbon nanosheets for efficient oxygen electrocatalysis and rechargeable aqueous/solid-state Zn–air batteries

The ultrathin porous nanosheet structure and optimized N and P dual-coordinated Co active sites enable high performances of CoSA/NPC in oxygen electrocatalysis and rechargeable aqueous and flexible solid-state ZABs.

Atomically precise alloy nanoclusters: syntheses, structures, and properties.

Metal nanoclusters fill the gap between discrete atoms and plasmonic nanoparticles, providing unique opportunities for investigating the quantum effects and precise structure-property correlations at the atomic level. As a versatile strategy, alloying can largely improve the physicochemical performances compared to the corresponding homo-metal nanoclusters, and thus benefit the applications of such nanomaterials. In this review, we highlight the achievements of atomically precise alloy nanoclusters, and summarize the alloying principles and fundamentals, including the synthetic methods, site-preferences for different heteroatoms in the templates, and alloying-induced structure and property changes. First, based on various Au or Ag nanocluster templates, heteroatom doping modes are presented. The templates with electronic shell-closing configurations tend to maintain their structures during doping, while the others may undergo transformation and give rise to alloy nanoclusters with new structures. Second, alloy nanoclusters of specific magic sizes are reviewed. The arrangement of different atoms is related to the symmetry of the structures; that is, different atoms are symmetrically located in the nanoclusters of smaller sizes, and evolve into shell-by-shell structures at larger sizes. Then, we elaborate on the alloying effects in terms of optical, electrochemical, electroluminescent, magnetic and chiral properties, as well as the stability and reactivity via comparisons between the doped nanoclusters and their homo-metal counterparts. For example, central heteroatom-induced photoluminescence enhancement is emphasized. The applications of alloy nanoclusters in catalysis, chemical sensing, bio-labeling, and other fields are further discussed. Finally, we provide perspectives on existing issues and future efforts. Overall, this review provides a comprehensive synthetic toolbox and controllable doping modes so as to achieve more alloy nanoclusters with customized compositions, structures, and properties for applications. This review is based on publications available up to February 2020.

Spectral structure and solution of fractional hydrogen atom difference equations

In this study, discrete fractional hydrogen atom (DFHA) operators are presented. Hydrogen atom differential equations have series solution due to having singularity and also obtaining a series solution for DFHA equations have some difficulties, for this reason, we study to obtain solution of DFHA equations by means of nabla Laplace transform. In addition to all these, we show self-adjointness of the DFHA operator and some spectral properties, like orthogonality of distinct eigenfunctions, reality of eigenvalues. Finally, we find an analytical solution of the problem under different q (t) potential functions, different fractional orders and different eigenvalues and the results obtained are illustrated by tables and simulations.

Stable Discrete Pt1(0) in Crown Ether with Ultra‐High Hydrosilylation Activity

AbstractObtaining reduced discrete metal atoms that are stable in liquid solvents byin‐situreduction of an ionic metal precursor has been a challenge until recently. A liquid surfactant polydimethylsiloxane‐polyethylene glycol (PDMS‐PEG) enabled the synthesis of stable discrete platinum atoms (Pt1) by reducing Pt(IV) and Pt(II) salts. Here we report the successful preparation of discrete mononuclear platinum atoms (Pt1) in a crown ether, [15]crown‐5, as a structurally much simpler solvent, and the prepared Pt1@[15]crown‐5 was demonstrated for ultra‐high catalytic activity and selectivity in hydrosilylation reactions. A combination of spectroscopic characterizations proves the reduced Pt species is Pt1(0) with partially positive charge.195Pt NMR and DFT calculation indicate the Pt1(0) is stabilized by thepseudooctahedral structure of ([15]crown‐5)PtCl−2H+2involving two adjacent oxygens from the crown ether ring, although the oxygens in the crown ether ring have been known to host and stabilize certain metal cations. The Pt1@[15]crown‐5 shows ultrahigh activity (TOF of 8.3×108 h−1) with excellent terminal adducts selectivity in catalytic olefin hydrosilylation. This catalyst was found to be highly stable under hydrosilylation conditions. For examples, the turnover number (TON) exceeded 1.0×109for hydrosilylation between 1‐octene and (Me3SiO)2MeSiH without showing sign of deactivation; the TON exceeded 2.0×108while the catalyst remained active for a catalytically more demanding reaction between styrene and (Me3SiO)2MeSiH.

Genesis of electron deficient Pt1(0) in PDMS-PEG aggregates

While numerous single atoms stabilized by support surfaces have been reported, the synthesis of in-situ reduced discrete metal atoms weakly coordinated and stabilized in liquid media is a more challenging goal. We report the genesis of mononuclear electron deficient Pt1(0) by reducing H2PtCl6 in liquid polydimethylsiloxane-polyethylene glycol (PDMS-PEG) (Pt1@PDMS-PEG). UV–Vis, far-IR, and X-ray photoelectron spectroscopies evidence the reduction of H2PtCl6. CO infrared, and 195Pt and 13C NMR spectroscopies provide strong evidence of Pt1(0), existing as a pseudo-octahedral structure of (R1OR2)2Pt(0)Cl2H2 (R1 and R2 are H, C, or Si groups accordingly). The weakly coordinated (R1OR2)2Pt(0)Cl2H2 structure and electron deficient Pt1(0) have been validated by comparing experimental and DFT calculated 195Pt NMR spectra. The H+ in protic state and the Cl− together resemble HCl as the weak coordination. Neutralization by a base causes the formation of Pt nanoparticles. The Pt1@PDMS-PEG shows ultrahigh activity in olefin hydrosilylation with excellent terminal adducts selectivity.

Dynamic vibration phase reversal transition in discrete time-translational symmetry broken cold atoms

We experimentally demonstrate vibration phase reversal transition in a discrete time-translational symmetry broken cold atomic system by the application of a pulsed bias-field opposite to the existing phase of the symmetry broken vibrational state. The reversal transition depends on the strength hp and the duration Δt of the applied pulse. Consequently, we obtain a hp−Δt phase boundary with a divergent relaxation time τ due to the critical slowdown behavior. Interestingly, the dependence of the dynamic phase boundary and relaxation time on the noise-induced switching rate implies that the system is out of equilibrium, though not so in the Ising model of a spin system.

Catechol and 1,2,4,5-tetrahydroxybenzene functionalized cyclodiphosphazane ligands: synthesis, structural studies, and transition metal complexes.

Syntheses of two novel cyclodiphosphazane derivatives appended on catechol and 1,2,4,5-tetrahydroxy benzene, [{(μ-N(tBu)P)2(C6H4O2)}] (1) and [{((μ-N(tBu)P)2)2(μ-C6H2O4)}] (2), are described. Reactions of 1 with copper(i) halides led to the isolation of one-dimensional (1-D) and two-dimensional (2-D) coordination polymers, depending on the reaction conditions, metal-to-ligand ratio and CuX (X = Cl, Br or I) employed. The 1 : 1 reaction between 1 and CuCl yielded a 1-D coordination polymer [{(μ-N(tBu)P)2(C6H4O2)}{Cu(μ2-Cl)(NCCH3)}2]n (3) containing [Cu(μ2-Cl)]2 rhombus units. Similar reactions of 1 with CuBr and CuI produced rare 1-D coordination polymers [{(μ-N(tBu)P)2(C6H4O2)}{CuX(NCCH3)}]n (4, X = Br; 5, X = I) with discrete copper atoms linked by bridging cyclodiphosphazane ligands. However, the reactions of 1 with CuX (X = Cl, Br or I) in 1 : 2 molar ratios afforded 2-D coordination polymers [{(μ-N(tBu)P)2(C6H4O2)}2{Cu4(μ3-X)4}]n (6, X = Cl; 7, X = Br and 8, X = I) containing cuboids [Cu4(μ3-X)4] with 1 linking such units. Treatment of 1 with [RuCl2(η6-p-cymene)]2, [Rh(COD)Cl]2 and [Pd(η3-C3H5)Cl]2 in 1 : 1 molar ratios produced dinuclear complexes [{(μ-N(tBu)P)2(C6H4O2)}{RuCl2(η6-p-cymene)}2] (9), [{(μ-N(tBu)P)2(C6H4O2)}{RhCl(COD)}2] (10) and [{(μ-N(tBu)P)2(C6H4O2)}{PdCl(η3-C3H5)}2] (11), respectively. The reaction between 1 and [AuCl(SMe2)] in a 1 : 2 ratio yielded a dinuclear complex [{(μ-N(tBu)P)2(C6H4O2)}{AuCl}2] (12). The reactions of 2 with [RuCl2(η6-p-cymene)]2, [Rh(COD)Cl]2 and [Pd(η3-C3H5)Cl]2 in 1 : 2 molar ratios afforded tetranuclear complexes [{((μ-N(tBu)P)2)2(μ-C6H2O4)}{RuCl2(η6-p-cymene)}4] (13), [{((μ-N(tBu)P)2)2(μ-C6H2O4)}{RhCl(COD)}4] (14) and [{((μ-N(tBu)P)2)2(μ-C6H2O4)}{PdCl(η3-C3H5)}4] (15), respectively. The reaction of 2 with [AuCl(SMe2)] also afforded a tetranuclear complex [{((μ-N(tBu)P)2)2(μ-C6H2O4)}{AuCl}4] (16). In all these complexes, ligands preferred a bridged bidentate mode of coordination. Compounds 3-8 are the rare examples of 1-D and 2-D copper(i) coordination polymers containing cyclodiphosphazane ligands. The crystal structures of 2-8, and 15 were established by X-ray diffraction studies.

Representationalism in Nietzsche’s Early Physics: Cosmology and Sensation in the Zeitatomenlehre

Abstract Nietzsche’s 1873 fragment, the Zeitatomenlehre, posits a temporal conception of action at a distance where space is reduced to a single point and time consists only in a series of discrete atoms. Taken as a physical doctrine that destroys all spatial difference, this conception raises serious conflicts with the rest of his work. I describe and situate this theory within the historical context of debates over action at a distance in nineteenth-century physics, distinguish it from physical theories influential on Nietzsche, and argue that these conflicts can be resolved only by viewing it in the anti-metaphysical phenomenalist and representational terms that he also expressed in his early work.

The Role and Potential Dangers of Visualisation when Learning about Sub-Microscopic Explanations in Chemistry Education

The core of theory-driven chemistry education consists of the constant shift between the different representational domains of chemical thinking: the macroscopic, the sub-microscopic, and the symbolic domains. Because the sub-microscopic domain can neither be seen nor directly visualised, it requires specific forms of visualisation, i.e. pictures andanimations illustrating the model-based level of discrete particles, atoms, or molecular structures. This paper considers the central role visualisations play when learning about the model-based, sub-microscopic level, but it also reflects the dangers inherent in employing insufficiently examined, poorly considered, or even misleading visualisations. This is outlined using different examples taken from both textbooks for lower secondary chemistry education (for students aged 10 to 15) and from the internet. Implications for structuring and using sub-micro visualisations in chemistry education are also given.