Jacek Dziedzic

Jacek Dziedzic
University of Southampton · Division of Chemistry

PhD

About

43
Publications
20,642
Reads
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704
Citations
Introduction
My main research interests: (1) linear-scaling density functional theory, (2) QM/MM, particularly with DFT and polarisable force fields, (3) implicit solvation methods, particularly in the context of DFT, (4) Hartree-Fock exchange and hybrid functionals, (5) molecular dynamics. I am one of the main developers of ONETEP (a linear-scalnig DFT code). In my spare time I enjoy playing guitar, reading and music.
Additional affiliations
November 2016 - present
University of Southampton
Position
  • Research Associate
October 2012 - present
Gdansk University of Technology
Position
  • Professor (Assistant)
October 2009 - November 2016
University of Southampton
Position
  • PostDoc Position
Education
October 2002 - September 2009
Gdansk University of Technology
Field of study
  • Solid state physics
October 1997 - September 2002
Gdansk University of Technology
Field of study
  • Computational physics

Publications

Publications (43)
Article
Full-text available
We present an implicit solvent model for ab initio electronic structure calculations which is fully self-consistent and is based on direct solution of the nonhomogeneous Poisson equation. The solute cavity is naturally defined in terms of an isosurface of the electronic density according to the formula of Fattebert and Gygi (J. Comp. Chem. 23, 6 (2...
Article
Full-text available
We present a method for the calculation of four-centre two-electron repulsion integrals in terms of localised non-orthogonal generalised Wannier functions (NGWFs). Our method has been implemented in the ONETEP program and is used to compute the Hartree-Fock exchange energy component of Hartree-Fock and Density Functional Theory (DFT) calculations w...
Article
We report on the structure and mass transport properties of liquid Al–Cu alloys predicted by two recently-developed empirical many-body potentials: MEAM (Jelinek et al., 2012) and EAM-ADP (Apostol and Mishin, 2011), and by the well-known Gupta potential. Total and partial pair correlation functions, angular distribution functions, densities, coordi...
Article
We extend our recently developed quantum-mechanical/molecular mechanics (QM/MM) approach [Dziedzic et al., J. Chem. Phys. 145, 124106 (2016)] to enable in situ optimization of the localized orbitals. The quantum subsystem is described with onetep linear-scaling density functional theory and the classical subsystem - with the AMOEBA polarizable forc...
Article
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 the density matrix, which is constructed from spatially localized orbitals we call Non-orthogonal Generalized Wannier Functions (NGWFs), expres...
Article
Li nucleation on graphite anode probed using large-scale grand-canonical density functional theory simulations in electrolyte environment under applied voltage in Li-ion batteries.
Article
We extend our linear-scaling approach for the calculation of Hartree-Fock exchange energy using localized, in-situ-optimized orbitals to leverage massive parallelism. Our approach has been implemented in the ONETEP density functional theory framework, which employs a~basis of non-orthogonal generalized Wannier Functions (NGWFs) to achieve linear sc...
Article
Lithium metal plating is a critical safety issue in Li-ion cells with graphite anodes, and contributes significantly to ageing, drastically limiting the lifetime and inducing capacity loss. Nonetheless, the nucleation mechanism of metallic Li on graphite anodes is still poorly understood. But in-depth understanding is needed to rationally design mi...
Article
Progress in electrochemical technologies, such as automotive batteries, supercapacitors, and fuel cells, depends greatly on developing improved charged interfaces between electrodes and electrolytes. The rational development of such interfaces can benefit from the atomistic understanding of the materials involved by first-principles quantum mechani...
Article
Full-text available
Density functional theory (DFT) is often used for simulating extended materials such as infinite crystals or surfaces, under periodic boundary conditions (PBCs). In such calculations, when the simulation cell has non-zero charge, electrical neutrality has to be imposed, and this is often done via a uniform background charge of opposite sign (“jelli...
Preprint
Density functional theory (DFT) is often used for simulating extended materials such as infinite crystals or surfaces, under periodic boundary conditions (PBCs). In such calculations, when the simulation cell has non-zero charge, electrical neutrality has to be imposed and this is often done via a uniform background charge of opposite sign (`jelliu...
Article
Full-text available
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 may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here we evaluate the ability of the AMOEBA polarizable force field, as well a...
Article
We present the implementation of a hybrid continuum-atomistic model for including the effects of surrounding electrolyte in large-scale density functional theory (DFT) calculations within the ONETEP linear-scaling DFT code, which allows the simulation of large complex systems such as electrochemical interfaces. The model represents the electrolyte...
Preprint
div> 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 may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here we evaluate the ability of the AMOEBA polarizable force field, as...
Preprint
We present the implementation of a hybrid continuum-atomistic model for including the effects of surrounding electrolyte in large-scale density functional theory (DFT) calculations within the ONETEP linear-scaling DFT code, which allows the simulation of large complex systems such as electrochemical interfaces. The model represents the electrolyte...
Article
The presence of icosahedral ordering in liquid copper at temperatures close to the melting point is now wellestablished both experimentally and through computer simulation. However, a more elaborate analysis of local icosahedral and icosahedron-like structures, together with a system for classifying such structures based on some measure of “icosahe...
Article
Full-text available
The solution of the Poisson equation is a crucial step in electronic structure calculations, yielding the electrostatic potential—a key component of the quantum mechanical Hamiltonian. In recent decades, theoretical advances and increases in computer performance have made it possible to simulate the electronic structure of extended systems in compl...
Article
We present a method for computing excitation energies for molecules in solvent, based on the combination of a minimal parameter implicit solvent model and the equation-of-motion coupled-cluster singles and doubles method (EOM-CCSD). In this method, the solvent medium is represented by a smoothly varying dielectric function, constructed directly fro...
Technical Report
Full-text available
Implicit solvent models provide a simple, yet accurate means to incorporate solvent effects into electronic structure calculations. Such models avoid the computational expense of explicitly modelling solvent molecules by representing the solvent implicitly, for example as a polarizable dielectric medium. In this report, we describe the implementati...
Article
The importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the...
Article
Iterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles...
Article
Statistical block copolymers, composed of donor (D) and acceptor (A) blocks, are a novel type of material for organic photovoltaics (OPVs) devices. In particular a new series of polymers based on PBTZT-stat-BDTT-8, recently developed by Merck, offers high solubility in different solvents, and a high power conversion efficiency (PCE) in different de...
Article
We present a novel quantum mechanical/molecular mechanics (QM/MM) approach in which a quantum subsystem is coupled to a classical subsystem described by the AMOEBA polarizable force field. Our approach permits mutual polarization between the QM and MM subsystems, effected through multipolar electrostatics. Self-consistency is achieved for both the...
Article
Central-force decompositions are fundamental to the calculation of stress fields in atomic systems by means of Hardy stress. We derive expressions for a central-force decomposition of the spline-based modified embedded atom method (s-MEAM) potential. The expressions are subsequently simplified to a form that can be readily used in molecular-dynamic...
Article
Full-text available
Linear‐scaling density functional theory simulation of methylated imogolite nanotubes (NTs) elucidates the interplay between wall‐polarization, bands separation, charge‐transfer excitation, and tunable electrostatics inside and outside the NT‐cavity. The results suggest that integration of polarization‐enhanced selective photocatalysis and chemical...
Article
Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulati...
Article
Full-text available
We report a linear-scaling density functional theory (DFT) study of the structure, wall-polarization absolute band-alignment and optical absorption of several, recently synthesized, open-ended imogolite (Imo) nanotubes (NTs), namely single-walled (SW) aluminosilicate (AlSi), SW aluminogermanate (AlGe), SW methylated aluminosilicate (AlSi-Me), and d...
Article
We propose a novel, highly-efficient approach for the evaluation of bond-orientational order parameters (BOPs). Our approach exploits the properties of spherical harmonics and Wigner 3j-symbols to reduce the number of terms in the expressions for BOPs, and employs simultaneous interpolation of normalised associated Legendre polynomials and trigonom...
Article
Density functional theory molecular dynamics (DFT-MD) provides an efficient framework for accurately computing several kinds of spectra. The major benefit of DFT-MD approaches lies in the ability to naturally take into account the effects of temperature and anharmonicity, without having to introduce any ad hoc or a posteriori corrections. Consequen...
Article
AbsttractIn drug optimisation calculations, the Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) method can be used to compute free energies of binding of ligands to proteins. The method involves the evaluation of the energy of configurations in an implicit solvent model. One source of errors is the force field used, which can potential...
Article
Recently, variants of implicit solvation models for first principles electronic structure calculations based on a direct solution of the nonhomogeneous Poisson equation in real space have been developed. These implicit solvation models are very elegant from a physical point of view as the solute cavity is defined directly via isosurfaces of the ele...
Article
Full-text available
We present a comparison of methods for treating the electrostatic interactions of finite, isolated systems within periodic boundary conditions (PBCs), within density functional theory (DFT), with particular emphasis on linear-scaling (LS) DFT. Often, PBCs are not physically realistic but are an unavoidable consequence of the choice of basis set and...
Article
Full-text available
The learn-on-the-fly (LOTF) method [ G. Csànyi et al. Phys. Rev. Lett. 93 175503 (2004)] serves to seamlessly embed quantum-mechanical computations within a molecular-dynamics framework by continual local retuning of the potential’s parameters so that it reproduces the quantum-mechanical forces. In its current formulation, it is suitable for system...
Article
Full-text available
Speech recognition is a process of converting the acoustic signal into a set of words, whereas voice command recognition consists in the correct identification of voice commands, usually single words. Voice command recognition systems are widely used in the military, control systems, electronic devices, such as cellular phones, or by people with di...
Article
Full-text available
Body impact-contact dynamics is a classical subject in mechanics. Most of the papers on the subject are based on a kinematical or impulse-exchange approach. In this paper a different approach has been adopted. It consists in assigning a constitutive description for the contact forces between the boundaries of bodies which get close to each other. I...
Article
Molecular-dynamics (MD) simulations constitute an important tool in the study of nanoscale metallic systems, especially so in the face of the difficulties plaguing their experimental analysis. Main limitations of the MD method stem from the empirical nature of the potentials employed, their functional form which is postulated ad hoc, and its classi...
Article
We present the results of molecular-dynamics simulations of repeated interactions of a realistically-shaped cutting edge with a model, infinitely hard grain. The model edge is composed of several hundred thousand atoms of an fcc metal treated with the Sutton–Chen potential, moving with a constant speed of 20ms−1. Plastic deformations appearing upon...
Article
A tight-binding (TB) driven molecular-dynamics (MD) simulation of liquid gold in a periodic supercell was performed using our recently developed computer code. The structure of the obtained liquid is discussed and compared with the available empirical data and results of other simulations, in terms of pair correlation functions, angular distributio...
Article
Full-text available
Cross-scaling simulations of nanoindentation of copper with an infinitely hard tool, em-ploying molecular dynamics concurrently augmented with tight-binding calculations, have been conducted for three crystal orientations of the workmaterial. The effect of introducing tight-binding into the calculation on the normal force experienced by the indente...
Article
Ultra-precision machining of metals, the breaking of nanowires under tensile stress and fracture of nanoscale materials are examples of technologically important processes which are both extremely difficult and costly to investigate experimentally. We describe a multiscale method for the simulation of such systems in which the energetically active...
Article
A liquid Ge0.25Si0.75 alloy was simulated by means of the molecular dynamics method, using the Stillinger–Weber potential. The influence of precise parametrization of the three-body term in the unlike-species interactions on the alloy structure was studied and found to be significant. Differences in the parameters of only a few percent have led to...
Conference Paper
Germanate glasses containing oxides of heavy metals such as PbO, Bi2O3, have been studied for many years due to their interesting optical and electrical properties. We have investigated the structure of lead-germanate glasses using combined EXAFS (extended X-ray absorption fine structure) and MD (molecular dynamics) methods. We describe the local s...

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