A5005828580- Advanced Chemical Physics Studies
- Spectroscopy and Quantum Chemical Studies
- Protein Structure and Dynamics
- Machine Learning in Materials Science
- Advancements in Battery Materials
- Electrochemical Analysis and Applications
- Advanced Battery Materials and Technologies
- X-ray Diffraction in Crystallography
- Electrocatalysts for Energy Conversion
- Molecular Junctions and Nanostructures
- Crystallization and Solubility Studies
- Analytical Chemistry and Sensors
- Catalytic Processes in Materials Science
- Electrostatics and Colloid Interactions
- Quantum and electron transport phenomena
- nanoparticles nucleation surface interactions
- DNA and Nucleic Acid Chemistry
- Advanced NMR Techniques and Applications
- Conducting polymers and applications
- Crystallography and molecular interactions
- Inorganic Fluorides and Related Compounds
- Organic Electronics and Photovoltaics
- Semiconductor materials and devices
- Computational Drug Discovery Methods
- Material Dynamics and Properties
University of Southampton
2016-2025
The Faraday Institution
2020-2024
Gdańsk University of Technology
2020-2024
Lancaster University
2024
Culham Science Centre
2020
University of California, Berkeley
2019
Lanzhou University of Technology
2017
University of Oxford
2005-2017
University of Cambridge
1998-2006
Curtin University
2006
We present ONETEP (order-N electronic total energy package), a density functional program for parallel computers whose computational cost scales linearly with the number of atoms and processors. is based on our reformulation plane wave pseudopotential method which exploits localization that inherent in systems nonvanishing band gap. summarize theoretical developments enable direct optimization strictly localized quantities expressed terms delocalized basis. These same lead us to physical way...
We present an overview of the onetep program for linear-scaling density functional theory (DFT) calculations with large basis set (plane-wave) accuracy on parallel computers. The DFT energy is computed from matrix, which constructed spatially localized orbitals we call Non-orthogonal Generalized Wannier Functions (NGWFs), expressed in terms periodic sinc (psinc) functions. During calculation, both matrix and NGWFs are optimized localization constraints. By taking advantage localization, able...
Current research challenges in areas such as energy and bioscience have created a strong need for Density Functional Theory (DFT) calculations on metallic nanostructures of hundreds to thousands atoms provide understanding at the atomic level technologically important processes catalysis magnetic materials. Linear-scaling DFT methods with insulators are now reaching maturity. However not applicable metals, where continuum states through chemical potential their partial occupancies...
Silanol groups at the silica-water interface determine not only surface charge, but also have an important role in binding of ions and biomolecules. As pH is increased above 2, silica develops a net negative charge primarily due to deprotonation silanol group. An improved understanding energetics mechanisms this fundamentally process would further relevant dynamics.Density Functional Theory ab initio molecular dynamics geometry optimisations were used investigate neutralisation charging...
The VV10 and rVV10 nonlocal correlation functionals are consistently implemented assessed, with the goal of determining if functional can replace in recently developed B97M-V density functional, to give B97M-rV functional. Along way, four simultaneously tested: VV10, rVV10, B97M-V, B97M-rV. An initial assessment is carried out across S22 data set, short-range damping variable, b, varied for all order determine sensitivity empirical parameter. results this test indicate that a value b = 6...
We present a reformulation of the plane-wave pseudopotential method for insulators. This new approach allows us to perform density-functional calculations by solving directly ``nonorthogonal generalized Wannier functions'' rather than extended Bloch states. outline theory on which our is based and test variety systems. Comparison results with standard code shows that they are equivalent. Apart from usual advantages such as applicability any lattice symmetry high accuracy, also benefits...
We study the hydration of actinyl cations, uranyl UO22+ and plutonyl PuO22+, by performing Kohn−Sham Density Functional Theory calculations using a new quantum chemistry codeMAGIC. The have been performed on separate species, complexes AcO22+·nH2O (Ac = U, Pu n 4, 5, 6), in gas aqueous phases. liquid-state environmental effects are included via simple cavity model self-consistent reaction field method. find that solvent crucial. By this, we mean model, alone, will be incapable giving insight...
We present a novel quantum mechanical/molecular mechanics (QM/MM) approach in which subsystem is coupled to classical described by the AMOEBA polarizable force field. Our permits mutual polarization between QM and MM subsystems, effected through multipolar electrostatics. Self-consistency achieved for both subsystems total energy minimization scheme. provide an expression Hamiltonian of QM/MM system, we minimize using gradient methods. The onetep linear-scaling DFT approach, makes use...
Linear-scaling electronic structure methods are essential for calculations on large systems. Some of these approaches use a systematic basis set, the completeness which may be tuned with an adjustable parameter similar to energy cut-off plane-wave techniques. The search ground state in such suffers from ill-conditioning is related kinetic contribution total and results unacceptably slow convergence. We present general preconditioning scheme overcome this implement it within our own...
We present a comparison of methods for treating the electrostatic interactions finite, isolated systems within periodic boundary conditions (PBCs), Density Functional Theory (DFT), with particular emphasis on linear-scaling (LS) DFT. Often, PBCs are not physically realistic but an unavoidable consequence choice basis set and efficacy using Fourier transforms to compute Hartree potential. In such cases effects calculations need be avoided, so that results obtained represent open rather than...
We present an implicit solvent model for ab initio electronic structure calculations which is fully self-consistent and based on direct solution of the nonhomogeneous Poisson equation. The solute cavity naturally defined in terms isosurface density according to formula Fattebert Gygi (J. Comp. Chem. 23, 6 (2002)). While this depends only two parameters, we demonstrate that by using appropriate boundary conditions dispersion-repulsion contributions, solvation energies obtained extensive test...
Biomolecular simulations with atomistic detail are often required to describe interactions chemical accuracy for applications such as the calculation of free energies binding or reactions in enzymes. Force fields typically used this task but these rely on extensive parameterisation which cases can lead limited and transferability, example ligands unusual functional groups. These limitations be overcome first principles calculations methods density theory (DFT) at a much higher computational...
The use of the Zwanzig equation in calculation single-step perturbations to provide first-principles (ab initio) quantum mechanics (QM) correction terms molecular (MM) free energy cycles is well established. A rigorous test ability converge such calculations would be very useful this context. In work, we perform a direct assessment convergence MM QM perturbation, by attempting reverse perturbation. This required generation extensive dynamics trajectories, using density functional theory...
A new method for finite-temperature density functional theory calculations which significantly increases the number of atoms that can be simulated in metallic systems is presented. self-consistent, direct minimization technique used to obtain Helmholtz free energy electronic system, described terms a set non-orthogonal, localized functions are optimized situusing periodic-sinc basis set, equivalent plane waves. Most parts calculation, including demanding operation building Hamiltonian...
We present a hybrid MPI-OpenMP implementation of Linear-Scaling Density Functional Theory within the ONETEP code. illustrate its performance on range high computing (HPC) platforms comprising shared-memory nodes with fast interconnect. Our work has focused applying OpenMP parallelism to routines which dominate computational load, attempting where possible parallelize different loops from those already parallelized MPI. This includes 3D FFT box operations, sparse matrix algebra calculation...
Many studies of heterogeneous catalysis, both experimental and computational, make use idealized structures such as extended surfaces or regular polyhedral nanoparticles. This simplification neglects the morphological diversity in real commercial oxygen reduction reaction (ORR) catalysts used fuel-cell cathodes. Here we introduce an approach that combines 3D nanoparticle obtained from high-throughput high-precision electron microscopy with density functional theory. Discrepancies between...
Significance Tuberculosis is a major global pandemic responsible for more deaths than any other infectious disease, yet no effective vaccine exists. Here, we demonstrate CD1b expression within human tuberculous granulomas, supporting role lipid antigen presentation in host immunity to infection. presents mycolates, the dominant Mycobacterium tuberculosis (Mtb) cell wall class and key virulence factors, αβ T cells. We reveal that mycolate tail moieties, distal head group, are antigenic...
Crystal structure prediction involves a search of complex configurational space for local minima corresponding to stable crystal structures, which can be performed efficiently using atom-atom force fields the assessment intermolecular interactions. However, challenging systems, limitations in accuracy prevent reliable relative thermodynamic stability potential while cost fully quantum mechanical approaches limit applications methods. We present method rapidly improve field lattice energies...
Implicit solvent models are a computationally efficient method of representing solid/liquid interfaces prevalent in electrocatalysis, energy storage, and materials science. However, electronic structure changes induced at the metallic surface by dielectric continuum not fully understood. To address this, we perform DFT calculations for Pt(111)/water interface, order to compare Poisson–Boltzmann solvation methods with ab initio molecular dynamics (AIMD) simulations explicit solvent. We show...
The chemical structure of a molecule influences the molecular conformation in solid-state affecting crystal packing, which turn drives charge carrier transport anisotropy.
Preorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and it may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here, we evaluate ability AMOEBA polarizable force field, well additive Amber ff14SB Charmm C36m models, describe present site peptidyl-prolyl isomerase cyclophilin A. We compare mechanical those calculated fully...
The ensemble of structures generated by molecular mechanics (MM) simulations is determined the functional form force field employed and its parameterization. For a given form, quality parameterization crucial will determine how accurately we can compute observable properties from simulations. While accurate parameterizations are available for biomolecules, such as proteins or DNA, new molecules, drug candidates, particularly challenging these may involve groups interactions which parameters...
Quantum mechanical binding free energies based on thousands of full-protein DFT calculations are tractable, reproducible and converge well.