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1. Determination of the nitrogen vacancy as a shallow compensating center in GaN doped with divalent metals

Author

Buckeridge, J., Catlow, C. R. A., Scanlon, D. O., Keal, T. W., Sherwood, P., Miskufova, M., Walsh, A., Woodley, S. M., and Sokol, A. A.

Subjects
Condensed Matter - Materials Science
Abstract

We report accurate energetics of defects introduced in GaN on doping with divalent metals, focussing on the technologically important case of Mg doping, using a model which takes into consideration both the effect of hole localisation and dipolar polarisation of the host material, and includes a well-defined reference level. Defect formation and ionisation energies show that divalent dopants are counterbalanced in GaN by nitrogen vacancies and not by holes, which explains both the difficulty in achieving p-type conductivity in GaN and the associated major spectroscopic features, including the ubiquitous 3.46 eV photoluminescence line, a characteristic of all lightly divalent metal-doped GaN materials that has also been shown to occur in pure GaN samples. Our results give a comprehensive explanation for the observed behaviour of GaN doped with low concentrations of divalent metals in good agreement with relevant experiment., Comment: 6 pages, 3 figures

Published
2014
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3. Buckeridgeet al.Reply

Author

Buckeridge, J., primary, Catlow, C. R. A., additional, Scanlon, D. O., additional, Keal, T. W., additional, Sherwood, P., additional, Miskufova, M., additional, Walsh, A., additional, Woodley, S. M., additional, and Sokol, A. A., additional

Published
2015
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5. Choice of exchange-correlation functional for computing NMR indirect spin-spin coupling constants

Author

Keal, T. W., Helgaker, T., Salek, Pawel, Tozer, D. J., Keal, T. W., Helgaker, T., Salek, Pawel, and Tozer, D. J.

Abstract

The choice of exchange-correlation functional for the determination of indirect nuclear spin-spin coupling constants in density-functional theory is considered. In an assessment of one-bond (1)J(CH) couplings, the PBE functional was recently shown [S.N. Maximoff, J.E. Peralta, V. Barone, G.E. Scuseria, J. Chem. Theory Comput. 1 (2005) 541] to perform well, significantly outperforming B3LYP. For couplings involving N, 0, and F atoms in simple molecules, we demonstrate that the opposite is observed; PBE is considerably less accurate than B3LYP. By contrast, the B97-2 and B97-3 semi-empirical functionals provide good, consistent quality couplings for all these atom types in an extensive assessment., QC 20100525

Published
2006
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6. Assessment of a Coulomb-attenuated exchange-correlation energy functional

Author

Peach, M. J. G., Helgaker, T., Salek, Pawel, Keal, T. W., Lutnaes, O. B., Tozer, D. J., Handy, N. C., Peach, M. J. G., Helgaker, T., Salek, Pawel, Keal, T. W., Lutnaes, O. B., Tozer, D. J., and Handy, N. C.

Abstract

The recently proposed CAM-B3LYP exchange-correlation energy functional, based on a partitioning of the r(12)(-1) operator in the exchange interaction into long- and short-range components, is assessed for the determination of molecular thermochemistry, structures, and second order response properties. Rydberg and charge transfer excitation energies and static electronic polarisabilities are notably improved over the standard B3LYP functional; classical reaction barriers also improve. Ionisation potentials, bond lengths, NMR shielding constants and indirect spin-spin coupling constants are comparable with the two functionals. CAM-B3LYP atomisation energies and diatomic harmonic vibrational wavenumbers are less accurate than those of B3LYP. Future research directions are outlined., QC 20100525

Published
2005
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7. Materials and Molecular Modeling at the Exascale

Author

Thomas W. Keal, Alin-Marin Elena, Alexey A. Sokol, Karen Stoneham, Matt I. J. Probert, Clotilde S. Cucinotta, David J. Willock, Andrew J. Logsdail, Andrea Zen, Phil J. Hasnip, Ian J. Bush, Matthew Watkins, Dario Alfe, Chris-Kriton Skylaris, Basile F. E. Curchod, Qiong Cai, Scott M. Woodley, Keal, T. W., Elena, A. -M., Sokol, A. A., Stoneham, K., Probert, M. I. J., Cucinotta, C. S., Willock, D. J., Logsdail, A. J., Zen, A., Hasnip, P. J., Bush, I. J., Watkins, M., Alfe', D., Skylaris, C. -K., Curchod, B. F. E., Cai, Q., and Woodley, S. M.

Subjects
General Computer Science, General Engineering
Abstract

Progression of computational resources towards exascale computing makes possible simulations of unprecedented accuracy and complexity in the fields of materials and molecular modelling (MMM), allowing high fidelity in silico experiments on complex materials of real technological interest. However, this presents demanding challenges for the software used, especially the exploitation of the huge degree of parallelism available on exascale hardware, and the associated problems of developing effective workflows and data management on such platforms. As part of the UKs ExCALIBUR exascale computing initiative, the UK-led MMM Design and Development Working Group has worked with the broad MMM community to identify a set of high priority application case studies which will drive future exascale software developments. We present an overview of these case studies, categorized by the methodological challenges which will be required to realize them on exascale platforms, and discuss the exascale requirements, software challenges and impact of each application area.

Published
2022
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8. Buckeridge et al. Reply:.

Author

Buckeridge, J., Catlow, C. R. A., Scanlon, D. O., Keal, T. W., Sherwood, P., Miskufova, M., Walsh, A., Woodley, S. M., and Sokol, A. A.

Subjects
*NITROGEN, *GALLIUM nitride, *SEMICONDUCTOR doping
Abstract

A response from the authors of the article "Determination of the Nitrogen Vacancy as a Shallow Compensating Center in GaN Doped with Divalent Metals" in the 2015 issue is presented.

Published
2015
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9. A STAG2-PAXIP1/PAGR1 axis suppresses lung tumorigenesis.

Author

Ashkin EL, Tang YJ, Xu H, Hung KL, Belk JA, Cai H, Lopez SS, Dolcen DN, Hebert JD, Li R, Ruiz PA, Keal T, Andrejka L, Chang HY, Petrov DA, Dixon JR, Xu Z, and Winslow MM

Subjects
Humans, Animals, Cell Line, Tumor, Mice, Gene Expression Regulation, Neoplastic, CRISPR-Cas Systems, Antigens, Nuclear metabolism, Antigens, Nuclear genetics, Tumor Suppressor Proteins metabolism, Tumor Suppressor Proteins genetics, Cohesins, Lung Neoplasms pathology, Lung Neoplasms metabolism, Lung Neoplasms genetics, Cell Cycle Proteins metabolism, Cell Cycle Proteins genetics, Carcinogenesis genetics, Carcinogenesis metabolism
Abstract

The cohesin complex is a critical regulator of gene expression. STAG2 is the most frequently mutated cohesin subunit across several cancer types and is a key tumor suppressor in lung cancer. Here, we coupled somatic CRISPR-Cas9 genome editing and tumor barcoding with an autochthonous oncogenic KRAS-driven lung cancer model and showed that STAG2 is uniquely tumor-suppressive among all core and auxiliary cohesin components. The heterodimeric complex components PAXIP1 and PAGR1 have highly correlated effects with STAG2 in human lung cancer cell lines, are tumor suppressors in vivo, and are epistatic to STAG2 in oncogenic KRAS-driven lung tumorigenesis in vivo. STAG2 inactivation elicits changes in gene expression, chromatin accessibility, and 3D genome conformation that impact the cancer cell state. Gene expression and chromatin accessibility similarities between STAG2- and PAXIP1-deficient neoplastic cells further relate STAG2-cohesin to PAXIP1/PAGR1. These findings reveal a STAG2-PAXIP1/PAGR1 tumor-suppressive axis and uncover novel PAXIP1-dependent and PAXIP1-independent STAG2-cohesin-mediated mechanisms of lung tumor suppression., (© 2024 Ashkin et al.)

Published
2025
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10. A STAG2-PAXIP1/PAGR1 axis suppresses lung tumorigenesis.

Author

Ashkin EL, Tang YJ, Xu H, Hung KL, Belk J, Cai H, Lopez S, Dolcen DN, Hebert JD, Li R, Ruiz PA, Keal T, Andrejka L, Chang HY, Petrov DA, Dixon JR, Xu Z, and Winslow MM

Abstract

The cohesin complex is a critical regulator of gene expression. STAG2 is the most frequently mutated cohesin subunit across several cancer types and is a key tumor suppressor in lung cancer. Here, we coupled somatic CRISPR-Cas9 genome editing and tumor barcoding with an autochthonous oncogenic KRAS-driven lung cancer model and show that STAG2 is uniquely tumor suppressive among all core and auxiliary cohesin components. The heterodimeric complex components PAXIP1 and PAGR1 have highly correlated effects with STAG2 in human lung cancer cell lines, are tumor suppressors in vivo , and are epistatic to STAG2 in oncogenic KRAS-driven lung tumorigenesis in vivo . STAG2 inactivation elicits changes in gene expression, chromatin accessibility and 3D genome conformation that impact cancer cell state. Gene expression and chromatin accessibility similarities between STAG2- and PAXIP1-deficient neoplastic cells further relates STAG2-cohesin to PAXIP1/PAGR1. These findings reveal a STAG2-PAXIP1/PAGR1 tumor-suppressive axis and uncover novel PAXIP1-dependent and PAXIP1-independent STAG2-cohesin mediated mechanisms of lung tumor suppression., Summary: STAG2 is a frequently mutated cohesin subunit across several cancers and one of the most important functional suppressors of lung adenocarcinoma. Our findings underscore important roles of STAG2 in suppressing lung tumorigenesis and highlight a STAG2-PAXIP1/PAGR1 tumor-suppressive program that may transcend cancer type.

Published
2024
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