Location Of Atoms Research Articles

Non-Adiabatic Excited-State Time-Dependent GW (TDGW) Molecular Dynamics Simulation of Nickel-Atom Aided Photolysis of Methane to Produce a Hydrogen Molecule

Methane photolysis is a very important initiation reaction from the perspective of hydrogen production for alternative energy applications. In our recent work, we demonstrated using our recently developed novel method, non-adiabatic excited-state time-dependent GW (TDGW) molecular dynamics (MD), how the decomposition reaction of methane into a methyl radical and a hydrogen atom was captured accurately via the time-tracing of all quasiparticle levels. However, this process requires a large amount of photoabsorption energy (PAE ∼10.2 eV). Moreover, only one hydrogen atom is produced via a single photon absorption. Transition metal atoms can be used as agents for photochemical reactions, to reduce this optical gap and facilitate an easier pathway for hydrogen production. Here, we explore the photolysis of methane in the presence of a Ni atom by employing TDGW-MD. We show two possibilities for hydrogen-atom ejection with respect to the location of the Ni atom, towards the Ni side or away from it. We demonstrate that only the H ejection away from the Ni side facilitates the formation of a hydrogen molecule with the quasiparticle level corresponding to it having an energy close to the negative ionization potential of an isolated H2 molecule. This is achieved at a PAE of 8.4 eV which is lower compared to that of pristine methane. The results obtained in this work are an encouraging step towards transition metal-mediated hydrogen production via photolysis of hydrocarbons.

Improved Dopant Fraction Variance Estimation in Statistical ALCHEMI Based on Correct Error Propagation Rule.

This report revisits the statistical atom location by channeling enhanced microanalysis (St-ALCHEMI) method, correcting the dopant site occupancy error by applying an appropriate error propagation rule. A revised equation for calculating the uncertainty in the determined dopant fractions is proposed. The revised equation is expected to correct the uncertainty in the determined dopant fractions, which is particularly significant in cases of low dopant concentrations and variable dopant occupancies across inequivalent host atomic sites. The approach is validated using Eu-doped Ca2SnO4 as a typical model system.

Superposition of standing waves induced ultra high-resolution atom localization

Abstract In this study, we have theoretically demonstrated ultra-high resolution two-dimensional atom localization within a three-level $\lambda$-type atomic medium via superposition of asymmetric and symmetric standing wave fields. Our analysis provides understanding into the precise spatial localization of atomic positions at the atomic level, utilizing advanced theoretical approaches and principles of quantum mechanics. The dynamical behavior of a three-level atomic system is thoroughly analyzed using the density matrix formalism within the realm of quantum mechanics. A theoretical approach is constructed to describe the interaction between the system and external fields, specifically a control field and a probe field. The absorption spectrum of the probe field is thoroughly examined to clarify the spatial
localization of the atom within the proposed configuration. We have theoretically investigated that symmetric and asymmetric superposition phenomena significantly influence the localized peaks within a two-dimensional spatial domain. Specifically, the emergence of one and two sharp localized peaks has been observed within a region of one wavelength domain. We observed notable influences of the intensity of the control field, probe field detuning, and decay rates on atom localization. Ultimately, we have achieved an unprecedented level of ultra-high resolution and precision in localizing an atom within an area smaller than λ/35×λ/35. These findings hold promise for potential applications in domains such as Bose-Einstein condensation, nanolithography, laser cooling, trapping of neutral atoms, and the measurement of center-of-mass wave-functions.

Design, Synthesis, Physicochemical Properties, and Biological Activity of Thymidine Compounds Attached to 5,8-Quinolinedione Derivatives as Potent DT-Diaphorase Substrates.

After heart disease, cancer is the second-leading cause of death worldwide. The most effective method of cancer treatment is target therapy. One of the potential goals of therapy could be DT-diaphorase, which reduces quinone moiety to hydroquinone, and reactive oxygen species are create as a byproduct. The obtaining of hybrid compounds containing the quinone moiety and other bioactive compounds leads to new derivatives which can activate DT-diaphorase. The aim of this research was the synthesis and characterization of new hybrids of 5,8-quinolinedione with thymidine derivatives. The analysis of the physicochemical properties shows a strong relationship between the structure and properties of the tested compounds. The enzymatic assay shows that hybrids are good substrates of NQO1 protein. The analysis of the structure-activity relationship shows that the localization of nitrogen atoms influences the enzymatic conversion rate. The analysis was supplemented by a molecular docking study. Comparing the results of the enzymatic assay and the molecular docking presents a strong correlation between the enzymatic conversion rate and the scoring value.

Covalent Organic Frameworks in Computational Design of Second-Harmonic Generation Materials: Role of Tetrel Atoms and Their Interactions.

Modern approaches to the design of nonlinear optical materials often rely on computational techniques. Here, we discuss the effects of the variation in the center tetrel atoms, Tt = C, Si, or Ge, in a series of covalent organic frameworks of the COF-102 family. The effects of halogen substitution, Hal = Cl, Br, or I on intramolecular tetrel bonding are also discussed. The characteristics of the calculated electron density have been implemented to describe the features of the electron distribution around the central fragment involving a tetrahedral tetrel atom. The effect of the central Tt atom leads to a dramatic change in the character of electron delocalization on the Tt-Car bond with aromatic rings. The location of the halogen atom at the ortho-position of the aromatic ring leads to the formation of tetrel bonds, halogen bonds, or other noncovalent interactions. The changes in the second-order electric susceptibility χ(2) have been studied in order to describe the strength of nonlinear optical properties within the periodic couple-perturbed Kohn-Sham approach. A counterintuitive trend for the χ(2) decrease is observed upon substitution of H > Cl > Br > I at the ortho-position of the phenyl ring. This is due to the corresponding elongation of the Tt-Car bond.

Prediction of the Cu oxidation state from EELS and XAS spectra using supervised machine learning

Electron energy loss spectroscopy (EELS) and X-ray absorption spectroscopy (XAS) provide detailed information about bonding, distributions and locations of atoms, and their coordination numbers and oxidation states. However, analysis of XAS/EELS data often relies on matching an unknown experimental sample to a series of simulated or experimental standard samples. This limits analysis throughput and the ability to extract quantitative information from a sample. In this work, we have trained a random forest model capable of predicting the oxidation state of copper based on its L-edge spectrum. Our model attains an R2 score of 0.85 and a root mean square error of 0.24 on simulated data. It has also successfully predicted experimental L-edge EELS spectra taken in this work and XAS spectra extracted from the literature. We further demonstrate the utility of this model by predicting simulated and experimental spectra of mixed valence samples generated by this work. This model can be integrated into a real-time EELS/XAS analysis pipeline on mixtures of copper-containing materials of unknown composition and oxidation state. By expanding the training data, this methodology can be extended to data-driven spectral analysis of a broad range of materials.

Efficient control of high-precision three-dimensional atom localization via probe absorption in a five-level phase-coherent atomic system

We propose a new scheme for high-precision three-dimensional (3D) atom localization by observing the spatially modulated absorption of a weak probe field operating in a partially closed-loop dependent five-level atomic system. Different spatial structures of localization patterns are presented by controlling the Rabi frequency, detuning, and field-induced collective phase-coherence with a variety of superposed standing wave field configurations. Our results highlight that 100% detection probability of atom is possible in the present model in many ways with high precision measurement of spatial absorption. It has been shown that, in the presence of standing wave fields, position information of the atom with maximum detection probability can be efficiently controlled by employing the travelling-wave field in the system. In the present work, we note that the maximum detection probability of the atom is attainable with the limit of spatial resolution better than λ/50. The efficacy of the present model is to find its application in atom nanolithography and atom-imaging having importance in quantum information processing.

Energy distributions of Frenkel–Kontorova-type atomic chains: Transition from conservative to dissipative dynamics

We investigate energy distributions of Frenkel–Kontorova-type atomic chains generated from large number of independent identically distributed (iid) random initial atomic positionings under two cases. In the first case, atoms at the free-end chains without dissipation (conservative case) are only coupled to one other atom, whereas each atom inside the bulk is coupled to its 2 nearest neighbors. Here, atoms located at the chain are all at the same type. Such kind of systems can be modelled by conservative standard map. We show that, when the coupling is non-linear (which leads chaotic arrangement of the atoms) for energy distribution, the Boltzmann–Gibbs statistical mechanics is constructed, namely, exponential form emerges as Boltzmann factor P(E)∝e−βE. However, when the coupling is linear (which leads linear arrangement of the atoms) the Boltzmann–Gibbs statistical mechanics fails and the exponential distribution is replaced by a q-exponential form, which generalizes the Boltzmann factor as P(E)∝eq−βqE=[1−(1−q)βqE]1/(1−q). We also show for each type of atom localization with N number of atoms, β (or βq) values can be given as a function of 1/N. In the second case, although the couplings among the atoms are exactly the same as the previous case, atoms located at the chain are now considered as being at different types. We show that, for energy distribution of such linear chains, each of the distributions corresponding to different dissipation parameters (γ) are in the q-exponential form. Moreover, we numerically verify that βq values can be given as a linear function of 1/∑n=1N(1−γ)(n−2). On the other hand, although energy distributions of the chaotic chains for different dissipation parameters are in exponential form, a linear scaling between β and γ values cannot be obtained. This scaling is possible if the energies of the chains are scaled with 1/(1−γ)−N. For both cases, clear data collapses among distributions are evident.

Optical tomography and coherence of a cavity interacting with two time-dependent position qubits

Optical tomography is a widely used method for estimating complex information. It provides a monotonic relation between the coherent field states density and their corresponding probability distributions. This approach is critical for validating any quantum information processing system’s implementation. This paper explores the optical tomography and coherence dynamics for a cavity interacting with two two-level atoms having time-dependent locations. We analyze the dynamics of the photon-field states, as two moving atoms enter a cavity filled with two superposed coherent states. The von-Neumann entropy dynamics illustrates how interaction couplings between the two atoms and cavity can give rise to entangled states under the effects of the atom-field couplings and the time-dependent atomic location parameter. Aside from coherence, the interactions between the cavity and atoms are essential for producing nonclassical proprieties in optical tomography. Furthermore, we investigate the dynamics of optical tomography densities with respect to the couplings between atoms and photons for time-dependent atomic location. Our results show that the couplings between atoms and cavity not only accelerate but also improve the processes involved in generating nonclassical optical tomography and coherence dynamics.

Developments of Pyrrolo[2,3-d]pyrimidines with Pharmaceutical Potential

: In terms of fused heterocyclic compounds, pyrrolopyrimidines, and their substituted analogs are among the most extensively explored scaffolds. Based on the location of the nitrogen atom in the pyrrole ring, pyrrolopyrimidines have different isomers. This study deals only with the pyrrolo[2,3-d]pyrimidine isomer. Several techniques are represented and discussed in this review for producing pyrrolo[2,3-d]pyrimidine derivatives. The first one is the cyclization of the pyrimidine ring on the pyrrole ring through the reaction of β-enaminonitrile, β-enaminoester or β-enaminoamide of the pyrrole ring with different bifunctional reagents such as formic acid, acetic acid, acetic anhydride, formamide, isothiocyanate, urea, thiourea, and carbon disulfide. The second technique includes cyclization of the pyrrole ring on the pyrimidine ring via the treatment of pyrimidine, aminopyrimidine, diamino-pyrimidine, or triamino-pyrimidine with different reagents such as nitroalkenes, alkynes, aldehydes, and acid chlorides. In addition, different reaction methodologies like one pot, two-step, and threestep synthetic methodologies were reported. The last technique for producing pyrrolo[2,3-d]pyrimidine derivatives is through miscellaneous reactions. This review also includes the interactions of pyrrolo[2,3- d]pyrimidines at different active centers of the pyrrole ring with different reagents to form N-alkylated, Nglycosylated, C-5, and C-6 adducts. Besides, the interactions on the pyrimidine ring to form chloro, hydrazino, and amino-imino derivatives were also discussed. The amino-imino derivatives are key intermediates for the preparation of tricyclic pyrrolotriazolopyrimidines. Finally, the pharmaceutical and biological properties of some pyrrolo[2,3-d]pyrimidine derivatives have also been mentioned. This information can be utilized to design novel diverse pyrrolopyrimidine derivatives for recent challenges in pharmaceutical and medical studies to develop the already existing drugs or discover new ones.

Efficient control of three-dimensional atom localization via probe absorption in a phase-coherent atomic medium

Efficient control of three-dimensional atom localization via probe absorption in a phase-coherent atomic medium

Machine Learning-Assisted Precision Manufacturing of Atom Qubits in Silicon.

Donor-based qubits in silicon, manufactured using scanning tunneling microscope (STM) lithography, provide a promising route to realizing full-scale quantum computing architectures. This is due to the precision of donor placement, long coherence times, and scalability of the silicon material platform. The properties of multiatom quantum dot qubits, however, depend on the exact number and location of the donor atoms within the quantum dots. In this work, we develop machine learning techniques that allow accurate and real-time prediction of the donor number at the qubit site during STM patterning. Machine learning image recognition is used to determine the probability distribution of donor numbers at the qubit site directly from STM images during device manufacturing. Models in excess of 90% accuracy are found to be consistently achieved by mitigating overfitting through reduced model complexity, image preprocessing, data augmentation, and examination of the intermediate layers of the convolutional neural networks. The results presented in this paper constitute an important milestone in automating the manufacture of atom-based qubits for computation and sensing applications.

A dataset of alternately located segments in protein crystal structures

Protein Data Bank (PDB) files list the relative spatial location of atoms in a protein structure as the final output of the process of fitting and refining to experimentally determined electron density measurements. Where experimental evidence exists for multiple conformations, atoms are modelled in alternate locations. Programs reading PDB files commonly ignore these alternate conformations by default leaving users oblivious to the presence of alternate conformations in the structures they analyze. This has led to underappreciation of their prevalence, under characterisation of their features and limited the accessibility to this high-resolution data representing structural ensembles. We have trawled PDB files to extract structural features of residues with alternately located atoms. The output includes the distance between alternate conformations and identifies the location of these segments within the protein chain and in proximity of all other atoms within a defined radius. This dataset should be of use in efforts to predict multiple structures from a single sequence and support studies investigating protein flexibility and the association with protein function.

Subsurface Single‐atom Catalyst Enabled by Mechanochemical Synthesis for Oxidation Chemistry

Single‐atom catalysts have garnered significant attention due to their exceptional atom utilization and unique properties. However, the practical application of these catalysts is often impeded by challenges such as sintering‐induced instability and poisoning of isolated atoms due to strong gas adsorption. In this study, we employed the mechanochemical method to insert single Cu atoms into the subsurface of Fe2O3 support. By manipulating the location of single atoms at the surface or subsurface, catalysts with distinct adsorption properties and reaction mechanisms can be achieved. It was observed that the subsurface Cu single atoms in Fe2O3 remained isolated under both oxidation and reduction environments, whereas surface Cu single atoms on Fe2O3 experienced sintering under reduction conditions. The unique properties of these subsurface single‐atom catalysts call for innovations and new understandings in catalyst design.

Subsurface Single-Atom Catalyst Enabled by Mechanochemical Synthesis for Oxidation Chemistry.

Single-atom catalysts have garnered significant attention due to their exceptional atom utilization and unique properties. However, the practical application of these catalysts is often impeded by challenges such as sintering-induced instability and poisoning of isolated atoms due to strong gas adsorption. In this study, we employed the mechanochemical method to insert single Cu atoms into the subsurface of Fe2O3 support. By manipulating the location of single atoms at the surface or subsurface, catalysts with distinct adsorption properties and reaction mechanisms can be achieved. It was observed that the subsurface Cu single atoms in Fe2O3 remained isolated under both oxidation and reduction environments, whereas surface Cu single atoms on Fe2O3 experienced sintering under reduction conditions. The unique properties of these subsurface single-atom catalysts call for innovations and new understandings in catalyst design.

Compressing generalized trajectories of molecular motion for efficient detection of chemical interactions

Molecular Dynamics (MD) simulation is often used to study properties of various chemical interactions in domains such as drug discovery and development, particularly when executing real experimental studies is costly and/or unsafe. Studying the motion of trajectories of molecules/atoms generated from MD simulations provides a detailed atomic level spatial location of every atom for every time frame in the experiment. The analysis of this data leads to an atomic and molecular level understanding of interactions among the constituents of the system of interest. However, the data is extremely large and poses storage and processing challenges in the querying and analysis of associated atom level motion trajectories. We take a first step towards applying domain-specific generalization techniques for the data representation, subsequently used for applying trajectory compression algorithms towards reducing the storage requirements and speeding up the processing of within-distance queries over MD simulation data. We demonstrate that this generalization-aware compression, when applied to the dataset used in this case study, yields significant improvements in terms of data reduction and processing time without sacrificing the effectiveness of within-distance queries for threshold-based detection of molecular events of interest, such as the formation of Hydrogen Bonds (H-Bonds).

A modified phase-retrieval algorithm to facilitate automatic de novo macromolecular structure determination in single-wavelength anomalous diffraction.

The success of experimental phasing in macromolecular crystallography relies primarily on the accurate locations of heavy atoms bound to the target crystal. To improve the process of substructure determination, a modified phase-retrieval algorithm built on the framework of the relaxed alternating averaged reflection (RAAR) algorithm has been developed. Importantly, the proposed algorithm features a combination of the π-half phase perturbation for weak reflections and enforces the direct-method-based tangent formula for strong reflections in reciprocal space. The proposed algorithm is extensively demonstrated on a total of 100 single-wavelength anomalous diffraction (SAD) experimental datasets, comprising both protein and nucleic acid structures of different qualities. Compared with the standard RAAR algorithm, the modified phase-retrieval algorithm exhibits significantly improved effectiveness and accuracy in SAD substructure determination, highlighting the importance of additional constraints for algorithmic performance. Furthermore, the proposed algorithm can be performed without human intervention under most conditions owing to the self-adaptive property of the input parameters, thus making it convenient to be integrated into the structural determination pipeline. In conjunction with the IPCAS software suite, we demonstrated experimentally that automatic de novo structure determination is possible on the basis of our proposed algorithm.

DFT Atomic‐Scale Insight into Pt/Cu Single Atom Alloy Clusters Supported on γ‐Al2O3: The Effect of Hydrogen Environment

Single atom alloy (SAA) clusters formed by anchoring single atoms in small supported host clusters are emerging as catalysts with high performance. In this work, density functional theory (DFT) calculations and ab‐initio molecular dynamics (AIMD) simulations are performed to study the stability and the structure evolution of γ‐alumina‐supported platinum/copper SAA clusters of sub‐nanometer size in hydrogen environment. Due to the strong dynamic nature of both Cu cluster and anchored Pt single atom and their evolving interaction with the support, different isomers with different geometric and energetic properties are predicted. Extensive sampling through AIMD simulations reveals strong effect of hydrogen on the location of Pt single atom and strong variation of the cluster shape, evolving from 3D to concave and planar shapes wetting the alumina support. Interfacial site location of Pt single atom is found to be hydrogen coverage dependent. When the hydrogen coverage increases, the Pt single atom located preferentially at the interfacial site is pulled up by hydrogen atoms toward the upper surface Cu layers. The interaction of Pt/Cu cluster with alumina is predicted to decrease with increasing hydrogen coverage. Finally, electronic structure analysis reveals dramatic effect of hydrogen on the metallic nature of the catalysts.

High-precision two- and three- dimensional atom localization in a microwave and radio-frequency driven Δ∇ system

We introduce a new approach for precise and high-resolution two-dimensional (2D) and three-dimensional (3D) atom localization in a four-level Δ∇ atomic system driven by microwave (M) and radio frequency (R) fields. In the proposed work, additional microwave and radio-frequency fields are utilized for an efficient control of the localization precision. Due to the spatially varying atom-field interaction, the probe susceptibility become position dependent and therefore, one can directly ascertain the position probability distribution of an atom by analyzing the probe spectra. The phase-sensitive property of the atomic system plays a significant role in substantially reducing the uncertainty associated with atom position measurements. We have studied the system behavior through the analysis of dressed states, which forms the basis for its physical interpretation. The increase in precision for measuring the atom’s position is a result of interference between one-photon excitation and the phase-dependent three-photon excitation arising from the closed interacting contour within the laser-driven atomic system, as demonstrated through both numerical calculations and qualitative analyses. The findings indicate that precise sub-wavelength atom localization can be attained by appropriately adjusting the system parameters. Also, the optimal adjustment of these parameters can lead to 100% probability of locating the atom at a particular position within 2D and 3D subspaces.

Steric interaction of iridium sites towards efficient oxygen and hydrogen evolution

Transition metal materials that loaded with trace of Iridium (Ir) are widely accepted as effective catalysts for oxygen evolution (OER) and hydrogen evolution reaction (HER), in which the Ir atoms exposed on the surface can directly affect the electrocatalytic reaction. However, this neglects the Ir – Ir interaction of distinct locations, which may be benefit for the fine-tuning of electronic structure. Herein, we changed the locations (surface and inside) of Ir atoms in the cobalt oxide (Co3O4@NC), and investigated their alkaline OER and HER performances. Combined with X-ray photoelectron spectroscopy (XPS), X-ray absorption spectroscopy (XAS) and theoretical calculations, we infer that the steric interaction induced by the surface – internal Ir sites can weaken the Ir-O bond and optimize the adsorption of intermediates on catalyst surface with a negative shift of d-band center, enabling the surface-Ir sites with lower energy barrier for water dissociation and hydrogen adsorption for HER. Therefore, the as-prepared Irw-Co3O4@NC with surface − inside Ir distribution significantly improve the HER without degrading OER performance, with low overpotential of −173 / −71 mV for HER at −10 mA/cm2 in 0.1 M KOH / 1.0 M KOH, and 244 / 249 mV at 10 mA/cm2 for OER.