Efeitos da defaunação na comunidades de pequenos mamíferos na Mata Atlântica

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Estudo comparativo da diversidade de vespas sociais (Hymenoptera, Vespidae) em mata ciliar e cultura de cana-de-açúcar na região de Ipeúna - SP

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Diversidade de mamíferos de médio e grande porte e sua relação com o mosaico vegetacional na fazenda experimental Edgárdia, Unesp, Botucatu/SP

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Composição, riqueza e abundância de espécies de anfíbios na região do médio rio Xingú

Este estudo teve como objetivo inventariar a fauna de anfíbios nos diferentes hábitats da região do Médio Rio Xingu. Para tanto, foram selecionadas seis localidades, sendo as amostragens realizadas em três incursões, entre novembro de 2007 e março de 2008, totalizando 48 dias. Foram identificados seis tipos de hábitats na região amostrada: floresta de terra-firme, floresta sazonalmente alagável (várzea), margem do rio, “pedral”, lagoa e área alterada. Para a coleta de dados foram utilizadas duas metodologias: armadilhas de interceptação e queda e procura ativa. As armadilhas foram instaladas apenas nas áreas de floresta de terra-firme, enquanto a procura ativa foi empregada em todos os tipos de hábitats identificados. As amostragens resultaram no registro de 56 espécies de anfíbios e outras oito espécies foram identificadas e registradas em estudos anteriores na área. A diversidade e riqueza de espécies foram maiores na localidade Caracol, onde predominou a floresta de terra-firme, e menor na localidade Ilha Grande, dominada por floresta sazonalmente alagável. Foram registrados nove modos reprodutivos na área de estudo, sendo todos observados na floresta de terra-firme e apenas três nos “pedrais”, o que parece refletir a baixa heterogeneidade ambiental dessa área. Para comparar as localidades estudadas foram realizadas duas análises de similaridade, uma para cada metodologia de coleta utilizada. A análise de similaridade dos dados de procura ativa apontou maior semelhança na composição das espécies entre as áreas de floresta de terra-firme do que entre os outros hábitats. A análise de agrupamento realizada entre a composição de espécies obtida nesse estudo e outros levantamentos realizados na Amazônia agrupou esta área com outra também localizada no Médio Xingu.

Mamíferos de médio e grande porte do Parque Nacional das nascentes do Rio Parnaíba, Brasil

O Parque Nacional das Nascentes do Rio Parnaíba está localizado na divisa dos Estados do Piauí, Maranhão, Tocantins e Bahia. Para verificar a composição, riqueza, abundância relativa e padrão de atividade da mastofauna de médio e grande porte do Parque, bem como a utilização das fitofisionomias presentes na área por essas espécies, foi realizado um inventário utilizando armadilhas-fotográficas, entrevistas semi-estruturadas e métodos complemetares de amostragem. Foi registrado um total de 37 espécies de mamíferos de médio e grande porte, distribuídos em 14 famílias e sete ordens. Vinte dessas espécies foram registradas por meio de armadilhas-fotográficas, 16 por meio de avistamentos e vestígios (rastros, fezes e carcaças), e todas por meio de entrevistas com moradores da região. O estimador de riqueza nãoparamétrico Jackknife1 calculou 22 espécies (D.P. ± 1,41) para o Parque. Quanto às fitofisionomias, apenas mata de galeria e cerrado sensu stricto apresentaram diferença significativa quanto à riqueza e abundância relativa. Dentre as espécies registradas no Parque, as raposas Cerdocyon thous e Lycalopex vetulus foram as mais abundantes, respectivamente. Quanto ao uso do habitat, somente Cerdocyon thous e Mazama gouazoubira apresentaram diferença significativa entre as fitofisionomias, sendo a primeira de hábito generalista e registrada principalmente em áreas de cerrado sensu stricto, e a segunda mais freqüente em áreas de vegetação mais densa (cerradão). No que diz respeito à composição de espécies, a análise de agrupamento indicou as áreas de cerradão e cerrado sensu stricto como as de maior similaridade, o que provavelmente se deve à maior semelhança florística entre esses ambientes. A análise de composição regional mostrou que o Parque apresenta uma maior similaridade quanto à composição de espécies com as UCs localizadas no Sul do Estado do Piauí (E.E. de Uruçuí-Una e PARNA da Serra das Confusões) do que com as demais áreas de Cerrado.

História natural e ecologia das serpentes da Floresta Nacional de Caxiuanã e áreas adjacentes, Pará, Brasil

A busca por padrões de estrutura e composição das comunidades é essencial para prover informações que permitam o manejo sustentado de populações e monitoramento de atividades antrópicas. Na região neotropical, onde ocorre grande riqueza de espécies e complexas relações ecológicas entre elas, estudos envolvendo ofidiofauna ainda são escassos, o que faz com que o entendimento dos processos responsáveis pela estruturação de suas comunidades ainda seja incipiente. No Brasil, vários trabalhos foram desenvolvidos na tentativa de explicitar os fenômenos responsáveis pelos padrões de ocorrência e interações das espécies de serpentes. Objetivando esclarecer quais os fatores que determinam os padrões observados e que afinidades (ecológicas e/ou históricas) as espécies compartilham, foi realizado estudo da taxocenose de serpentes da FLONA de Caxiuanã e áreas adjacentes, durante os anos de 2005 e 2006. Utilizou-se conjuntamente quatro métodos de amostragem (Procura Limitada por Tempo-PLT, Encontros Ocasionais-EO, Armadilhas de Interceptação e Queda-AIQ e Coletas por Terceiros-CT), em cinco áreas (IBAMA e Caquajó, no interior da FLONA de Caxiuanã; Enseada e dois pontos com influência antrópica: Marinaú e Mojuá, estando esses três últimos localizados em áreas adjacentes à FLONA. Foram registrados 378 espécimes distribuídos em cinco famílias, 35 gêneros e 50 espécies. Com os novos registros obtidos nesse estudo, o número de espécies de serpentes para a FLONA de Caxiuanã e áreas adjacentes passa de 63 para 69. Os métodos que apresentaram melhor desempenho em número de indivíduos foram PLT (199/378) e CT (159/378). EO (11/378) e AIQ (9/378) foram os métodos menos eficazes. A riqueza estimada (Jackknife 1), a partir de dados obtidos através de PLT, foi de 56 (+ ou – 4) espécies. O número de espécies estimado para as áreas preservadas foi maior que para áreas antropizadas. A composição das espécies de serpentes da área estudada apresentou maior similaridade com outras taxocenoses de áreas amazônicas. As espécies mais abundantes, acessadas através de PLT, foram Imantodes cenchoa, Corallus hortulanus e Leptodeira annulata. Quando todos os métodos foram considerados, Bothrops atrox, Imantodes cenchoa e Corallus hortulanus foram as espécies mais representadas. As áreas mais antropizadas, localizadas fora da FLONA (Marinaú e Mojuá), apresentaram menores abundância e riqueza de espécies em comparação com áreas protegidas, localizadas no interior da FLONA. Nove espécies foram consideradas potencialmente especialistas: Lachesis muta (pequenos mamíferos), Atractus schach (minhocas), Dipsas catesbyi (moluscos - lesmas), Helicops trivitatus e Hydrops triangularis (peixes), Siphlophis compressus (lagartos), Xenopholis scalaris, Taeniophallus brevirostris (anfíbios anuros) e Tantilla melanocephala (centopéias). Os itens mais acessados foram “lagartos”, “anfíbios anuros” e “pequenos mamíferos”. Serpentes com hábitos primária ou exclusivamente diurnas prevaleceram na comunidade analisada. A ausência de sazonalidade reprodutiva foi característica da maioria das espécies e isso se deve, muito provavelmente, à pouca diferença na temperatura ao longo do ano. A taxocenose de serpentes da FLONA de Caxiuanã e áreas adjacentes está, basicamente, formada por grupos contendo espécies onde, em geral, hábitos diários e de dieta estão sobrepostos. Além dos diversos fatores ecológicos, também fatores históricos, como adaptações morfológicas das espécies, têm grande influência na composição da taxocenose analisada. A grande dificuldade na realização de estudos de comunidades de serpentes está na escassez de dados das espécies, portanto torna-se imperioso que estudos de Ecologia e História Natural continuem sendo exaustivamente conduzidos em uma mesma localidade, objetivando a elucidação dos padrões de respostas aos diversos fatores relacionados à existência das espécies nos diferentes biomas.

Non-volant mammals from Nucleo Santa Virginia, Serra do Mar State Park, Sao Paulo, Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Estimating abundance of killer whales in the nearshore waters of the Gulf of Alaska and Aleutian Islands using line-transect sampling

Killer whale (Orcinus orca Linnaeus, 1758) abundance in the North Pacific is known only for a few populations for which extensive longitudinal data are available, with little quantitative data from more remote regions. Line-transect ship surveys were conducted in July and August of 2001–2003 in coastal waters of the western Gulf of Alaska and the Aleutian Islands. Conventional and Multiple Covariate Distance Sampling methods were used to estimate the abundance of different killer whale ecotypes, which were distinguished based upon morphological and genetic data. Abundance was calculated separately for two data sets that differed in the method by which killer whale group size data were obtained. Initial group size (IGS) data corresponded to estimates of group size at the time of first sighting, and post-encounter group size (PEGS) corresponded to estimates made after closely approaching sighted groups.

A Model-Based Approach for Making Ecological Inference from Distance Sampling Data

We consider a fully model-based approach for the analysis of distance sampling data. Distance sampling has been widely used to estimate abundance (or density) of animals or plants in a spatially explicit study area. There is, however, no readily available method of making statistical inference on the relationships between abundance and environmental covariates. Spatial Poisson process likelihoods can be used to simultaneously estimate detection and intensity parameters by modeling distance sampling data as a thinned spatial point process. A model-based spatial approach to distance sampling data has three main benefits: it allows complex and opportunistic transect designs to be employed, it allows estimation of abundance in small subregions, and it provides a framework to assess the effects of habitat or experimental manipulation on density. We demonstrate the model-based methodology with a small simulation study and analysis of the Dubbo weed data set. In addition, a simple ad hoc method for handling overdispersion is also proposed. The simulation study showed that the model-based approach compared favorably to conventional distance sampling methods for abundance estimation. In addition, the overdispersion correction performed adequately when the number of transects was high. Analysis of the Dubbo data set indicated a transect effect on abundance via Akaike’s information criterion model selection. Further goodness-of-fit analysis, however, indicated some potential confounding of intensity with the detection function.

SAMPLING OF CORN TO ASSESS BIRD DAMAGE: A Preliminary Review of a Comprehensive Study

"How large a sample is needed to survey the bird damage to corn in a county in Ohio or New Jersey or South Dakota?" Like those in the Bureau of Sport Fisheries and Wildlife and the U.S.D.A. who have been faced with a question of this sort we found only meager information on which to base an answer, whether the problem related to a county in Ohio or to one in New Jersey, or elsewhere. Many sampling methods and rates of sampling did yield reliable estimates but the judgment was often intuitive or based on the reasonableness of the resulting data. Later, when planning the next study or survey, little additional information was available on whether 40 samples of 5 ears each or 5 samples of 200 ears should be examined, i.e., examination of a large number of small samples or a small number of large samples. What information is needed to make a reliable decision? Those of us involved with the Agricultural Experiment Station regional project concerned with the problems of bird damage to crops, known as NE-49, thought we might supply an ans¬wer if we had a corn field in which all the damage was measured. If all the damage were known, we could then sample this field in various ways and see how the estimates from these samplings compared to the actual damage and pin-point the best and most accurate sampling procedure. Eventually the investigators in four states became involved in this work1 and instead of one field we were able to broaden the geographical base by examining all the corn ears in 2 half-acre sections of fields in each state, 8 sections in all. When the corn had matured well past the dough stage, damage on each corn ear was assessed, without removing the ear from the stalk, by visually estimating the percent of the kernel surface which had been destroyed and rating it in one of 5 damage categories. Measurements (by row-centimeters) of the rows of kernels pecked by birds also were made on selected ears representing all categories and all parts of each field section. These measurements provided conversion factors that, when fed into a computer, were applied to the more than 72,000 visually assessed ears. The machine now had in its memory and could supply on demand a map showing each ear, its location and the intensity of the damage.

Fiber architecture in remodeled myocardium revealed with a quantitative diffusion CMR tractography framework and histological validation

Background: The study of myofiber reorganization in the remote zone after myocardial infarction has been performed in 2D. Microstructural reorganization in remodeled hearts, however, can only be fully appreciated by considering myofibers as continuous 3D entities. The aim of this study was therefore to develop a technique for quantitative 3D diffusion CMR tractography of the heart, and to apply this method to quantify fiber architecture in the remote zone of remodeled hearts. Methods: Diffusion Tensor CMR of normal human, sheep, and rat hearts, as well as infarcted sheep hearts was performed ex vivo. Fiber tracts were generated with a fourth-order Runge-Kutta integration technique and classified statistically by the median, mean, maximum, or minimum helix angle (HA) along the tract. An index of tract coherence was derived from the relationship between these HA statistics. Histological validation was performed using phase-contrast microscopy. Results: In normal hearts, the subendocardial and subepicardial myofibers had a positive and negative HA, respectively, forming a symmetric distribution around the midmyocardium. However, in the remote zone of the infarcted hearts, a significant positive shift in HA was observed. The ratio between negative and positive HA variance was reduced from 0.96 +/- 0.16 in normal hearts to 0.22 +/- 0.08 in the remote zone of the remodeled hearts (p<0.05). This was confirmed histologically by the reduction of HA in the subepicardium from -52.03 degrees +/- 2.94 degrees in normal hearts to -37.48 degrees +/- 4.05 degrees in the remote zone of the remodeled hearts (p < 0.05). Conclusions: A significant reorganization of the 3D fiber continuum is observed in the remote zone of remodeled hearts. The positive (rightward) shift in HA in the remote zone is greatest in the subepicardium, but involves all layers of the myocardium. Tractography-based quantification, performed here for the first time in remodeled hearts, may provide a framework for assessing regional changes in the left ventricle following infarction.

The release of zinc and lead from mine tailings

Mining and processing of metal ores are important causes of soil and groundwater contamination in many regions worldwide. Metal contaminations are a serious risk for the environment and human health. The assessment of metal contaminations in the soil is therefore an important task. A common approach to assess the environmental risk emanating from inorganic contaminations to soil and groundwater is the use of batch or column leaching tests. In this regard, the suitability of leaching tests is a controversial issue. In the first part of this work the applicability and comparability of common leaching tests in the scope of groundwater risk assessment of inorganic contamination is reviewed and critically discussed. Soil water sampling methods (the suction cup method and centrifugation) are addressed as an alternative to leaching tests. Reasons for limitations of the comparability of leaching test results are exposed and recommendations are given for the expedient application of leaching tests for groundwater risk assessment. Leaching tests are usually carried out in open contact with the atmosphere disregarding possible changes of redox conditions. This can affect the original metal speciation and distribution, particularly when anoxic samples are investigated. The influence of sample storage on leaching test results of sulfide bearing anoxic material from a former flotation dump is investigated in a long-term study. Since the oxidation of the sulfide-bearing samples leads to a significant overestimation of metal release, a feasible modification for the conduction of common leaching tests for anoxic material is proposed, where oxidation is prevented efficiently. A comparison of leaching test results to soil water analyzes have shown that the modified saturation soil extraction (SSE) is found to be the only of the tested leaching procedures, which can be recommended for the assessment of current soil water concentrations at anoxic sites if direct investigation of the soil water is impossible due to technical reasons. The vertical distribution and speciation of Zn and Pb in the flotation residues as well as metal concentrations in soil water and plants were investigated to evaluate the environmental risk arising from this site due to the release of metals. The variations in pH and inorganic C content show an acidification of the topsoil with pH values down to 5.5 in the soil and a soil water pH of 6 in 1 m depth. This is due to the oxidation of sulfides and depletion in carbonates. In the anoxic subsoil pH conditions are still neutral and soil water collected with suction cups is in equilibrium with carbonate minerals. Results from extended x-ray absorption fine-structure (EXAFS) spectroscopy confirm that Zn is mainly bound in sphalerite in the subsoil and weathering reactions lead to a redistribution of Zn in the topsoil. A loss of 35% Zn and S from the topsoil compared to the parent material with 10 g/kg Zn has been observed. 13% of total Zn in the topsoil can be regarded as mobile or easily mobilizable according to sequential chemical extractions (SCE). Zn concentrations of 10 mg/L were found in the soil water, where pH is acidic. Electron supply and the buffer capacity of the soil were identified as main factors controlling Zn mobility and release to the groundwater. Variable Pb concentrations up to 30 µg/L were observed in the soil water. In contrast to Zn, Pb is enriched in the mobile fraction of the oxidized topsoil by a factor of 2 compared to the subsoil with 2 g/kg Pb. 80% of the cation exchange capacity in the topsoil is occupied by Pb. Therefore, plant uptake and bioavailability are of major concern. If the site is not prevented from proceeding acidification in the future, a significant release of Zn, S, and Pb to the groundwater has to be expected. Results from this study show that the assessment of metal release especially from sulfide bearing anoxic material requires an extensive comprehension of leaching mechanisms on the one hand and on weathering processes, which influence the speciation and the mobility of metals, on the other hand. Processes, which may change redox and pH conditions in the future, have to be addressed to enable sound decisions for soil and groundwater protection and remediation.

Einsatz eines Aerosolmassenspektrometers während der CYPHEX-Kampagne und zur Methodenentwicklung einer Echtzeitquantifizierung gasförmiger Amine

Atmosphärische Aerosole haben einen starken Einfluss auf das Klima, der bisher nur grundlegend verstanden ist und weiterer Forschung bedarf. Das atmosphärische Verhalten der Aerosolpartikel hängt maßgeblich von ihrer Größe und chemischen Zusammensetzung ab. Durch Reflexion, Absorption und Streuung des Sonnenlichtes verändern sie den Strahlungshaushalt der Erde direkt und durch ihre Einflussnahme auf die Wolkenbildung indirekt. Besonders gealterte, stark oxidierte organische Aerosole mit großem Sauerstoff-zu-Kohlenstoff-Verhältnis wirken als effektive Wolkenkondensationskeime. Neben primären Aerosolpartikeln, die direkt partikelförmig in die Atmosphäre gelangen, spielen sekundäre Aerosolpartikel eine große Rolle, die aus Vorläufergasen in der Atmosphäre entstehen. Aktuelle Forschungsergebnisse legen nahe, dass kurzkettige aliphatische Amine bei Nukleationsprozessen beteiligt sind und somit die Partikelneubildung vielerorts mitsteuern. Um die Rolle von Aminen in der Atmosphäre besser erforschen und industrielle Emissionen kontrollieren zu können, bedarf es einer zuverlässigen Methode zur Echtzeitquantifizierung gasförmiger Amine mit hoher Zeitauflösung und niedriger Nachweisgrenze.rnDas hochauflösende Flugzeit-Aerosolmassenspektrometer (HR-ToF-AMS) bietet die Möglichkeit, atmosphärische Partikel in Echtzeit zu analysieren. Dabei werden Größe, Menge und grundlegende chemische Zusammensetzung erfasst. Anorganische Aerosolbestandteile können eindeutig zugeordnet werden. Es ist jedoch kaum möglich, einzelne organische Verbindungen in den komplizierten Massenspektren atmosphärischer Aerosole zu identifizieren und quantifizieren.rnIn dieser Arbeit wird atmosphärisches Aerosol untersucht, das im Westen Zyperns während der CYPHEX-Kampagne mit einem HR-ToF-AMS gemessen wurde. An diesem Standort ist vor allem stark gealtertes Aerosol vorzufinden, das aus Zentral- und Westeuropa stammt. Lokale Einflüsse spielen fast keine Rolle. Es wurde eine durchschnittliche Massenkonzentration von 10,98 μg/m3 gefunden, zusammengesetzt aus 57 % Sulfat, 30 % organischen Bestandteilen, 12 % Ammonium, < 1 % Nitrat und < 1 % Chlorid, bezogen auf das Gewicht. Der Median des vakuum-aerodynamischen Durchmessers betrug 446,25 nm. Es wurde sehr acides Aerosol gefunden, dessen anorganische Bestandteile weitgehend der Zusammensetzung von Ammoniumhydrogensulfat entsprachen. Tag-Nacht-Schwankungen in der Zusammensetzung wurden beobachtet. Die Sulfatkonzentration und die Acidität zeigten tagsüber Maxima und nachts Minima. Konzentrationsschwankungen an Nitrat und Chlorid zeigten einen weniger ausgeprägten Rhythmus, Maxima fallen aber immer mit Minima der Sulfatkonzentration, Aerosolacidität und Umgebungstemperatur zusammen. Organische Aerosolbestandteile entsprachen stark gealtertem, schwerflüchtigem oxidiertem organischem Aerosol. Es wurde eine interne Mischung der Partikel beobachtet, die ebenfalls meist bei alten Aerosolen auftritt.rnUm mit dem HR-ToF-AMS auch einzelne organische Verbindungen identifizieren und quantifizieren zu können, wurde eine Methode entwickelt, mit der man Amine der Gasphase selektiv in künstlich erzeugte Phosphorsäurepartikel aufnimmt und so für die HR-ToF-AMS-Messung zugänglich macht. Dadurch kombiniert man die Vorteile der Online-Messung des HR-ToF-AMS mit den Vorteilen klassischer Offline-Probenahmen. So können in Echtzeit sehr einfache Massenspektren gemessen werden, in denen störende Komponenten abgetrennt sind, während die Analyten eindeutig identifiziert werden können. Systeme dieser Art wurden GTRAP-AMS (Gaseous compound TRapping in Artificially-generated Particles – Aerosol Mass Spectrometry) genannt. Kalibrierungen für (Mono)Methylamin, Dimethylamin, Trimethylamin, Diethylamin und Triethylamin ergaben Nachweisgrenzen im ppt-Bereich bei einer Zeitauflösung von 3 min. Kammerexperimente zur Aminemission von Pflanzen zeigten eine gute Übereinstimmung des neu entwickelten Systems mit einer Gasdiffusionsabscheider-Offline-Probenahme und anschließender ionenchromatographischer Analyse. Beide Methoden zeigten Reaktionen der Pflanzen auf eine Veränderung der Lichtverhältnisse, während erhöhte Ozonkonzentrationen die Aminemission nicht veränderten. Die GTRAP-AMS-Methode eignet sich bereits für die Messung von Umgebungsluftkonzentrationen an einigen Orten, für die meisten Orte reicht die Nachweisgrenze allerdings noch nicht aus. Die Technik könnte bereits zur Echtzeitkontrolle industrieller Abgasemissionen eingesetzt werden.

Comparison of bacterial plaque samples from titanium implant and tooth surfaces by different methods

Studies have shown similarities in the microflora between titanium implants or tooth sites when samples are taken by gingival crevicular fluid (GCF) sampling methods. The purpose of the present study was to study the microflora from curette and GCF samples using the checkerboard DNA-DNA hybridization method to assess the microflora of patients who had at least one oral osseo-integrated implant and who were otherwise dentate. Plaque samples were taken from tooth/implant surfaces and from sulcular gingival surfaces with curettes, and from gingival fluid using filter papers. A total of 28 subjects (11 females) were enrolled in the study. The mean age of the subjects was 64.1 years (SD+/-4.7). On average, the implants studied had been in function for 3.7 years (SD+/-2.9). The proportion of Streptococcus oralis (P<0.02) and Fusobacterium periodonticum (P<0.02) was significantly higher at tooth sites (curette samples). The GCF samples yielded higher proportions for 28/40 species studies (P-values varying between 0.05 and 0.001). The proportions of Tannerella forsythia (T. forsythensis), and Treponema denticola were both higher in GCF samples (P<0.02 and P<0.05, respectively) than in curette samples (implant sites). The microbial composition in gingival fluid from samples taken at implant sites differed partly from that of curette samples taken from implant surfaces or from sulcular soft tissues, providing higher counts for most bacteria studied at implant surfaces, but with the exception of Porphyromonas gingivalis. A combination of GCF and curette sampling methods might be the most representative sample method.

Proteins in silico-modeling and sampling

Proteins are linear chain molecules made out of amino acids. Only when they fold to their native states, they become functional. This dissertation aims to model the solvent (environment) effect and to develop & implement enhanced sampling methods that enable a reliable study of the protein folding problem in silico. We have developed an enhanced solvation model based on the solution to the Poisson-Boltzmann equation in order to describe the solvent effect. Following the quantum mechanical Polarizable Continuum Model (PCM), we decomposed net solvation free energy into three physical terms– Polarization, Dispersion and Cavitation. All the terms were implemented, analyzed and parametrized individually to obtain a high level of accuracy. In order to describe the thermodynamics of proteins, their conformational space needs to be sampled thoroughly. Simulations of proteins are hampered by slow relaxation due to their rugged free-energy landscape, with the barriers between minima being higher than the thermal energy at physiological temperatures. In order to overcome this problem a number of approaches have been proposed of which replica exchange method (REM) is the most popular. In this dissertation we describe a new variant of canonical replica exchange method in the context of molecular dynamic simulation. The advantage of this new method is the easily tunable high acceptance rate for the replica exchange. We call our method Microcanonical Replica Exchange Molecular Dynamic (MREMD). We have described the theoretical frame work, comment on its actual implementation, and its application to Trp-cage mini-protein in implicit solvent. We have been able to correctly predict the folding thermodynamics of this protein using our approach.