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At least 1,441 records · Page 80

Self-consistent implementation of locally scaled self-interaction-correction method

Recently proposed local self-interaction correction (LSIC) method is a one-electron self-interaction-correction (SIC) method that uses an iso-orbital indicator to apply the SIC at each point in space by scaling the exchange–correlation and Coulomb energy densities. The LSIC method is exact for the one-electron densities, also recovers the uniform electron gas limit of the uncorrected density functional approximation, and reduces to the well-known Perdew–Zunger SIC (PZSIC) method as a special case. This article presents the self-consistent implementation of the LSIC method using the ratio of Weizsäcker and Kohn–Sham kinetic energy densities as an iso-orbital indicator. The atomic forces as well as the forces on the Fermi-Löwdin orbitals are also implemented for the LSIC energy functional. Results show that LSIC with the simplest local spin density functional predicts atomization energies of the AE6 dataset better than some of the most widely used generalized-gradient-approximation (GGA) functional and barrier heights of the BH6 database better than some of the most widely used hybrid functionals. The LSIC method [a mean absolute error (MAE) of 0.008 Å] predicts bond lengths of a small set of molecules better than the PZSIC-LSDA (MAE 0.042 Å) and LSDA (0.011 Å). Furthermore, this work shows that accurate results can be obtained from the simplest density functional by removing the self-interaction-errors using an appropriately designed SIC method.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Causal interaction in high frequency turbulence at the biosphere–atmosphere interface: Structural behavior

High-frequency (e.g., 10 Hz) eddy covariance measurements are typically used to estimate fluxes at the land–atmosphere interface at timescales of 15–60 min. These multivariate data contain information about the interdependency at high frequency between the interacting variables such as wind, humidity, temperature, and CO 2⁠ . We use data at 10 Hz from an eddy covariance instrument located at 25 m above agricultural land in the Midwestern US, which offers an opportunity to move beyond the traditional spectral analyses to explore causal dependency among variables. In this study, we quantify the structure of inter-dependencies of interacting variables at high frequency represented by a directed acyclic graph (DAG). We compare DAGs to investigate changes in structural differences in causal interactions. We then apply a distance-based classification and -means clustering approach to identify the evolution of the causal structure represented by a DAG. Our method selects an unbiased number of clusters of similar structures and characterizes the similarities and differences between them. We explore a range of dynamic behavior using data from a clear sky day and during a solar eclipse in 2017. Our results show well-defined clusters of similar causal dependencies as the system evolves. Furthermore, our approach provides a methodological framework to understand how causal dependence in turbulence manifests in high-frequency data when represented through a DAG.

54 ENVIRONMENTAL SCIENCES↗

Causal interaction in high frequency turbulence at the biosphere–atmosphere interface: Structure–function coupling

At the biosphere–atmosphere interface, nonlinear interdependencies among components of an ecohydrological complex system can be inferred using multivariate high frequency time series observations. Information flow among these interacting variables allows us to represent the causal dependencies in the form of a directed acyclic graph (DAG). Here, we use high frequency multivariate data at 10 Hz from an eddy covariance instrument located at 25 m above agricultural land in the Midwestern US to quantify the evolutionary dynamics of this complex system using a sequence of DAGs by examining the structural dependency of information flow and the associated functional response. We investigate whether functional differences correspond to structural differences or if there are no functional variations despite the structural differences. We base our analysis on the hypothesis that causal dependencies are instigated through information flow, and the resulting interactions sustain the dynamics and its functionality. To test our hypothesis, we build upon causal structure analysis in the companion paper to characterize the information flow in similarly clustered DAGs from 3-min non-overlapping contiguous windows in the observational data. We characterize functionality as the nature of interactions as discerned through redundant, unique, and synergistic components of information flow. Through this analysis, we find that in turbulence at the biosphere–atmosphere interface, the variables that control the dynamic character of the atmosphere as well as the thermodynamics are driven by non-local conditions, while the scalar transport associated with CO and H 2 O is mainly driven by short-term local conditions.

58 GEOSCIENCES↗

Spin-state gaps and self-interaction-corrected density functional approximations: Octahedral Fe(II) complexes as case study

Accurate prediction of a spin-state energy difference is crucial for understanding the spin crossover phenomena and is very challenging for density functional approximations, especially for local and semi-local approximations due to delocalization errors. Here, we investigate the effect of the self-interaction error removal from the local spin density approximation (LSDA) and Perdew–Burke–Ernzerhof generalized gradient approximation on the spin-state gaps of Fe(II) complexes with various ligands using recently developed locally scaled self-interaction correction (LSIC) by Zope et al. [J. Chem. Phys. 151, 214108 (2019)]. The LSIC method is exact for one-electron density, recovers the uniform electron gas limit of the underlying functional, and approaches the well-known Perdew–Zunger self-interaction correction (PZSIC) as a particular case when the scaling factor is set to unity. Our results, when compared with reference diffusion Monte Carlo results, show that the PZSIC method significantly overestimates spin-state gaps favoring low spin states for all ligands and does not improve upon density functional approximations. The perturbative LSIC-LSDA using PZSIC densities significantly improves the gaps with a mean absolute error of 0.51 eV but slightly overcorrects for the stronger CO ligands. Finally, the quasi-self-consistent LSIC-LSDA, such as coupled-cluster single double and perturbative triple [CCSD(T)], gives a correct sign of spin-state gaps for all ligands with a mean absolute error of 0.56 eV, comparable to that of CCSD(T) (0.49 eV).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Electronic structure theory on modeling short-range noncovalent interactions between amino acids

While short-range noncovalent interactions (NCIs) are proving to be of importance in many chemical and biological systems, these atypical bindings happen within the so-called van der Waals envelope and pose an enormous challenge for current computational methods. We introduce SNCIAA, a database of 723 benchmark interaction energies of short-range noncovalent interactions between neutral/charged amino acids originated from protein x-ray crystal structures at the “gold standard” coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory with a mean absolute binding uncertainty less than 0.1 kcal/mol. Subsequently, a systematic assessment of commonly used computational methods, such as the second-order Møller−Plesset theory (MP2), density functional theory (DFT), symmetry-adapted perturbation theory (SAPT), composite electronic-structure methods, semiempirical approaches, and the physical-based potentials with machine learning (IPML) on SNCIAA is carried out. It is shown that the inclusion of dispersion corrections is essential even though these dimers are dominated by electrostatics, such as hydrogen bondings and salt bridges. Overall, MP2, ωB97M-V, and B3LYP+D4 turned out to be the most reliable methods for the description of short-range NCIs even in strongly attractive/repulsive complexes. SAPT is also recommended in describing short-range NCIs only if the δMP2 correction has been included. The good performance of IPML for dimers at close-equilibrium and long-range conditions is not transferable to the short-range. We expect that SNCIAA will assist the development/improvement/validation of computational methods, such as DFT, force-fields, and ML models, in describing NCIs across entire potential energy surfaces (short-, intermediate-, and long-range NCIs) on the same footing.

Chemistry↗

Resonant interactions involving local vibrational modes in crystals

When an impurity with a light mass is inserted into a crystal, it can undergo a high-frequency oscillation referred to as a local vibrational mode (LVM). A Fermi resonance may occur between the LVM and lower-frequency modes of the defect. The LVM may also interact with phonons or the electromagnetic field. Understanding these interactions can help model and control diffusion, defect reactions, and thermal conductivity. LVMs have been probed in semiconductors using pressure and alloying as experimental parameters, resulting in anticrossing between localized and extended vibrational modes. Furthermore, these types of vibrational interactions could play an important role in the stability and thermal properties of organic–inorganic hybrid semiconductors. The coupling between an LVM and electromagnetic wave yields an “LVM polariton,” an excitation that has significant vibrational and electric-field amplitudes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Radiation and heat transport in divergent shock–bubble interactions

Shock–bubble interactions (SBIs) are important across a wide range of physical systems. In inertial confinement fusion, interactions between laser-driven shocks and micro-voids in both ablators and foam targets generate instabilities that are a major obstacle in achieving ignition. Experiments imaging the collapse of such voids at high energy densities (HED) are constrained by spatial and temporal resolution, making simulations a vital tool in understanding these systems. In this study, we benchmark several radiation and thermal transport models in the xRAGE hydrodynamic code against experimental images of a collapsing mesoscale void during the passage of a 300 GPa shock. We also quantitatively examine the role of transport physics in the evolution of the SBI. This allows us to understand the dynamics of the interaction at timescales shorter than experimental imaging framerates. We find that all radiation models examined reproduce empirical shock velocities within experimental error. Radiation transport is found to reduce shock pressures by providing an additional energy pathway in the ablation region, but this effect is small (∼1% of total shock pressure). Employing a flux-limited Spitzer model for heat conduction, we find that flux limiters between 0.03 and 0.10 produce agreement with experimental velocities, suggesting that the system is well-within the Spitzer regime. Higher heat conduction is found to lower temperatures in the ablated plasma and to prevent secondary shocks at the ablation front, resulting in weaker primary shocks. Finally, we confirm that the SBI-driven instabilities observed in the HED regime are baroclinically driven, as in the low energy case.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Effect of penetrant–polymer interactions and shape on the motion of molecular penetrants in dense polymer networks

The diffusion of dilute molecular penetrants within polymers plays a crucial role in the advancement of material engineering for applications such as coatings and membrane separations. The potential of highly cross-linked polymer networks in these applications stems from their capacity to adjust the size and shape selectivity through subtle changes in network structures. In this paper, we use molecular dynamics simulation to understand the role of penetrant shape (aspect ratios) and its interaction with polymer networks on its diffusivity. We characterize both local penetrant hopping and the long-time diffusive motion for penetrants and consider different aspect ratios and penetrant–network interaction strengths at a variety of cross-link densities and temperatures. The shape affects the coupling of penetrant motion to the cross-link density- and temperature-dependent structural relaxation of networks and also affects the way a penetrant experiences the confinement from the network meshes. The attractive interaction between the penetrant and network primarily affects the former since only the system of dilute limit is of present interest. These results offer fundamental insights into the intricate interplay between penetrant characteristics and polymer network properties and also suggest future directions for manipulating polymer design to enhance the separation efficiency.

Chemistry↗

Effect of electron–electron interactions on the emission characteristics of ultracold, nanoscale photoemission-based electron sources

For nearly 60 years, cold field emitters have been the source of choice for electron microscopy due to their high brightness and relatively low energy spread. In this paper, we have examined an alternative: nanoscale electron sources based on near-threshold photoemission. While these sources have not yet been realized, they hold the potential to produce significantly brighter beams than cold field emitters. We model electron–electron Coulomb interactions in beams emitted from such sources to calculate the impact of these interactions on the brightness and the energy spread. Our results show that these sources can theoretically deliver more than an order of magnitude brighter electron beams compared to cold field emitters along with more than an order of magnitude smaller energy spread, before being limited by the Coulomb interactions. Electron sources with such high brightness and low energy spread would be transformational for electron microscopy, enabling electron energy loss-based vibrational spectroscopy at the sub-nanometer scale.

Gevorkyan, G S↗

Classification of dynamical Lie algebras generated by spin interactions on undirected graphs

Dynamical Lie algebras (DLAs) are a versatile tool for various topics that span from the expressibility-trainability of variational quantum algorithms (VQAs), to simulation of many body Hamiltonians. Quantum gates and most of the Hamiltonians of interest consist of local interactions; therefore, the analysis of all possible DLAs generated by 1- and 2-local operators is crucial for quantum simulation and VQAs on current hardware. Previously in [R. Wiersema et al ., npj Quantum Inf. 10 , 110 (2024)], we analyzed the DLAs on linear, circular and all-to-all topologies, and obtained results about their dimensions and algebraic structure. Here, in this work, we extend our analysis into any possible hardware topology and provide a classification of all DLAs generated by Pauli strings on any undirected interaction graph. Our results indicate that the DLAs depend solely on whether the connectivity or interaction graph is bipartite or not. In addition, we find that the non-trivial polynomially scaling DLAs appear only on 1D line or circle topologies, and all other DLAs have dimensions scaling exponentially with the system size. Together with the current VQA literature, our results imply that either the majority of VQAs are non-trainable, or we are yet to understand the role of DLAs on the trainability of VQAs.

Algebraic structures↗

Interplay of ferromagnetic and antiferromagnetic interactions in epitaxial Co 3 ZnN

Antiperovskite nitrides with the general formula M 3 AN have attracted significant attention due to their tunable electronic and magnetic properties. Among them are many cobalt-based compounds predicted to exhibit high thermodynamic stability and intriguing magnetic behavior. Here, we report the synthesis and magnetic characterization of epitaxial Co3ZnN thin films grown by radio frequency sputtering on SrTiO 3 (STO) and MgO substrates. X-ray diffraction confirms phase-pure (00l)-oriented films with cube-on-cube epitaxy on STO, with a c-lattice parameter of 3.752 Å. Magnetic measurements reveal clear hysteresis at 2 K with a coercive field of ∼0.11 T and a small net moment of 0.108 μ B /f.u., suggesting either a canted antiferromagnetic (AFM) or ferrimagnetic (FiM) configuration. Temperature-dependent magnetization measurements show a transition near 25 K, with strong AFM interactions with Curie–Weiss temperature (Θ) = −80.13 K. Complementary density functional theory and Monte Carlo simulations indicate a ferromagnetic (FM) ground state, with the FM–AFM energy difference decreasing systematically with increasing supercell size, consistent with competition between FM and AFM/FiM interactions. These results highlight Co3ZnN as a magnetically complex antiperovskite nitride with competing exchange interactions.

36 MATERIALS SCIENCE↗

Phase field dislocation dynamics formulation coupled with Fourier based micromechanics solver and its application to grain boundary–dislocation interactions

A new phase field dislocation dynamics (PFDD) formulation for homogeneous and heterogeneous materials is presented, which couples micromechanical solvers and the time-dependent Ginzburg–Landau equation. The strain fields are obtained from the micromechanical solver by solving the Lippmann–Schwinger equation and then used to define energy terms to model the evolution of the dislocations. Grain boundary (GB)–dislocation interactions are studied using the coupled PFDD formulation and by describing GBs as inclusions. GB energy and stiffness tensors are computed from molecular statics simulations, and a newly proposed lattice energy term that is dependent on the GB energy is considered in the calculations. Interaction of a screw dislocation with minimum energy and metastable states of low and high angle ⟨110⟩ symmetric tilt grain boundaries are studied. We show good agreement between predictions from our PFDD formulation and molecular dynamics simulations of grain boundary–dislocation interactions.

36 MATERIALS SCIENCE↗

Role of electron correlation on the adenine dimer interaction for non-equilibrium geometries: a benchmark Quantum Monte Carlo study

The accurate description of non-covalent interactions is critical for understanding the structure, dynamics, and eventual function of biomolecules. The adenine dimer serves as a benchmark system for computational methods due to its role in nucleic acid structures and its rich conformational landscape. In this study, we employ benchmark diffusion quantum Monte Carlo (DMC) methods to investigate the relative energies and role of electron correlation on a set of adenine dimer conformations generated via a search of the potential energy landscape using the global optimizer algorithm. Relative DMC energies are compared against a wide range of density functional theory (DFT) approximation results. We find that although most of the DFT functionals perform well for low-energy structures, their accuracy varies significantly for higher-energy conformations, including stacked and T-shaped structures. A large fraction of the variation is due to the treatment of the van der Waals interaction. BLYP, B3LYP, and PBE0 significantly improve with added D4 dispersion, while the recent r2SCAN-D4 and ωB97M-V functionals show the least scatter and closest agreement with the DMC. These findings highlight the delicate nature of these interactions in biomolecular systems and provide guidance for simulations of their structure and dynamics and for the development of machine learned interatomic potentials.

Washburn, Laurel [ORNL] (ORCID:0000000324179335)↗

Dimer interaction in the Hv1 proton channel

The voltage-gated proton channel Hv1 is a member of the voltage-gated ion channel superfamily, which stands out in design: It is a dimer of two voltage-sensing domains (VSDs), each containing a pore pathway, a voltage sensor (S4), and a gate (S1) and forming its own ion channel. Opening of the two channels in the dimer is cooperative. Part of the cooperativity is due to association between coiled-coil domains that extend intracellularly from the S4s. Interactions between the transmembrane portions of the subunits may also contribute, but the nature of transmembrane packing is unclear. Using functional analysis of a mutagenesis scan, biochemistry, and modeling, we find that the subunits form a dimer interface along the entire length of S1, and also have intersubunit contacts between S1 and S4. These interactions exert a strong effect on gating, in particular on the stability of the open state. Our results suggest that gating in Hv1 is tuned by extensive VSD–VSD interactions between the gates and voltage sensors of the dimeric channel.

59 BASIC BIOLOGICAL SCIENCES↗

Regulating phase behavior of nanoparticle assemblies through engineering of DNA-mediated isotropic interactions

Self-assembly of isotropically interacting particles into desired crystal structures could allow for creating designed functional materials via simple synthetic means. However, the ability to use isotropic particles to assemble different crystal types remains challenging, especially for generating low-coordinated crystal structures. Here, we demonstrate that isotropic pairwise interparticle interactions can be rationally tuned through the design of DNA shells in a range that allows transition from common, high-coordinated FCC-CuAu and BCC-CsCl lattices, to more exotic symmetries for spherical particles such as the SC-NaCl lattice and to low-coordinated crystal structures (i.e., cubic diamond, open honeycomb). The combination of computational and experimental approaches reveals such a design strategy using DNA-functionalized nanoparticles and successfully demonstrates the realization of BCC-CsCl, SC-NaCl, and a weakly ordered cubic diamond phase. The study reveals the phase behavior of isotropic nanoparticles for DNA–shell tunable interaction, which, due to the ease of synthesis is promising for the practical realization of non-close-packed lattices.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Structures and membrane interactions of native serotonin transporter in complexes with psychostimulants

The serotonin transporter (SERT) is a member of the SLC6 neurotransmitter transporter family that mediates serotonin reuptake at presynaptic nerve terminals. SERT is the target of both therapeutic antidepressant drugs and psychostimulant substances such as cocaine and methamphetamines, which are small molecules that perturb normal serotonergic transmission by interfering with serotonin transport. Despite decades of studies, important functional aspects of SERT such as the oligomerization state of native SERT and its interactions with potential proteins remain unresolved. Here, we develop methods to isolate SERT from porcine brain (pSERT) using a mild, nonionic detergent, utilize fluorescence-detection size-exclusion chromatography to investigate its oligomerization state and interactions with other proteins, and employ single-particle cryo-electron microscopy to elucidate the structures of pSERT in complexes with methamphetamine or cocaine, providing structural insights into psychostimulant recognition and accompanying pSERT conformations. Methamphetamine and cocaine both bind to the central site, stabilizing the transporter in an outward open conformation. We also identify densities attributable to multiple cholesterol or cholesteryl hemisuccinate (CHS) molecules, as well as to a detergent molecule bound to the pSERT allosteric site. Under our conditions of isolation, we find that pSERT is best described as a monomeric entity, isolated without interacting proteins, and is ensconced by multiple cholesterol or CHS molecules.

59 BASIC BIOLOGICAL SCIENCES↗

First principles band structure of interacting phosphorus and boron/aluminum δ -doped layers in silicon

Silicon can be heavily doped with phosphorus in a single atomic layer (a δ layer), significantly altering the electronic structure of the conduction bands within the material. Recent progress has also made it possible to further dope silicon with acceptor-based δ layers using either boron or aluminum, making it feasible to create devices with interacting δ layers with opposite polarity. Using density functional theory, we calculate the electronic structure of a phosphorus-based δ layer interacting with a boron or aluminum δ layer, varying the distances between the δ layers. At separations 1 nm and smaller, the dopant potentials overlap and largely cancel each other out, leading to an electronic structure closely mimicking intrinsic silicon. At separations greater than 1 nm, the two δ layers behave independently of one another, with an equivalent electronic structure to a p–n diode with an intrinsic layer taking the place of the depletion region. One mechanism for charge transfer between δ layers at larger distances could be tunneling, where we see a tunneling probability exceeding what would be seen for a standard silicon 1.1 eV triangular barrier, indicating that the interaction between delta layers may enhance tunneling compared to a traditional junction.

delta layers↗

Identification of a network of nonlinear interactions as a mechanism triggering the onset of edge localized modes

Edge localized modes (ELMs) remain a critical issue for the lifetime of in-vessel components of fusion reactors such as ITER. We study ELMs triggered when the pedestal parameters are below the peeling-ballooning limit. These ELMs occur while the pedestal recovers after an ELM crash. We identify a mechanism by which a non-linear perturbation involving many active triads—a network of non-linear interactions – leads to the triggering of these ELMs. Each active triad leads to the non-linear transfer of energy between three waves, such that the network of non-linear interactions lead to a transfer of energy between many waves. The triggering of this non-linear perturbation systematically coincides with a pedestal perturbation induced by the neutral beam injection beams and localized near the magnetic surface of safety factor q = 5. Among the non-linear interactions detected during the ELM by a bi-coherence analysis, the most active triad involves a slow frequency that is qualitatively consistent with a geodesic acoustic mode located at the same location, i.e., near the q = 5 surface.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗