Insights into mechanism kinematics for protein motion simulation

Background: The high demanding computational requirements necessary to carry out protein motion simulations make it difficult to obtain information related to protein motion. On the one hand, molecular dynamics simulation requires huge computational resources to achieve satisfactory motion simulations. On the other hand, less accurate procedures such as interpolation methods, do not generate realistic morphs from the kinematic point of view. Analyzing a protein's movement is very similar to serial robots; thus, it is possible to treat the protein chain as a serial mechanism composed of rotational degrees of freedom. Recently, based on this hypothesis, new methodologies have arisen, based on mechanism and robot kinematics, to simulate protein motion. Probabilistic roadmap method, which discretizes the protein configurational space against a scoring function, or the kinetostatic compliance method that minimizes the torques that appear in bonds, aim to simulate protein motion with a reduced computational cost. Results: In this paper a new viewpoint for protein motion simulation, based on mechanism kinematics is presented. The paper describes a set of methodologies, combining different techniques such as structure normalization normalization processes, simulation algorithms and secondary structure detection procedures. The combination of all these procedures allows to obtain kinematic morphs of proteins achieving a very good computational cost-error rate, while maintaining the biological meaning of the obtained structures and the kinematic viability of the obtained motion. Conclusions: The procedure presented in this paper, implements different modules to perform the simulation of the conformational change suffered by a protein when exerting its function. The combination of a main simulation procedure assisted by a secondary structure process, and a side chain orientation strategy, allows to obtain a fast and reliable simulations of protein motion.

Devir-câmera: A relação dos estudantes com os equipamentos de produção de imagens em movimento

Esta pesquisa tem como objetivo cartografar o devir câmera de um grupo de produção audiovisual para verificar de que forma as novas tecnologias de captura produzem uma transformação na relação com as imagens que poderá ser considerada como produção de uma nova subjetividade. Encaramos como devir câmera o resultado do acoplamento estudante/ câmera de vídeo em suas várias manifestações tecnológicas (handycams, câmeras de fotografia digitais, telefones celulares). Como nosso objeto de pesquisa é formado por alunos de ensino médio-técnico e de graduação, também pretendemos apontar possibilidades para a utilização do audiovisual na educação atuando na construção de novos territórios existenciais, no sentido de gerar processos de singularização através da educação pela arte. Nosso campo conceitual tomará consistência através do uso de autores como Gilles Deleuze, Felix Guattari, Michel Foucault; Kastrup, Escóssia, Benevides, Passos, Suely Rolnik; Michael Hardt, Toni Negri, Peter Pal Pelbart, Gilbert Simondon, McLuhan, Pierre Lévy; Jonathan Crary, Pierre Barboza, e Phillipe Dubois, além da bibliografia técnica/tecnológica da área.

BotCam: a baited camera system for nonextractive monitoring of bottomfish species

A stereo-video baited camera system (BotCam) has been developed as a fishery-independent tool to monitor and study deepwater fish species and their habitat. During testing, BotCam was deployed primarily in water depths between 100 and 300 m for an assessment of its use in monitoring and studying Hawaiian bottomfish species. Details of the video analyses and data from the pilot study with BotCam in Hawai`i are presented. Multibeam bathymetry and backscatter data were used to delineate bottomfish habitat strata, and a stratified random sampling design was used for BotCam deployment locations. Video data were analyzed to assess relative fish abundance and to measure f ish size composition. Results corroborate published depth ranges and zones of the target species, as well as their habitat preferences. The results indicate that BotCam is a promising tool for monitoring and studying demersal fish populations associated with deepwater habitats to a depth of 300 m, at mesohabitat scales. BotCam is a flexible, nonextractive, and economical means to better understand deepwater ecosystems and improve science-based ecosystem approaches to management.

Use of stereo camera systems for assessment of rockfish abundance in untrawlable areas and for recording pollock behavior during midwater trawls

We describe the application of two types of stereo camera systems in fisheries research, including the design, calibration, analysis techniques, and precision of the data obtained with these systems. The first is a stereo video system deployed by using a quick-responding winch with a live feed to provide species- and size- composition data adequate to produce acoustically based biomass estimates of rockfish. This system was tested on the eastern Bering Sea slope where rockfish were measured. Rockfish sizes were similar to those sampled with a bottom trawl and the relative error in multiple measurements of the same rockfish in multiple still-frame images was small. Measurement errors of up to 5.5% were found on a calibration target of known size. The second system consisted of a pair of still-image digital cameras mounted inside a midwater trawl. Processing of the stereo images allowed fish length, fish orientation in relation to the camera platform, and relative distance of the fish to the trawl netting to be determined. The video system was useful for surveying fish in Alaska, but it could also be used broadly in other situations where it is difficult to obtain species-composition or size-composition information. Likewise, the still-image system could be used for fisheries research to obtain data on size, position, and orientation of fish.