Linear Scaling Density Matrix Real Time TDDFT: Propagator Unitarity \& Matrix Truncation

Real time, density matrix based, time dependent density functional theory proceeds through the propagation of the density matrix, as opposed to the Kohn-Sham orbitals. It is possible to reduce the computational workload by imposing spatial cut-off radii on sparse matrices, and the propagation of the density matrix in this manner provides direct access to the optical response of very large systems, which would be otherwise impractical to obtain using the standard formulations of TDDFT. Following a brief summary of our implementation, along with several benchmark tests illustrating the validity of the method, we present an exploration of the factors affecting the accuracy of the approach. In particular we investigate the effect of basis set size and matrix truncation, the key approximation used in achieving linear scaling, on the propagator unitarity and optical spectra. Finally we illustrate that, with an appropriate density matrix truncation range applied, the computational load scales linearly with the system size and discuss the limitations of the approach.Comment: Accepted for publication in J. Chem. Phy

DSSC Anchoring Groups: A Surface Dependent Decision

Electrodes in dye sensitised solar cells (DSSCs) are typically nanocrystalline anatase TiO2 with a majority (101) surface exposed. Generally the sensitising dye employs a carboxylic anchoring moiety through which it adheres to the TiO2 surface. Recent interest in exploiting the properties of differing TiO2 electrode morphologies, such as rutile nanorods exposing the (110) surface and anatase electrodes with high percentages of the (001) surface exposed, begs the question of whether this anchoring strategy is best, irrespective of the majority surface exposed. Here we address this question by presenting density functional theory calculations contrasting the binding properties of two promising anchoring groups, phosphonic acid and boronic acid, to that of carboxylic acid. Anchor-electrode interactions are studied for the pro- totypical anatase (101) surface, along with the anatase (001) and rutile (110) surfaces. Finally the effect of using these alternative anchoring groups to bind a typical coumarin dye (NKX- 2311) to these TiO2 substrates is examined. Significant differences in the binding properties are found depending on both the anchor and surface, illustrating that the choice of anchor is necessarily dependent upon the surface exposed in the electrode. In particular the boronic acid is found to show the potential to be an excellent anchor choice for electrodes exposing the anatase (001) surface.Comment: 44 pages, 15 figures, accepted by J. Phys.:Condens. Matter. Coordinates for structures available via figshar

Intrinsic Oxygen Vacancy and Extrinsic Aluminium Dopant Interplay: A Route to the Restoration of Defective TiO2_2

Density functional theory (DFT) and DFT corrected for on-site Coulomb interactions (DFT+U) calculations are presented on Aluminium doping in bulk TiO$_2$ and the anatase (101) surface. Particular attention is paid to the mobility of oxygen vacancies throughout the doped TiO$_2$ lattice, as a means by which charge compensation of trivalent dopants can occur. The effect that Al doping of TiO$_2$ electrodes has in dye sensitised solar cells is explained as a result of this mobility and charge compensation. Substitutional defects in which one Al3+ replaces one Ti4+ are found to introduce valence band holes, while intrinsic oxygen vacancies are found to introduce states in the band-gap. Coupling two of these substitutional defects with an oxygen vacancy results in exothermic defect formation which maintain charge neutrality. Nudged elastic band calculations have been performed to investigate the formation of these clustered defects in the (101) surface by oxygen vacancy diffusion, with the resulting potential energy surface suggesting energetic gains with small diffusion barriers. Efficiency in- creases observed in dye sensitised solar cells as a result of aluminium doping of TiO$_2$ electrodes are investigated by adsorbing the tetrahydroquinoline C2-1 chromophore on the defective surfaces. Adsorption on the clustered extrinsic Al3+ and intrinsic oxygen vacancy defects are found to behave as if adsorbed on a clean surface, with vacancy states not present, while adsorption on the oxygen vacancy results in a down shift of the dye localised states within the band-gap and defect states being present below the conduction band edge. Aluminium doping therefore acts as a benign dopant for 'cleaning' TiO$_2$ through oxygen vacancy diffusion.Comment: 32 pages, 15 figures, accepted for publication by J. Phys. Chem.

crystal-torture: A Crystal Tortuosity Module

crystal_torture: A crystal structure analysis code, allowing site tortuosity to be calculated.This work was funded by EPSRC Grant No. EP/N004302/1, and was supported with fund- ing from the Faraday Institution (faraday.ac.uk; EP/S003053/1), grant number FIRG003. B.J.M. acknowledges support from the Royal Society (UF130329)

Anion-polarisation--directed short-range-order in antiperovskite Li2_2FeSO

Short-range ordering in cation-disordered cathodes can have a significant effect on their electrochemical properties. Here, we characterise the cation short-range order in the antiperovskite cathode material Li$_2$FeSO, using density functional theory, Monte Carlo simulations, and synchrotron X-ray pair-distribution-function data. We predict partial short-range cation-ordering, characterised by favourable OLi$_4$Fe$_2$ oxygen coordination with a preference for polar cis-OLi$_4$Fe$_2$ over non-polar trans-OLi$_4$Fe$_2$ configurations. This preference for polar cation configurations produces long-range disorder, in agreement with experimental data. The predicted short-range-order preference contrasts with that for a simple point-charge model, which instead predicts preferential trans-OLi$_4$Fe$_2$ oxygen coordination and corresponding long-range crystallographic order. The absence of long-range order in Li$_2$FeSO can therefore be attributed to the relative stability of cis-OLi$_4$Fe$_2$ and other non-OLi$_4$Fe$_2$ oxygen-coordination motifs. We show that this effect is associated with the polarisation of oxide and sulfide anions in polar coordination environments, which stabilises these polar short-range cation orderings. We propose similar anion-polarisation-directed short-range-ordering may be present in other heterocationic materials that contain cations with different formal charges. Our analysis also illustrates the limitations of using simple point-charge models to predict the structure of cation-disordered materials, where other factors, such as anion polarisation, may play a critical role in directing both short- and long-range structural correlations

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

DFT Dataset for "Interfacial Strain Effects on Lithium Diffusion Pathways in the Spinel Solid Electrolyte Li-Doped MgAl2O4"

This dataset contains inputs and outputs for the VASP calculations described in the manuscript "Interfacial Strain Effects on Lithium Diffusion Pathways in the Spinel Solid Electrolyte Li-Doped MgAl2O4", and scripts for extracting the appropriate resulting data into .csv files, for further analysis. For more information see: C. O’Rourke and B. J. Morgan, "Interfacial Strain Effects on Lithium Diffusion Pathways in the Spinel Solid Electrolyte Li-Doped MgAl2O4" The repository consists of 1. Input and output files for a series of VASP calculations. 2. A series of Python command-line scripts for extracting relevant data from these DFT calculations, and collating them in .csv files

DSSC Anchoring Groups

<p>Structures for study of DSSC binding to titania surfaces depending on acid binding groups</p

DFT Dataset for "Interfacial Strain Effects on Lithium Diffusion Pathways in the Spinel Solid Electrolyte Li-Doped MgAl2O4"

This dataset contains inputs and outputs for the VASP calculations described in the manuscript "Interfacial Strain Effects on Lithium Diffusion Pathways in the Spinel Solid Electrolyte Li-Doped MgAl2O4", and scripts for extracting the appropriate resulting data into .csv files, for further analysis. For more information see: C. O’Rourke and B. J. Morgan, "Interfacial Strain Effects on Lithium Diffusion Pathways in the Spinel Solid Electrolyte Li-Doped MgAl2O4" The repository consists of 1. Input and output files for a series of VASP calculations. 2. A series of Python command-line scripts for extracting relevant data from these DFT calculations, and collating them in .csv files

Data Analysis for "Interfacial Strain Effects on Lithium Diffusion Pathways in the Spinel Solid Electrolyte Li-Doped MgAl2O4"

This repository contains data analysis that supports the findings reported in C. O’Rourke and B. J. Morgan, “Interfacial Strain Effects on Lithium Diffusion Pathways in the Spinel Solid Electrolyte Li-Doped MgAl2O4”, and code for plotting figures in this paper. The repository consists of - A series of .csv files, containing data extracted from VASP calculations. The inputs and outputs for the source VASP calculations, along with scripts for extracting the relevant data, are available at the University of Bath Data Archive (https://doi.org/10.15125/BATH-00438). - A Jupyter notebook that constructs the figures in the manuscript from the .csv data