Atomistic mechanisms for the ordered growth of Co nano-dots on Au(788): comparison of VT-STM experiments and multi-scaled calculations

Hetero-epitaxial growth on a strain-relief vicinal patterned substrate has revealed unprecedented 2D long range ordered growth of uniform cobalt nanostructures. The morphology of a Co sub-monolayer deposit on a Au(111) reconstructed vicinal surface is analyzed by Variable Temperature Scanning Tunneling Microscopy (VT-STM) experiments. A rectangular array of nano-dots (3.8 nm x 7.2 nm) is found for a particularly large deposit temperature range lying from 60 K to 300 K. Although the nanodot lattice is stable at room temperature, this paper focus on the early stage of ordered nucleation and growth at temperatures between 35 K and 480 K. The atomistic mechanisms leading to the nanodots array are elucidated by comparing statistical analysis of VT-STM images with multi-scaled numerical calculations combining both Molecular Dynamics for the quantitative determination of the activation energies for the atomic motion and the Kinetic Monte Carlo method for the simulations of the mesoscopic time and scale evolution of the Co submonolayer

The effect of monomer evaporation on a simple model of submonolayer growth

We present a model for thin film growth by particle deposition that takes into account the possible evaporation of the particles deposited on the surface. Our model focuses on the formation of two-dimensional structures. We find that the presence of evaporation can dramatically affect the growth kinetics of the film, and can give rise to regimes characterized by different ``growth'' exponents and island size distributions. Our results are obtained by extensive computer simulations as well as through a simple scaling approach and the analysis of rate equations describing the system. We carefully discuss the relationship of our model with previous studies by Venables and Stoyanov of the same physical situation, and we show that our analysis is more general.Comment: 41 pages including figures, Revtex, to be published in Physical Review

Mass-Transport Models with Multiple-Chipping Processes

We study mass-transport models with multiple-chipping processes. The rates of these processes are dependent on the chip size and mass of the fragmenting site. In this context, we consider k-chip moves (where k = 1, 2, 3, ....); and combinations of 1-chip, 2-chip and 3-chip moves. The corresponding mean-field (MF) equations are solved to obtain the steady-state probability distributions, P (m) vs. m. We also undertake Monte Carlo (MC) simulations of these models. The MC results are in excellent agreement with the corresponding MF results, demonstrating that MF theory is exact for these models.Comment: 18 pages, 4 figures, To appear in European Physical Journal

Transient thermal effects in solid noble gases as materials for the detection of Dark Matter

The transient phenomena produced in solid noble gases by the stopping of the recoils resulting from the elastic scattering processes of WIMPs from the galactic halo were modelled, as dependencies of the temperatures of lattice and electronic subsystems on the distance to the recoil's trajectory, and time from its passage. The peculiarities of these thermal transients produced in Ar, Kr and Xe were analysed for different initial temperatures and WIMP energies, and were correlated with the characteristics of the targets and with the energy loss of the recoils. The results were compared with the thermal spikes produced by the same WIMPs in Si and Ge. In the range of the energy of interest, up to tens of keV for the self-recoil, local phase transitions solid - liquid and even liquid - gas were found possible, and the threshold parameters were established.Comment: Minor corrections and updated references; accepted to JCA

Distribution and abundance of western gray whales during a seismic survey near Sakhalin Island, Russia

Exxon Neftegas Limited, operator of the Sakhalin-1 consortium, is developing oil and gas reserves on the continental shelf off northeast Sakhalin Island, Russia. DalMorNefteGeofizika (DMNG), on behalf of the Sakhalin-1 consortium, conducted a 3-D seismic survey of the Odoptu license area during 17 August-September 2001. A portion of the primary known feeding area of the endangered western gray whale (Eschrichtius robustus) is located adjacent to the seismic block. The data presented here were collected as part of daily monitoring to determine if there was any measurable effect of the seismic survey on the distribution and abundance of western gray whales. Mitigation and monitoring program included aerial surveys conducted between 19 July and 19 November using the methodology outlined by the Southern California High Energy Seismic Survey team (HESS). These surveys provided documentation of the distribution, abundance and bottom feeding activity of western gray whales in relation to seismic survey sounds. From an operations perspective, the aerial surveys provided near real-time data on the location of whales in and outside the feeding area, and documented whether whales were displaced out of an area normally used as feeding habitat. The objectives of this study were to assess (a) temporal changes in the distribution and abundance of gray whales in relation to seismic survey, and (b) the influence of seismic survey, environmental factors, and other variables on the distribution and abundance of gray whales within their preferred feeding area adjacent to Piltun Bay. Multiple regression analysis revealed a limited redistribution of gray whales southward within the Piltun feeding area when the seismic survey was fully operational. A total of five environmental and other variables unrelated to seismic survey (date and proxies of depth, sea state and visibility) and one seismic survey-related variable (seg3d, i.e., received sound energy accumulated over 3 days) had statistically significant effects on the distribution and abundance of gray whales. The distribution of two to four gray whales observed on the surface (i.e., about five to ten whales in total) has likely been affected by the seismic survey. However, the total number of gray whales observed within the Piltun feeding area remained stable during the seismic survey

Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens.

BackgroundTo determine differentially expressed and spliced RNA transcripts in chronic lymphocytic leukemia specimens a high throughput RNA-sequencing (HTS RNA-seq) analysis was performed.MethodsTen CLL specimens and five normal peripheral blood CD19+ B cells were analyzed by HTS RNA-seq. The library preparation was performed with Illumina TrueSeq RNA kit and analyzed by Illumina HiSeq 2000 sequencing system.ResultsAn average of 48.5 million reads for B cells, and 50.6 million reads for CLL specimens were obtained with 10396 and 10448 assembled transcripts for normal B cells and primary CLL specimens respectively. With the Cuffdiff analysis, 2091 differentially expressed genes (DEG) between B cells and CLL specimens based on FPKM (fragments per kilobase of transcript per million reads and false discovery rate, FDR q < 0.05, fold change >2) were identified. Expression of selected DEGs (n = 32) with up regulated and down regulated expression in CLL from RNA-seq data were also analyzed by qRT-PCR in a test cohort of CLL specimens. Even though there was a variation in fold expression of DEG genes between RNA-seq and qRT-PCR; more than 90 % of analyzed genes were validated by qRT-PCR analysis. Analysis of RNA-seq data for splicing alterations in CLL and B cells was performed by Multivariate Analysis of Transcript Splicing (MATS analysis). Skipped exon was the most frequent splicing alteration in CLL specimens with 128 significant events (P-value <0.05, minimum inclusion level difference >0.1).ConclusionThe RNA-seq analysis of CLL specimens identifies novel DEG and alternatively spliced genes that are potential prognostic markers and therapeutic targets. High level of validation by qRT-PCR for a number of DEG genes supports the accuracy of this analysis. Global comparison of transcriptomes of B cells, IGVH non-mutated CLL (U-CLL) and mutated CLL specimens (M-CLL) with multidimensional scaling analysis was able to segregate CLL and B cell transcriptomes but the M-CLL and U-CLL transcriptomes were indistinguishable. The analysis of HTS RNA-seq data to identify alternative splicing events and other genetic abnormalities specific to CLL is an added advantage of RNA-seq that is not feasible with other genome wide analysis

An efficient record linkage scheme using graphical analysis for identifier error detection

Integration of information on individuals (record linkage) is a key problem in healthcare delivery, epidemiology, and "business intelligence" applications. It is now common to be required to link very large numbers of records, often containing various combinations of theoretically unique identifiers, such as NHS numbers, which are both incomplete and error-prone

Flower preferences and pollen transport networks for cavity-nesting solitary bees: Implications for the design of agri-environment schemes.

Floral foraging resources are valuable for pollinator conservation on farmland, and their provision is encouraged by agri-environment schemes in many countries. Across Europe, wildflower seed mixtures are widely sown on farmland to encourage pollinators, but the extent to which key pollinator groups such as solitary bees exploit and benefit from these resources is unclear. We used high-throughput sequencing of 164 pollen samples extracted from the brood cells of six common cavity-nesting solitary bee species (Osmia bicornis, Osmia caerulescens, Megachile versicolor, Megachile ligniseca, Megachile centuncularis and Hylaeus confusus) which are widely distributed across the UK and Europe. We documented their pollen use across 19 farms in southern England, UK, revealing their forage plants and examining the structure of their pollen transport networks. Of the 32 plant species included currently in sown wildflower mixes, 15 were recorded as present within close foraging range of the bees on the study farms, but only Ranunculus acris L. was identified within the pollen samples. Rosa canina L. was the most commonly found of the 23 plant species identified in the pollen samples, suggesting that, in addition to providing a nesting resource for Megachile leafcutter bees, it may be an important forage plant for these species. Higher levels of connectance and nestedness were characteristic of pollen transport networks on farms with abundant floral resources, which may increase resilience to species loss. Our data suggest that plant species promoted currently by agri-environment schemes are not optimal for solitary bee foraging. If a diverse community of pollinators is to be supported on UK and European farmland, additional species such as R. canina should be encouraged to meet the foraging requirements of solitary bees

Formation of a stable deacagonal quasicrystalline Al-Pd-Mn surface layer

We report the in situ formation of an ordered equilibrium decagonal Al-Pd-Mn quasicrystal overlayer on the 5-fold symmetric surface of an icosahedral Al-Pd-Mn monograin. The decagonal structure of the epilayer is evidenced by x-ray photoelectron diffraction, low-energy electron diffraction and electron backscatter diffraction. This overlayer is also characterized by a reduced density of states near the Fermi edge as expected for quasicrystals. This is the first time that a millimeter-size surface of the stable decagonal Al-Pd-Mn is obtained, studied and compared to its icosahedral counterpart.Comment: Submitted to Phys. Ref. Lett. (18 July 2001

Self-diffusion of adatoms, dimers, and vacancies on Cu(100)

We use ab initio static relaxation methods and semi-empirical molecular-dynamics simulations to investigate the energetics and dynamics of the diffusion of adatoms, dimers, and vacancies on Cu(100). It is found that the dynamical energy barriers for diffusion are well approximated by the static, 0 K barriers and that prefactors do not depend sensitively on the species undergoing diffusion. The ab initio barriers are observed to be significantly lower when calculated within the generalized-gradient approximation (GGA) rather than in the local-density approximation (LDA). Our calculations predict that surface diffusion should proceed primarily via the diffusion of vacancies. Adatoms are found to migrate most easily via a jump mechanism. This is the case, also, of dimers, even though the corresponding barrier is slightly larger than it is for adatoms. We observe, further, that dimers diffuse more readily than they can dissociate. Our results are discussed in the context of recent submonolayer growth experiments of Cu(100).Comment: Submitted to the Physical Review B; 15 pages including postscript figures; see also http://www.centrcn.umontreal.ca/~lewi