Beyond metals: theoretical discovery of semiconducting MAX phases and their potential application in thermoelectrics.

MAX phase is a family of ceramic compounds, typically known for their metallic properties. However, we show here that some of them may be narrow bandgap semiconductors. Using a series of first-principles calculations, we have investigated the electronic structures of 861 dynamically stable MAX phases. Notably, Sc2SC, Y2SC, Y2SeC, Sc3AuC2, and Y3AuC2 have been identified as semiconductors with band gaps ranging from 0.2 to 0.5 eV. Furthermore, we have assessed the thermodynamic stability of these systems by generating ternary phase diagrams utilizing evolutionary algorithm techniques. Their dynamic stabilities are confirmed by phonon calculations. Additionally, we have explored the potential thermoelectric efficiencies of these materials by combining Boltzmann transport theory with first-principles calculations. The relaxation times are estimated using scattering theory. The zT coefficients for the aforementioned systems fall within the range of 0.5 to 2.5 at temperatures spanning from 300 to 700 K, indicating their suitability for high-temperature thermoelectric applications.

Non-adiabatic excited-state time-dependent GW molecular dynamics (TDGW) satisfying extended Koopmans' theorem: An accurate description of methane photolysis.

There is a longstanding difficulty that time-dependent density functional theory relying on adiabatic local density approximation is not applicable to the electron dynamics, for example, for an initially excited state, such as in photochemical reactions. To overcome this, we develop non-adiabatic excited-state time-dependent GW molecular dynamics (TDGW) on the basis of the extended quasiparticle theory. Replacing Kohn-Sham orbitals/energies with correlated, interacting quasiparticle orbitals/energies allows the full correspondence to the excited-state surfaces and corresponding total energies, with satisfying extended Koopmans' theorem. We demonstrate the power of TDGW using methane photolysis, CH4→CH3•+H, an important initiation reaction for combustion/pyrolysis and hydrogen production of methane. We successfully explore several possible pathways and show how this reaction dynamics is captured accurately through simultaneously time-tracing all quasiparticle levels. TDGW scales as O(NB3-4), where NB is the number of basis functions, which is distinctly advantageous to performing dynamics using configuration interaction and coupled cluster methods.

Modeling the SDF-1/CXCR4 protein using advanced artificial intelligence and antagonist screening for Japanese anchovy.

SDF-1/CXCR4 chemokine signaling are indispensable for cell migration, especially the Primordial Germ Cell (PGC) migration towards the gonadal ridge during early development. We earlier found that this signaling is largely conserved in the Japanese anchovy (Engraulis japonicus, EJ), and a mere treatment of CXCR4 antagonist, AMD3100, leads to germ cell depletion and thereafter gonad sterilization. However, the effect of AMD3100 was limited. So, in this research, we scouted for CXCR4 antagonist with higher potency by employing advanced artificial intelligence deep learning-based computer simulations. Three potential candidates, AMD3465, WZ811, and LY2510924, were selected and in vivo validation was conducted using Japanese anchovy embryos. We found that seven transmembrane motif of EJ CXCR4a and EJ CXCR4b were extremely similar with human homolog while the CXCR4 chemokine receptor N terminal (PF12109, essential for SDF-1 binding) was missing in EJ CXCR4b. 3D protein analysis and cavity search predicted the cavity in EJ CXCR4a to be five times larger (6,307 Å³) than that in EJ CXCR4b (1,241 Å³). Docking analysis demonstrated lower binding energy of AMD3100 and AMD3465 to EJ CXCR4a (Vina score -9.6) and EJ CXCR4b (Vina score -8.8), respectively. Furthermore, we observed significant PGC mismigration in microinjected AMD3465 treated groups at 10, 100 and 1 × 105 nM concentration in 48 h post fertilized embryos. The other three antagonists showed various degrees of PGC dispersion, but no significant effect compared to their solvent control at tested concentrations was observed. Cumulatively, our results suggests that AMD3645 might be a better candidate for abnormal PGC migration in Japanese anchovy and warrants further investigation.

Pattern recognition receptors involved in the immune system of hagfish (Eptatretus burgeri).

The initial defense against invading pathogenic microbes is the activation of innate immunity by binding of pattern recognition receptors (PRRs) to pathogen associated molecular patterns (PAMPs). To explain the action of PRRs from hagfish, one of the extant jawless vertebrates, we purified the GlcNAc recognition complex (GRC) from serum using GlcNAc-agarose. The GRC comprises four proteins of varying molecular masses: 19 kDa, 26 kDa, 27 kDa, and 31 kDa. Exposure of Escherichia coli to the GRC led to the phagocytic activation of macrophages, revealing the opsonic function of the GRC. The GRC in serum formed a large complex with a molecular mass of approximately 1200 kDa. The GRC bound to Escherichia coli but not to rabbit red blood cells, despite both having GlcNAc on their surface. These structural and binding properties are similar to those of mannose-binding lectin (MBL). The amino acid sequence of a portion of the 31 kDa protein in the GRC matched the amino acid sequence of variable lymphocyte receptor (VLR)-B in some place. According to the Western blot analysis, the 31 kDa protein was recognized by the anti-hagfish VLR-B antiserum. Based on the results, it appears that the GRC functions as a PRR like MBL and that its 31 kDa protein has a structure similar to that of VLR-B.

Extended quasiparticle approach to non-resonant and resonant X-ray emission spectroscopy.

The initial states of the secondary processes of X-ray emission spectroscopy (XES) and resonant inelastic X-ray scattering (RIXS) are highly excited eigenstates with a deep core hole after a X-ray photoelectron spectroscopy (XPS) process and a X-ray photoabsorption spectroscopy (XAS) process, respectively, so that the XES and RIXS calculation offers a good example of extended quasiparticle theory (EQPT) (K. Ohno, S. Ono and T. Isobe, J. Chem. Phys., 2017, 146, 084108) which is applicable to any initial exited eigenstate. We apply the standard one-shot GW + Bethe-Salpeter equation (BSE) approach in MBPT to this problem on the basis of EQPT and analyze XES and RIXS spectra for CH4, NH3, H2O, and CH3OH molecules. We also suggest a simpler approach only using the GW calculation without solving the BSE to compute the XES and RIXS energies, although it cannot give the spectral intensity. Moreover, according to extended Kohn-Sham theory (T. Nakashima, H. Raebiger and K. Ohno, Phys. Rev. B, 2021, 104, L201116), we give a justification and comment of applying the method relying on time-dependent density functional theory as well as the one-shot GW + BSE approach to this problem.

All-proportional solid solution versus two-phase coexistence in the Ti-V alloy by first-principles phase field and SQS methods.

The microstructures of the Ti-V alloy are studied by purely first-principles calculations without relying on any empirical or experimental parameter. The special quasirandom structure model is employed to treat the all-proportional solid solution [Formula: see text] phase, while the first-principles phase field method or its variant is employed to treat the coexistence phases. The linearity of the calculated local free energy against the integer Ti[Formula: see text]V[Formula: see text] composition in the cluster expansion method manifests a clear evidence of the solid solution behavior. From a detailed energy comparison, our results are consistent with the experimental fact that the Ti-V alloy is an all-proportional solid solution of the [Formula: see text] phase at high temperatures and exhibits an [Formula: see text] coexistence at low temperatures. Moreover, it is found that mosaic-type microstructures may appear as a metastable phase, as observed by many experiments. The first-principles criterion for the all-proportional solid solution behavior presented in this paper is very general and can be applied to any other binary or multi-component alloys.

High-throughput computational discovery of ternary-layered MAX phases and prediction of their exfoliation for formation of 2D MXenes.

The rush to synthesize novel two-dimensional (2D) materials has excited the research community studying ternary-layered carbide and nitride compounds, known as MAX phases, for the past two decades in the quest to develop new 2D material precursors. The objective of this study is to expand the family of MAX phases and to investigate their feasible exfoliation to generate 2D systems. To expand the family of MAX phases, we conduct systematic and fundamental research using elemental information and data from high-throughput density functional theory calculations performed on 1122 MAX candidates. Our results suggest that 466 MAX compounds can be synthesized, among which 136 MAX phases can be exfoliated to produce 26 MXenes. We investigate the transition metal or A elements that could be suitable for the formation of novel MAX phase carbides or nitrides and determine promising MAX phases that can be exfoliated to form 2D systems.

Estrogen receptor 2b is the major determinant of sex-typical mating behavior and sexual preference in medaka.

Male and female animals typically display innate sex-specific mating behaviors, which, in vertebrates, are highly dependent on sex steroid signaling. While estradiol-17ß (E2) signaling through estrogen receptor 2 (ESR2) serves to defeminize male mating behavior in rodents, the available evidence suggests that E2 signaling is not required in teleosts for either male or female mating behavior. Here, we report that female medaka deficient for Esr2b, a teleost ortholog of ESR2, are not receptive to males but rather court females, despite retaining normal ovarian function with an unaltered sex steroid milieu. Thus, contrary to both prevailing views in rodents and teleosts, E2/Esr2b signaling in the brain plays a decisive role in feminization and demasculinization of female mating behavior and sexual preference in medaka. Further behavioral testing showed that mutual antagonism between E2/Esr2b signaling and androgen receptor-mediated androgen signaling in adulthood induces and actively maintains sex-typical mating behaviors and preference. Our results also revealed that the female-biased sexual dimorphism in esr2b expression in the telencephalic and preoptic nuclei implicated in mating behavior can be reversed between males and females by altering the sex steroid milieu in adulthood, likely via mechanisms involving direct E2-induced transcriptional activation. In addition, Npba, a neuropeptide mediating female sexual receptivity, was found to act downstream of E2/Esr2b signaling in these brain nuclei. Collectively, these functional and regulatory mechanisms of E2/Esr2b signaling presumably underpin the neural mechanism for induction, maintenance, and reversal of sex-typical mating behaviors and sexual preference in teleosts, at least in medaka.

Creation of Mo/Tc@C60 and Au@C60 and molecular-dynamics simulations.

The formation of middle- and/or high-weight atom (Mo, Au)-incorporated fullerenes was investigated using radionuclides produced by nuclear reactions. From the trace radioactivities of 99Mo/99mTc or 194Au after high-performance liquid chromatography, it was found that the formation of endohedral and/or heterofullerene fullerenes in 99Mo/99mTc and 194Au atoms could occur by a recoil process following the nuclear reactions. Furthermore, the 99mTc (and 194Au) atoms recoiled against ß-decay remained present inside these cages. To confirm the produced materials experimentally, ab initio molecular dynamics (MD) simulations based on an all-electron mixed-basis approach were performed. The possibility of the formation of endohedral fullerenes containing Mo/Tc and Au atoms is verified; here, the formation of heterofullerenes is excluded by MD simulations. These findings suggest that radionuclides stably encapsulated by fullerenes could potentially play a valuable role in diagnostic nuclear medicine.

A first-principles phase field method for quantitatively predicting multi-composition phase separation without thermodynamic empirical parameter.

To design tailored materials, it is highly desirable to predict microstructures of alloys without empirical parameter. Phase field models (PFMs) rely on parameters adjusted to match experimental information, while first-principles methods cannot directly treat the typical length scale of 10 µm. Combining density functional theory, cluster expansion theory and potential renormalization theory, we derive the free energy as a function of compositions and construct a parameter-free PFM, which can predict microstructures in high-temperature regions of alloy phase diagrams. Applying this method to Ni-Al alloys at 1027 °C, we succeed in reproducing evolution of microstructures as a function of only compositions without thermodynamic empirical parameter. The resulting patterns including cuboidal shaped precipitations are in excellent agreement with the experimental microstructures in each region of the Ni-Al phase diagram. Our method is in principle applicable to any kind of alloys as a reliable theoretical tool to predict microstructures of new materials.

First principles calculations of surface dependent electronic structures: a study on ß-FeOOH and γ-FeOOH.

We report a theoretical study on iron oxyhydroxide (FeOOH). The FeOOH surface is expected to act as an efficient electrochemical catalyst for the oxygen evolution reaction (OER), because it is based on iron, an element of the fourth highest Clarke number. Experimentally, the OER activity of ß-FeOOH is known to be higher than that of γ-FeOOH. However, the details of the OER mechanism and the surface reactivities of the FeOOH polymorphs have not yet been fully understood. We performed first-principles calculations of bulk and surfaces of ß-FeOOH and γ-FeOOH using density functional theory, to investigate their electronic structures and catalytic activities. The calculations suggest that depending on the surface indices, several surfaces may be favored for catalytic activities.

Mass production of low-boiling point solvent- and water-soluble graphene by simple salt-assisted ball milling.

Developing a mass production method for graphene is essential for practical usage of this remarkable material. Direct exfoliation of graphite in a liquid is a promising approach for production of high quality graphene. However, this technique has three huge obstacles to be solved; limitation of solvent, low yield and low quality (i.e., multilayer graphene with a small size). Here, we found that soluble graphite produced by mechanochemical reaction with salts overcomes the above three drawbacks. Soluble graphite was exfoliated into monolayer graphene with more than 10% yield in five minutes of sonication. The modified graphite was easily exfoliated in a low-boiling point solvent such as acetone, alcohol and water without the aid of a surfactant. Molecular simulation revealed that the salt is adsorbed to the active carbon at the graphite edge. In the case of weak acid salts, the original bonding nature between the alkali ion and the base molecule is retained after the reaction. Thus, alkali metals are easily dissociated in a polar solvent, leading to negative charge of graphene, enabling the exfoliation of graphite in low boiling point solvents. The approach proposed here opens up a new door to practical usage of the attractive 2D material.

Accurate quasiparticle calculation of x-ray photoelectron spectra of solids.

It has been highly desired to provide an accurate and reliable method to calculate core electron binding energies (CEBEs) of crystals and to understand the final state screening effect on a core hole in high resolution x-ray photoelectron spectroscopy (XPS), because the ΔSCF method cannot be simply used for bulk systems. We propose to use the quasiparticle calculation based on many-body perturbation theory for this problem. In this study, CEBEs of band-gapped crystals, silicon, diamond, ß-SiC, BN, and AlP, are investigated by means of the GW approximation (GWA) using the full ω integration and compared with the preexisting XPS data. The screening effect on a deep core hole is also investigated in detail by evaluating the relaxation energy (RE) from the core and valence contributions separately. Calculated results show that not only the valence electrons but also the core electrons have an important contribution to the RE, and the GWA have a tendency to underestimate CEBEs due to the excess RE. This underestimation can be improved by introducing the self-screening correction to the GWA. The resulting C1s, B1s, N1s, Si2p, and Al2p CEBEs are in excellent agreement with the experiments within 1 eV absolute error range. The present self-screening corrected GW approach has the capability to achieve the highly accurate prediction of CEBEs without any empirical parameter for band-gapped crystals, and provide a more reliable theoretical approach than the conventional ΔSCF-DFT method.

Carbon Monoxide Hydrogenation on Ice Surfaces.

We have performed density functional calculations to investigate the carbon monoxide hydrogenation reaction (H+CO→HCO), which is important in interstellar clouds. We found that the activation energy of the reaction on amorphous ice is lower than that on crystalline ice. In the course of this study, we demonstrated that it is roughly possible to use the excitation energy of the reactant molecule (CO) in place of the activation energy. This relationship holds also for small water clusters at the CCSD level of calculation and the two-layer-level ONIOM (CCSD : X3LYP) calculation. Generally, since it is computationally demanding to estimate activation energies of chemical reactions in a circumstance of many water molecules, this relationship enables one to determine the activation energy of this reaction on ice surfaces from the knowledge of the excitation energy of CO only. Incorporating quantum-tunneling effects, we discuss the reaction rate on ice surfaces. Our estimate that the reaction rate on amorphous ice is almost twice as large as that on crystalline ice is qualitatively consistent with the experimental evidence reported by Hidaka et al. [Chem. Phys. Lett., 2008, 456, 36.].

First-principles study on the atomistic corrosion processes of iron.

The corrosion of iron presents an important scientific problem and a serious economic issue. It is also one of the most important subjects in materials science because it is basically an electrochemical process and closely related to other topics such as the electrocatalysis of the oxygen reduction reaction. So far, many studies have been conducted to address the corrosion of iron, a very complicated process that occurs when iron is exposed to oxygen and water. An important question is, at which site of the iron surface the corrosion starts and how it results in the final stage of the corrosion. In the present study, as an example of superficial defects, Fe dimers sticking out of Fe(100) surfaces are considered in order to understand the iron corrosion process from first-principles using density functional theory. We found that the Fe dimers spontaneously react with O2 and H2O to form Fe2(OH)4 + 4OH-. Here, it is interesting to note that the Fe dimer plays the role of a water splitting catalyst, because the space above it is always vacant and can accept oxygen molecules many times for reacting with the surrounding water molecules. Then, if the Fe2(OH)4 molecules are detached from the surface, they react with O2 to form Fe2O(OH)4 without an activation barrier, and, in turn, the Fe2O(OH)4 and H2O molecules react to form Fe2(OH)6 complexes with an activation energy of 0.653 eV. If these complexes further dissociate into Fe(OH)3 molecules, they react with each other to form Fe2O3·2H2O with an activation energy of 0.377 eV. This work may provide useful information on possible iron corrosion processes by water in the air.

Weakly spin-dependent band structures of antiferromagnetic perovskite LaMO3 (M = Cr, Mn, Fe).

We investigate the spin-dependent electronic states of antiferromagnetic (AFM) lanthanum chromite (LaCrO3), lanthanum manganite (LaMnO3), and lanthanum ferrite (LaFeO3) using spin-polarized first-principles density functional theory with Hubbard U correction. The band structures are calculated for 15 types of their different AFM structures. It is verified for these structures that there is a very simple rule to identify which wave number [Formula: see text] exhibits spin splitting or degeneracy in the band structure. This rule uses the symmetry operations that map the up-spin atoms onto the down-spin atoms. The resulting spin splitting is very small for the most stable spin configuration of the most stable experimental structure. We discuss a plausible benefit of this characteristic, i.e. the direction-independence of the spin current, in electrode applications.

Ovarian aromatase loss-of-function mutant medaka undergo ovary degeneration and partial female-to-male sex reversal after puberty.

Although estrogens have been generally considered to play a critical role in ovarian differentiation in non-mammalian vertebrates, the specific functions of estrogens during ovarian differentiation remain unclear. We isolated two mutants with premature stops in the ovarian aromatase (cyp19a1) gene from an N-ethyl-N-nitrosourea-based gene-driven mutagenesis library of the medaka, Oryzias latipes. In XX mutants, gonads first differentiated into normal ovaries containing many ovarian follicles that failed to accumulate yolk. Subsequently, ovarian tissues underwent extensive degeneration, followed by the appearance of testicular tissues on the dorsal side of ovaries. In the newly formed testicular tissue, strong expression of gsdf was detected in sox9a2-positive somatic cells surrounding germline stem cells suggesting that gsdf plays an important role in testicular differentiation during estrogen-depleted female-to-male sex reversal. We conclude that endogenous estrogens synthesized after fertilization are not essential for early ovarian differentiation but are critical for the maintenance of adult ovaries.

A simple derivation of the exact quasiparticle theory and its extension to arbitrary initial excited eigenstates.

The quasiparticle (QP) energies, which are minus of the energies required by removing or produced by adding one electron from/to the system, corresponding to the photoemission or inverse photoemission (PE/IPE) spectra, are determined together with the QP wave functions, which are not orthonormal and even not linearly independent but somewhat similar to the normal spin orbitals in the theory of the configuration interaction, by self-consistently solving the QP equation coupled with the equation for the self-energy. The electron density, kinetic, and all interaction energies can be calculated using the QP wave functions. We prove in a simple way that the PE/IPE spectroscopy and therefore this QP theory can be applied to an arbitrary initial excited eigenstate. In this proof, we show that the energy-dependence of the self-energy is not an essential difficulty, and the QP picture holds exactly if there is no relaxation mechanism in the system. The validity of the present theory for some initial excited eigenstates is tested using the one-shot GW approximation for several atoms and molecules.

A self-consistent GW approach to the van der Waals potential for a helium dimer.

van der Waals interaction between two helium (He) atoms is studied by calculating the total energy as a function of the He-He distance within the self-consistent GW approximation, which is expected to behave correctly in the long wavelength limit. In the Born-Oppenheimer (BO) approximation, the pair potential curve has its minimum value at 2.87 Å, which is somewhat larger than the local density approximation result, 2.40 Å, and is closer to previous quantum chemistry results. The expectation value for the interatomic distance, calculated by solving the Schrödinger equation for the two nuclei problem using the BO potential energy curve, is 30 Å, which is smaller but of the same order as previous experimental and theoretical results.

Relationship between cap structure and energy gap in capped carbon nanotubes.

Revealing a universal relation between geometrical structures and electronic properties of capped carbon nanotubes (CNTs) is one of the current objectives in nanocarbon community. Here, we investigate the local curvature of capped CNTs and define the cap region by a crossover behavior of the curvature energy versus the number of carbon atoms integrated from the tip to the tube region. Clear correlations among the energy gap of the cap localized states, the curvature energy, the number of carbon atoms in the cap region, and the number of specific carbon clusters are observed. The present analysis opens the way to understand the cap states.