1. |
- Palumbo, M., et al.
(författare)
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Thermodynamic modelling of crystalline unary phases
- 2014
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Ingår i: Physica status solidi. B, Basic research. - : Wiley. - 0370-1972 .- 1521-3951. ; 251:1, s. 14-32
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Tidskriftsartikel (refereegranskat)abstract
- Progress in materials science through thermodynamic modelling may rest crucially on access to a database, such as that developed by Scientific Group Thermodata Europe (SGTE) around 1990. It gives the Gibbs energy G(T) of the elements in the form of series as a function of temperature, i.e. essentially a curve fitting to experimental data. In the light of progress in theoretical understanding and first-principles calculation methods, the possibility for an improved database description of the thermodynamics of the elements has become evident. It is the purpose of this paper to provide a framework for such work. Lattice vibrations, which usually give the major contribution to G(T), are treated in some detail with a discussion of neutron scattering studies of anharmonicity in aluminium, first-principles calculations including ab initio molecular dynamics (AIMD), and the strength and weakness of analytic model representations of data. Similarly, electronic contributions to G(T) are treated on the basis of the density of states N(E) for metals, with emphasis on effects at high T. Further, we consider G(T) below 300K, which is not covered by SGTE. Other parts in the paper discuss metastable and dynamically unstable lattices, G(T) in the region of superheated solids and the requirement on a database in the calculation of phase diagrams.
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2. |
- Romagnoni, A, et al.
(författare)
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Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data
- 2019
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1, s. 10351-
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Tidskriftsartikel (refereegranskat)abstract
- Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machine learning (ML) approaches incited us to apply them to classify healthy and diseased people according to their genomic information. The Immunochip dataset containing 18,227 CD patients and 34,050 healthy controls enrolled and genotyped by the international Inflammatory Bowel Disease genetic consortium (IIBDGC) has been re-analyzed using a set of ML methods: penalized logistic regression (LR), gradient boosted trees (GBT) and artificial neural networks (NN). The main score used to compare the methods was the Area Under the ROC Curve (AUC) statistics. The impact of quality control (QC), imputing and coding methods on LR results showed that QC methods and imputation of missing genotypes may artificially increase the scores. At the opposite, neither the patient/control ratio nor marker preselection or coding strategies significantly affected the results. LR methods, including Lasso, Ridge and ElasticNet provided similar results with a maximum AUC of 0.80. GBT methods like XGBoost, LightGBM and CatBoost, together with dense NN with one or more hidden layers, provided similar AUC values, suggesting limited epistatic effects in the genetic architecture of the trait. ML methods detected near all the genetic variants previously identified by GWAS among the best predictors plus additional predictors with lower effects. The robustness and complementarity of the different methods are also studied. Compared to LR, non-linear models such as GBT or NN may provide robust complementary approaches to identify and classify genetic markers.
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3. |
- Saunders, C. N., et al.
(författare)
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Thermal expansion and phonon anharmonicity of cuprite studied by inelastic neutron scattering and ab initio calculations
- 2022
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Ingår i: Physical Review B. - : AMER PHYSICAL SOC. - 2469-9950 .- 2469-9969. ; 105:17
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Tidskriftsartikel (refereegranskat)abstract
- Inelastic neutron scattering measurements were performed with a time-of-flight chopper spectrometer to observe phonons in all parts of the Brillouin zone of a single crystal of cuprite Cu2O. We reduced the experimental data to phonon dispersions in the high-symmetry directions, and changes between 10 and 300 K are reported. In this paper, we show ab initio quasiharmonic (QH) and anharmonic (AH) calculations of phonon dispersions. We performed all AH calculations with a temperature-dependent effective potential method. Both QH and AH calculations account for the small negative thermal expansion of cuprite at low temperatures. However, the measured temperature-dependent phonon behavior was predicted more accurately with the AH calculations than the QH ones. Nevertheless, at 300 K, the cubic AH used in this paper did not entirely account for the experimental phonon dispersions in cuprite.
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