Spin-polarization-induced structural selectivity in Pd3X_3X and Pt3X_3X (X=3dX=3d) compounds

Spin-polarization is known to lead to important {\it magnetic} and {\it optical} effects in open-shell atoms and elemental solids, but has rarely been implicated in controlling {\it structural} selectivity in compounds and alloys. Here we show that spin-polarized electronic structure calculations are crucial for predicting the correct $T=0$ crystal structures for Pd$_3X$ and Pt$_3X$ compounds. Spin-polarization leads to (i) stabilization of the $L1_2$ structure over the $DO_{22}$ structure in Pt$_3$Cr, Pd$_3$Cr, and Pd$_3$Mn, (ii) to the stabilization of the $DO_{22}$ structure over the $L1_2$ structure in Pd$_3$Co and to (iii) ordering (rather than phase-separation) in Pt$_3$Co and Pd$_3$Cr. The results are analyzed in terms of first-principles local spin density calculations.Comment: 4 pages, REVTEX, 3 eps figures, to appear in PR

Reliability of panel-based mutational signatures for immune-checkpoint-inhibition efficacy prediction in non-small cell lung cancer

OBJECTIVES: Mutational signatures (MS) are gaining traction for deriving therapeutic insights for immune checkpoint inhibition (ICI). We asked if MS attributions from comprehensive targeted sequencing assays are reliable enough for predicting ICI efficacy in non-small cell lung cancer (NSCLC).METHODS: Somatic mutations of m = 126 patients were assayed using panel-based sequencing of 523 cancer-related genes. In silico simulations of MS attributions for various panels were performed on a separate dataset of m = 101 whole genome sequenced patients. Non-synonymous mutations were deconvoluted using COSMIC v3.3 signatures and used to test a previously published machine learning classifier.RESULTS: The ICI efficacy predictor performed poorly with an accuracy of 0.51 -0.09 +0.09, average precision of 0.52 -0.11 +0.11, and an area under the receiver operating characteristic curve of 0.50 -0.09 +0.10. Theoretical arguments, experimental data, and in silico simulations pointed to false negative rates (FNR) related to panel size. A secondary effect was observed, where deconvolution of small ensembles of point mutations lead to reconstruction errors and misattributions. CONCLUSION: MS attributions from current targeted panel sequencing are not reliable enough to predict ICI efficacy. We suggest that, for downstream classification tasks in NSCLC, signature attributions be based on whole exome or genome sequencing instead.</p

Point-charge electrostatics in disordered alloys

A simple analytic model of point-ion electrostatics has been previously proposed in which the magnitude of the net charge q_i on each atom in an ordered or random alloy depends linearly on the number N_i^(1) of unlike neighbors in its first coordination shell. Point charges extracted from recent large supercell (256-432 atom) local density approximation (LDA) calculations of Cu-Zn random alloys now enable an assessment of the physical validity and accuracy of the simple model. We find that this model accurately describes (i) the trends in q_i vs. N_i^(1), particularly for fcc alloys, (ii) the magnitudes of total electrostatic energies in random alloys, (iii) the relationships between constant-occupation-averaged charges and Coulomb shifts (i.e., the average over all sites occupied by either $A$ or $B$ atoms) in the random alloy, and (iv) the linear relation between the site charge q_i and the constant- charge-averaged Coulomb shift (i.e., the average over all sites with the same charge) for fcc alloys. However, for bcc alloys the fluctuations predicted by the model in the q_i vs. V_i relation exceed those found in the LDA supercell calculations. We find that (a) the fluctuations present in the model have a vanishing contribution to the electrostatic energy. (b) Generalizing the model to include a dependence of the charge on the atoms in the first three (two) shells in bcc (fcc) - rather than the first shell only - removes the fluctuations, in complete agreement with the LDA data. We also demonstrate an efficient way to extract charge transfer parameters of the generalized model from LDA calculations on small unit cells.Comment: 15 pages, ReVTeX galley format, 7 eps figures embedded using psfig, to be published in Phys. Rev.

Importance of Correlation Effects on Magnetic Anisotropy in Fe and Ni

We calculate magnetic anisotropy energy of Fe and Ni by taking into account the effects of strong electronic correlations, spin-orbit coupling, and non-collinearity of intra-atomic magnetization. The LDA+U method is used and its equivalence to dynamical mean-field theory in the static limit is emphasized. Both experimental magnitude of MAE and direction of magnetization are predicted correctly near U=4 eV for Ni and U=3.5 eV for Fe. Correlations modify one-electron spectra which are now in better agreement with experiments.Comment: 4 pages, 2 figure

Cation- and vacancy-ordering in Li_xCoO_2

Using a combination of first-principles total energies, a cluster expansion technique, and Monte Carlo simulations, we have studied the Li/Co ordering in LiCoO_2 and Li-vacancy/Co ordering in CoO_2. We find: (i) A ground state search of the space of substitutional cation configurations yields the (layered) CuPt structure as the lowest-energy state in the octahedral system LiCoO_2 (and CoO_2), in agreement with the experimentally observed phase. (ii) Finite temperature calculations predict that the solid-state order- disorder transitions for LiCoO_2 and CoO_2 occur at temperatures (~5100 K and ~4400 K, respectively) much higher than melting, thus making these transitions experimentally inaccessible. (iii) The energy of the reaction E(LiCoO_2) - E(CoO_2) - E(Li) gives the average battery voltage V of a Li_xCoO_2/Li cell. Searching the space of configurations for large average voltages, we find that CuPt (a monolayer superlattice) has a high voltage (V=3.78 V), but that this could be increased by cation randomization (V=3.99 V), partial disordering (V=3.86 V), or by forming a 2-layer Li_2Co_2O_4 superlattice along (V=4.90 V).Comment: 12 Pages, RevTeX galley format, 5 figures embedded using epsf Phys. Rev. B (in press, 1998

Electric fields and valence band offsets at strained [111] heterojunctions

[111] ordered common atom strained layer superlattices (in particular the common anion GaSb/InSb system and the common cation InAs/InSb system) are investigated using the ab initio full potential linearized augmented plane wave (FLAPW) method. We have focused our attention on the potential line-up at the two sides of the homopolar isovalent heterojunctions considered, and in particular on its dependence on the strain conditions and on the strain induced electric fields. We propose a procedure to locate the interface plane where the band alignment could be evaluated; furthermore, we suggest that the polarization charges, due to piezoelectric effects, are approximately confined to a narrow region close to the interface and do not affect the potential discontinuity. We find that the interface contribution to the valence band offset is substantially unaffected by strain conditions, whereas the total band line-up is highly tunable, as a function of the strain conditions. Finally, we compare our results with those obtained for [001] heterojunctions.Comment: 18 pages, Latex-file, to appear in Phys.Rev.

First-principles calculations of the self-trapped exciton in crystalline NaCl

The atomic and electronic structure of the lowest triplet state of the off-center (C2v symmetry) self-trapped exciton (STE) in crystalline NaCl is calculated using the local-spin-density (LSDA) approximation. In addition, the Franck-Condon broadening of the luminescence peak and the a1g -> b3u absorption peak are calculated and compared to experiment. LSDA accurately predicts transition energies if the initial and final states are both localized or delocalized, but 1 eV discrepancies with experiment occur if one state is localized and the other is delocalized.Comment: 4 pages with 4 embeddded figure

Theory of structural response to macroscopic electric fields in ferroelectric systems

We have developed and implemented a formalism for computing the structural response of a periodic insulating system to a homogeneous static electric field within density-functional perturbation theory (DFPT). We consider the thermodynamic potentials E(R,eta,e) and F(R,eta,e) whose minimization with respect to the internal structural parameters R and unit cell strain eta yields the equilibrium structure at fixed electric field e and polarization P, respectively. First-order expansion of E(R,eta,e) in e leads to a useful approximation in which R(P) and eta(P) can be obtained by simply minimizing the zero-field internal energy with respect to structural coordinates subject to the constraint of a fixed spontaneous polarization P. To facilitate this minimization, we formulate a modified DFPT scheme such that the computed derivatives of the polarization are consistent with the discretized form of the Berry-phase expression. We then describe the application of this approach to several problems associated with bulk and short-period superlattice structures of ferroelectric materials such as BaTiO3 and PbTiO3. These include the effects of compositionally broken inversion symmetry, the equilibrium structure for high values of polarization, field-induced structural phase transitions, and the lattice contributions to the linear and the non-linear dielectric constants.Comment: 19 pages, with 15 postscript figures embedded. Uses REVTEX4 and epsf macros. Also available at http://www.physics.rutgers.edu/~dhv/preprints/sai_pol/index.htm

A noncoding, regulatory mutation implicates HCFC1 in nonsyndromic intellectual disability

The discovery of mutations causing human disease has so far been biased toward protein-coding regions. Having excluded all annotated coding regions, we performed targeted massively parallel resequencing of the nonrepetitive genomic linkage interval at Xq28 of family MRX3. We identified in the binding site of transcription factor YY1 a regulatory mutation that leads to overexpression of the chromatin-associated transcriptional regulator HCFC1. When tested on embryonic murine neural stem cells and embryonic hippocampal neurons, HCFC1 overexpression led to a significant increase of the production of astrocytes and a considerable reduction in neurite growth. Two other nonsynonymous, potentially deleterious changes have been identified by X-exome sequencing in individuals with intellectual disability, implicating HCFC1 in normal brain function