Plasma-deposited Ge nanoisland films on Si : is Stranski–Krastanow fragmentation unavoidable?

The formation of Ge quantum dot arrays by deposition from a low-temperature plasma environment is investigated by kinetic Monte Carlo numerical simulation. It is demonstrated that balancing of the Ge influx from the plasma against surface diffusion provides an effective control of the surface processes and can result in the formation of very small densely packed quantum dots. In the supply-controlled mode, a continuous layer is formed which is then followed by the usual Stranski-Krastanow fragmentation with a nanocluster size of 10 nm. In the diffusion-controlled mode, with the oversupply relative to the surface diffusion rate, nanoclusters with a characteristic size of 3 nm are formed. Higher temperatures change the mode to supply controlled and thus encourage formation of the continuous layer that then fragments into an array of large size. The use of a high rate of deposition, easily accessible using plasma techniques, changes the mode to diffusion controlled and thus encourages formation of a dense array of small nanoislands.

Reducing building information fragmentation : a BIM-specifications approach

The world of Construction is changing, so too are the expectations of stakeholders regarding strategies for adapting existing resources (people, equipment and finances), processes and tools to the evolving needs of the industry. Building Information Modelling (BIM) is a data-rich, digital approach for representing building information required for design and construction. BIM tools play a crucial role and are instrumental to current approaches, by industry stakeholders, aimed at harnessing the power of a single information repository for improved project delivery and maintenance. Yet, building specifications - which document information on material quality, and workmanship requirements - remain distinctly separate from model information typically represented in BIM models. BIM adoption for building design, construction and maintenance is an industry-wide strategy aimed at addressing such concerns about information fragmentation. However, to effectively reduce inefficiencies due to fragmentation, BIM models require crucial building information contained in specifications. This paper profiles some specification tools which have been used in industry as a means of bridging the BIM-Specifications divide. We analyse the distinction between current attempts at integrating BIM and specifications and our approach which utilizes rich specification information embedded within objects in a product library as a method for improving the quality of information contained in BIM objects at various levels of model development.

Behavioural, population, and genetic processes affecting metapopulation dynamics of the Glanville fritillary butterfly

In my thesis I have been studying the effects of population fragmentation and extinction-recolonization dynamics on genetic and evolutionary processes in the Glanville fritillary butterfly (Melitaea cinxia). By conducting crosses within and among newly-colonized populations and using several fitness measures, I found a strong decrease in fitness following colonization by a few related individuals, and a strong negative relationship between parental relatedness and offspring fitness. Thereafter, I was interested in determining the number and relatedness of individuals colonizing new populations, which I did using a set of microsatellites I had previously developed for this species. Additionally, I am interested in the evolution of key life-history traits. By following the lifetime reproductive success of males emerging at different times in a semi-natural setup, I demonstrated that protandry is adaptive in males, and I was able to rule out, for M. cinxia, alternative incidental hypotheses evoked to explain the evolution of protandry in insects. Finally, in work I did together with Prof. Hanna Kokko, I am proposing bet-hedging as a new mechanism that could explain the evolution of polyandry in M. cinxia.

Characterisation of Landscape with Forest Fragmentation Dynamics

Land cover (LC) and land use (LU) dynamics induced by human and natural processes play a major role in global as well as regional patterns of landscapes influencing biodiversity, hydrology, ecology and climate. Changes in LC features resulting in forest fragmentations have posed direct threats to biodiversity, endangering the sustainability of ecological goods and services. Habitat fragmentation is of added concern as the residual spatial patterns mitigate or exacerbate edge effects. LU dynamics are obtained by classifying temporal remotely sensed satellite imagery of different spatial and spectral resolutions. This paper reviews five different image classification algorithms using spatio-temporal data of a temperate watershed in Himachal Pradesh, India. Gaussian Maximum Likelihood classifier was found to be apt for analysing spatial pattern at regional scale based on accuracy assessment through error matrix and ROC (receiver operating characteristic) curves. The LU information thus derived was then used to assess spatial changes from temporal data using principal component analysis and correspondence analysis based image differencing. The forest area dynamics was further studied by analysing the different types of fragmentation through forest fragmentation models. The computed forest fragmentation and landscape metrics show a decline of interior intact forests with a substantial increase in patch forest during 1972-2007.

Combined Electron Transfer Dissociation-Collision-Induced Dissociation Fragmentation in the Mass Spectrometric Distinction of Leucine, Isoleucine, and Hydroxyproline Residues in Peptide Natural Products

Distinctions between isobaric residues have been a major challenge in mass spectrometric peptide sequencing. Here, we propose a methodology for distinction among isobaric leucine, isoleucine, and hydroxyproline, a commonly found post-translationally modified amino acid with a nominal mass of 113 Da, through a combined electron transfer dissociation-collision-induced dissociation approach. While the absence of c and z(center dot) ions, corresponding to the Yyy-Xxx (Xxx = Leu, Ile, or Hyp) segment, is indicative of the presence of hydroxyproline, loss of isopropyl (Delta m = 43 Da) or ethyl radicals (Delta m = 29 Da), through collisional activation of z(center dot) radical ions, are characteristic of leucine or isoleucine, respectively. Radical migration processes permit distinctions even in cases where the specific e ions, corresponding to the Yyy-Leu or -Ile segments, are absent or of low intensity. This tandem mass spectrometric (MSn) method has been successfully implemented in a liquid chromatography MSn platform to determine the identity of 23 different isobaric residues from a mixture of five different peptides. The approach is convenient for distinction of isobaric residues from any crude peptide mixture, typically encountered in natural peptide libraries or proteomic analysis.

Investigation of Fundamental Processes Governing Secondary Organic Aerosol Formation in Laboratory Chambers

Our understanding of the processes and mechanisms by which secondary organic aerosol (SOA) is formed is derived from laboratory chamber studies. In the atmosphere, SOA formation is primarily driven by progressive photooxidation of SOA precursors, coupled with their gas-particle partitioning. In the chamber environment, SOA-forming vapors undergo multiple chemical and physical processes that involve production and removal via gas-phase reactions; partitioning onto suspended particles vs. particles deposited on the chamber wall; and direct deposition on the chamber wall. The main focus of this dissertation is to characterize the interactions of organic vapors with suspended particles and the chamber wall and explore how these intertwined processes in laboratory chambers govern SOA formation and evolution.

A Functional Group Oxidation Model (FGOM) that represents SOA formation and evolution in terms of the competition between functionalization and fragmentation, the extent of oxygen atom addition, and the change of volatility, is developed. The FGOM contains a set of parameters that are to be determined by fitting of the model to laboratory chamber data. The sensitivity of the model prediction to variation of the adjustable parameters allows one to assess the relative importance of various pathways involved in SOA formation.

A critical aspect of the environmental chamber is the presence of the wall, which can induce deposition of SOA-forming vapors and promote heterogeneous reactions. An experimental protocol and model framework are first developed to constrain the vapor-wall interactions. By optimal fitting the model predictions to the observed wall-induced decay profiles of 25 oxidized organic compounds, the dominant parameter governing the extent of wall deposition of a compound is identified, i.e., wall accommodation coefficient. By correlating this parameter with the molecular properties of a compound via its volatility, the wall-induced deposition rate of an organic compound can be predicted based on its carbon and oxygen numbers in the molecule.

Heterogeneous transformation of δ-hydroxycarbonyl, a major first-generation product from long-chain alkane photochemistry, is observed on the surface of particles and walls. The uniqueness of this reaction scheme is the production of substituted dihydrofuran, which is highly reactive towards ozone, OH, and NO3, thereby opening a reaction pathway that is not usually accessible to alkanes. A spectrum of highly-oxygenated products with carboxylic acid, ester, and ether functional groups is produced from the substituted dihydrofuran chemistry, thereby affecting the average oxidation state of the alkane-derived SOA.

The vapor wall loss correction is applied to several chamber-derived SOA systems generated from both anthropogenic and biogenic sources. Experimental and modeling approaches are employed to constrain the partitioning behavior of SOA-forming vapors onto suspended particles vs. chamber walls. It is demonstrated that deposition of SOA-forming vapors to the chamber wall during photooxidation experiments can lead to substantial and systematic underestimation of SOA. Therefore, it is likely that a lack of proper accounting for vapor wall losses that suppress chamber-derived SOA yields contribute substantially to the underprediction of ambient SOA concentrations in atmospheric models.

Electron-impact fragmentation of Cl2-

merged beam technique has been used to investigate the fragmentation of the Cl ion in collisions with electrons over an energy range of 0–200 eV. We have measured absolute cross sections for detachment, detachment plus dissociation and dissociation processes. Over the energy range studied, the dominant breakup mechanism is dissociation. Dissociation is relatively enhanced in the e–+Cl collision system due to the suppression of the normally dominant detachment process, as a result of the large difference between the equilibrium internuclear distances of the Cl2 and Cl ground state potential curves. A prominent structure is observed just above the threshold in the Cl–+Cl+e– dissociation channel. It is proposed that the structure is a resonance associated with production and rapid decay of an excited state of the doubly charged Cl ion. A plausible mechanism for production of the di-anionic state based on an excitation plus capture process is suggested.

Differential cross sections for fragmentation of positronium

Cross sections differential with respect to energy and angle of ejected positrons and electrons for Ps(ls) fragmentation in collision with He, Ne, Ar, Kr and Xe targets are reported. For Ne, Ar, Kr and Xe, only the case where the target is not excited (target elastic collisions) is considered. For He, fragmentation with target excitation/ionization (target inelastic collisions) is also studied. The impulse approximation has been used for target elastic fragmentation, the first Born approximation for target inelastic processes. (c) 2006 Elsevier B.V. All rights reserved.

Charge exchange and dissociative processes in collisions of slow He2+ ions with H2O molecules

Experimental and theoretical studies of one-electron capture in collisions of He2+ ions with H2O molecules have been carried out in the range 0.025-12 keV amu(-1) corresponding to typical solar wind velocities of 70-1523 km s(-1). Translational energy spectroscopy (TES), photon emission spectroscopy (PES), and fragment ion spectroscopy were employed to identify and quantify the collision mechanisms involved. Cross sections for selective single electron capture into n=1, 2, and 3 states of the He+ ion were obtained using TES while PES provided cross sections for capture into the He+(2p) and He+(3p) states. Our model calculations show that He+(n=2) and He+(n=3) formation proceeds via a single-electron process governed by the nucleus-electron interaction. In contrast, the He+(1s) formation mechanism involves an exothermic two-electron process driven by the electron-electron interaction, where the potential energy released by the electron capture is used to remove a second electron thereby resulting in fragmentation of the H2O molecule. This process is found to become increasingly important as the collision energy decreases. The experimental cross sections are found to be in reasonable agreement with cross sections calculated using the Demkov and Landau-Zener models.

LIAD-fs: A novel method for studies of ultrafast processes in gas phase neutral biomolecules

A new experimental technique for femtosecond (fs) pulse studies of gas phase biomolecules is reported. Using Laser-Induced Acoustic Desorption (LIAD) to produce a plume of neutral molecules, a time-delayed fs pulse is employed for ionisation/fragmentation, with subsequent products extracted and mass analysed electrostatically. By varying critical laser pulse parameters, this technique can be used to implement control over molecular fragmentation for a range of small biomolecules, with specific studies of amino acids demonstrated.

Insights into processes and deposits of hazardous vulcanian explosions at Soufrière Hills Volcano during 2008 and 2009 (Montserrat, West Indies)

During the Soufrière Hills eruption, vulcanian explosions have generally occurred 1) in episodic cycles; 2) isolated during pauses in extrusion, and 3) after major collapses of the dome. In a different eruptive context, significant vulcanian explosions occurred on 29 July 2008, 3 December 2008, and 3 January 2009. Deposits are pumiceous except for the 3 December event. We reconstructed the dispersal pattern of the deposits and their textural characteristics to evaluate erupted volume and vesicularity of the magma at fragmentation. We discuss the implications of these explosions in terms of eruptive processes and chronology, and the hazards posed by their sudden and often unheralded occurrence. We suggest that overpressurization of the conduit can develop over time-scales of months to weeks by a process of self-sealing of conduit walls and/or the cooling dome by silica polymorphs. This work provides new insights for understanding the generation of hazardous vulcanian explosions at andesitic volcanoes.

Endoparasitism in colonial hosts: patterns and processes

This study begins to redress our lack of knowledge of the interactions between colonial hosts and their parasites by focusing on a novel host-parasite system. Investigations of freshwater bryozoan populations revealed that infection by myxozoan parasites is widespread. Covert infections were detected in all 5 populations studied and were often at high prevalence while overt infections were observed in only 1. Infections were persistent in populations subject to temporal sampling. Negative effects of infection were identified but virulence was low. Infection did not induce mortality in the environmental conditions studied. However, the production of statoblasts (dormant propagules) was greatly reduced in bryozoans with overt infections in comparison to uninfected bryozoans. Overtly-infected bryozoans also grew more slowly and had low fission rates relative to colonies lacking overt infection. Bryozoans with covert infections were smaller than uninfected bryozoans. High levels of vertical transmission were achieved through colony fission and the infection of statoblasts. Increased fission rates may be a strategy for hosts to escape from parasites but the parasite can also exploit the fragmentation of colonial hosts to gain vertical transmission and dispersal. Our study provides evidence that opportunities and constraints for host-parasite co-evolution can be highly dependent on organismal body plans and that low virulence may be associated with exploitation of colonial hosts by endoparasites.

The impact of fragmentation and density regulation on forest succession in the Atlantic rain forest

The Atlantic Rain Forest, an important biodiversity hot spot, has faced severe habitat loss since the last century which has resulted in a highly fragmented landscape with a large number of small forest patches (<100 ha). For conservation planning it is essential to understand how current and future forest regeneration depends on ecological processes, fragment size and the connection to the regional seed pool. We have investigated the following questions by applying the forest growth simulation model FORMIND to the situation of the Atlantic Forest in the state of Sao Paulo, SE Brazil: (1) which set of parameters describing the local regeneration and level of density regulation can reproduce the biomass distribution and stem density of an old growth forest in a reserve? (2) Which additional processes apart from those describing the dynamics of an old growth forest, drive forest succession of small isolated fragments? (3) Which role does external seed input play during succession? Therefore, more than 300 tree species have been classified into nine plant functional types (PFTs), which are characterized by maximum potential height and shade tolerance. We differentiate between two seed dispersal modes: (i) local dispersal, i.e. all seedlings originated from fertile trees within the simulated area and (ii) external seed rain. Local seed dispersal has been parameterized following the pattern oriented approach, using biomass estimates of old growth forest. We have found that moderate density regulation is essential to achieve coexistence for a broad range of regeneration parameters. Considering the expected uncertainty and variability in the regeneration processes it is important that the forest dynamics are robust to variations in the regeneration parameters. Furthermore, edge effects such as increased mortality at the border and external seed rain have been necessary to reproduce the patterns for small isolated fragments. Overall, simulated biomass is much lower in the fragments compared to the continuous forest, whereas shade tolerant species are affected most strongly by fragmentation. Our simulations can supplement empirical studies by extrapolating local knowledge on edge effects of fragments to larger temporal and spatial scales. In particular our results show the importance of external seed rain and therefore highlight the importance of structural connectivity between regenerating fragments and mature forest stands. (C) 2009 Elsevier B.V. All rights reserved.

Forest structure in a mosaic of rainforest sites: The effect of fragmentation and recovery after clear cut

A variety of human-induced disturbances such as forest fragmentation and recovery after deforestation for pasture or agricultural activities have resulted in a complex landscape mosaic in the Una region of northeastern Brazil. Using a set of vegetation descriptors, we investigated the main structural changes observed in forest categories that comprise the major components of the regional landscape and searched for potential key descriptors that could be used to discriminate among different forest categories. We assessed the forest structure of five habitat categories defined as (I) interiors and (2) edges of large fragments of old-growth forest (>1000 ha), (3) interiors and (4) edges of small forest fragments (<100 ha), and (5) early secondary forests. Forest descriptors used here were: frequency of herbaceous lianas and woody climbers, number of standing dead trees, number of fallen trunks, litter depth, number of pioneer plants (early secondary and shade-intolerant species), vertical foliage stratification profile and distribution Of trees in different diameter classes. Edges and interiors of forest fragments were significantly different only in the number of standing dead trees. Secondary forests and edges of fragments showed differences in litter depth, fallen trunks and number of pioneer trees, and secondary forests were significantly different from fragment interiors in the number of standing dead trees and the number of pioneer trees. Horizontal and vertical structure evaluated via ordination analysis showed that fragment interiors, compared to secondary forests, were characterized by a greater number of medium (25-35 cm) and large (35-50 cm) trees and smaller numbers of thin trees (5-10 cm). There was great heterogeneity at the edges of small and large fragments, as these sites were distributed along almost the entire gradient. Most interiors of large and small fragments presented higher values of foliage densities at higher strata ( 15-20 m and at 20-25 m height), and lower densities at 1-5 m. All secondary forests and some fragment edge sites showed an opposite tendency. A discriminant function highlighted differences among forest categories, with transects of large fragment interiors and secondary forests representing two extremes along a disturbance gradient determined by foliage structure (densities at 15-20 m and 20-25 m), with the edges of both large and small fragments and the interiors of small fragments scattered across the gradient. The major underlying processes determining patterns of forest disturbance in the study region are discussed, highlighting the importance of forest fragments, independently of its size, as forests recovery after clear cut show a greatly distinct structure, with profound implications on fauna movements. (C) 2009 Elsevier BY. All rights reserved.