Showing papers by "Karlsruhe Institute of Technology published in 2014"

Phylogenomics resolves the timing and pattern of insect evolution

Abstract: Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.

Assessing agricultural risks of climate change in the 21st century in a global gridded crop model intercomparison

Abstract: Here we present the results from an intercomparison of multiple global gridded crop models (GGCMs) within the framework of the Agricultural Model Intercomparison and Improvement Project and the Inter-Sectoral Impacts Model Intercomparison Project. Results indicate strong negative effects of climate change, especially at higher levels of warming and at low latitudes; models that include explicit nitrogen stress project more severe impacts. Across seven GGCMs, five global climate models, and four representative concentration pathways, model agreement on direction of yield changes is found in many major agricultural regions at both low and high latitudes; however, reducing uncertainty in sign of response in mid-latitude regions remains a challenge. Uncertainties related to the representation of carbon dioxide, nitrogen, and high temperature effects demonstrated here show that further research is urgently needed to better understand effects of climate change on agricultural production and to devise targeted adaptation strategies.

The Dalton quantum chemistry program system

Abstract: Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, confi ...

Engineered nanoparticles interacting with cells: size matters

Abstract: With the rapid advancement of nanoscience and nanotechnology, detailed knowledge of interactions between engineered nanomaterials and cells, tissues and organisms has become increasingly important, especially in regard to possible hazards to human health. This review intends to give an overview of current research on nano-bio interactions, with a focus on the effects of NP size on their interactions with live cells. We summarize common techniques to characterize NP size, highlight recent work on the impact of NP size on active and passive cellular internalization and intracellular localization. Cytotoxic effects are also discussed.

What drives nematic order in iron-based superconductors?

Abstract: Nematic order in the iron-based superconductors breaks the symmetry between the x and y directions in the Fe plane. Beyond this, however, there is little consensus on how nematic order arises and whether it has an effect on superconductivity. This Review discusses the current theoretical and experimental state of the field.

Data-Driven Grasp Synthesis—A Survey

Abstract: We review the work on data-driven grasp synthesis and the methodologies for sampling and ranking candidate grasps. We divide the approaches into three groups based on whether they synthesize grasps for known, familiar, or unknown objects. This structure allows us to identify common object representations and perceptual processes that facilitate the employed data-driven grasp synthesis technique. In the case of known objects, we concentrate on the approaches that are based on object recognition and pose estimation. In the case of familiar objects, the techniques use some form of a similarity matching to a set of previously encountered objects. Finally, for the approaches dealing with unknown objects, the core part is the extraction of specific features that are indicative of good grasps. Our survey provides an overview of the different methodologies and discusses open problems in the area of robot grasping. We also draw a parallel to the classical approaches that rely on analytic formulations.

Microbial and animal rhodopsins: structures, functions, and molecular mechanisms.

Abstract: Organisms of all domains of life use photoreceptor proteins to sense and respond to light. The light-sensitivity of photoreceptor proteins arises from bound chromophores such as retinal in retinylidene proteins, bilin in biliproteins, and flavin in flavoproteins. Rhodopsins found in Eukaryotes, Bacteria, and Archaea consist of opsin apoproteins and a covalently linked retinal which is employed to absorb photons for energy conversion or the initiation of intra- or intercellular signaling.1 Both functions are important for organisms to survive and to adapt to the environment. While lower organisms utilize the family of microbial rhodopsins for both purposes, animals solely use a different family of rhodopsins, a specialized subset of G-protein-coupled receptors (GPCRs).1,2 Animal rhodopsins, for example, are employed in visual and nonvisual phototransduction, in the maintenance of the circadian clock and as photoisomerases.3,4 While sharing practically no sequence similarity, microbial and animal rhodopsins, also termed type-I and type-II rhodopsins, respectively, share a common architecture of seven transmembrane α-helices (TM) with the N- and C-terminus facing out- and inside of the cell, respectively (Figure ​(Figure11).1,5 Retinal is attached by a Schiff base linkage to the e-amino group of a lysine side chain in the middle of TM7 (Figures ​(Figures11 and ​and2).2). The retinal Schiff base (RSB) is protonated (RSBH+) in most cases, and changes in protonation state are integral to the signaling or transport activity of rhodopsins. Figure 1 Topology of the retinal proteins. (A) These membrane proteins contain seven α-helices (typically denoted helix A to G in microbial opsins and TM1 to 7 in the animal opsins) spanning the lipid bilayer. The N-terminus faces the outside of the cell ...

Precision Measurement of the Proton Flux in Primary Cosmic Rays from Rigidity 1 GV to 1.8 TV with the Alpha Magnetic Spectrometer on the International Space Station

Abstract: A precise measurement of the proton flux in primary cosmic rays with rigidity (momentum/charge) from 1 GV to 1.8 TV is presented based on 300 million events. Knowledge of the rigidity dependence of the proton flux is important in understanding the origin, acceleration, and propagation of cosmic rays. We present the detailed variation with rigidity of the flux spectral index for the first time. The spectral index progressively hardens at high rigidities.

Making Bertha Drive?An Autonomous Journey on a Historic Route

Abstract: 125 years after Bertha Benz completed the first overland journey in automotive history, the Mercedes Benz S-Class S 500 INTELLIGENT DRIVE followed the same route from Mannheim to Pforzheim, Germany, in fully autonomous manner. The autonomous vehicle was equipped with close-to-production sensor hardware and relied solely on vision and radar sensors in combination with accurate digital maps to obtain a comprehensive understanding of complex traffic situations. The historic Bertha Benz Memorial Route is particularly challenging for autonomous driving. The course taken by the autonomous vehicle had a length of 103 km and covered rural roads, 23 small villages and major cities (e.g. downtown Mannheim and Heidelberg). The route posed a large variety of difficult traffic scenarios including intersections with and without traffic lights, roundabouts, and narrow passages with oncoming traffic. This paper gives an overview of the autonomous vehicle and presents details on vision and radar-based perception, digital road maps and video-based self-localization, as well as motion planning in complex urban scenarios.

Three Decades of Driver Assistance Systems: Review and Future Perspectives

Abstract: This contribution provides a review of fundamental goals, development and future perspectives of driver assistance systems. Mobility is a fundamental desire of mankind. Virtually any society strives for safe and efficient mobility at low ecological and economic costs. Nevertheless, its technical implementation significantly differs among societies, depending on their culture and their degree of industrialization. A potential evolutionary roadmap for driver assistance systems is discussed. Emerging from systems based on proprioceptive sensors, such as ABS or ESC, we review the progress incented by the use of exteroceptive sensors such as radar, video, or lidar. While the ultimate goal of automated and cooperative traffic still remains a vision of the future, intermediate steps towards that aim can be realized through systems that mitigate or avoid collisions in selected driving situations. Research extends the state-of-the-art in automated driving in urban traffic and in cooperative driving, the latter addressing communication and collaboration between different vehicles, as well as cooperative vehicle operation by its driver and its machine intelligence. These steps are considered important for the interim period, until reliable unsupervised automated driving for all conceivable traffic situations becomes available. The prospective evolution of driver assistance systems will be stimulated by several technological, societal and market trends. The paper closes with a view on current research fields.

Electrically driven nuclear spin resonance in single-molecule magnets

Abstract: Recent advances in addressing isolated nuclear spins have opened up a path toward using nuclear-spin–based quantum bits. Local magnetic fields are normally used to coherently manipulate the state of the nuclear spin; however, electrical manipulation would allow for fast switching and spatially confined spin control. Here, we propose and demonstrate coherent single nuclear spin manipulation using electric fields only. Because there is no direct coupling between the spin and the electric field, we make use of the hyperfine Stark effect as a magnetic field transducer at the atomic level. This quantum-mechanical process is present in all nuclear spin systems, such as phosphorus or bismuth atoms in silicon, and offers a general route toward the electrical control of nuclear-spin–based devices.

Both CRISPR/Cas-based nucleases and nickases can be used efficiently for genome engineering in Arabidopsis thaliana.

Abstract: Engineered nucleases can be used to induce site-specific double-strand breaks (DSBs) in plant genomes Thus, homologous recombination (HR) can be enhanced and targeted mutagenesis can be achieved by error-prone non-homologous end-joining (NHEJ) Recently, the bacterial CRISPR/Cas9 system was used for DSB induction in plants to promote HR and NHEJ Cas9 can also be engineered to work as a nickase inducing single-strand breaks (SSBs) Here we show that only the nuclease but not the nickase is an efficient tool for NHEJ-mediated mutagenesis in plants We demonstrate the stable inheritance of nuclease-induced targeted mutagenesis events in the ADH1 and TT4 genes of Arabidopsis thaliana at frequencies from 25 up to 700% Deep sequencing analysis revealed NHEJ-mediated DSB repair in about a third of all reads in T1 plants In contrast, applying the nickase resulted in the reduction of mutation frequency by at least 740-fold Nevertheless, the nickase is able to induce HR at similar efficiencies as the nuclease or the homing endonuclease I-SceI Two different types of somatic HR mechanisms, recombination between tandemly arranged direct repeats as well as gene conversion using the information on an inverted repeat could be enhanced by the nickase to a similar extent as by DSB-inducing enzymes Thus, the Cas9 nickase has the potential to become an important tool for genome engineering in plants It should not only be applicable for HR-mediated gene targeting systems but also by the combined action of two nickases as DSB-inducing agents excluding off-target effects in homologous genomic regions

Coherent terabit communications with microresonator Kerr frequency combs.

Abstract: Optical frequency combs have the potential to revolutionize terabit communications1. Generation of Kerr combs in nonlinear microresonators2 represents a particularly promising option3 enabling line spacings of tens of GHz. However, such combs may exhibit strong phase noise4-6, which has made high-speed data transmission impossible up to now. Here we demonstrate that systematic adjustment of pump conditions for low phase noise4,7-9 enables coherent data transmission with advanced modulation formats that pose stringent requirements on the spectral purity of the comb. In a first experiment, we encode a data stream of 392 Gbit/s on a Kerr comb using quadrature phase shift keying (QPSK) and 16-state quadrature amplitude modulation (16QAM). A second experiment demonstrates feedback-stabilization of the comb and transmission of a 1.44 Tbit/s data stream over up to 300 km. The results show that Kerr combs meet the highly demanding requirements of coherent communications and thus offer an attractive solution towards chip-scale terabit/s transceivers.

Net carbon uptake has increased through warming-induced changes in temperate forest phenology

Abstract: The timing of life-history events has a strong impact on ecosystems. Now, analysis of the phenology of temperate forests in the eastern US indicates that in the case of an earlier spring and a later autumn, carbon uptake (photosynthesis) increases considerably more than carbon release (respiration).

Selecting optimal partitioning schemes for phylogenomic datasets

Abstract: Partitioning involves estimating independent models of molecular evolution for different subsets of sites in a sequence alignment, and has been shown to improve phylogenetic inference. Current methods for estimating best-fit partitioning schemes, however, are only computationally feasible with datasets of fewer than 100 loci. This is a problem because datasets with thousands of loci are increasingly common in phylogenetics. We develop two novel methods for estimating best-fit partitioning schemes on large phylogenomic datasets: strict and relaxed hierarchical clustering. These methods use information from the underlying data to cluster together similar subsets of sites in an alignment, and build on clustering approaches that have been proposed elsewhere. We compare the performance of our methods to each other, and to existing methods for selecting partitioning schemes. We demonstrate that while strict hierarchical clustering has the best computational efficiency on very large datasets, relaxed hierarchical clustering provides scalable efficiency and returns dramatically better partitioning schemes as assessed by common criteria such as AICc and BIC scores. These two methods provide the best current approaches to inferring partitioning schemes for very large datasets. We provide free open-source implementations of the methods in the PartitionFinder software. We hope that the use of these methods will help to improve the inferences made from large phylogenomic datasets.

Description and performance of track and primary-vertex reconstruction with the CMS tracker

Abstract: A description is provided of the software algorithms developed for the CMS tracker both for reconstructing charged-particle trajectories in proton-proton interactions and for using the resulting tracks to estimate the positions of the LHC luminous region and individual primary-interaction vertices. Despite the very hostile environment at the LHC, the performance obtained with these algorithms is found to be excellent. For tt events under typical 2011 pileup conditions, the average track-reconstruction efficiency for promptly-produced charged particles with transverse momenta of p_T > 0.9GeV is 94% for pseudorapidities of |η| < 0.9 and 85% for 0.9 < |η| < 2.5. The inefficiency is caused mainly by hadrons that undergo nuclear interactions in the tracker material. For isolated muons, the corresponding efficiencies are essentially 100%. For isolated muons of p_T = 100GeV emitted at |η| < 1.4, the resolutions are approximately 2.8% in p_T, and respectively, 10μm and 30μm in the transverse and longitudinal impact parameters. The position resolution achieved for reconstructed primary vertices that correspond to interesting pp collisions is 10–12μm in each of the three spatial dimensions. The tracking and vertexing software is fast and flexible, and easily adaptable to other functions, such as fast tracking for the trigger, or dedicated tracking for electrons that takes into account bremsstrahlung.

Karst water resources in a changing world: Review of hydrological modeling approaches

Abstract: Karst regions represent 7–12% of the Earth's continental area, and about one quarter of the global population is completely or partially dependent on drinking water from karst aquifers. Climate simulations project a strong increase in temperature and a decrease of precipitation in many karst regions in the world over the next decades. Despite this potentially bleak future, few studies specifically quantify the impact of climate change on karst water resources. This review provides an introduction to karst, its evolution, and its particular hydrological processes. We explore different conceptual models of karst systems and how they can be translated into numerical models of varying complexity and therefore varying data requirements and depths of process representation. We discuss limitations of current karst models and show that at the present state, we face a challenge in terms of data availability and information content of the available data. We conclude by providing new research directions to develop and evaluate better prediction models to address the most challenging problems of karst water resources management, including opportunities for data collection and for karst model applications at so far unprecedented scales.

High-speed plasmonic phase modulators

Abstract: A phase modulator that is only 29 µm long and operates at 65 GHz is demonstrated using plasmonics and the Pockels effect in a nonlinear polymer. The device operates across a 120-nm-wide wavelength range centred on 1,550 nm and at temperatures up to 85 °C.

High Statistics Measurement of the Positron Fraction in Primary Cosmic Rays of 0.5-500 GeV with the Alpha Magnetic Spectrometer on the International Space Station

Abstract: A precision measurement by AMS of the positron fraction in primary cosmic rays in the energy range from 0.5 to 500 GeV based on 10.9 million positron and electron events is presented. This measurement extends the energy range of our previous observation and increases its precision. The new results show, for the first time, that above ∼200 GeV the positron fraction no longer exhibits an increase with energy.

Implications of incorporating N cycling and N limitations on primary production in an individual-based dynamic vegetation model

Abstract: . The LPJ-GUESS dynamic vegetation model uniquely combines an individual- and patch-based representation of vegetation dynamics with ecosystem biogeochemical cycling from regional to global scales. We present an updated version that includes plant and soil N dynamics, analysing the implications of accounting for C–N interactions on predictions and performance of the model. Stand structural dynamics and allometric scaling of tree growth suggested by global databases of forest stand structure and development were well reproduced by the model in comparison to an earlier multi-model study. Accounting for N cycle dynamics improved the goodness of fit for broadleaved forests. N limitation associated with low N-mineralisation rates reduces productivity of cold-climate and dry-climate ecosystems relative to mesic temperate and tropical ecosystems. In a model experiment emulating free-air CO2 enrichment (FACE) treatment for forests globally, N limitation associated with low N-mineralisation rates of colder soils reduces CO2 enhancement of net primary production (NPP) for boreal forests, while some temperate and tropical forests exhibit increased NPP enhancement. Under a business-as-usual future climate and emissions scenario, ecosystem C storage globally was projected to increase by ca. 10%; additional N requirements to match this increasing ecosystem C were within the high N supply limit estimated on stoichiometric grounds in an earlier study. Our results highlight the importance of accounting for C–N interactions in studies of global terrestrial N cycling, and as a basis for understanding mechanisms on local scales and in different regional contexts.

B(s,d)→ℓ(+)ℓ(-) in the standard model with reduced theoretical uncertainty.

Abstract: We combine our new results for the O(αem) and O(αs2) corrections to Bs,d→l+l-, and present updated branching ratio predictions for these decays in the standard model. Inclusion of the new corrections removes major theoretical uncertainties of perturbative origin that have just begun to dominate over the parametric ones. For the recently observed muonic decay of the Bs meson, our calculation gives B¯(Bs→μ+μ-)=(3.65±0.23)×10-9.

An elasto-mechanical unfeelability cloak made of pentamode metamaterials

Abstract: Cloaking of a range of stimuli have been demonstrated in various metamaterials recently. Here, the authors report mechanical cloaking in a pentamode structure, leading to ‘unfeelability’ of a core in an elasto-mechanical core-shell system.

Electron and Positron Fluxes in Primary Cosmic Rays Measured with the Alpha Magnetic Spectrometer on the International Space Station

Abstract: Precision measurements by the Alpha Magnetic Spectrometer on the International Space Station of the primary cosmic-ray electron flux in the range 0.5 to 700 GeV and the positron flux in the range 0.5 to 500 GeV are presented. The electron flux and the positron flux each require a description beyond a single power-law spectrum. Both the electron flux and the positron flux change their behavior at ∼30 GeV but the fluxes are significantly different in their magnitude and energy dependence. Between 20 and 200 GeV the positron spectral index is significantly harder than the electron spectral index. The determination of the differing behavior of the spectral indices versus energy is a new observation and provides important information on the origins of cosmic-ray electrons and positrons.

3D Traffic Scene Understanding From Movable Platforms

Abstract: In this paper, we present a novel probabilistic generative model for multi-object traffic scene understanding from movable platforms which reasons jointly about the 3D scene layout as well as the location and orientation of objects in the scene. In particular, the scene topology, geometry, and traffic activities are inferred from short video sequences. Inspired by the impressive driving capabilities of humans, our model does not rely on GPS, lidar, or map knowledge. Instead, it takes advantage of a diverse set of visual cues in the form of vehicle tracklets, vanishing points, semantic scene labels, scene flow, and occupancy grids. For each of these cues, we propose likelihood functions that are integrated into a probabilistic generative model. We learn all model parameters from training data using contrastive divergence. Experiments conducted on videos of 113 representative intersections show that our approach successfully infers the correct layout in a variety of very challenging scenarios. To evaluate the importance of each feature cue, experiments using different feature combinations are conducted. Furthermore, we show how by employing context derived from the proposed method we are able to improve over the state-of-the-art in terms of object detection and object orientation estimation in challenging and cluttered urban environments.

Protein corona formation around nanoparticles – from the past to the future

Abstract: The protein adsorption layer (a.k.a. the “protein corona”) that forms on the surface of colloidal nanoparticles plays an important role in their interaction with living matter. Thus, characterization of the protein corona is of utmost importance for understanding how exposure to nanoparticles affects the biological responses of cells and organisms. Although a lot of experimental studies have been reported in this direction, a comprehensive picture is still missing, in particular due to the multitude of different scenarios under which experiments have been performed. In this review an analysis of existing experimental data about the protein corona, and an outline for required future work will be given. In particular we review how existing simple analytical models such as the adopted Hill model may help to extract quantitative data from such experiments such as equilibrium dissociation and kinetic coefficients. Careful quantitative assessment of equilibrium and kinetic properties would allow for a comparison of protein binding data from the vast array of engineered nanoparticles, so that basic principles could be revealed. This review outlines that the field is in dire need of more quantitative studies to further our understanding of protein corona formation and its biological consequences.

High-strength cellular ceramic composites with 3D microarchitecture

Abstract: To enhance the strength-to-weight ratio of a material, one may try to either improve the strength or lower the density, or both. The lightest solid materials have a density in the range of 1,000 kg/m3; only cellular materials, such as technical foams, can reach considerably lower values. However, compared with corresponding bulk materials, their specific strength generally is significantly lower. Cellular topologies may be divided into bending- and stretching-dominated ones. Technical foams are structured randomly and behave in a bending-dominated way, which is less weight efficient, with respect to strength, than stretching-dominated behavior, such as in regular braced frameworks. Cancellous bone and other natural cellular solids have an optimized architecture. Their basic material is structured hierarchically and consists of nanometer-size elements, providing a benefit from size effects in the material strength. Designing cellular materials with a specific microarchitecture would allow one to exploit the structural advantages of stretching-dominated constructions as well as size-dependent strengthening effects. In this paper, we demonstrate that such materials may be fabricated. Applying 3D laser lithography, we produced and characterized micro-truss and -shell structures made from alumina–polymer composite. Size-dependent strengthening of alumina shells has been observed, particularly when applied with a characteristic thickness below 100 nm. The presented artificial cellular materials reach compressive strengths up to 280 MPa with densities well below 1,000 kg/m3.