Unfolding Rates for the Diffusion-Collision Model

In the diffusion-collision model, the unfolding rates are given by the likelihood of secondary structural cluster dissociation. In this work, we introduce an unfolding rate calculation for proteins whose secondary structural elements are $\alpha$-helices, modeled from thermal escape over a barrier which arises from the free energy in buried hydrophobic residues. Our results are in good agreement with currently accepted values for the attempt rate.Comment: Shorter version of cond-mat/0011024 accepted for publication in PR

Low-temperature dynamical simulation of spin-boson systems

The dynamics of spin-boson systems at very low temperatures has been studied using a real-time path-integral simulation technique which combines a stochastic Monte Carlo sampling over the quantum fluctuations with an exact treatment of the quasiclassical degrees of freedoms. To a large degree, this special technique circumvents the dynamical sign problem and allows the dynamics to be studied directly up to long real times in a numerically exact manner. This method has been applied to two important problems: (1) crossover from nonadiabatic to adiabatic behavior in electron transfer reactions, (2) the zero-temperature dynamics in the antiferromagnetic Kondo region 1/2<K<1 where K is Kondo's parameter.Comment: Phys. Rev. B (in press), 28 pages, 6 figure

Congested Traffic States in Empirical Observations and Microscopic Simulations

We present data from several German freeways showing different kinds of congested traffic forming near road inhomogeneities, specifically lane closings, intersections, or uphill gradients. The states are localized or extended, homogeneous or oscillating. Combined states are observed as well, like the coexistence of moving localized clusters and clusters pinned at road inhomogeneities, or regions of oscillating congested traffic upstream of nearly homogeneous congested traffic. The experimental findings are consistent with a recently proposed theoretical phase diagram for traffic near on-ramps [D. Helbing, A. Hennecke, and M. Treiber, Phys. Rev. Lett. {\bf 82}, 4360 (1999)]. We simulate these situations with a novel continuous microscopic single-lane model, the ``intelligent driver model'' (IDM), using the empirical boundary conditions. All observations, including the coexistence of states, are qualitatively reproduced by describing inhomogeneities with local variations of one model parameter. We show that the results of the microscopic model can be understood by formulating the theoretical phase diagram for bottlenecks in a more general way. In particular, a local drop of the road capacity induced by parameter variations has practically the same effect as an on-ramp.Comment: Now published in Phys. Rev. E. Minor changes suggested by a referee are incorporated; full bibliographic info added. For related work see http://www.mtreiber.de/ and http://www.helbing.org

Habitat requirements of Tetanocera elata (Diptera: Sciomyzidae): case study of a dry meadow in western Ireland

Terrestrial slugs are pervasive pests of agriculture throughout temperate regions and have the potential to disrupt the germination of seedlings, cause damage to fruiting bodies of crops, and vector plant pathogens. Tetanocera elata Fabricius (Diptera: Sciomyzidae), a widely distributed Palaearctic species, is an obligate mesoparasitoid and predator of pestiferous slugs including Deroceras reticulatum Müller (Stylommatophora: Agriolimacidae). It has the potential to be developed as a native natural enemy in a conservation biological control programme as an alternative to chemical molluscicides. To better understand the ecological requirements of this species, a detailed observational study was conducted at a site in the west of Ireland possessing naturally occurring T. elata populations. Comparison of local patches where T. elata were recovered revealed no association with plant community composition. Taller dead vegetation was associated with T. elata presence throughout the site. Within the area of greatest T. elata aggregation, there was a significantly greater percentage cover of dead vegetation where T. elata occurred. Abundance of T. elata was also significantly correlated to hedgerow proximity. Results of this study are directly applicable for the design of a conservation biological control programme, which effectively satisfies the principal habitat requirements of T. elata populations

O desenvolvimento embrionário da Piapara, Leporinus elongatus (Pisces, Anostomidae), utilizando técnicas de histologia, microscopia eletrônica de varredura e imunológicas empregando marcadores ósseos

Resumo O desenvolvimento embrionário dos peixes é de grande importância para a piscicultura e na reintrodução de espécies ameaçadas de extinção em seus ambientes, e seu conhecimento constitui uma importante maneira para minimizar doenças e mortalidades dessas espécies. Com o auxílio de técnicas como a Microscopia Eletrônica de Varredura (MEV) e a imuno-histoquimica para identificar proteínas ósseas, foi possível avaliar as fases de desenvolvimento com mais riqueza de detalhes, facilitando a compreensão de hábitos e da biologia da espécie. Neste trabalho pudemos observar a ontogenia e osteogênese da Piapara (Leporinus elongatus), desde a fecundação até a fase juvenil, sendo evidenciadas estruturas importantes como o tamanho do vitelo, essencial para a nutrição do embrião; o fechamento do blastóporo, evento principal da embriogênese, que indica as taxas de fertilização; a metamorfose, que indica a formação dos primeiros e principais órgãos do animal e a formação de sua estrutura óssea. As Proteínas Ósseas Morfogenéticas (BMP-2 e BMP-4), moléculas essenciais reguladoras no desenvolvimento embrionário e na formação óssea, foram observadas apenas no estádio larval até o período juvenil, não sendo evidenciadas nos estágios anteriores. Os resultados desse trabalho trouxeram novas informações quanto à biologia do desenvolvimento dessa espécie, que certamente poderão auxiliar no aprimoramento de técnicas reprodutivas visando uma melhora na sua produção seja para fins comerciais ou de repovoamento

Aspects of microbial communities in peatland carbon cycling under changing climate and land use pressures

This is the final version. Available on open access from the Finnish Peatland Society via the DOI in this record. Globally, major efforts are being made to restore peatlands to maximise their resilience to anthropogenic climate change, which puts continuous pressure on peatland ecosystems and modifies the geography of the environmental envelope that underpins peatland functioning. A probable effect of climate change is reduction in the waterlogged conditions that are key to peatland formation and continued accumulation of carbon (C) in peat. C sequestration in peatlands arises from a delicate imbalance between primary production and decomposition, and microbial processes are potentially pivotal in regulating feedbacks between environmental change and the peatland C cycle. Increased soil temperature, caused by climate warming or disturbance of the natural vegetation cover and drainage, may result in reductions of long-term C storage via changes in microbial community composition and metabolic rates. Moreover, changes in water table depth alter the redox state and hence have broad consequences for microbial functions, including effects on fungal and bacterial communities especially methanogens and methanotrophs. This article is a perspective review of the effects of climate change and ecosystem restoration on peatland microbial communities and the implications for C sequestration and climate regulation. It is authored by peatland scientists, microbial ecologists, land managers and non-governmental organisations who were attendees at a series of three workshops held at The University of Manchester (UK) in 2019–2020. Our review suggests that the increase in methane flux sometimes observed when water tables are restored is predicated on the availability of labile carbon from vegetation and the absence of alternative terminal electron acceptors. Peatland microbial communities respond relatively rapidly to shifts in vegetation induced by climate change and subsequent changes in the quantity and quality of below-ground C substrate inputs. Other consequences of climate change that affect peatland microbial communities and C cycling include alterations in snow cover and permafrost thaw. In the face of rapid climate change, restoration of a resilient microbiome is essential to sustaining the climate regulation functions of peatland systems. Technological developments enabling faster characterisation of microbial communities and functions support progress towards this goal, which will require a strongly interdisciplinary approach.Natural Environment Research Council (NERC