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At least 541 records · Page 30

Spatio-temporal patterning of extensile active stresses in microtubule-based active fluids

Abstract Microtubule-based active fluids exhibit turbulent-like autonomous flows, which are driven by the molecular motor powered motion of filamentous constituents. Controlling active stresses in space and time is an essential prerequisite for controlling the intrinsically chaotic dynamics of extensile active fluids. We design single-headed kinesin molecular motors that exhibit optically enhanced clustering and thus enable precise and repeatable spatial and temporal control of extensile active stresses. Such motors enable rapid, reversible switching between flowing and quiescent states. In turn, spatio-temporal patterning of the active stress controls the evolution of the ubiquitous bend instability of extensile active fluids and determines its critical length dependence. Combining optically controlled clusters with conventional kinesin motors enables one-time switching from contractile to extensile active stresses. These results open a path towards real-time control of the autonomous flows generated by active fluids.

36 MATERIALS SCIENCE↗

Influence of solar forcing, climate variability and modes of low-frequency atmospheric variability on summer floods in Switzerland

The higher frequency of severe flood events in Switzerland in recent decades has given fresh impetus to the study of flood patterns and their possible forcing mechanisms, particularly in mountain environments. This paper presents a new index of summer flood damage that considers severe and catastrophic summer floods in Switzerland between 1800 and 2009, and explores the influence of external forcings on flood frequencies. In addition, links between floods and low-frequency atmospheric variability patterns are examined. The flood damage index provides evidence that the 1817–1851, 1881–1927, 1977–1990 and 2005–present flood clusters occur mostly in phase with palaeoclimate proxies. The cross-spectral analysis documents that the periodicities detected in the coherency and phase spectra of 11 (Schwabe cycle) and 104 years (Gleissberg cycle) are related to a high frequency of flooding and solar activity minima, whereas the 22-year cyclicity detected (Hale cycle) is associated with solar activity maxima and a decrease in flood frequency. The analysis of low-frequency atmospheric variability modes shows that Switzerland lies close to the border of the principal summer mode. The Swiss river catchments situated on the centre and southern flank of the Alps are affected by atmospherically unstable areas defined by the positive phase of the pattern, while those basins located in the northern slope of the Alps are predominantly associated with the negative phase of the pattern. Furthermore, a change in the low-frequency atmospheric variability pattern related to the major floods occurred over the period from 1800 to 2009; the summer principal mode persists in the negative phase during the last cool pulses of the Little Ice Age (1817–1851 and 1881–1927 flood clusters), whereas the positive phases of the mode prevail during the warmer climate of the last 4 decades (flood clusters from 1977 to present).

54 ENVIRONMENTAL SCIENCES↗

Deletion analysis of the itaconic acid biosynthesis gene cluster components in Aspergillus pseudoterreus ATCC32359

The filamentous fungus Aspergillus terreus has been successfully used for industrial production of itaconic acid (IA) for many years. The IA biosynthesis pathway has recently been characterized at a molecular genetic level as an IA gene cluster (IA cluster) by a clone-based transcriptomic approach. The cluster consists of four genes, including genes for cis-aconitic acid decarboxylase (cadA), a predicted transcription factor (tf), mitochondrial organic acid transporter (mttA), and MFS (Major Facilitator Superfamily) type transporter (mfsA). In this research, we performed EST (Expressed Sequence Tag) analysis and systematic gene deletions to investigate the role of those genes in IA biosynthesis in A. pseudoterreus ATCC32359. EST analysis showed a similar expression pattern among those four genes that was distinct from neighbouring genes and further confirmed that they belong to the same biosynthesis cluster. Systematic gene deletion analysis demonstrated that tf, cadA, mttA, and mfsA genes in the cluster are essential for IA production. Deletion of any of them will either completely abolish the IA production or dramatically decrease amount of IA produced. More importantly, a significant amount of aconitic acid was detected in the cadA deletion strain but not in the other deletion strains. Therefore, the cadA deletion strain is a novel microorganism host for production of aconitic acid and other value-added chemicals from lignocellulosic biomass.

Deng, Shuang↗

Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes

In this work, we analyzed the community structure and metabolic potential of sediment microbial communities in high-latitude coastal environments subjected to low to moderate levels of chronic pollution. Subtidal sediments from four low-energy inlets located in polar and subpolar regions from both Hemispheres were analyzed using large-scale 16S rRNA gene and metagenomic sequencing. Communities showed high diversity (Shannon’s index 6.8 to 10.2), with distinct phylogenetic structures (<40% shared taxa at the Phylum level among regions) but similar metabolic potential in terms of sequences assigned to KOs. Environmental factors (mainly salinity, temperature, and in less extent organic pollution) were drivers of both phylogenetic and functional traits. Bacterial taxa correlating with hydrocarbon pollution included families of anaerobic or facultative anaerobic lifestyle, such as Desulfuromonadaceae, Geobacteraceae, and Rhodocyclaceae. In accordance, biomarker genes for anaerobic hydrocarbon degradation (bamA, ebdA, bcrA, and bssA) were prevalent, only outnumbered by alkB, and their sequences were taxonomically binned to the same bacterial groups. BssA-assigned metagenomic sequences showed an extremely wide diversity distributed all along the phylogeny known for this gene, including bssA sensu stricto, nmsA, assA, and other clusters from poorly or not yet described variants. This work increases our understanding of microbial community patterns in cold coastal sediments, and highlights the relevance of anaerobic hydrocarbon degradation processes in subtidal environments.

metagenomic↗

Convective Biases in the US DOE Global Storm‐Resolving Model: Insights From Regionally Refined Simulations During the CACTI Campaign

Accurately simulating convective processes in complex terrain remains a critical challenge for global storm-resolving models (GSRMs). This study systematically evaluates moist convective biases in the Regionally Refined Mesh configuration of the U.S. Department of Energy Simple Cloud-Resolving E3SM Atmosphere Model (RRM-SCREAM) using comprehensive observations and large-eddy simulations from the Cloud, Aerosol, and Complex Terrain Interactions (CACTI) campaign in the mountainous area of central Argentina. Comparisons of simulations with high-resolution observations and reanalysis data indicate that RRM-SCREAM effectively captures large-scale meteorological patterns, including regional atmospheric gradients and diurnal variability. However, RRM-SCREAM disproportionately produces smaller precipitation clusters referred to as “popcorn convection,” and exaggerated rainfall intensities compared to observations and reference models. Detailed examination of a representative orographic shallow-to-deep convective transition case shows that RRM-SCREAM delays initial shallow convection growth due to lower-tropospheric dryness and sustained convective inhibition, but once triggered, deep convection becomes overly vigorous with excessively strong vertical velocities and elevated cloud ice content, linked to a thermodynamic structure characterized by suppressed low-level moistening and excessive upper-level moisture retention. Our results highlight specific deficiencies in the model representation of convective vertical velocity, cloud microphysical processes, and convective precipitation organization within RRM-SCREAM. Addressing these biases is essential for improving the predictions of convective clouds and precipitation in the global high-resolution atmospheric models.

Su, Tianning [Lawrence Livermore National Laborato↗

Nanoscale mapping of heterogeneity of the polarization reversal in lead-free relaxor–ferroelectric ceramic composites

Relaxor/ferroelectric ceramic/ceramic composites have shown to be promising in generating large electromechanical strain at moderate electric fields. However, the mechanisms of polarization and strain coupling between grains of different nature in the composites remain unclear. To rationalize the coupling mechanisms we performed advanced piezoresponse force microscopy (PFM) studies of 0.92BNT-0.06BT-0.02KNN/0.93BNT-0.07BT (ergodic/non-ergodic relaxor) composites. PFM is able to distinguish grains of different phases by characteristic domain patterns. Polarization switching has been probed locally, on a sub-grain scale. k-Means clustering analysis applied to arrays of local hysteresis loops reveals variations of polarization switching characteristics between the ergodic and non-ergodic relaxor grains. Here, we report a different set of switching parameters for grains in the composites as opposed to the pure phase samples. These results confirm ceramic/ceramic composites to be a viable approach to tailor the piezoelectric properties and optimize the macroscopic electromechanical characteristics.

36 MATERIALS SCIENCE↗

Imaging collective behavior in an rf-SQUID metamaterial tuned by DC and RF magnetic fields

In this study, we examine the collective behavior of two-dimensional nonlinear superconducting metamaterials using a non-contact spatially resolved imaging technique. The metamaterial is made up of sub-wavelength nonlinear oscillators in a strongly coupled 27x27 planar array of radio-frequency Superconducting QUantum Interference Devices (rf SQUIDs). By using low-temperature laser scanning microscopy we image microwave currents in the driven SQUIDs while in non-radiating dark modes and identify the clustering and uniformity of like-oscillating meta-atoms. We follow the rearrangement of coherent patterns due to meta-atom resonant frequency tuning as a function of external dc and rf magnetic flux bias. We find that the rf current distribution across the SQUID array at zero dc flux and small rf flux reveals a low degree of coherence. By contrast, the spatial coherence improves dramatically upon increasing of rf flux amplitude, in agreement with simulation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Explosive nucleation and growth of Pb islands on Ge(111) below room temperature via collective diffusion

Nucleation is a fundamental process in nature controlling phase transitions and pattern formation. Classical nucleation is based on the gradual aggregation of diffusing atoms after a critical cluster size is reached. Contrary to these expectations, we have observed in real time the formation of perfect Pb(111) islands with more than 10 5 atoms emerging out of the compressed wetting layer within a few seconds during growth of Pb on Ge(111) below room temperature. Pb deposited on Ge(111) in a temperature range between −30 °C and 10 °C exhibited explosive nucleation of height-selected islands upon reaching a critical coverage of 1.33 ± 0.07 ML with respect to Ge(111). Island nucleation was fueled by the 2% compression of the Pb wetting layer at the critical coverage. The island areas grew linearly with time, exhibiting collective diffusion, where thousands of atoms follow correlated, non-random walk diffusion. The total growth rate was higher with increasing temperature. Density functional theory simulations of the chemical potential and binding sites of the Pb/Ge(111) system give insight into the role of the compression of the wetting layer and the strain within the growing Pb layers, which explain this nonclassical behavior of the system.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Simulation and performance of an artificial retina for 40 MHz track reconstruction

We present the results of a detailed simulation of the artificial retina pattern-recognition algorithm, designed to reconstruct events with hundreds of charged-particle tracks in pixel and silicon detectors at LHCb with LHC crossing frequency of 40 MHz. Performances of the artificial retina algorithm are assessed using the official Monte Carlo samples of the LHCb experiment. We found performances for the retina pattern-recognition algorithm comparable with the full LHCb reconstruction algorithm.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

A Convolutional Neural Network Neutrino Event Classifier

Convolutional neural networks (CNNs) have been widely applied in the computer vision community to solve complex problems in image recognition and analysis. We describe an application of the CNN technology to the problem of identifying particle interactions in sampling calorimeters used commonly in high energy physics and high energy neutrino physics in particular. Following a discussion of the core concepts of CNNs and recent innovations in CNN architectures related to the field of deep learning, we outline a specific application to the NOvA neutrino detector. This algorithm, CVN (Convolutional Visual Network) identifies neutrino interactions based on their topology without the need for detailed reconstruction and outperforms algorithms currently in use by the NOvA collaboration.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Fault Diagnosis of Power Systems Using Intelligent Systems

The power system operator's need for a reliable power delivery system calls for a real-time or near-real-time Al-based fault diagnosis tool. Such a tool will allow NASA ground controllers to re-establish a normal or near-normal degraded operating state of the EPS (a DC power system) for Space Station Alpha by isolating the faulted branches and loads of the system. And after isolation, re-energizing those branches and loads that have been found not to have any faults in them. A proposed solution involves using the Fault Diagnosis Intelligent System (FDIS) to perform near-real time fault diagnosis of Alpha's EPS by downloading power transient telemetry at fault-time from onboard data loggers. The FDIS uses an ANN clustering algorithm augmented with a wavelet transform feature extractor. This combination enables this system to perform pattern recognition of the power transient signatures to diagnose the fault type and its location down to the orbital replaceable unit. FDIS has been tested using a simulation of the LeRC Testbed Space Station Freedom configuration including the topology from the DDCU's to the electrical loads attached to the TPDU's. FDIS will work in conjunction with the Power Management Load Scheduler to determine what the state of the system was at the time of the fault condition. This information is used to activate the appropriate diagnostic section, and to refine if necessary the solution obtained. In the latter case, if the FDIS reports back that it is equally likely that the faulty device as 'start tracker #1' and 'time generation unit,' then based on a priori knowledge of the system's state, the refined solution would be 'star tracker #1' located in cabinet ITAS2. It is concluded from the present studies that artificial intelligence diagnostic abilities are improved with the addition of the wavelet transform, and that when such a system such as FDIS is coupled to the Power Management Load Scheduler, a faulty device can be located and isolated from the rest of the system. The benefit of these studies provides NASA with the ability to quickly restore the operating status of a space station from a critical state to a safe degraded mode, thereby saving costs in experimentation rescheduling, fault diagnostics, and prevention of loss-of-life.

Momoh, James A.↗

Crowd cluster data in the USA for analysis of human response to COVID-19 events and policies

We provide data on daily social contact intensity of clusters of people at different types of Points of Interest (POI) by zip code in Florida and California. This data is obtained by aggregating fine-scaled details of interactions of people at the spatial resolution of 10 m, which is then normalized as a social contact index. We also provide the distribution of cluster sizes and average time spent in a cluster by POI type. This data will help researchers perform fine-scaled, privacy-preserving analysis of human interaction patterns to understand the drivers of the COVID-19 epidemic spread and mitigation. Current mobility datasets either provide coarse-level metrics of social distancing, such as radius of gyration at the county or province level, or traffic at a finer scale, neither of which is a direct measure of contacts between people. We use anonymized, de-identified, and privacy-enhanced location-based services (LBS) data from opted-in cell phone apps, suitably reweighted to correct for geographic heterogeneities, and identify clusters of people at non-sensitive public areas to estimate fine-scaled contacts.

60 APPLIED LIFE SCIENCES↗

Incomplete segregation of endorgan-specific vestibular ganglion cells in mice and rats

The endorgan-specific distribution of vestibular ganglion cells was studied in neonatal and postnatal rats and mice using indocarbocyanine dye (DiI) and dextran amines for retrograde and anterograde labeling. Retrograde DiI tracing from the anterior vertical canal labeled neurons scattered throughout the whole superior vestibular ganglion, with denser labeling at the dorsal and central regions. Horizontal canal neurons were scattered along the dorsoventral axis with more clustering toward the dorsal and ventral poles of this axis. Utricular ganglion cells occupied predominantly the central region of the superior vestibular ganglion. This utricular population overlapped with both the anterior vertical and horizontal canals' ganglion cells. Posterior vertical canal neurons were clustered in the posterior part of the inferior vestibular ganglion. The saccular neurons were distributed in the two parts of the vestibular ganglion, the superior and inferior ganglia. Within the inferior ganglion, the saccular neurons were clustered in the anterior part. In the superior ganglion, the saccular neurons were widely scattered throughout the whole ganglion with more numerous neurons at the posterior half. Small and large neurons were labeled from all endorgans. Examination of the fiber trajectory within the superior division of the vestibular nerve showed no clear lamination of the fibers innervating the different endorgans. These results demonstrate an overlapping pattern between the different populations within the superior ganglion, while in the inferior ganglion, the posterior canal and saccular neurons show tighter clustering but incomplete segregation. This distribution implies that the ganglion cells are assigned for their target during development in a stochastic rather than topographical fashion.

NASA Discipline Developmental Biology↗

Spatiotemporal Characteristics and Propagation of Summer Extreme Precipitation Events over United States: A Complex Network Analysis

Complex Network (CN) is a graph-theory based depiction of relation shared by various elements of a complex-dynamical system such as the atmosphere. Here we applied the concept of CN to understand the directionality and topological structure of summer extreme precipitation events (SEPEs) over the conterminous United States (CONUS). The SEPEs are calculated based on the 95th percentile daily rainfall at 0.5ox0.5o spatial resolution for CONUS to investigate the multi-dimensional characteristics of precipitation extremes. The derived CN coefficients (e.g., betweenness centrality, clustering coefficient, orientation, and network divergence) reveal important structural and dynamical information about the topology of the SEPEs and improve understanding of the dominant meteorological patterns. The initiation and propagation of SEPEs from the source-zones to the sink-zones are identified. The SEPEs are influenced by topography, dominant wind patterns, and moisture sources in terms of their topological structure and spatial dynamics.

Mondal, Somnath↗

Dynamic phases, clustering, and chain formation for driven disk systems in the presence of quenched disorder

In this paper, we numerically examine the dynamic phases and pattern formation of two-dimensional monodisperse repulsive disks driven over random quenched disorder. We show that there is a series of distinct dynamic regimes as a function of increasing drive, including a clogged or pile-up phase near depinning, a homogeneous disordered flow state, and a dynamically phase separated regime consisting of high-density crystalline regions surrounded by a low density of disordered disks. At the highest drives the disks arrange into one-dimensional moving chains. The phase separated regime has parallels with the phase separation observed in active matter systems, but arises from a distinct mechanism consisting of the combination of nonequilibrium fluctuations with density-dependent mobility. We discuss the pronounced differences between this system and previous studies of driven particles with longer-range repulsive interactions moving over random substrates, such as superconducting vortices or electron crystals, where dynamical phase separation and distinct one-dimensional moving chains are not observed. Finally, our results should be generic to a broad class of systems in which the particle-particle interactions are short ranged, such as sterically interacting colloids or Yukawa particles with strong screening driven over random pinning arrays, superconducting vortices in the limit of small penetration depths, or quasi-two-dimensional granular matter flowing over rough landscapes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Message Passing vs. Shared Address Space on a Cluster of SMPs

The convergence of scalable computer architectures using clusters of PCs (or PC-SMPs) with commodity networking has become an attractive platform for high end scientific computing. Currently, message-passing and shared address space (SAS) are the two leading programming paradigms for these systems. Message-passing has been standardized with MPI, and is the most common and mature programming approach. However message-passing code development can be extremely difficult, especially for irregular structured computations. SAS offers substantial ease of programming, but may suffer from performance limitations due to poor spatial locality, and high protocol overhead. In this paper, we compare the performance of and programming effort, required for six applications under both programming models on a 32 CPU PC-SMP cluster. Our application suite consists of codes that typically do not exhibit high efficiency under shared memory programming. due to their high communication to computation ratios and complex communication patterns. Results indicate that SAS can achieve about half the parallel efficiency of MPI for most of our applications: however, on certain classes of problems SAS performance is competitive with MPI. We also present new algorithms for improving the PC cluster performance of MPI collective operations.

Shan, Hongzhang↗

Multi-scale visual analysis of time-varying electrocorticography data via clustering of brain regions

There exists a need for effective and easy-to-use software tools supporting the analysis of complex Electrocorticography (ECoG) data. Understanding how epileptic seizures develop or identifying diagnostic indicators for neurological diseases require the in-depth analysis of neural activity data from ECoG. Such data is multi-scale and is of high spatio-temporal resolution. Comprehensive analysis of this data should be supported by interactive visual analysis methods that allow a scientist to understand functional patterns at varying levels of granularity and comprehend its time-varying behavior. We introduce a novel multi-scale visual analysis system, ECoG ClusterFlow, for the detailed exploration of ECoG data. Our system detects and visualizes dynamic high-level structures, such as communities, derived from the time-varying connectivity network. The system supports two major views: 1) an overview summarizing the evolution of clusters over time and 2) an electrode view using hierarchical glyph-based design to visualize the propagation of clusters in their spatial, anatomical context. We present case studies that were performed in collaboration with neuroscientists and neurosurgeons using simulated and recorded epileptic seizure data to demonstrate our system's effectiveness. ECoG ClusterFlow supports the comparison of spatio-temporal patterns for specific time intervals and allows a user to utilize various clustering algorithms. Neuroscientists can identify the site of seizure genesis and its spatial progression during various the stages of a seizure. Our system serves as a fast and powerful means for the generation of preliminary hypotheses that can be used as a basis for subsequent application of rigorous statistical methods, with the ultimate goal being the clinical treatment of epileptogenic zones.

60 APPLIED LIFE SCIENCES↗

Scalable Pattern Matching in Metadata Graphs via Constraint Checking

Pattern matching is a fundamental tool for answering complex graph queries. Unfortunately, existing solutions have limited capabilities: They do not scale to process large graphs and/or support only a restricted set of search templates or usage scenarios. Moreover, the algorithms at the core of the existing techniques are not suitable for today’s graph processing infrastructures relying on horizontal scalability and shared-nothing clusters, as most of these algorithms are inherently sequential and difficult to parallelize. In this article we present an algorithmic pipeline that bases pattern matching on constraint checking. The key intuition is that each vertex and edge participating in a match has to meet a set of constraints implicitly specified by the search template. These constraints can be verified independently and typically are less expensive to compute than searching the full template. The pipeline we propose generates these constraints and iterates over them to eliminate all the vertices and edges that do not participate in any match, thus reducing the background graph to a subgraph that is the union of all template matches—the complete set of all vertices and edges that participate in at least one match. Additional analysis can be performed on this annotated, reduced graph, such as full match enumeration, match counting, or computing vertex/edge centrality. Furthermore, a vertex-centric formulation for constraint checking algorithms exists, and this makes it possible to harness existing high-performance, vertex-centric graph processing frameworks. This technique (i) enables highly scalable pattern matching in metadata (labeled) graphs; (ii) supports arbitrary patterns with 100% precision; (iii) enables tradeoffs between precision and time-to-solution, while always selects all vertices and edges that participate in matches, thus offering 100% recall; and (iv) supports a set of popular data analytics scenarios. We implement our approach on top of HavoqGT, an open-source asynchronous graph processing framework, and demonstrate its advantages through strong and weak scaling experiments on massive scale real-world (up to 257 billion edges) and synthetic (up to 4.4 trillion edges) labeled graphs, respectively, and at scales (1,024 nodes / 36,864 cores), orders of magnitude larger than used in the past for similar problems. This article serves two purposes: First, it synthesises the knowledge accumulated during a long-term project. Second, it presents new system features, usage scenarios, optimizations, and comparisons with related work that strengthen the confidence that pattern matching based on iterative pruning via constraint checking is an effective and scalable approach in practice. The new contributions include the following: (i) We demonstrate the ability of the constraint checking approach to efficiently support two additional search scenarios that often emerge in practice, interactive incremental search and exploratory search. (ii) We empirically compare our solution with two additional state-of-the-art systems, Arabsque and TriAD. (iii) We show the ability of our solution to accommodate a more diverse range of datasets with varying properties, e.g., scale, skewness, label distribution, and match frequency. (iv) We introduce or extend a number of system features (e.g., work aggregation, load balancing, and the ability to cap the generated traffic) and design optimizations and demonstrate their advantages with respect to improving performance and scalability. (v) We present bottleneck analysis and insights into artifacts that influence performance. (vi) We present a theoretical complexity argument that motivates the performance gains we observe.

97 MATHEMATICS AND COMPUTING↗