Atomic Interactions Research Articles

Monte Carlo Simulations of the Interaction of 55Mn with 14.7-MeV Protons Produced by D+3He Fusion Reaction

The global energy crisis and climate change pose significant challenges for the future of humankind. To address these issues, clean energy sources are being promoted, with nuclear energy being an effective solution. The development of fission reactors and the promising advancements in fusion reactor technology provide potential solutions. However, challenges related to security and costs remain. This study focuses on the interaction between 55Mn and protons at 14.7 MeV using Monte Carlo simulations. Various Monte Carlo codes, including TALYS-1.96, GEANT4 (for GEometry ANd Tracking), PHITS-3.31 (for Particle and Heavy Ion Transport Code System), SRIM-2013 (for Stopping and Range of Ions in Matter), and ATIMA v1 41 (for ATomic Interaction with MAtter), were employed to investigate different interaction mechanisms. The research aims to understand the impact of these interactions on reactor performance, particularly in the context of the fusion facility. Manganese-containing steels play a crucial role in enhancing efficiency, durability, and safety in fusion reactors. The findings contribute to ongoing research and development activities in the field of nuclear energy.

Superfluid excitations in rotating two-dimensional ring traps

We studied a rotating Bose–Einstein condensate confined in ring trap configurations that can be produced starting with a bubble trap confinement, approximated by a Mexican hat and shift harmonic oscillator potentials. Using a variational technique and perturbation theory, we determined the vortex configurations in this system by varying the interparticle interaction and the angular velocity of the atomic cloud. We found that the phase diagram of the system has macrovortex structures for small positive values of the interaction parameter, and the charge of the central vortex increases with rotation. Strengthening the atomic interaction makes the macrovortex unstable, and it decays into multiple singly charged vortices that arrange themselves in a lattice configuration. We also look for experimentally realizable methods to determine the vortex configuration without relying upon absorption imaging since the structures are not always visible in the latter. More specifically, we study how the vortex distribution affects the collective modes of the condensate by solving the Gross–Pitaevskii equation numerically and by analytical predictions using the sum-rule approach for the frequencies of the modes. These results reveal important signatures to characterize the macrovortices and vortex lattice transitions in the experiments.

Fast simulation for interacting four-level Rydberg atoms: electromagnetically induced transparency and Autler-Townes splitting

Quantum sensing using Rydberg atoms is an emerging technology for precise measurement of electric fields. However, most existing computational methods are all based on a single-particle model and neglect Rydberg-Rydberg interaction between atoms. In this study, we introduce the interaction term into the conventional four-level optical Bloch equations. By incorporating fast iterations and solving for the steady-state solution efficiently, we avoid the computation of a massive 4 N × 4 N dimensional matrix. Additionally, we apply the Doppler frequency shift to each atom used in the calculation, eliminating the requirement for an additional Doppler iteration. These schemes allow for the calculation of the interaction between 7000 atoms around one minute. Based on the many-body model, we investigate the Rydberg-Rydberg interaction of Rydberg atoms under different atomic densities. Furthermore, we compare our results with the literature data of a three-level system and the experimental results of our own four-level system. The results demonstrate the validity of our model, with an effective error of 4.59% compared to the experimental data. Finally, we discover that the many-body model better predicts the linear range for measuring electric fields than the single-particle model, making it highly applicable in precise electric field measurements.

Rydberg Platform for Nonergodic Chiral Quantum Dynamics.

We propose a mechanism for engineering chiral interactions in Rydberg atoms via a directional antiblockade condition, where an atom can change its state only if an atom to its right (or left) is excited. The scalability of our scheme enables us to explore the many-body dynamics of kinetically constrained models with unidirectional character. We observe nonergodic behavior via either scars, confinement, or localization, upon simply tuning the strength of two driving fields acting on the atoms. We discuss how our mechanism persists in the presence of classical noise and how the degree of chirality in the interactions can be tuned, opening towards the frontier of directional, strongly correlated, quantum mechanics using neutral atoms arrays.

Work hardening in colloidal crystals

Colloidal crystals exhibit interesting properties1–4 that are in many ways analogous to their atomic counterparts. They have the same crystal structures2,5–7, undergo the same phase transitions8–10, and possess the same crystallographic defects11–14. In contrast to these structural properties, the mechanical properties of colloidal crystals are quite different from those of atomic systems. For example, unlike in atomic systems, the elasticity of hard-sphere colloidal crystals is purely entropic15; as a result, they are so soft that they can be melted just by stirring16,17. Moreover, crystalline materials deform plastically when subjected to increasing shear and become stronger because of the ubiquitous process of work hardening18; but this has so far never been observed in colloidal crystals, to our knowledge. Here we show that hard-sphere colloidal crystals exhibit work hardening. Moreover, despite their softness, the shear strength of colloidal crystals can increase and approach the theoretical limit for crystals, a value reached in very few other materials so far. We use confocal microscopy to show that the strength of colloidal crystals increases with dislocation density, and ultimately reaches the classic Taylor scaling behaviour for atomic materials19–21, although hard-sphere interactions lack the complexity of atomic interactions. We demonstrate that Taylor hardening arises through the formation of dislocation junctions22. The Taylor hardening regime, however, is established only after a transient phase, and it ceases when the colloidal crystals become so hard that the strain is localized within a thin boundary layer in which slip results from an unconventional motion of dislocations. The striking resemblance between colloidal and atomic crystals, despite the many orders of magnitude difference in particle size and shear modulus, demonstrates the universality of work hardening.

Direct Fabrication of Atomically Defined Pores in MXenes Using Feedback-Driven STEM.

Controlled fabrication of nanopores in 2D materials offer the means to create robust membranes needed for ion transport and nanofiltration. Techniques for creating nanopores have relied upon either plasma etching or direct irradiation; however, aberration-corrected scanning transmission electron microscopy (STEM) offers the advantage of combining a sub-Å sized electron beam for atomic manipulation along with atomic resolution imaging. Here, a method for automated nanopore fabrication is utilized with real-time atomic visualization to enhance the mechanistic understanding of beam-induced transformations. Additionally, an electron beam simulation technique, Electron-Beam Simulator (E-BeamSim) is developed to observe the atomic movements and interactions resulting from electron beam irradiation. Using the MXene Ti3C2Tx, the influence of temperature on nanopore fabrication is explored by tracking atomic transformations and find that at room temperature the electron beam irradiation induces random displacement and results in titanium pileups at the nanopore edge, which is confirmed by E-BeamSim. At elevated temperatures, after removal of the surface functional groups and with the increased mobility of atoms results in atomic transformations that lead to the selective removal of atoms layer by layer. This work can lead to the development of defect engineering techniques within functionalized MXene layers and other 2D materials.

Imidazole[1,5-a]pyridine derivatives as EGFR tyrosine kinase inhibitors unraveled by umbrella sampling and steered molecular dynamics simulations

Although the use of the tyrosine kinase inhibitors (TKIs) has been proved that it can save live in a cancer treatment, the currently used drugs bring in many undesirable side-effects. Therefore, the search for new drugs and an evaluation of their efficiency are intensively carried out. Recently, a series of eighteen imidazole[1,5-a]pyridine derivatives were synthetized by us, and preliminary analyses pointed out their potential to be an important platform for pharmaceutical development owing to their promising actions as anticancer agents and enzyme (kinase, HIV-protease,…) inhibitors. In the present theoretical study, we further analyzed their efficiency in using a realistic scenario of computational drug design. Our protocol has been developed to not only observe the atomistic interaction between the EGFR protein and our 18 novel compounds using both umbrella sampling and steered molecular dynamics simulations, but also determine their absolute binding free energies. Calculated properties of the 18 novel compounds were in detail compared with those of two known drugs, erlotinib and osimertinib, currently used in cancer treatment. Inspiringly the simulation results promote three imidazole[1,5-a]pyridine derivatives as promising inhibitors into a further step of clinical trials.

First-principles investigation of Cu/Ti-TM/Si (TM=W, Ru) interfaces: Role of Ti-TM binary alloys as diffusion barrier layers

This study employs first-principles calculations to investigate the role of Ti-TM (TM=W, Ru) binary alloys as diffusion barrier layers in Cu/Ti-TM/Si interfaces, which are critical for enhancing the performance and reliability of microelectronic devices. The calculated results reveal that TiRu and Ti4W12 alloys exhibit exceptional stability and low contact resistance, outperforming traditional Cu/Si interfaces. The introduction of these alloys into the interface structure results in a reduced Cu s-d coupling effect, which is pivotal for inhibiting Cu diffusion. Additionally, the presence of pseudogap features and enhanced electron distribution at the interface indicate strong atomic interactions, contributing to the formation of covalent bonds and further improving barrier properties. The findings suggest that TiRu and Ti4W12 alloys are promising candidates for diffusion barrier layers, offering a balance of low contact resistance, thermal stability, and effective Cu diffusion inhibition. Therefore, from the results, it is concluded that the formation of the new interface structure will improve performance in various aspects, and thus the strategy can be applied in various directions, such as new energy materials, electronic materials, and so on. In addition, the combination of the previous work and the present work suggests that Ti-based alloys have the potential to be used as diffusion barrier materials.

Characterization of Z cluster connectivity in CuZr metallic glasses.

Previous studies have proposed that the backbone of metallic glasses consists mainly of high-centrosymmetric structures, particularly Z clusters, which are responsible for the strength of the glass matrix. However, exploring these networks involves medium-range order analysis, a topic still not fully understood in the literature. This study investigates the atomic connectivity of CuZr metallic glasses by analyzing Z clusters using complex networks to establish their relationship with the mechanical behavior. Our results reveal higher connectivity and larger network sizes in the sample exhibiting the most pronounced stress overshoot, while the opposite trend is observed in samples with less pronounced stress overshoot. Metrics, such as density and clustering coefficient, further validate the correlation between Z cluster connectivity and mechanical behavior. These findings underscore the critical role of Z cluster connectivity in understanding the mechanical response of metallic glasses. Molecular dynamics simulations were conducted using the LAMMPS software. Atomic interactions in Cu Zr metallic glasses were modeled using the embedded atom method, and compression tests were performed to assess the mechanical response. Atomic connectivity was examined through complex network analysis based on Z clusters, utilizing the NetworkX library for the Python programming language. Within this framework, parameters such as the average coordination number, network size, and network density were calculated, revealing the relationship between the interpenetrating Z cluster structure and the mechanical response of the samples.

CytoSIP: an annotated structural atlas for interactions involving cytokines or cytokine receptors

Therapeutic agents targeting cytokine-cytokine receptor (CK-CKR) interactions lead to the disruption in cellular signaling and are effective in treating many diseases including tumors. However, a lack of universal and quick access to annotated structural surface regions on CK/CKR has limited the progress of a structure-driven approach in developing targeted macromolecular drugs and precision medicine therapeutics. Herein we develop CytoSIP (Single nucleotide polymorphisms (SNPs), Interface, and Phenotype), a rich internet application based on a database of atomic interactions around hotspots in experimentally determined CK/CKR structural complexes. CytoSIP contains: (1) SNPs on CK/CKR; (2) interactions involving CK/CKR domains, including CK/CKR interfaces, oligomeric interfaces, epitopes, or other drug targeting surfaces; and (3) diseases and phenotypes associated with CK/CKR or SNPs. The database framework introduces a unique tri-level SIP data model to bridge genetic variants (atomic level) to disease phenotypes (organism level) using protein structure (complexes) as an underlying framework (molecule level). Customized screening tools are implemented to retrieve relevant CK/CKR subset, which reduces the time and resources needed to interrogate large datasets involving CK/CKR surface hotspots and associated pathologies. CytoSIP portal is publicly accessible at https://CytoSIP.biocloud.top, facilitating the panoramic investigation of the context-dependent crosstalk between CK/CKR and the development of targeted therapeutic agents.

Calculating structure factors of protein solutions by atomistic modeling of protein-protein interactions

We present a method, FMAPS(q), for calculating the structure factor, S(q), of a protein solution, by extending our fast Fourier transform-based modeling of atomistic protein-protein interactions (FMAP) approach. The interaction energy consists of steric, nonpolar attractive, and electrostatic terms that are additive among all pairs of atoms between two protein molecules. In the present version, we invoke the free-rotation approximation, such that the structure factor is given by the Fourier transform of the protein center-center distribution function gC(R). At low protein concentrations, gC(R) can be approximated as e−βW(R), where W(R) is the potential of mean force along the center-center distance R. We calculate W(R) using FMAPB2, a member of the FMAP class of methods that is specialized for the second virial coefficient [Qin and Zhou, J Phys Chem B 123 (2019) 8203–8215]. For higher protein concentrations, we obtain S(q) by a modified random-phase approximation, which is a perturbation around the steric-only energy function. Without adjusting any parameters, the calculated structure factors for lysozyme and bovine serum albumin at various ionic strengths, temperatures, and protein concentrations are all in reasonable agreement with those measured by small-angle X-ray or neutron scattering. This initial success motivates further developments, including removing approximations and parameterizing the interaction energy function.

Effects of classical drivings on the power broadening of atomic lineshapes

In the framework of the Jaynes–Cummings model, we investigate how atomic lineshapes are affected by coherently driving the atom–field interaction. We pay particular attention to the two-level atom interaction with a thermal cavity field when both are influenced by external classical fields. Adopting a density matrix formalism, we calculate the average atomic inversion and demonstrate how the corresponding lineshapes vary as a function of the average number of thermal photons and the atom–field classical coupling. Furthermore, we compare these results with those obtained from the standard Jaynes–Cummings model and validate our findings through numerical calculations.

Bifunctional Pt dual atoms for overall water splitting

While dual-atom catalysts benefiting from synergetic interatomic interactions have inspired the development of emerging catalysts, the role of atomic interactions on the catalytic selectivity and activity has yet to be clearly discovered. Herein, two-types of Pt dual-atom active sites, Pt dimers (2Pt) with an interatomic distance of 2.6 Å and Pt pairs (Pt2) at a distance of 0.9 Å, are fabricated by anchoring onto cationic vacancy-rich nickel-based hydroxide (Pt@NiFeCo-E). It reveals that 2Pt sites are favorable for hydrogen evolution reaction (HER) while Pt2 sites are active towards oxygen evolution reaction (OER). The coexistence of two types of Pt dual atoms endows the bifunctional activity, which reached an overpotential of 14 mV@10 mA cm−2 for HER, an overpotential of 234 mV@100 mA cm−2 for OER, and an effective overall water splitting reaction (OWS) in alkaline at an overpotential of 1.42 V to reach 10 mA cm−2 and at 100 mA cm−2 for 50 h. This work not only clarifies a new mechanism in manipulating the selectivity of dual-atom catalysts via controlling the interatomic distance, but also paves a pathway for designing novel high-efficient bifunctional catalysts.

Energy spectrum and superfluidity breakdown of Bose–Einstein condensates in optical lattice under density-dependent artificial gauge field

Nonlinear feedback between the gauge field and the material field can yield novel quantum phenomena. Here, the interplay between a density-dependent artificial gauge field and Bose–Einstein condensates (BECs) trapped in an optical lattice is studied. The energy spectrum and superfluidity represented by energetic and dynamical stabilities of the system are systematically discussed. A density-dependent artificial gauge field with a back-action between the BECs dynamics and the gauge field induces an effective atomic interaction that depends on the quasi-momentum and density of the condensates, resulting in a symmetry-broken energy spectrum and exotic stability phase diagram, that is, the system is only stable in a certain range of atoms density and under a limited lattice strength. The density-dependent artificial gauge field changes the sequence for the emergence of energetic and dynamical instability and the regimes of the energetic and dynamical instabilities are significantly separated, offering an efficient way to examine the energetic and dynamical instabilities of superfluids separately. In particular, the density-dependent artificial gauge field, as a mechanism for transferring momentum to the fluid, results in dynamic instability of the condensates even in free space. Our results provide deep insights into the dynamical response of superfluid systems to gauge fields and have potential applications for the coherent control of exotic superfluid states.

Quantum entropic exchange at avoided crossings due to laser–atom interaction

In the present study, we detail the entropic characteristics of a dressed atom, wherein the atom undergoes an interaction with a monochromatic laser beam. Our investigation of the laser–atom interplay employs a well-established non-perturbative quasi-energy methodology, allowing us to discern the dressed wavefunctions and quasi-energies of the laser-dressed atom. Utilizing these dressed wavefunctions as a foundation, we systematically examine various entropic measures, observing their behaviour for laser frequency and intensity. The selection of levels within the system adheres to the criteria dictated by the selection rules governing transitions between these levels. Our exploration focuses on the interplay between Shannon entropy and other entropic metrics, with their fluctuations intricately tied to the phenomenon of avoided crossings. As the laser amplitude intensifies, the AC Stark effect takes centre stage, exerting influence over the sharp or smooth variations in Shannon entropy at these avoided crossings. Furthermore, we delineate the correlation between the number of levels considered and the identification of avoided crossings. Our present analysis sheds light on the intricate dynamics in the dressed atom system, enhancing our understanding of the interplay between laser-induced dressing and entropic measures.

Influence of Ti Vacancy Defects on the Dissolution of O-Adsorbed Ti(0001) Surface: A First-Principles Study

To investigate the dissolution mechanism of Ti metal, ab initio calculations were conducted to observe the impact of Ti vacancy defects on the O-adsorbed Ti(0001) surface, focusing on the formation energies of Ti vacancy, geometric structures, and electronic structures. The surface structures subsequent to Ti dissolution were simulated by introducing a Ti cavity on both clean and O-adsorbed Ti(0001) surfaces. Our findings indicated that Ti vacancy formation energies and electrochemical dissolution potential on the O-adsorbed Ti(0001) surface surpassed those on the clean surface, and they increased with increasing O coverage. This suggested that O adsorption inhibited Ti dissolution and enhanced O atom interaction with the Ti surface as O coverage increased. Furthermore, at higher O coverage, Ti vacancies contributed to the strengthening of Ti-O bonds on the O-adsorbed Ti(0001) surface, indicating that Ti dissolution aided in stabilizing the Ti surface. The formation of Ti vacancies brought the atomic ratio of Ti to O on the Ti surface closer to that of TiO2, potentially explaining the increased stability of the structure with Ti vacancies.

Anti-Jaynes–Cummings interaction of a two-level atom with squeezed light: photon statistics, atomic population inversion and entropy of entanglement

Anti-Jaynes–Cummings interaction of a two-level atom with squeezed light: photon statistics, atomic population inversion and entropy of entanglement

Crystallography applications: A comprehensive review

Crystallography is an essential scientific technique profoundly influencing our understanding of atomic and molecular structures in materials, providing insights into the arrangement and interactions of atoms. This review highlights crystallographys extensive applications across chemistry, biology, physics, and materials science, emphasizing its critical role and adaptability. The paper traces crystallographys historical development, outlines its fundamental principles, and celebrates its significant milestones and contributions to science. By revealing the complex structures and functions of compounds, from simple molecules to complex macromolecules, crystallography has catalyzed advancements in drug development, material innovation, and fundamental scientific understanding. The paper asserts crystallographys continued prominence in scientific research, with its application and influence steadily growing. Its pivotal in enhancing our understanding of matter, driving technological and material advancements, and offering solutions to complex scientific questions. Moreover, the review addresses the current challenges and future directions of crystallography, pointing out potential areas for innovation and improvement. As technology advances, crystallographys significance in various scientific disciplines remains indispensable, solidifying its position as a cornerstone of scientific inquiry and discovery. The paper concludes by reinforcing the techniques vital role in pushing the boundaries of science and technology.

Selective Gold Precipitation by a Tertiary Diamide Driven by Thermodynamic Control.

The simple diamide ligand L was previously shown to selectively precipitate gold from acidic solutions typical of e-waste leach streams, with precipitation of gallium, iron, tin, and platinum possible under more forcing conditions. Herein, we report direct competition experiments to afford the order of selectivity. Thermal analysis indicates that the gold-, gallium-, and iron-containing precipitates present as the most thermodynamically stable structures at room temperature, while the tin-containing structure does not. Computational modeling established that the precipitation process is thermodynamically driven, with ion exchange calculations matching the observed experimental selectivity ordering. Calculations also show that the stretched ligand conformation seen in the X-ray crystal structure of the gold-containing precipitate is more strained than in the structures of the other metal precipitates, indicating that intermolecular interactions likely dictate the selectivity ordering. This was confirmed through a combination of Hirshfeld, noncovalent interaction (NCI), and quantum theory of atoms in molecules (QTAIM) analyses, which highlight favorable halogen···halogen contacts between metalates and pseudo-anagostic C-H···metal interactions in the crystal structure of the gold-containing precipitate.

Evaluating polyester resin as a viable substitute for PMMA in computed tomography dosimetry phantoms

The current study aimed to evaluate the suitability of polyester resin as an alternative material to polymethyl methacrylate (PMMA) for computed tomography (CT) dosimetry phantoms using the GEANT4/GATE Monte Carlo simulation platform. Cylindrical phantoms (32 cm diameter) constructed of polyester resin and PMMA were simulated and compared in terms of atomic composition, effective atomic number, electron density, mass density, and photon interaction mechanisms. Weighted CT dose index (CTDIw) values were calculated for each phantom at 80, 110, and 130 kVp tube voltages based on measurements of CTDI100,c and CTDI100,p. Results demonstrated that the physical properties of polyester closely matched those of PMMA, and the polyester phantom displayed equivalent dosimetric behavior to the PMMA phantom at all tube voltages tested. CTDIw values from the polyester phantom were within 1.4 % of the PMMA phantom across all tube voltages. Conversion coefficients were derived to equate polyester CTDIw values to PMMA dose equivalents. This study found that a polyester resin phantom exhibited radiation dosimetry commensurate with the standard PMMA phantom for CT dose assessment. Consequently, polyester resin represents a viable substitute material when PMMA is unavailable for construction of CT dosimetry phantoms.