dr hab. inż. Jacek Dziedzic
Publikacje
Filtry
wszystkich: 39
Katalog Publikacji
-
The ONETEP linear-scaling density functional theory program
PublikacjaWe present an overview of the ONETEP program for linear-scaling density functional theory (DFT) calculations with large basis set (planewave) 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), expressed in terms of periodic sinc (psinc) functions. During the calculation, both the...
-
Advanced Potential Energy Surfaces for Molecular Simulation
PublikacjaAdvanced 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 simulations: the computational cost of the theoretical models, a paucity of approximate models...
-
Electrostatic interactions in finite systems treated with periodic boundary conditions: Application to linear-scaling density functional theory
PublikacjaWe 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 the efficacy of using Fourier transforms to compute the Hartree potential. In such...
-
TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field
PublikacjaWe 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 QM and MM subsystems through a total energy minimization scheme. We provide an expression...
-
Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site
PublikacjaIn drug optimization 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 potentially lead to large errors due to the restrictions in accuracy imposed by its empirical nature....
-
Large-scale DFT calculations in implicit solvent-A case study on the T4 lysozyme L99A/M102Q protein
PublikacjaW ostatnich latach zaproponowano szereg modeli typu implicit solvent, ktore bazują na bezpośrednim rozwiązaniu niejednorodnego równania Poissona w przestrzeni rzeczywistej. Modele te charakteryzują się elegancją, ponieważ wnęka, w której umieszczona jest molekuła substancji rozpuszczanej zdefiniowana jest bezpośrednio w funkcji gęstości elektronowej, a rozkład ładunku jest w sposób samouzgodniony polaryzowany dzięki reakcji dielektryka,...
-
DL_MG: A Parallel Multigrid Poisson and Poisson–Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution
PublikacjaThe 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 complex environments. This requires the solution of more complicated variants of the...
-
The potential of imogolite nanotubes as (co-)photocatalysts: a linear-scaling density functional theory study
PublikacjaWe 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 double-walled (DW) AlGe NTs. Simulations with three different semi-local and dispersion-corrected...
-
Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis
PublikacjaThe 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 AMOEBA force field, in which the total energy of the system is variationally minimized...
-
Chemically Selective Alternatives to Photoferroelectrics for Polarization-Enhanced Photocatalysis: The Untapped Potential of Hybrid Inorganic Nanotubes
PublikacjaLinear-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 separation into one overall dipole-free material should be possible.
-
The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
PublikacjaPreorganization 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 the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric...
-
Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory
PublikacjaIterative 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. The computational effort of the self-consistency procedure can be reduced by re-using...
-
Linear-scaling calculation of Hartree-Fock exchange energy with Non-orthogonal Generalised Wannier Functions
PublikacjaWe 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 imple- mented in the ONETEP program and is used to compute the Hartree-Fock exchange energy component of Hartree-Fock and Density Functional Theory (DFT) calculations with hybrid exchange-correlation functionals. As the NGWFs are optimised in situ...
-
Structure and properties of liquid Al–Cu alloys: Empirical potentials compared
PublikacjaWe 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, coordination numbers and self-diffusion coefficients are compared with published experimental...
-
Mutually polarizable QM/MM model with in situ optimized localized basis functions
PublikacjaWe 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 force field. The two subsystems interact via multipolar electrostatics and are fully...
-
Anharmonic Infrared Spectroscopy through the Fourier Transform of Time Correlation Function Formalism in ONETEP
PublikacjaDensity functional theory molecular dynamics (DFT-MD) provides an efficient framework for accurately computing several types of spectra. The major benefit of DFTMD 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. Consequently, computational spectroscopy based on DFT-MD approaches plays a pivotal role in...
-
Practical Approach to Large-Scale Electronic Structure Calculations in Electrolyte Solutions via Continuum-Embedded Linear-Scaling Density Functional Theory
PublikacjaWe present the implementation of a hybrid continuum-atomistic model for including the effects of a surrounding electrolyte in large-scale density functional theory (DFT) calculations within the Order-N Electronic Total Energy Package (ONETEP) linear-scaling DFT code, which allows the simulation of large complex systems such as electrochemical interfaces. The model represents the electrolyte ions as a scalar field and the solvent...
-
Mechanism of Li nucleation at graphite anodes and mitigation strategies
PublikacjaLithium 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 mitigation measures. In this work, we conducted FirstPrinciples studies to elucidate...
-
Li nucleation on the graphite anode under potential control in Li-ion batteries
PublikacjaApplication of Li-ion batteries in electric vehicles requires improved safety, increased lifetime and high charging rates. One of the most commonly used intercalation anode material for Li-ion batteries, graphite, is vulnerable to Li nucleation, a side reaction which competes with the intercalation process and leads to loss of reversible capacity of the battery, ageing and short-circuits. In this study, we deploy a combined grand...
-
Electrochemistry from first-principles in the grand canonical ensemble
PublikacjaProgress 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 mechanical simulations with Density Functional Theory (DFT). However, such simulations are...
wyświetlono 1569 razy