Ab Initio Simulation Methods Research Articles

Ab initiosimulations of geometrical frustration in supercooled liquid Fe and Fe-based metallic glass

We investigate short range order in liquid and supercooled liquid Fe and Fe-based metallic glass using ab initio simulation methods. We analyze the data to quantify the degree of local icosahedral and polytetrahedral order and to understand the role of alloying in controlling the degree of geometric frustration. Comparing elemental Fe to Cu [P. Ganesh and M. Widom, Phys. Rev. B 74, 134205 (2006)] we find that the degree of icosahedral order is greater in Fe than in Cu, possibly because icosahedral disclination line defects are more easily incorporated into bcc environments than fcc. In Fe-based metallic glass-forming alloys ($\mathrm{FeB}$ and $\mathrm{FeZrB}$) we find that introducing small concentrations of small B atoms and large Zr atoms controls the frustration of local icosahedral order.

Voids in Hydrogenated Amorphous Silicon: A Comparison of ab initio Simulations and Proton NMR Studies

ABSTRACTRecently, a new hydrogen NMR signal has been observed in a number of PECVD prepared hydrogenated amorphous silicon (a-Si:H) films of varying quality. It is speculated that the signal is the consequence of a dipolar-coupled hydrogen pair separated, on average, by 1.8 ± 0.1 Å. To elucidate the possible bonding configurations responsible for the NMR data of ref. [1], we have used ab initio simulation methods to determine a set of relaxed structures of a-Si:H with varying void sizes and H-concentrations. Models containing two isolated hydrogen atoms indicate a preferred H-H distance of approximately 1.8 Å when the two atoms bond to nearest neighbor silicon atoms. This separation also occurs for models containing small, hydrogenated voids, but the configurations giving rise to this H-H distance do not appear to be unique. For larger voids, a proton separation of about 2.4Å is seen, as noted previously [2]. There appears to be consistency between the computed structures and the NMR data for configurations consisting of isolated hydrogen pairs or for clusters of an even number of hydrogen atoms with the constraint that the average H-H distance is 1.8 Å. In this paper, we will discuss the most probable bonding configurations of clustered hydrogen based upon the extent of the NMR data and simulated structures.

Structural and electronic properties of an abrupt4H−SiC(0001)∕SiO2interface model: Classical molecular dynamics simulations and density functional calculations

Using a density functional approach, we study structural and electronic properties of the 4H(0001)-SiC/SiO2 interface. Through the sequential use of classical and ab initio simulation methods, we generate an abrupt model structure which describes the transition between crystalline SiC and amorphous SiO2 without showing any coordination defect. The first step in our generation procedure consists in identifying suitable interfacial bonding patterns which account for the bond density reduction across the interface. In the second step, the connection to amorphous SiO2 is achieved through classical molecular dynamics. The atomic positions are then relaxed within a generalized gradient approximation of density functional theory. The final model structure shows good structural parameters and an oxide density typical of amorphous SiO2. We investigate the electronic structure of the generated model interface through the local density of states obtained with hybrid density functionals. In our atomically abrupt interface model, the full oxide band gap is recovered at a distance of similar to 5 A from the interface. This extent is in good agreement with estimates derived from internal photoemission measurements and provides support for the abrupt nature of the interface. We obtained band offsets through two different procedures: by evaluating the local density of states and by aligning the band extrema through the local electrostatic potential. Band offsets calculated with various functionals are compared to experimental values. The best agreement is achieved for a hybrid functional in which a screened Coulomb potential is used in the Hartree-Fock exchange term. For this case, the calculated band offsets underestimate the experimental values by similar to 25%, but agree with experiment within a few percent when expressed with respect to the oxide band gap.

Real-Space Multigrid Method for Linear-Response Quantum Transport in Molecular Electronic Devices

We present a self-consistent ab initio simulation method to calculate coherent quantum transport through a molecule connected to metal electrodes in the linear-response regime. Density-functional theory (DFT) is applied to the metal-molecule-metal system. The molecule and the metal electrodes are treated on the same footing as one extended molecule. The Full Approximation Scheme (FAS) nonlinear multigrid technique is used to accelerate convergence in a nonorthogonal localized orbital basis. The Landauer formula is employed to calculate the current with the transmission function obtained from a Green's function calculation. The current-voltage characteristics of a benzene-1,4-dithiolate (BDT) extended molecule are studied as an example, and our results are compared to other theoretical calculations. We also show that a recently formulated constrained-current formalism is invariant to a reversal in the imposed current. Hence, the predicted voltage drop must be zero. This suggests the theory must be modified to properly treat possible nonlinearities in the nonzero current case

Energy level reordering and stability of MPb 12 clusters: An interplay between geometry and electronic structure

In this work we demonstrate the influence of an impurity atom in tuning the stability of Pb 13 cluster. For this purpose we have investigated the electronic and geometric structure of MPb 12 (M = Pb, C, Al, Mg) clusters using the ab initio molecular dynamics simulation method. The energy gap between the highest occupied and lowest unoccupied energy levels of Pb 13 and MgPb 12 is estimated to be 0.95 and 2.3 eV, respectively. The significant increase in the energy gap is resulted from the energy level reordering of Pb 13 by the incorporation of Mg atom. Further investigations of the stability of MPb 12 clusters reveal that the interplay between the atomic and electronic structure is crucial to understand the stability of small size clusters.

Constant pressure Langevin dynamics: theory and application

The method of constant pressure Langevin dynamics is reviewed. The particular utility of the method for ab-initio simulation is discussed. Example results for both semi-empirical and ab-initio systems are given.

Light‐induced global structural changes in phytochrome A regulating photomorphogenesis in plants

Phytochromes are photoreceptor proteins that monitor the light environment and regulate a variety of photomorphogenic responses to optimize the growth and development of plants. Phytochromes comprise N-terminal photosensory and C-terminal regulatory domains. They are mutually photoconvertible between a red-light-absorbing (Pr) and a far-red-light-absorbing (Pfr) form. Their interconversion by light stimuli initiates downstream signaling cascades. Here we report the molecular structures of pea phytochrome A lacking the N-terminal 52 amino-acid residues in the Pr and Pfr forms studied by small-angle X-ray scattering. A new purification protocol yielded monodispersive sample solutions. The molecular mass and the maximum dimension of Pr determined from scattering data indicated its dimeric association. The molecular structure of Pr predicted by applying the ab initio simulation method to the scattering profile was approximated as a stack of two flat bodies, comprising two lobes assignable to the functional regions. Scattering profiles recorded under red-light irradiation showed small but definite changes from those of Pr. The molecular dimensions and predicted molecular structure of Pfr suggest global structural changes such as movement of the C-terminal domains in the Pr-to-Pfr phototransformation. Red-light-induced structural changes in Pfr were reversible, mostly due to thermal relaxation processes.

Fundamental absorption frequency from quasi-classical direct ab initio molecular dynamics: diatomic molecule

A new approach is proposed to extract the fundamental absorption frequency from classical molecular dynamics simulation in which the oscillator amplitude is specified by setting the total energy equal to the harmonic zero-point energy. This approach is applied to D 2 molecule. The fundamental absorption frequency and the anharmonic constant of D 2, obtained from the quasi-classical direct ab initio molecular dynamics simulation method with the full Configuration Interaction level of theory with the aug-cc-pVTZ basis set, compare well with the experimentally observed values.

Ab initiomolecular dynamics simulation of femtosecond laser-induced structural modification in vitreous silica

Femtosecond laser pulse induced structural changes in silica glass and their role in changing the refractive index of the glass have been investigated using ab initio molecular dynamics simulation methods based on finite-temperature density functional theory. The average nearest-neighbor Si-O, Si-Si, and O-O distances are found to increase during laser irradiation due to the weakening of bonds resulting from the thermalization of electrons. These changes in the nearest-neighbor distances are almost completely recovered during the postirradiation evolution of the glass structure. However, persistent structural changes are found to involve the formation of three-coordinated Si atoms and nonbridging oxygens that correspond to the defect species of Si ${E}^{\ensuremath{'}}$ centers and nonbridging oxygen hole centers, respectively. These defects give rise to optical absorptions that increase the refractive index of silica glass through a Kramers-Kronig mechanism.

Some recent trends in computer simulations of aqueous double layers

Recent molecular simulations of the electric double layer between an aqueous and a metallic phase are reviewed. Several trends in the field can be identified: (i) the increasing use of ab initio simulation methods, most notably the Car-Parrinello method, allows to combine a statistical mechanical description of the double layer with a description of elementary chemical processes on the electronic structure level; (ii) the application of free-energy methods in one and (recently) two dimensions to describe chemical reactivity within and beyond the framework of the Marcus theory of electron transfer; and (iii) at high concentrations, direct simulations of two-phase systems with an aqueous solution and a charged or uncharged solid phase or surface can model the entire double layer region.

Data Mining Approach to Ab-Initio Prediction of Crystal Structure

ABSTRACTPredicting crystal structure is one of the most fundamental problems in materials science and a key early step in computational materials design. Ab initio simulation methods are a powerful tool for predicting crystal structure, but are too slow to explore the extremely large space of possible structures for new alloys. Here we describe ongoing work on a novel method (Data Mining of Quantum Calculations, or DMQC) that applies data mining techniques to existing ab initio data in order to increase the efficiency of crystal structure prediction for new alloys. We find about a factor of three speedup in ab intio prediction of crystal structures using DMQC as compared to naïve random guessing. This study represents an extension of work done by Curtarolo, et al. [1] to a larger library of data.

An ab initio based structure model of i(Al–Pd–Mn)

We illustrate how ab initio numerical simulation methods can be used to check and improve structure models for i(Al–Pd–Mn). By focusing our study on the optimization of a small approximant, we obtain a number of general structural and compositional rules simple enough to be applicable to the quasicrystalline structure itself.

Conformational and solvation aspects of the chorismate–prephenate rearrangement studied by ab initio electronic structure and simulation methods

The effect of water on the energetics of the Claisen rearrangement of chorismate to prephenate has been investigated with both a continuum model (PCM) and explicit solvation within a Monte Carlo (MC) free energy perturbation (FEP) treatment. Both models are surprisingly similar in their quantitative predictions. Solvation is shown to increase the conformational flexibility in the reactant by reducing the energy difference between the diequatorial and diaxial structures, and to lead to a considerable reduction in the barrier to the reaction. The estimate of the activation barrier, 22 kcal mol-1, is very close to the experimental value of 24.5 kcal mol-1. The implications of the various possible conformers on kinetic isotope effects are discussed.

Electronic materials process modeling

This report focuses on current needs in the process modeling of materials used in electronic and optoelectronic device fabrication and provides specific recommendations in addressing these needs. The establishment of relationships between materials structure and processing is identified as the critical modeling need in the electronics industry. A hierarchical modeling approach is suggested aiming at the development of efficient and robust process simulators with predictive capabilities and, thus, providing modeling tools for development of optimal materials processing strategies. This approach is based on linking a variety of existing theoretical and computational methods which include: ab initio, semi-empirical, and empirical atomic-scale simulation methods for accurate calculation of materials properties and mechanistic physical understanding; microstructural-scale thermodynamic, transport, and kinetic modeling; and macroscopic process-specific process simulation. Issues of interdisciplinary communication and collaboration and exploratory research for new materials are also addressed.

Structure of diamond(100) stepped surfaces from ab initio calculations

We present theoretical studies of relaxations of monoatomic and steps on the diamond(100)-(21) surface employing an ab initio molecular dynamics simulation method that is based on density functional theory. Stable dimer structures are found in the upper and lower planes of the step surfaces in agreement with experiment. Significant atomic relaxations occur near the step edges of and stepped surfaces induced by the creation of the steps. Atomic H adsorption on these step surfaces to form monohydride structures is energetically favourable. We also simulate the presence of radical sites near the step edges of , and and local reconstruction involving the dimer containing the radical sites is found. Electronic charge density profiles of the filled states near the Fermi level show features associated with the dimer structures.

Ab-initio simulation of phase transformations under pressure

We have recently devised a new method for ab initio simulation of solid-solid phase transformation under pressure. The method is here applied to the study of ice at Mbar pressure, the solid-state polymerization of acetylene under pressure and the generation of ta-C: H from compression of polyacetylene.