Collective dipole excitations in sodium clusters

Some properties of small and medium sodium clusters are described within the RPA approach using a projected spherical single particle basis. The oscillator strengths calculated with a Schiff-like dipole transition operator and folded with Lorentzian functions are used to calculate the photoabsorbtion cross section spectra. The results are further employed to establish the dependence of the plasmon frequency on the number of cluster components. Static electric polarizabilities of the clusters excited in a RPA dipole state are also calculated. Comparison of our results with the corresponding experimental data show an overall good agreement.Comment: 23 pages, 5 figure

Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity

Most computational methods that infer somatic copy number alterations (SCNAs) from bulk sequencing of DNA analyse tumour samples individually. However, the sequencing of multiple tumour samples from a patient's disease is an increasingly common practice. We introduce Refphase, an algorithm that leverages this multi-sampling approach to infer haplotype-specific copy numbers through multi-sample phasing. We demonstrate Refphase's ability to infer haplotype-specific SCNAs and characterise their intra-tumour heterogeneity, to uncover previously undetected allelic imbalance in low purity samples, and to identify parallel evolution in the context of whole genome doubling in a pan-cancer cohort of 336 samples from 99 tumours