Explainable machine learning for materials discovery: predicting the potentially formable Nd-Fe-B crystal structures and extracting the structure-stability relationship.

New Nd-Fe-B crystal structures can be formed via the elemental substitution of -- host structures, including lanthanides (), transition metals () and light elements, = B, C, N and O. The 5967 samples of ternary -- materials that are collected are then used as the host structures. For each host crystal structure, a substituted crystal structure is created by substituting all lanthanide sites with Nd, all transition metal sites with Fe and all light-element sites with B.

Computational study of positron annihilation parameters for cation mono-vacancies and vacancy complexes in nitride semiconductor alloys.

We calculate positron annihilation parameters, namely the S and W parameters from the Doppler broadening spectroscopy and the positron lifetime [Formula: see text], for defect-free states as well as cation mono-vacancies and vacancy complexes in nitride semiconductor alloys AlGaN, InGaN and AlInN. The obtained distributions of these parameters differ from compound to compound. Especially, the S-W relation for InGaN is very different from that for AlGaN.

Is it possible for short peptide composed of positively- and negatively-charged "hydrophilic" amino acid residue-clusters to form metastable "hydrophobic" packing?

We theoretically and experimentally analyzed a conformational ensemble of a small, characteristic polypeptide consisting of positively- and negatively-charged amino acid residue clusters, (Lys)9(Glu)9(Lys)9, designed based on the supercoiled DNA-recognition (SDR) domain, with the capability of preferentially binding to supercoiled DNA. Advanced molecular dynamics (MD) simulations coupled with a generalized ensemble technique revealed that substantial amounts of ordered, helical structures were present at the boundaries of the Lys and Glu segments in the obtained conformational ensemble. In fact, the helical content of the peptide calculated from our MD simulations was consistent with that estimated from our experimental analysis employing circular dichroism (CD) spectroscopy.

Learning structure-property relationship in crystalline materials: A study of lanthanide-transition metal alloys.

We have developed a descriptor named Orbital Field Matrix (OFM) for representing material structures in datasets of multi-element materials. The descriptor is based on the information regarding atomic valence shell electrons and their coordination. In this work, we develop an extension of OFM called OFM1.

Machine learning reveals orbital interaction in materials.

We propose a novel representation of materials named an 'orbital-field matrix (OFM)', which is based on the distribution of valence shell electrons. We demonstrate that this new representation can be highly useful in mining material data. Experimental investigation shows that the formation energies of crystalline materials, atomization energies of molecular materials, and local magnetic moments of the constituent atoms in bimetal alloys of lanthanide metal and transition-metal can be predicted with high accuracy using the OFM.

Quantum transport localization through graphene.

Localization of atomic defect-induced electronic transport through a single graphene layer is calculated using a full-valence electronic structure description as a function of the defect density and taking into account the atomic-scale deformations of the layer. The elementary electronic destructive interferences leading to Anderson localization are analyzed. The low-voltage current intensity decreases with increasing length and defect density, with a calculated localization length ζ = 3.

Novel mixture model for the representation of potential energy surfaces.

We demonstrate that knowledge of chemical physics on a materials system can be automatically extracted from first-principles calculations using a data mining technique; this information can then be utilized to construct a simple empirical atomic potential model. By using unsupervised learning of the generative Gaussian mixture model, physically meaningful patterns of atomic local chemical environments can be detected automatically. Based on the obtained information regarding these atomic patterns, we propose a chemical-structure-dependent linear mixture model for estimating the atomic potential energy.

Direct theoretical evidence for weaker correlations in electron-doped and Hg-based hole-doped cuprates.

Many important questions for high-Tc cuprates are closely related to the insulating nature of parent compounds. While there has been intensive discussion on this issue, all arguments rely strongly on, or are closely related to, the correlation strength of the materials. Clear understanding has been seriously hampered by the absence of a direct measure of this interaction, traditionally denoted by U.

Contact conductance of a graphene nanoribbon with its graphene nano-electrodes.

Electronically contacted between two graphene nano-electrodes, the contact conductance (G0) of a graphene nanoribbon (GNR) molecular wire is calculated using mono-electronic Elastic Scattering Quantum Chemistry (ESQC) theory. Different nano-electrode contact geometries are considered ranging from a top face to face van der Waals contact to an adiabatic funnel like planar chemical bonding. The Tamm state contributions to the GNR-graphene nano-electrode electronic interactions are discussed as a function of the molecular orbital hybridization.

Quasiparticle self-consistent GW study of cuprates: electronic structure, model parameters, and the two-band theory for Tc.

Despite decades of progress, an understanding of unconventional superconductivity still remains elusive. An important open question is about the material dependence of the superconducting properties. Using the quasiparticle self-consistent GW method, we re-examine the electronic structure of copper oxide high-Tc materials.

High performance organic field-effect transistors based on single-crystal microribbons and microsheets of solution-processed dithieno[3,2-b:2',3'-d]thiophene derivatives.

We present π-conjugated dithieno[3,2-b:2',3'-d]thiophene derivatives that act as high-performance p-type organic semiconductors. These molecules self-organize into single-crystal microribbons or microsheets. High carrier mobilities of up to 10.

A theoretical investigation of the functional role of the axial methionine ligand of the Cu(A) site in cytochrome c oxidase.

The functional roles of the amino acid residues of the Cu(A) site in bovine cytochrome c oxidase (CcO) were investigated by utilizing hybrid quantum mechanics (QM)/molecular mechanics (MM) calculations. The energy levels of the molecular orbitals (MOs) involving Cu d(zx) orbitals unexpectedly increased, as compared with those found previously with a simplified model system lacking the axial Met residue (i.e.

Modulation of electronic structures of bases through DNA recognition of protein.

The effects of environmental structures on the electronic states of functional regions in a fully solvated DNA·protein complex were investigated using combined ab initio quantum mechanics/molecular mechanics calculations. A complex of a transcriptional factor, PU.1, and the target DNA was used for the calculations.

Re-examination of half-metallic ferromagnetism for doped LaMnO(3) in a quasiparticle self-consistent GW method.

We apply the quasiparticle self-consistent GW (QSGW) method to a cubic virtual-crystal alloy La(1-x)Ba(x)MnO(3) as a theoretical representative for colossal magnetoresistive perovskite manganites. The QSGW predicts it as a fully polarized half-metallic ferromagnet for a wide range of x and lattice constant. Calculated density of states and dielectric functions are consistent with experiments.

Transport properties of a biphenyl-based molecular junction system-the electrode metal dependence.

We investigate the transport properties of a biphenyl-dithiol molecule sandwiched between electrodes made of metal Y (Y = Cu, Ag and Au) using the non-equilibrium Green's function method based on a density functional theory. The electrode metal Y has an influence on the coupling between the molecule and electrodes, and thus on the transmission peak height. For the transmission T(Y) at the Fermi energy, we obtain T(Cu)∼T(Ag) View Article and Find Full Text PDF

Dependence of the conduction of a single biphenyl dithiol molecule on the dihedral angle between the phenyl rings and its application to a nanorectifier.

The transport properties of a biphenyl dithiol (BPD) molecule sandwiched between two gold electrodes are studied using the nonequilibrium Green's function method based on the density functional theory. In particular, their dependence on the dihedral angle (phi=90 degrees -180 degrees ) between two phenyl rings is investigated. While the dihedral-angle dependence of the density of states projected on the BPD molecular orbitals is small, the transport properties change dramatically with phi.

Electronic structure of DNA nucleobases and their dinucleotides explored by soft X-ray spectroscopy.

The electronic structures of a series of DNA nucleobases and their dinucleotides were investigated by N 1s X-ray absorption, X-ray photoemission, and resonant X-ray emission spectroscopy. Resonant X-ray emission spectra of the guanine base and its dinucleotide indicate that it has a weak structure at the lowest binding energy; at this energy, it isolates from the main valence band and forms the HOMO state. This indicates that the HOMO state is localized in the guanine base, as claimed by valence and core photoemissions and expected from theoretical predictions.

Theoretical investigation on electron transport through an organic molecule: effect of the contact structure.

Knowing how the contact geometry influences the conductance of a molecular wire junction requires both a precise determination of the molecule/metallic-electrode interface structure and an evaluation of the conductance for different contact geometries with a fair accuracy. With a greatly improved method to solve the Lippmann-Schwinger equation, we are able to include at least one atomic layer of each electrode into the extended molecule. The artificial effect of the jellium model used for the electrodes is therefore significantly reduced.