Systematically improvable optimized atomic basis sets for {\it ab inito} calculations

We propose a unique scheme to construct fully optimized atomic basis sets for density-functional calculations. The shapes of the radial functions are optimized by minimizing the {\it spillage} of the wave functions between the atomic orbital calculations and the converged plane wave calculations for dimer systems. The quality of the bases can be systematically improved by increasing the size of the bases within the same framework. The scheme is easy to implement and very flexible. We have done extensive tests of this scheme for wide variety of systems. The results show that the obtained atomic basis sets are very satisfactory for both accuracy and transferability

Atom-projected and angular momentum resolved density of states in the ONETEP code

Local and angular momentum projected densities of states (DOS) are invaluable sources of information that can be obtained from density functional theory calculations. In this work, we describe a theoretical framework within ONETEP's linear-scaling DFT formalism that allows the calculation of local (atom-projected) and angular momentum projected density of states l-p-DOS. We describe four different bases that can be used for projecting the DOS with angular momentum resolution and perform a set of tests to compare them. We validate the results obtained with ONETEP's l-p-DOS against the plane-wave DFT code CASTEP. Comparable results between ONETEP's and CASTEP's charge spilling parameters are observed when we use pseudo-atomic orbitals as the projection basis sets. In general, the charge spilling parameters show remarkably low values for projections using non-contracted spherical waves as the angular momentum resolved basis. We also calculate the d-band and d-band centres for Pt atoms in (1 1 1) facets of cuboctahedral Pt nanoparticles of increasing size, which is an example of l-p-DOS application commonly used as an electronic descriptor in heterogeneous catalysis. Interestingly, the different projection bases lead to similar conclusions, showing the reliability of the implemented method for such studies. The implementation of these methods in a linear-scaling framework such as ONETEP provides another tool for analysing the electronic structure of complex nanostructured materials

Linear-scaling density-functional theory with tens of thousands of atoms: Expanding the scope and scale of calculations with ONETEP

ONETEP is an ab initio electronic structure package for total energy calculations within density-functional theory. It combines ‘linear scaling’, in that the total computational effort scales only linearly with system size, with ‘plane-wave’ accuracy, in that the convergence of the total energy is systematically improvable in the manner typical of conventional plane-wave pseudopotential methods. We present recent progress on improving the performance, and thus in effect the feasible scope and scale, of calculations with ONETEP on parallel computers comprising large clusters of commodity servers. Our recent improvements make calculations of tens of thousands of atoms feasible, even on fewer than 100 cores. Efficient scaling with number of atoms and number of cores is demonstrated up to 32,768 atoms on 64 cores.<br/

Dynamic behaviour of the silica-water-bio electrical double layer in the presence of a divalent electrolyte

Electronic devices are becoming increasingly used in chemical- and bio-sensing applications and therefore understanding the silica-electrolyte interface at the atomic scale is becoming increasingly important. For example, field-effect biosensors (BioFETs) operate by measuring perturbations in the electric field produced by the electrical double layer due to biomolecules binding on the surface. In this paper, explicit-solvent atomistic calculations of this electric field are presented and the structure and dynamics of the interface are investigated in different ionic strengths using molecular dynamics simulations. Novel results from simulation of the addition of DNA molecules and divalent ions are also presented, the latter of particular importance in both physiological solutions and biosensing experiments. The simulations demonstrated evidence of charge inversion, which is known to occur experimentally for divalent electrolyte systems. A strong interaction between ions and DNA phosphate groups was demonstrated in mixed electrolyte solutions, which are relevant to experimental observations of device sensitivity in the literature. The bound DNA resulted in local changes to the electric field at the surface; however, the spatial- and temporal-mean electric field showed no significant change. This result is explained by strong screening resulting from a combination of strongly polarised water and a compact layer of counterions around the DNA and silica surface. This work suggests that the saturation of the Stern layer is an important factor in determining BioFET response to increased salt concentration and provides novel insight into the interplay between ions and the electrical double layer

Lithium intercalation edge effects and doping implications for graphite anodes

The interface between the electrolyte and graphite anodes plays an important role for lithium (Li) intercalation and has significant impact on the charging/discharging performance of Lithium-Ion Batteries (LIBs). However, atomistic understanding of interface effects that would allow the interface to be rationally optimized for application needs is largely missing. Here we comprehensively study the energetics of Li intercalation near the main non-basal surfaces of graphite, namely the armchair and zigzag edges. We find that edge sites at both surfaces bind Li more strongly than in the bulk of graphite. Therefore, lithiation of these sites is expected to proceed at higher voltages than in the bulk. Furthermore, this effect is significantly more pronounced at the zigzag edge compared to the armchair edge due to its unique electronic structure. The “peculiar” topologically stabilized electronic surface state found at zigzag edges strongly interacts with Li, thereby changing Li diffusion behavior at the surface as well. Finally, we investigate boron (B)/nitrogen (N) doping as a promising strategy to tune the Li intercalation behavior at both edge systems, which could lead to enhanced intercalation kinetics in B/N doped graphite anodes

O(N) methods in electronic structure calculations

Linear scaling methods, or O(N) methods, have computational and memory requirements which scale linearly with the number of atoms in the system, N, in contrast to standard approaches which scale with the cube of the number of atoms. These methods, which rely on the short-ranged nature of electronic structure, will allow accurate, ab initio simulations of systems of unprecedented size. The theory behind the locality of electronic structure is described and related to physical properties of systems to be modelled, along with a survey of recent developments in real-space methods which are important for efficient use of high performance computers. The linear scaling methods proposed to date can be divided into seven different areas, and the applicability, efficiency and advantages of the methods proposed in these areas is then discussed. The applications of linear scaling methods, as well as the implementations available as computer programs, are considered. Finally, the prospects for and the challenges facing linear scaling methods are discussed.Comment: 85 pages, 15 figures, 488 references. Resubmitted to Rep. Prog. Phys (small changes

Dimensionality of Carbon Nanomaterials Determines the Binding and Dynamics of Amyloidogenic Peptides: Multiscale Theoretical Simulations

Experimental studies have demonstrated that nanoparticles can affect the rate of protein self-assembly, possibly interfering with the development of protein misfolding diseases such as Alzheimer's, Parkinson's and prion disease caused by aggregation and fibril formation of amyloid-prone proteins. We employ classical molecular dynamics simulations and large-scale density functional theory calculations to investigate the effects of nanomaterials on the structure, dynamics and binding of an amyloidogenic peptide apoC-II(60-70). We show that the binding affinity of this peptide to carbonaceous nanomaterials such as C60, nanotubes and graphene decreases with increasing nanoparticle curvature. Strong binding is facilitated by the large contact area available for π-stacking between the aromatic residues of the peptide and the extended surfaces of graphene and the nanotube. The highly curved fullerene surface exhibits reduced efficiency for π-stacking but promotes increased peptide dynamics. We postulate that the increase in conformational dynamics of the amyloid peptide can be unfavorable for the formation of fibril competent structures. In contrast, extended fibril forming peptide conformations are promoted by the nanotube and graphene surfaces which can provide a template for fibril-growth