Showing papers by "University of Stuttgart published in 2015"

Thermodynamic uncertainty relation for biomolecular processes.

Abstract: Biomolecular systems like molecular motors or pumps, transcription and translation machinery, and other enzymatic reactions, can be described as Markov processes on a suitable network. We show quite generally that, in a steady state, the dispersion of observables, like the number of consumed or produced molecules or the number of steps of a motor, is constrained by the thermodynamic cost of generating it. An uncertainty $\ensuremath{\epsilon}$ requires at least a cost of $2{k}_{B}T/{\ensuremath{\epsilon}}^{2}$ independent of the time required to generate the output.

Improving f-element single molecule magnets

Abstract: Ever since the discovery that certain manganese clusters retain their magnetisation for months at low temperatures, there has been intense interest in molecular nanomagnets because of potential applications in data storage, spintronics, quantum computing, and magnetocaloric cooling. In this Tutorial Review, we summarise some key historical developments, and centre our discussion principally on the increasing trend to exploit the large magnetic moments and anisotropies of f-element ions. We focus on the important theme of strategies to improve these systems with the ultimate aim of developing materials for ultra-high-density data storage devices. We present a critical discussion of key parameters to be optimised, as well as of experimental and theoretical techniques to be used to this end.

Coherent control of single spins in silicon carbide at room temperature

Abstract: Defects in silicon carbide have recently been proposed as bright single-photon sources. It is now shown that they can be used as sources of single electron spins having long coherence times at room temperature. Spins in solids are cornerstone elements of quantum spintronics1. Leading contenders such as defects in diamond2,3,4,5 or individual phosphorus dopants in silicon6 have shown spectacular progress, but either lack established nanotechnology or an efficient spin/photon interface. Silicon carbide (SiC) combines the strength of both systems5: it has a large bandgap with deep defects7,8,9 and benefits from mature fabrication techniques10,11,12. Here, we report the characterization of photoluminescence and optical spin polarization from single silicon vacancies in SiC, and demonstrate that single spins can be addressed at room temperature. We show coherent control of a single defect spin and find long spin coherence times under ambient conditions. Our study provides evidence that SiC is a promising system for atomic-scale spintronics and quantum technology.

Interrelation of Oxidative Stress and Inflammation in Neurodegenerative Disease: Role of TNF

Abstract: Neuroinflammation and mitochondrial dysfunction are common features of chronic neurodegenerative diseases of the central nervous system. Both conditions can lead to increased oxidative stress by excessive release of harmful reactive oxygen and nitrogen species (ROS and RNS), which further promote neuronal damage and subsequent inflammation resulting in a feed-forward loop of neurodegeneration. The cytokine tumor necrosis factor (TNF), a master regulator of the immune system, plays an important role in the propagation of inflammation due to the activation and recruitment of immune cells via its receptor TNF receptor 1 (TNFR1). Moreover, TNFR1 can directly induce oxidative stress by the activation of ROS and RNS producing enzymes. Both TNF-induced oxidative stress and inflammation interact and cooperate to promote neurodegeneration. However, TNF plays a dual role in neurodegenerative disease, since stimulation via its second receptor, TNFR2, is neuroprotective and promotes tissue regeneration. Here we review the interrelation of oxidative stress and inflammation in the two major chronic neurodegenerative diseases, Alzheimer's and Parkinson's disease, and discuss the dual role of TNF in promoting neurodegeneration and tissue regeneration via its two receptors.

A Switchable Mid-Infrared Plasmonic Perfect Absorber with Multispectral Thermal Imaging Capability.

Abstract: A switchable perfect absorber with multispectral thermal imaging capability is presented. Aluminum nanoantenna arrays above a germanium antimony telluride (GST) spacer layer and aluminum mirror provide efficient wavelength-tunable absorption in the mid-infrared. Utilizing the amorphous-to-crystalline phase transition in GST, this device offers switchable absorption with strong reflectance contrast at resonance and large phase-change-induced spectral shifts.

Ongoing hydrothermal activities within Enceladus

Abstract: Analysis of silicon-rich, nanometre-sized dust particles near Saturn shows them to consist of silica, which was initially embedded in icy grains emitted from Enceladus’ subsurface waters and released by sputter erosion in Saturn’s E ring; their properties indicate their ongoing formation and transport by high-temperature hydrothermal reactions from the ocean floor and up into the plume of Enceladus. Hsiang-Wen Hsu et al. have analysed the silicon-rich, nanometre-sized dust stream particles in the Saturnian system using the Cosmic Dust Analyser (CDA) onboard the Cassini spacecraft. With the help of experiments and modelling, the particles are interpreted as silica grains that were initially embedded in the icy plume emitted from subsurface waters on Enceladus and released by sputter erosion in Saturn's E ring. Their properties indicate their formation and transport by high-temperature hydrothermal reactions from the ocean floor and up into the plume of Enceladus. Detection of sodium-salt-rich ice grains emitted from the plume of the Saturnian moon Enceladus suggests that the grains formed as frozen droplets from a liquid water reservoir that is, or has been, in contact with rock1,2. Gravitational field measurements suggest a regional south polar subsurface ocean of about 10 kilometres thickness located beneath an ice crust 30 to 40 kilometres thick3. These findings imply rock–water interactions in regions surrounding the core of Enceladus. The resulting chemical ‘footprints’ are expected to be preserved in the liquid and subsequently transported upwards to the near-surface plume sources, where they eventually would be ejected and could be measured by a spacecraft4. Here we report an analysis of silicon-rich, nanometre-sized dust particles5,6,7,8 (so-called stream particles) that stand out from the water-ice-dominated objects characteristic of Saturn. We interpret these grains as nanometre-sized SiO2 (silica) particles, initially embedded in icy grains emitted from Enceladus’ subsurface waters and released by sputter erosion in Saturn’s E ring. The composition and the limited size range (2 to 8 nanometres in radius) of stream particles indicate ongoing high-temperature (>90 °C) hydrothermal reactions associated with global-scale geothermal activity that quickly transports hydrothermal products from the ocean floor at a depth of at least 40 kilometres up to the plume of Enceladus.

Subpicotesla Diamond Magnetometry

Abstract: Magnetic fields play roles in a variety of scientific and medical applications. Using solid-state spins in diamond, researchers experimentally demonstrate the measurement of magnetic fields as small as 100 fT in a tiny sensor volume.

Single-protein spin resonance spectroscopy under ambient conditions

Abstract: Magnetic resonance is essential in revealing the structure and dynamics of biomolecules. However, measuring the magnetic resonance spectrum of single biomolecules has remained an elusive goal. We demonstrate the detection of the electron spin resonance signal from a single spin-labeled protein under ambient conditions. As a sensor, we use a single nitrogen vacancy center in bulk diamond in close proximity to the protein. We measure the orientation of the spin label at the protein and detect the impact of protein motion on the spin label dynamics. In addition, we coherently drive the spin at the protein, which is a prerequisite for studies involving polarization of nuclear spins of the protein or detailed structure analysis of the protein itself.

Direct evidence for dominant bond-directional interactions in a honeycomb lattice iridate Na2IrO3

Abstract: Honeycomb iridates have been proposed as experimental realizations of the Kitaev model. An X-ray scattering study presents evidence for bond-directional interactions in Na2IrO3, a key requirement to make the connection with Kitaev physics possible.

Making existing production systems Industry 4.0-ready

Abstract: This paper presents an approach to how existing production systems that are not Industry 4.0-ready can be expanded to participate in an Industry 4.0 factory. Within this paper, a concept is presented how production systems can be discovered and included into an Industry 4.0 (I4.0) environment, even though they did not have I4.0-interfaces when they have been manufactured. The concept is based on a communication gateway and an information server. Besides the concept itself, this paper presents a validation that demonstrates applicability of the developed concept.

Atom based RF electric field sensing

Abstract: Atom-based measurements of length, time, gravity, inertial forces and electromagnetic fields are receiving increasing attention. Atoms possess properties that suggest clear advantages as self calibrating platforms for measurements of these quantities. In this review, we describe work on a new method for measuring radio frequency (RF) electric fields based on quantum interference using either Cs or Rb atoms contained in a dielectric vapor cell. Using a bright resonance prepared within an electromagnetically induced transparency window it is possible to achieve high sensitivities, <1 μV cm−1 Hz−1/2, and detect small RF electric fields μV cm−1 with a modest setup. Some of the limitations of the sensitivity are addressed in the review. The method can be used to image RF electric fields and can be adapted to measure the vector electric field amplitude. Extensions of Rydberg atom-based electrometry for frequencies up to the terahertz regime are described.

Active Chiral Plasmonics.

Abstract: Active control over the handedness of a chiral metamaterial has the potential to serve as key element for highly integrated polarization engineering approaches, polarization sensitive imaging devices, and stereo display technologies. However, this is hard to achieve as it seemingly involves the reconfiguration of the metamolecule from a left-handed into a right-handed enantiomer and vice versa. This type of mechanical actuation is intricate and usually neither monolithically realizable nor viable for high-speed applications. Here, enabled by the phase change material Ge3Sb2Te6 (GST-326), we demonstrate a tunable and switchable mid-infrared plasmonic chiral metamaterial in a proof-of-concept experiment. A large tunability range of the circular dichroism response from λ = 4.15 to 4.90 μm is achieved, and we experimentally demonstrate that the combination of a passive bias-type chiral layer with the active chiral metamaterial allows for switchable chirality, that is, the reversal of the circular dichroism si...

Electron flow in reaction mechanisms--revealed from first principles.

Abstract: The “curly arrow” of Robinson and Ingold is the primary tool for describing and rationalizing reaction mechanisms. Despite this approach’s ubiquity and stellar success, its physical basis has never been clarified and a direct connection to quantum chemistry has never been found. Here we report that the bond rearrangements expressed by curly arrows can be directly observed in ab initio computations, as transformations of intrinsic bond orbitals (IBOs) along the reaction coordinate. Our results clarify that curly arrows are rooted in physical reality—a notion which has been challenged before—and show how quantum chemistry can directly establish reaction mechanisms in intuitive terms and unprecedented detail.

Failure mechanisms of additively manufactured porous biomaterials: Effects of porosity and type of unit cell

Abstract: Since the advent of additive manufacturing techniques, regular porous biomaterials have emerged as promising candidates for tissue engineering scaffolds owing to their controllable pore architecture and feasibility in producing scaffolds from a variety of biomaterials. The architecture of scaffolds could be designed to achieve similar mechanical properties as in the host bone tissue, thereby avoiding issues such as stress shielding in bone replacement procedure. In this paper, the deformation and failure mechanisms of porous titanium (Ti6Al4V) biomaterials manufactured by selective laser melting from two different types of repeating unit cells, namely cubic and diamond lattice structures, with four different porosities are studied. The mechanical behavior of the above-mentioned porous biomaterials was studied using finite element models. The computational results were compared with the experimental findings from a previous study of ours. The Johnson–Cook plasticity and damage model was implemented in the finite element models to simulate the failure of the additively manufactured scaffolds under compression. The computationally predicted stress–strain curves were compared with the experimental ones. The computational models incorporating the Johnson–Cook damage model could predict the plateau stress and maximum stress at the first peak with less than 18% error. Moreover, the computationally predicted deformation modes were in good agreement with the results of scaling law analysis. A layer-by-layer failure mechanism was found for the stretch-dominated structures, i.e. structures made from the cubic unit cell, while the failure of the bending-dominated structures, i.e. structures made from the diamond unit cells, was accompanied by the shearing bands of 45°.

Logic-geometric programming: an optimization-based approach to combined task and motion planning

Abstract: We consider problems of sequential robot manipulation (aka. combined task and motion planning) where the objective is primarily given in terms of a cost function over the final geometric state, rather than a symbolic goal description. In this case we should leverage optimization methods to inform search over potential action sequences. We propose to formulate the problem holistically as a 1st- order logic extension of a mathematical program: a non-linear constrained program over the full world trajectory where the symbolic state-action sequence defines the (in-)equality constraints. We tackle the challenge of solving such programs by proposing three levels of approximation: The coarsest level introduces the concept of the effective end state kinematics, parametrically describing all possible end state configurations conditional to a given symbolic action sequence. Optimization on this level is fast and can inform symbolic search. The other two levels optimize over interaction keyframes and eventually over the full world trajectory across interactions. We demonstrate the approach on a problem of maximizing the height of a physically stable construction from an assortment of boards, cylinders and blocks.

Highly multiplexed profiling of single-cell effector functions reveals deep functional heterogeneity in response to pathogenic ligands

Abstract: Despite recent advances in single-cell genomic, transcriptional, and mass-cytometric profiling, it remains a challenge to collect highly multiplexed measurements of secreted proteins from single cells for comprehensive analysis of functional states. Herein, we combine spatial and spectral encoding with polydimethylsiloxane (PDMS) microchambers for codetection of 42 immune effector proteins secreted from single cells, representing the highest multiplexing recorded to date for a single-cell secretion assay. Using this platform to profile differentiated macrophages stimulated with lipopolysaccharide (LPS), the ligand of Toll-like receptor 4 (TLR4), reveals previously unobserved deep functional heterogeneity and varying levels of pathogenic activation. Uniquely protein profiling on the same single cells before and after LPS stimulation identified a role for macrophage inhibitory factor (MIF) to potentiate the activation of LPS-induced cytokine production. Advanced clustering analysis identified functional subsets including quiescent, polyfunctional fully activated, partially activated populations with different cytokine profiles. This population architecture is conserved throughout the cell activation process and prevails as it is extended to other TLR ligands and to primary macrophages derived from a healthy donor. This work demonstrates that the phenotypically similar cell population still exhibits a large degree of intrinsic heterogeneity at the functional and cell behavior level. This technology enables full-spectrum dissection of immune functional states in response to pathogenic or environmental stimulation, and opens opportunities to quantify deep functional heterogeneity for more comprehensive and accurate immune monitoring.

Enzymatically active biomimetic micropropellers for the penetration of mucin gels

Abstract: In the body, mucus provides an important defense mechanism by limiting the penetration of pathogens. It is therefore also a major obstacle for the efficient delivery of particle-based drug carriers. The acidic stomach lining in particular is difficult to overcome because mucin glycoproteins form viscoelastic gels under acidic conditions. The bacterium Helicobacter pylori has developed a strategy to overcome the mucus barrier by producing the enzyme urease, which locally raises the pH and consequently liquefies the mucus. This allows the bacteria to swim through mucus and to reach the epithelial surface. We present an artificial system of reactive magnetic micropropellers that mimic this strategy to move through gastric mucin gels by making use of surface-immobilized urease. The results demonstrate the validity of this biomimetic approach to penetrate biological gels, and show that externally propelled microstructures can actively and reversibly manipulate the physical state of their surroundings, suggesting that such particles could potentially penetrate native mucus.

Convolutional Neural Network for Paraphrase Identification

Abstract: We present a new deep learning architecture Bi-CNN-MI for paraphrase identification (PI). Based on the insight that PI requires comparing two sentences on multiple levels of granularity, we learn multigranular sentence representations using convolutional neural network (CNN) and model interaction features at each level. These features are then the input to a logistic classifier for PI. All parameters of the model (for embeddings, convolution and classification) are directly optimized for PI. To address the lack of training data, we pretrain the network in a novel way using a language modeling task. Results on the MSRP corpus surpass that of previous NN competitors.

Self-propulsion of a catalytically active particle near a planar wall: from reflection to sliding and hovering.

Abstract: Micron-sized particles moving through a solution in response to self-generated chemical gradients serve as model systems for studying active matter. Their far-reaching potential applications will require the particles to sense and respond to their local environment in a robust manner. The self-generated hydrodynamic and chemical fields, which induce particle motion, probe and are modified by that very environment, including confining boundaries. Focusing on a catalytically active Janus particle as a paradigmatic example, we predict that near a hard planar wall such a particle exhibits several scenarios of motion: reflection from the wall, motion at a steady-state orientation and height above the wall, or motionless, steady “hovering.” Concerning the steady states, the height and the orientation are determined both by the proportion of catalyst coverage and the interactions of the solutes with the different “faces” of the particle. Accordingly, we propose that a desired behavior can be selected by tuning these parameters via a judicious design of the particle surface chemistry.

Cell death stages in single apoptotic and necrotic cells monitored by Raman microspectroscopy

Abstract: Although apoptosis and necrosis have distinct features, the identification and discrimination of apoptotic and necrotic cell death in vitro is challenging. Immunocytological and biochemical assays represent the current gold standard for monitoring cell death pathways; however, these standard assays are invasive, render large numbers of cells and impede continuous monitoring experiments. In this study, both room temperature (RT)-induced apoptosis and heat-triggered necrosis were analyzed in individual Saos-2 and SW-1353 cells by utilizing Raman microspectroscopy. A targeted analysis of defined cell death modalities, including early and late apoptosis as well as necrosis, was facilitated based on the combination of Raman spectroscopy with fluorescence microscopy. Spectral shifts were identified in the two cell lines that reflect biochemical changes specific for either RT-induced apoptosis or heat-mediated necrosis. A supervised classification model specified apoptotic and necrotic cell death based on single cell Raman spectra. To conclude, Raman spectroscopy allows a non-invasive, continuous monitoring of cell death, which may help shedding new light on complex pathophysiological or drug-induced cell death processes.

Minimization principles for the coupled problem of Darcy–Biot-type fluid transport in porous media linked to phase field modeling of fracture

Abstract: This work develops new minimization and saddle point principles for the coupled problem of Darcy–Biot-type fluid transport in porous media at fracture. It shows that the quasi-static problem of elastically deforming, fluid-saturated porous media is related to a minimization principle for the evolution problem. This two-field principle determines the rate of deformation and the fluid mass flux vector. It provides a canonically compact model structure, where the stress equilibrium and the inverse Darcy's law appear as the Euler equations of a variational statement. A Legendre transformation of the dissipation potential relates the minimization principle to a characteristic three field saddle point principle, whose Euler equations determine the evolutions of deformation and fluid content as well as Darcy's law. A further geometric assumption results in modified variational principles for a simplified theory, where the fluid content is linked to the volumetric deformation. The existence of these variational principles underlines inherent symmetries of Darcy–Biot theories of porous media. This can be exploited in the numerical implementation by the construction of time- and space-discrete variational principles, which fully determine the update problems of typical time stepping schemes. Here, the proposed minimization principle for the coupled problem is advantageous with regard to a new unconstrained stable finite element design, while space discretizations of the saddle point principles are constrained by the LBB condition. The variational principles developed provide the most fundamental approach to the discretization of nonlinear fluid–structure interactions, showing symmetric systems in algebraic update procedures. They also provide an excellent starting point for extensions towards more complex problems. This is demonstrated by developing a minimization principle for a phase field description of fracture in fluid-saturated porous media. It is designed for an incorporation of alternative crack driving forces, such as a convenient criterion in terms of the effective stress. The proposed setting provides a modeling framework for the analysis of complex problems such as hydraulic fracture. This is demonstrated by a spectrum of model simulations.

Nanoscale nuclear magnetic imaging with chemical contrast

Abstract: A nitrogen–vacancy centre in diamond can be used as a probe in a scanning probe microscope to image different chemical species on various substrates.

Interest Group Success in the European Union: When (and Why) Does Business Lose?

Abstract: Business lobbying is widespread in the European Union (EU). But because not all lobbying is successful, the following question arises: When does business win and when does it lose in the context of legislative policy making in the EU? We argue that business actors are, overall, less successful than citizen groups in the European policy process. However, they can protect their interests if interest group conflict is low or the role of the European Parliament is restricted. A new data set on the positions of more than 1,000 non-state actors with respect to 70 legislative acts proposed by the European Commission between 2008 and 2010 allows us to evaluate this argument. Empirical support for our expectations is highly robust. Our findings have implications for the literature on legislative decision-making in the EU and for research on non-state actors in international organizations.

When attention is not scarce - detecting boredom from mobile phone usage

Abstract: Boredom is a common human emotion which may lead to an active search for stimulation. People often turn to their mobile phones to seek that stimulation. In this paper, we tackle the challenge of automatically inferring boredom from mobile phone usage. In a two-week in-the-wild study, we collected over 40,000,000 usage logs and 4398 boredom self-reports of 54 mobile phone users. We show that a user-independent machine-learning model of boredom --leveraging features related to recency of communication, usage intensity, time of day, and demographics-- can infer boredom with an accuracy (AUCROC) of up to 82.9%. Results from a second field study with 16 participants suggest that people are more likely to engage with recommended content when they are bored, as inferred by our boredom-detection model. These findings enable boredom-triggered proactive recommender systems that attune their users' level of attention and need for stimulation.

Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies

Abstract: Phenotypic plasticity is important in adaptation and shapes the evolution of organisms. However, we understand little about what aspects of the genome are important in facilitating plasticity. Eusocial insect societies produce plastic phenotypes from the same genome, as reproductives (queens) and nonreproductives (workers). The greatest plasticity is found in the simple eusocial insect societies in which individuals retain the ability to switch between reproductive and nonreproductive phenotypes as adults. We lack comprehensive data on the molecular basis of plastic phenotypes. Here, we sequenced genomes, microRNAs (miRNAs), and multiple transcriptomes and methylomes from individual brains in a wasp (Polistes canadensis) and an ant (Dinoponera quadriceps) that live in simple eusocial societies. In both species, we found few differences between phenotypes at the transcriptional level, with little functional specialization, and no evidence that phenotype-specific gene expression is driven by DNA methylation or miRNAs. Instead, phenotypic differentiation was defined more subtly by nonrandom transcriptional network organization, with roles in these networks for both conserved and taxon-restricted genes. The general lack of highly methylated regions or methylome patterning in both species may be an important mechanism for achieving plasticity among phenotypes during adulthood. These findings define previously unidentified hypotheses on the genomic processes that facilitate plasticity and suggest that the molecular hallmarks of social behavior are likely to differ with the level of social complexity.

A permanent, asymmetric dust cloud around the Moon

Abstract: Observations are reported of a permanent, asymmetric dust cloud around the Moon, caused by impacts of high-speed cometary dust particles on eccentric orbits, as opposed to particles of asteroidal origin following near-circular paths striking the Moon at lower speeds. Before its planned demise on lunar impact in April 2014, NASA's Lunar Atmosphere and Dust Environment Explorer (LADEE) spent some seven months orbiting the Moon's equator, collecting dust particles for spectroscopic analysis. Sketches made by the Apollo 17 astronauts famously showed a lunar horizon glow, triggering suggestions that electrostatic lofting might be generating dense clouds of small dust particles high above the lunar surface. In this first report on the observations made by the Lunar Dust Experiment (LDEX) onboard LADEE, Mihaly Horanyi et al. find no evidence for such clouds. However, they have detected a permanent asymmetric dust cloud around the Moon, supplied by secondary ejecta dust particles produced by the continual surface impacts of high-speed cometary dust particles in eccentric orbits, as opposed to particles of asteroidal origin following near-circular paths and striking the Moon at lower speeds. The lunar surface is exposed to the same stream of interplanetary dust particles as the Earth, and the LDEX data show that the density of the lunar ejecta cloud increases during meteor showers such as the Geminids. Interplanetary dust particles hit the surfaces of airless bodies in the Solar System, generating charged1 and neutral2 gas clouds, as well as secondary ejecta dust particles3. Gravitationally bound ejecta clouds that form dust exospheres were recognized by in situ dust instruments around the icy moons of Jupiter4 and Saturn5, but have hitherto not been observed near bodies with refractory regolith surfaces. High-altitude Apollo 15 and 17 observations of a ‘horizon glow’ indicated a putative population of high-density small dust particles near the lunar terminators6,7, although later orbital observations8,9 yielded upper limits on the abundance of such particles that were a factor of about 104 lower than that necessary to produce the Apollo results. Here we report observations of a permanent, asymmetric dust cloud around the Moon, caused by impacts of high-speed cometary dust particles on eccentric orbits, as opposed to particles of asteroidal origin following near-circular paths striking the Moon at lower speeds. The density of the lunar ejecta cloud increases during the annual meteor showers, especially the Geminids, because the lunar surface is exposed to the same stream of interplanetary dust particles. We expect all airless planetary objects to be immersed in similar tenuous clouds of dust.