61 research outputs found

    Constraint methods for determining pathways and free energy of activated processes

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    Activated processes from chemical reactions up to conformational transitions of large biomolecules are hampered by barriers which are overcome only by the input of some free energy of activation. Hence, the characteristic and rate-determining barrier regions are not sufficiently sampled by usual simulation techniques. Constraints on a reaction coordinate r have turned out to be a suitable means to explore difficult pathways without changing potential function, energy or temperature. For a dense sequence of values of r, the corresponding sequence of simulations provides a pathway for the process. As only one coordinate among thousands is fixed during each simulation, the pathway essentially reflects the system's internal dynamics. From mean forces the free energy profile can be calculated to obtain reaction rates and insight in the reaction mechanism. In the last decade, theoretical tools and computing capacity have been developed to a degree where simulations give impressive qualitative insight in the processes at quantitative agreement with experiments. Here, we give an introduction to reaction pathways and coordinates, and develop the theory of free energy as the potential of mean force. We clarify the connection between mean force and constraint force which is the central quantity evaluated, and discuss the mass metric tensor correction. Well-behaved coordinates without tensor correction are considered. We discuss the theoretical background and practical implementation on the example of the reaction coordinate of targeted molecular dynamics simulation. Finally, we compare applications of constraint methods and other techniques developed for the same purpose, and discuss the limits of the approach

    The History of Makassan Trepang Fishing and Trade

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    The Malayan term trepang describes a variety of edible holothurians commonly known as sea cucumbers. Although found in temperate and tropical marine waters all over the world, the centre of species diversity and abundance are the shallow coastal waters of Island Southeast Asia. For at least 300 years, trepang has been a highly priced commodity in the Chinese market. Originally, its fishing and trade was a specialized business, centred on the town of Makassar in South Sulawesi (Indonesia). The rise of trepang fishing in the 17th century added valuable export merchandize to the rich shallow seas surrounding the islands of Southeast Asia. This enabled local communities to become part of large trading networks and greatly supported their economic development. In this article, we follow Makassan trepang fishing and trading from its beginning until the industrialization of the fishery and worldwide depletion of sea cucumbers in the 20th century. Thereby, we identify a number of characteristics which trepang fishing shares with the exploitation of other marine resources, including (1) a strong influence of international markets, (2) the role of patron-client relationships which heavily influence the resource selection, and (3) the roving-bandit-syndrome, where fishermen exploit local stocks of valuable resources until they are depleted, and then move to another area. We suggest that understanding the similarities and differences between historical and recent exploitation of marine resources is an important step towards effective management solutions

    Operational space weather service for GNSS precise positioning

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    The ionospheric plasma can significantly influence the propagation of radio waves and the ionospheric disturbances are capable of causing range errors, rapid phase and amplitude fluctuations (radio scintillations) of satellite signals that may lead to degradation of the system performance, its accuracy and reliability. The cause of such disturbances should be sought in the processes originating in the Sun. Numerous studies on these phenomena have been already carried out at a broad international level, in order to measure/estimate these space weather induced effects, to forecast them, and to understand and mitigate their impact on present-day technological systems. <P style="line-height: 20px;"> SWIPPA (Space Weather Impact on Precise Positioning Applications) is a pilot project jointly supported by the German Aerospace Centre (DLR) and the European Space Agency (ESA). The project aims at establishing, operating, and evaluating a specific space-weather monitoring service that can possibly lead to improving current positioning applications based on Global Navigation Satellite Systems (GNSS). This space weather service provides GNSS users with essential expert information delivered in the form of several products - maps of TEC values, TEC spatial and temporal gradients, alerts for ongoing/oncoming ionosphere disturbances, etc

    On developing a new ionospheric perturbation index for space weather operations

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    To better and faster quantify the strength and impact of the ionospheric perturbations, we propose a new index for operational use in communication/navigation systems. Presented here is the analysis of selected events of strong disturbances observed with techniques based on Global Navigation Satellite Systems (GNSS) in order to show some insufficiencies when using existing geomagnetic indices. We found that the GNSS Total Electron Content (TEC) measurements and/or derivatives are outstanding candidates for defining a new ionospheric perturbation index, more specialised and therefore more effective. It is believed that the standardization and usage of the proposed perturbation index, together with other indices of similar nature, can prove helpful in reducing the space weather impact on the GNSS-based navigation and positioning
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