Publications (167)621.27 Total impact
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ABSTRACT: We placed isoflurane, a general anaesthetic, inside palmitoyloleoylphosphatidylcholine (POPC) bilayers at clinical concentration, and performed molecular dynamics simulations at atmospheric and raised pressures, using two different thermodynamic ensembles. We also performed a simulation of this system with isoflurane at ten times the clinical concentration. We found that isoflurane did not aggregate inside POPC membranes at 20 MPa, nor at 40 MPa. The implications of these findings for pressure reversal is discussed, in light of the highpressure neurological syndrome. 

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ABSTRACT: We have used ab initio total energy plane wave pseudopotential methods to perform the first completely ab initio investigation of the atomic and electronic structure of a grain boundary in a transition metal oxide. The ∑ = 15 (210)[001] tilt boundary in rutile TiG2 is studied using the conjugate gradients iterative minimisation technique for performing total energy calculations within the LDA and pseudopotential approximations. The stability of the experimentally observed translation state of the boundary is confirmed, and some insight is gained into its electronic structure. 

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ABSTRACT: The microscopic structure of a tilt and a twist boundary in germanium are explored using a stateoftheart total energy calculation. The structure of the tilt boundary (Σ = 5 (310)) is found to be simple as it exhibits a well defined minimum energy structure, consistent with previous experimental and theoretical results on this and other tilt boundaries. The structure of the twist boundary (Σ = 5 (100)), however, is found to be very complex. The boundary bonds are distorted and weak, and their weakness makes the twist boundary exhibit a wealth of local energy minima. The different types of energy minima for the twist boundaries are identified and studied in some detail. We summarize the consequence of the orientation of the two crystal grains upon the microscopic structure of the boundaries, and speculate about future applications.  [Show abstract] [Hide abstract]
ABSTRACT: Plane wave basis sets are widely used in ab initio electronic structure calculations even though such an expansion in terms of extended states does not provide a natural way of quantifying local atomic properties. To overcome this deficiency we have implemented a scheme for projection of plane wave states onto a localised basis set. This approach is used to calculate atomic charges and bond populations, and is illustrated by application to a selection of small molecules. Finally, we calculate the changes in these quantities induced by adsorption of a molecule onto a zeolite substrate. Thus, using the procedure described in this paper, plane wave calculations can yield the same information as traditional quantum chemical methods.  [Show abstract] [Hide abstract]
ABSTRACT: An ab initio density functional theory study is reported of the conformational energy map of acetylcholine, with respect to the two central dihedral angles of the molecule. The acetylcholine molecule pays a central role in neurotransmission and has been studied widely using semiempirical computational modelling. The ab initio results are compared with a number of previous investigations and with experiment. The ab initio data indicate that the most stable conformation of acetylcholine is the trans, gauche arrangement of the central dihedral angles. Furthermore, Mulliken population analysis of the electronic structure of the molecule in this conformation indicates that the positive charge of the molecule is spread over the exterior of the cationic head of the molecule.  [Show abstract] [Hide abstract]
ABSTRACT: We present calculations of formation energies of defects in an ionic solid (Al(2)O(3)) extrapolated to the dilute limit, corresponding to a simulation cell of infinite size. The largescale calculations required for this extrapolation are enabled by developments in the approach to parallel sparse matrix algebra operations, which are central to linearscaling densityfunctional theory calculations. The computational cost of manipulating sparse matrices, whose sizes are determined by the large number of basis functions present, is greatly improved with this new approach. We present details of the sparse algebra scheme implemented in the ONETEP code using hierarchical sparsity patterns, and demonstrate its use in calculations on a wide range of systems, involving thousands of atoms on hundreds to thousands of parallel processes. 
Article: Proteinprotein interaction from linearscaling firstprinciples quantummechanical calculations
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ABSTRACT: A modification of the MMPBSA technique for calculating binding affinities of biomolecular complexes is presented. Classical molecular dynamics is used to explore the motion of the extended interface between two peptides derived from the BRC4 repeat of BRCA2 and the eukaryotic recombinase RAD51. The resulting trajectory is sampled using the linearscaling density functional theory code, onetep, to determine from first principles, and with high computational efficiency, the relative free energies of binding of the ˜2800 atom receptorligand complexes. This new method provides the basis for computational interrogation of proteinprotein and proteinligand interactions, within fields ranging from chemical biological studies to small molecule binding behaviour, with both unprecedented chemical accuracy and affordable computational expense. 
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ABSTRACT: ONETEP is an ab initio electronic structure package for total energy calculations within densityfunctional theory. It combines ‘linear scaling’, in that the total computational effort scales only linearly with system size, with ‘planewave’ accuracy, in that the convergence of the total energy is systematically improvable in the manner typical of conventional planewave 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.  [Show abstract] [Hide abstract]
ABSTRACT: When a brittle material is loaded to the limit of its strength, it fails by the nucleation and propagation of a crack. The conditions for crack propagation are created by stress concentration in the region of the crack tip and depend on macroscopic parameters such as the geometry and dimensions of the specimen. The way the crack propagates, however, is entirely determined by atomicscale phenomena, because brittle crack tips are atomically sharp and propagate by breaking the variously oriented interatomic bonds, one at a time, at each point of the moving crack front. The physical interplay of multiple length scales makes brittle fracture a complex 'multiscale' phenomenon. Several intermediate scales may arise in more complex situations, for example in the presence of microdefects or grain boundaries. The occurrence of various instabilities in crack propagation at very high speeds is well known, and significant advances have been made recently in understanding their origin. Here we investigate lowspeed propagation instabilities in silicon using quantummechanical hybrid, multiscale modelling and singlecrystal fracture experiments. Our simulations predict a cracktip reconstruction that makes lowspeed crack propagation unstable on the (111) cleavage plane, which is conventionally thought of as the most stable cleavage plane. We perform experiments in which this instability is observed at a range of low speeds, using an experimental technique designed for the investigation of fracture under low tensile loads. Further simulations explain why, conversely, at moderately high speeds crack propagation on the (110) cleavage plane becomes unstable and deflects onto (111) planes, as previously observed experimentally.  [Show abstract] [Hide abstract]
ABSTRACT: ONETEP is a linear scaling code for performing firstprinciples total energy calculations within densityfunctional theory (DFT). The method is based on the densitymatrix formulation of DFT and involves the iterative minimization of the total energy with respect to a set of local orbitals and a density kernel. An overview is given of the kernel optimization methods proposed in the literature and implemented in ONETEP, focusing in particular on the constraints of compatibility, idempotency and normalization that must be applied. A method is proposed for locating the chemical potential which may be useful in applying the normalization constraint and analysing the electronic structure near the Fermi level.  [Show abstract] [Hide abstract]
ABSTRACT: Ab initio calculations are presented of the cohesive energies of aluminium in a number of diverse hypothetical structures which span a wide range of the coordination number, C, from C = 0 to C = 12. The calculations have been performed to investigate the nature of multiatom bonding, its dependence on C and to form a database for testing and developing empirical and semiempirical models. The results support the saturation of cohesive energy for large C predicted by several simple theoretical models. Calculations on the same structures using semiempirical schemes suggest that these methods might have a greater degree of accuracy than had previously been believed.  [Show abstract] [Hide abstract]
ABSTRACT: An overview is presented of the method used to parallelize a set of total energy pseudopotential codes on a 64node i860 Meiko Computing Surface and a 32node Intel iPSC/860 Hypercube. These codes have been used to calculate the surface energies and relaxed structures of the 3 × 3, 5 × 5 and 7 × 7 Takayanagi reconstructions of the (111) surface of silicon. It is found that the 7 × 7 reconstruction has the lowest energy and that structural trends across the series of reconstructions can be related to the degree of charge transfer from the adatoms to the rest atoms.  [Show abstract] [Hide abstract]
ABSTRACT: Basis set superposition error (BSSE) in densityfunctional calculations occurs when the extended Kohn–Sham orbitals are expanded in localised basis sets, but is absent when a planewave basis is used. Elimination of BSSE is essential for the accurate description of intermolecular forces. Linearscaling methods are formulated in terms of local orbitals, making planewaves an inappropriate choice of basis. In this work the BSSE in linearscaling methods is studied in the context of hydrogen bonds. In particular it is shown that BSSE is eliminated by optimizing the local orbitals in situ using a systematic basis set equivalent to a set of planewaves.  [Show abstract] [Hide abstract]
ABSTRACT: We review the main features of a recently proposed molecular dynamics method in which quantum mechanical calculations are embedded in a classical force model within a unified scheme free of boundary region and transferability problems. The scheme is based on the idea of augmenting a parametrized analytic force model by incorporating in it the quantum mechanical information necessary to compute accurate trajectories. This is achieved through a suitable fitting procedure in which the parameters of a classical interatomic force field are adjusted at run time to reproduce highaccuracy results which are computed separately on system subsets by tightbinding or DFTbased “black box” computing engines.  [Show abstract] [Hide abstract]
ABSTRACT: This paper provides a general overview of the methodology implemented in onetep (OrderN Electronic Total Energy Package), a parallel densityfunctional theory code for largescale firstprinciples quantummechanical calculations. The distinctive features of onetep are linearscaling in both computational effort and resources, obtained by making wellcontrolled approximations which enable simulations to be performed with planewave accuracy. Titanium dioxide clusters of increasing size designed to mimic surfaces are studied to demonstrate the accuracy and scaling of onetep.
Publication Stats
17k  Citations  
621.27  Total Impact Points  
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Institutions

19902015

University of Cambridge
 • Department of Physics: Cavendish Laboratory
 • Theory of Condensed Matter (TCM)
Cambridge, England, United Kingdom


1998

Technical University of Denmark
 Department of Physics
København, Capital Region, Denmark


19851998

Massachusetts Institute of Technology
 Department of Physics
Cambridge, Massachusetts, United States


1994

ChristianAlbrechtsUniversität zu Kiel
Kiel, SchleswigHolstein, Germany 
The University of Edinburgh
 School of Physics and Astronomy
Edinburgh, Scotland, United Kingdom


1993

Cardiff University
Cardiff, Wales, United Kingdom 
Oak Ridge National Laboratory
 Solid State Division
Oak Ridge, Florida, United States


19921993

University of Bath
 Department of Physics
Bath, England, United Kingdom


1991

Los Andes University (Colombia)
Μπογκοτά, Bogota D.C., Colombia
