41 research outputs found
Point defects and clustering in uranium dioxide by LSDA+U calculations
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
beta-U4O9. Finally we generalize the point defect model to the independent
clusters approximation to include clustering effects, the impact on defect
populations is discussed.Comment: 20 pages, 12 figure
Computational Analysis of the Interaction Energies between Amino Acid Residues of the Measles Virus Hemagglutinin and Its Receptors
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