A comprehensive investigation on point defects and their clustering behavior in nonstoichiometric uranium dioxide UO2±x is carried out using LSDA+U method based on density functional theory. Accurate energetic information and charge transfers available so far are obtained. With these energies that have improved more than 50% over that of pure GGA and LDA, we show the density functional theory predicts the predominance of oxygen defects over uranium ones at any compositions, which is possible only after treated the localized 5f electrons properly. Calculations also suggest an upper bound of x ∼ 0.03 for oxygen clusters to start off. The volume change induced by point uranium defects is monotonic but nonlinear, whereas for oxygen defects, increase x always reduces the system volume linearly, except dimers that require extra space for accommodation, which has been identified as meta-stable ionic molecule. Though oxygen dimers usually occupy Willis O ′′ sites and mimic a single oxygen in energetics and charge state, they are rare at ambient conditions. Its decomposition process and vibrational properties have been studied carefully. To obtain a general clustering mechanism in anion-excess fluorites systematically, we also analyze the local stabilities of possible basic clustering modes of oxygen defects. The result shows an unified way to understand the structure of Willis type and cuboctahedral clusters in UO2+x and β-U4O9. Finally we generalize the point defect model to the independent clusters approximation to include clustering effects, the impact on defect populations is discussed.

A first-principles calculation for uranium dioxide (UO 2 ) in an antiferromagnetic structure with four types of point defects, uranium vacancy, oxygen vacancy, uranium interstitial, and oxygen interstitial, has been performed by the projector-augmented-wave method with generalized gradient approximation combined with the Hubbard U correction. Defect formation energies are estimated under lattice relaxation for supercells containing 1, 2, and 8 unit cells of UO 2 . The electronic structure, the atomic displacement and the stability of defected systems are obtained, and the effects of cell sizes on these properties are discussed. The results form a self-consistent dataset of formation energies and atomic distance variations of various point defects in UO 2 with relatively high precision. We show that a supercell with 8 UO 2 unit cells or larger is necessary to investigate the defect behavior with reliable precision, since point defects have a wide-ranging effect, not only on the first nearest neighbor atoms of the defect, but on the second neighbors and on more distant atoms.

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Measles virus (MV) causes an acute and highly devastating contagious disease in humans. Employing the crystal structures of three human receptors, signaling lymphocyte-activation molecule (SLAM), CD46, and Nectin-4, in complex with the measles virus hemagglutinin (MVH), we elucidated computationally the details of binding energies between the amino acid residues of MVH and those of the receptors with an ab initio fragment molecular orbital (FMO) method. The calculated inter-fragment interaction energies (IFIEs) revealed a number of significantly interacting amino acid residues of MVH that played essential roles in binding to the receptors. As predicted from previously reported experiments, some important amino-acid residues of MVH were shown to be common but others were specific to interactions with the three receptors. Particularly, some of the (non-polar) hydrophobic residues of MVH were found to be attractively interacting with multiple receptors, thus indicating the importance of the hydrophobic pocket for intermolecular interactions (especially in the case of Nectin-4). In contrast, the electrostatic interactions tended to be used for specific molecular recognition. Furthermore, we carried out FMO calculations for in silico experiments of amino acid mutations, finding reasonable agreements with virological experiments concerning the substitution effect of residues. Thus, the present study demonstrates that the electron-correlated FMO method is a powerful tool to search exhaustively for amino acid residues that contribute to interactions with receptor molecules. It is also applicable for designing inhibitors of MVH and engineered MVs for cancer therapy.