Atomic Interactions Research Articles

Teaching protein structure and function through molecular visualization.

The function of proteins is governed by their three-dimensional structure. This structure is determined by the chemical characteristics and atomic interactions of amino acids. Students of biochemistry, with a particular focus on protein chemistry, benefit from looking at protein structures and understanding how proteins are built and fold. Due to their three-dimensional nature, static two-dimensional representations in textbooks can be limiting to student learning. Here, we developed a series of tutorials that introduce students to molecular graphics software. The students are challenged to apply the software to look at proteins and to get a deeper understanding of how amino acid properties are linked to structure. We also familiarize students with some of the latest tools in computational structural biology. Students performed the tutorials with visual enthusiasm and reported general satisfaction in being able to visualize theoretical concepts learned during lectures. We further stimulated student engagement by allowing space for self-exploration. We share the tutorial instructions for other teachers to build on them, and we also offer suggestions for further improvement based on student feedback. In summary, we present a series of tutorials aimed at students of an advanced course in protein biochemistry to enable them to explore the universe of protein structures and how those relate to function.

Investigating the structural, electronic, and optical properties of the novel double perovskite K2AgBiI6 using DFT

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.

Exploring the local structure of molten Al-Zr-Y(Si) alloys using ab initio molecular dynamics

Accelerating the diffusion rate of Zr in aluminum and suppressing Zr segregation during solidification are crucial for enhancing the heat resistance of Al-Zr alloys. In this study, ab initio molecular dynamics simulations were employed to investigate the local structure of molten Al-Zr-Y(Si) alloys and the morphology of the liquid/substrate interface. By examining the atomic interactions, the mechanism by which Si addition improves Zr segregation during solidification and accelerates Zr diffusion was revealed. The results indicate that the interaction between Si and Zr is significantly stronger than that with other alloying elements such as Al, Y, and Zr itself. The introduction of Si had a discernible detrimental effect on Zr-Zr bonds, as Zr atoms exhibited a preference for bonding with Si atoms, consequently promoting cluster formation. This phenomenon resulted in the fragmentation of large Zr clusters into smaller ones. Moreover, the inclusion of Si atoms notably augmented the diffusion coefficient of Zr atoms within the Al-Zr-Y alloy. Analysis of the solid-liquid interface unveiled a noteworthy dragging effect, where Si atoms prominently pulled Zr atoms into the liquid phase at the interface's forefront.

Assignment of a Physical Energy Scale for the Dimensionless Interaction Energies within the PRIME20 Peptide Model.

We present a calibration scheme to determine the conversion factors from a coarse-grained stochastic approximation Monte Carlo approach using the PRIME20 peptide interaction model into atomistic force-field interaction energies at full explicit aqueous solvation. The conversion from coarse-grained to atomistic structures was done according to our previously established inverse coarse-graining protocol. We provide a physical energy scale for both the backbone hydrogen bonding interactions and the sidechain interactions by correlating the dimensionless energy descriptors of the PRIME20 model with the energies averaged over molecular dynamics simulations. The conversion factor for these interactions turns out to be around 2kJ/mol for the backbone interactions, and zero for the sidechain interactions. We discuss these surprisingly small values in terms of their molecular interpretation.

Transition metal embedded MoS2 as efficient trifunctional electrocatalyst: A computational study

In the advancement of electrochemical energy systems, multifunctional catalysts for the oxygen reduction reaction (ORR), hydrogen evolution reaction (HER), and oxygen evolution reaction (OER) are indispensable. Moreover, catalysts produced by incorporating transition metals into two-dimensional materials via substitutional modification have demonstrated remarkable efficacy. The present study examines the prospective uses of transition metal (TM= Nb, Co, In, and Re) dopants comprising 10% Niobium, Rhenium, Cobalt, and Indium in 2D MoS2. The density functional theory has been utilized to study the atomic level interaction. Based on the result, it can be observed that Nb-doped MoS2 has a ΔGH value of 0.06 eV, which signifies its remarkable HER capability when compared to pristine MoS2 and other doped versions. Our analysis for OER and ORR activities reveals that Co doped MoS2 exhibit superior performance compared to both the pristine and other doped versions of TM-MoS2, with an overpotential value ɳOER = 1.00 V and ɳORR = 0.77 V. A modification in electronic properties is examined by analysing the partial density of states during the HER and OER processes. The number of potential candidates suggested by the present findings will aid in the development of TM-doped MoS2-based electrocatalysts.

Insights into the Single Atom and Support Interaction in Electrocatalytic Oxygen Evolution Reaction

Insights into the Single Atom and Support Interaction in Electrocatalytic Oxygen Evolution Reaction

Competing nucleation pathways in nanocrystal formation

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.

Structural investigation of the complexation between vitamin B12 and per- and polyfluoroalkyl substances: Insights into degradation using density functional theory

Environmental remediation of per- and polyfluoroalkyl substances (PFAS) has become a significant research topic in recent years due to the fact that these materials are omnipresent, resistant to degradation and thus environmentally persistent. Unfortunately, they have also been shown to cause health concerns. PFAS are widely used in industrial applications and consumer products. Vitamin B12 (B12) has been identified as being catalytically active towards a variety of halogenated compounds such as PFAS. It has also been shown to be effective when using sulfide as a reducing agent for B12. This is promising as sulfide is readily available in the environment. However, there are many unknowns with respect to PFAS interactions with B12. These include the reaction mechanism and B12's specificity for PFAS with certain functionalization(s). In order to understand the specificity of B12 towards branched PFAS, we examined the atomistic interactions between B12 and eight different PFAS molecules using Density Functional Theory (B3LYP/cc-pVDZ). The PFAS test set included linear PFAS and their branched analogs, carboxylic acid and sulfonic acid headgroups, and aromatic and non-aromatic cyclic structures. Conformational analyses were carried out to determine the lowest energy configurations. This analysis showed that small chain PFAS such as perfluorobutanoic acid interact with the cobalt center of B12. Bulkier PFAS prefer to interact with the amine and carbonyl groups on the sidechains of the B12 ring system. Furthermore, computed complexation energies determined that, in general, branched PFAS (e.g. perfluoro-5-methylheptane sulfonic acid) interact more strongly than linear molecules (e.g. perfluorooctanesulfonic acid). Our results indicate that it may be possible to alter the interactions between B12 and PFAS by synthetically modifying the sidechains of the ring structure.

Cooperative Decay of an Ensemble of Atoms in a One-Dimensional Chain with a Single Excitation

We propose a new expression of the cooperative decay rate of a one-dimensional chain of N two-level atoms in the single-excitation configuration. From it, the interference nature of superradiance and subradiance arises naturally, without the need to solve the eigenvalue problem of the atom–atom interaction Green function. The cooperative decay rate can be interpreted as the imaginary part of the expectation value of the effective non-Hermitian Hamiltonian of the system, evaluated over a generalized Dicke state of N atoms in the single-excitation manifold. Whereas the subradiant decay rate is zero for an infinite chain, it decreases as 1/N for a finite chain. A simple approximated expression for the cooperative decay rate is obtained as a function of the lattice constant d and the atomic number N. The results are obtained first for the scalar model and then extended to the vectorial light model, assuming all the dipoles aligned.

Diffusion enhancement by spontaneous formation of Frenkel defects in NaCl-type high-entropy materials

High-entropy materials (HEMs) are attracting attention due to their exceptional properties, such as enhanced mechanical toughness, irradiation resistance, ionic conductivity, and thermoelectric performance. Although diffusion is an important phenomenon as it is closely related to these physical properties of materials, there is a lack of understanding of the mechanisms of diffusion due to the complexity of the atomic interactions in HEMs. Here, we investigates diffusion mechanisms in PbTe-based HEMs AgInSnPbBiTe5, focusing on the role of indium (In). Molecular dynamics simulations reveal that In+ spontaneously forms Frenkel defect and enhancing diffusion not only of In+ but also other cations. Furthermore, as a result of enhanced diffusion, short-range order is formed by structural relaxation. This insight not only enhances comprehension of HEMs diffusion mechanisms but also develops HEMs with properties such as self-healing from damage and high ion permeability, advancing the field of material science.

Making molecules in cavity.

Free molecules undergo processes with photons; in particular, they can undergo photoionization and photodissociation, which are relevant processes in nature and laboratory. Recently, it has been shown that in a cavity, the reverse process of photoionization, namely, electron capture becomes highly probable. The underlying mechanism is the formation of a hybrid resonance state. In this work, we demonstrate that the idea of enhanced reverse processes is more general. We discuss the case of the reverse process of photodissociation, namely, making a molecule out of separate atoms in a cavity. For bound electronic states, the interaction of atoms and molecules with quantum light as realized in cavities is known to give rise to the formation of hybrid light-matter states (usually called polaritons). In the scenarios discussed here, the hybrid light-matter states are resonance (metastable) states, which decay into the continuum of either electrons or of the fragments of a molecule. Resonances can substantially enhance the outcome of processes. In addition to the new resonant mechanism of molecule formation, the impact of the hybrid resonances on the scattering cross section of the atoms can be dramatic.

The Effective Separation of Gallium, Vanadium, and Aluminum from a Simulated Bayer Solution by Resin Exchange.

The effective recovery of gallium from wastewater discharge in the Bayer process is promising for the long-term development of gallium resources. The adsorption and desorption behavior of gallium (Ga), vanadium (V), and aluminum (Al) ions on a strong acidic styrene cation exchange resin (JK resin) from a simulated Bayer solution was systematically investigated by static experiments. The results showed that the optimum conditions for separating Ga from V and Al were at low temperatures and short contact times, with 78.30%, 15.16%, and 6.63% of the adsorption efficiency at 25 °C and 60 min, respectively, for Ga, V, and Al. The adsorption kinetics of Ga3+ conformed to the pseudo-second order model, and the static saturation adsorption capacity was 18.25 mg/g. The Langmuir model fitted the adsorption isotherm of gallium well, and the maximum adsorption capacity was 1.11 mg/g at 25 °C. FT-IR spectroscopy and XPS showed that the mechanism of the Ga3+ adsorption was only related to the interaction of the oxygen atoms of the amide oxime group (C=NOH). The separation of Ga, V, and Al can be achieved by desorbing 98% of Al with low concentrations of ammonia and 90% of Ga with low concentrations of hydrochloric acid. The results indicate that JK resin is an efficient adsorbent for separating gallium and vanadium in alkaline solutions.

Accelerating Fourth-Generation Machine Learning Potentials Using Quasi-Linear Scaling Particle Mesh Charge Equilibration.

Machine learning potentials (MLPs) have revolutionized the field of atomistic simulations by describing atomic interactions with the accuracy of electronic structure methods at a small fraction of the cost. Most current MLPs construct the energy of a system as a sum of atomic energies, which depend on information about the atomic environments provided in the form of predefined or learnable feature vectors. If, in addition, nonlocal phenomena like long-range charge transfer are important, fourth-generation MLPs need to be used, which include a charge equilibration (Qeq) step to take the global structure of the system into account. This Qeq can significantly increase the computational cost and thus can become a computational bottleneck for large systems. In this Article, we present a highly efficient formulation of Qeq that does not require the explicit computation of the Coulomb matrix elements, resulting in a quasi-linear scaling method. Moreover, our approach also allows for the efficient calculation of energy derivatives, which explicitly consider the global structure-dependence of the atomic charges as obtained from Qeq. Due to its generality, the method is not restricted to MLPs and can also be applied within a variety of other force fields.

Interaction Effects on the Dynamical Anderson Metal-Insulator Transition Using Kicked Quantum Gases.

Understanding the interplay of interaction and disorder in quantum transport poses long-standing scientific challenges for theory and experiment. While highly controlled ultracold atomic platforms combining atomic interactions with spatially disordered lattices have led to remarkable advances, the extension of such controlled studies to phenomena in high-dimensional disordered systems, such as the three-dimensional Anderson metal-insulator transition has been limited. Kicked quantum gases provide an alternate experimental platform that captures the Anderson model in momentum space and features dynamical localization as the analog of Anderson localization. Here, we utilize a momentum space lattice platform using quasiperiodically kicked ultracold atomic gases to experimentally investigate interaction effects on the three-dimensional dynamical Anderson metal-insulator transition. We observe interaction-driven subdiffusion and a divergence of delocalization onset time on approaching the phase boundary. Mean-field numerical simulations show qualitative agreement with experimental observations, but with significant quantitative deviations.

Avalanche Terahertz Photon Detection in a Rydberg Tweezer Array.

We propose a protocol for the amplified detection of low-intensity terahertz radiation using Rydberg tweezer arrays. The protocol offers single photon sensitivity together with a low dark count rate. It is split into two phases: during a sensing phase, it harnesses strong terahertz-range transitions between highly excited Rydberg states to capture individual terahertz photons. During an amplification phase it exploits the Rydberg facilitation mechanism which converts a single terahertz photon into a substantial signal of Rydberg excitations. We discuss a concrete realization based on realistic atomic interaction parameters, develop a comprehensive theoretical model that incorporates the motion of trapped atoms and study the many-body dynamics using tensor network methods.

Restrictions of microwave electrometry due to nonlocal interactions in Rydberg atoms

Restrictions of microwave electrometry due to nonlocal interactions in Rydberg atoms

Magnetic splitting induced ferromagnetism in chromium-doped HfSe2

Two-dimensional (2D) magnetic layered materials have gained significant interest in spintronic for memory storage devices. Herein, the electronic and magnetic properties of high-quality single crystals of chromium (Cr)-doped hafnium diselenide were studied. The electronic study indicated that the Cr-doped HfSe2 reveals the semiconducting nature with a proper bandgap as identified by angle-resolved photoemission spectroscopy and first-principle density functional theory (DFT) calculations. The magnetic results indicate that the HfSe₂ exhibited ferromagnetic characteristics with the substitution of Cr atoms in a perpendicular direction. The Cr-doped HfSe2 sample shows a ferromagnetic phase below ∼58 K, indicating the critical temperature (Tc) of magnetic order, while above this temperature, it shows a paramagnetic phase that can follow the Curie-Weiss Law. It can be seen that the magnetic moment is approximately 0.16 emu/g at 5 K, which further decreases with increasing temperature until 60 K and then transforms to a paramagnetic phase. The sample can clearly show a weak out-of-plane magnetic anisotropy with a coercivity of around 50.56 Oe and a saturation magnetization value of 0.029 emu/g. Convincingly, it was observed from the ARPES results that the valence band is split due to the spin-orbit interaction of Cr atoms, which can induce ferromagnetic order. At the same time, the temperature-dependent ARPES data shows that the splitting is higher below the Tc, while it is weaker above the Tc. The DFT results revealed that near the Fermi level, the spin-up and spin-down are spin-polarized with asymmetric trends. It can be observed that substituting Cr on the octahedral sites of Hf atoms influences the electron spin order created by Hf vacancies (as validated by the magnetic coupling measured by electron paramagnetic resonance spectroscopy experiments), which can change the magnetic alignment to induce the magnetism in HfSe2. This study highlights that doping transition metal in HfSe2 has promising potential for future applications, especially in memory devices and spintronic technologies.

Ratchet loading and multi-ensemble operation in an optical lattice clock

We demonstrate programmable control over the spatial distribution of ultra-cold atoms confined in an optical lattice. The control is facilitated through a combination of spatial manipulation of the magneto-optical trap and atomic population shelving to a metastable state. We first employ the technique to load an extended (5 mm) atomic sample with uniform density in an optical lattice clock (OLC), reducing atomic interactions and realizing remarkable frequency homogeneity across the atomic cloud. We also prepare multiple spatially separated atomic ensembles, and realize multi-ensemble clock operation within the standard one-dimensional (1D) OLC architecture. Leveraging this technique, we prepare two oppositely spin-polarized ensembles that are independently addressable, offering a platform for implementing spectroscopic protocols for enhanced tracking of local oscillator phase. Finally, we demonstrate a relative fractional frequency instability at one second of 2.4(1)×10−17 between two ensembles, useful for characterization of intra-lattice differential systematics.

TEM-processed defect densities in single-layer TMDCs and their substrate-dependent signature in PL and Raman spectroscopy

The optical properties of the direct-bandgap transition metal dichalcogenides (TMDCs) MoS2 and WS2 are heavily influenced by their atomic defect structure and substrate interaction. In this work we use low-voltage chromatic and spherical aberration (CC/CS)-corrected high-resolution transmission electron microscopy to simultaneously create and image chalcogen vacancies in TMDCs. However, correlating the defect structure, produced and analyzed using transmission electron microscopy (TEM), with optical spectroscopy often presents challenges because of very different fields of view and sample platforms involved. Here we employ a reverse transfer technique to transfer electron-irradiated single-layer MoS2 and WS2 from the TEM grid to various substrates for subsequent optical examination. The dynamics of defect creation are studied in atomic resolution on a separate sample, which allows to apply the derived statistics to larger irradiated areas on the other samples. The intensity of both the defect-bound exciton peak in photoluminescence (PL) and the defect-induced LA(M) mode in Raman spectra increase with defect density. The best substrates for defect-density determination by optical spectroscopy are polystyrene for PL and SiC and Si/SiO2 for Raman spectroscopy. These investigations represent an important step towards the quantification of defects using solely optical spectroscopy, paving the way for fast, reliable, and automatable optical quality control of optoelectronic devices.

Fine-tuned protein-lipid interactions in biological membranes: exploration and implications of the ORMDL-ceramide negative feedback loop in the endoplasmic reticulum.

Biological membranes consist of a lipid bilayer in which integral membrane proteins are embedded. Based on the compositional complexity of the lipid species found in membranes, and on their specific and selective interactions with membrane proteins, we recently suggested that membrane bilayers can be best described as "finely-tuned molecular machines." We now discuss one such set of lipid-protein interactions by describing a negative feedback mechanism operating in the de novo sphingolipid biosynthetic pathway, which occurs in the membrane of the endoplasmic reticulum, and describe the atomic interactions between the first enzyme in the pathway, namely serine palmitoyl transferase, and the product of the fourth enzyme in the pathway, ceramide. We explore how hydrogen-bonding and hydrophobic interactions formed between Asn13 and Phe63 in the serine palmitoyl transferase complex and ceramide can influence the ceramide content of the endoplasmic reticulum. This example of finely-tuned biochemical interactions raises intriguing mechanistic questions about how sphingolipids and their biosynthetic enzymes could have evolved, particularly in light of their metabolic co-dependence.