Nowadays, the most adopted model for the design and control of soft robots is the piecewise constant curvature model, with its consolidated benefits and drawbacks. In this work, an alternative model ...for multisection soft manipulator dynamics is presented based on a discrete Cosserat approach, in which the continuous Cosserat model is discretized by assuming a piecewise constant strain along the soft arm. As a consequence, the soft manipulator state is described by a finite set of constant strains. This approach has several advantages with respect to the existing models. First, it takes into account shear and torsional deformations, which are both essential to cope with out-of-plane external loads. Furthermore, it inherits desirable geometrical and mechanical properties of the continuous Cosserat model, such as intrinsic parameterization and greater generality. Finally, this approach allows to extend to soft manipulators, the recursive composite-rigid-body and articulated-body algorithms, whose performances are compared through a cantilever beam simulation. The soundness of the model is demonstrated through extensive simulation and experimental results.
DNA metabarcoding offers new perspectives in biodiversity research. This recently developed approach to ecosystem study relies heavily on the use of next‐generation sequencing (NGS) and thus calls ...upon the ability to deal with huge sequence data sets. The obitools package satisfies this requirement thanks to a set of programs specifically designed for analysing NGS data in a DNA metabarcoding context. Their capacity to filter and edit sequences while taking into account taxonomic annotation helps to set up tailor‐made analysis pipelines for a broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses. The obitools package is distributed as an open source software available on the following website: http://metabarcoding.org/obitools. A Galaxy wrapper is available on the GenOuest core facility toolshed: http://toolshed.genouest.org.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
The robotics community has seen an exponential growth in the level of complexity of the theoretical tools presented for the modeling of soft robotics devices. Different solutions have been presented ...to overcome the difficulties related to the modeling of soft robots, often leveraging on other scientific disciplines, such as continuum mechanics, computational mechanics, and computer graphics. These theoretical and computational foundations are often taken for granted and this leads to an intricate literature that, consequently, has rarely been the subject of a complete review. For the first time, we present here a structured overview of all the approaches proposed so far to model soft robots. The chosen classification, which is based on their theoretical and numerical grounds, allows us to provide a critical analysis about their uses and applicability. This will enable robotics researchers to learn the basics of these modeling techniques and their associated numerical methods, but also to have a critical perspective on their uses.
This article addresses the dynamic modeling of geometrically exact sliding Cosserat rods. Such systems need to consider non-material time-varying domains to which the Lagrangian view point of solid ...mechanics is inappropriate. In the article here presented, we use the geometrically exact model of inextensible Kirchhoff rods along a non-material domain whose time variations are not necessarily imposed but are governed by the dynamics, i.e. depend on the configuration of the rod. To progress through derivation, we use the variational calculus on Lie group introduced by Poincaré, and apply it to an extension of Hamilton’s principle holding for open rod systems, which is derived in the article. This extended variational principle uses a moving non-material tube across which the material rod slides. The resulting closed formulation of sliding rods dynamics takes the form of a set of non-material Cosserat–Poincaré’s partial differential equations governing the time-evolution of the cross-section pause of the non-material tube, coupled with an ordinary Lagrange’s differential equation for the sliding motion of the rod across the tube. While emphasize is on the dynamic formulations, the modeling approach is numerically illustrated on a few examples related to the so called sliding spaghetti problem.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The best known analytical model of swimming was originally developed by Lighthill and is known as the large amplitude elongated body theory (LAEBT). Recently, this theory has been improved and ...adapted to robotics through a series of studies ranging from hydrodynamic modeling to mobile multibody system dynamics. This article marks a further step towards the Lighthill theory. The LAEBT is applied to one of the best bio-inspired swimming robots yet built: the AmphiBot III, a modular anguilliform swimming robot. To that end, we apply a Newton–Euler modeling approach and focus our attention on the model of hydrodynamic forces. This model is numerically integrated in real time by using an extension of the Newton–Euler recursive forward dynamics algorithm for manipulators to a robot without a fixed base. Simulations and experiments are compared on undulatory gaits and turning maneuvers for a wide range of parameters. The discrepancies between modeling and reality do not exceed 16% for the swimming speed, while requiring only the one-time calibration of a few hydrodynamic parameters. Since the model can be numerically integrated in real time, it has significantly superior accuracy compared with computational speed ratio, and is, to the best of our knowledge, one of the most accurate models that can be used in real-time. It should provide an interesting tool for the design and control of swimming robots. The approach is presented in a self contained manner, with the concern to help the reader not familiar with fluid dynamics to get insight both into the physics of swimming and the mathematical tools that can help its modeling.
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There is a growing interest on the study of continuum parallel robots (CPRs) due to their higher stiffness and better dynamics capacities than serial continuum robots (SCRs). Several works have ...focused on the computation of their geometrico- and kinemato-static models that can be sorted into two main categories. Models based on the continuous Cosserat equations are very accurate but assessing elastic stability with them is tricky, and discretized models allow easily checking the elastic stability, but they require a large number of elastic variables to be accurate. In this article, we extend an approach based on assumed strain modes developed for the dynamics of SCRs to the statics of CPRs. This method is able to predict the robot configuration with an excellent accuracy with a very limited number of elastic variables, contrary to other discretization methods. The method is also more than 100 times faster than finite differences for a better prediction accuracy. Finally, it is possible to assess the robot elastic stability by only checking the Hessian of the potential energy as for any discretization method, thus making the analysis of this property simpler than for the continuous Cosserat model. All results are validated through simulations on two case studies.
Environmental DNA (eDNA) metabarcoding is increasingly used to study the present and past biodiversity. eDNA analyses often rely on amplification of very small quantities or degraded DNA. To avoid ...missing detection of taxa that are actually present (false negatives), multiple extractions and amplifications of the same samples are often performed. However, the level of replication needed for reliable estimates of the presence/absence patterns remains an unaddressed topic. Furthermore, degraded DNA and PCR/sequencing errors might produce false positives. We used simulations and empirical data to evaluate the level of replication required for accurate detection of targeted taxa in different contexts and to assess the performance of methods used to reduce the risk of false detections. Furthermore, we evaluated whether statistical approaches developed to estimate occupancy in the presence of observational errors can successfully estimate true prevalence, detection probability and false‐positive rates. Replications reduced the rate of false negatives; the optimal level of replication was strongly dependent on the detection probability of taxa. Occupancy models successfully estimated true prevalence, detection probability and false‐positive rates, but their performance increased with the number of replicates. At least eight PCR replicates should be performed if detection probability is not high, such as in ancient DNA studies. Multiple DNA extractions from the same sample yielded consistent results; in some cases, collecting multiple samples from the same locality allowed detecting more species. The optimal level of replication for accurate species detection strongly varies among studies and could be explicitly estimated to improve the reliability of results.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
The availability of hundreds of bacterial genomes allowed a comparative genomic study of the Type VI Secretion System (T6SS), recently discovered as being involved in pathogenesis. By combining ...comparative and phylogenetic approaches using more than 500 prokaryotic genomes, we characterized the global T6SS genetic structure in terms of conservation, evolution and genomic organization.
This genome wide analysis allowed the identification of a set of 13 proteins constituting the T6SS protein core and a set of conserved accessory proteins. 176 T6SS loci (encompassing 92 different bacteria) were identified and their comparison revealed that T6SS-encoded genes have a specific conserved genetic organization. Phylogenetic reconstruction based on the core genes showed that lateral transfer of the T6SS is probably its major way of dissemination among pathogenic and non-pathogenic bacteria. Furthermore, the sequence analysis of the VgrG proteins, proposed to be exported in a T6SS-dependent way, confirmed that some C-terminal regions possess domains showing similarities with adhesins or proteins with enzymatic functions.
The core of T6SS is composed of 13 proteins, conserved in both pathogenic and non-pathogenic bacteria. Subclasses of T6SS differ in regulatory and accessory protein content suggesting that T6SS has evolved to adapt to various microenvironments and specialized functions. Based on these results, new functional hypotheses concerning the assembly and function of T6SS proteins are proposed.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The Type VI secretion system (T6SS) is a widespread weapon dedicated to the delivery of toxin proteins into eukaryotic and prokaryotic cells. The 13 T6SS subunits assemble a cytoplasmic contractile ...structure anchored to the cell envelope by a membrane-spanning complex. This structure is evolutionarily, structurally and functionally related to the tail of contractile bacteriophages. In bacteriophages, the tail assembles onto a protein complex, referred to as the baseplate, that not only serves as a platform during assembly of the tube and sheath, but also triggers the contraction of the sheath. Although progress has been made in understanding T6SS assembly and function, the composition of the T6SS baseplate remains mostly unknown. Here, we report that six T6SS proteins-TssA, TssE, TssF, TssG, TssK and VgrG-are required for proper assembly of the T6SS tail tube, and a complex between VgrG, TssE,-F and-G could be isolated. In addition, we demonstrate that TssF and TssG share limited sequence homologies with known phage components, and we report the interaction network between these subunits and other baseplate and tail components. In agreement with the baseplate being the assembly platform for the tail, fluorescence microscopy analyses of functional GFP-TssF and TssK-GFP fusion proteins show that these proteins assemble stable and static clusters on which the sheath polymerizes. Finally, we show that recruitment of the baseplate to the apparatus requires initial positioning of the membrane complex and contacts between TssG and the inner membrane TssM protein.
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