Energetics and atomic mechanisms of dislocation nucleation in strained epitaxial layers

We study numerically the energetics and atomic mechanisms of misfit dislocation nucleation and stress relaxation in a two-dimensional atomistic model of strained epitaxial layers on a substrate with lattice misfit. Relaxation processes from coherent to incoherent states for different transition paths are studied using interatomic potentials of Lennard-Jones type and a systematic saddle point and transition path search method. The method is based on a combination of repulsive potential minimization and the Nudged Elastic Band method. For a final state with a single misfit dislocation, the minimum energy path and the corresponding activation barrier are obtained for different misfits and interatomic potentials. We find that the energy barrier decreases strongly with misfit. In contrast to continuous elastic theory, a strong tensile-compressive asymmetry is observed. This asymmetry can be understood as manifestation of asymmetry between repulsive and attractive branches of pair potential and it is found to depend sensitively on the form of the potential.Comment: 11 pages, 9 figures, to appear in Phys. Rev.

Effect of molecular and electronic structure on the light harvesting properties of dye sensitizers

The systematic trends in structural and electronic properties of perylene diimide (PDI) derived dye molecules have been investigated by DFT calculations based on projector augmented wave (PAW) method including gradient corrected exchange-correlation effects. TDDFT calculations have been performed to study the visible absorbance activity of these complexes. The effect of different ligands and halogen atoms attached to PDI were studied to characterize the light harvesting properties. The atomic size and electronegativity of the halogen were observed to alter the relaxed molecular geometries which in turn influenced the electronic behavior of the dye molecules. Ground state molecular structure of isolated dye molecules studied in this work depends on both the halogen atom and the carboxylic acid groups. DFT calculations revealed that the carboxylic acid ligands did not play an important role in changing the HOMO-LUMO gap of the sensitizer. However, they serve as anchor between the PDI and substrate titania surface of the solar cell or photocatalyst. A commercially available dye-sensitizer, ruthenium bipyridine (RuBpy), was also studied for electronic and structural properties in order to make a comparison with PDI derivatives for light harvesting properties. Results of this work suggest that fluorinated, chlorinated, brominated, and iyodinated PDI compounds can be useful as sensitizers in solar cells and in artificial photosynthesis.Comment: Single pdf file, 14 pages with 7 figures and 4 table

The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein

The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling approach, and the resulting potential energy surface is visualized by constructing disconnectivity graphs. Owing to topological constraints, the low-lying portion of the landscape consists of three distinct regions, corresponding to the native knotted state and to configurations where either the N- or C-terminus is not yet folded into the knot. The fastest folding pathways from denatured states exhibit early formation of the N-terminus portion of the knot and a rate-determining step where the C-terminus is incorporated. The low-lying minima with the N-terminus knotted and the C-terminus free therefore constitute an off-pathway intermediate for this model. The insertion of both the N- and C-termini into the knot occur late in the folding process, creating large energy barriers that are the rate limiting steps in the folding process. When compared to other protein folding proteins of a similar length, this system folds over six orders of magnitude more slowly.Comment: 19 page

Molecular Dynamics Studies of Dislocations in CdTe Crystals from a New Bond Order Potential

Cd1-xZnxTe (CZT) crystals are the leading semiconductors for radiation detection, but their application is limited by the high cost of detector-grade materials. High crystal costs primarily result from property non-uniformity that causes low manufacturing yield. While tremendous efforts have been made in the past to reduce Te inclusions / precipitates in CZT, this has not resulted in an anticipated improvement in material property uniformity. Moreover, it is recognized that in addition to Te particles, dislocation cells can also cause electric field perturbation and the associated property non-uniformity. Further improvement of the material, therefore, requires that dislocations in CZT crystals be understood and controlled. Here we use a recently developed CZT bond order potential to perform representative molecular dynamics simulations to study configurations, energies, and mobilities of 29 different types of possible dislocations in CdTe (i.e., x = 1) crystals. An efficient method to derive activation free energies and activation volumes of thermally activated dislocation motion will be explored. Our focus gives insight into understanding important dislocations in the material, and gives guidance toward experimental efforts for improving dislocation network structures in CZT crystals

Equilibrium molecular thermodynamics from Kirkwood sampling.

We present two methods for barrierless equilibrium sampling of molecular systems based on the recently proposed Kirkwood method (J. Chem. Phys. 2009, 130, 134102). Kirkwood sampling employs low-order correlations among internal coordinates of a molecule for random (or non-Markovian) sampling of the high dimensional conformational space. This is a geometrical sampling method independent of the potential energy surface. The first method is a variant of biased Monte Carlo, where Kirkwood sampling is used for generating trial Monte Carlo moves. Using this method, equilibrium distributions corresponding to different temperatures and potential energy functions can be generated from a given set of low-order correlations. Since Kirkwood samples are generated independently, this method is ideally suited for massively parallel distributed computing. The second approach is a variant of reservoir replica exchange, where Kirkwood sampling is used to construct a reservoir of conformations, which exchanges conformations with the replicas performing equilibrium sampling corresponding to different thermodynamic states. Coupling with the Kirkwood reservoir enhances sampling by facilitating global jumps in the conformational space. The efficiency of both methods depends on the overlap of the Kirkwood distribution with the target equilibrium distribution. We present proof-of-concept results for a model nine-atom linear molecule and alanine dipeptide.This research was funded by the European Research Council and EPSRC grant EP/I001352/1. Y.O. was supported, in part, by the JSPS Grant-in-Aid for Scientific Research on Innovative Areas (“Dynamical Ordering and Integrated Functions”).This is the final published version. It first appeared at http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.5b01800

Modeling evaporation, ion-beam assist, and magnetron sputtering of thin metal films over realistic time scales

This article was published in the journal, Physical Review B [© American Physical Society] and the definitive version is available at: http://dx.doi.org/10.1103/PhysRevB.86.035416A long-time-scale dynamics technique has been used to model the evaporation, ion-beam assist, and magnetron sputtering of thin metal films over realistic time scales. Two fcc metals have been investigated: silver and aluminum. We illustrate how the technique can be used to model growth of these films over experimental time scales, while investigating individual growth mechanisms and surface diffusion events. Long-time dynamics is achieved through an on-the-fly kinetic Monte Carlo method, which determines diffusion pathways and barriers, in parallel, with no prior knowledge of the involved transitions. It was found that Ag has the ability to grow smooth surfaces, using several mechanisms including multiple-atom concerted motion, exchange mechanisms, and damage and repair systems. Ag {111} and {100} grew dense, complete, and crystalline film when sputtering was simulated, whereas evaporation produced incomplete layers. The inclusion of Ar in the ion-beam-assisted evaporation of Ag {111} aided growth by transferring more energy to the surface atoms allowing increased diffusion. Al {111}, however, shows slightly different patterns; growth via evaporation and magnetron sputtering shows only slight differences and the inclusion of the ion-beam assist actually damages the film beyond repair, producing subsurface Ar clusters where Al atoms were displaced creating voids throughout the film. Al {100}, similar to Ag {100}, grows denser and more complete film when grown via sputtering rather than evaporation. Results show that the energy of the deposition method used plays a vital role in the resulting thin film and substrate quality

Quasi-continuous Interpolation Scheme for Pathways between Distant Configurations

A quasi-continuous interpolation (QCI) scheme is introduced for characterizing physically realistic initial pathways from which to initiate transition state searches and construct kinetic transition networks. Applications are presented for peptides, proteins, and a morphological transformation in an atomic cluster. The first step in each case involves end point alignment, and we describe the use of a shortest augmenting path algorithm for optimizing permutational isomers. The QCI procedure then employs an interpolating potential, which preserves the covalent bonding framework for the biomolecules and includes repulsive terms between unconstrained atoms. This potential is used to identify an interpolating path by minimizing contributions from a connected set of images, including terms corresponding to minima in the interatomic distances between them. This procedure detects unphysical geometries in the line segments between images. The most difficult cases, where linear interpolation would involve chain crossings, are treated by growing the structure an atom at a time using the interpolating potential. To test the QCI procedure, we carry through a series of benchmark calculations where the initial interpolation is coupled to explicit transition state searches to produce complete pathways between specified local minima.This work was supported by the Engineering and Physical Sciences Research Council [grant number EP/H042660/1]This document is the unedited Author’s version of a Submitted Work that was subsequently accepted for publication in the Journal of Chemical Theory and Computation, copyright © American Chemical Society after peer review. To access the final edited and published work see http://dx.doi.org/10.1021/ct300483

Human impact on the hydroenvironment of Lake Parishan, SW Iran, through the late Holocene

A multiproxy record from Lake Parishan, SW Iran, shows human impact on the lake and its catchment over the last 4000 years. The Parishan record provides evidence of changes in lake hydrology, from ostracod, diatom and isotope analyses, that are directly linked to human activity in the catchment; recorded by pollen and charcoal and supported by regional archaeological and historical data. The lake ostracod fauna is particularly sensitive to human induced catchment alterations and allow us to identify changes in catchment hydrology that are due to more than a simple change in precipitation: evaporation state. Oxygen isotope data from endogenic carbonates follow these faunal changes but also displays a longer trend to more positive values through the period, coincident with regional patterns of water balance for the late Holocene in the eastern Mediterranean

O(N) methods in electronic structure calculations

Linear scaling methods, or O(N) methods, have computational and memory requirements which scale linearly with the number of atoms in the system, N, in contrast to standard approaches which scale with the cube of the number of atoms. These methods, which rely on the short-ranged nature of electronic structure, will allow accurate, ab initio simulations of systems of unprecedented size. The theory behind the locality of electronic structure is described and related to physical properties of systems to be modelled, along with a survey of recent developments in real-space methods which are important for efficient use of high performance computers. The linear scaling methods proposed to date can be divided into seven different areas, and the applicability, efficiency and advantages of the methods proposed in these areas is then discussed. The applications of linear scaling methods, as well as the implementations available as computer programs, are considered. Finally, the prospects for and the challenges facing linear scaling methods are discussed.Comment: 85 pages, 15 figures, 488 references. Resubmitted to Rep. Prog. Phys (small changes