Krylov Subspace Method for Molecular Dynamics Simulation based on Large-Scale Electronic Structure Theory

For large scale electronic structure calculation, the Krylov subspace method is introduced to calculate the one-body density matrix instead of the eigenstates of given Hamiltonian. This method provides an efficient way to extract the essential character of the Hamiltonian within a limited number of basis set. Its validation is confirmed by the convergence property of the density matrix within the subspace. The following quantities are calculated; energy, force, density of states, and energy spectrum. Molecular dynamics simulation of Si(001) surface reconstruction is examined as an example, and the results reproduce the mechanism of asymmetric surface dimer.Comment: 7 pages, 3 figures; corrected typos; to be published in Journal of the Phys. Soc. of Japa

Split-off dimer defects on the Si(001)2x1 surface

Dimer vacancy (DV) defect complexes in the Si(001)2x1 surface were investigated using high-resolution scanning tunneling microscopy and first principles calculations. We find that under low bias filled-state tunneling conditions, isolated 'split-off' dimers in these defect complexes are imaged as pairs of protrusions while the surrounding Si surface dimers appear as the usual 'bean-shaped' protrusions. We attribute this to the formation of pi-bonds between the two atoms of the split-off dimer and second layer atoms, and present charge density plots to support this assignment. We observe a local brightness enhancement due to strain for different DV complexes and provide the first experimental confirmation of an earlier prediction that the 1+2-DV induces less surface strain than other DV complexes. Finally, we present a previously unreported triangular shaped split-off dimer defect complex that exists at SB-type step edges, and propose a structure for this defect involving a bound Si monomer.Comment: 8 pages, 7 figures, submitted to Phys. Rev.

The role of electronic correlation in the Si(100) reconstruction: a quantum Monte Carlo study

Recent low-temperature scanning tunneling experiments have challenged the generally accepted picture of buckled silicon dimers as the ground state reconstruction of the Si(100) surface. Together with the symmetric dimer model of the surface suggested by quantum chemistry calculations on small clusters, these findings question our general understanding of electronic correlations at surfaces and its proper description within density functional theory. We present quantum Monte Carlo calculations on large cluster models of the symmetric and buckled surface, and conclude that buckling remains energetically more favorable even when the present-day best treatment of electronic correlation is employed.Comment: 5 pages, Revtex, 10 figure

Single- and two-phase flow simulation based on equivalent pore network extracted from micro-CT images of sandstone core

Due to the intricate structure of porous rocks, relationships between porosity or saturation and petrophysical transport properties classically used for reservoir evaluation and recovery strategies are either very complex or nonexistent. Thus, the pore network model extracted from the natural porous media is emphasized as a breakthrough to predict the fluid transport properties in the complex micro pore structure. This paper presents a modified method of extracting the equivalent pore network model from the three-dimensional micro computed tomography images based on the maximum ball algorithm. The partition of pore and throat are improved to avoid tremendous memory usage when extracting the equivalent pore network model. The porosity calculated by the extracted pore network model agrees well with the original sandstone sample. Instead of the Poiseuille’s law used in the original work, the Lattice-Boltzmann method is employed to simulate the single- and two- phase flow in the extracted pore network. Good agreements are acquired on relative permeability saturation curves of the simulation against the experiment results

Density-functional study of hydrogen chemisorption on vicinal Si(001) surfaces

Relaxed atomic geometries and chemisorption energies have been calculated for the dissociative adsorption of molecular hydrogen on vicinal Si(001) surfaces. We employ density-functional theory, together with a pseudopotential for Si, and apply the generalized gradient approximation by Perdew and Wang to the exchange-correlation functional. We find the double-atomic-height rebonded D_B step, which is known to be stable on the clean surface, to remain stable on partially hydrogen-covered surfaces. The H atoms preferentially bind to the Si atoms at the rebonded step edge, with a chemisorption energy difference with respect to the terrace sites of >sim 0.1 eV. A surface with rebonded single atomic height S_A and S_B steps gives very similar results. The interaction between H-Si-Si-H mono-hydride units is shown to be unimportant for the calculation of the step-edge hydrogen-occupation. Our results confirm the interpretation and results of the recent H_2 adsorption experiments on vicinal Si surfaces by Raschke and Hoefer described in the preceding paper.Comment: 13 pages, 8 figures, submitted to Phys. Rev. B. Other related publications can be found at http://www.rz-berlin.mpg.de/th/paper.htm

Phase Separation of Crystal Surfaces: A Lattice Gas Approach

We consider both equilibrium and kinetic aspects of the phase separation (``thermal faceting") of thermodynamically unstable crystal surfaces into a hill--valley structure. The model we study is an Ising lattice gas for a simple cubic crystal with nearest--neighbor attractive interactions and weak next--nearest--neighbor repulsive interactions. It is likely applicable to alkali halides with the sodium chloride structure. Emphasis is placed on the fact that the equilibrium crystal shape can be interpreted as a phase diagram and that the details of its structure tell us into which surface orientations an unstable surface will decompose. We find that, depending on the temperature and growth conditions, a number of interesting behaviors are expected. For a crystal in equilibrium with its vapor, these include a low temperature regime with logarithmically--slow separation into three symmetrically--equivalent facets, and a higher temperature regime where separation proceeds as a power law in time into an entire one--parameter family of surface orientations. For a crystal slightly out of equilibrium with its vapor (slow crystal growth or etching), power--law growth should be the rule at late enough times. However, in the low temperature regime, the rate of separation rapidly decreases as the chemical potential difference between crystal and vapor phases goes to zero.Comment: 16 pages (RevTex 3.0); 12 postscript figures available on request ([email protected]). Submitted to Physical Review E. SFU-JDSDJB-94-0

Single nucleotide polymorphisms unravel hierarchical divergence and signatures of selection among Alaskan sockeye salmon (Oncorhynchus nerka) populations

<p>Abstract</p> <p>Background</p> <p>Disentangling the roles of geography and ecology driving population divergence and distinguishing adaptive from neutral evolution at the molecular level have been common goals among evolutionary and conservation biologists. Using single nucleotide polymorphism (SNP) multilocus genotypes for 31 sockeye salmon (<it>Oncorhynchus nerka</it>) populations from the Kvichak River, Alaska, we assessed the relative roles of geography (discrete boundaries or continuous distance) and ecology (spawning habitat and timing) driving genetic divergence in this species at varying spatial scales within the drainage. We also evaluated two outlier detection methods to characterize candidate SNPs responding to environmental selection, emphasizing which mechanism(s) may maintain the genetic variation of outlier loci.</p> <p>Results</p> <p>For the entire drainage, Mantel tests suggested a greater role of geographic distance on population divergence than differences in spawn timing when each variable was correlated with pairwise genetic distances. Clustering and hierarchical analyses of molecular variance indicated that the largest genetic differentiation occurred between populations from distinct lakes or subdrainages. Within one population-rich lake, however, Mantel tests suggested a greater role of spawn timing than geographic distance on population divergence when each variable was correlated with pairwise genetic distances. Variable spawn timing among populations was linked to specific spawning habitats as revealed by principal coordinate analyses. We additionally identified two outlier SNPs located in the major histocompatibility complex (MHC) class II that appeared robust to violations of demographic assumptions from an initial pool of eight candidates for selection.</p> <p>Conclusions</p> <p>First, our results suggest that geography and ecology have influenced genetic divergence between Alaskan sockeye salmon populations in a hierarchical manner depending on the spatial scale. Second, we found consistent evidence for diversifying selection in two loci located in the MHC class II by means of outlier detection methods; yet, alternative scenarios for the evolution of these loci were also evaluated. Both conclusions argue that historical contingency and contemporary adaptation have likely driven differentiation between Kvichak River sockeye salmon populations, as revealed by a suite of SNPs. Our findings highlight the need for conservation of complex population structure, because it provides resilience in the face of environmental change, both natural and anthropogenic.</p

Increased Inter-Colony Fusion Rates Are Associated with Reduced COI Haplotype Diversity in an Invasive Colonial Ascidian Didemnum vexillum

Considerable progress in our understanding of the population genetic changes associated with biological invasions has been made over the past decade. Using selectively neutral loci, it has been established that reductions in genetic diversity, reflecting founder effects, have occurred during the establishment of some invasive populations. However, some colonial organisms may actually gain an ecological advantage from reduced genetic diversity because of the associated reduction in inter-colony conflict. Here we report population genetic analyses, along with colony fusion experiments, for a highly invasive colonial ascidian, Didemnum vexillum. Analyses based on mitochondrial cytochrome oxidase I (COI) partial coding sequences revealed two distinct D. vexillum clades. One COI clade appears to be restricted to the probable native region (i.e., north-west Pacific Ocean), while the other clade is present in widely dispersed temperate coastal waters around the world. This clade structure was supported by 18S ribosomal DNA (rDNA) sequence data, which revealed a one base-pair difference between the two clades. Recently established populations of D. vexillum in New Zealand displayed greatly reduced COI genetic diversity when compared with D. vexillum in Japan. In association with this reduction in genetic diversity was a significantly higher inter-colony fusion rate between randomly paired New Zealand D. vexillum colonies (80%, standard deviation ±18%) when compared with colonies found in Japan (27%, standard deviation ±15%). The results of this study add to growing evidence that for colonial organisms reductions in population level genetic diversity may alter colony interaction dynamics and enhance the invasive potential of newly colonizing species