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The diffusion of proteins is significantly affected by macromolecular crowding. Molecular simulations accounting for protein interactions at atomic resolution are useful for characterizing the diffusion patterns in crowded environments. We present a comprehensive analysis of protein diffusion under different crowding conditions based on our recent docking-based approach simulating an intracellular crowded environment by sampling the intermolecular energy landscape using the Markov Chain Monte Carlo protocol. The procedure was extensively benchmarked, and the results are in very good agreement with the available experimental and theoretical data. The translational and rotational diffusion rates were determined for different types of proteins under crowding conditions in a broad range of concentrations. A protein system representing most abundant protein types in the E. coli cytoplasm was simulated, as well as large systems of other proteins of varying sizes in heterogeneous and self-crowding solutions. Dynamics of individual proteins was analyzed as a function of concentration and different diffusion rates in homogeneous and heterogeneous crowding. Smaller proteins diffused faster in heterogeneous crowding of larger molecules, compared to their diffusion in the self-crowded solution. Larger proteins displayed the opposite behavior, diffusing faster in the self-crowded solution. The results show the predictive power of our structure-based simulation approach for long timescales of cell-size systems at atomic resolution. [ABSTRACT FROM AUTHOR]

We describe a method to compute photon–matter interaction and atomic dynamics with x-ray lasers using a hybrid code based on classical molecular dynamics and collisional-radiative calculations. The forces between the atoms are dynamically determined based on changes to their electronic occupations and the formation of a free electron cloud created from the irradiation of photons in the x-ray spectrum. The rapid transition from neutral solid matter to dense plasma phase allows the use of screened potentials, reducing the number of non-bonded interactions. In combination with parallelization through domain decomposition, the hybrid code handles large-scale molecular dynamics and ionization. This method is applicable for large enough samples (solids, liquids, proteins, viruses, atomic clusters, and crystals) that, when exposed to an x-ray laser pulse, turn into a plasma in the first few femtoseconds of the interaction. We present four examples demonstrating the applicability of the method. We investigate the non-thermal heating and scattering of bulk water and damage-induced dynamics of a protein crystal using an x-ray pump–probe scheme. In both cases, we compare to the experimental data. For single particle imaging, we simulate the ultrafast dynamics of a methane cluster exposed to a femtosecond x-ray laser. In the context of coherent diffractive imaging, we study the fragmentation as given by an x-ray pump–probe setup to understand the evolution of radiation damage in the time range of hundreds of femtoseconds. [ABSTRACT FROM AUTHOR]

As the most important solvent, water has been at the center of interest since the advent of computer simulations. While early molecular dynamics and Monte Carlo simulations had to make use of simple model potentials to describe the atomic interactions, accurate ab initio molecular dynamics simulations relying on the first-principles calculation of the energies and forces have opened the way to predictive simulations of aqueous systems. Still, these simulations are very demanding, which prevents the study of complex systems and their properties. Modern machine learning potentials (MLPs) have now reached a mature state, allowing us to overcome these limitations by combining the high accuracy of electronic structure calculations with the efficiency of empirical force fields. In this Perspective, we give a concise overview about the progress made in the simulation of water and aqueous systems employing MLPs, starting from early work on free molecules and clusters via bulk liquid water to electrolyte solutions and solid–liquid interfaces. [ABSTRACT FROM AUTHOR]

The quantum Drude oscillator (QDO) model has been widely used as an efficient surrogate to describe the electric response properties of matter as well as long-range interactions in molecules and materials. Most commonly, QDOs are coupled within the dipole approximation so that the Hamiltonian can be exactly diagonalized, which forms the basis for the many-body dispersion method [Phys. Rev. Lett. 108, 236402 (2012)]. The dipole coupling is efficient and allows us to study non-covalent many-body effects in systems with thousands of atoms. However, there are two limitations: (i) the need to regularize the interaction at short distances with empirical damping functions and (ii) the lack of multipolar effects in the coupling potential. In this work, we convincingly address both limitations of the dipole-coupled QDO model by presenting a numerically exact solution of the Coulomb-coupled QDO model by means of quantum Monte Carlo methods. We calculate the potential-energy surfaces of homogeneous QDO dimers, analyzing their properties as a function of the three tunable parameters: frequency, reduced mass, and charge. We study the coupled-QDO model behavior at short distances and show how to parameterize this model to enable an effective description of chemical bonds, such as the covalent bond in the H2 molecule. [ABSTRACT FROM AUTHOR]

In this work, we propose a linear machine learning force matching approach that can directly extract pair atomic interactions from ab initio calculations in amorphous structures. The local feature representation is specifically chosen to make the linear weights a force field as a force/potential function of the atom pair distance. Consequently, this set of functions is the closest representation of the ab initio forces, given the two-body approximation and finite scanning in the configurational space. We validate this approach in amorphous silica. Potentials in the new force field (consisting of tabulated Si–Si, Si–O, and O–O potentials) are significantly different than existing potentials that are commonly used for silica, even though all of them produce the tetrahedral network structure and roughly similar glass properties. This suggests that the commonly used classical force fields do not offer fundamentally accurate representations of the atomic interaction in silica. The new force field furthermore produces a lower glass transition temperature (Tg ∼ 1800 K) and a positive liquid thermal expansion coefficient, suggesting the extraordinarily high Tg and negative liquid thermal expansion of simulated silica could be artifacts of previously developed classical potentials. Overall, the proposed approach provides a fundamental yet intuitive way to evaluate two-body potentials against ab initio calculations, thereby offering an efficient way to guide the development of classical force fields. [ABSTRACT FROM AUTHOR]

Biomedical network learning offers fresh prospects for expediting drug repositioning. However, traditional network architectures struggle to quantify the relationship between micro-scale drug spatial structures and corresponding macro-scale biomedical networks, limiting their ability to capture key pharmacological properties and complex biomedical information crucial for drug screening and therapeutic discovery. Moreover, challenges such as difficulty in capturing long-range dependencies hinder current network-based approaches. To address these limitations, we introduce the Spatial Hierarchical Network, modeling molecular 3D structures and biological associations into a unified network. We propose an end-to-end framework, SpHN-VDA, integrating spatial hierarchical information through triple attention mechanisms to enhance machine understanding of molecular functionality and improve the accuracy of virus-drug association identification. SpHN-VDA outperforms leading models across three datasets, particularly excelling in out-of-distribution and cold-start scenarios. It also exhibits enhanced robustness against data perturbation, ranging from 20% to 40%. It accurately identifies critical motifs for binding sites, even without protein residue annotations. Leveraging reliability of SpHN-VDA, we have identified 25 potential candidate drugs through gene expression analysis and CMap. Molecular docking experiments with the SARS-CoV-2 spike protein further corroborate the predictions. This research highlights the broad potential of SpHN-VDA to enhance drug repositioning and identify effective treatments for various diseases. The Spatial Hierarchical Network model enhances drug repositioning by quantifying and integrating 3D spatial network with biomedical network information and offers interpretations from biological relationships down to atomic interactions. [ABSTRACT FROM AUTHOR]

Decreased presence or activity of human SLC26A4 at the plasma membrane is a common cause of hearing loss. SLC26A4 (Pendrin) is necessary for normal reabsorption of endolymph, the fluid bathing the inner ear. We identified the μ2 subunit of adaptor protein 2 (AP-2) complex required for clathrin-mediated endocytosis as a protein-partner of SLC26A4 involved in regulating its plasma membrane abundance. We showed that, in the endolymphatic sac, where fluid reabsorption occurs, SLC26A4 is localized along the apical microvilli of mitochondria-rich cells, in contact with the endolymph, and associated with clathrin-coated pits where μ2 and AP-2 are present. Based on SLC26A4 structure, the elements involved in SLC26A4-μ2 interaction were identified and validated experimentally, allowing modeling of this interaction at the atomic level. Pharmacological inhibition of clathrin-mediated endocytosis led to an increased plasma membrane abundance of hemagglutinin-tagged SLC26A4 virally or endogenously expressed in mitochondria-rich cells. These results indicate that the SLC26A4-μ2 interaction regulates SLC26A4 abundance at the apical surface of mitochondria-rich cells. [ABSTRACT FROM AUTHOR]

Quantitatively probing the ultimate limit of near-field enhancement around plasmonic nanostructures remains elusive, despite more than five decades since the discovery of surface-enhanced Raman scattering. Theoretical calculations have predicted an ultimate near-field enhancement exceeding 1000 using the best plasmonic material silver, but experimental estimations disperse by orders of magnitude. Here, we design a high-quality silver plasmonic nanocavity with atomic precision and precisely quantify the upper limit of near-field enhancement in ~1 nm junctions. A hot-spot averaged Raman enhancement of 4.27 × 1010 is recorded with a small fluctuation, corresponding to an averaged electric field enhancement larger than 1000 times. This result quantitatively delineates the ultimate limit of plasmonic field enhancement around plasmonic nanostructures, establishing a foundation for diverse plasmon-enhanced processes and strong light-matter interactions at the atomic scale. The authors develop a quantitative probe for plasmonic near-field enhancement in a ~ 1 nm gap based on a MoS2-spaced silver nanocube-on-mirror nanocavity. They derive an enhancement factor of ~1644, representing an upper limit for local near-field plasmonic enhancement in the visible/near-infrared. [ABSTRACT FROM AUTHOR]

X-ray spectra are pivotal for understanding chemical bonding and atomic interactions in materials. Particularly, valence-to-core (VtC) electronic transitions and satellite peaks within X-ray spectra provide insights into valence states and chemical environments. This study focuses on the multi-vacancy satellite peaks, Si KβIII and KβIV, and their application in analyzing silicate minerals in igneous rocks. A wavelength dispersive X-ray fluorescence (WD-XRF) spectrometer, commonly employed for chemical analysis of geological samples, was utilized in this study. The Si KβIII and KβIV peaks were selected due to their VtC transitions and multi-vacancy origin, offering enhanced sensitivity to the chemical environment. We examined 41 certified reference materials (CRMs) of igneous rocks, demonstrating the capaβility of these satellite peaks to reveal detailed chemical and structural information. A strong correlation was found βetween the chemical composition of silicate minerals and the intensities along with chemical shifts of the Si KβIII and KβIV peaks. We developed a regression model to predict mineral concentrations, validating the method with CRMs. The results suggest that the spectral region of the Si KβIII and KβIV peaks serves as a distinctive fingerprint for identifying silicate minerals in igneous rocks. [ABSTRACT FROM AUTHOR]

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Extrinsic dilute magnetic semiconductors achieve magnetic functionality through tailored interaction between a semiconducting matrix and a non‐magnetic dopant. The absence of intrinsic magnetic impurities makes this approach promising to investigate the newly emerging field of 2D dilute magnetic semiconductors. Here the first realization of an extrinsic 2D DMS in Pt‐doped WS2 is demonstrated. A bottom‐up synthesis approach yields a uniform and highly crystalline monolayer where platinum selectively occupies the tungsten sub‐lattice. The orbital overlap between W 4d and Pt 5d results in spin‐selective hybrid states that produce a strong valley‐Zeeman splitting. Combined experimental and theoretical results show that this interaction yields a sizable ferromagnetic response with a Curie temperature ≈375 K. These results open up a new route toward 2D magnetic properties through tailoring of atomic interactions for future applications in spintronics and magnetic nanoactuation. [ABSTRACT FROM AUTHOR]

In this groundbreaking study, we unveil the remarkable structural, electronic, and optical Properties of the newly discovered double perovskite material, K2AgBiI6, presenting a paradigm shift in materials science. The unique crystal structure and diverse atomic interactions inherent in this double perovskite make it an up-and-coming candidate for various technological applications, particularly in photovoltaics; owing to its stability and resistance to heat and humidity, we aim to shed light on the extraordinary potential of K2AgBiI6. Our study provides valuable insights for researchers engaged in tailored material design. We anticipate that the exceptional electronic properties of K2AgBiI6 will not only redefine the boundaries of materials engineering but also catalyze unprecedented advances in sustainable technology. Employing the powerful computational tool CASTEP, we conducted detailed electronic structure calculations within the framework of Density Functional Theory (DFT) to unravel the electronic properties of the double perovskite K2AgBiI6. Our investigation thoroughly explored structural properties, band structure, total density of states (DOS), and partial density of states (PDOS). Furthermore, we systematically examined the influence of different exchange-correlation functionals, including LDA, GGA, and m-GGA, on the electronic and optical features of the material by presenting a comparative analysis of these approximations. [ABSTRACT FROM AUTHOR]

Understanding the functions of metal ions in biological systems is crucial for many aspects of research, including deciphering their roles in diseases and potential therapeutic use. Structural information about the molecular or atomic details of these interactions, generated by methods like X-ray crystallography, cryo-electron microscopy, or nucleic magnetic resonance, frequently provides details that no other method can. As with any experimental method, they have inherent limitations that sometimes lead to an erroneous interpretation. This manuscript highlights different aspects of structural data available for metal-protein complexes. We examine the quality of modeling metal ion binding sites across different structure determination methods, where different kinds of errors stem from, and how they can impact correct interpretations and conclusions. [ABSTRACT FROM AUTHOR]

Monotypic catalytic site for bifunctional hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) at low overpotential is a grand challenge in alkaline water splitting. Herein, a new strategy of dual‐type atomic site‐support interaction is reported, in which ruthenium heteroatoms are in situ implanted into both the N‐C nanosheet matrix (Ru1‐N‐C) and supported Co2P nanoparticle lattice (Ru2‐P‐Co) for boosting alkaline water splitting. It is found that the Ru1‐N‐C and Ru2‐P‐Co can give rise to a synergistic effect for boosting HER and OER catalysis. Density functional theory calculations disclose that for HER, the Ru‐functionalized Co sites in Co2P assume the task of expediting H2O adsorption‐dissociation, and the adjacent coordination unsaturated Ru1‐N‐C sites can facilitate the following H2 desorption kinetic. The study found that the hydrogen spillover mechanism contributes to an ultralow HER polarization of 69 mV at 10 mA cm−2. While for OER, due to electronegativity discrepancies, the doped Ru within Co2P triggers electronic coupling, thereby efficiently tuning Ru d‐band center. This grants its electronic characteristic preferred for modulating rate‐determining step of OER to reduce the corresponding energy barrier, leading to superior OER catalytic activity. This work offers new understandings into catalyzing different reactions with multiple intermediate adsorptions by different atomic site‐support interplays. [ABSTRACT FROM AUTHOR]

In this study, the elastic properties of the newly discovered mechanoluminescence (ML) material LixZn1−xO:Nd3+ are investigated by first‐principles calculations. The elastic properties such as Young's modulus, bulk modulus, and shear modulus are calculated from the elastic tensor. As a result of investigating the phase stability of LixZn1−xO:Nd3+, it indicates that the wurtzite ZnO phase is stable in the Li additive range of 0 ≤ x ≤ 0.44, and an excess addition caused a structural transition to the h‐BN structure. Besides, elastic properties, such as Young's modulus, bulk modulus, and shear modulus of LixZn1−xO:Nd3+ are decreased with increasing Li concentration in the examined range of 0 ≤ x ≤ 0.44. Furthermore, it reveals from bonding analysis between cation and anion that the bonding strength of Li─O bonding for the covalent bonding is weaker than that of Zn─O bonding. The elastic softening derives from atomic interaction in the covalent bonding. Therefore, it concludes that elastic softening is promoted by the increase in Li─O bonding with weak covalent bonding as the Li concentration increases. [ABSTRACT FROM AUTHOR]

All‐solid‐state Li‐metal battery (ASSLB) represents advantageous energy storage system for automotive applications. For ASSLB, inorganic solid electrolyte is essential in determining safety and cycling performance. However, significant challenges persist in practical construction of ASSLB with optimized electrolyte. Specifically, electrolyte's structural instability influencing its electrochemical performance remains critical issue within typical operating temperatures for ASSLB in electric vehicles. Herein, this challenge is fundamentally addressed by substituting trace amount of lithium with cadmium, which lacks crystal field stabilization energy. This strategy of atomic interaction modification has induced electrolyte's structural distortion and electronic alteration by deliberately introducing disorder at local lithium sites. Li symmetric cell with cadmium‐substituted antiperovskite solid electrolyte exhibits outstanding critical current density of 11.5 mA cm−2 (5.75 mAh cm−2) and excellent stability for 3000 h at 10.0 mA cm−2 (5.0 mAh cm−2). This study highlights explicit research direction for breakthrough of ASSLB, focusing on understanding how local distortion affects complex inorganic materials. [ABSTRACT FROM AUTHOR]

Main‐group layered binary semiconductors, in particular, the III–VI alloys in the binary Ga–Te system are attracting increasing interest for a range of practical applications. The III–VI semiconductor, monoclinic gallium monotelluride (m‐GaTe), has been recently used in high‐sensitivity photodetectors/phototransistors and electronic memory applications due to its anisotropic properties yielding superior optical and electrical performance. Despite these applications, the origin of such anisotropy, namely the complex structural and bonding environments in GaTe nanostructures remain to be fully understood. In the present work, a comprehensive atomic‐scale characterization of m‐GaTe is reported by element‐resolved atomic‐scale microscopy experiments, enabling a direct measure of the in‐plane anisotropy at the sub‐Angstrom level. It is shown that these experimental images compare well with the results of first‐principles modeling. Quantum‐chemical bonding analyses provide a detailed picture of the atomic neighbor interactions within the layers, revealing that vertical GaGa homopolar bonds get stronger when they are distorted and rotated, inducing the strong in‐plane anisotropy. Beyond GaTe, using a systematic screening over the Materials Project database, the four additional low‐symmetric layered crystals with similar distorted tetrahedral patterns are identified, indicating that the homopolar‐bond‐induced anisotropy is a more generic feature in these layered van der Waals (vdW) materials. [ABSTRACT FROM AUTHOR]

The first-principles calculation was applied to predict the critical velocity of Cu/Al cold-spray bonding for the first time. The bonding mechanism of cold-spray was clarified by analyzing the energy variation and atomic interaction during the cold-spray impact process. Our results showed that the shear deformation played a key role in the cold-spray bonding. The atomic interaction determined the effective absorption of impact kinetic energy and finally determined the successful bonding of the cold-spray. The heterogeneous atoms absorbed the impact kinetic energy by interatomic attraction to achieve cold-spray bonding, while the homogeneous atoms absorbed the impact kinetic energy by the deformation of interface layers. An excellent agreement between the predicted critical velocity and the experimental one could be obtained, especially for the heterogeneous material cold-spray. Our present method proved to be a simple and highly efficient computing method in critical velocity prediction. Most importantly, the critical velocity for cold-spray could be predicted without using any empirical or experimental parameters. [ABSTRACT FROM AUTHOR]

Despite numerous efforts from numerical approaches to complement experimental measurements, several fundamental challenges have still hindered one's ability to truly provide an atomistic picture of the nucleation process in nanocrystals. Among them, our study resolves three obstacles: (1) Machine-learning force fields including long-range interactions able to capture the finesse of the underlying atomic interactions, (2) Data-driven characterization of the local ordering in a complex structural landscape associated with several crystal polymorphs and (3) Comparing results from a large range of temperatures using both brute-force and rare-event sampling. Altogether, our simulation strategy has allowed us to study zinc oxide crystallization from nano-droplet melt. Remarkably, our results show that different nucleation pathways compete depending on the investigated degree of supercooling. [ABSTRACT FROM AUTHOR]

Interstitial filling of light atoms strongly affects the electronic structure and adsorption properties of the parent catalyst due to ligand and ensemble effects. Different from the conventional doping and surface modification, constructing ordered intermetallic structures is more promising to overcome the dissolution and reconstruction of active sites through strong interactions generated by atomic periodic arrangement, achieving joint improvement in catalytic activity and stability. However, for tightly arranged metal lattices, such as iridium (Ir), obtaining ordered filling atoms and further unveiling their interstitial effects are still limited by highly activated processes. Herein, we report a high‐temperature molten salt assisted strategy to form the intermetallic Ir−B compounds (IrB1.1) with ordered filling by light boron (B) atoms. The B residing in the interstitial lattice of Ir constitutes favorable adsorption surfaces through a donor‐acceptor architecture, which has an optimal free energy uphill in rate‐determining step (RDS) of oxygen evolution reaction (OER), resulting in enhanced activity. Meanwhile, the strong coupling of Ir−B structural units suppresses the demetallation and reconstruction behavior of Ir, ensuring catalytic stability. Such B‐induced interstitial effects endow IrB1.1 with higher OER performance than commercial IrO2, which is further validated in proton exchange membrane water electrolyzers (PEMWEs). [ABSTRACT FROM AUTHOR]

Switchable adhesion, a phenomenon characterized by the ability to transition between attachment and detachment states under external stimuli, has recently gained popularity in various advanced devices. The realization of the desired functionalities on such surfaces relies on intricate interfacial designs. A general understanding of the commonalities and distinctions among these designs can foster the development of refined switchable adhesion interfaces (SAIs). To address this, this review first examines adhesion interfaces by focusing on the fundamental interactions at the atomic/molecular level, adhesion models, and their correlation with the diverse forces/bonds that dominate the adhesion behaviors. The latest progress in SAIs based on various forces/bonds, including electrostatic force, van der Waals force, capillary force, chemical bond, and suction force, is then discussed with regard to their specific design strategies, such as structures, components, and triggers. Additionally, an extensive overview of the broad applications of SAIs in fields ranging from space to biomedicine is provided, along with an exploration of the prevailing challenges and potential opportunities. With the rapid progress that has been made in state‐of‐the‐art mechanisms and design strategies, SAIs are expected to undergo booming development in the foreseeable future. [ABSTRACT FROM AUTHOR]

The performance of the recently suggested projected atomic orbitals (PAO) approach as the virtual space in excited state projection-based embedding applications is analysed. The role of the parameters in the PAO generation is discussed and the impact of different choices is evaluated on the ground state of the stacked formaldehyde and pyrrole dimers. A comparison of excitation energies obtained with PAOs and localised virtual orbitals is given and the role of diffuse basis functions is discussed using a benchmark set from previous studies. [ABSTRACT FROM AUTHOR]

The discovery of the electron in 1897 by J. J. Thomson meant that the atom was no longer the smallest unit of matter. This led to a set of responses both experimental and theoretical which consolidated a new branch of physics—atomic physics. What were the tools available at the time to address atomic physics and how were they deployed? The research begins with Thomson who sought to describe a structure of the atom that accommodates both mechanical and electromagnetic properties, but he had little experimental data to base it on. It was indeed an experimental finding which paved the way for the modern conception of the structure of the atom—Rutherford's scattering experiment. A complex relation between theory and experiment in a new domain of physics is uncovered. While the revolutionary discovery of the electron was the result of a classical propagation experiment, the discovery of the concentrated charge at the center of the atom was an outcome of a scattering experiment—a bombardment technique. This technique has turned out to be the hallmark of experimental atomic physics. [ABSTRACT FROM AUTHOR]

In three dimensions, dipole–dipole interactions which alter atomic level shifts and spontaneous decay rates only persist over distances comparable to the wavelength of the emitted light. In this paper we show that it is possible to significantly extend the range of these interactions with the help of a partially transparent asymmetric mirror interface. Suppose two two-level atoms are placed on opposite sides of the interface, each at the position of the mirror image of the other. In this case, their emitted light interferes almost exactly as it would when the atoms are right next to each other. Hence their dipole–dipole interaction assumes an additional maximum, even when the actual distance of the atoms is several orders of magnitude larger than the transition wavelength. Although the resulting ultralong-range interactions are in general relatively weak, we expect them to find applications in quantum technology, like non-invasive quantum sensing. [ABSTRACT FROM AUTHOR]

This study reveals the impact resistance of shear thickening gel (STG) impregnated four‐layer regular angle interlocking fabrics (AIF) composites. The effects of STG parameters, including reaction time, reaction temperature, and reaction ratio, on the rheological characterization and mechanical properties of STG/AIF flexible composites were investigated. The results show that the increase in STG parameters accelerated the formation of BO crosslink bonds within the STG. The energy storage modulus of STG increased by three orders of magnitude for a reaction temperature of 230°C, a reaction time of 9 h, and a reaction ratio of 12.5%. STG had an obvious shear thickening effect. The coupling effect of STG and AIF increases the inter‐yarn friction. The shear thickening effect of STG and the deformation of AIF fabric synergistically absorbed the impact energy, and the energy absorption rate reached 95.6%. The material surface was not significantly damaged after the low‐velocity impact. The STG/AIF flexible composites showed excellent impact energy absorption properties. Highlights: A new high‐energy absorption and impact resistance composite was prepared.Increased STG reaction ratio and temperature promoted its internal reaction.B and O atomic interactions enhance the rheological properties of STG.STG and fabric synergistically improve the impact resistance. [ABSTRACT FROM AUTHOR]

Correlated and uncorrelated Debye-Waller factors and correlation function in atomic vibrations described by mean square relative displacement, mean square displacement, and displacement displacement correlation function, respectively, have been studied based on correlated and uncorrelated Einstein models, including many-body effects. The impact of many-body effects in the derived analytical expressions of the above-considered quantities is realized by using the effective potentials of the derived Einstein models, which take into account the contributions of all nearest neighbors of vibrating atoms. The Morse potential is used to describe the single-pair atomic interactions. The difference between the correlated Debye-Waller factor and the uncorrelated one is considered to be the source of the correlation effect described by the correlation function, which is temperature and crystal-type-dependent. The larger such difference is, the stronger the correlation effect it generates. The numerical results for the Cu crystal agree with experimental results and with those calculated using other theories. [ABSTRACT FROM AUTHOR]

After explorations in a diversity of single-atom nanozymes (SAzymes), developing dual-centered SAzymes becomes a promising approach for superior catalytic performance. But confusing mechanisms including atomic coordination, spatial configuration, and metal–metal atom interaction hinder the development and design of SAzymes. Herein, a dual-centered Fe-Cu-Nx SAzyme exhibits excellent peroxidase (POD)- and catalase (CAT)-like activities with d-band center (εd) coordination of Fe and Cu in multiple reaction stages, which plays a critical role in the adsorption of H2O2 molecule and H2O and O2 release. Therefore, the d-band center coordination, which can be represented by εd(Fe)–εd(Cu) shifts, leads to the competition between one-side and bilateral adsorption, which determines the favorable reaction path with lower energy barriers. Based on experimental statistics, simulated formation energies, and reaction barriers, 3 configurations, Fe-Cu-N6-I, Fe-Cu-N8-II, and Fe-Cu-N8-III, are modeled and validated. Impressively, configuration-dependent catalytic selectivity and the competition between one-side and bilateral adsorption can be unveiled by d-band center coordination paradigm analysis. Theoretical simulations suggest that the unsymmetrical charge distribution over the three Fe-Cu configurations could tune the adsorption strength compared with the counterparts FeN4 and CuN4. The present work provides a potential route for optimizing enzyme-like catalysis by designing the dual- or even triple-metal SAzymes, which demonstrates the large space to modulate the metal atomic configuration and interaction. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Full landscapes of atomic interactions, including strong chemical bonds, intramolecular noncovalent and intermolecular, were calculated for a series of six highly polymorphic compounds, all of which exhibit pronounced biological activity: sulfapyridine, sulfamerazine, sulfamethoxazole, sulfathiazole, chlorpropamide and tolbutamide. To ensure strict and unambiguous characterization of atomic bonding, the method of molecular Voronoi–Dirichlet polyhedra (MVDP) was employed. Conformational differences among molecules within polymorphic families were quantified in terms of the peculiarities of the intramolecular noncovalent interactions being realized. On the basis of the k–Φ criterion all the studied molecules were proved to show unique systems of intramolecular noncovalent interactions thus being unique conformers. The relative importance of intramolecular noncovalent interactions, which have the maximum effect on the conformation of the respective molecules, was assessed. Good correlation was observed between the characteristics of π stacking calculated using the MVDP method and experimental polymorphic transition temperatures of sulfamethoxazole. The ratio of crystal volume with respect to strong chemical bonds, intramolecular noncovalent and intermolecular interactions for a large amount of unrelated compounds was analyzed. [ABSTRACT FROM AUTHOR]

Many of the most exciting materials discoveries in fundamental condensed matter physics are made in systems hosting some degree of intrinsic disorder. While disorder has historically been regarded as something to be avoided in materials design, it is often of central importance to correlated and quantum materials. This is largely driven by the conceptual and theoretical ease to handle, predict, and understand highly uniform systems that exhibit complex interactions, symmetries, and band structures. In this Perspective, we highlight how flipping this paradigm has enabled exciting possibilities in the emerging field of high entropy materials, focusing primarily on high entropy oxide and chalcogenide quantum materials. These materials host high levels of cation or anion compositional disorder while maintaining unexpectedly uniform single crystal lattices. The diversity of atomic scale interactions of spin, charge, orbital, and lattice degrees of freedom are found to emerge into coherent properties on much larger length scales. Thus, altering the variance and magnitudes of the atomic scale properties through elemental selection can open new routes to tune global correlated phases, such as magnetism, metal–insulator transitions, ferroelectricity, and even emergent topological responses. The strategy of embracing disorder in this way provides a much broader pallet from which functional states can be designed for next-generation microelectronic and quantum information systems. [ABSTRACT FROM AUTHOR]

Context: 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. Methods: Molecular dynamics simulations were conducted using the LAMMPS software. Atomic interactions in Cu 50 Zr 50 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. [ABSTRACT FROM AUTHOR]

Cryptophycins are microtubule-targeting agents (MTAs) that belong to the most potent antimitotic compounds known to date; however, their exact molecular mechanism of action remains unclear. Here, we present the 2.2 Å resolution X-ray crystal structure of a potent cryptophycin derivative bound to the αβ-tubulin heterodimer. The structure addresses conformational issues present in a previous 3.3 Å resolution cryoelectron microscopy structure of cryptophycin-52 bound to the maytansine site of β-tubulin. It further provides atomic details on interactions of cryptophycins, which had not been described previously, including ones that are in line with structure-activity relationship studies. Interestingly, we discovered a second cryptophycin-binding site that involves the T5-loop of β-tubulin, a critical secondary structure element involved in the exchange of the guanosine nucleotide and in the formation of longitudinal tubulin contacts in microtubules. Cryptophycins are the first natural ligands found to bind to this new "βT5-loop site” that bridges the maytansine and vinca sites. Our results offer unique avenues to rationally design novel MTAs with the capacity to modulate T5-loop dynamics and to simultaneously engage multiple β-tubulin binding sites. [ABSTRACT FROM AUTHOR]

The evolution of ideas concerning the nature of hydrogen embrittlement of engineering metallic materials is described based on a number of the proposed hypotheses and corresponding experiments. The main attention is paid to two of them, namely hydrogen-enhanced decohesion (HEDE) and hydrogen-enhanced localized plasticity (HELP). Recent attempts to interconnect the both models as HELP + HEDE and HELP-mediated HEDE ones are also estimated. A conclusion is made that HELP model is preferential for understanding the entire array of experimental data with a caveat that it is necessary to consider the chemical nature of hydrogen atoms and view them not only as point defects. Based on the studies of hydrogen effect on the atomic interactions in iron, nickel, titanium, and its alloys, it is shown that the electron approach to HELP phenomenon adequately describes two competitive features of hydrogen behavior in metals: increased brittleness and enhanced plasticity. Due to the increase in the concentration of free electrons, hydrogen decreases the elasticity moduli, which causes the crystal lattice to soften. For this reason, the formation of hydrogen atmospheres around the dislocations decreases the start stress of dislocation sources, as well as line tension of emitted dislocations, enhancing thereby their mobility, and weakens repulsion between dislocations in their pile-ups. The range of temperatures and strain rates in which hydrogen embrittlement occurs is controlled by the enthalpies of hydrogen atoms' diffusion and their binding to dislocations. The resulting consequences for mechanical properties depend on the short-range atomic order, SRO, which inherently occurs in the metallic solid solutions and localizes plastic deformation both in the cases of short-range atomic ordering and of short-range atomic decomposition. Hydrogen enhances slip localization because of its different solubility in the submicrovolumes of short-range decomposed solid solutions. If SRO is absent or not remarkably formed, the hydrogen-increased concentration of free electrons results in enhanced plasticity. Available positive hydrogen effects on the plasticity of titanium β-alloys and austenitic steels are presented and interpreted. [ABSTRACT FROM AUTHOR]

AgCrO 2 nanoparticles incorporated with magnesium were synthesized by a hydrothermal method and its response to ethylene glycol vapor was improved, with a remarkable detection limited down to ppm level. This hybrid oxide also exhibits a high selectivity and response (16.2–10 ppm ethylene glycol) at low operation temperature of 120 °C with short response/recovery time (32s/130s). Based on the microstructural characterizations including X-ray diffraction, electron microscope observation and X-ray photoelectron spectroscope probing, the first-principles calculation of the gas-oxide system was performed to elucidate the sensing enhancement by Mg hybridization. It started with the adsorption of gas to the superficial Ag atom in the vicinity of doped Mg, which was then followed by dehydrogenation resulting in electrons releasing and charge transfer through the adatom bond and supplementary route towards a terminal Ag atom. This work provided a new perspective to the atomic interaction between the specific gas molecules and sensitive oxide layer, which delivered approaches of chemiresistive material system optimization for advanced gas sensing application. [ABSTRACT FROM AUTHOR]

To facilitate the transition of quantum effects from the controlled laboratory environment to practical real-world applications, there is a pressing need for scalable platforms. One promising strategy involves integrating thermal vapors with nanostructures designed to manipulate atomic interactions. In this tutorial, we aim to gain deeper insights into this by examining the behavior of thermal vapors that are confined within nanocavities or waveguides and exposed to near-resonant light. We explore the interactions between atoms in confined dense thermal vapors. Our investigation reveals deviations from the predictions of continuous electrodynamics models, including density-dependent line shifts and broadening effects. In particular, our results demonstrate that by carefully controlling the saturation of single atoms and the interactions among multiple atoms using nanostructures, along with controlling the geometry of the atomic cloud, it becomes possible to manipulate the effective optical nonlinearity of the entire atomic ensemble. This capability renders the hybrid thermal atom-nanophotonic platform a distinctive and valuable one for manipulating the collective effect and achieving substantial optical nonlinearities. [ABSTRACT FROM AUTHOR]

The sensitivity of atom interferometers depends on their ability to realize long pulse separation times and prevent loss of contrast by limiting the expansion of the atomic ensemble within the interferometer beam through matter-wave collimation. Here we investigate the impact of atomic interactions on collimation by applying a lensing protocol to a 39K Bose-Einstein condensate at different scattering lengths. Tailoring interactions, we measure energies corresponding to (340 ± 12) pK in one direction. Our results are supported by an accurate simulation, which allows us to extrapolate a 2D ballistic expansion energy of (438 ± 77) pK. Based on our findings we propose an advanced scenario, which enables 3D expansion energies below 16 pK by implementing an additional pulsed delta-kick. Our results pave the way to realize ensembles with more than 1 × 105 atoms and 3D energies in the two-digit pK range in typical dipole trap setups without the need for micro-gravity or long baseline environments. Precision measurements with atom interferometers benefit from reducing the expansion rate of the atomic ensemble within the interferometric beam through matter-wave collimation. Here we demonstrate a collimation method based on time-averaged optical potentials and tunable interactions, realizing expansion energies of a few hundred picokelvin. [ABSTRACT FROM AUTHOR]

This dataset represents a collection of pocket-centric structural data related to protein-protein interactions (PPIs) and PPI-related ligand binding sites. The dataset includes high-quality structural information on more than 23,000 pockets, 3,700 proteins on more than 500 organisms, and nearly 3500 ligands that can aid researchers in the fields of bioinformatics, structural biology, and drug discovery. It encompasses a diverse set of PPI complexes with more than 1,700 unique protein families including some with associated ligands, enabling detailed investigations into molecular interactions at the atomic level. This article introduces an indispensable resource designed to unlock the full potential of PPIs while pioneering a novel metric for pocket similarity for hypothesizing protein partners repurposing. [ABSTRACT FROM AUTHOR]

Diabetes is a degenerative disease caused by either the body's inability to use insulin adequately or the pancreas's failure to release enough insulin. Diabetes is a glucose metabolic imbalance produced by the phosphodiesterase family of protein inositol monophosphatase (IMPase). Inositol monophosphatase, an enzyme involved in the phosphatidylinositol signalling pathway, is encoded by the IMPA1 gene. Homology Modelling is used to create a 3D model of the IMPA1 protein (target). The FASTA sequence for the IMPase protein (265 amino acids) (Uniprot ID H0YBL1) is obtained from the Uniprot server. Jpred, and NCBI Blast servers are used to search for templates. Based on the query coverage (92%) and E-score, the protein with the PDB ID-1IMA is identified as a potential template. The structural alignment (by ClustalW) submitted to the SWISS-MODEL service yields a 3D model. The Swiss PDB viewer is used to minimise energy (E = - 10099.60 kcal/mole). Procheck, ERRAT, and the VERIFY 3D server validate the model. The Ramachandran plot of the 3D model indicates that 93.5% of the amino acids are in the allowed region and none are in the forbidden region. The ERRAT result shows an overall quality factor of up to 96.17% for non-bonded atomic interactions. According to NCBI blast, the conserved domain is between 60 - 245 amino acids. The servers (ACTIVE SITE FINDER,) indicate binding pockets in the hydrophobic area, and Swiss dock is used to determine the active residues by protein - small ligand (Natural substrate, Fructose Biphosphatase-FBPase receptor) docking to identify the active site residues (Asp 90 and Thr-95) based on visualisations and a Swiss energy value. The glucose metabolism can be stopped by blocking these residues. Key Words: Diabetes, Phosphodiesterase family, Homology Modelling. [ABSTRACT FROM AUTHOR]

This study employs a combined computational and experimental approach to elucidate the mechanisms governing the interaction between lignin and urea, impacting lignin dissolution and subsequent aggregation behavior. Molecular dynamics (MD) simulations reveal how the urea concentration and temperature influence lignin conformation and interactions. Higher urea concentrations and temperatures promote lignin dispersion by disrupting intramolecular interactions and enhancing solvation. Density functional theory (DFT) calculations quantitatively assess the interaction energy between lignin and urea, supporting the findings from MD simulations. Anti-solvent precipitation demonstrates that increasing the urea concentration hinders the self-assembly of lignin nanoclusters. The findings provide valuable insights for optimizing lignin biorefinery processes by tailoring the urea concentration and temperature for efficient extraction and dispersion. Understanding the influence of urea on lignin behavior opens up avenues for designing novel lignin-based materials with tailored properties. This study highlights the potential for the synergetic application of MD simulations and DFT calculations to unravel complex material interactions at the atomic level. [ABSTRACT FROM AUTHOR]

Understanding the structure and function of intermediate filaments (IFs) is necessary in order to explain why more than 70 related IF genes have evolved in vertebrates while maintaining such dramatically tissue-specific expression. Desmin is a member of the large multigene family of IF proteins and is specifically expressed in myocytes. In an effort to elucidate its muscle-specific behavior, we have used a yeast two-hybrid system in order to identify desmin's head binding partners. We described a mitochondrial and a lysosomal protein, NADH ubiquinone oxidoreductase core subunit S2 (NDUFS2), and saposin D, respectively, as direct desmin binding partners. In silico analysis indicated that both interactions at the atomic level occur in a very similar way, by the formation of a three-helix bundle with hydrophobic interactions in the interdomain space and hydrogen bonds at R16 and S32 of the desmin head domain. The interactions, confirmed also by GST pull-down assays, indicating the necessity of the desmin head domain and, furthermore, point out its role in function of mitochondria and lysosomes, organelles which are disrupted in myopathies due to desmin head domain mutations. [ABSTRACT FROM AUTHOR]

This study investigates the effects of increasing PbO concentration on the Al2O3–PbO–B2O3–SiO2 glasses' physical, mechanical and gamma ray shielding properties. PbO addition leads to higher density and molar mass, making the glass denser. However, molar volume decreases, indicating a more compact structure. Interatomic distances and ion concentration change, strengthening atomic interactions. Oxygen molar volume increases, but packing density drops with more PbO, impacting the glass lattice. Optical basicity rises, suggesting improved electron transport and optical behavior. Electronegativity decreases, and electronic polarizability increases with higher PbO content, rendering the glass more electron-donating and sensitive to external electric fields.This study investigates glass mechanical properties using the Makishima–Mackenzie model. As PbO concentration rises, elastic moduli consistently decrease, signifying increased flexibility in glass structures. The mass attenuation coefficients (MAC) of the chosen glasses were evaluated in the 0.284–1.333 MeV energy range. It was found that increased PbO content leads to a corresponding MAC enhancement. The MAC values at 0.284 MeV were 0.297 and 0.349 cm2/g, while at 0.511 MeV they varied between 0.124 and 0.135 cm2/g. It was found that Glass Pb47.5 sample, which contains a higher amount of PbO compared to the other glasses, had the highest MAC at all energies. The results showed that the PbO has a notable impact on the MAC and thus on the radiation attenuation performance at lower energy. Moreover, increased glass density led to a corresponding LAC increase, which at 0.284 MeV increased from 1.269 cm−1 for Pb32.5 to 1.898 cm−1 for Pb47.5. According to the LAC results, one simple means of enhancing the glasses' radiation shielding properties is utilizing a high PbO percentage. This paper aims to illuminate silicate glasses' radiation shielding abilities. The paper will investigate the efficiency under specific conditions, like high-energy radiation. Moreover, it will explore innovative methods to enhance their shielding competence, concreting the way for a better yet effective radiation shielding approach. [ABSTRACT FROM AUTHOR]

In our work, we have explored the phase space nonlinear coherent-Kerr-cavity nonclassicality and purity loss induced by off-resonant intensity-dependent cavity-qubit interactions under atomic spontaneous-emission dissipation effect. The generation of the cavity purity loss (mixedness) dynamics, by using von Neumann entropy, is linked to the nonclassicality's Wigner distribution dynamics, which is investigated at spastic times chosen based on the von Neumann entropy's cavity dynamics. The temporal evolution of the largest negativity of the Wigner distribution is investigated under the physical system effects of the qubit spontaneous-emission dissipation, the detuning as well as the coherent-Kerr-cavity nonlinearity. The growths and the stability of the purity loss and the Wigner distribution negativity loss have the same behaviors. They depend on the Kerr-like nonlinearity and the dissipation couplings. These losses and their stability can be enhanced by increasing the dissipation coupling. It is found that the nonclassicality's phase space Wigner quasi-probability distribution and the mixedness of the generated coherent-Kerr-cavity states are highly sensitive to the physical system effects. [ABSTRACT FROM AUTHOR]

Numerous researchers in the energy field are engaged in a competitive race to advance hydrogen as a clean and environmentally friendly fuel. Studies have been conducted on the different aspects of hydrogen, including its production, storage, transportation and utilization. The catalytic methane decomposition technique for hydrogen production is an environmentally friendly process that avoids generating carbon dioxide gas, which contributes to the greenhouse effect. Catalysts play a crucial role in facilitating rapid, cost-effective and efficient production of hydrogen using this technique. In this study, reactive molecular dynamics simulations were employed to examine the impact of Pt7 cluster decoration on the surface of a Ni (110) catalyst, referred to as Pt7-Ni (110), on the rates of methane dissociation and molecular hydrogen production. The reactive force field was employed to model the atomic interactions that enabled the formation and dissociation of chemical bonds. Our reactive molecular dynamics simulations using the Pt7-Ni (110) catalyst revealed a notable decrease in the number of methane molecules, specifically ~11.89 molecules per picosecond. The rate was approximately four times higher than that of the simulation system utilizing a Ni (110) catalyst and approximately six times higher than that of the pure methane, no-catalyst system. The number of hydrogen molecules generated during a simulation period of 150 000 fs was greater on the Pt7-Ni (110) surface than in both the Ni (110) and pure methane systems. This was due to the presence of numerous dissociated hydrogen atoms on the Pt7-Ni (110) surface. [ABSTRACT FROM AUTHOR]

Understanding hydrogen incorporation into palladium requires detailed knowledge of surface and subsurface structure and atomic interactions as surface hydrogen is being embedded. Using density functional theory (DFT), we examine the energies of hydrogen layers of varying coverage adsorbed on Pd(111). We find that H–H and H–Pd interactions promote the formation of the well-known 3 × 3 phases but also favor an unreported (3 × 3) phase at high H coverages for which we present experimental evidence. We relate the stability of isolated H vacancies of the (3 × 3) phase to the need of H2 molecules to access bare Pd before they can dissociate. Following higher hydrogen dosage, we observe initial steps of hydride formation, starting with small clusters of subsurface hydrogen. The interaction between H and Pd is complicated by the persistent presence of carbon at the surface. X-ray photoelectron spectroscopy experiments show that trace amounts of carbon, emerging from the Pd bulk despite many surface cleaning cycles, become mobile enough to repopulate the C-depleted surface at temperatures above 200 K. When exposed to hydrogen, these surface carbon atoms react to form benzene, as evidenced by scanning tunneling microscopy observations interpreted with DFT. [ABSTRACT FROM AUTHOR]

Synthetic dimensions, wherein dynamics occurs in a set of internal states, have found great success in recent years in exploring topological effects in cold atoms and photonics. However, the phenomena thus far explored have largely been restricted to the non-interacting or weakly interacting regimes. Here, we extend the synthetic dimensions playbook to strongly interacting systems of Rydberg atoms prepared in optical tweezer arrays. We use precise control over driving microwave fields to introduce a tunable U(1) flux in a four-site lattice of coupled Rydberg levels. We find highly coherent dynamics, in good agreement with theory. Single atoms show oscillatory dynamics controllable by the gauge field. Small arrays of interacting atoms exhibit behavior suggestive of the emergence of ergodic and arrested dynamics in the regimes of intermediate and strong interactions, respectively. These demonstrations pave the way for future explorations of strongly interacting dynamics and many-body phases in Rydberg synthetic lattices. Weak and non-interacting systems have been previously explored in synthetic dimensions. Here the authors demonstrate strong atomic interaction in synthetic dimensions using an array of Rydberg atoms. [ABSTRACT FROM AUTHOR]

The absolute mass of neutrinos and their nature are presently unknown. Aggregate matter has a coherent weak charge leading to a repulsive interaction mediated by a neutrino pair. The virtual neutrinos are non-relativistic at micron distances, giving a distinct behavior for Dirac versus Majorana mass terms. This effective potential allows for the disentanglement of the Dirac or Majorana nature of the neutrino via magnitude and distance dependence. We propose an experiment to search for this potential based on the concept that the density-dependent interaction of an atomic probe with a material source in one arm of an atomic clock interferometer generates a differential phase. The appropriate geometry of the device is selected using the saturation of the weak potential as a guide. The proposed experiment has the added benefit of being sensitive to gravity at micron distances. A strategy to suppress the competing Casimir–Polder interaction, depending on the electronic structure of the material source, as well as a way to compensate the gravitational interaction in the two arms of the interferometer is discussed. [ABSTRACT FROM AUTHOR]

The optical properties and Landau quantisations in twisted bilayer graphene are investigated using a generalised tight-binding model that takes into account all interlayer and intralayer atomic interactions in the Moire superlattice. The system is a zero-gap semiconductor with double-degenerate Dirac-cone structures, and saddle-point energy dispersions appear at low energies for small twisting angles. The magnetic quantisation phenomena in this system are rich and unique, with Landau-level subgroups specified owing to specific Moire zone folding through modulation of the stacking angles. The Landau-level spectrum shows hybridised characteristics associated with those in monolayer, as well as AA and AB stackings. The detailed analysis explores the complex relations among the different sublattices on the same and different graphene layers. [ABSTRACT FROM AUTHOR]

Context: Density functional theory (DFT) was used to investigate the effects of varying carbon doping concentrations on the electronic and optical properties of SnS2-doped systems. The findings show that a doping concentration of 3.7% in SnS2 results in the highest structural stability and the lowest formation energy. A pure SnS2 monolayer is an indirect bandgap semiconductor, and the result reveals that increasing carbon doping correlates with a gradual reduction in the system's bandgap. The density of states analysis reveals that the valence band comprises C-2p, S-3p, and Sn-5p orbitals, whereas the conduction band consists of S-3p, Sn-5 s, and C-2p orbitals. Furthermore, doping concentration appears to cause a redshift in both the absorption coefficient and reflection peaks, which both decrease as doping concentration increases. Methods: The calculations for this study were performed using DFT within the CASTEP module of Materials Studio Segall et al. J Phys: Condens Matter 14(11):2717, 2002. The system parameters and structures were optimized to determine the electronic structure and optical properties. Geometric optimization and calculations were carried out with the generalized gradient approximation plane-wave pseudopotential method and the Perdew-Burke-Ernzerhof functional Perdew et al. Phys Rev Lett 80(4):891–891, 1998. The parameters for structural optimization included a plane-wave expansion cutoff energy set at 500 eV and a k-point mesh of 6 × 6 × 1 for Brillouin zone integration. The electronic convergence criteria were established at 1.0 × 10-5 eV/atom for the unit cell energy and 1.0 × 10-6 eV/atom for self-consistency. The internal stress deviation was maintained below 0.05 GPa, the atomic force interactions were kept under 0.03 eV/Å, and atomic displacements during geometric optimization were confined to less than 0.001 Å. To calculate the properties of the SnS2 monolayer, a vacuum spacing of 15 Å along the z-axis was introduced to prevent interactions between adjacent layers. [ABSTRACT FROM AUTHOR]

Studying the photoinduced changes of materials with atomic-scale spatial resolution can provide a fundamental understanding of light-matter interaction. A long-standing impediment has been the detrimental thermal effects on the stability of the tunneling gap from intensity-modulated laser irradiation of the scanning tunneling microscope junction. Photoinduced DC current transduces photons to an electric current and is widely applied in optoelectronics as switches and signal transmission. Our results revealed the origin of the light-induced DC current and related it to the two-level population dynamics and related nonlinearity in the conductance of a single molecule. Here, we compensated for the near-visible laser-induced thermal effects to demonstrate photoinduced DC current spectroscopy and microscopy and to observe the persistent photoconductivity of a two-level pyrrolidine molecule. The methodology can be generally applied to the coupling of light to scan probes to investigate light-matter interactions at the atomic scale. [ABSTRACT FROM AUTHOR]

Context: Density functional theory (DFT) was used to investigate the effects of varying carbon doping concentrations on the electronic and optical properties of SnS2-doped systems. The findings show that a doping concentration of 3.7% in SnS2 results in the highest structural stability and the lowest formation energy. A pure SnS2 monolayer is an indirect bandgap semiconductor, and the result reveals that increasing carbon doping correlates with a gradual reduction in the system's bandgap. The density of states analysis reveals that the valence band comprises C-2p, S-3p, and Sn-5p orbitals, whereas the conduction band consists of S-3p, Sn-5 s, and C-2p orbitals. Furthermore, doping concentration appears to cause a redshift in both the absorption coefficient and reflection peaks, which both decrease as doping concentration increases. Methods: The calculations for this study were performed using DFT within the CASTEP module of Materials Studio Segall et al. J Phys: Condens Matter 14(11):2717, 2002. The system parameters and structures were optimized to determine the electronic structure and optical properties. Geometric optimization and calculations were carried out with the generalized gradient approximation plane-wave pseudopotential method and the Perdew-Burke-Ernzerhof functional Perdew et al. Phys Rev Lett 80(4):891–891, 1998. The parameters for structural optimization included a plane-wave expansion cutoff energy set at 500 eV and a k-point mesh of 6 × 6 × 1 for Brillouin zone integration. The electronic convergence criteria were established at 1.0 × 10-5 eV/atom for the unit cell energy and 1.0 × 10-6 eV/atom for self-consistency. The internal stress deviation was maintained below 0.05 GPa, the atomic force interactions were kept under 0.03 eV/Å, and atomic displacements during geometric optimization were confined to less than 0.001 Å. To calculate the properties of the SnS2 monolayer, a vacuum spacing of 15 Å along the z-axis was introduced to prevent interactions between adjacent layers. [ABSTRACT FROM AUTHOR]