Computational studies of the gramicidin channel

Ion channels are highly specific membrane-spanning protein structures which serve to facilitate the passage of selected ions across the lipid barrier. In the past decade, molecular dynamics simulations based on atomic models and realistic microscopic interactions with explicit solvent and membrane lipids have been used to gain insight into the function of these complex systems. These calculations have considerably expanded our view of ion permeation at the microscopic level. This Account will mainly focus on computational studies of the gramicidin A channel, one of the simplest and best characterized molecular pore.     

A dynamics formulation of general constrained robots

The complexity of a standard compact-in-form Lagrangian dynamical expression is proportional to the fourth power of the number of degrees of freedom (DOF) of a robotic system. This fact challenges both simulation and control of robots with hyper degrees of freedom. In this paper, a systematic approach for deriving the dynamical expression of so-called general constrained robots is proposed. This proposed approach has two main features. First, it uses the subsystem dynamics such as the dynamics of joints and rigid links to construct the dynamical expression of the entire robotic system in a closed form. The complexity of the resulted dynamic expression is linearly proportional to the number of DOF of a robotic system. Second, it extends the standard dynamical form and properties of the conventional single-arm constrained robots to a class of more general robotic systems including the coordinated multiple-arm robotic systems. Three spaces, namely the general joint space, the general task space, and the extended subsystems space, are connected through corresponding velocity/force mapping matrices.An erratum to this article can be found at     

ANTARES: The HTR/VHTR project at Framatome ANP

Framatome ANP is developing a very high temperature reactor (VHTR), relying on its previous experience with high temperature reactor concepts, from its participation in the MODUL and the GT-MHR designs. While being a major actor in the nuclear reactor business with proven light water technology, AREVA wishes to be ready to meet the new challenges calling for small grid requirements, high temperature process heat and cogeneration. The Framatome ANP VHTR design for electricity production is based on an indirect cycle coupled to an “off-the-shelf” combined cycle gas turbine. Although direct cycle HTRs are being promoted for their high efficiency, preliminary evaluations show that the Framatome ANP design efficiency is on par with a direct cycle while avoiding power generation system (PGS) developments and keeping the PGS contamination free. Moreover, the nuclear heat source of the indirect cycle could also be used to meet the heat supplies from a standard design for multiple applications.     

Mammalian Exocrine Secretions. XII: Constituents of Interdigital Secretions of Bontebok, Damaliscus dorcas dorcas, and Blesbok, D. d. phillipsi

In addition to the nine compounds identified in the interdigital secretion of the bontebok, Damaliscus dorcas dorcas, in a previous study, 76 compounds belonging to different compound types, were identified in the interdigital secretions of the bontebok and the blesbok, D. d. phillipsi. These compounds include alkanes, alcohols, aldehydes, ketones, fatty acids, terpenoids, -lactones, an isopropyl ester, long-chain hydroxyesters, 2-substituted pyridines, phenols, steroids, and dimethylsulfone. No qualitative differences were found between secretions from the two sexes or from animals from different habitats. Although no attempt was made to correlate territorial behavior or other behavioral phenomena with the qualitative composition of interdigital secretions from individual animals, available information seems to indicate that quantitative differences probably do not have a major semiochemical function. Only two species of bacteria, Bacillus brevis and Planococcus citreus, were found in the interdigital pouches of male and female members of the two subspecies, regardless of the habitat of the animals. B. brevis synthesized, among other unidentified constituents, (Z)-3-penten-2-ol, 2-hexanone, 2-octanone, 2-nonanone, tetradecanoic acid, pentadecanoic acid, heptadecanoic acid, octadecanoic acid, (Z)-9-hexadecenoic acid, and isopropyl hexadecanoate in vitro, while P. citreus produced, among others, the -lactones dodecan-4-olide and (Z)-6-dodecen-4-olide, which is one of the major constituents of the interdigital secretions of both subspecies. Some components of the interdigital secretions are not present in the interdigital glandular tissue, and the possibility is discused that these compounds could be produced by microbiological activity in the interdigital pouch.     

Digital Image Correlation: from Displacement Measurement to Identification of Elastic Properties – a Review

Abstract:  The current state of the art of digital image correlation, where displacements can be determined for values less than one pixel, enables one to better characterise the behaviour of materials and the response of structures to external loads. A general presentation of the extraction of displacement fields from pictures taken at different instants during an experiment is given. Different strategies can be followed to determine subpixel displacements. New identification procedures are then devised making use of full-field measurements. A priori or a posteriori routes can be followed. They are illustrated on the analysis of a Brazilian disk test.     

Understanding coronary artery movement: a knowledge-based approach

The aim of this paper is to describe a knowledge-based system that interprets three-dimensional (3D) coronary artery movement, using data from digital subtraction angiography image sequences. Dynamic information obtained from artery centerline 3D reconstruction and optical flow estimation, is classified according to experimental evidence indicating that artery displacements are quasi-homogeneous by a segment analysis. Characteristic motion features like displacement direction, perpendicular/radial components, rotation direction, curvature and torsion are qualitatively described from an image sequence using symbolic labels. These facts are then related and interpreted using anatomical-functional knowledge provided by a specialist, as well as spatial and temporal knowledge, applying spatio-temporal reasoning schemes. Facts, knowledge and reasoning rules are stated in a declarative form. Detailed examples of local and global interpretation results, using a real reconstructed angiographic biplane image sequence are presented in order to illustrate how our system suitably interprets coronary artery dynamic behavior.     

Identification of Pneumocystis carinii f. sp. hominis gene sequences in filtered air in hospital environments

To evaluate the risk of a nosocomial spread of Pneumocystis carinii f. sp. hominis (P. carinii hominis), air filter samples from rooms of P. carinii pneumonia (PCP) patients, adjacent corridors, and other hospital environments have been investigated for the presence of P. carinii hominis. Amplified DNA from air filters and sputum or bronchoalveolar lavage samples from the PCP patients have been genotyped with the P. carinii hominis genes of the mitochondrial large-subunit (mtLSU) rRNA and the internal transcribed spacers (ITS1 and ITS2) of the rRNA. Genotypes of the two loci were identified by direct sequencing, and for site 85 of the mtLSU locus, three allele-specific PCR assays were used. P. carinii hominis DNA was identified in the air of five of seven PCP patient rooms and in the air of two of four air filtrations from the ward corridors. The P. carinii hominis genotypes were the same in four of the five room air samples as those in the corresponding patients, suggesting a risk of person-to-person transmission of P. carinii hominis from PCP patients. Three of 16 air samples collected in infectious disease wards without the presence of PCP patients and one sample from a cardiology unit in a separate hospital building were also positive, which further strengthens the possibility of acquisition of P. carinii hominis from the environment.