Robustness to Algorithmic Singularities and Sensitivity in Computational Kinematics

A robust approach to computational kinematics intended to cope with algorithmic singularities is introduced in this article. The approach is based on the reduction of the original system of equations to a subsystem of bivariate equations, as opposed to the multivariate polynomial reduction leading to the characteristic univariate polynomial. The effectiveness of the approach is illustrated for the exact function-generation synthesis of planar, spherical, and spatial four-bar linkages. Some numerical examples are provided for the case of the spherical four-bar function generator with six precision points to show the benefits of the proposed method with respect to methods reported in the literature.The first author acknowledges the support of Universidad Politecnica de Valencia, research project PAID-00-09. The second author acknowledges the support of McGill University by means of a James McGill Professorship.Gracia Calandin, LI.; Angeles, J. (2011). Robustness to Algorithmic Singularities and Sensitivity in Computational Kinematics. Proceedings of the Institution of Mechanical Engineers part C - Journal of Mechanical Engineering Science. 225(4):987-999. doi:10.1243/09544062JMES2464S9879992254Raghavan, M., & Roth, B. (1993). Inverse Kinematics of the General 6R Manipulator and Related Linkages. Journal of Mechanical Design, 115(3), 502-508. doi:10.1115/1.2919218Lee, H. Y., Woernle, C., & Hiller, M. (1991). A Complete Solution for the Inverse Kinematic Problem of the General 6R Robot Manipulator. Journal of Mechanical Design, 113(4), 481-486. doi:10.1115/1.2912808Innocenti, C., & Parenti-Castelli, V. (1993). Echelon form solution of direct kinematics for the general fully-parallel spherical wrist. Mechanism and Machine Theory, 28(4), 553-561. doi:10.1016/0094-114x(93)90035-tGosselin, C. M., Sefrioui, J., & Richard, M. J. (1994). On the Direct Kinematics of Spherical Three-Degree-of-Freedom Parallel Manipulators of General Architecture. Journal of Mechanical Design, 116(2), 594-598. doi:10.1115/1.2919419Alizade, R. I., & Kilit, Ö. (2005). Analytical synthesis of function generating spherical four-bar mechanism for the five precision points. Mechanism and Machine Theory, 40(7), 863-878. doi:10.1016/j.mechmachtheory.2004.12.010Cervantes-Sánchez, J. J., Gracia, L., Rico-Martínez, J. M., Medellín-Castillo, H. I., & González-Galván, E. J. (2009). A novel and efficient kinematic synthesis approach of the spherical 4R function generator for five and six precision points. Mechanism and Machine Theory, 44(11), 2020-2037. doi:10.1016/j.mechmachtheory.2009.05.006Angeles, J. (2007). Fundamentals of Robotic Mechanical Systems. Mechanical Engineering Series. doi:10.1007/978-0-387-34580-2Bai, S., Hansen, M. R., & Angeles, J. (2009). A robust forward-displacement analysis of spherical parallel robots. Mechanism and Machine Theory, 44(12), 2204-2216. doi:10.1016/j.mechmachtheory.2009.07.005Sommese, A. J., & Wampler, C. W. (2005). The Numerical Solution of Systems of Polynomials Arising in Engineering and Science. doi:10.1142/5763Forsythe, G. E. (1970). Pitfalls in Computation, or why a Math Book isn’t Enough. The American Mathematical Monthly, 77(9), 931. doi:10.2307/2318109Angeles, J., Hommel, G., & Kovács, P. (Eds.). (1993). Computational Kinematics. Solid Mechanics and Its Applications. doi:10.1007/978-94-015-8192-9Yang, A. T., & Freudenstein, F. (1964). Application of Dual-Number Quaternion Algebra to the Analysis of Spatial Mechanisms. Journal of Applied Mechanics, 31(2), 300-308. doi:10.1115/1.3629601Gupta, K. C., & Beloiu, A. S. (1998). Branch and circuit defect elimination in spherical four-bar linkages. Mechanism and Machine Theory, 33(5), 491-504. doi:10.1016/s0094-114x(97)00078-

Buildup and dephasing of Floquet-Bloch bands on subcycle time scales

Strong light fields have created spectacular opportunities to tailor novel functionalities of solids. Floquet-Bloch states can form under periodic driving of electrons and enable exotic quantum phases. On subcycle time scales, lightwaves can simultaneously drive intraband currents and interband transitions, which enable high-harmonic generation (HHG) and pave the way towards ultrafast electronics. Yet, the interplay of intra- and interband excitations as well as their relation with Floquet physics have been key open questions as dynamical aspects of Floquet states have remained elusive. Here we provide this pivotal link by pioneering the ultrafast buildup of Floquet-Bloch bands with time- and angle-resolved photoemission spectroscopy. We drive surface states on a topological insulator with mid-infrared fields - strong enough for HHG - and directly monitor the transient band structure with subcycle time resolution. Starting with strong intraband currents, we observe how Floquet sidebands emerge within a single optical cycle; intraband acceleration simultaneously proceeds in multiple sidebands until high-energy electrons scatter into bulk states and dissipation destroys the Floquet bands. Quantum nonequilibrium calculations explain the simultaneous occurrence of Floquet states with intra- and interband dynamics. Our joint experiment-theory study opens up a direct time-domain view of Floquet physics and explores the fundamental frontiers of ultrafast band-structure engineering.Comment: 45 pages, 4 figures, 10 extended data figure

Enhancement of the helium resonance lines in the solar atmosphere by suprathermal electron excitation II: non-Maxwellian electron distributions

In solar EUV spectra the He I and He II resonance lines show unusual behaviour and have anomalously high intensities compared with other transition region lines. The formation of the helium resonance lines is investigated through extensive non-LTE radiative transfer calculations. The model atmospheres of Vernazza, Avrett & Loeser are found to provide reasonable matches to the helium resonance line intensities but significantly over-estimate the intensities of other transition region lines. New model atmospheres have been developed from emission measure distributions derived by Macpherson & Jordan, which are consistent with SOHO observations of transition region lines other than those of helium. These models fail to reproduce the observed helium resonance line intensities by significant factors. The possibility that non-Maxwellian electron distributions in the transition region might lead to increased collisional excitation rates in the helium lines is studied. Collisional excitation and ionization rates are re-computed for distribution functions with power law suprathermal tails which may form by the transport of fast electrons from high temperature regions. Enhancements of the helium resonance line intensities are found, but many of the predictions of the models regarding line ratios are inconsistent with observations. These results suggest that any such departures from Maxwellian electron distributions are not responsible for the helium resonance line intensities.Comment: 23 pages, 11 figures, accepted to appear in MNRAS, LaTeX uses mn.st

Structure and biochemical composition of desmosomes and tonofilaments isolated from calf muzzle epidermis.

Complexes of plasma membrane segments with desmosomes and attached tonofilaments were separated from the stratum spinosum cells of calf muzzle by means of moderately alkaline buffers of low ionic strength and mechanical homogenization. These structures were further fractionated by the use of various treatments including sonication, sucrose gradient centrifugaton, and extraction with buffers containing high concentrations of salt, urea, citric acid, or detergents. Subfractions enriched in desmosome-tonofilament-complexes and tonofilament fragments were studied in detail. The desmosome structures such as the midline, the trilaminar membrane profile, and the desmosomal plaque appeared well preserved and were notably resistant to the various treatments employed. Fractions containing desmosome-tonofilament complexes were invariably dominated by the nonmembranous proteins of the tonofilaments which appeared as five major polypeptide bands (apparent molecular weights: 48,000; 51,000; 58,000; 60,000; 68,000) present in molar ratios of approx. 2:1:1:2:2. Four of these polypeptide bands showed electrophoretic mobilities similar to those of prekeratin polypeptides from bovine hoof. However, the largest polypeptide (68,000 mol wt) migrated significantly less in polyacrylamide gels than the largest component of the hoof prekeratin (~ 63,000 mol wt). In addition, a series of minor bands, including carbohydrate-containing proteins, were identified and concluded to represent constituents of the desmosomal membrane. The analysis of protein-bound carbohydrates (total 270 μg/mg phospholipid in desmosomeenriched desmosome-enriched showed the presence of relatively high amounts of glucosamine, mannose, galactose, and sialic acids. These data as well as the lipid composition (e.g. high ratio of cholesterol to phospholipids, relatively high contents of sphingomyelin and gangliosides, and fatty acid pattern) indicate that the desmosomal membrane is complex in protein and lipid composition and has a typical plasma membrane character. The similarity of the desmosome-associated tonofilaments to prekeratin filaments and other forms of intermediate-sized filaments is discussed.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Mitochondrial Data in Monocot Phylologenetics

Mitochondrial sequences are an important source of data in animal phylogenetics, equivalent in importance to plastid sequences in plants. However, in recent years plant systematists have begun exploring the mitochondrial genome as a source of phylogenetically useful characters. The plant mitochondrial genome is renowned for its variability in size, structure, and gene organization, but this need not be of concern for the application of sequence data in phylogenetics. However, the incorporation of reverse transcribed mitochondrial genes ( processed paralogs ) and the recurring transfer of genes from the mitochondrion to the nucleus are evolutionary events that must be taken into account. RNA editing of mitochondrial genes is sometimes considered a problem in phylogenetic reconstruction, but we regard it only as a mechanism that may increase variability at edited sites and change the codon position bias accordingly. Additionally, edited sites may prove a valuable tool in identifying processed paralogs. An overview of genes and sequences used in phylogenetic studies of angiosperms is presented. In the monocots, a large amount of mitochondrial sequence data is being collected together with sequence data from plastid and nuclear genes, thus offering an opportunity to compare data from different genomic compartments. The mitochondrial and plastid data are incongruent when organelle gene trees are reconstructed. Possible reasons for the observed incongruence involve sampling of paralogous sequences and highly divergent substitution rates, potentially leading to longbranch attraction. The above problems are addressed in Acorales, Alismatales, Poales, Liliaceae, the Anthericum clade (in Agavaceae), and in some achlorophyllous taxa

Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

Recent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth–death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.Universidad de Costa Rica/[814-B8-257]/UCR/Costa RicaUniversidad de Costa Rica/[814-B6-140]/UCR/Costa RicaIDEA WILD/[]//Estados UnidosSociedad Colombiana de Orquideología/[]/SCO/ColombiaFundação de Amparo à Pesquisa do Estado de São Paulo/[11/08308-9]/FAPESP/BrasilFundação de Amparo à Pesquisa do Estado de São Paulo/[13/19124-1]/FAPESP/BrasilSwiss Orchid Foundation/[]//SuizaRoyal Botanic Gardens, Kew/[]//InglaterraSwedish Research Council/[2019-05191]//SueciaSwedish Foundation for Strategic Research/[FFL15-0196]/SSF/SueciaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Jardín Botánico Lankester (JBL