Femtosecond dynamics of molecules and clusters

The real-time dynamics of multiphoton ionization and fragmentation of molecules - Na_2 , Na_3 - and clusters - Na_n, Hg_n - has been studied in molecular beam experiments employing ion and electron spectroscopy together with femtosecond pump-probe techniques. Experiments with Na_2 and Na_3 reveal unexpected features of the dynamics of the absorption of several photons as seen in the one- and three dimensional vibrational wave packet motion in different potential surfaces and in high laser fields. Cluster size dependent studies of physical properties such as absorption resonances, lifetimes and decay channels have been performed using tunable femtosecond light pulses in resonance enhanced multiphoton ionization (REMPI) of the cluster size under investigation. This method failed in ns-laser experiments due to the ultrafast decay of the studied cluster. For Na_n, cluster we find that for cluster sizes n \le 21 molecular excitations and properties prevail over collective excitations of plasmon-like resonances. In the case of Hg_n cluster prompt formation of singly and doubly charged cluster are observed up to n \approx 60. The transient multiphoton ionization spectra show a 'short' time wave packet dynamics, which is identical for singly and doubly charged mercury clusters while the 'long' time fragmentation dynamics is different.

Quantum tunneling fragmentation model

A nonthermal quantum mechanical statistical fragmentation model based on tunneling of particles through potential barriers is studied in compact two- and three-dimensional systems. It is shown that this fragmentation dynamics gives origin to several static and dynamic scaling relations. The critical exponents are found and compared with those obtained in classical statistical models of fragmentation of general interest, in particular with thermal fragmentation involving classical processes over potential barriers. Besides its general theoretical interest, the fragmentation dynamics discussed here is complementary to classical fragmentation dynamics of interest in chemical kinetics and can be useful in the study of a number of other dynamic processes such as nuclear fragmentation. ©2000 The American Physical Society.

Femtosecond real-time probing of reactions

Femtosecond reaction dynamics of OClO in a supersonic molecular beam are reported. The system is excited to the A^2A_2 state with a femtosecond pulse, covering a range of excitation in the symmetric stretch between v_1 = 17 to v_1 = 11 (308-352 nm). A time-delayed femtosecond probe pulse ionizes the OClO, and OClO^+ is detected. This ion has not been observed in previous experiments because of its ultrafast fragmentation. Transients are reported for the mass of the parent OClO as well as the mass of the ClO. Apparent biexponential decays are observed and related to the fragmentation dynamics: OClO+hv \rightarrow (OClO)^{(++)*} \rightarrow ClO+O \rightarrow Cl+O_2. Clusters of OClO with water (OClO)_n (H_2 0)_m with n from 1 to 3 and m from 0 to 3 are also observed. The dynamics of the fragmentation reveal the nuclear motions and the electronic coupling between surfaces. The time scale for bond breakage is in the range of 300-500 fs, depending on v_1; surface crossing to form new intermediates is a pathway for the two channels of fragmentation: ClO+O (primary) and Cl+O_2 (minor). Comparisons with results of ab initio calculations are made.

Elemetary processes of radiation damage in organic molecules of biological interest

It was observed in the ‘80s that the radiation damage on biological systems strongly depends on processes occurring at the microscopic level, involving the elementary constituents of biological cells. Since then, lot of attention has been paid to study elementary processes of photo- and ion-chemistry of isolated organic molecule of biological interest. This work fits in this framework and aims to study the radiation damage mechanisms induced by different types of radiations on simple halogenated biomolecules used as radiosensitizers in radiotherapy. The research is focused on the photofragmentation of halogenated pyrimidine molecules (5Br-pyrimidine, 2Br-pyrimidine and 2Cl-pyrimidine) in the VUV range and on the 12C4+ ion-impact fragmentation of the 5Br-uracil and its homogeneous and hydrated clusters. Although halogen substituted pyrimidines have similar structure to the pyrimidine molecule, their photodissociation dynamics is quite different. These targets have been chosen with the purpose of investigating the effect of the specific halogen atom and site of halogenation on the fragmentation dynamics. Theoretical and experimental studies have highlighted that the site of halogenation and the type of halogen atom, lead either to the preferential breaking of the pyrimidinic ring or to the release of halogen/hydrogen radicals. The two processes can subsequently trigger different mechanisms of biological damage. To understand the effect of the environment on the fragmentation dynamic of the single molecule, the ion-induced fragmentation of homogenous and hydrated clusters of 5Br-uracil have been studied and compared to similar studies on the isolated molecule. The results show that the “protective effect” of the environment on the single molecule hold in the homogeneous clusters, but not in the hydrated clusters, where several hydrated fragments have been observed. This indicates that the presence of water molecules can inhibit some fragmentation channels and promote the keto-enol tautomerization, which is very important in the mutagenesis of the DNA.

Análise da paisagem e das alterações de uso/ocupação do solo no Lubango e arredores

A cartografia temática surge como um aliado indispensável ao estudo e conhecimento do estado da paisagem e dos ecossistemas terrestres. Angola é um país com uma enorme lacuna em termos de informação cartográfica para suporte a diversas actividades desenvolvidas em várias áreas. É por isso necessária informação sobre a superfície terrestre que registe as alterações temporais ocorridas nos ecossistemas e identifique os factores que estão na sua origem de forma a implementar medidas que permitam uma gestão mais sustentável do seu enorme território. O presente estudo foi realizado no sector Sudoeste de Angola, abrangendo os municípios do Lubango, Humpata e Chibia, com uma área aproximada de 9600 km2. Os objectivos foram: a) cartografar o coberto do solo e monitorizar as alterações ocorridas na área de estudo no período 1990-2010, b) analisar e interpretar as alterações da estrutura da paisagem nos últimos 20 anos usando cartografia de ocupação do solo, produzida recorrendo a imagens de satélite, e métricas da paisagem, e c) quantificar e examinar a relação entre a fragmentação da paisagem e os factores geradores. A metodologia utilizada no estudo é composta por duas partes, sendo a primeira dedicada às operações de processamento e interpretação de imagens de satélite Landsat e, a segunda dedicada à produção de novas métricas de fragmentação da paisagem com recurso à ferramenta SIG utilizando operações de álgebra de mapas. O comportamento da fragmentação é analisado, à luz do efeito dos fatores ambientais e socioeconómicas ao nível da região. Os resultados obtidos, através da aplicação de técnicas de deteção remota e usando imagens Landsat TM e ETM+, permitiram a elaboração de mapas de coberto do solo, onde se distinguiram 8 classes temáticas e espectralmente diferentes. Verificou-se em termos globais que aproximadamente 38% da área sofreu algum tipo de alteração no período estudado, sendo as classes de miombo e áreas cultivadas as que mais alterações sofreram. A fragmentação da paisagem foi avaliada através da implementação de novas métricas, mostrando os resultados, que no período 1990-2000, a fragmentação foi superior à que se verificou entre 2000-2010. A nível espacial, a dinâmica de fragmentação foi mais acentuada, entre 1990-2000, na Humpata e, entre 2000-2010, no Lubango; ANALYSIS OF LANDSCAPE AND LAND USE LAND COVER CHANGE IN LUBANGO AND SURROUNDINGS ABSTRACT: Thematic cartography shows up as an essential ally in the study and knowledge of the state of landscapes and terrestrial ecosystems. Angola is a country with an enormous lack of cartographic information to support the several activities carried out in a variety of areas. This is the reason information on the earth’s surface is necessary, registering alterations which occur over time in ecosystems and identifying the associated factors in its origin, so as to implement metrics that allow a more sustainable management of its enormous territory. This study was carried out in the Southeast of Angola in the Lubango, Humpata and Chibia Municipalities, with an area of approximately 9600 km2. Our objectives were the following: a) land cover mapping and land cover changes monitoring over the period 1990 to 2010 using Landsat images, b) to analyze and interpret landscape structures changes using land cover maps, and landscapes metrics, and c) to quantify and to examine the relationship between landscape fragmentation and its drivers. The methodology developed in the study has two parts, the first includes Landsat satellite images processing and interpretation and, the second the production of new landscape fragmentation metrics with support to a GIS tool and algebraic mapping operations. The fragmentation behavior is analyzed, taking into account the effect of environmental and socioeconomic factors at a regional level. The results allowed obtaining land cover maps, in which 8 spectrally different thematic classes were distinguished. It was observed that 38% of the area suffered some type of alteration in the studied period, with higher changes observed in the classes of miombo and agriculture. Landscapes fragmentation results, evaluated through the implementation of new metrics, show that, values are greater in the period 1990-2000 than in 2000-2010. At municipality level, fragmentation dynamics were more accentuated in Humpata between 1990 -2000 and in Lubango between 2000 -2010.

The Armc10/SVH gene: Genome context, regulation of mitochondrial dynamics and protection against Aβ-induced mitochondrial fragmentation

Mitochondrial function and dynamics are essential for neurotransmission, neural function and neuronal viability. Recently, we showed that the eutherian-specific Armcx gene cluster (Armcx1-6 genes), located in the X chromosome, encodes for a new family of proteins that localise to mitochondria, regulating mitochondrial trafficking. The Armcx gene cluster evolved by retrotransposition of the Armc10 gene mRNA, which is present in all vertebrates and is considered to be the ancestor gene. Here we investigate the genomic organisation, mitochondrial functions and putative neuroprotective role of the Armc10 ancestor gene. The genomic context of the Armc10 locus shows considerable syntenic conservation among vertebrates, and sequence comparisons and CHIP-data suggest the presence of at least three conserved enhancers. We also show that the Armc10 protein localises to mitochondria and that it is highly expressed in the brain. Furthermore, we show that Armc10 levels regulate mitochondrial trafficking in neurons, but not mitochondrial aggregation, by controlling the number of moving mitochondria. We further demonstrate that the Armc10 protein interacts with the KIF5/Miro1-2/Trak2 trafficking complex. Finally, we show that overexpression of Armc10 in neurons prevents A beta-induced mitochondrial fission and neuronal death. Our data suggest both conserved and differential roles of the Armc10/Armcx gene family in regulating mitochondrial dynamics in neurons, and underscore a protective effect of the Armc10 gene against A beta-induced toxicity. Overall, our findings support a further degree of regulation of mitochondrial dynamics in the brain of more evolved mammals.

The Armc10/SVH gene: Genome context, regulation of mitochondrial dynamics and protection against Aβ-induced mitochondrial fragmentation

Mitochondrial function and dynamics are essential for neurotransmission, neural function and neuronal viability. Recently, we showed that the eutherian-specific Armcx gene cluster (Armcx1-6 genes), located in the X chromosome, encodes for a new family of proteins that localise to mitochondria, regulating mitochondrial trafficking. The Armcx gene cluster evolved by retrotransposition of the Armc10 gene mRNA, which is present in all vertebrates and is considered to be the ancestor gene. Here we investigate the genomic organisation, mitochondrial functions and putative neuroprotective role of the Armc10 ancestor gene. The genomic context of the Armc10 locus shows considerable syntenic conservation among vertebrates, and sequence comparisons and CHIP-data suggest the presence of at least three conserved enhancers. We also show that the Armc10 protein localises to mitochondria and that it is highly expressed in the brain. Furthermore, we show that Armc10 levels regulate mitochondrial trafficking in neurons, but not mitochondrial aggregation, by controlling the number of moving mitochondria. We further demonstrate that the Armc10 protein interacts with the KIF5/Miro1-2/Trak2 trafficking complex. Finally, we show that overexpression of Armc10 in neurons prevents A beta-induced mitochondrial fission and neuronal death. Our data suggest both conserved and differential roles of the Armc10/Armcx gene family in regulating mitochondrial dynamics in neurons, and underscore a protective effect of the Armc10 gene against A beta-induced toxicity. Overall, our findings support a further degree of regulation of mitochondrial dynamics in the brain of more evolved mammals.

Femtosecond dynamics of molecular and cluster ionization and fragmentation

The real-time dynamics of molecular (Na_2 . Na_3) and cluster Na_n (n=4-2l) multiphoton ionization and -fragmentation has been studied in beam experiments applying femtosecond pump-probe techniques in combination with ion and electron spectroscopy. Wave packet motion in the dimer Na_2 reveals two independent multiphoton ionization processes while the higher dimensional motion in the trimer Na_3 reflects the chaotic vibrational motion in this floppy system. The first studies of cluster properties (energy, bandwidth and lifetime of intermediate resonances Na^*_n) ) with femtosecond laser pulses give a striking illustration of the transition from "molecule-like" excitations to "surfaceplasma"-like resonances for increasing cluster sizes. Time-resolved fragmentation of cluster ions Na_n^* indicate that direct photo-induced fragmentation processes are more important at short times than the statistical unimolecular decay.

How predation and landscape fragmentation affect vole population dynamics

Background: Microtine species in Fennoscandia display a distinct north-south gradient from regular cycles to stable populations. The gradient has often been attributed to changes in the interactions between microtines and their predators. Although the spatial structure of the environment is known to influence predator-prey dynamics of a wide range of species, it has scarcely been considered in relation to the Fennoscandian gradient. Furthermore, the length of microtine breeding season also displays a north-south gradient. However, little consideration has been given to its role in shaping or generating population cycles. Because these factors covary along the gradient it is difficult to distinguish their effects experimentally in the field. The distinction is here attempted using realistic agent-based modelling. Methodology/Principal Findings: By using a spatially explicit computer simulation model based on behavioural and ecological data from the field vole (Microtus agrestis), we generated a number of repeated time series of vole densities whose mean population size and amplitude were measured. Subsequently, these time series were subjected to statistical autoregressive modelling, to investigate the effects on vole population dynamics of making predators more specialised, of altering the breeding season, and increasing the level of habitat fragmentation. We found that fragmentation as well as the presence of specialist predators are necessary for the occurrence of population cycles. Habitat fragmentation and predator assembly jointly determined cycle length and amplitude. Length of vole breeding season had little impact on the oscillations. Significance: There is good agreement between our results and the experimental work from Fennoscandia, but our results allow distinction of causation that is hard to unravel in field experiments. We hope our results will help understand the reasons for cycle gradients observed in other areas. Our results clearly demonstrate the importance of landscape fragmentation for population cycling and we recommend that the degree of fragmentation be more fully considered in future analyses of vole dynamics.

Using indicators of deforestation and land-use dynamics to support conservation strategies: A case study of central Rondonia, Brazil

In Rondonia State, Brazil, settlement processes have cleared 68,000 km 2 of tropical forests since the 1970s. The intensity of deforestation has differed by region depending on driving factors like roads and economic activities. Different histories of land-use activities and rates of change have resulted in mosaics of forest patches embedded in an agricultural matrix. Yet, most assessments of deforestation and its effects on vegetation, soil and water typically focus on landscape patterns of current conditions, yet historical deforestation dynamics can influence current conditions strongly. Here, we develop and describe the use of four land-use dynamic indicators to capture historical land-use changes of catchments and to measure the rate of deforestation (annual deforestation rate), forest regeneration level (secondary forest mean proportion), time since disturbance (mean time since deforestation) and deforestation profile (deforestation profile curvature). We used the proposed indices to analyze a watershed located in central Rondonia. Landsat TM and ETM+ images were used to produce historical land-use maps of the last 18 years, each even year from 1984 to 2002 for 20 catchments. We found that the land-use dynamics indicators are able to distinguish catchments with different land-use change profiles. Four categories of historical land-use were identified: old and dominant pasture cover on small properties, recent deforestation and dominance of secondary growth, old extensive pastures and large forest remnants and, recent deforestation, pasture and large forest remnants. Knowing historical deforestation processes is important to develop appropriate conservation strategies and define priorities and actions for conserving forests currently under deforestation. (C) 2009 Elsevier B.V. All rights reserved.

Fragmentation of a Neotropical migratory fish population by a century-old dam

Loss of connectivity in impounded rivers is among the impacts imposed by dams, and mitigation measures such as fish passages might not accomplish their purpose of reestablishing an efficient bi-directional gene flow in the fish populations affected. As a consequence, fish populations remain fragmented, and a new interpopulational structure may develop, with increased risk of reduced genetic diversity and stochastic extinction. In order to evaluate the effects of the Gavio Peixoto Dam, which was constructed almost a century ago on the Jacar,-Gua double dagger u River in the Upper Parana River basin, Brazil, a comparative morphometric study was undertaken on the populations of the Neotropical migratory characid fish Salminus hilarii living up- and downstream of this dam. Population dynamics, spatial segregation, and habitat use by different age classes were monitored for 2 years. We found that segregation caused by the dam and long periods with no efficient connection by fish passages have led to fragmentation and interpopulational structuring of S. hilarii, as revealed by canonical variable analysis of morphometric features. The fish populations occupying the up- and downstream sections have succeeded in performing short-distance reproductive migrations in the main river and tributaries, have found suitable habitats for completing their life cycle, and have been able to maintain distinct small-sized populations so far.

A generalised dynamic model for char particle gasification with structure evolution and peripheral fragmentation

A generalised model for the prediction of single char particle gasification dynamics, accounting for multi-component mass transfer with chemical reaction, heat transfer, as well as structure evolution and peripheral fragmentation is developed in this paper. Maxwell-Stefan analysis is uniquely applied to both micro and macropores within the framework of the dusty-gas model to account for the bidisperse nature of the char, which differs significantly from the conventional models that are based on a single pore type. The peripheral fragmentation and random-pore correlation incorporated into the model enable prediction of structure/reactivity relationships. The occurrence of chemical reaction within the boundary layer reported by Biggs and Agarwal (Chem. Eng. Sci. 52 (1997) 941) has been confirmed through an analysis of CO/CO2 product ratio obtained from model simulations. However, it is also quantitatively observed that the significance of boundary layer reaction reduces notably with the reduction of oxygen concentration in the flue gas, operational pressure and film thickness. Computations have also shown that in the presence of diffusional gradients peripheral fragmentation occurs in the early stages on the surface, after which conversion quickens significantly due to small particle size. Results of the early commencement of peripheral fragmentation at relatively low overall conversion obtained from a large number of simulations agree well with experimental observations reported by Feng and Bhatia (Energy & Fuels 14 (2000) 297). Comprehensive analysis of simulation results is carried out based on well accepted physical principles to rationalise model prediction. (C) 2001 Elsevier Science Ltd. AH rights reserved.

Disease, habitat fragmentation and conservation

Habitat loss and the resultant fragmentation of remaining habitat is the primary cause of loss of biological diversity. How do these processes affect the dynamics of parasites and pathogens? Hess has provided some important insights into this problem using metapopulation models for pathogens that exhibit 'S-I' dynamics; for example, pathogens such as rabies in which the host population may be divided into susceptible and infected individuals. A major assumption of Hess's models is that infected patches become extinct, rather than recovering and becoming resistant to future infections. In this paper, we build upon this framework in two different ways: first, we examine the consequences of including patches that are resistant to infection; second, we examine the consequences of including a second species of host that can act as a reservoir for the pathogen. Both of these effects are likely to be important from a conservation perspective. The results of both sets of analysis indicate that the benefits of corridors and other connections that allow species to disperse through the landscape far outweigh the possible risks of increased pathogen transmission. Even in the commonest case, where harmful pathogens are maintained by a common reservoir host, increased landscape connectance still allows greater coexistence and persistence of a threatened or endangered host.

Polymer indentation with mesoscopic molecular dynamics

Indentation tests are used to determine the hardness of a material, e.g., Rockwell, Vickers, or Knoop. The indentation process is empirically observed in the laboratory during these tests; the mechanics of indentation is insufficiently understood. We have performed first molecular dynamics computer simulations of indentation resistance of polymers with a chain structure similar to that of high density polyethylene (HDPE). A coarse grain model of HDPE is used to simulate how the interconnected segments respond to an external force imposed by an indenter. Results include the time-dependent measurement of penetration depth, recovery depth, and recovery percentage, with respect to indenter force, indenter size, and indentation time parameters. The simulations provide results that are inaccessible experimentally, including continuous evolution of the pertinent tribological parameters during the entire indentation process.

Gastrointestinal symbionts of chimpanzees in Cantanhez National Park, Guinea-Bissau with respect to habitat fragmentation

One of the major factors threatening chimpanzees (Pan troglodytes verus) in Guinea-Bissau is habitat fragmentation. Such fragmentation may cause changes in symbiont dynamics resulting in increased susceptibility to infection, changes in host specificity and virulence. We monitored gastrointestinal symbiotic fauna of three chimpanzee subpopulations living within Cantanhez National Park (CNP) in Guinea Bissau in the areas with different levels of anthropogenic fragmentation. Using standard coproscopical methods (merthiolate-iodine formalin concentration and Sheather's flotation) we examined 102 fecal samples and identified at least 13 different symbiotic genera (Troglodytella abrassarti, Troglocorys cava, Blastocystis spp., Entamoeba spp., Iodamoeba butschlii, Giardia intestinalis, Chilomastix mesnili, Bertiella sp., Probstmayria gombensis, unidentified strongylids, Strongyloides stercoralis, Strongyloides fuelleborni, and Trichuris sp.). The symbiotic fauna of the CNP chimpanzees is comparable to that reported for other wild chimpanzee populations, although CNP chimpanzees have a higher prevalence of Trichuris sp. Symbiont richness was higher in chimpanzee subpopulations living in fragmented forests compared to the community inhabiting continuous forest area. We reported significantly higher prevalence of G. intestinalis in chimpanzees from fragmented areas, which could be attributed to increased contact with humans and livestock.