Comparative survey of the relative impact of mRNA features on local ribosome profiling read density

Ribosome profiling (Ribo-seq), a promising technology for exploring ribosome decoding rates, is characterized by the presence of infrequent high peaks in ribosome footprint density and by long alignment gaps. Here, to reduce the impact of data heterogeneity we introduce a simple normalization method, Ribo-seq Unit Step Transformation (RUST). RUST is robust and outperforms other normalization techniques in the presence of heterogeneous noise. We illustrate how RUST can be used for identifying mRNA sequence features that affect ribosome footprint densities globally. We show that a few parameters extracted with RUST are sufficient for predicting experimental densities with high accuracy. Importantly the application of RUST to 30 publicly available Ribo-seq data sets revealed a substantial variation in sequence determinants of ribosome footprint frequencies, questioning the reliability of Ribo-seq as an accurate representation of local ribosome densities without prior quality control. This emphasizes our incomplete understanding of how protocol parameters affect ribosome footprint densities.

Inter-ELM evolution of the edge current density profile on the ASDEX upgrade tokamak

The sudden decrease of plasma stored energy and subsequent power deposition on the first wall of a tokamak due to edge localised modes (ELMs) is potentially detrimental to the success of a future fusion reactor. Understanding and control of ELMs is critical for the longevity of these devices and also to maximise their performance. The commonly accepted picture of ELMs posits a critical pressure gradient and current density in the plasma edge, above which coupled magnetohy drodynamic peeling-ballooning modes become unstable. Much analysis has been presented in recent years on the spatial and temporal evolution of the edge pressure gradient. However, the edge current density has typically been overlooked due to the difficulties in measuring this quantity. In this thesis, a novel method of current density recovery is presented, using the equilibrium solver CLISTE to reconstruct a high resolution equilibrium utilising both external magnetic and internal edge kinetic data measured on the ASDEX Upgrade tokamak. The evolution of the edge current density relative to an ELM crash is presented, showing that a resistive delay in the buildup of the current density is unlikely. An uncertainty analysis shows that the edge current density can be determined with an accuracy consistent with that of the kinetic data used. A comparison with neoclassical theory demonstrates excellent agreement be- tween the current density determined by CLISTE and the calculated profiles. Three ELM mitigation regimes are investigated: Type-II ELMs, ELMs sup- pressed by external magnetic perturbations, and Nitrogen seeded ELMs. In the first two cases, the current density is found to decrease as mitigation on- sets, indicating a more ballooning-like plasma behaviour. In the latter case, the flux surface averaged current density can decrease while the local current density increases, providing a mechanism to suppress both the peeling and ballooning modes.

Precursor adsorption on copper surfaces as the first step during the deposition of copper: a density functional study with van der Waals correction

Copper dimethylamino-2-propoxide [Cu(dmap)2] is used as a precursor for low-temperature atomic layer deposition (ALD) of copper thin films. Chemisorption of the precursor is the necessary first step of ALD, but it is not known in this case whether there is selectivity for adsorption sites, defects, or islands on the substrate. Therefore, we study the adsorption of the Cu(dmap)2 molecule on the different sites on flat and rough Cu surfaces using PBE, PBE-D3, optB88-vdW, and vdW-DF2 methods. We found the relative order of adsorption energies for Cu(dmap)2 on Cu surfaces is Eads (PBE-D3) > Eads (optB88-vdW) > Eads (vdW-DF2) > Eads (PBE). The PBE and vdW-DF2 methods predict one chemisorption structure, while optB88-vdW predicts three chemisorption structures for Cu(dmap)2 adsorption among four possible adsorption configurations, whereas PBE-D3 predicts a chemisorbed structure for all the adsorption sites on Cu(111). All the methods with and without van der Waals corrections yield a chemisorbed molecule on the Cu(332) step and Cu(643) kink because of less steric hindrance on the vicinal surfaces. Strong distortion of the molecule and significant elongation of Cu–N bonds are predicted in the chemisorbed structures, indicating that the ligand–Cu bonds break during the ALD of Cu from Cu(dmap)2. The molecule loses its initial square-planar structure and gains linear O–Cu–O bonding as these atoms attach to the surface. As a result, the ligands become unstable and the precursor becomes more reactive to the coreagent. Charge redistribution mainly occurs between the adsorbate O–Cu–O bond and the surface. Bader charge analysis shows that electrons are donated from the surface to the molecule in the chemisorbed structures, so that the Cu center in the molecule is partially reduced.