Single-Atom Control of Arsenic Incorporation in Silicon for High-Yield Artificial Lattice Fabrication.

Artificial lattices constructed from individual dopant atoms within a semiconductor crystal hold promise to provide novel materials with tailored electronic, magnetic, and optical properties. These custom-engineered lattices are anticipated to enable new, fundamental discoveries in condensed matter physics and lead to the creation of new semiconductor technologies including analog quantum simulators and universal solid-state quantum computers. This work reports precise and repeatable, substitutional incorporation of single arsenic atoms into a silicon lattice.

Origin of Ferroelectric Domain Wall Alignment with Surface Trenches in Ultrathin Films.

Engraving trenches on the surfaces of ultrathin ferroelectric (FE) films and superlattices promises control over the orientation and direction of FE domain walls (DWs). Through exploiting the phenomenon of DW-surface trench (ST) parallel alignment, systems where DWs are known for becoming electrical conductors could now become useful nanocircuits using only standard lithographical techniques. Despite this clear application, the microscopic mechanism responsible for the alignment phenomenon has remained elusive.

Insight into the Charge Density Wave Gap from Contrast Inversion in Topographic STM Images.

Charge density waves (CDWs) are understood in great detail in one dimension, but they remain largely enigmatic in two-dimensional systems. In particular, numerous aspects of the associated energy gap and the formation mechanism are not fully understood. Two long-standing riddles are the amplitude and position of the CDW gap with respect to the Fermi level (E_{F}) and the frequent absence of CDW contrast inversion (CI) between opposite bias scanning tunneling microscopy (STM) images.

Notes on density matrix perturbation theory.

Density matrix perturbation theory (DMPT) is known as a promising alternative to the Rayleigh-Schrödinger perturbation theory, in which the sum-over-states (SOS) is replaced by algorithms with perturbed density matrices as the input variables. In this article, we formulate and discuss three types of DMPT, with two of them based only on density matrices: the approach of Kussmann and Ochsenfeld [J. Chem.

Blue moon ensemble simulation of aquation free energy profiles applied to mono and bifunctional platinum anticancer drugs.

Aquation free energy profiles of neutral cisplatin and cationic monofunctional derivatives, including triaminochloroplatinum(II) and cis-diammine(pyridine)chloroplatinum(II), were computed using state of the art thermodynamic integration, for which temperature and solvent were accounted for explicitly using density functional theory-based canonical molecular dynamics (DFT-MD). For all the systems, the "inverse-hydration" where the metal center acts as an acceptor of hydrogen bond has been observed. This has motivated to consider the inversely bonded solvent molecule in the definition of the reaction coordinate required to initiate the constrained DFT-MD trajectories.

Large scale and linear scaling DFT with the CONQUEST code.

We survey the underlying theory behind the large-scale and linear scaling density functional theory code, conquest, which shows excellent parallel scaling and can be applied to thousands of atoms with diagonalization and millions of atoms with linear scaling. We give details of the representation of the density matrix and the approach to finding the electronic ground state and discuss the implementation of molecular dynamics with linear scaling. We give an overview of the performance of the code, focusing in particular on the parallel scaling, and provide examples of recent developments and applications.

Author Correction: Gate controlling of quantum interference and direct observation of anti-resonances in single molecule charge transport.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

DFT study of undoped and As-doped Si nanowires approaching the bulk limit.

The electronic properties of pure and As-doped Si nanowires (NWs) with radii up to 9.53 nm are studied using large scale density functional theory (DFT) calculations. We show that, for the undoped NWs, the DFT bandgap reduces with increasing diameter and converges to its bulk value, a trend in agreement with experimental data.

Gate controlling of quantum interference and direct observation of anti-resonances in single molecule charge transport.

Quantum interference can profoundly affect charge transport in single molecules, but experiments can usually measure only the conductance at the Fermi energy. Because, in general, the most pronounced features of the quantum interference are not located at the Fermi energy, it is highly desirable to probe charge transport in a broader energy range. Here, by means of electrochemical gating, we measure the conductance and map the transmission functions of single molecules at and around the Fermi energy, and study signatures associated with constructive and destructive interference.

High-accuracy large-scale DFT calculations using localized orbitals in complex electronic systems: the case of graphene-metal interfaces.

Over many years, computational simulations based on density functional theory (DFT) have been used extensively to study many different materials at the atomic scale. However, its application is restricted by system size, leaving a number of interesting systems without a high-accuracy quantum description. In this work, we calculate the electronic and structural properties of a graphene-metal system significantly larger than in previous plane-wave calculations with the same accuracy.

Structural properties of silicon-germanium and germanium-silicon core-shell nanowires.

Core-shell nanowires made of Si and Ge can be grown experimentally with excellent control for different sizes of both core and shell. We have studied the structural properties of Si/Ge and Ge/Si core-shell nanowires aligned along the [Formula: see text] direction, with diameters up to 10.2 nm and varying core to shell ratios, using linear scaling density functional theory.

Local Real-Space View of the Achiral 1T-TiSe_{2} 2×2×2 Charge Density Wave.

The transition metal dichalcogenide 1T-TiSe_{2}-two-dimensional layered material undergoing a commensurate 2×2×2 charge density wave (CDW) transition with a weak periodic lattice distortion (PLD) below ≈200  K. Scanning tunneling microscopy (STM) combined with intentionally introduced interstitial Ti atoms allows us to go beyond the usual spatial resolution of STM and to intimately probe the three-dimensional character of the PLD. Furthermore, the inversion-symmetric achiral nature of the CDW in the z direction is revealed, contradicting the claimed existence of helical CDW stacking and associated chiral order.

Reaction paths of alane dissociation on the Si(0 0 1) surface.

Building on our earlier study, we examine the kinetic barriers to decomposition of alane, AlH, on the Si(0 0 1) surface, using the nudged elastic band approach within density functional theory. We find that the initial decomposition to AlH with two H atoms on the surface proceeds without a significant barrier. There are several pathways available to lose the final hydrogen, though these present barriers of up to 1 eV.

Atomic layer doping of Mn magnetic impurities from surface chains at a Ge/Si hetero-interface.

We realize Mn δ-doping into Si and Si/Ge interfaces using Mn atomic chains on Si(001). Highly sensitive X-ray absorption fine structure techniques reveal that encapsulation at room temperature prevents the formation of silicides/germanides while maintaining one-dimensional anisotropic structures. This is revealed by studying both the incident X-ray polarization dependence and post-annealing effects.

Effects of the Hubbard U on density functional-based predictions of BiFeO properties.

First principles studies of multiferroic materials, such as bismuth ferrite (BFO), require methods that extend beyond standard density functional theory (DFT). The DFT  +  U method is one such extension that is widely used in the study of BFO. We present a systematic study of the effects of the U parameter on the structural, ferroelectric and electronic properties of BFO.

Canonical-ensemble extended Lagrangian Born-Oppenheimer molecular dynamics for the linear scaling density functional theory.

We discuss the development and implementation of a constant temperature (NVT) molecular dynamics scheme that combines the Nosé-Hoover chain thermostat with the extended Lagrangian Born-Oppenheimer molecular dynamics (BOMD) scheme, using a linear scaling density functional theory (DFT) approach. An integration scheme for this canonical-ensemble extended Lagrangian BOMD is developed and discussed in the context of the Liouville operator formulation. Linear scaling DFT canonical-ensemble extended Lagrangian BOMD simulations are tested on bulk silicon and silicon carbide systems to evaluate our integration scheme.

Efficient Calculation of Electronic Structure Using O(N) Density Functional Theory.

We propose an efficient way to calculate the electronic structure of large systems by combining a large-scale first-principles density functional theory code, Conquest, and an efficient interior eigenproblem solver, the Sakurai-Sugiura method. The electronic Hamiltonian and charge density of large systems are obtained by Conquest, and the eigenstates of the Hamiltonians are then obtained by the Sakurai-Sugiura method. Applications to a hydrated DNA system and adsorbed P molecules and Ge hut clusters on large Si substrates demonstrate the applicability of this combination on systems with 10,000+ atoms with high accuracy and efficiency.

Alane adsorption and dissociation on the Si(0 0 1) surface.

We used DFT to study the energetics of the decomposition of alane, AlH, on the Si(0 0 1) surface, as the acceptor complement to PH. Alane forms a dative bond with the raised atoms of silicon surface dimers, via the Si atom lone pair. We calculated the energies of various structures along the pathway of successive dehydrogenation events following adsorption: AlH, AlH and Al, finding a gradual, significant decrease in energy.

Raoult's law revisited: accurately predicting equilibrium relative humidity points for humidity control experiments.

The humidity surrounding a sample is an important variable in scientific experiments. Biological samples in particular require not just a humid atmosphere but often a relative humidity (RH) that is in equilibrium with a stabilizing solution required to maintain the sample in the same state during measurements. The controlled dehydration of macromolecular crystals can lead to significant increases in crystal order, leading to higher diffraction quality.

Dopant activation mechanism of Bi wire-δ-doping into Si crystal, investigated with wavelength dispersive fluorescence x-ray absorption fine structure and density functional theory.

We successfully characterized the local structures of Bi atoms in a wire-δ-doped layer (1/8 ML) in a Si crystal, using wavelength dispersive fluorescence x-ray absorption fine structure at the beamline BL37XU, in SPring-8, with the help of density functional theory calculations. It was found that the burial of Bi nanolines on the Si(0 0 1) surface, via growth of Si capping layer at 400 °C by molecular beam epitaxy, reduced the Bi-Si bond length from [Formula: see text] to [Formula: see text] Å. We infer that following epitaxial growth the Bi-Bi dimers of the nanoline are broken, and the Bi atoms are located at substitutional sites within the Si crystal, leading to the shorter Bi-Si bond lengths.

Stripe and Short Range Order in the Charge Density Wave of 1T-Cu_{x}TiSe_{2}.

We study the impact of Cu intercalation on the charge density wave (CDW) in 1T-Cu_{x}TiSe_{2} by scanning tunneling microscopy and spectroscopy. Cu atoms, identified through density functional theory modeling, are found to intercalate randomly on the octahedral site in the van der Waals gap and to dope delocalized electrons near the Fermi level. While the CDW modulation period does not depend on Cu content, we observe the formation of charge stripe domains at low Cu content (x<0.

Communication: Generalized canonical purification for density matrix minimization.

A Lagrangian formulation for the constrained search for the N-representable one-particle density matrix based on the McWeeny idempotency error minimization is proposed, which converges systematically to the ground state. A closed form of the canonical purification is derived for which no a posteriori adjustment on the trace of the density matrix is needed. The relationship with comparable methods is discussed, showing their possible generalization through the hole-particle duality.

Efficient Calculations with Multisite Local Orbitals in a Large-Scale DFT Code CONQUEST.

Multisite local orbitals, which are formed from linear combinations of pseudoatomic orbitals from a target atom and its neighbor atoms, have been introduced in the large-scale density functional theory calculation code CONQUEST. Multisite local orbitals correspond to local molecular orbitals so that the number of required local orbitals can be minimal. The multisite support functions are determined by using the localized filter diagonalization (LFD) method [ Phys.

Stable and Efficient Linear Scaling First-Principles Molecular Dynamics for 10000+ Atoms.

The recent progress of linear-scaling or O(N) methods in density functional theory (DFT) is remarkable. Given this, we might expect that first-principles molecular dynamics (FPMD) simulations based on DFT could treat more realistic and complex systems using the O(N) technique. However, very few examples of O(N) FPMD simulations exist to date, and information on the accuracy and reliability of the simulations is very limited.