Evaluating boundary dependent errors in QM/MM simulations.

Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations provide a powerful tool for studying chemical reactions, especially in complex biochemical systems. In most works to date, the quantum region is kept fixed throughout the simulation and is defined in an ad hoc way based on chemical intuition and available computational resources. The simulation errors associated with a given choice of the quantum region are, however, rarely assessed in a systematic manner. Here we study the dependence of two relevant quantities on the QM region size: the force error at the center of the QM region and the free energy of a proton transfer reaction. Taking lysozyme as our model system, we find that in an apolar region the average force error rapidly decreases with increasing QM region size. In contrast, the average force error at the polar active site is considerably higher, exhibits large oscillations and decreases more slowly, and may not fall below acceptable limits even for a quantum region radius of 9.0 A. Although computation of free energies could only be afforded until 6.0 A, results were found to change considerably within these limits. These errors demonstrate that the results of QM/MM calculations are heavily affected by the definition of the QM region (not only its size), and a convergence test is proposed to be a part of setting up QM/MM simulations.

可见光波段双层浮雕型导模共振滤波器设计与分析

基于傅里叶模式理论分析了双层浮雕型导模共振光栅的共振效应,分别讨论了光栅的槽深、剩余厚度、周期以及填充系数对峰值反射率、带宽、旁带反射率的影响.数据计算表明,欠刻蚀情形的误差宽容度远远优于过刻蚀情形,两者在光栅槽深相对误差小于15%的范围内,都能保证共振峰的衍射效率高于99.5%,在相同的误差范围内,共振峰线宽的相对误差将分别达到7%和60%,因此厚度误差集中反映在对共振线宽的改变上.另外,光栅周期和填充系数的变化将明显改变共振峰中心波长和线宽.

Smoked marine fish from Western Region, Ghana: a value chain assessment

The value chain analysis of ths report focused on smoked marine fish- overwhelmingly the most important fish product originating in Western Region, Ghana. Smoked fish from Western Region is mainly destined for the domestic market where demand is very strong. Small quantities of smoked fish are destined for markets in Togo, Benin and Nigeria. The underlying objective of the fisheries value chain analysis is to identify opportunities for growth in the fisheries value chain, with an emphasis on those opportunities that have the potential to generate significant additional livelihoods, particularly at the level of the fishing communities and for low-income groups. The results from the value chain analysis will be used to identify pilot interventions to promote those livelihood outcomes. The main focus for the study is smoked fish (major species/product forms) destined for domestic markets. However, work will also be undertaken on the fresh fish trade and frozen fish to find out more about the significance of these value chains.

Prediction and confirmation of seasonal migration of Pacific sardine (Sardinops sagax) in the California Current Ecosystem

During the last century, the population of Pacific sardine (Sardinops sagax) in the California Current Ecosystem has exhibited large fluctuations in abundance and migration behavior. From approximately 1900 to 1940, the abundance of sardine reached 3.6 million metric tons and the “northern stock” migrated from offshore of California in the spring to the coastal areas near Oregon, Washington, and Vancouver Island in the summer. In the 1940s, the sardine stock collapsed and the few remaining sardine schools concentrated in the coastal region off southern California, year-round, for the next 50 years. The stock gradually recovered in the late 1980s and resumed its seasonal migration between regions off southern California and Canada. Recently, a model was developed which predicts the potential habitat for the northern stock of Pacific sardine and its seasonal dynamics. The habitat predictions were successfully validated using data from sardine surveys using the daily egg production method; scientific trawl surveys off the Columbia River mouth; and commercial sardine landings off Oregon, Washington, and Vancouver Island. Here, the predictions of the potential habitat and seasonal migration of the northern stock of sardine are validated using data from “acoustic–trawl” surveys of the entire west coast of the United States during the spring and summer of 2008. The estimates of sardine biomass and lengths from the two surveys are not significantly different between spring and summer, indicating that they are representative of the entire stock. The results also confirm that the model of potential sardine habitat can be used to optimally apply survey effort and thus minimize random and systematic sampling error in the biomass estimates. Furthermore, the acoustic–trawl survey data are useful to estimate concurrently the distributions and abundances of other pelagic fishes.

Measurements of resistance and reactance in fish with the use of bioelectrical impedance analysis: sources of error

New technologies can be riddled with unforeseen sources of error, jeopardizing the validity and application of their advancement. Bioelectrical impedance analysis (BIA) is a new technology in fisheries research that is capable of estimating proximate composition, condition, and energy content in fish quickly, cheaply, and (after calibration) without the need to sacrifice fish. Before BIA can be widely accepted in fisheries science, it is necessary to identify sources of error and determine a means to minimize potential errors with this analysis. We conducted controlled laboratory experiments to identify sources of errors within BIA measurements. We concluded that electrode needle location, procedure deviations, user experience, time after death, and temperature can affect resistance and reactance measurements. Sensitivity analyses showed that errors in predictive estimates of composition can be large (>50%) when these errors are experienced. Adherence to a strict protocol can help avoid these sources of error and provide BIA estimates that are both accurate and precise in a field or laboratory setting.

Variation in the isotopic signatures of juvenile gray snapper (Lutjanus griseus) from five southern Florida region

Measurements of 18O/16O and 13C/12C ratios in the carbonate of juvenile gray snapper (Lutjanus griseus) sagittal otoliths collected during 2001–2005 from different southern Florida regions indicated significant variations in the ratios between Florida Bay and surrounding areas. Annual differences in isotopic composition were also observed. Classification accuracy of individual otoliths to a region averaged 80% (63% to 96%), thereby enabling the probability of assigning an unknown individual to the appropriate juvenile nursery habitat. Identification of isotopic signatures in the otoliths of gray snapper from Florida Bay and adjacent ecosystems may be important for distinguishing specific portions of the bay that are crucial nursery grounds for juveniles. Separation of gray snapper between geographic regions and nursery sites is possible and has the potential to establish a link between adult gray snapper present on offshore reefs and larvae and juveniles at nursery habitats in Florida Bay or adjacent areas.