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The SIESTA method for ab initio order-N materials simulation

TLDR
In this paper, a selfconsistent density functional method using standard norm-conserving pseudopotentials and a flexible, numerical linear combination of atomic orbitals basis set, which includes multiple-zeta and polarization orbitals, was developed and implemented.
Abstract
We have developed and implemented a selfconsistent density functional method using standard norm-conserving pseudopotentials and a flexible, numerical linear combination of atomic orbitals basis set, which includes multiple-zeta and polarization orbitals. Exchange and correlation are treated with the local spin density or generalized gradient approximations. The basis functions and the electron density are projected on a real-space grid, in order to calculate the Hartree and exchange-correlation potentials and matrix elements, with a number of operations that scales linearly with the size of the system. We use a modified energy functional, whose minimization produces orthogonal wavefunctions and the same energy and density as the Kohn-Sham energy functional, without the need for an explicit orthogonalization. Additionally, using localized Wannier-like electron wavefunctions allows the computation time and memory required to minimize the energy to also scale linearly with the size of the system. Forces and stresses are also calculated efficiently and accurately, thus allowing structural relaxation and molecular dynamics simulations.

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Oxygen reduction reactions on pure and nitrogen-doped graphene: a first-principles modeling.

TL;DR: In this paper, the authors explored the energy barrier of oxygen reduction over pristine and nitrogen-doped graphene with different amounts of nitrogen doping and found that the maximal coverage of doped graphene is lower and depends on the corrugation of graphene.
Journal ArticleDOI

Density Functional Investigation of Thioepoxidated and Thiolated Graphene

TL;DR: In this article, the SH group is dissociatively bonded to bare edges and hydrogen-terminated zigzag edges prefer to bind the SH groups to these edges, while the single vacancy defect site has the highest affinity for the SH radical.
Journal ArticleDOI

Electrostatic complementarity in an aldose reductase complex from ultra-high-resolution crystallography and first-principles calculations

TL;DR: The charge density refinement of the protein was performed with the program mopro by using the transferability principle and the database of charge density parameters built from crystallographic analyses of peptides and amino acids, and the potentials obtained directly from the database are in excellent agreement with the experimental ones.
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Controlled manipulation of single atoms and small molecules using the scanning tunnelling microscope

TL;DR: In this article, the authors review manipulation of single molecules by scanning tunnelling microscopes, in particular vertical manipulation, lateral manipulation, and inelastic electron tunneling (IET) manipulation.
References
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Journal ArticleDOI

Generalized Gradient Approximation Made Simple

TL;DR: A simple derivation of a simple GGA is presented, in which all parameters (other than those in LSD) are fundamental constants, and only general features of the detailed construction underlying the Perdew-Wang 1991 (PW91) GGA are invoked.
Journal ArticleDOI

Special points for brillouin-zone integrations

TL;DR: In this article, a method for generating sets of special points in the Brillouin zone which provides an efficient means of integrating periodic functions of the wave vector is given, where the integration can be over the entire zone or over specified portions thereof.
Journal ArticleDOI

Self-Consistent Equations Including Exchange and Correlation Effects

TL;DR: In this paper, the Hartree and Hartree-Fock equations are applied to a uniform electron gas, where the exchange and correlation portions of the chemical potential of the gas are used as additional effective potentials.
Book

Classical Electrodynamics

Book

Introduction to solid state physics

TL;DR: In this paper, the Hartree-Fock Approximation of many-body techniques and the Electron Gas Polarons and Electron-phonon Interaction are discussed.
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