Thermal diffusion in molecular dynamics simulations of thin film diamond deposition

Molecular dynamics simulations of carbon atom depositions are used to investigate energy diffusion from the impact zone. A modified Stillinger-Weber potential models the carbon interactions for both sp2 and sp3 bonding. Simulations were performed on 50 eV carbon atom depositions onto the (111) surface of a 3.8 x 3.4 x 1.0 nm diamond slab containing 2816 atoms in 11 layers of 256 atoms each. The bottom layer was thermostated to 300 K. At every 100th simulation time step (27 fs), the average local kinetic energy, and hence local temperature, is calculated. To do this the substrate is divided into a set of 15 concentric hemispherical zones, each of thickness one atomic diameter (0.14 nm) and centered on the impact point. A 50-eV incident atom heats the local impact zone above 10 000 K. After the initial large transient (200 fs) the impact zone has cooled below 3000 K, then near 1000 K by 1 ps. Thereafter the temperature profile decays approximately as described by diffusion theory, perturbed by atomic scale fluctuations. A continuum model of classical energy transfer is provided by the traditional thermal diffusion equation. The results show that continuum diffusion theory describes well energy diffusion in low energy atomic deposition processes, at distance and time scales larger than 1.5 nm and 1-2 ps, beyond which the energy decays essentially exponentially. (C) 1998 Published by Elsevier Science S.A. All rights reserved.

Dynamics of a mesoscopic charge quantum bit under continuous quantum measurement

We present the conditional quantum dynamics of an electron tunneling between two quantum dots subject to a measurement using a low transparency point contact or tunnel junction. The double dot system forms a single qubit and the measurement corresponds to a continuous in time readout of the occupancy of the quantum dot. We illustrate the difference between conditional and unconditional dynamics of the qubit. The conditional dynamics is discussed in two regimes depending on the rate of tunneling through the point contact: quantum jumps, in which individual electron tunneling current events can be distinguished, and a diffusive dynamics in which individual events are ignored, and the time-averaged current is considered as a continuous diffusive variable. We include the effect of inefficient measurement and the influence of the relative phase between the two tunneling amplitudes of the double dot/point contact system.

Quantum dynamics of spin polarized optoelectronic processes

We study the quantum dynamics of the emission of multimodal polarized light in light emitting devices (LED) due to spin polarized carriers injection. We present the equations for photon number and carrier numbers, and calculate the polarisation degree of the light generated by LED. (C) 2002 Elsevier Science B.V. All rights reserved.

Impact of land-use on soil organic matter quality in south-western Australia - characterization with C-13 CP/MAS NMR spectroscopy

The influence of change in land-use from native vegetation to pasture (20-71 yr after conversion), and subsequent change from pasture to eucalypt plantation (7-10 yr after conversion) on soil organic matter quality was investigated using C-13 CP/MAS NMR spectroscopy. We studied surface soil (0-10 cm) from six sites representing a range of soil, and climate types from south-western Australia. Total C in the samples ranged from 1.6 to 5.5%, but the relative proportions of the four primary spectral regions (alkyl, O-alkyl, aromatic and carboxylic) were similar across the sites, and changes due to land-use at each site were relatively minor. Main impacts of changed land-use were higher O-alkyl (carbohydrate) material under pasture than under native vegetation and plantation (P = 0.048), and lower aromatic C under pasture than under native vegetation (P = 0.027). The decrease in aromatic C in pasture soils was related to time since clearing. (C) 2002 Elsevier Science Ltd. All rights reserved.

Soil attributes dynamics evaluation after prescribed burning practice in northwestern Portugal forest

The Portuguese northern forests are often and severely affected by wildfires during the summer season. These occurrences affect significant and rudely all ecosystems, namely soil, fauna and flora. Preventive actions such as prescribed burnings and clear-cut logging are frequently used and have showed a significant reduction of the natural wildfires occurrences. In Portugal, and due to some technical and operational conditions, prescribed burnings in forests are the most common preventive action used to reduce the existing fuel hazard. The overall impacts of this preventive action on Portuguese ecosystems are complex and not fully understood. This work reports to the study of a prescribed burning impact in soil chemical properties, namely pH, humidity and organic matter, by monitoring the soil self-recovery capacity. The experiments were carried out in soil cover over a natural site of Andaluzitic schist, in Gramelas, Caminha, Portugal, who was able to maintain itself intact from prescribed burnings from four years. The composed soil samples were collected from five plots at three different layers (0-3cm, 3-6cm and 6-18cm) 1 day before prescribed fire and after the prescribed fire. The results have shown that the dynamic equilibrium in soil was affected significantly.

Advanced instrumentation for superheated liquid detectors in dark matter searches

Dissertação para obtenção do Grau de Doutor em Engenharia Física

Flood pulse and spatial dynamics of mercury in sediments in Puruzinho lake, Brazilian Amazon

The study was conducted in Puruzinho lake (Humaitá, AM) considering seasonal periods of rainy and dry in way to elucidate the flood pulse importance in the deposition, remobilization and distributions of mercury and organic matter in bottom sediments in the Madeira River Basin (Brazilian Amazon). Bottom sediments and soils samples were analyzed for total mercury and organic matter. Mercury concentrations obtained in bottom sediment were 32.20-146.40 ng g-1 and organic matter values were 3.5 - 18.0%. The main region for accumulation of mercury and organic matter was in the central and deepest lake area In the rainy season there was a greater distribution of Hg and organic matter, mainly controlled by means of income of the Madeira river water during flooding, while the predominant process in the dry season was the remobilization of total Hg due to the resuspension of bottom sediments.

Population dynamics of 0-group flounder (Platichthys flesus L.) in Galway Bay, West of Ireland and the value of flounder from shore angling tourism in Ireland

The economic value of flounder from shore angling around Ireland was assessed. Flounder catches from shore angling tournaments around Ireland were related to domestic and overseas shore angling expenditure in order to determine an economic value for the species. Temporal trends in flounder angling catches, and specimen (trophy) flounder reports were also investigated. Flounder was found to be the most caught shore angling species in competitions around Ireland constituting roughly one third of the shore angling competition catch although this did vary by area. The total value of flounder from shore angling tourism was estimated to be of the order of €8.4 million. No significant temporal trends in flounder angling catches and specimen reports were found. Thus there is no evidence from the current study for any decline in flounder stocks. The population dynamics of 0-group flounder during the early benthic stage was investigated at estuarine sites in Galway Bay, west of Ireland. Information was analysed from the March to June sampling period over five years (2002 to 2006). Spatial and temporal variations in settlement and population length structure were analysed between beach and river habitats and sites. Settlement of flounder began from late March to early May of each year, most commonly in April. Peak settlement was usually in April or early May. Settlement was recorded earlier than elsewhere, although most commonly was similar to the southern part of the UK and northern France. Settlement was generally later in tidal rivers than on sandy beaches. Abundance of 0-group flounder in Galway Bay did not exhibit significant inter -annual variability. 0-group flounder were observed in dense aggregations of up to 105 m'2, which were patchy in distribution. Highest densities of 0-group flounder were recorded in limnetic and oligohaline areas as compared with the lower densities in polyhaline and to a lesser extent mesohaline areas. Measurements to of salinity allowed the classification of beaches, and tidal river sections near the mouth, into a salinity based scheme for length comparisons. Beaches were classified as polyhaline,the lower section of rivers as mesohaline, and the middle and upper sections as oligohaline. Over the March to June sampling period 0-group flounder utilised different sections at different length ranges and were significantly larger in more upstream sections. During initial settlement in April, 0-group flounder of 8-10 mm (standard length, SL) were present in abundance on polyhaline sandy beaches. By about 10mm (SL), flounder were present in all polyhaline, mesohaline and (oligohaline) sections. 0-group flounder became absent or in insignificant numbers in polyhaline and mesohaline sections in a matter of weeks after first appearance. From April to June, 0-group flounder of 12-30mm (SL) were found in more upstream locations in the oligohaline sections. About one month (May or June) after initial settlement, 0-group flounder became absent from the oligohaline sections. Concurrently, flounder start to reappear in mesohaline and polyhaline areas at approximately 30mm (SL) in June. The results indicate 0-group flounder in the early benthic stage are associated with low salinity areas, but as they grow, this association diminishes. Results strongly suggest that migration of 0-group flounder between habitats takes place during the early benthic phase.

White matter maturation reshapes structural connectivity in the late developing human brain.

From toddler to late teenager, the macroscopic pattern of axonal projections in the human brain remains largely unchanged while undergoing dramatic functional modifications that lead to network refinement. These functional modifications are mediated by increasing myelination and changes in axonal diameter and synaptic density, as well as changes in neurochemical mediators. Here we explore the contribution of white matter maturation to the development of connectivity between ages 2 and 18 y using high b-value diffusion MRI tractography and connectivity analysis. We measured changes in connection efficacy as the inverse of the average diffusivity along a fiber tract. We observed significant refinement in specific metrics of network topology, including a significant increase in node strength and efficiency along with a decrease in clustering. Major structural modules and hubs were in place by 2 y of age, and they continued to strengthen their profile during subsequent development. Recording resting-state functional MRI from a subset of subjects, we confirmed a positive correlation between structural and functional connectivity, and in addition observed that this relationship strengthened with age. Continuously increasing integration and decreasing segregation of structural connectivity with age suggests that network refinement mediated by white matter maturation promotes increased global efficiency. In addition, the strengthening of the correlation between structural and functional connectivity with age suggests that white matter connectivity in combination with other factors, such as differential modulation of axonal diameter and myelin thickness, that are partially captured by inverse average diffusivity, play an increasingly important role in creating brain-wide coherence and synchrony.

Dynamics of a paleoecosystem reef associated with oceanic change in carbonate sedimentary regime and carbon cycling (Oxfordian, Swiss Jura)

Herein we report an analysis of an Oxfordian (Upper Jurassic) paleoreef located in the Swiss Jura Mountains. The paleoreef is located in a Middle Oxfordian transitional interval in which sedimentation switched from marl-dominated to carbonate-dominated deposits. The paleoecosystem is composed of four successive fossil communities characterized by microsolenid corals and organisms that specialized in suspension feeding. Carbon isotopes measured from echinoid spine carbonates exhibit a positive trend from similar to 1.0 parts per thousand to 2.5 parts per thousand in delta(13)C values from the base to the top of the paleoreef. Comparison of delta(13)C curves with organic matter and belemnites shows different patterns not compatible with a global variation of the carbon cycle. Similar fossil assemblages and stratigraphic sequences identical in age are found along the continental margin of the Tethys-Atlantic Ocean. This biolithostratigraphic succession corresponds to increasing delta(13)C values of marine and biogenic carbonates, to the transition from marl-dominated to carbonate-dominated deposits, and to the development of carbonate platforms, which together suggest a change in the carbon cycling regime within the Tethys-Atlantic Ocean system.

HIV-1 reverse transcriptase connection domain mutations: dynamics of emergence and implications for success of combination antiretroviral therapy.

BACKGROUND: Factors promoting the emergence of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) connection domain mutations and their effect on antiretroviral therapy (ART) are still largely undetermined. We investigated this matter by analyzing genotypic resistance tests covering 400 amino acid positions in the RT of HIV-1 subtype B viruses and corresponding treatment histories and laboratory measurements. METHODS: The emergence of connection domain mutations was studied in 334 patients receiving monotherapy or dual therapy with thymidine analogues at the time of the genotypic resistance test. Response to subsequent combination ART (cART) was analyzed using Cox regression for 291 patients receiving unboosted protease inhibitors. Response was defined by ever reaching an HIV RNA level <50 copies/mL during the first cART. RESULTS: The connection domain mutations N348I, R356K, R358K, A360V, and A371V were more frequently observed in ART-exposed than ART-naive patients, of which only N348I and A360V were nonpolymorphic (with a prevalence of <1.5% in untreated patients). N348I correlated with M184V and predominantly occurred in patients receiving lamivudine and zidovudine concomitantly. A360V was not associated with specific drug combinations and was found to emerge later than M184V or thymidine analogue mutations. Nonpolymorphic connection domain mutations were rarely detected in the absence of established drug resistance mutations in ART-exposed individuals (prevalence, <1%). None of the 5 connection domain mutations associated with treatment showed a statistically significant effect on response to cART. CONCLUSIONS: Despite their frequent emergence, connection domain mutations did not show large detrimental effects on response to cART. Currently, routine implementation of connection domain sequencing seems unnecessary for developed health care settings.

Predicting current and future biological invasions: both native and invaded ranges matter.

The classical approach to predicting the geographical extent of species invasions consists of training models in the native range and projecting them in distinct, potentially invasible areas. However, recent studies have demonstrated that this approach could be hampered by a change of the realized climatic niche, allowing invasive species to spread into habitats in the invaded ranges that are climatically distinct from those occupied in the native range. We propose an alternative approach that involves fitting models with pooled data from all ranges. We show that this pooled approach improves prediction of the extent of invasion of spotted knapweed (Centaurea maculosa) in North America on models based solely on the European native range. Furthermore, it performs equally well on models based on the invaded range, while ensuring the inclusion of areas with similar climate to the European niche, where the species is likely to spread further. We then compare projections from these models for 2080 under a severe climate warming scenario. Projections from the pooled models show fewer areas of intermediate climatic suitability than projections from the native or invaded range models, suggesting a better consensus among modelling techniques and reduced uncertainty.

Does money matter in shaping domestic business cycles? An international investigation (with appendices)

We study the contribution of money to business cycle fluctuations in the US,the UK, Japan, and the Euro area using a small scale structural monetary business cycle model. Constrained likelihood-based estimates of the parameters areprovided and time instabilities analyzed. Real balances are statistically importantfor output and inflation fluctuations. Their contribution changes over time. Models giving money no role provide a distorted representation of the sources of cyclicalfluctuations, of the transmission of shocks and of the events of the last 40 years.

The structural dynamics of output growth and inflation: some international evidence

We examine the dynamics of output growth and inflation in the US, Euro area and UK using a structural time varying coefficient VAR. There are important similarities in structural inflation dynamics across countries; output growth dynamics differ. Swings in the magnitude of inflation and output growth volatilities and persistences are accounted for by a combination of three structural shocks. Changes over time in the structure of the economy are limited and permanent variations largely absent. Changes in the volatilities of structural shocks matter.

Do expectations matter? The Great Moderation revisited

We examine the role of expectations in the Great Moderation episode. We derive theoretical restrictions in a New-Keynesian model and test them using measures of expectations obtained from survey data, the Greenbook and bond markets. Expectations explain the dynamics of inflation and of interest rates but their importance is roughly unchanged over time. Systems with and without expectations display similar reduced form characteristics. Including or excluding expectations hardly changes the economic explanation of the Great Moderation. Results are robust to changes in the structure of the empirical model.