Fundamental Design Principles for Transcription-Factor-Based Metabolite Biosensors.

PubMed

Mannan, Ahmad A; Liu, Di; Zhang, Fuzhong; Oyarzún, Diego A

2017-10-20

Metabolite biosensors are central to current efforts toward precision engineering of metabolism. Although most research has focused on building new biosensors, their tunability remains poorly understood and is fundamental for their broad applicability. Here we asked how genetic modifications shape the dose-response curve of biosensors based on metabolite-responsive transcription factors. Using the lac system in Escherichia coli as a model system, we built promoter libraries with variable operator sites that reveal interdependencies between biosensor dynamic range and response threshold. We developed a phenomenological theory to quantify such design constraints in biosensors with various architectures and tunable parameters. Our theory reveals a maximal achievable dynamic range and exposes tunable parameters for orthogonal control of dynamic range and response threshold. Our work sheds light on fundamental limits of synthetic biology designs and provides quantitative guidelines for biosensor design in applications such as dynamic pathway control, strain optimization, and real-time monitoring of metabolism.

Beaked Whale Habitat Characterization and Prediction

DTIC Science & Technology

2005-09-30

trying to develop a better understanding of beaked whale distribution. For long - range planning, the static habitat prediction maps provide a broad... whale presence ranged from 79.3% to 100.0% for the static models and 85.7% to 94.5% for the dynamic models. Beaked whale habitat prediction has been...submerged for such long periods of time that there is a high probability that they will never surface within the visual range of observers aboard a

Structure and Dynamics of Dinucleosomes Assessed by Atomic Force Microscopy

DOE PAGES

Filenko, Nina A.; Palets, Dmytro B.; Lyubchenko, Yuri L.

2012-01-01

Dynamics of nucleosomes and their interactions are important for understanding the mechanism of chromatin assembly. Internucleosomal interaction is required for the formation of higher-order chromatin structures. Although H1 histone is critically involved in the process of chromatin assembly, direct internucleosomal interactions contribute to this process as well. To characterize the interactions of nucleosomes within the nucleosome array, we designed a dinucleosome and performed direct AFM imaging. The analysis of the AFM data showed dinucleosomes are very dynamic systems, enabling the nucleosomes to move in a broad range along the DNA template. Di-nucleosomes in close proximity were observed, but their populationmore » was low. The use of the zwitterionic detergent, CHAPS, increased the dynamic range of the di-nucleosome, facilitating the formation of tight di-nucleosomes. The role of CHAPS and similar natural products in chromatin structure and dynamics is also discussed.« less

Monitoring wetland inundation dynamics in response to weather variability in the Chesapeake Bay watershed

USDA-ARS?s Scientific Manuscript database

Wetlands provide a broad range of ecosystem services, including flood control, water purification, groundwater replenishment, and biodiversity support. The provision of these services, which are especially valued in the Chesapeake Bay Watershed, is largely controlled by varying levels of wetness. ...

Dynamics at Intermediate Time Scales and Management of Ecological Populations

DTIC Science & Technology

2017-05-10

thinking about the importance of transients is to recognize the importance of serial autocorrelation in time of forcing terms over realistic ecological time...rich areas helps produce divergent home range responses bet - ween individuals from difference age classes. This model has broad applications for

Transformation of Patriarchal Regimes, Literacy, and Schooling

ERIC Educational Resources Information Center

Miller, Pavla

2003-01-01

Literacy has been among the most publicly contested domains in gender struggles; the way that history of literacy is gendered and interpreted makes a difference to the way reading and writing is thought of today. Broadly understood, gender signals a wide range of concerns with subjectivities, social relations, and historical dynamics. Literacy…

TRANSFERABLE DISCHARGE PERMITS FOR CONTROL OF SO2 EMISSIONS FROM ILLINOIS POWER PLANTS (JOURNAL VERSION)

EPA Science Inventory

The paper discusses the use of a large scale simulation model in evaluating various policy alternatives for reducing SO2 emissions from Illinois electric power plants for a broad range of nuclear power capacity addition scenarios. A dynamic simulation of a transferable discharge ...

THE HUBBLE WIDE FIELD CAMERA 3 TEST OF SURFACES IN THE OUTER SOLAR SYSTEM: SPECTRAL VARIATION ON KUIPER BELT OBJECTS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fraser, Wesley C.; Brown, Michael E.; Glass, Florian, E-mail: wesley.fraser@nrc.ca

2015-05-01

Here, we present additional photometry of targets observed as part of the Hubble Wide Field Camera 3 (WFC3) Test of Surfaces in the Outer Solar System. Twelve targets were re-observed with the WFC3 in the optical and NIR wavebands designed to complement those used during the first visit. Additionally, all of the observations originally presented by Fraser and Brown were reanalyzed through the same updated photometry pipeline. A re-analysis of the optical and NIR color distribution reveals a bifurcated optical color distribution and only two identifiable spectral classes, each of which occupies a broad range of colors and has correlatedmore » optical and NIR colors, in agreement with our previous findings. We report the detection of significant spectral variations on five targets which cannot be attributed to photometry errors, cosmic rays, point-spread function or sensitivity variations, or other image artifacts capable of explaining the magnitude of the variation. The spectrally variable objects are found to have a broad range of dynamical classes and absolute magnitudes, exhibit a broad range of apparent magnitude variations, and are found in both compositional classes. The spectrally variable objects with sufficiently accurate colors for spectral classification maintain their membership, belonging to the same class at both epochs. 2005 TV189 exhibits a sufficiently broad difference in color at the two epochs that span the full range of colors of the neutral class. This strongly argues that the neutral class is one single class with a broad range of colors, rather than the combination of multiple overlapping classes.« less

In vitro fermentation of lupin seeds (Lupinus albus) and broad beans (Vicia faba): dynamic modulation of the intestinal microbiota and metabolomic output.

PubMed

Gullón, Patricia; Gullón, Beatriz; Tavaria, Freni; Vasconcelos, Marta; Gomes, Ana Maria

2015-10-01

Broad beans (Vicia faba) and lupin seeds (Lupinus albus) are legumes rich in a wide range of compounds, which may represent a useful dietary approach for modulating the human gut microbiome. In this work, after in vitro digestion, legume samples were used as carbon sources in anaerobic batch cultures to evaluate their impact on the intestinal microbiota composition and on their metabolic products. The fermentations were monitored by a decrease in pH, generation of short chain fatty acids (SCFA) and lactate and the changes in the dynamic bacterial populations by fluorescence in situ hybridization (FISH). The total SCFA at the end of fermentation was 81.52 mM for lupin seeds and 78.41 mM for broad beans accompanied by a decrease of the pH for both legumes. The microbial groups that increased significantly (P < 0.05) were Bifidobacterium spp., Lactobacillus-Enterococcus, Atopobium, Bacteroides-Pretovella, Clostridium coccoides-Eubacterium rectale, Faecalibacterium prausnitzii and Roseburia intestinalis. This impact on the intestinal microbiota suggests that lupin seeds and broad beans may be used in the development of novel functional foods, which can be included in dietary strategies for human health promotion.

Broadband cross-polarization-based heteronuclear dipolar recoupling for structural and dynamic NMR studies of rigid and soft solids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kharkov, B. B.; Chizhik, V. I.; Dvinskikh, S. V., E-mail: sergeid@kth.se

2016-01-21

Dipolar recoupling is an essential part of current solid-state NMR methodology for probing atomic-resolution structure and dynamics in solids and soft matter. Recently described magic-echo amplitude- and phase-modulated cross-polarization heteronuclear recoupling strategy aims at efficient and robust recoupling in the entire range of coupling constants both in rigid and highly dynamic molecules. In the present study, the properties of this recoupling technique are investigated by theoretical analysis, spin-dynamics simulation, and experimentally. The resonance conditions and the efficiency of suppressing the rf field errors are examined and compared to those for other recoupling sequences based on similar principles. The experimental datamore » obtained in a variety of rigid and soft solids illustrate the scope of the method and corroborate the results of analytical and numerical calculations. The technique benefits from the dipolar resolution over a wider range of coupling constants compared to that in other state-of-the-art methods and thus is advantageous in studies of complex solids with a broad range of dynamic processes and molecular mobility degrees.« less

Introduction to focus issue: intrinsic and designed computation: information processing in dynamical systems--beyond the digital hegemony.

PubMed

Crutchfield, James P; Ditto, William L; Sinha, Sudeshna

2010-09-01

How dynamical systems store and process information is a fundamental question that touches a remarkably wide set of contemporary issues: from the breakdown of Moore's scaling laws--that predicted the inexorable improvement in digital circuitry--to basic philosophical problems of pattern in the natural world. It is a question that also returns one to the earliest days of the foundations of dynamical systems theory, probability theory, mathematical logic, communication theory, and theoretical computer science. We introduce the broad and rather eclectic set of articles in this Focus Issue that highlights a range of current challenges in computing and dynamical systems.

Calculations of the Performance of Explosive Impulse Generators

DTIC Science & Technology

1979-08-01

low impedance material such as lexan or some other plastic between the tungsten and the titanium, the stress is reduced even further. As we said...codes modeled after the HEMP family of codes^ cur- rently in use at the Lawrence Livermore Laboratory. The codes have a broad range of capabilities...for problems involving the dynamics of fluid and solid continua. They contain a full range of material property models including elastic- plastic flow

MDANSE: An Interactive Analysis Environment for Molecular Dynamics Simulations.

PubMed

Goret, G; Aoun, B; Pellegrini, E

2017-01-23

The MDANSE software-Molecular Dynamics Analysis of Neutron Scattering Experiments-is presented. It is an interactive application for postprocessing molecular dynamics (MD) simulations. Given the widespread use of MD simulations in material and biomolecular sciences to get a better insight for experimental techniques such as thermal neutron scattering (TNS), the development of MDANSE has focused on providing a user-friendly, interactive, graphical user interface for analyzing many trajectories in the same session and running several analyses simultaneously independently of the interface. This first version of MDANSE already proposes a broad range of analyses, and the application has been designed to facilitate the introduction of new analyses in the framework. All this makes MDANSE a valuable tool for extracting useful information from trajectories resulting from a wide range of MD codes.

Dynamics of a broad-band quantum cascade laser: from chaos to coherent dynamics and mode-locking

NASA Astrophysics Data System (ADS)

Columbo, L. L.; Barbieri, S.; Sirtori, C.; Brambilla, M.

2018-02-01

The dynamics of a multimode Quantum Cascade Laser, is studied in a model based on effective semiconductor Maxwell-Bloch equations, encompassing key features for the radiationmedium interaction such as an asymmetric, frequency dependent, gain and refractive index as well as the phase-amplitude coupling provided by the Henry factor. By considering the role of the free spectral range and Henry factor, we develop criteria suitable to identify the conditions which allow to destabilize, close to threshold, the traveling wave emitted by the laser and lead to chaotic or regular multimode dynamics. In the latter case our simulations show that the field oscillations are associated to self-confined structures which travel along the laser cavity, bridging mode-locking and solitary wave propagation. In addition, we show how a RF modulation of the bias current leads to active mode-locking yielding high-contrast, picosecond pulses. Our results compare well with recent experiments on broad-band THz-QCLs and may help understanding the conditions for the generation of ultrashort pulses and comb operation in Mid-IR and THz spectral regions

Dynamic microscopy of nanoscale cluster growth at the solid-liquid interface.

PubMed

Williamson, M J; Tromp, R M; Vereecken, P M; Hull, R; Ross, F M

2003-08-01

Dynamic processes at the solid-liquid interface are of key importance across broad areas of science and technology. Electrochemical deposition of copper, for example, is used for metallization in integrated circuits, and a detailed understanding of nucleation, growth and coalescence is essential in optimizing the final microstructure. Our understanding of processes at the solid-vapour interface has advanced tremendously over the past decade due to the routine availability of real-time, high-resolution imaging techniques yielding data that can be compared quantitatively with theory. However, the difficulty of studying the solid-liquid interface leaves our understanding of processes there less complete. Here we analyse dynamic observations--recorded in situ using a novel transmission electron microscopy technique--of the nucleation and growth of nanoscale copper clusters during electrodeposition. We follow in real time the evolution of individual clusters, and compare their development with simulations incorporating the basic physics of electrodeposition during the early stages of growth. The experimental technique developed here is applicable to a broad range of dynamic phenomena at the solid-liquid interface.

Long-Range Interactions Restrict Water Transport in Pyrophyllite Interlayers

DOE PAGES

Zarzycki, Piotr; Gilbert, Benjamin

2016-04-27

Water diffusion within smectite clay interlayers is reduced by confinement and hence is highly determined by the interlayer spacings that are adopted during swelling. However, a molecular understanding of the short-and long-range forces governing interlayer water structure and dynamics is lacking. Using molecular dynamics simulations of water intercalated between pyrophyllite (smectite prototype) layers we provide a detailed picture of the variation of interlayered water mobility accompanying smectite expansion. Subtle changes in hydrogen bond network structure cause significant changes in water mobility that is greater for stable hydration states and reduced for intermediate separations. By studying pyrophyllite with and without externalmore » water we reveal that long-range electrostatic forces apply a restraining effect upon interlayer water mobility. Our findings are relevant for broad range of confining nanostructures with walls thin enough to permit long-range interactions that could affect the mobility of confined solvent molecules and solute species.« less

Long-Range Interactions Restrict Water Transport in Pyrophyllite Interlayers

PubMed Central

Zarzycki, Piotr; Gilbert, Benjamin

2016-01-01

Water diffusion within smectite clay interlayers is reduced by confinement and hence is highly determined by the interlayer spacings that are adopted during swelling. However, a molecular understanding of the short- and long-range forces governing interlayer water structure and dynamics is lacking. Using molecular dynamics simulations of water intercalated between pyrophyllite (smectite prototype) layers we provide a detailed picture of the variation of interlayered water mobility accompanying smectite expansion. Subtle changes in hydrogen bond network structure cause significant changes in water mobility that is greater for stable hydration states and reduced for intermediate separations. By studying pyrophyllite with and without external water we reveal that long-range electrostatic forces apply a restraining effect upon interlayer water mobility. Our findings are relevant for broad range of confining nanostructures with walls thin enough to permit long-range interactions that could affect the mobility of confined solvent molecules and solute species. PMID:27118164

Determining landscape extent for succession and disturbance simulation modeling

Treesearch

Eva C. Karau; Robert E. Keane

2007-01-01

Dividing regions into manageable landscape units presents special problems in landscape ecology and land management. Ideally, a landscape should be large enough to capture a broad range of vegetation, environmental and disturbance dynamics, but small enough to be useful for focused management objectives. The purpose of this study was to determine the optimal landscape...

Temporal-contrast measurements of a white-light-seeded noncollinear optical parametric amplifier

DOE PAGES

Bromage, J.; Dorrer, C.; Zuegel, J. D.

2015-09-01

Ultra-intense optical parametric chirped-pulse systems require front ends with broad bandwidth and high temporal contrast. Temporal cross-correlation measurements of a white-light–seeded noncollinear optical parametric amplifier (NOPA) show that its prepulse contrast exceeds the 120 dB dynamic range of the broadband NOPA-based cross-correlator.

The Systemic Vision of the Educational Learning

ERIC Educational Resources Information Center

Lima, Nilton Cesar; Penedo, Antonio Sergio Torres; de Oliveira, Marcio Mattos Borges; de Oliveira, Sonia Valle Walter Borges; Queiroz, Jamerson Viegas

2012-01-01

As the sophistication of technology is increasing, also increased the demand for quality in education. The expectation for quality has promoted broad range of products and systems, including in education. These factors include the increased diversity in the student body, which requires greater emphasis that allows a simple and dynamic model in the…

Spatiotemporal variation in resource selection: Insights from the American marten (Martes Americana)

Treesearch

Andrew J. Shirk; Martin G. Raphael; Samuel A. Cushman

2014-01-01

Behavioral and genetic adaptations to spatiotemporal variation in habitat conditions allow species to maximize their biogeographic range and persist over time in dynamic environments. An understanding of these local adaptations can be used to guide management and conservation of populations over broad extents encompassing diverse habitats. This understanding is often...

Temporal Modulation of Stem Cell Activity Using Magnetoactive Hydrogels.

PubMed

Abdeen, Amr A; Lee, Junmin; Bharadwaj, N Ashwin; Ewoldt, Randy H; Kilian, Kristopher A

2016-10-01

Cell activity is coordinated by dynamic interactions with the extracellular matrix, often through stimuli-mediated spatiotemporal stiffening and softening. Dynamic changes in mechanics occur in vivo through enzymatic or chemical means, processes which are challenging to reconstruct in cell culture materials. Here a magnetoactive hydrogel material formed by embedding magnetic particles in a hydrogel matrix is presented whereby elasticity can be modulated reversibly by attenuation of a magnetic field. Orders of magnitude change in elasticity using low magnetic fields are shown and reversibility of stiffening with simple permanent magnets is demonstrated. The broad applicability of this technique is demonstrated with two therapeutically relevant bioactivities in mesenchymal stem cells: secretion of proangiogenic molecules, and dynamic control of osteogenesis. The ability to reversibly stiffen cell culture materials across the full spectrum of soft tissue mechanics, using simple materials and commercially available permanent magnets, makes this approach viable for a broad range of laboratory environments. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cardiorespiratory dynamics: sensitivity of the on-transition to endurance-training status.

PubMed

Taylor, N A; Osborne, M A; Bube, T L; Stocks, J M

1999-10-01

This project investigated the sensitivity of oxygen uptake (VO(2)) dynamics to training-induced physiological changes, across a broad spectrum of endurance-training histories. Forty subjects participated: sedentary (n = 10), active healthy (n = 10), regular runners (n = 10), and competitive distance runners (n = 10). Subjects completed a cycle step-function protocol, to elicit a steady state at 60% maximal work rate. Breath-by-breath data were collected for VO(2) and cardiac frequency (f(c)), and modelled mathematically, and used to determine the average response times to attain 20%, 40%, 60%, 80% and 100% of the respective steady states. The between-group comparisons for both VO(2) and f(c) revealed significantly faster response times to 40%, 60%, 80% and 100% of the induced response, for the better trained subjects (P < 0.05). In general, this technique permitted differentiation between the VO(2) and f(c) response dynamics of non-elite subjects from a broad range of endurance-training histories, with differences becoming more pronounced as subjects approached the steady state.

A molecular dynamics study of polymer/graphene interfacial systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rissanou, Anastassia N.; Harmandaris, Vagelis

2014-05-15

Graphene based polymer nanocomposites are hybrid materials with a very broad range of technological applications. In this work, we study three hybrid polymer/graphene interfacial systems (polystyrene/graphene, poly(methyl methacrylate)/graphene and polyethylene/graphene) through detailed atomistic molecular dynamics (MD) simulations. Density profiles, structural characteristics and mobility aspects are being examined at the molecular level for all model systems. In addition, we compare the properties of the hybrid systems to the properties of the corresponding bulk ones, as well as to theoretical predictions.

Dynamic modulus estimation and structural vibration analysis.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gupta, A.

1998-11-18

Often the dynamic elastic modulus of a material with frequency dependent properties is difficult to estimate. These uncertainties are compounded in any structural vibration analysis using the material properties. Here, different experimental techniques are used to estimate the properties of a particular elastomeric material over a broad frequency range. Once the properties are determined, various structures incorporating the elastomer are analyzed by an interactive finite element method to determine natural frequencies and mode shapes. Then, the finite element results are correlated with results obtained by experimental modal analysis.

Scaling behavior of immersed granular flows

NASA Astrophysics Data System (ADS)

Amarsid, L.; Delenne, J.-Y.; Mutabaruka, P.; Monerie, Y.; Perales, F.; Radjai, F.

2017-06-01

The shear behavior of granular materials immersed in a viscous fluid depends on fluid properties (viscosity, density), particle properties (size, density) and boundary conditions (shear rate, confining pressure). Using computational fluid dynamics simulations coupled with molecular dynamics for granular flow, and exploring a broad range of the values of parameters, we show that the parameter space can be reduced to a single parameter that controls the packing fraction and effective friction coefficient. This control parameter is a modified inertial number that incorporates viscous effects.

Proceedings of the U.S. Army Symposium on Gun Dynamics (5th) Held in Rensselaerville, New York on 23-25 September 1987

DTIC Science & Technology

1987-09-01

have shown that gun barrel heating, and hence thermal expansion , is both axially and circumferentially asymmetric. Circumferential, or cross-barrel...element code, which ended in the selection of ABAQUS . The code will perform static, dynamic, and thermal anal- ysis on a broad range of structures...analysis may be performed by a user supplied FORTRAN subroutine which is automatically linked to the code and supplements the stand- ard ABAQUS

Dynamic compression of synthetic diamond windows (final report for LDRD project 93531).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dolan, Daniel H.,

2008-09-01

Diamond is an attractive dynamic compression window for many reasons: high elastic limit,large mechanical impedance, and broad transparency range. Natural diamonds, however, aretoo expensive to be used in destructive experiments. Chemical vapor deposition techniquesare now able to produce large single-crystal windows, opening up many potential dynamiccompression applications. This project studied the behavior of synthetic diamond undershock wave compression. The results suggest that synthetic diamond could be a usefulwindow in this field, though complete characterization proved elusive.3

From theory to field experiments

NASA Astrophysics Data System (ADS)

de Vos, Bram

2016-04-01

Peter Raats' achievements in Haren (NL) 1986-1997 were based on a solid theoretical insight in hydrology and transport process in soil. However, Peter was also the driving force behind many experimental studies and applied research. This will be illustrated by a broad range of examples ranging from the dynamics of composting processes of organic material; modelling and monitoring nutrient leaching at field-scale; wind erosion; water and nutrient dynamics in horticultural production systems; oxygen diffusion in soils; and processes of water and nutrient uptake by plant roots. Peter's leadership led to may new approaches and the introduction of innovative measurement techniques in Dutch research; ranging from TDR to nutrient concentration measurements in closed fertigation systems. This presentation will give a brief overview how Peter's theoretical and mathematical insights accelerated this applied research.

The HelCat dual-source plasma device.

PubMed

Lynn, Alan G; Gilmore, Mark; Watts, Christopher; Herrea, Janis; Kelly, Ralph; Will, Steve; Xie, Shuangwei; Yan, Lincan; Zhang, Yue

2009-10-01

The HelCat (Helicon-Cathode) device has been constructed to support a broad range of basic plasma science experiments relevant to the areas of solar physics, laboratory astrophysics, plasma nonlinear dynamics, and turbulence. These research topics require a relatively large plasma source capable of operating over a broad region of parameter space with a plasma duration up to at least several milliseconds. To achieve these parameters a novel dual-source system was developed utilizing both helicon and thermionic cathode sources. Plasma parameters of n(e) approximately 0.5-50 x 10(18) m(-3) and T(e) approximately 3-12 eV allow access to a wide range of collisionalities important to the research. The HelCat device and initial characterization of plasma behavior during dual-source operation are described.

Broadband mid-infrared measurements for shock induced chemistry

NASA Astrophysics Data System (ADS)

McGrane, Shawn; Bowlan, Pamela; Brown, Kathryn; Bolme, Cynthia; Cawkwell, Marc

2017-06-01

Vibrational absorption spectroscopy across the mid-infrared range is a ubiquitous diagnostic of chemical effects due to its sensitivity to small variations in bonding. At the high temperatures and pressures relevant to shock induced chemistry, vibrational spectral peaks become very broad, and accessing as much spectral range as possible with high time resolution can significantly aid in deducing chemical dynamics. Here, we report experiments using broadband (<500 cm-1 to >2000 cm-1) mid-infrared femtosecond supercontinua created by four wave mixing in filaments to perform absorption spectroscopy. These broadband mid-infrared supercontinua are detected through upconversion to visible light. Initial efforts to utilize these methods for measurement of chemical dynamics in shocked nitromethane will be reported.

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids.

PubMed

Aradi, Bálint; Niklasson, Anders M N; Frauenheim, Thomas

2015-07-14

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. For systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can be applied to a broad range of problems in materials science, chemistry, and biology.

Using ultrashort terahertz pulses to directly probe spin dynamics in insulating antiferromagnets

NASA Astrophysics Data System (ADS)

Bowlan, P.; Trugman, S. A.; Yarotski, D. A.; Taylor, A. J.; Prasankumar, R. P.

2018-05-01

Terahertz pulses are a direct and general probe of ultrafast spin dynamics in insulating antiferromagnets (AFM). This is shown by using optical-pump, THz-probe spectroscopy to directly track AFM spin dynamics in the hexagonal multiferroic HoMnO3 and the orthorhombic multiferroic TbMnO3. Our studies show that despite the different structural and spin orders in these materials, THz pulses can unambiguously resolve spin dynamics after optical photoexcitation. We believe that this approach is quite general and can be applied to a broad range of materials with different AFM spin alignments, providing a novel non-contact approach for probing AFM order with femtosecond temporal resolution.

Unifying latitudinal gradients in range size and richness across marine and terrestrial systems

PubMed Central

Tomašových, Adam; Kennedy, Jonathan D.; Betzner, Tristan J.; Kuehnle, Nicole Bitler; Edie, Stewart; Kim, Sora; Supriya, K.; White, Alexander E.; Rahbek, Carsten; Huang, Shan; Price, Trevor D.; Jablonski, David

2016-01-01

Many marine and terrestrial clades show similar latitudinal gradients in species richness, but opposite gradients in range size—on land, ranges are the smallest in the tropics, whereas in the sea, ranges are the largest in the tropics. Therefore, richness gradients in marine and terrestrial systems do not arise from a shared latitudinal arrangement of species range sizes. Comparing terrestrial birds and marine bivalves, we find that gradients in range size are concordant at the level of genera. Here, both groups show a nested pattern in which narrow-ranging genera are confined to the tropics and broad-ranging genera extend across much of the gradient. We find that (i) genus range size and its variation with latitude is closely associated with per-genus species richness and (ii) broad-ranging genera contain more species both within and outside of the tropics when compared with tropical- or temperate-only genera. Within-genus species diversification thus promotes genus expansion to novel latitudes. Despite underlying differences in the species range-size gradients, species-rich genera are more likely to produce a descendant that extends its range relative to the ancestor's range. These results unify species richness gradients with those of genera, implying that birds and bivalves share similar latitudinal dynamics in net species diversification. PMID:27147094

Vespertilionid bats control the width of their biosonar sound beam dynamically during prey pursuit

PubMed Central

Jakobsen, Lasse; Surlykke, Annemarie

2010-01-01

Animals using sound for communication emit directional signals, focusing most acoustic energy in one direction. Echolocating bats are listening for soft echoes from insects. Therefore, a directional biosonar sound beam greatly increases detection probability in the forward direction and decreases off-axis echoes. However, high directionality has context-specific disadvantages: at close range the detection space will be vastly reduced, making a broad beam favorable. Hence, a flexible system would be very advantageous. We investigated whether bats can dynamically change directionality of their biosonar during aerial pursuit of insects. We trained five Myotis daubentonii and one Eptesicus serotinus to capture tethered mealworms and recorded their echolocation signals with a multimicrophone array. The results show that the bats broaden the echolocation beam drastically in the terminal phase of prey pursuit. M. daubentonii increased the half-amplitude angle from approximately 40° to approximately 90° horizontally and from approximately 45° to more than 90° vertically. The increase in beam width is achieved by lowering the frequency by roughly one octave from approximately 55 kHz to approximately 27.5 kHz. The E. serotinus showed beam broadening remarkably similar to that of M. daubentonii. Our results demonstrate dynamic control of beam width in both species. Hence, we propose directionality as an explanation for the frequency decrease observed in the buzz of aerial hawking vespertilionid bats. We predict that future studies will reveal dynamic control of beam width in a broad range of acoustically communicating animals. PMID:20643943

Vespertilionid bats control the width of their biosonar sound beam dynamically during prey pursuit.

PubMed

Jakobsen, Lasse; Surlykke, Annemarie

2010-08-03

Animals using sound for communication emit directional signals, focusing most acoustic energy in one direction. Echolocating bats are listening for soft echoes from insects. Therefore, a directional biosonar sound beam greatly increases detection probability in the forward direction and decreases off-axis echoes. However, high directionality has context-specific disadvantages: at close range the detection space will be vastly reduced, making a broad beam favorable. Hence, a flexible system would be very advantageous. We investigated whether bats can dynamically change directionality of their biosonar during aerial pursuit of insects. We trained five Myotis daubentonii and one Eptesicus serotinus to capture tethered mealworms and recorded their echolocation signals with a multimicrophone array. The results show that the bats broaden the echolocation beam drastically in the terminal phase of prey pursuit. M. daubentonii increased the half-amplitude angle from approximately 40 degrees to approximately 90 degrees horizontally and from approximately 45 degrees to more than 90 degrees vertically. The increase in beam width is achieved by lowering the frequency by roughly one octave from approximately 55 kHz to approximately 27.5 kHz. The E. serotinus showed beam broadening remarkably similar to that of M. daubentonii. Our results demonstrate dynamic control of beam width in both species. Hence, we propose directionality as an explanation for the frequency decrease observed in the buzz of aerial hawking vespertilionid bats. We predict that future studies will reveal dynamic control of beam width in a broad range of acoustically communicating animals.

Fire on the mountain: birds and burns in the Rocky Mountains

Treesearch

Natasha B. Kotliar; Victoria A. Saab; Richard L. Hutto

2005-01-01

The diversity of climate and topography across the Rocky Mountains has resulted in a broad spectrum of fire regimes ranging from frequent, low-severity fires to infrequent stand-replacement events. Such variation in fire history contributes to landscape structure and dynamics, and in turn can influence subsequent fire behavior (Allen et al. 2002). In essence,...

Reduction of soluble nitrogen and mobilization of plant nutrients in soils from U.S. northern Great Plains agroecosystems by phenolic compounds

USDA-ARS?s Scientific Manuscript database

Phenolic plant secondary metabolites actively participate in a broad range of important reactions that affect livestock, plants and soil. In soil, phenolic compounds can affect nutrient dynamics and mobility of metals but their role in northern Great Plains agroecosystems is largely unknown. We eval...

Microclimate predicts within-season distribution dynamics of montane forest birds

Treesearch

Sarah J.K. Frey; Adam S. Hadley; Matthew G. Betts; Mark Robertson

2016-01-01

Aim: Climate changes are anticipated to have pervasive negative effects on biodiversity and are expected to necessitate widespread range shifts or contractions. Such projections are based upon the assumptions that (1) species respond primarily to broad-scale climatic regimes, or (2) that variation in climate at fine spatial scales is less relevant at coarse spatial...

FMR-driven spin pumping in Y3Fe5O12-based structures

NASA Astrophysics Data System (ADS)

Yang, Fengyuan; Hammel, P. Chris

2018-06-01

Ferromagnetic resonance driven spin pumping, a topic of steadily increasing interest since its emergence over two decades ago, remains one of the most exciting research fields in condensed matter physics. Among the many materials that have been explored for spin pumping, yttrium iron garnet (YIG) is one of the most extensively studied because of its exceptionally low magnetic damping and insulating nature. There is a great amount of literature in the spin pumping and related research fields, too broad for this review to cover. In this Topical Review, we focus on the YIG-based spin pumping results carried out by our groups, including: the mechanism and technical details of our off-axis sputtering technique for the growth of single-crystalline YIG epitaxial films with a high degree ordering, experimental evidence for the high quality of the YIG films, spin pumping results from YIG into various transition metals and their heterostructures, dynamic spin transport in YIG/antiferromagnet hybrid structures, intralayer spin pumping by localized spin wave modes confined by a micromagnetic probe, dynamic spin coupling between YIG and nitrogen-vacancy centers in diamond, parametric spin pumping from high-wavevector spin waves in YIG, and localized spin wave mode behavior in broadly tunable spatially complex magnetic configurations. These results build on the power and versatility of YIG spin pumping to improve our understanding of spin dynamics, spin currents, spin Hall physics, spin–orbit coupling, dynamic magnetic coupling, and the relationship between these phenomena in a broad range of materials, geometries, and settings.

Hierarchical coarse-graining model for photosystem II including electron and excitation-energy transfer processes.

PubMed

Matsuoka, Takeshi; Tanaka, Shigenori; Ebina, Kuniyoshi

2014-03-01

We propose a hierarchical reduction scheme to cope with coupled rate equations that describe the dynamics of multi-time-scale photosynthetic reactions. To numerically solve nonlinear dynamical equations containing a wide temporal range of rate constants, we first study a prototypical three-variable model. Using a separation of the time scale of rate constants combined with identified slow variables as (quasi-)conserved quantities in the fast process, we achieve a coarse-graining of the dynamical equations reduced to those at a slower time scale. By iteratively employing this reduction method, the coarse-graining of broadly multi-scale dynamical equations can be performed in a hierarchical manner. We then apply this scheme to the reaction dynamics analysis of a simplified model for an illuminated photosystem II, which involves many processes of electron and excitation-energy transfers with a wide range of rate constants. We thus confirm a good agreement between the coarse-grained and fully (finely) integrated results for the population dynamics. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Auditory expectation: the information dynamics of music perception and cognition.

PubMed

Pearce, Marcus T; Wiggins, Geraint A

2012-10-01

Following in a psychological and musicological tradition beginning with Leonard Meyer, and continuing through David Huron, we present a functional, cognitive account of the phenomenon of expectation in music, grounded in computational, probabilistic modeling. We summarize a range of evidence for this approach, from psychology, neuroscience, musicology, linguistics, and creativity studies, and argue that simulating expectation is an important part of understanding a broad range of human faculties, in music and beyond. Copyright © 2012 Cognitive Science Society, Inc.

Technical Competencies Applied in Experimental Fluid Dynamics

NASA Astrophysics Data System (ADS)

Tagg, Randall

2017-11-01

The practical design, construction, and operation of fluid dynamics experiments require a broad range of competencies. Three types are instrumental, procedural, and design. Respective examples would be operation of a spectrum analyzer, soft-soldering or brazing flow plumbing, and design of a small wind tunnel. Some competencies, such as the selection and installation of pumping systems, are unique to fluid dynamics and fluids engineering. Others, such as the design and construction of electronic amplifiers or optical imaging systems, overlap with other fields. Thus the identification and development of learning materials and methods for instruction are part of a larger effort to identify competencies needed in active research and technical innovation.

Demodulation System for Fiber Optic Bragg Grating Dynamic Pressure Sensing

NASA Technical Reports Server (NTRS)

Lekki, John D.; Adamovsky, Grigory; Floyd, Bertram

2001-01-01

Fiber optic Bragg gratings have been used for years to measure quasi-static phenomena. In aircraft engine applications there is a need to measure dynamic signals such as variable pressures. In order to monitor these pressures a detection system with broad dynamic range is needed. This paper describes an interferometric demodulator that was developed and optimized for this particular application. The signal to noise ratio was maximized through temporal coherence analysis. The demodulator was incorporated in a laboratory system that simulates conditions to be measured. Several pressure sensor configurations incorporating a fiber optic Bragg grating were also explored. The results of the experiments are reported in this paper.

Dynamics of a broad-band quantum cascade laser: from chaos to coherent dynamics and mode-locking.

PubMed

Columbo, L L; Barbieri, S; Sirtori, C; Brambilla, M

2018-02-05

The dynamics of a multimode quantum cascade laser, are studied in a model based on effective semiconductor Maxwell-Bloch equations, encompassing key features for the radiation-medium interaction such as an asymmetric frequency dependent gain and refractive index as well as the phase-amplitude coupling provided by the linewidth enhancement factor. By considering its role and that of the free spectral range, we find the conditions in which the traveling wave emitted by the laser at the threshold can be destabilized by adjacent modes, thus leading the laser emission towards chaotic or regular multimode dynamics. In the latter case our simulations show that the field oscillations are associated to self-confined structures which travel along the laser cavity, bridging mode-locking and solitary wave propagation. In addition, we show how a RF modulation of the bias current leads to active mode-locking yielding high-contrast, picosecond pulses. Our results compare well with recent experiments on broad-band THz-QCLs and may help in the understanding of the conditions for the generation of ultrashort pulses and comb operation in mid-IR and THz spectral regions.

NMR contributions to structural dynamics studies of intrinsically disordered proteins☆

PubMed Central

Konrat, Robert

2014-01-01

Intrinsically disordered proteins (IDPs) are characterized by substantial conformational plasticity. Given their inherent structural flexibility X-ray crystallography is not applicable to study these proteins. In contrast, NMR spectroscopy offers unique opportunities for structural and dynamic studies of IDPs. The past two decades have witnessed significant development of NMR spectroscopy that couples advances in spin physics and chemistry with a broad range of applications. This article will summarize key advances in basic physical-chemistry and NMR methodology, outline their limitations and envision future R&D directions. PMID:24656082

Why interdisciplinary research enriches the study of crime. Comment on "Statistical physics of crime: A review" by M.R. D'Orsogna and M. Perc

NASA Astrophysics Data System (ADS)

Donnay, Karsten

2015-03-01

The past several years have seen a rapidly growing interest in the use of advanced quantitative methodologies and formalisms adapted from the natural sciences to study a broad range of social phenomena. The research field of computational social science [1,2], for example, uses digital artifacts of human online activity to cast a new light on social dynamics. Similarly, the studies reviewed by D'Orsogna and Perc showcase a diverse set of advanced quantitative techniques to study the dynamics of crime. Methods used range from partial differential equations and self-exciting point processes to agent-based models, evolutionary game theory and network science [3].

Dynamical systems model and discrete element simulations of a tapped granular column

NASA Astrophysics Data System (ADS)

Rosato, A. D.; Blackmore, D.; Tricoche, X. M.; Urban, K.; Zuo, L.

2013-06-01

We present an approximate dynamical systems model for the mass center trajectory of a tapped column of N uniform, inelastic, spheres (diameter d), in which collisional energy loss is governed by the Walton-Braun linear loading-unloading soft interaction. Rigorous analysis of the model, akin to the equations for the motion of a single bouncing ball on a vibrating plate, reveals a parameter γ≔2aω2(1+e)/g that gauges the dynamical regimes and their transitions. In particular, we find bifurcations from periodic to chaotic dynamics that depend on frequency ω, amplitude a/d of the tap. Dynamics predicted by the model are also qualitatively observed in discrete element simulations carried out over a broad range of the tap parameters.

The fluid dynamics of atmospheric clouds

NASA Astrophysics Data System (ADS)

Randall, David A.

2017-11-01

Clouds of many types are of leading-order importance for Earth's weather and climate. This importance is most often discussed in terms of the effects of clouds on radiative transfer, but the fluid dynamics of clouds are at least equally significant. Some very small-scale cloud fluid-dynamical processes have significant consequences on the global scale. These include viscous dissipation near falling rain drops, and ``buoyancy reversal'' associated with the evaporation of liquid water. Major medium-scale cloud fluid-dynamical processes include cumulus convection and convective aggregation. Planetary-scale processes that depend in an essential way on cloud fluid dynamics include the Madden-Julian Oscillation, which is one of the largest and most consequential weather systems on Earth. I will attempt to give a coherent introductory overview of this broad range of phenomena.

Quantitative mass imaging of single biological macromolecules.

PubMed

Young, Gavin; Hundt, Nikolas; Cole, Daniel; Fineberg, Adam; Andrecka, Joanna; Tyler, Andrew; Olerinyova, Anna; Ansari, Ayla; Marklund, Erik G; Collier, Miranda P; Chandler, Shane A; Tkachenko, Olga; Allen, Joel; Crispin, Max; Billington, Neil; Takagi, Yasuharu; Sellers, James R; Eichmann, Cédric; Selenko, Philipp; Frey, Lukas; Riek, Roland; Galpin, Martin R; Struwe, Weston B; Benesch, Justin L P; Kukura, Philipp

2018-04-27

The cellular processes underpinning life are orchestrated by proteins and their interactions. The associated structural and dynamic heterogeneity, despite being key to function, poses a fundamental challenge to existing analytical and structural methodologies. We used interferometric scattering microscopy to quantify the mass of single biomolecules in solution with 2% sequence mass accuracy, up to 19-kilodalton resolution, and 1-kilodalton precision. We resolved oligomeric distributions at high dynamic range, detected small-molecule binding, and mass-imaged proteins with associated lipids and sugars. These capabilities enabled us to characterize the molecular dynamics of processes as diverse as glycoprotein cross-linking, amyloidogenic protein aggregation, and actin polymerization. Interferometric scattering mass spectrometry allows spatiotemporally resolved measurement of a broad range of biomolecular interactions, one molecule at a time. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Counter-ions dynamics in highly plastic and conducting compounds of poly(aniline). A quasi-elastic neutron scattering study.

PubMed

Djurado, David; Bée, Marc; Sniechowski, Maciej; Howells, Spencer; Rannou, Patrice; Pron, Adam; Travers, J P; Luzny, Wojciech

2005-03-21

Proton dynamics in films of poly(aniline) "plastdoped" with di-esters of sulfophthalic (or sulfosuccinic) acids have been investigated by using quasi-elastic neutron scattering techniques. A broad time range (10(-13)-10(-9) s) has been explored by using four different spectrometers. In this time range, the dynamics is exclusively due to protons attached to the flexible tails of the counter-ions. A model of limited diffusion in spheres whose radii are distributed in size gives a realistic view of the geometry of molecular motions. However, it is found that the characteristic times of these motions are widely distributed over several orders of magnitude. The time decay of the intermediate scattering function is well described by a time power law. This behaviour is qualitatively discussed in connection with the structure of the systems and by comparison with other so-called complex systems.

Components of spatial and temporal soil variation at Canyonlands National Park: Implications for P dynamics and cheatgrass (Bromus tectorum) performance

Treesearch

Mark Miller; Jayne Belnap; Susan Beatty; Bruce Webb

2001-01-01

From January 1997 through October 1998, research was conducted at Canyonlands National Park to investigate soil traits responsible for distinct spatial patterns of cheatgrass (Bromus tectorum) occurrence. Field experiments were conducted at sites representing a broad range of soil conditions and cheatgrass abundances. Standard physicochemical soil measures in...

Revisiting the Americas: Teaching and Learning the Geography of the Western Hemisphere. Pathways in Geography Series, Title No. 4.

ERIC Educational Resources Information Center

Martinson, Tom, Ed.; Brooker-Gross, Susan, Ed.

This book, issued in observance of the Columbus Quincentennial and on the occasion of the 27th International Geographical Congress, addresses a broad range of contemporary topics including environmental change, dynamics of the world economy, human needs, wants and rights, political order and change, and contemporary cultures. The format is one of…

Water dynamics in rigid ionomer networks.

PubMed

Osti, N C; Etampawala, T N; Shrestha, U M; Aryal, D; Tyagi, M; Diallo, S O; Mamontov, E; Cornelius, C J; Perahia, D

2016-12-14

The dynamics of water within ionic polymer networks formed by sulfonated poly(phenylene) (SPP), as revealed by quasi-elastic neutron scattering (QENS), is presented. These polymers are distinguished from other ionic macromolecules by their rigidity and therefore in their network structure. QENS measurements as a function of temperature as the fraction of ionic groups and humidity were varied have shown that the polymer molecules are immobile while absorbed water molecules remain dynamic. The water molecules occupy multiple sites, either bound or loosely constrained, and bounce between the two. With increasing temperature and hydration levels, the system becomes more dynamic. Water molecules remain mobile even at subzero temperatures, illustrating the applicability of the SPP membrane for selective transport over a broad temperature range.

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materialsmore » science, chemistry, and biology.« less

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

DOE PAGES

Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

2015-06-26

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materialsmore » science, chemistry, and biology.« less

Microbial Nanoculture as an Artificial Microniche

NASA Astrophysics Data System (ADS)

Niepa, Tagbo H. R.; Hou, Likai; Jiang, Hongyuan; Goulian, Mark; Koo, Hyun; Stebe, Kathleen J.; Lee, Daeyeon

2016-08-01

Microbes self-organize in microcolonies while transitioning to a sessile form within a protective biofilm matrix. To enable the detailed study of microbial dynamics within these microcolonies, new sessile culture systems are needed that sequester cells and mimic their complex growth conditions and interactions. We present a new nanoliter-scale sessile culture system that is easily implemented via microfluidics-enabled fabrication. Hundreds of thousands of these nanocultures can be easily generated and imaged using conventional or confocal microscopy. Each nanoculture begins as a several nanoliter droplet of suspended cells, encapsulated by a polydimethylsiloxane (PDMS) membrane. The PDMS shell provides long-lasting mechanical support, enabling long term study, and is selectively permeable to small molecules including antibiotics, signaling molecules and functional fluorescent probes. Thus, as microcolonies mature within the nanocultures, they can be stressed or interrogated using selected probes to characterize cell physiological properties, antibiotic susceptibilities, and antagonistic interactions. We demonstrate this platform by investigating broad ranges of microcolony dynamics, including direct and indirect bacterial-fungal interactions. This versatile new tool has broad potential for addressing biological questions associated with drug resistance, chronic infections, microbiome dynamics, and antibiotic discovery.

Microbial Nanoculture as an Artificial Microniche

PubMed Central

Niepa, Tagbo H. R.; Hou, Likai; Jiang, Hongyuan; Goulian, Mark; Koo, Hyun; Stebe, Kathleen J.; Lee, Daeyeon

2016-01-01

Microbes self-organize in microcolonies while transitioning to a sessile form within a protective biofilm matrix. To enable the detailed study of microbial dynamics within these microcolonies, new sessile culture systems are needed that sequester cells and mimic their complex growth conditions and interactions. We present a new nanoliter-scale sessile culture system that is easily implemented via microfluidics-enabled fabrication. Hundreds of thousands of these nanocultures can be easily generated and imaged using conventional or confocal microscopy. Each nanoculture begins as a several nanoliter droplet of suspended cells, encapsulated by a polydimethylsiloxane (PDMS) membrane. The PDMS shell provides long-lasting mechanical support, enabling long term study, and is selectively permeable to small molecules including antibiotics, signaling molecules and functional fluorescent probes. Thus, as microcolonies mature within the nanocultures, they can be stressed or interrogated using selected probes to characterize cell physiological properties, antibiotic susceptibilities, and antagonistic interactions. We demonstrate this platform by investigating broad ranges of microcolony dynamics, including direct and indirect bacterial-fungal interactions. This versatile new tool has broad potential for addressing biological questions associated with drug resistance, chronic infections, microbiome dynamics, and antibiotic discovery. PMID:27476816

Microbial Nanoculture as an Artificial Microniche.

PubMed

Niepa, Tagbo H R; Hou, Likai; Jiang, Hongyuan; Goulian, Mark; Koo, Hyun; Stebe, Kathleen J; Lee, Daeyeon

2016-08-01

Microbes self-organize in microcolonies while transitioning to a sessile form within a protective biofilm matrix. To enable the detailed study of microbial dynamics within these microcolonies, new sessile culture systems are needed that sequester cells and mimic their complex growth conditions and interactions. We present a new nanoliter-scale sessile culture system that is easily implemented via microfluidics-enabled fabrication. Hundreds of thousands of these nanocultures can be easily generated and imaged using conventional or confocal microscopy. Each nanoculture begins as a several nanoliter droplet of suspended cells, encapsulated by a polydimethylsiloxane (PDMS) membrane. The PDMS shell provides long-lasting mechanical support, enabling long term study, and is selectively permeable to small molecules including antibiotics, signaling molecules and functional fluorescent probes. Thus, as microcolonies mature within the nanocultures, they can be stressed or interrogated using selected probes to characterize cell physiological properties, antibiotic susceptibilities, and antagonistic interactions. We demonstrate this platform by investigating broad ranges of microcolony dynamics, including direct and indirect bacterial-fungal interactions. This versatile new tool has broad potential for addressing biological questions associated with drug resistance, chronic infections, microbiome dynamics, and antibiotic discovery.

The origin of ultra diffuse galaxies: stellar feedback and quenching

NASA Astrophysics Data System (ADS)

Chan, T. K.; Kereš, D.; Wetzel, A.; Hopkins, P. F.; Faucher-Giguère, C.-A.; El-Badry, K.; Garrison-Kimmel, S.; Boylan-Kolchin, M.

2018-05-01

We test if the cosmological zoom-in simulations of isolated galaxies from the FIRE project reproduce the properties of ultra diffuse galaxies (UDGs). We show that outflows that dynamically heat galactic stars, together with a passively aging stellar population after imposed quenching, naturally reproduce the observed population of red UDGs, without the need for high spin halos, or dynamical influence from their host cluster. We reproduce the range of surface brightness, radius and absolute magnitude of the observed red UDGs by quenching simulated galaxies at a range of different times. They represent a mostly uniform population of dark matter-dominated dwarf galaxies with M* ˜ 108 M⊙, low metallicity and a broad range of ages; the more massive the UDGs, the older they are. The most massive red UDG in our sample (M* ˜ 3 × 108M⊙) requires quenching at z ˜ 3 when its halo reached Mh ˜ 1011 M⊙. Our simulated UDGs form with normal stellar-to-halo ratios and match the central enclosed masses and the velocity dispersions of the observed UDGs. Enclosed masses remain largely fixed across a broad range of quenching times because the central regions of their dark matter halos complete their growth early. If our simulated dwarfs are not quenched, they evolve into bluer low-surface brightness galaxies with M/L similar to observed field dwarfs. While our simulation sample covers a limited range of formation histories and halo masses, we predict that UDG is a common, and perhaps even dominant, galaxy type around M* ˜ 108 M⊙, both in the field and in clusters.

The origin of ultra diffuse galaxies: stellar feedback and quenching

NASA Astrophysics Data System (ADS)

Chan, T. K.; Kereš, D.; Wetzel, A.; Hopkins, P. F.; Faucher-Giguère, C.-A.; El-Badry, K.; Garrison-Kimmel, S.; Boylan-Kolchin, M.

2018-07-01

We test if the cosmological zoom-in simulations of isolated galaxies from the FIRE project reproduce the properties of ultra diffuse galaxies (UDGs). We show that outflows that dynamically heat galactic stars, together with a passively aging stellar population after imposed quenching, naturally reproduce the observed population of red UDGs, without the need for high spin haloes, or dynamical influence from their host cluster. We reproduce the range of surface brightness, radius, and absolute magnitude of the observed red UDGs by quenching simulated galaxies at a range of different times. They represent a mostly uniform population of dark matter-dominated dwarf galaxies with M* ˜ 108 M⊙, low metallicity, and a broad range of ages; the more massive the UDGs, the older they are. The most massive red UDG in our sample (M* ˜ 3 × 108 M⊙) requires quenching at z ˜ 3 when its halo reached Mh ˜ 1011 M⊙. Our simulated UDGs form with normal stellar-to-halo ratios and match the central enclosed masses and the velocity dispersions of the observed UDGs. Enclosed masses remain largely fixed across a broad range of quenching times because the central regions of their dark matter haloes complete their growth early. If our simulated dwarfs are not quenched, they evolve into bluer low surface brightness galaxies with M/L similar to observed field dwarfs. While our simulation sample covers a limited range of formation histories and halo masses, we predict that UDG is a common, and perhaps even dominant, galaxy type around M* ˜ 108 M⊙, both in the field and in clusters.

Heterogeneous Nature of Relaxation Dynamics of Room-Temperature Ionic Liquids (EMIm) 2[Co(NCS) 4] and (BMIm) 2[Co(NCS) 4

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hensel-Bielowka, Stella; Wojnarowska, Zaneta; Dzida, Marzena

2015-08-11

Dynamic crossover above T g has been recognized as a characteristic feature of molecular dynamics of liquids approaching glass transition. Experimentally, it is manifested as a change in Vogel–Fulcher–Tammann dependence or a breakdown of the Stokes–Einstein and related relations. In this study, we report the exception from this rather general pattern of behavior. By means of dielectric, ultrasonic, rheological, and calorimetric methods, dynamics of two good ionic conductors (BMIm) 2[Co(NCS) 4] and (EMIm) 2[Co(NCS) 4] of less common stoichiometry (2:1) was studied in a very broad temperature range. However, none of the mentioned dynamic changes was observed in the entiremore » studied temperature range. On the contrary, the single VFT and the same fractional Walden coefficient were found for conductivity and viscosity changes over 12 decades. Finally and moreover, ultrasonic studies revealed that the data at temperatures which cover the normal liquid region cannot be fitted by a single exponential decay, and the Cole–Cole function should be used instead.« less

Heterogeneous nature of relaxation dynamics of room-temperature ionic liquids (EMIm) 2[Co(NCS) 4] and (BMIm) 2[Co(NCS) 4

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hensel-Bielowka, Stella; Wojnarowska, Zaneta E.; Dzida, Marzena

2015-08-11

Dynamic crossover above T g has been recognized as a characteristic feature of molecular dynamics of liquids approaching glass transition. Experimentally, it is manifested as a change in Vogel Fulcher Tammann dependence or a breakdown of the Stokes Einstein and related relations. In this paper, we report the exception from this rather general pattern of behavior. By means of dielectric, ultrasonic, rheological, and calorimetric methods, dynamics of two good ionic conductors (BMIm) 2[Co(NCS) 4] and (EMIm) 2[Co(NCS) 4] of less common stoichiometry (2:1) was studied in a very broad temperature range. However, none of the mentioned dynamic changes was observedmore » in the entire studied temperature range. On the contrary, the single VFT and the same fractional Walden coefficient were found for conductivity and viscosity changes over 12 decades. Furthermore, ultrasonic studies revealed that the data at temperatures which cover the normal liquid region cannot be fitted by a single exponential decay, and the Cole Cole function should be used instead.« less

Tunable meta-atom using liquid metal embedded in stretchable polymer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Peng; Yang, Siming; Wang, Qiugu

2015-07-07

Reconfigurable metamaterials have great potential to alleviate complications involved in using passive metamaterials to realize emerging electromagnetic functions, such as dynamical filtering, sensing, and cloaking. This paper presents a new type of tunable meta-atoms in the X-band frequency range (8–12 GHz) toward reconfigurable metamaterials. The meta-atom is made of all flexible materials compliant to the surface of an interaction object. It uses a liquid metal-based split-ring resonator as its core constituent embedded in a highly flexible elastomer. We demonstrate that simple mechanical stretching of the meta-atom can lead to the great flexibility in reconfiguring its resonance frequency continuously over moremore » than 70% of the X-band frequency range. The presented meta-atom technique provides a simple approach to dynamically tune response characteristics of metamaterials over a broad frequency range.« less

Water Dynamics in the Hydration Shells of Biomolecules

PubMed Central

2017-01-01

The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water. PMID:28248491

Molecular dynamics studies of polyurethane nanocomposite hydrogels

NASA Astrophysics Data System (ADS)

Strankowska, J.; Piszczyk, Ł.; Strankowski, M.; Danowska, M.; Szutkowski, K.; Jurga, S.; Kwela, J.

2013-10-01

Polyurethane PEO-based hydrogels have a broad range of biomedical applicability. They are attractive for drug-controlled delivery systems, surgical implants and wound healing dressings. In this study, a PEO based polyurethane hydrogels containing Cloisite® 30B, an organically modified clay mineral, was synthesized. Structure of nanocomposite hydrogels was determined using XRD technique. Its molecular dynamics was studied by means of NMR spectroscopy, DMA and DSC analysis. The mechanical properties and thermal stability of the systems were improved by incorporation of clay and controlled by varying the clay content in polymeric matrix. Molecular dynamics of polymer chains depends on interaction of Cloisite® 30B nanoparticles with soft segments of polyurethanes. The characteristic nanosize effect is observed.

Fluctuations of global energy release and crackling in nominally brittle heterogeneous fracture.

PubMed

Barés, J; Hattali, M L; Dalmas, D; Bonamy, D

2014-12-31

The temporal evolution of mechanical energy and spatially averaged crack speed are both monitored in slowly fracturing artificial rocks. Both signals display an irregular burstlike dynamics, with power-law distributed fluctuations spanning a broad range of scales. Yet, the elastic power released at each time step is proportional to the global velocity all along the process, which enables defining a material-constant fracture energy. We characterize the intermittent dynamics by computing the burst statistics. This latter displays the scale-free features signature of crackling dynamics, in qualitative but not quantitative agreement with the depinning interface models derived for fracture problems. The possible sources of discrepancies are pointed out and discussed.

Competition-Driven Network Dynamics: Emergence of a Scale-Free Leadership Structure and Collective Efficiency

NASA Astrophysics Data System (ADS)

Anghel, M.; Toroczkai, Zoltán; Bassler, Kevin E.; Korniss, G.

2004-02-01

Using the minority game as a model for competition dynamics, we investigate the effects of interagent communications across a network on the global evolution of the game. Agent communication across this network leads to the formation of an influence network, which is dynamically coupled to the evolution of the game, and it is responsible for the information flow driving the agents' actions. We show that the influence network spontaneously develops hubs with a broad distribution of in-degrees, defining a scale-free robust leadership structure. Furthermore, in realistic parameter ranges, facilitated by information exchange on the network, agents can generate a high degree of cooperation making the collective almost maximally efficient.

Transonic aerodynamic design experience

NASA Technical Reports Server (NTRS)

Bonner, E.

1989-01-01

Advancements have occurred in transonic numerical simulation that place aerodynamic performance design into a relatively well developed status. Efficient broad band operating characteristics can be reliably developed at the conceptual design level. Recent aeroelastic and separated flow simulation results indicate that systematic consideration of an increased range of design problems appears promising. This emerging capability addresses static and dynamic structural/aerodynamic coupling and nonlinearities associated with viscous dominated flows.

Waves and instability in the atmosphere of Mars: NASA planetary atmospheres program

NASA Technical Reports Server (NTRS)

Barnes, Jeffrey R.

1990-01-01

A broad range of phenomena were addressed by the study including the following: (1) polar warming; (2) forced stationary waves; (3) gravity waves; (4) transient baroclinic eddies; and (5) radiative-dynamical instabilities. A variety of numerical models have been employed in these studies, as well as analytical approaches. Some of the most significant results from this work are very briefly summarized.

Far-IR transparency and dynamic infrared signature control with novel conducting polymer systems

NASA Astrophysics Data System (ADS)

Chandrasekhar, Prasanna; Dooley, T. J.

1995-09-01

Materials which possess transparency, coupled with active controllability of this transparency in the infrared (IR), are today an increasingly important requirement, for varied applications. These applications include windows for IR sensors, IR-region flat panel displays used in camouflage as well as in communication and sight through night-vision goggles, coatings with dynamically controllable IR-emissivity, and thermal conservation coatings. Among stringent requirements for these applications are large dynamic ranges (color contrast), 'multi-color' or broad-band characteristics, extended cyclability, long memory retention, matrix addressability, small area fabricability, low power consumption, and environmental stability. Among materials possessing the requirements for variation of IR signature, conducting polymers (CPs) appear to be the only materials with dynamic, actively controllable signature and acceptable dynamic range. Conventional CPs such as poly(alkyl thiophene), poly(pyrrole) or poly(aniline) show very limited dynamic range, especially in the far-IR, while also showing poor transparency. We have developed a number of novel CP systems ('system' implying the CP, the selected dopant, the synthesis method, and the electrolyte) with very wide dynamic range (up to 90% in both important IR regions, 3 - 5 (mu) and 8 - 12 (mu) ), high cyclability (to 105 cycles with less than 10% optical degradation), nearly indefinite optical memory retention, matrix addressability of multi-pixel displays, very wide operating temperature and excellent environmental stability, low charge capacity, and processability into areas from less than 1 mm2 to more than 100 cm2. The criteria used to design and arrive at these CP systems, together with representative IR signature data, are presented in this paper.

Communication: Microsecond dynamics of the protein and water affect electron transfer in a bacterial bc1 complex

NASA Astrophysics Data System (ADS)

Martin, Daniel R.; Matyushov, Dmitry V.

2015-04-01

Cross-membrane electron transport between cofactors localized in proteins of mitochondrial respiration and bacterial photosynthesis is the source of all biological energy. The statistics and dynamics of nuclear fluctuations in these protein/membrane/water heterogeneous systems are critical for their energetic efficiency. The results of 13 μs of atomistic molecular dynamics simulations of the membrane-bound bc1 bacterial complex are analyzed here. The reaction is affected by a broad spectrum of nuclear modes, with the slowest dynamics in the range of time-scales ˜0.1-1.6 μs contributing half of the reaction reorganization energy. Two reorganization energies are required to describe protein electron transfer due to dynamical arrest of protein conformations on the observation window. This mechanistic distinction allows significant lowering of activation barriers for reactions in proteins.

Homeostatic enhancement of sensory transduction

PubMed Central

Milewski, Andrew R.; Ó Maoiléidigh, Dáibhid; Salvi, Joshua D.; Hudspeth, A. J.

2017-01-01

Our sense of hearing boasts exquisite sensitivity, precise frequency discrimination, and a broad dynamic range. Experiments and modeling imply, however, that the auditory system achieves this performance for only a narrow range of parameter values. Small changes in these values could compromise hair cells’ ability to detect stimuli. We propose that, rather than exerting tight control over parameters, the auditory system uses a homeostatic mechanism that increases the robustness of its operation to variation in parameter values. To slowly adjust the response to sinusoidal stimulation, the homeostatic mechanism feeds back a rectified version of the hair bundle’s displacement to its adaptation process. When homeostasis is enforced, the range of parameter values for which the sensitivity, tuning sharpness, and dynamic range exceed specified thresholds can increase by more than an order of magnitude. Signatures in the hair cell’s behavior provide a means to determine through experiment whether such a mechanism operates in the auditory system. Robustness of function through homeostasis may be ensured in any system through mechanisms similar to those that we describe here. PMID:28760949

Integrated decision-making about housing, energy and wellbeing: a qualitative system dynamics model.

PubMed

Macmillan, Alexandra; Davies, Michael; Shrubsole, Clive; Luxford, Naomi; May, Neil; Chiu, Lai Fong; Trutnevyte, Evelina; Bobrova, Yekatherina; Chalabi, Zaid

2016-03-08

The UK government has an ambitious goal to reduce carbon emissions from the housing stock through energy efficiency improvements. This single policy goal is a strong driver for change in the housing system, but comes with positive and negative "unintended consequences" across a broad range of outcomes for health, equity and environmental sustainability. The resulting policies are also already experiencing under-performance through a failure to consider housing as a complex system. This research aimed to move from considering disparate objectives of housing policies in isolation to mapping the links between environmental, economic, social and health outcomes as a complex system. We aimed to support a broad range of housing policy stakeholders to improve their understanding of housing as a complex system through a collaborative learning process. We used participatory system dynamics modelling to develop a qualitative causal theory linking housing, energy and wellbeing. Qualitative interviews were followed by two interactive workshops to develop the model, involving representatives from national and local government, housing industries, non-government organisations, communities and academia. More than 50 stakeholders from 37 organisations participated. The process resulted in a shared understanding of wellbeing as it relates to housing; an agreed set of criteria against which to assess to future policy options; and a comprehensive set of causal loop diagrams describing the housing, energy and wellbeing system. The causal loop diagrams cover seven interconnected themes: community connection and quality of neighbourhoods; energy efficiency and climate change; fuel poverty and indoor temperature; household crowding; housing affordability; land ownership, value and development patterns; and ventilation and indoor air pollution. The collaborative learning process and the model have been useful for shifting the thinking of a wide range of housing stakeholders towards a more integrated approach to housing. The qualitative model has begun to improve the assessment of future policy options across a broad range of outcomes. Future work is needed to validate the model and increase its utility through computer simulation incorporating best quality data and evidence. Combining system dynamics modelling with other methods for weighing up policy options, as well as methods to support shifts in the conceptual frameworks underpinning policy, will be necessary to achieve shared housing goals across physical, mental, environmental, economic and social wellbeing.

Bifurcation phenomena in an impulsive model of non-basal testosterone regulation

NASA Astrophysics Data System (ADS)

Zhusubaliyev, Zhanybai T.; Churilov, Alexander N.; Medvedev, Alexander

2012-03-01

Complex nonlinear dynamics in a recent mathematical model of non-basal testosterone regulation are investigated. In agreement with biological evidence, the pulsatile (non-basal) secretion of testosterone is modeled by frequency and amplitude modulated feedback. It is shown that, in addition to already known periodic motions with one and two pulses in the least period of a closed-loop system solution, cycles of higher periodicity and chaos are present in the model in hand. The broad range of exhibited dynamic behaviors makes the model highly promising in model-based signal processing of hormone data.

The effect of sampling techniques used in the multiconfigurational Ehrenfest method

NASA Astrophysics Data System (ADS)

Symonds, C.; Kattirtzi, J. A.; Shalashilin, D. V.

2018-05-01

In this paper, we compare and contrast basis set sampling techniques recently developed for use in the ab initio multiple cloning method, a direct dynamics extension to the multiconfigurational Ehrenfest approach, used recently for the quantum simulation of ultrafast photochemistry. We demonstrate that simultaneous use of basis set cloning and basis function trains can produce results which are converged to the exact quantum result. To demonstrate this, we employ these sampling methods in simulations of quantum dynamics in the spin boson model with a broad range of parameters and compare the results to accurate benchmarks.

Small-World Network Spectra in Mean-Field Theory

NASA Astrophysics Data System (ADS)

Grabow, Carsten; Grosskinsky, Stefan; Timme, Marc

2012-05-01

Collective dynamics on small-world networks emerge in a broad range of systems with their spectra characterizing fundamental asymptotic features. Here we derive analytic mean-field predictions for the spectra of small-world models that systematically interpolate between regular and random topologies by varying their randomness. These theoretical predictions agree well with the actual spectra (obtained by numerical diagonalization) for undirected and directed networks and from fully regular to strongly random topologies. These results may provide analytical insights to empirically found features of dynamics on small-world networks from various research fields, including biology, physics, engineering, and social science.

The effect of sampling techniques used in the multiconfigurational Ehrenfest method.

PubMed

Symonds, C; Kattirtzi, J A; Shalashilin, D V

2018-05-14

In this paper, we compare and contrast basis set sampling techniques recently developed for use in the ab initio multiple cloning method, a direct dynamics extension to the multiconfigurational Ehrenfest approach, used recently for the quantum simulation of ultrafast photochemistry. We demonstrate that simultaneous use of basis set cloning and basis function trains can produce results which are converged to the exact quantum result. To demonstrate this, we employ these sampling methods in simulations of quantum dynamics in the spin boson model with a broad range of parameters and compare the results to accurate benchmarks.

Predicting and testing continental vertical motion histories since the Paleozoic

NASA Astrophysics Data System (ADS)

Zhang, Nan; Zhong, Shijie; Flowers, Rebecca M.

2012-02-01

Dynamic topography at the Earth's surface caused by mantle convection can affect a range of geophysical and geological observations including bathymetry, sea-level change, continental flooding, sedimentation and erosion. These observations provide important constraints on and test of mantle dynamic models. Based on global mantle convection models coupled with the surface plate motion history, we compute dynamic topography and its history for the last 400 Ma associated with Pangea assembly and breakup, with particular focus on cratonic regions. We propose that burial-unroofing histories of cratons inferred from thermochronology data can be used as a new diagnostic to test dynamic topography and mantle dynamic models. Our models show that there are currently two broad dynamic topography highs in the Pacific and Africa for the present-day Earth that are associated with the broad, warm structures (i.e., superplumes) in the deep mantle, consistent with previous proposals of dynamical support for the Pacific and African superswells. Our models reveal that Pangea assembly and breakup, by affecting subduction and mantle upwelling processes, have significant effects on continental vertical motions. Our models predict that the Slave craton in North America subsides before Pangea assembly at 330 Ma but uplifts significantly from 330 Ma to 240 Ma in response to pre-Pangea subduction and post-assembly mantle warming. The Kaapvaal craton of Africa is predicted to undergo uplift from ~180 Ma to 90 Ma after Pangea breakup, but its dynamic topography remains stable for the last 90 Ma. The predicted histories of elevation change for the Slave and Kaapvaal cratons compare well with the burial-unroofing histories inferred from thermochronology studies, thus supporting our dynamic models including the development of the African superplume mantle structure. The vertical motion histories for other cratons can provide further tests of and constraints on our mantle dynamic models.

Predicting and testing continental vertical motion histories since the Paleozoic

NASA Astrophysics Data System (ADS)

Zhang, N.; Zhong, S.; Flowers, R. M.

2011-12-01

Dynamic topography at the Earth's surface caused by mantle convection can affect a range of geophysical and geological observations including bathymetry, sea-level change, continental flooding, sedimentation and erosion. These observations provide important constraints on and test of mantle dynamic models. Based on global mantle convection models coupled with the surface plate motion history, we compute dynamic topography and its history for the last 400 Ma associated with Pangea assembly and breakup, with particular focus on continental cratonic regions. We propose that burial-unroofing histories of continental cratons inferred from thermochronology data can be used as a new diagnostic to test dynamic topography and mantle dynamic models. Our models show that there are currently two broad dynamic topography highs in the Pacific and Africa for the present-day Earth that are associated with the broad, warm structures (i.e., superplumes) in the deep mantle, consistent with previous proposals of dynamical support for the Pacific and African superswells. Our models reveal that Pangea assembly and breakup, by affecting subduction and mantle upwelling processes, have significant effects on continental vertical motions. Our models predict that the Slave craton in North America subsides before Pangea assembly at 330 Ma but uplifts significantly from 330 Ma to 240 Ma in response to pre-Pangea subduction and post-assembly mantle warming. The Kaapvaal craton of Africa is predicted to undergo uplift from ~180 Ma to 90 Ma after Pangea breakup, but its dynamic topography remains stable for the last 90 Ma. The predicted histories of elevation change for the Slave and Kaapvaal cratons compare well with the burial-unroofing histories inferred from thermochronology studies, thus supporting our dynamic models including the development of the African superplume mantle structure. The vertical motion histories for other cratons can provide further tests and constraints on our mantle dynamic models.

The influence of interspecific interactions on species range expansion rates

USGS Publications Warehouse

Svenning, Jens-Christian; Gravel, Dominique; Holt, Robert D.; Schurr, Frank M.; Thuiller, Wilfried; Münkemüller, Tamara; Schiffers, Katja H.; Dullinger, Stefan; Edwards, Thomas C.; Hickler, Thomas; Higgins, Steven I.; Nabel, Julia E.M.S.; Pagel, Jörn; Normand, Signe

2014-01-01

Ongoing and predicted global change makes understanding and predicting species’ range shifts an urgent scientific priority. Here, we provide a synthetic perspective on the so far poorly understood effects of interspecific interactions on range expansion rates. We present theoretical foundations for how interspecific interactions may modulate range expansion rates, consider examples from empirical studies of biological invasions and natural range expansions as well as process-based simulations, and discuss how interspecific interactions can be more broadly represented in process-based, spatiotemporally explicit range forecasts. Theory tells us that interspecific interactions affect expansion rates via alteration of local population growth rates and spatial displacement rates, but also via effects on other demographic parameters. The best empirical evidence for interspecific effects on expansion rates comes from studies of biological invasions. Notably, invasion studies indicate that competitive dominance and release from specialized enemies can enhance expansion rates. Studies of natural range expansions especially point to the potential for competition from resident species to reduce expansion rates. Overall, it is clear that interspecific interactions may have important consequences for range dynamics, but also that their effects have received too little attention to robustly generalize on their importance. We then discuss how interspecific interactions effects can be more widely incorporated in dynamic modeling of range expansions. Importantly, models must describe spatiotemporal variation in both local population dynamics and dispersal. Finally, we derive the following guidelines for when it is particularly important to explicitly represent interspecific interactions in dynamic range expansion forecasts: if most interacting species show correlated spatial or temporal trends in their effects on the target species, if the number of interacting species is low, and if the abundance of one or more strongly interacting species is not closely linked to the abundance of the target species.

The influence of interspecific interactions on species range expansion rates.

PubMed

Svenning, Jens-Christian; Gravel, Dominique; Holt, Robert D; Schurr, Frank M; Thuiller, Wilfried; Münkemüller, Tamara; Schiffers, Katja H; Dullinger, Stefan; Edwards, Thomas C; Hickler, Thomas; Higgins, Steven I; Nabel, Julia E M S; Pagel, Jörn; Normand, Signe

2014-12-01

Ongoing and predicted global change makes understanding and predicting species' range shifts an urgent scientific priority. Here, we provide a synthetic perspective on the so far poorly understood effects of interspecific interactions on range expansion rates. We present theoretical foundations for how interspecific interactions may modulate range expansion rates, consider examples from empirical studies of biological invasions and natural range expansions as well as process-based simulations, and discuss how interspecific interactions can be more broadly represented in process-based, spatiotemporally explicit range forecasts. Theory tells us that interspecific interactions affect expansion rates via alteration of local population growth rates and spatial displacement rates, but also via effects on other demographic parameters. The best empirical evidence for interspecific effects on expansion rates comes from studies of biological invasions. Notably, invasion studies indicate that competitive dominance and release from specialized enemies can enhance expansion rates. Studies of natural range expansions especially point to the potential for competition from resident species to reduce expansion rates. Overall, it is clear that interspecific interactions may have important consequences for range dynamics, but also that their effects have received too little attention to robustly generalize on their importance. We then discuss how interspecific interactions effects can be more widely incorporated in dynamic modeling of range expansions. Importantly, models must describe spatiotemporal variation in both local population dynamics and dispersal. Finally, we derive the following guidelines for when it is particularly important to explicitly represent interspecific interactions in dynamic range expansion forecasts: if most interacting species show correlated spatial or temporal trends in their effects on the target species, if the number of interacting species is low, and if the abundance of one or more strongly interacting species is not closely linked to the abundance of the target species.

The influence of interspecific interactions on species range expansion rates

PubMed Central

Svenning, Jens-Christian; Gravel, Dominique; Holt, Robert D.; Schurr, Frank M.; Thuiller, Wilfried; Münkemüller, Tamara; Schiffers, Katja H.; Dullinger, Stefan; Edwards, Thomas C.; Hickler, Thomas; Higgins, Steven I.; Nabel, Julia E. M. S.; Pagel, Jörn; Normand, Signe

2014-01-01

Ongoing and predicted global change makes understanding and predicting species’ range shifts an urgent scientific priority. Here, we provide a synthetic perspective on the so far poorly understood effects of interspecific interactions on range expansion rates. We present theoretical foundations for how interspecific interactions may modulate range expansion rates, consider examples from empirical studies of biological invasions and natural range expansions as well as process-based simulations, and discuss how interspecific interactions can be more broadly represented in process-based, spatiotemporally explicit range forecasts. Theory tells us that interspecific interactions affect expansion rates via alteration of local population growth rates and spatial displacement rates, but also via effects on other demographic parameters. The best empirical evidence for interspecific effects on expansion rates comes from studies of biological invasions. Notably, invasion studies indicate that competitive dominance and release from specialized enemies can enhance expansion rates. Studies of natural range expansions especially point to the potential for competition from resident species to reduce expansion rates. Overall, it is clear that interspecific interactions may have important consequences for range dynamics, but also that their effects have received too little attention to robustly generalize on their importance. We then discuss how interspecific interactions effects can be more widely incorporated in dynamic modeling of range expansions. Importantly, models must describe spatiotemporal variation in both local population dynamics and dispersal. Finally, we derive the following guidelines for when it is particularly important to explicitly represent interspecific interactions in dynamic range expansion forecasts: if most interacting species show correlated spatial or temporal trends in their effects on the target species, if the number of interacting species is low, and if the abundance of one or more strongly interacting species is not closely linked to the abundance of the target species. PMID:25722537

Influence of Microstructure on Micro-/Nano-Mechanical Measurements of Select Model Transparent Poly(urethane urea) Elastomers

DTIC Science & Technology

2012-12-17

results. Furthermore, instrumented impact indentation is also utilized for elucidation of dynamic damping characteristics in these PUUs. REPORT... characteristics in these PUUs. Published by Elsevier Ltd. 1. Introduction Elastomers are versatile materials that are vital to a broad range of...industrial, medical, and military applications, particularly in the areas of coating, adhesives, foams , and composite structures [1]. More specifically, high

Dynamic Response and Failure Mechanisms of Layered Ceramic-Elastomer-Polymer/Metal Composites

DTIC Science & Technology

2010-08-20

characterization of each material constituent of interest, i.e., polyurea and DH-36 steel, over broad ranges of deformation rates, strains, and temperature of...metal-metal, metal- polyurea -metal and polyurea -ceramic composites. New steel plate designs with different thicknesses were employed to avoid tearing...of the sample at its supporting ring. New experiments support the hypothesis that the steel- polyurea sandwich samples show a noticeably better

Quantum mechanical free energy profiles with post-quantization restraints: Binding free energy of the water dimer over a broad range of temperatures

NASA Astrophysics Data System (ADS)

Bishop, Kevin P.; Roy, Pierre-Nicholas

2018-03-01

Free energy calculations are a crucial part of understanding chemical systems but are often computationally expensive for all but the simplest of systems. Various enhanced sampling techniques have been developed to improve the efficiency of these calculations in numerical simulations. However, the majority of these approaches have been applied using classical molecular dynamics. There are many situations where nuclear quantum effects impact the system of interest and a classical description fails to capture these details. In this work, path integral molecular dynamics has been used in conjunction with umbrella sampling, and it has been observed that correct results are only obtained when the umbrella sampling potential is applied to a single path integral bead post quantization. This method has been validated against a Lennard-Jones benchmark system before being applied to the more complicated water dimer system over a broad range of temperatures. Free energy profiles are obtained, and these are utilized in the calculation of the second virial coefficient as well as the change in free energy from the separated water monomers to the dimer. Comparisons to experimental and ground state calculation values from the literature are made for the second virial coefficient at higher temperature and the dissociation energy of the dimer in the ground state.

Quantum mechanical free energy profiles with post-quantization restraints: Binding free energy of the water dimer over a broad range of temperatures.

PubMed

Bishop, Kevin P; Roy, Pierre-Nicholas

2018-03-14

Free energy calculations are a crucial part of understanding chemical systems but are often computationally expensive for all but the simplest of systems. Various enhanced sampling techniques have been developed to improve the efficiency of these calculations in numerical simulations. However, the majority of these approaches have been applied using classical molecular dynamics. There are many situations where nuclear quantum effects impact the system of interest and a classical description fails to capture these details. In this work, path integral molecular dynamics has been used in conjunction with umbrella sampling, and it has been observed that correct results are only obtained when the umbrella sampling potential is applied to a single path integral bead post quantization. This method has been validated against a Lennard-Jones benchmark system before being applied to the more complicated water dimer system over a broad range of temperatures. Free energy profiles are obtained, and these are utilized in the calculation of the second virial coefficient as well as the change in free energy from the separated water monomers to the dimer. Comparisons to experimental and ground state calculation values from the literature are made for the second virial coefficient at higher temperature and the dissociation energy of the dimer in the ground state.

A swinging seesaw as a novel model mechanism for time-dependent hormesis under dose-dependent stimulatory and inhibitory effects: A case study on the toxicity of antibacterial chemicals to Aliivibrio fischeri.

PubMed

Sun, Haoyu; Calabrese, Edward J; Zheng, Min; Wang, Dali; Pan, Yongzheng; Lin, Zhifen; Liu, Ying

2018-08-01

Hormesis occurs frequently in broadly ranging biological areas (e.g. plant biology, microbiology, biogerontology), toxicology, pharmacology and medicine. While numerous mechanisms (e.g. receptor and pathway mediated pathway responses) account for stimulatory and inhibitory features of hormetic dose responses, the vast majority emphasizes the inclusion of many doses but only one timepoint or use of a single optimized dose that is assessed over a broad range of timepoints. In this paper, a toxicity study was designed using a large number of properly spaced doses with responses determined over a large number of timepoints, which could help us reveal the underlying mechanism of hormesis. We present the results of a dose-time-response study on hormesis using five antibacterial chemicals on the bioluminescence of Aliivibrio fischeri, measuring expression of protein mRNA based on quorum sensing, simulating bioluminescent reaction and analyzing toxic actions of test chemicals. The findings show dose-time-dependent responses conforming to the hormetic dose-response model, while revealing unique response dynamics between agent induced stimulatory and inhibitory effects within bacterial growth phase dynamics. These dynamic dose-time features reveal a type of biological seesaw model that integrates stimulatory and inhibitory responses within unique growth phase, dose and time features, which has faultlessly explained the time-dependent hormetic phenomenon induced by five antibacterial chemicals (characterized by low-dose stimulation and high-dose inhibition). This study offers advances in understanding cellular dynamics, the biological integration of diverse and opposing responses and their role in evolutionary adaptive strategies to chemicals, which can provide new insight into the mechanistic investigation of hormesis. Copyright © 2018 Elsevier Ltd. All rights reserved.

Magnetic Excitations and Continuum of a Possibly Field-Induced Quantum Spin Liquid in α -RuCl3

NASA Astrophysics Data System (ADS)

Wang, Zhe; Reschke, S.; Hüvonen, D.; Do, S.-H.; Choi, K.-Y.; Gensch, M.; Nagel, U.; Rõõm, T.; Loidl, A.

2017-12-01

We report on terahertz spectroscopy of quantum spin dynamics in α -RuCl3 , a system proximate to the Kitaev honeycomb model, as a function of temperature and magnetic field. We follow the evolution of an extended magnetic continuum below the structural phase transition at Ts 2=62 K . With the onset of a long-range magnetic order at TN=6.5 K , spectral weight is transferred to a well-defined magnetic excitation at ℏω1=2.48 meV , which is accompanied by a higher-energy band at ℏω2=6.48 meV . Both excitations soften in a magnetic field, signaling a quantum phase transition close to Bc=7 T , where a broad continuum dominates the dynamical response. Above Bc, the long-range order is suppressed, and on top of the continuum, emergent magnetic excitations evolve. These excitations follow clear selection rules and exhibit distinct field dependencies, characterizing the dynamical properties of a possibly field-induced quantum spin liquid.

Analysis encapsulation of fiber Bragg gratings into polydimethylsiloxane for the needs of dynamic weighing

NASA Astrophysics Data System (ADS)

Fajkus, M.; Nedoma, J.; Martinek, R.; Novak, M.; Jargus, J.; Vasinek, V.

2017-05-01

Authors of the article focused on the possible encapsulation method of fiber Bragg gratings (FBGs) for the needs of dynamic weighing. For monitoring the parameters, we used broad-spectrum light source LED (Light-Emitting Diode) with a central wavelength of 1550 nm and optical spectrum analyzer with sampling rate 300 Hz. For encapsulation of used FBGs was chosen a specific material polymer polydimethylsiloxane (PDMS). A characteristic feature of this material is very high mechanical resistance, chemical resistance and temperature stability in the range of values -60 °C to + 200 °C. The combination of characteristic advantages of optical fibers (electromagnetic immunity) with stated properties of PDMS gives us the innovative type of encapsulated sensor which could be used for example for the needs of dynamic weighing in worsened or potentially hazardous conditions. This type of monitoring weighing is fully dielectric. Experimental measurements were carried out in laboratory conditions in the weight range of 35 up to 180 kg.

Mathematical Modeling of Microbial Community Dynamics: A Methodological Review

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Hyun-Seob; Cannon, William R.; Beliaev, Alex S.

Microorganisms in nature form diverse communities that dynamically change in structure and function in response to environmental variations. As a complex adaptive system, microbial communities show higher-order properties that are not present in individual microbes, but arise from their interactions. Predictive mathematical models not only help to understand the underlying principles of the dynamics and emergent properties of natural and synthetic microbial communities, but also provide key knowledge required for engineering them. In this article, we provide an overview of mathematical tools that include not only current mainstream approaches, but also less traditional approaches that, in our opinion, can bemore » potentially useful. We discuss a broad range of methods ranging from low-resolution supra-organismal to high-resolution individual-based modeling. Particularly, we highlight the integrative approaches that synergistically combine disparate methods. In conclusion, we provide our outlook for the key aspects that should be further developed to move microbial community modeling towards greater predictive power.« less

Chloride ions induce order-disorder transition at water-oxide interfaces

NASA Astrophysics Data System (ADS)

Deshmukh, Sanket; Kamath, Ganesh; Ramanathan, Shriram; Sankaranarayanan, Subramanian K. R. S.

2013-12-01

Water can form quasi-two-dimensional ordered layers near a solid interface. The solvation dynamics and ionic transport phenomena through this ordered water structure is of direct relevance to a variety of problems in interface science. Molecular dynamics simulations are used to study the impact of local fluctuation of the chloride ion density in the vicinity of an oxide surface on the structure and dynamics of water layers. We demonstrate that local increase in chloride ions beyond a threshold concentration near the water-MgO (100) interface introduces an order-disorder transition of this two-dimensional layered network into bulklike water, leading to increased diffusional characteristics and reduced hydrogen bonding lifetimes. We find that the extent of this order-disorder transition can be tuned by modifying the defect chemistry and nature of the underlying substrate. The kinetic fluidity resulting from order-disorder transition at high chloride ion concentration has significance for a broad range of phenomena, ranging from freezing point depression of brine to onset of aqueous corrosion.

Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range.

PubMed

Bachmann, Julie; Raue, Andreas; Schilling, Marcel; Böhm, Martin E; Kreutz, Clemens; Kaschek, Daniel; Busch, Hauke; Gretz, Norbert; Lehmann, Wolf D; Timmer, Jens; Klingmüller, Ursula

2011-07-19

Cellular signal transduction is governed by multiple feedback mechanisms to elicit robust cellular decisions. The specific contributions of individual feedback regulators, however, remain unclear. Based on extensive time-resolved data sets in primary erythroid progenitor cells, we established a dynamic pathway model to dissect the roles of the two transcriptional negative feedback regulators of the suppressor of cytokine signaling (SOCS) family, CIS and SOCS3, in JAK2/STAT5 signaling. Facilitated by the model, we calculated the STAT5 response for experimentally unobservable Epo concentrations and provide a quantitative link between cell survival and the integrated response of STAT5 in the nucleus. Model predictions show that the two feedbacks CIS and SOCS3 are most effective at different ligand concentration ranges due to their distinct inhibitory mechanisms. This divided function of dual feedback regulation enables control of STAT5 responses for Epo concentrations that can vary 1000-fold in vivo. Our modeling approach reveals dose-dependent feedback control as key property to regulate STAT5-mediated survival decisions over a broad range of ligand concentrations.

Flavivirus structural heterogeneity: implications for cell entry.

PubMed

Rey, Félix A; Stiasny, Karin; Heinz, Franz X

2017-06-01

The explosive spread of Zika virus is the most recent example of the threat imposed to human health by flaviviruses. High-resolution structures are available for several of these arthropod-borne viruses, revealing alternative icosahedral organizations of immature and mature virions. Incomplete proteolytic maturation, however, results in a cloud of highly heterogeneous mosaic particles. This heterogeneity is further expanded by a dynamic behavior of the viral envelope glycoproteins. The ensemble of heterogeneous and dynamic infectious particles circulating in infected hosts offers a range of alternative possible receptor interaction sites at their surfaces, potentially contributing to the broad flavivirus host-range and variation in tissue tropism. The potential synergy between heterogeneous particles in the circulating cloud thus provides an additional dimension to understand the unanticipated properties of Zika virus in its recent outbreaks. Copyright © 2017 Elsevier B.V. All rights reserved.

Notes on a broad-band variant of the NCER seismic data multiplex system for use with field tape recorders

USGS Publications Warehouse

Eaton, Jerry P.

1976-01-01

Tests of the standard NCER multiplex system recorded and played back on both the Bell and Howell 3700B (about 0.1% tape speed variation) and on the Sony TC-126 cassette recorder (about 1% tape speed variation) showed that subtractive compensation employing a reference frequency multiplexed on the data track was remarkably effective in reducing tape-speed-variation-induced noise 1 and, hence, in increasing the dynamic range of the record/playback system. Further tests suggested that the 0 to 30 Hz bandwidth of the standard system (8 data channels) might be increased substantially, at the 'price' of reducing the number of data channels to 3 or 4, without serious loss of dynamic range if subtractive compensation could be implemented effectively with the broader-band system.

Improved laser-based triangulation sensor with enhanced range and resolution through adaptive optics-based active beam control.

PubMed

Reza, Syed Azer; Khwaja, Tariq Shamim; Mazhar, Mohsin Ali; Niazi, Haris Khan; Nawab, Rahma

2017-07-20

Various existing target ranging techniques are limited in terms of the dynamic range of operation and measurement resolution. These limitations arise as a result of a particular measurement methodology, the finite processing capability of the hardware components deployed within the sensor module, and the medium through which the target is viewed. Generally, improving the sensor range adversely affects its resolution and vice versa. Often, a distance sensor is designed for an optimal range/resolution setting depending on its intended application. Optical triangulation is broadly classified as a spatial-signal-processing-based ranging technique and measures target distance from the location of the reflected spot on a position sensitive detector (PSD). In most triangulation sensors that use lasers as a light source, beam divergence-which severely affects sensor measurement range-is often ignored in calculations. In this paper, we first discuss in detail the limitations to ranging imposed by beam divergence, which, in effect, sets the sensor dynamic range. Next, we show how the resolution of laser-based triangulation sensors is limited by the interpixel pitch of a finite-sized PSD. In this paper, through the use of tunable focus lenses (TFLs), we propose a novel design of a triangulation-based optical rangefinder that improves both the sensor resolution and its dynamic range through adaptive electronic control of beam propagation parameters. We present the theory and operation of the proposed sensor and clearly demonstrate a range and resolution improvement with the use of TFLs. Experimental results in support of our claims are shown to be in strong agreement with theory.

Biophysical dynamics in disorderly environments.

PubMed

Nelson, David R

2012-01-01

Three areas where time-independent disorder plays a key role in biological dynamics far from equilibrium are reviewed. We first discuss the anomalous localization dynamics that arises when a single species spreads in space and time via diffusion and fluid advection in the presence of frozen heterogeneities in the growth rate. Next we treat the unzipping of double-stranded DNA as a function of force and temperature, a challenge that must be surmounted every time a cell divides. Heterogeneity in the DNA sequence dominates the physics of single-molecule force-extension curves for a broad range of forces upon approaching a sharp unzipping transition. The dynamics of the unzipping fork exhibits anomalous drift and diffusion in a similar range above this transition, with energy barriers that scale as the square root of the genome size. Finally, we describe how activated peptidoglycan strand extension sites, called dislocations in materials science, can mediate the growth of bacterial cell walls. Enzymatically driven circumferential motions of a few dozen of these defects are sufficient to describe the exponential elongation rates observed in experiments on Escherichia coli in a nutrient-rich environment. However, long-range elastic forces transmitted by the peptidoglycan meshwork cause the moving dislocations to interact not only with each other, but also with a disorderly array of frozen, inactivated strand ends.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fedrigo, Anna, E-mail: anna.fedrigo@nbi.ku.dk; Istituto dei Sistemi Complessi, Consiglio Nazionale delle Ricerche, 50019 Sesto Fiorentino; European Spallation Source ESS AB, SE-221 00 Lund

VESPA, Vibrational Excitation Spectrometer with Pyrolytic-graphite Analysers, aims to probe molecular excitations via inelastic neutron scattering. It is a thermal high resolution inverted geometry time-of-flight instrument designed to maximise the use of the long pulse of the European Spallation Source. The wavelength frame multiplication technique was applied to provide simultaneously a broad dynamic range (about 0-500 meV) while a system of optical blind choppers allows to trade flux for energy resolution. Thanks to its high flux, VESPA will allow the investigation of dynamical and in situ experiments in physical chemistry. Here we describe the design parameters and the corresponding McStasmore » simulations.« less

HINDERED DIFFUSION OF COAL LIQUIDS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Theodore T. Tsotsis; Muhammad Sahimi; Ian A. Webster

1996-01-01

It was the purpose of the project described here to carry out careful and detailed investigations of petroleum and coal asphaltene transport through model porous systems under a broad range of temperature conditions. The experimental studies were to be coupled with detailed, in-depth statistical and molecular dynamics models intended to provide a fundamental understanding of the overall transport mechanisms and a more accurate concept of the asphaltene structure. The following discussion describes some of our accomplishments.

Sustaining Pinus flexilis ecosystems of the southern Rocky Mountains (USA) in the presence of Cronartium ribicola and Dendroctonus ponderosae in a changing climate

Treesearch

Anna W. Schoettle; Richard A. Sniezko; Kelly S. Burns

2009-01-01

Limber pine, Pinus flexilis James, is characterized by a patchy distribution that displays metapopulation dynamics and spans a broad latitudinal and elevational range in North America (Webster and Johnson 2000). In the southern Rocky Mountains limber pine grows from below the forest-grassland ecotone up to the forest-alpine ecotone, from ~1600 m above sea level in the...

High-order Discontinuous Element-based Schemes for the Inviscid Shallow Water Equations: Spectral Multidomain Penalty and Discontinuous Galerkin Methods

DTIC Science & Technology

2011-07-19

multidomain methods, Discontinuous Galerkin methods, interfacial treatment ∗ Jorge A. Escobar-Vargas, School of Civil and Environmental Engineering, Cornell...Click here to view linked References 1. Introduction Geophysical flows exhibit a complex structure and dynamics over a broad range of scales that...hyperbolic problems, where the interfacial patching was implemented with an upwind scheme based on a modified method of characteristics. This approach

Robust, synergistic regulation of human gene expression using TALE activators.

PubMed

Maeder, Morgan L; Linder, Samantha J; Reyon, Deepak; Angstman, James F; Fu, Yanfang; Sander, Jeffry D; Joung, J Keith

2013-03-01

Artificial activators designed using transcription activator-like effector (TALE) technology have broad utility, but previous studies suggest that these monomeric proteins often exhibit low activities. Here we demonstrate that TALE activators can robustly function individually or in synergistic combinations to increase expression of endogenous human genes over wide dynamic ranges. These findings will encourage applications of TALE activators for research and therapy, and guide design of monomeric TALE-based fusion proteins.

Shortening the HIV-1 TAR RNA Bulge by a Single Nucleotide Preserves Motional Modes over a Broad Range of Time Scales.

PubMed

Merriman, Dawn K; Xue, Yi; Yang, Shan; Kimsey, Isaac J; Shakya, Anisha; Clay, Mary; Al-Hashimi, Hashim M

2016-08-16

Helix-junction-helix (HJH) motifs are flexible building blocks of RNA architecture that help define the orientation and dynamics of helical domains. They are also frequently involved in adaptive recognition of proteins and small molecules and in the formation of tertiary contacts. Here, we use a battery of nuclear magnetic resonance techniques to examine how deleting a single bulge residue (C24) from the human immunodeficiency virus type 1 (HIV-1) transactivation response element (TAR) trinucleotide bulge (U23-C24-U25) affects dynamics over a broad range of time scales. Shortening the bulge has an effect on picosecond-to-nanosecond interhelical and local bulge dynamics similar to that casued by increasing the Mg(2+) and Na(+) concentration, whereby a preexisting two-state equilibrium in TAR is shifted away from a bent flexible conformation toward a coaxial conformation, in which all three bulge residues are flipped out and flexible. Surprisingly, the point deletion minimally affects microsecond-to-millisecond conformational exchange directed toward two low-populated and short-lived excited conformational states that form through reshuffling of bases pairs throughout TAR. The mutant does, however, adopt a slightly different excited conformational state on the millisecond time scale, in which U23 is intrahelical, mimicking the expected conformation of residue C24 in the excited conformational state of wild-type TAR. Thus, minor changes in HJH topology preserve motional modes in RNA occurring over the picosecond-to-millisecond time scales but alter the relative populations of the sampled states or cause subtle changes in their conformational features.

Wide-spectral/dynamic-range skin-compatible phototransistors enabled by floated heterojunction structures with surface functionalized SWCNTs and amorphous oxide semiconductors.

PubMed

Hwang, Insik; Kim, Jaehyun; Lee, Minkyung; Lee, Min-Wook; Kim, Hee-Joong; Kwon, Hyuck-In; Hwang, Do Kyung; Kim, Myunggil; Yoon, Haeyoung; Kim, Yong-Hoon; Park, Sung Kyu

2017-11-09

Purified semiconducting single-walled carbon nanotubes (sc-SWCNTs) have been researched for optoelectronic applications due to their high absorption coefficient from the visible to even the near-infrared (NIR) region. Nevertheless, the insufficient electrical characteristics and incompatibility with conventional CMOS processing have limited their wide utilization in this emerging field. Here, we demonstrate highly detective and wide spectral/dynamic range phototransistors incorporating floated heterojunction active layers which are composed of low-temperature sol-gel processed n-type amorphous indium gallium zinc oxide (a-IGZO) stacked with a purified p-type sc-SWCNT layer. To achieve a high and broad spectral/dynamic range photo-response of the heterogeneous transistors, photochemically functionalized sc-SWCNT layers were carefully implemented onto the a-IGZO channel area with a floating p-n heterojunction active layer, resulting in the suppression of parasitic charge leakage and good bias driven opto-electrical properties. The highest photosensitivity (R) of 9.6 × 10 2 A W -1 and a photodetectivity (D*) of 4 × 10 14 Jones along with a dynamic range of 100-180 dB were achieved for our phototransistor in the spectral range of 400-780 nm including continuous and minimal frequency independent behaviors. More importantly, to demonstrate the diverse application of the ultra-flexible hybrid photosensor platform as skin compatible electronics, the sc-SWCNT/a-IGZO phototransistors were fabricated on an ultra-thin (∼1 μm) polyimide film along with a severe static and dynamic electro-mechanical test. The skin-like phototransistors showed excellent mechanical stability such as sustainable good electrical performance and high photosensitivity in a wide dynamic range without any visible cracks or damage and little noise interference after being rolled-up on the 150 μm-thick optical fiber as well as more than 1000 times cycling.

The virtual brain: 30 years of video-game play and cognitive abilities.

PubMed

Latham, Andrew J; Patston, Lucy L M; Tippett, Lynette J

2013-09-13

Forty years have passed since video-games were first made widely available to the public and subsequently playing games has become a favorite past-time for many. Players continuously engage with dynamic visual displays with success contingent on the time-pressured deployment, and flexible allocation, of attention as well as precise bimanual movements. Evidence to date suggests that both brief and extensive exposure to video-game play can result in a broad range of enhancements to various cognitive faculties that generalize beyond the original context. Despite promise, video-game research is host to a number of methodological issues that require addressing before progress can be made in this area. Here an effort is made to consolidate the past 30 years of literature examining the effects of video-game play on cognitive faculties and, more recently, neural systems. Future work is required to identify the mechanism that allows the act of video-game play to generate such a broad range of generalized enhancements.

The virtual brain: 30 years of video-game play and cognitive abilities

PubMed Central

Latham, Andrew J.; Patston, Lucy L. M.; Tippett, Lynette J.

2013-01-01

Forty years have passed since video-games were first made widely available to the public and subsequently playing games has become a favorite past-time for many. Players continuously engage with dynamic visual displays with success contingent on the time-pressured deployment, and flexible allocation, of attention as well as precise bimanual movements. Evidence to date suggests that both brief and extensive exposure to video-game play can result in a broad range of enhancements to various cognitive faculties that generalize beyond the original context. Despite promise, video-game research is host to a number of methodological issues that require addressing before progress can be made in this area. Here an effort is made to consolidate the past 30 years of literature examining the effects of video-game play on cognitive faculties and, more recently, neural systems. Future work is required to identify the mechanism that allows the act of video-game play to generate such a broad range of generalized enhancements. PMID:24062712

Computational Re-design of Synthetic Genetic Oscillators for Independent Amplitude and Frequency Modulation.

PubMed

Tomazou, Marios; Barahona, Mauricio; Polizzi, Karen M; Stan, Guy-Bart

2018-04-25

To perform well in biotechnology applications, synthetic genetic oscillators must be engineered to allow independent modulation of amplitude and period. This need is currently unmet. Here, we demonstrate computationally how two classic genetic oscillators, the dual-feedback oscillator and the repressilator, can be re-designed to provide independent control of amplitude and period and improve tunability-that is, a broad dynamic range of periods and amplitudes accessible through the input "dials." Our approach decouples frequency and amplitude modulation by incorporating an orthogonal "sink module" where the key molecular species are channeled for enzymatic degradation. This sink module maintains fast oscillation cycles while alleviating the translational coupling between the oscillator's transcription factors and output. We characterize the behavior of our re-designed oscillators over a broad range of physiologically reasonable parameters, explain why this facilitates broader function and control, and provide general design principles for building synthetic genetic oscillators that are more precisely controllable. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

X-ray Scattering Combined with Coordinate-Based Analyses for Applications in Natural and Artificial Photosynthesis

PubMed Central

Tiede, David M.; Mardis, Kristy L.; Zuo, Xiaobing

2009-01-01

Advances in x-ray light sources and detectors have created opportunities for advancing our understanding of structure and structural dynamics for supramolecular assemblies in solution by combining x-ray scattering measurement with coordinate-based modeling methods. In this review the foundations for x-ray scattering are discussed and illustrated with selected examples demonstrating the ability to correlate solution x-ray scattering measurements to molecular structure, conformation, and dynamics. These approaches are anticipated to have a broad range of applications in natural and artificial photosynthesis by offering possibilities for structure resolution for dynamic supramolecular assemblies in solution that can not be fully addressed with crystallographic techniques, and for resolving fundamental mechanisms for solar energy conversion by mapping out structure in light-excited reaction states. PMID:19636808

Dynamic stiffness of chemically and physically ageing rubber vibration isolators in the audible frequency range: Part 2—waveguide solution

NASA Astrophysics Data System (ADS)

Kari, Leif

2017-09-01

The dynamic stiffness of a chemically and physically ageing rubber vibration isolator in the audible frequency range is modelled as a function of ageing temperature, ageing time, actual temperature, time, frequency and isolator dimension. In particular, the dynamic stiffness for an axially symmetric, homogeneously aged rubber vibration isolator is derived by waveguides where the eigenmodes given by the dispersion relation for an infinite cylinder satisfying traction free radial surface boundary condition are matched to satisfy the displacement boundary conditions at the lateral surface ends of the finite rubber cylinder. The constitutive equations are derived in a companion paper (Part 1). The dynamic stiffness is calculated over the whole audible frequency range 20-20,000 Hz at several physical ageing times for a temperature history starting at thermodynamic equilibrium at +25°C and exposed by a sudden temperature step down to -60°C and at several chemical ageing times at temperature +25°C with simultaneous molecular network scission and reformation. The dynamic stiffness results are displaying a strong frequency dependence at a short physical ageing time, showing stiffness magnitude peaks and troughs, and a strong physical ageing time dependence, showing a large stiffness magnitude increase with the increased physical ageing time, while the peaks and troughs are smoothed out. Likewise, stiffness magnitude peaks and troughs are frequency-shifted with increased chemical ageing time. The developed model is possible to apply for dynamic stiffness prediction of rubber vibration isolator over a broad audible frequency range under realistic environmental condition of chemical ageing, mainly attributed to oxygen exposure from outside and of physical ageing, primarily perceived at low-temperature steps.

Emergence, evolution and scaling of online social networks.

PubMed

Wang, Le-Zhi; Huang, Zi-Gang; Rong, Zhi-Hai; Wang, Xiao-Fan; Lai, Ying-Cheng

2014-01-01

Online social networks have become increasingly ubiquitous and understanding their structural, dynamical, and scaling properties not only is of fundamental interest but also has a broad range of applications. Such networks can be extremely dynamic, generated almost instantaneously by, for example, breaking-news items. We investigate a common class of online social networks, the user-user retweeting networks, by analyzing the empirical data collected from Sina Weibo (a massive twitter-like microblogging social network in China) with respect to the topic of the 2011 Japan earthquake. We uncover a number of algebraic scaling relations governing the growth and structure of the network and develop a probabilistic model that captures the basic dynamical features of the system. The model is capable of reproducing all the empirical results. Our analysis not only reveals the basic mechanisms underlying the dynamics of the retweeting networks, but also provides general insights into the control of information spreading on such networks.

The Metastable Brain

PubMed Central

Tognoli, Emmanuelle; Kelso, J. A. Scott

2014-01-01

Neural ensembles oscillate across a broad range of frequencies and are transiently coupled or “bound” together when people attend to a stimulus, perceive, think and act. This is a dynamic, self-assembling process, with parts of the brain engaging and disengaging in time. But how is it done? The theory of Coordination Dynamics proposes a mechanism called metastability, a subtle blend of integration and segregation. Tendencies for brain regions to express their individual autonomy and specialized functions (segregation, modularity) coexist with tendencies to couple and coordinate globally for multiple functions (integration). Although metastability has garnered increasing attention, it has yet to be demonstrated and treated within a fully spatiotemporal perspective. Here, we illustrate metastability in continuous neural and behavioral recordings, and we discuss theory and experiments at multiple scales suggesting that metastable dynamics underlie the real-time coordination necessary for the brain's dynamic cognitive, behavioral and social functions. PMID:24411730

Dynamics of contact line depinning during droplet evaporation based on thermodynamics.

PubMed

Yu, Dong In; Kwak, Ho Jae; Doh, Seung Woo; Ahn, Ho Seon; Park, Hyun Sun; Kiyofumi, Moriyama; Kim, Moo Hwan

2015-02-17

For several decades, evaporation phenomena have been intensively investigated for a broad range of applications. However, the dynamics of contact line depinning during droplet evaporation has only been inductively inferred on the basis of experimental data and remains unclear. This study focuses on the dynamics of contact line depinning during droplet evaporation based on thermodynamics. Considering the decrease in the Gibbs free energy of a system with different evaporation modes, a theoretical model was developed to estimate the receding contact angle during contact line depinning as a function of surface conditions. Comparison of experimentally measured and theoretically modeled receding contact angles indicated that the dynamics of contact line depinning during droplet evaporation was caused by the most favorable thermodynamic process encountered during constant contact radius (CCR mode) and constant contact angle (CCA mode) evaporation to rapidly reach an equilibrium state during droplet evaporation.

Dark-field-based observation of single-nanoparticle dynamics on a supported lipid bilayer for in situ analysis of interacting molecules and nanoparticles.

PubMed

Lee, Young Kwang; Kim, Sungi; Nam, Jwa-Min

2015-01-12

Observation of single plasmonic nanoparticles in reconstituted biological systems allows us to obtain snapshots of dynamic processes between molecules and nanoparticles with unprecedented spatiotemporal resolution and single-molecule/single-particle-level data acquisition. This Concept is intended to introduce nanoparticle-tethered supported lipid bilayer platforms that allow for the dynamic confinement of nanoparticles on a two-dimensional fluidic surface. The dark-field-based long-term, stable, real-time observation of freely diffusing plasmonic nanoparticles on a lipid bilayer enables one to extract a broad range of information about interparticle and molecular interactions throughout the entire reaction period. Herein, we highlight important developments in this context to provide ideas on how molecular interactions can be interpreted by monitoring dynamic behaviors and optical signals of laterally mobile nanoparticles. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

General solution to inhomogeneous dephasing and smooth pulse dynamical decoupling

NASA Astrophysics Data System (ADS)

Zeng, Junkai; Deng, Xiu-Hao; Russo, Antonio; Barnes, Edwin

2018-03-01

In order to achieve the high-fidelity quantum control needed for a broad range of quantum information technologies, reducing the effects of noise and system inhomogeneities is an essential task. It is well known that a system can be decoupled from noise or made insensitive to inhomogeneous dephasing dynamically by using carefully designed pulse sequences based on square or delta-function waveforms such as Hahn spin echo or CPMG. However, such ideal pulses are often challenging to implement experimentally with high fidelity. Here, we uncover a new geometrical framework for visualizing all possible driving fields, which enables one to generate an unlimited number of smooth, experimentally feasible pulses that perform dynamical decoupling or dynamically corrected gates to arbitrarily high order. We demonstrate that this scheme can significantly enhance the fidelity of single-qubit operations in the presence of noise and when realistic limitations on pulse rise times and amplitudes are taken into account.

Dynamical effects in Bragg coherent x-ray diffraction imaging of finite crystals

NASA Astrophysics Data System (ADS)

Shabalin, A. G.; Yefanov, O. M.; Nosik, V. L.; Bushuev, V. A.; Vartanyants, I. A.

2017-08-01

We present simulations of Bragg coherent x-ray diffractive imaging (CXDI) data from finite crystals in the frame of the dynamical theory of x-ray diffraction. The developed approach is based on a numerical solution of modified Takagi-Taupin equations and can be applied for modeling of a broad range of x-ray diffraction experiments with finite three-dimensional crystals of arbitrary shape also in the presence of strain. We performed simulations for nanocrystals of a cubic and hemispherical shape of different sizes and provided a detailed analysis of artifacts in the Bragg CXDI reconstructions introduced by the dynamical diffraction. Based on our theoretical analysis we developed an analytical procedure to treat effects of refraction and absorption in the reconstruction. Our results elucidate limitations for the kinematical approach in the Bragg CXDI and suggest a natural criterion to distinguish between kinematical and dynamical cases in coherent x-ray diffraction on a finite crystal.

Electrically tunable metasurface perfect absorbers for ultrathin mid-infrared optical modulators.

PubMed

Yao, Yu; Shankar, Raji; Kats, Mikhail A; Song, Yi; Kong, Jing; Loncar, Marko; Capasso, Federico

2014-11-12

Dynamically reconfigurable metasurfaces open up unprecedented opportunities in applications such as high capacity communications, dynamic beam shaping, hyperspectral imaging, and adaptive optics. The realization of high performance metasurface-based devices remains a great challenge due to very limited tuning ranges and modulation depths. Here we show that a widely tunable metasurface composed of optical antennas on graphene can be incorporated into a subwavelength-thick optical cavity to create an electrically tunable perfect absorber. By switching the absorber in and out of the critical coupling condition via the gate voltage applied on graphene, a modulation depth of up to 100% can be achieved. In particular, we demonstrated ultrathin (thickness < λ0/10) high speed (up to 20 GHz) optical modulators over a broad wavelength range (5-7 μm). The operating wavelength can be scaled from the near-infrared to the terahertz by simply tailoring the metasurface and cavity dimensions.

Relation of short-range and long-range lithium ion dynamics in glass-ceramics: Insights from 7Li NMR field-cycling and field-gradient studies

NASA Astrophysics Data System (ADS)

Haaks, Michael; Martin, Steve W.; Vogel, Michael

2017-09-01

We use various 7Li NMR methods to investigate lithium ion dynamics in 70Li 2S-30 P 2S5 glass and glass-ceramic obtained from this glass after heat treatment. We employ 7Li spin-lattice relaxometry, including field-cycling measurements, and line-shape analysis to investigate short-range ion jumps as well as 7Li field-gradient approaches to characterize long-range ion diffusion. The results show that ceramization substantially enhances the lithium ion mobility on all length scales. For the 70Li 2S-30 P 2S5 glass-ceramic, no evidence is found that bimodal dynamics result from different ion mobilities in glassy and crystalline regions of this sample. Rather, 7Li field-cycling relaxometry shows that dynamic susceptibilities in broad frequency and temperature ranges can be described by thermally activated jumps governed by a Gaussian distribution of activation energies g (Ea) with temperature-independent mean value Em=0.43 eV and standard deviation σ =0.07 eV . Moreover, use of this distribution allows us to rationalize 7Li line-shape results for the local ion jumps. In addition, this information about short-range ion dynamics further explains 7Li field-gradient results for long-range ion diffusion. In particular, we quantitatively show that, consistent with our experimental results, the temperature dependence of the self-diffusion coefficient D is not described by the mean activation energy Em of the local ion jumps, but by a significantly smaller apparent value whenever the distribution of correlation times G (logτ ) of the jump motion derives from an invariant distribution of activation energies and, hence, continuously broadens upon cooling. This effect occurs because the harmonic mean, which determines the results of diffusivity or also conductivity studies, continuously separates from the peak position of G (logτ ) when the width of this distribution increases.

Graph-based linear scaling electronic structure theory.

PubMed

Niklasson, Anders M N; Mniszewski, Susan M; Negre, Christian F A; Cawkwell, Marc J; Swart, Pieter J; Mohd-Yusof, Jamal; Germann, Timothy C; Wall, Michael E; Bock, Nicolas; Rubensson, Emanuel H; Djidjev, Hristo

2016-06-21

We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.

Graph-based linear scaling electronic structure theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Niklasson, Anders M. N., E-mail: amn@lanl.gov; Negre, Christian F. A.; Cawkwell, Marc J.

2016-06-21

We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.

Summary Report of the Summer Conference of the DARPA-Materials Research Council Held in La Jolla, California on 6-30 July 1987

DTIC Science & Technology

1987-07-01

that any array detector have very broad dynamic range. iv.) Analytical methods used in extracting structural data from experimental observations from...important influence on magnet design and on specialized magnetic devices ( SQUID devices) and forms the basis for promising electronic devices ’Josephson...printable inks using 123 powders. (2) Control of interfacial reactions between the superconductors and the dielectric. (3) Development of suitable

An Empirical Study of Combining Communicating Processes in a Parallel Discrete Event Simulation

DTIC Science & Technology

1990-12-01

dynamics of the cost/performance criteria which typically made up computer resource acquisition decisions . offering a broad range of tradeoffs in the way... prcesses has a significant impact on simulation performance. It is the hypothesis of this 3-4 SYSTEM DECOMPOSITION PHYSICAL SYSTEM 1: N PHYSICAL PROCESS 1...EMPTY)) next-event = pop(next-event-queue); lp-clock = next-event - time; Simulate next event departure- consume event-enqueue new event end while; If no

A systematic investigation of aluminium ion speciation at high temperature. Part 1. Solution studies.

PubMed

Shafran, Kirill L; Perry, Carole C

2005-06-21

Speciation diagrams of aluminium ions in aqueous solution (0.2 M) at high temperature (90 degrees C) have been obtained from 48 h time-resolved multi-batch titration experiments monitored by 27Al NMR spectroscopy, potentiometry and dynamic light scattering. The quantitative speciation patterns and kinetic data obtained offer a dynamic picture of the distribution of soluble and insoluble Al species as a function of hydrolysis ratio h(h=[OH-]/[Al3+]) over a very broad range of conditions (-1.0 < or =h < or = 4.0). Monomeric, small oligomeric, tridecameric (the 'Al13-mer') and the recently characterised 30-meric aluminium species (the 'Al30-mer') as well as aluminium hydroxide have been identified and quantified. The Al13-mer species dominates over a relatively broad range of hydrolysis ratios (1.5 < or =h< or = 2.7) during the first 6 h of experiment, but are gradually replaced by Al30-mers at longer reaction times. Kinetic profiles indicate that the formation of the Al30-mer is limited by the disappearance of the Al13 species at mildly acidic conditions. The estimated rate constants of both hydrolytic processes show good internal correlation at h> or = 1.5. The effect of local perturbations leading to the formation of aluminium hydroxide below the electroneutrality point (h= 3.0) has been estimated quantitatively.

Evolution and selection of river networks: Statics, dynamics, and complexity

PubMed Central

Rinaldo, Andrea; Rigon, Riccardo; Banavar, Jayanth R.; Maritan, Amos; Rodriguez-Iturbe, Ignacio

2014-01-01

Moving from the exact result that drainage network configurations minimizing total energy dissipation are stationary solutions of the general equation describing landscape evolution, we review the static properties and the dynamic origins of the scale-invariant structure of optimal river patterns. Optimal channel networks (OCNs) are feasible optimal configurations of a spanning network mimicking landscape evolution and network selection through imperfect searches for dynamically accessible states. OCNs are spanning loopless configurations, however, only under precise physical requirements that arise under the constraints imposed by river dynamics—every spanning tree is exactly a local minimum of total energy dissipation. It is remarkable that dynamically accessible configurations, the local optima, stabilize into diverse metastable forms that are nevertheless characterized by universal statistical features. Such universal features explain very well the statistics of, and the linkages among, the scaling features measured for fluvial landforms across a broad range of scales regardless of geology, exposed lithology, vegetation, or climate, and differ significantly from those of the ground state, known exactly. Results are provided on the emergence of criticality through adaptative evolution and on the yet-unexplored range of applications of the OCN concept. PMID:24550264

Frontiers of two-dimensional correlation spectroscopy. Part 2. Perturbation methods, fields of applications, and types of analytical probes

NASA Astrophysics Data System (ADS)

Noda, Isao

2014-07-01

Noteworthy experimental practices, which are advancing forward the frontiers of the field of two-dimensional (2D) correlation spectroscopy, are reviewed with the focus on various perturbation methods currently practiced to induce spectral changes, pertinent examples of applications in various fields, and types of analytical probes employed. Types of perturbation methods found in the published literature are very diverse, encompassing both dynamic and static effects. Although a sizable portion of publications report the use of dynamic perturbatuions, much greater number of studies employ static effect, especially that of temperature. Fields of applications covered by the literature are also very broad, ranging from fundamental research to practical applications in a number of physical, chemical and biological systems, such as synthetic polymers, composites and biomolecules. Aside from IR spectroscopy, which is the most commonly used tool, many other analytical probes are used in 2D correlation analysis. The ever expanding trend in depth, breadth and versatility of 2D correlation spectroscopy techniques and their broad applications all point to the robust and healthy state of the field.

Particle and Blood Cell Dynamics in Oscillatory Flows Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Juan M. Restrepo

2008-09-01

Our aim has been to uncover fundamental aspects of the suspension and dislodgement of particles in wall-bounded oscillatory flows, in flows characterized by Reynolds numbers en- compassing the situation found in rivers and near shores (and perhaps in some industrial processes). Our research tools are computational and our coverage of parameter space fairly broad. Computational means circumvent many complications that make the measurement of the dynamics of particles in a laboratory setting an impractical task, especially on the broad range of parameter space we plan to report upon. The impact of this work on the geophysical problem of sedimentation ismore » boosted considerably by the fact that the proposed calculations can be considered ab-initio, in the sense that little to no modeling is done in generating dynamics of the particles and of the moving fluid: we use a three-dimensional Navier Stokes solver along with straightforward boundry conditions. Hence, to the extent that Navier Stokes is a model for an ideal incompressible isotropic Newtonian fluid, the calculations yield benchmark values for such things as the drag, buoyancy, and lift of particles, in a highly controlled environment. Our approach will be to make measurements of the lift, drag, and buoyancy of particles, by considering progressively more complex physical configurations and physics.« less

Nonlinear spatio-temporal filtering of dynamic PET data using a four-dimensional Gaussian filter and expectation-maximization deconvolution

NASA Astrophysics Data System (ADS)

Floberg, J. M.; Holden, J. E.

2013-02-01

We introduce a method for denoising dynamic PET data, spatio-temporal expectation-maximization (STEM) filtering, that combines four-dimensional Gaussian filtering with EM deconvolution. The initial Gaussian filter suppresses noise at a broad range of spatial and temporal frequencies and EM deconvolution quickly restores the frequencies most important to the signal. We aim to demonstrate that STEM filtering can improve variance in both individual time frames and in parametric images without introducing significant bias. We evaluate STEM filtering with a dynamic phantom study, and with simulated and human dynamic PET studies of a tracer with reversible binding behaviour, [C-11]raclopride, and a tracer with irreversible binding behaviour, [F-18]FDOPA. STEM filtering is compared to a number of established three and four-dimensional denoising methods. STEM filtering provides substantial improvements in variance in both individual time frames and in parametric images generated with a number of kinetic analysis techniques while introducing little bias. STEM filtering does bias early frames, but this does not affect quantitative parameter estimates. STEM filtering is shown to be superior to the other simple denoising methods studied. STEM filtering is a simple and effective denoising method that could be valuable for a wide range of dynamic PET applications.

Dynamic Scaling of Colloidal Gel Formation at Intermediate Concentrations

DOE PAGES

Zhang, Qingteng; Bahadur, Divya; Dufresne, Eric M.; ...

2017-10-25

Here, we have examined the formation and dissolution of gels composed of intermediate volume-fraction nanoparticles with temperature-dependent short-range attractions using small-angle x-ray scatter- ing (SAXS), x-ray photon correlation spectroscopy (XPCS), and rheology to obtain nanoscale and macroscale sensitivity to structure and dynamics. Gel formation after temperature quenches to the vicinity of the rheologically-determined gel temperature, T gel, was characterized via the slow-down of dynamics and changes in microstructure observed in the intensity autocorrelation functions and structure factor, respectively, as a function of quench depth (ΔT = T quench - T gel), wave vector, and formation time (t f). We findmore » similar patterns in the slow-down of dynamics that maps the wave-vector-dependent dynamics at a particular ΔT and t f to that at other ΔTs and t fs via an effective scaling temperature, Ts. A single Ts applies to a broad range of ΔT and tf but does depend on the particle size. The rate of formation implied by the scaling is a far stronger function of ΔT than that of the attraction strength between colloids. Finally, we interpret this strong temperature de- pendence in terms of changes in cooperative bonding required to form stable, energetically favored, local structures.« less

Dynamic Scaling of Colloidal Gel Formation at Intermediate Concentrations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Qingteng; Bahadur, Divya; Dufresne, Eric M.

Here, we have examined the formation and dissolution of gels composed of intermediate volume-fraction nanoparticles with temperature-dependent short-range attractions using small-angle x-ray scatter- ing (SAXS), x-ray photon correlation spectroscopy (XPCS), and rheology to obtain nanoscale and macroscale sensitivity to structure and dynamics. Gel formation after temperature quenches to the vicinity of the rheologically-determined gel temperature, T gel, was characterized via the slow-down of dynamics and changes in microstructure observed in the intensity autocorrelation functions and structure factor, respectively, as a function of quench depth (ΔT = T quench - T gel), wave vector, and formation time (t f). We findmore » similar patterns in the slow-down of dynamics that maps the wave-vector-dependent dynamics at a particular ΔT and t f to that at other ΔTs and t fs via an effective scaling temperature, Ts. A single Ts applies to a broad range of ΔT and tf but does depend on the particle size. The rate of formation implied by the scaling is a far stronger function of ΔT than that of the attraction strength between colloids. Finally, we interpret this strong temperature de- pendence in terms of changes in cooperative bonding required to form stable, energetically favored, local structures.« less

Formulation of image quality prediction criteria for the Viking lander camera

NASA Technical Reports Server (NTRS)

Huck, F. O.; Jobson, D. J.; Taylor, E. J.; Wall, S. D.

1973-01-01

Image quality criteria are defined and mathematically formulated for the prediction computer program which is to be developed for the Viking lander imaging experiment. The general objective of broad-band (black and white) imagery to resolve small spatial details and slopes is formulated as the detectability of a right-circular cone with surface properties of the surrounding terrain. The general objective of narrow-band (color and near-infrared) imagery to observe spectral characteristics if formulated as the minimum detectable albedo variation. The general goal to encompass, but not exceed, the range of the scene radiance distribution within single, commandable, camera dynamic range setting is also considered.

"Group IV Nanomembranes, Nanoribbons, and Quantum Dots: Processing, Characterization, and Novel Devices"

DOE Office of Scientific and Technical Information (OSTI.GOV)

liu, feng

This theoretical project has been carried out in close interaction with the experimental project at UW-Madison under the same title led by PI Max Lagally and co-PI Mark Eriksson. Extensive computational studies have been performed to address a broad range of topics from atomic structure, stability, mechanical property, to electronic structure, optoelectronic and transport properties of various nanoarchitectures in the context of Si and other solid nanomembranes. These have been done by using combinations of different theoretical and computational approaches, ranging from first-principles calculations and molecular dynamics (MD) simulations to finite-element (FE) analyses and continuum modeling.

Dynamic and diverse sugar signaling

PubMed Central

Li, Lei; Sheen, Jen

2016-01-01

Sugars fuel life and exert numerous regulatory actions that are fundamental to all life forms. There are two principal mechanisms underlie sugar “perception and signal transduction” in biological systems. Direct sensing and signaling is triggered via sugar-binding sensors with a broad range of affinity and specificity, whereas sugar-derived bioenergetic molecules and metabolites modulate signaling proteins and indirectly relay sugar signals. This review discusses the emerging sugar signals and potential sugar sensors discovered in plant systems. The findings leading to informative understanding of physiological regulation by sugars are considered and assessed. Comparative transcriptome analyses highlight the primary and dynamic sugar responses and reveal the convergent and specific regulators of key biological processes in the sugar-signaling network. PMID:27423125

Probing messenger RNA conformational heterogeneity using single-molecule fluorescence anisotropy

NASA Astrophysics Data System (ADS)

Sinha, Deepak; Sastry, Srikanth; Shivashankar, G. V.

2006-03-01

In this letter we describe a method to probe biomolecular conformations and their dynamics at the single molecule level. We show, using fluorescence anisotropy based methods, that the hydrodynamic volume of biomolecules captures the intrinsic heterogeneity within a population. Population distributions of conformations and their dynamics are studied by making anisotropy measurements on one molecule at a time within a confocal volume. The mean anisotropy of mRNA is lowered on addition of salt while the spread remains the same. The intrinsic heterogeneity is revealed when conformational transitions are frozen, resulting in a drastic increase in the spread of the anisotropy. These studies reveal that mRNA samples a broad range of conformations.

Photoionization Modeling

NASA Technical Reports Server (NTRS)

Kallman, T.

2010-01-01

Warm absorber spectra are characterized by the many lines from partially ionized intermediate-Z elements, and iron, detected with the grating instruments on Chandra and XMM-Newton. If these ions are formed in a gas which is in photoionization equilibrium, they correspond to a broad range of ionization parameters, although there is evidence for certain preferred values. A test for any dynamical model for these outflows is to reproduce these properties, at some level of detail. In this paper we present a statistical analysis of the ionization distribution which can be applied both the observed spectra and to theoretical models. As an example, we apply it to our dynamical models for warm absorber outflows, based on evaporation from the molecular torus.

Femtosecond movies of water near interfaces at sub-Angstrom resolution

NASA Astrophysics Data System (ADS)

Coridan, Robert; Hwee Lai, Ghee; Schmidt, Nathan; Abbamonte, Peter; Wong, Gerard C. L.

2010-03-01

The behavior of liquid water near interfaces with nanoscopic variations in chemistry influences a broad range of phenomena in biology. Using inelastic x-ray scattering (IXS) data from 3rd-generation synchrotron x-ray sources, we reconstruct the Greens function of liquid water, which describes the å-scale spatial and femtosecond-scale temporal evolution of density fluctuations. We extend this response function formalism to reconstruct the evolution of hydration structures near dynamic surfaces with different charge distributions, in order to define more precisely the molecular signature of hydrophilicity and hydrophobicity. Moreover, we investigate modifications to surface hydration structures and dynamics as the size of hydrophilic and hydrophobic patches are varied.

Atomistic simulations of TeO₂-based glasses: interatomic potentials and molecular dynamics.

PubMed

Gulenko, Anastasia; Masson, Olivier; Berghout, Abid; Hamani, David; Thomas, Philippe

2014-07-21

In this work we present for the first time empirical interatomic potentials that are able to reproduce TeO2-based systems. Using these potentials in classical molecular dynamics simulations, we obtained first results for the pure TeO2 glass structure model. The calculated pair distribution function is in good agreement with the experimental one, which indicates a realistic glass structure model. We investigated the short- and medium-range TeO2 glass structures. The local environment of the Te atom strongly varies, so that the glass structure model has a broad Q polyhedral distribution. The glass network is described as weakly connected with a large number of terminal oxygen atoms.

Multiphase Equations of State for Polymer Materials at High Dynamic Pressures

NASA Astrophysics Data System (ADS)

Khishchenko, Konstantin V.

2015-06-01

Equations of state for materials over a wide range of pressures and temperatures are necessary for numerical simulations of shock-wave processes in condensed matter. Accuracy of calculation results is determined mainly by adequacy of equation of state of a medium. In this work, a new multiphase equation-of-state model is proposed with taking into account the polymorphic phase transformations, melting and evaporation. Thermodynamic calculations are carried out for 2 polymer materials (polymethylmethacrylate and polytetrafluoroethylene) in a broad region of the phase diagram. Obtained results are presented in comparison with available data of experiments at high dynamic pressures in shock and release waves. This work is supported by RSF, Grant 14-50-00124.

Exact law for homogeneous compressible Hall magnetohydrodynamics turbulence

NASA Astrophysics Data System (ADS)

Andrés, N.; Galtier, S.; Sahraoui, F.

2018-01-01

We derive an exact law for three-dimensional (3D) homogeneous compressible isothermal Hall magnetohydrodynamic turbulence, without the assumption of isotropy. The Hall current is shown to introduce new flux and source terms that act at the small scales (comparable or smaller than the ion skin depth) to significantly impact the turbulence dynamics. The law provides an accurate means to estimate the energy cascade rate over a broad range of scales covering the magnetohydrodynamic inertial range and the sub-ion dispersive range in 3D numerical simulations and in in situ spacecraft observations of compressible turbulence. This work is particularly relevant to astrophysical flows in which small-scale density fluctuations cannot be ignored such as the solar wind, planetary magnetospheres, and the interstellar medium.

The dynamics of biogeographic ranges in the deep sea.

PubMed

McClain, Craig R; Hardy, Sarah Mincks

2010-12-07

Anthropogenic disturbances such as fishing, mining, oil drilling, bioprospecting, warming, and acidification in the deep sea are increasing, yet generalities about deep-sea biogeography remain elusive. Owing to the lack of perceived environmental variability and geographical barriers, ranges of deep-sea species were traditionally assumed to be exceedingly large. In contrast, seamount and chemosynthetic habitats with reported high endemicity challenge the broad applicability of a single biogeographic paradigm for the deep sea. New research benefiting from higher resolution sampling, molecular methods and public databases can now more rigorously examine dispersal distances and species ranges on the vast ocean floor. Here, we explore the major outstanding questions in deep-sea biogeography. Based on current evidence, many taxa appear broadly distributed across the deep sea, a pattern replicated in both the abyssal plains and specialized environments such as hydrothermal vents. Cold waters may slow larval metabolism and development augmenting the great intrinsic ability for dispersal among many deep-sea species. Currents, environmental shifts, and topography can prove to be dispersal barriers but are often semipermeable. Evidence of historical events such as points of faunal origin and climatic fluctuations are also evident in contemporary biogeographic ranges. Continued synthetic analysis, database construction, theoretical advancement and field sampling will be required to further refine hypotheses regarding deep-sea biogeography.

The dynamics of biogeographic ranges in the deep sea

PubMed Central

McClain, Craig R.; Hardy, Sarah Mincks

2010-01-01

Anthropogenic disturbances such as fishing, mining, oil drilling, bioprospecting, warming, and acidification in the deep sea are increasing, yet generalities about deep-sea biogeography remain elusive. Owing to the lack of perceived environmental variability and geographical barriers, ranges of deep-sea species were traditionally assumed to be exceedingly large. In contrast, seamount and chemosynthetic habitats with reported high endemicity challenge the broad applicability of a single biogeographic paradigm for the deep sea. New research benefiting from higher resolution sampling, molecular methods and public databases can now more rigorously examine dispersal distances and species ranges on the vast ocean floor. Here, we explore the major outstanding questions in deep-sea biogeography. Based on current evidence, many taxa appear broadly distributed across the deep sea, a pattern replicated in both the abyssal plains and specialized environments such as hydrothermal vents. Cold waters may slow larval metabolism and development augmenting the great intrinsic ability for dispersal among many deep-sea species. Currents, environmental shifts, and topography can prove to be dispersal barriers but are often semipermeable. Evidence of historical events such as points of faunal origin and climatic fluctuations are also evident in contemporary biogeographic ranges. Continued synthetic analysis, database construction, theoretical advancement and field sampling will be required to further refine hypotheses regarding deep-sea biogeography. PMID:20667884

Temperature drives abundance fluctuations, but spatial dynamics is constrained by landscape configuration: Implications for climate-driven range shift in a butterfly.

PubMed

Fourcade, Yoan; Ranius, Thomas; Öckinger, Erik

2017-10-01

Prediction of species distributions in an altered climate requires knowledge on how global- and local-scale factors interact to limit their current distributions. Such knowledge can be gained through studies of spatial population dynamics at climatic range margins. Here, using a butterfly (Pyrgus armoricanus) as model species, we first predicted based on species distribution modelling that its climatically suitable habitats currently extend north of its realized range. Projecting the model into scenarios of future climate, we showed that the distribution of climatically suitable habitats may shift northward by an additional 400 km in the future. Second, we used a 13-year monitoring dataset including the majority of all habitat patches at the species northern range margin to assess the synergetic impact of temperature fluctuations and spatial distribution of habitat, microclimatic conditions and habitat quality, on abundance and colonization-extinction dynamics. The fluctuation in abundance between years was almost entirely determined by the variation in temperature during the species larval development. In contrast, colonization and extinction dynamics were better explained by patch area, between-patch connectivity and host plant density. This suggests that the response of the species to future climate change may be limited by future land use and how its host plants respond to climate change. It is, thus, probable that dispersal limitation will prevent P. armoricanus from reaching its potential future distribution. We argue that models of range dynamics should consider the factors influencing metapopulation dynamics, especially at the range edges, and not only broad-scale climate. It includes factors acting at the scale of habitat patches such as habitat quality and microclimate and landscape-scale factors such as the spatial configuration of potentially suitable patches. Knowledge of population dynamics under various environmental conditions, and the incorporation of realistic scenarios of future land use, appears essential to provide predictions useful for actions mitigating the negative effects of climate change. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

Enzyme specificity under dynamic control

NASA Astrophysics Data System (ADS)

Ota, Nobuyuki; Agard, David A.

2002-03-01

The contributions of conformational dynamics to substrate specificity have been examined by the application of principal component analysis to molecular dynamics trajectories of alpha-lytic protease. The wild-type alpha-lytic protease is highly specific for substrates with small hydrophobic side chains at the specificity pocket, while the Met190Ala binding pocket mutant has a much broader specificity, actively hydrolyzing substrates ranging from Ala to Phe. We performed a principal component analysis using 1-nanosecond molecular dynamics simulations using solvent boundary condition. We found that the walls of the wild-type substrate binding pocket move in tandem with one another, causing the pocket size to remain fixed so that only small substrates are recognized. In contrast, the M190A mutant shows uncoupled movement of the binding pocket walls, allowing the pocket to sample both smaller and larger sizes, which appears to be the cause of the observed broad specificity. The results suggest that the protein dynamics of alpha-lytic protease may play a significant role in defining the patterns of substrate specificity.

Dynamics of individual perceptual decisions

PubMed Central

Clark, Torin K.; Lu, Yue M.; Karmali, Faisal

2015-01-01

Perceptual decision making is fundamental to a broad range of fields including neurophysiology, economics, medicine, advertising, law, etc. Although recent findings have yielded major advances in our understanding of perceptual decision making, decision making as a function of time and frequency (i.e., decision-making dynamics) is not well understood. To limit the review length, we focus most of this review on human findings. Animal findings, which are extensively reviewed elsewhere, are included when beneficial or necessary. We attempt to put these various findings and data sets, which can appear to be unrelated in the absence of a formal dynamic analysis, into context using published models. Specifically, by adding appropriate dynamic mechanisms (e.g., high-pass filters) to existing models, it appears that a number of otherwise seemingly disparate findings from the literature might be explained. One hypothesis that arises through this dynamic analysis is that decision making includes phasic (high pass) neural mechanisms, an evidence accumulator and/or some sort of midtrial decision-making mechanism (e.g., peak detector and/or decision boundary). PMID:26467513

Coherent exciton-vibrational dynamics and energy transfer in conjugated organics

DOE PAGES

Nelson, Tammie R.; Ondarse-Alvarez, Dianelys; Oldani, Nicolas; ...

2018-06-13

Coherence, signifying concurrent electron-vibrational dynamics in complex natural and man-made systems, is currently a subject of intense study. Understanding this phenomenon is important when designing carrier transport in optoelectronic materials. Here, excited state dynamics simulations reveal a ubiquitous pattern in the evolution of photoexcitations for a broad range of molecular systems. Symmetries of the wavefunctions define a specific form of the non-adiabatic coupling that drives quantum transitions between excited states, leading to a collective asymmetric vibrational excitation coupled to the electronic system. This promotes periodic oscillatory evolution of the wavefunctions, preserving specific phase and amplitude relations across the ensemble ofmore » trajectories. The simple model proposed here explains the appearance of coherent exciton-vibrational dynamics due to non-adiabatic transitions, which is universal across multiple molecular systems. The observed relationships between electronic wavefunctions and the resulting functionalities allows us to understand, and potentially manipulate, excited state dynamics and energy transfer in molecular materials.« less

Coherent exciton-vibrational dynamics and energy transfer in conjugated organics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nelson, Tammie R.; Ondarse-Alvarez, Dianelys; Oldani, Nicolas

Coherence, signifying concurrent electron-vibrational dynamics in complex natural and man-made systems, is currently a subject of intense study. Understanding this phenomenon is important when designing carrier transport in optoelectronic materials. Here, excited state dynamics simulations reveal a ubiquitous pattern in the evolution of photoexcitations for a broad range of molecular systems. Symmetries of the wavefunctions define a specific form of the non-adiabatic coupling that drives quantum transitions between excited states, leading to a collective asymmetric vibrational excitation coupled to the electronic system. This promotes periodic oscillatory evolution of the wavefunctions, preserving specific phase and amplitude relations across the ensemble ofmore » trajectories. The simple model proposed here explains the appearance of coherent exciton-vibrational dynamics due to non-adiabatic transitions, which is universal across multiple molecular systems. The observed relationships between electronic wavefunctions and the resulting functionalities allows us to understand, and potentially manipulate, excited state dynamics and energy transfer in molecular materials.« less

Performance of the NIST goniocolorimeter with a broad-band source and multichannel charged coupled device based spectrometer.

PubMed

Podobedov, V B; Miller, C C; Nadal, M E

2012-09-01

The authors describe the NIST high-efficiency instrument for measurements of bidirectional reflectance distribution function of colored materials, including gonioapparent materials such as metallic and pearlescent coatings. The five-axis goniospectrometer measures the spectral reflectance of samples over a wide range of illumination and viewing angles. The implementation of a broad-band source and a multichannel CCD spectrometer corrected for stray light significantly increased the efficiency of the goniometer. In the extended range of 380 nm to 1050 nm, a reduction of measurement time from a few hours to a few minutes was obtained. Shorter measurement time reduces the load on the precise mechanical assembly ensuring high angular accuracy over time. We describe the application of matrix-based correction of stray light and the extension of effective dynamic range of measured fluxes to the values of 10(6) to 10(7) needed for the absolute characterization of samples. The measurement uncertainty was determined to be 0.7% (k = 2), which is comparable with similar instruments operating in a single channel configuration. Several examples of reflectance data obtained with the improved instrument indicate a 0.3% agreement compared to data collected with the single channel configuration.

The co-evolutionary dynamics of directed network of spin market agents

NASA Astrophysics Data System (ADS)

Horváth, Denis; Kuscsik, Zoltán; Gmitra, Martin

2006-09-01

The spin market model [S. Bornholdt, Int. J. Mod. Phys. C 12 (2001) 667] is generalized by employing co-evolutionary principles, where strategies of the interacting and competitive traders are represented by local and global couplings between the nodes of dynamic directed stochastic network. The co-evolutionary principles are applied in the frame of Bak-Sneppen self-organized dynamics [P. Bak, K. Sneppen, Phys. Rev. Lett. 71 (1993) 4083] that includes the processes of selection and extinction actuated by the local (node) fitness. The local fitness is related to orientation of spin agent with respect to the instant magnetization. The stationary regime is formed due to the interplay of self-organization and adaptivity effects. The fat tailed distributions of log-price returns are identified numerically. The non-trivial model consequence is the evidence of the long time market memory indicated by the power-law range of the autocorrelation function of volatility with exponent smaller than one. The simulations yield network topology with broad-scale node degree distribution characterized by the range of exponents 1.3<γin<3 coinciding with social networks.

Complex structural dynamics of nanocatalysts revealed in Operando conditions by correlated imaging and spectroscopy probes

DOE PAGES

Li, Y.; Zakharov, D.; Zhao, S.; ...

2015-06-29

Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction—ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. Lastly,more » this method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes.« less

The Hubble Space Telescope high speed photometer

NASA Technical Reports Server (NTRS)

Vancitters, G. W., Jr.; Bless, R. C.; Dolan, J. F.; Elliot, J. L.; Robinson, E. L.; White, R. L.

1988-01-01

The Hubble Space Telescope will provide the opportunity to perform precise astronomical photometry above the disturbing effects of the atmosphere. The High Speed Photometer is designed to provide the observatory with a stable, precise photometer with wide dynamic range, broad wavelenth coverage, time resolution in the microsecond region, and polarimetric capability. Here, the scientific requirements for the instrument are examined, the unique design features of the photometer are explored, and the improvements to be expected over the performance of ground-based instruments are projected.

Inference of Stochastic Nonlinear Oscillators with Applications to Physiological Problems

NASA Technical Reports Server (NTRS)

Smelyanskiy, Vadim N.; Luchinsky, Dmitry G.

2004-01-01

A new method of inferencing of coupled stochastic nonlinear oscillators is described. The technique does not require extensive global optimization, provides optimal compensation for noise-induced errors and is robust in a broad range of dynamical models. We illustrate the main ideas of the technique by inferencing a model of five globally and locally coupled noisy oscillators. Specific modifications of the technique for inferencing hidden degrees of freedom of coupled nonlinear oscillators is discussed in the context of physiological applications.

New applications of the renormalization group method in physics: a brief introduction.

PubMed

Meurice, Y; Perry, R; Tsai, S-W

2011-07-13

The renormalization group (RG) method developed by Ken Wilson more than four decades ago has revolutionized the way we think about problems involving a broad range of energy scales such as phase transitions, turbulence, continuum limits and bifurcations in dynamical systems. The Theme Issue provides articles reviewing recent progress made using the RG method in atomic, condensed matter, nuclear and particle physics. In the following, we introduce these articles in a way that emphasizes common themes and the universal aspects of the method.

Foam Rolling for Delayed-Onset Muscle Soreness and Recovery of Dynamic Performance Measures

PubMed Central

Pearcey, Gregory E. P.; Bradbury-Squires, David J.; Kawamoto, Jon-Erik; Drinkwater, Eric J.; Behm, David G.; Button, Duane C.

2015-01-01

Context: After an intense bout of exercise, foam rolling is thought to alleviate muscle fatigue and soreness (ie, delayed-onset muscle soreness [DOMS]) and improve muscular performance. Potentially, foam rolling may be an effective therapeutic modality to reduce DOMS while enhancing the recovery of muscular performance. Objective: To examine the effects of foam rolling as a recovery tool after an intense exercise protocol through assessment of pressure-pain threshold, sprint time, change-of-direction speed, power, and dynamic strength-endurance. Design: Controlled laboratory study. Setting: University laboratory. Patients or Other Participants: A total of 8 healthy, physically active males (age = 22.1 ± 2.5 years, height = 177.0 ± 7.5 cm, mass = 88.4 ± 11.4 kg) participated. Intervention(s): Participants performed 2 conditions, separated by 4 weeks, involving 10 sets of 10 repetitions of back squats at 60% of their 1-repetition maximum, followed by either no foam rolling or 20 minutes of foam rolling immediately, 24, and 48 hours postexercise. Main Outcome Measure(s): Pressure-pain threshold, sprint speed (30-m sprint time), power (broad-jump distance), change-of-direction speed (T-test), and dynamic strength-endurance. Results: Foam rolling substantially improved quadriceps muscle tenderness by a moderate to large amount in the days after fatigue (Cohen d range, 0.59 to 0.84). Substantial effects ranged from small to large in sprint time (Cohen d range, 0.68 to 0.77), power (Cohen d range, 0.48 to 0.87), and dynamic strength-endurance (Cohen d = 0.54). Conclusions: Foam rolling effectively reduced DOMS and associated decrements in most dynamic performance measures. PMID:25415413

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.

PubMed

Šponer, Jiří; Bussi, Giovanni; Krepl, Miroslav; Banáš, Pavel; Bottaro, Sandro; Cunha, Richard A; Gil-Ley, Alejandro; Pinamonti, Giovanni; Poblete, Simón; Jurečka, Petr; Walter, Nils G; Otyepka, Michal

2018-04-25

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.

The terrestrial plasma source - A new perspective in solar-terrestrial processes from Dynamics Explorer

NASA Technical Reports Server (NTRS)

Chappell, Charles R.

1988-01-01

The geospace environment has been viewed as a mixing bowl for plasmas of both solar and terrestrial origin. The present perspective on the nature of the supply mechanisms has undergone a radical evolution over the past decade, particularly during the five years of the Dynamics Explorer mission. During this period, the terrestrial source has increased in importance in both magnitude and character of ionospheric outflow. These outflows include the classical polar wind, the cleft ion fountain, the auroral ion fountain, and the polar cap. The earth can be envisioned as a multifaceted fountain which ejects particles from different spatial locations spread around the globe. These particles exhibit a range of masses from 1 to 32 amu and a range of energies from 1 eV to 10 keV. The total flux of this ionospheric outflow is very large: adequate to supply the entire magnetospheric particle population. And the implications of the outflow are significant across a broad spectrum of solar-terrestrial processes ranging from sources of magnetospheric plasmas, to influences on ionospheric density and temperature structure, to energy transfer in phenomena such as stable auroral red arcs. The Dynamics Explorer mission has made a major contribution in the characterization of the terrestrial plasma source.

Exploring Anomalous Polarization Dynamics in Organometallic Halide Perovskites

DOE PAGES

Ahmadi, Mahshid; Collins, Liam; Puretzky, Alexander; ...

2018-01-22

Organometallic halide perovskites (OMHPs) have attracted broad attention as prospective materials for optoelectronic applications. Among the many anomalous properties of these materials, of special interest are the ferroelectric properties including both classical and relaxor-like components, as a potential origin of slow dynamics, field enhancement, and anomalous mobilities. Here, ferroelectric properties of the three representative OMHPs are explored, including FAPb xSn 1–xI 3 (x = 0, x = 0.85) and FA 0.85MA 0.15PbI 3 using band excitation piezoresponse force microscopy and contact mode Kelvin probe force microscopy, providing insight into long- and short-range dipole and charge dynamics in these materials andmore » probing ferroelectric density of states. Furthermore, second-harmonic generation in thin films of OMHPs is observed, providing a direct information on the noncentrosymmetric polarization in such materials. Overall, the data provide strong evidence for the presence of ferroelectric domains in these systems; however, the domain dynamics is suppressed by fast ion dynamics. These materials hence present the limit of ferroelectric materials with spontaneous polarization dynamically screened by ionic and electronic carriers.« less

High frequency, multi-axis dynamic stiffness analysis of a fractionally damped elastomeric isolator using continuous system theory

NASA Astrophysics Data System (ADS)

Fredette, Luke; Singh, Rajendra

2017-02-01

A spectral element approach is proposed to determine the multi-axis dynamic stiffness terms of elastomeric isolators with fractional damping over a broad range of frequencies. The dynamic properties of a class of cylindrical isolators are modeled by using the continuous system theory in terms of homogeneous rods or Timoshenko beams. The transfer matrix type dynamic stiffness expressions are developed from exact harmonic solutions given translational or rotational displacement excitations. Broadband dynamic stiffness magnitudes (say up to 5 kHz) are computationally verified for axial, torsional, shear, flexural, and coupled stiffness terms using a finite element model. Some discrepancies are found between finite element and spectral element models for the axial and flexural motions, illustrating certain limitations of each method. Experimental validation is provided for an isolator with two cylindrical elements (that work primarily in the shear mode) using dynamic measurements, as reported in the prior literature, up to 600 Hz. Superiority of the fractional damping formulation over structural or viscous damping models is illustrated via experimental validation. Finally, the strengths and limitations of the spectral element approach are briefly discussed.

Exploring Anomalous Polarization Dynamics in Organometallic Halide Perovskites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahmadi, Mahshid; Collins, Liam; Puretzky, Alexander

Organometallic halide perovskites (OMHPs) have attracted broad attention as prospective materials for optoelectronic applications. Among the many anomalous properties of these materials, of special interest are the ferroelectric properties including both classical and relaxor-like components, as a potential origin of slow dynamics, field enhancement, and anomalous mobilities. Here, ferroelectric properties of the three representative OMHPs are explored, including FAPb xSn 1–xI 3 (x = 0, x = 0.85) and FA 0.85MA 0.15PbI 3 using band excitation piezoresponse force microscopy and contact mode Kelvin probe force microscopy, providing insight into long- and short-range dipole and charge dynamics in these materials andmore » probing ferroelectric density of states. Furthermore, second-harmonic generation in thin films of OMHPs is observed, providing a direct information on the noncentrosymmetric polarization in such materials. Overall, the data provide strong evidence for the presence of ferroelectric domains in these systems; however, the domain dynamics is suppressed by fast ion dynamics. These materials hence present the limit of ferroelectric materials with spontaneous polarization dynamically screened by ionic and electronic carriers.« less

Dielectric Study of Alcohols Using Broadband Terahertz Time Domain Spectroscopy (THz-TDS).

NASA Astrophysics Data System (ADS)

Sarkar, Sohini; Saha, Debasis; Banerjee, Sneha; Mukherjee, Arnab; Mandal, Pankaj

2016-06-01

Broadband Terahertz-Time Domain Spectroscopy (THz-TDS) (1-10 THz) has been utilized to study the complex dielectric properties of methanol, ethanol, 1-propanol, 2-propanol, 1-butanol, and 1-octanol. Previous reports on dielectric study of alcohols were limited to 5 THz. At THz (1 THz = 33.33 wn = 4 meV) frequency range (0.1 to 15 THz), the molecular reorientation and several intermolecular vibrations (local oscillation of dipoles) may coexist and contribute to the overall liquid dynamics. We find that the Debye type relaxations barely contribute beyond 1 THz, rather three harmonic oscillators dominate the entire spectral range. To get insights on the modes responsible for the observed absorption in THz frequency range, we performed all atom molecular dynamics (MD) using OPLS force field and ab initio quantum calculations. Combined experimental and theoretical study reveal that the complex dielectric functions of alcohols have contribution from a) alkyl group oscillation within H-bonded network ( 1 THz), b) intermolecular H-bond stretching ( 5 THz) , and c) librational motions in alcohols. The present work, therefore, complements all previous studies on alcohols at lower frequencies and provides a clear picture on them in a broad spectral range from microwave to 10 THz.

Self-shadowing effects of slim accretion disks in active galactic nuclei: the diverse appearance of the broad-line region

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jian-Min; Qiu, Jie; Du, Pu

2014-12-10

Supermassive black holes in active galactic nuclei (AGNs) undergo a wide range of accretion rates, which lead to diversity of appearance. We consider the effects of anisotropic radiation from accretion disks on the broad-line region (BLR) from the Shakura-Sunyaev regime to slim disks with super-Eddington accretion rates. The geometrically thick funnel of the inner region of slim disks produces strong self-shadowing effects that lead to very strong anisotropy of the radiation field. We demonstrate that the degree of anisotropy of the radiation fields grows with increasing accretion rate. As a result of this anisotropy, BLR clouds receive different spectral energymore » distributions depending on their location relative to the disk, resulting in the diverse observational appearance of the BLR. We show that the self-shadowing of the inner parts of the disk naturally produces two dynamically distinct regions of the BLR, depending on accretion rate. These two regions manifest themselves as kinematically distinct components of the broad Hβ line profile with different line widths and fluxes, which jointly account for the Lorentzian profile generally observed in narrow-line Seyfert 1 galaxies. In the time domain, these two components are expected to reverberate with different time lags with respect to the varying ionizing continuum, depending on the accretion rate and the viewing angle of the observer. The diverse appearance of the BLR due to the anisotropic ionizing energy source can be tested by reverberation mapping of Hβ and other broad emission lines (e.g., Fe II), providing a new tool to diagnose the structure and dynamics of the BLR. Other observational consequences of our model are also explored.« less

Altered dynamics of broad-leaved tree species in a Chinese subtropical montane mixed forest: the role of an anomalous extreme 2008 ice storm episode.

PubMed

Ge, Jielin; Xiong, Gaoming; Wang, Zhixian; Zhang, Mi; Zhao, Changming; Shen, Guozhen; Xu, Wenting; Xie, Zongqiang

2015-04-01

Extreme climatic events can trigger gradual or abrupt shifts in forest ecosystems via the reduction or elimination of foundation species. However, the impacts of these events on foundation species' demography and forest dynamics remain poorly understood. Here we quantified dynamics for both evergreen and deciduous broad-leaved species groups, utilizing a monitoring permanent plot in a subtropical montane mixed forest in central China from 2001 to 2010 with particular relevance to the anomalous 2008 ice storm episode. We found that both species groups showed limited floristic alterations over the study period. For each species group, size distribution of dead individuals approximated a roughly irregular and flat shape prior to the ice storm and resembled an inverse J-shaped distribution after the ice storm. Furthermore, patterns of mortality and recruitment displayed disequilibrium behaviors with mortality exceeding recruitment for both species groups following the ice storm. Deciduous broad-leaved species group accelerated overall diameter growth, but the ice storm reduced evergreen small-sized diameter growth. We concluded that evergreen broad-leaved species were more susceptible to ice storms than deciduous broad-leaved species, and ice storm events, which may become more frequent with climate change, might potentially threaten the perpetuity of evergreen-dominated broad-leaved forests in this subtropical region in the long term. These results underscore the importance of long-term monitoring that is indispensible to elucidate causal links between forest dynamics and climatic perturbations.

Altered dynamics of broad-leaved tree species in a Chinese subtropical montane mixed forest: the role of an anomalous extreme 2008 ice storm episode

PubMed Central

Ge, Jielin; Xiong, Gaoming; Wang, Zhixian; Zhang, Mi; Zhao, Changming; Shen, Guozhen; Xu, Wenting; Xie, Zongqiang

2015-01-01

Extreme climatic events can trigger gradual or abrupt shifts in forest ecosystems via the reduction or elimination of foundation species. However, the impacts of these events on foundation species' demography and forest dynamics remain poorly understood. Here we quantified dynamics for both evergreen and deciduous broad-leaved species groups, utilizing a monitoring permanent plot in a subtropical montane mixed forest in central China from 2001 to 2010 with particular relevance to the anomalous 2008 ice storm episode. We found that both species groups showed limited floristic alterations over the study period. For each species group, size distribution of dead individuals approximated a roughly irregular and flat shape prior to the ice storm and resembled an inverse J-shaped distribution after the ice storm. Furthermore, patterns of mortality and recruitment displayed disequilibrium behaviors with mortality exceeding recruitment for both species groups following the ice storm. Deciduous broad-leaved species group accelerated overall diameter growth, but the ice storm reduced evergreen small-sized diameter growth. We concluded that evergreen broad-leaved species were more susceptible to ice storms than deciduous broad-leaved species, and ice storm events, which may become more frequent with climate change, might potentially threaten the perpetuity of evergreen-dominated broad-leaved forests in this subtropical region in the long term. These results underscore the importance of long-term monitoring that is indispensible to elucidate causal links between forest dynamics and climatic perturbations. PMID:25897387

Caffeine-catalyzed gels.

PubMed

DiCiccio, Angela M; Lee, Young-Ah Lucy; Glettig, Dean L; Walton, Elizabeth S E; de la Serna, Eva L; Montgomery, Veronica A; Grant, Tyler M; Langer, Robert; Traverso, Giovanni

2018-07-01

Covalently cross-linked gels are utilized in a broad range of biomedical applications though their synthesis often compromises easy implementation. Cross-linking reactions commonly utilize catalysts or conditions that can damage biologics and sensitive compounds, producing materials that require extensive post processing to achieve acceptable biocompatibility. As an alternative, we report a batch synthesis platform to produce covalently cross-linked materials appropriate for direct biomedical application enabled by green chemistry and commonly available food grade ingredients. Using caffeine, a mild base, to catalyze anhydrous carboxylate ring-opening of diglycidyl-ether functionalized monomers with citric acid as a tri-functional crosslinking agent we introduce a novel poly(ester-ether) gel synthesis platform. We demonstrate that biocompatible Caffeine Catalyzed Gels (CCGs) exhibit dynamic physical, chemical, and mechanical properties, which can be tailored in shape, surface texture, solvent response, cargo release, shear and tensile strength, among other potential attributes. The demonstrated versatility, low cost and facile synthesis of these CCGs renders them appropriate for a broad range of customized engineering applications including drug delivery constructs, tissue engineering scaffolds, and medical devices. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Reservoir Computing Beyond Memory-Nonlinearity Trade-off.

PubMed

Inubushi, Masanobu; Yoshimura, Kazuyuki

2017-08-31

Reservoir computing is a brain-inspired machine learning framework that employs a signal-driven dynamical system, in particular harnessing common-signal-induced synchronization which is a widely observed nonlinear phenomenon. Basic understanding of a working principle in reservoir computing can be expected to shed light on how information is stored and processed in nonlinear dynamical systems, potentially leading to progress in a broad range of nonlinear sciences. As a first step toward this goal, from the viewpoint of nonlinear physics and information theory, we study the memory-nonlinearity trade-off uncovered by Dambre et al. (2012). Focusing on a variational equation, we clarify a dynamical mechanism behind the trade-off, which illustrates why nonlinear dynamics degrades memory stored in dynamical system in general. Moreover, based on the trade-off, we propose a mixture reservoir endowed with both linear and nonlinear dynamics and show that it improves the performance of information processing. Interestingly, for some tasks, significant improvements are observed by adding a few linear dynamics to the nonlinear dynamical system. By employing the echo state network model, the effect of the mixture reservoir is numerically verified for a simple function approximation task and for more complex tasks.

Heliospotlight: An Information Resource for Heliophysics

NASA Astrophysics Data System (ADS)

Young, C.; Wawro, M.; Schenk, L. C.

2013-12-01

The NASA Goddard Heliophysics Science Division (HSD) EPO and mission websites are rich with content covering the broad subject of heliophysics. This includes detailed information for many age groups, a large range of descriptive imagery and dynamic video and interactive material. The weakness of all this content is that it is scattered over so many websites as opposed to being organized and focused in one user friendly location. The website heliospotlight.org is being developed to address all these concerns, leveraging the vast content already developed while using state-of-the-art web technologies. This will provide a rich user experience simultaneously tailoring to the needs of the broad audience of students, educators, scientists, journalists and the general public. The website will use well supported, open source technologies enabling future flexibility and expansion. HSD EPO will support the development of this information resource.

Black Hole Safari: Tracking Populations and Hunting Big Game

NASA Astrophysics Data System (ADS)

McConnell, N. J.

2013-10-01

Understanding the physical connection, or lack thereof, between the growth of galaxies and supermassive black holes is a key challenge in extragalactic astronomy. Dynamical studies of nearby galaxies are building a census of black hole masses across a broad range of galaxy types and uncovering statistical correlations between galaxy bulge properties and black hole masses. These local correlations provide a baseline for studying galaxies and black holes at higher redshifts. Recent measurements have probed the extremes of the supermassive black hole population and introduced surprises that challenge simple models of black hole and galaxy co-evolution. Future advances in the quality and quantity of dynamical black hole mass measurements will shed light upon the growth of massive galaxies and black holes in different cosmic environments.

Nonparametric Inference of Doubly Stochastic Poisson Process Data via the Kernel Method

PubMed Central

Zhang, Tingting; Kou, S. C.

2010-01-01

Doubly stochastic Poisson processes, also known as the Cox processes, frequently occur in various scientific fields. In this article, motivated primarily by analyzing Cox process data in biophysics, we propose a nonparametric kernel-based inference method. We conduct a detailed study, including an asymptotic analysis, of the proposed method, and provide guidelines for its practical use, introducing a fast and stable regression method for bandwidth selection. We apply our method to real photon arrival data from recent single-molecule biophysical experiments, investigating proteins' conformational dynamics. Our result shows that conformational fluctuation is widely present in protein systems, and that the fluctuation covers a broad range of time scales, highlighting the dynamic and complex nature of proteins' structure. PMID:21258615

Nonparametric Inference of Doubly Stochastic Poisson Process Data via the Kernel Method.

PubMed

Zhang, Tingting; Kou, S C

2010-01-01

Doubly stochastic Poisson processes, also known as the Cox processes, frequently occur in various scientific fields. In this article, motivated primarily by analyzing Cox process data in biophysics, we propose a nonparametric kernel-based inference method. We conduct a detailed study, including an asymptotic analysis, of the proposed method, and provide guidelines for its practical use, introducing a fast and stable regression method for bandwidth selection. We apply our method to real photon arrival data from recent single-molecule biophysical experiments, investigating proteins' conformational dynamics. Our result shows that conformational fluctuation is widely present in protein systems, and that the fluctuation covers a broad range of time scales, highlighting the dynamic and complex nature of proteins' structure.

Car-Parrinello molecular dynamics study of the melting behaviors of n-atom (n = 6, 10) graphene quantum dots

NASA Astrophysics Data System (ADS)

Shekaari, Ashkan; Abolhassani, Mohammad Reza

2017-06-01

First-principles molecular dynamics has been applied to inquire into the melting behaviors of n-atom (n = 6, 10) graphene quantum dots (GQD6 and zigzag GQD10) within the temperature range of T = 0-500 K. The temperature dependence of the geometry of each quantum dot is thoroughly evaluated via calculating the related shape deformation parameters and the eigenvalues of the quadrupole tensors. Examining the variations of some phase-transition indicators such as root-mean-square bond length fluctuations and mean square displacements broadly proposes the value of Tm = 70 K for the melting point of GQD6 while a continuous, two-stage phase transition has been concluded for zigzag GQD10.

Fluid and particle transport of a hairy structure

NASA Astrophysics Data System (ADS)

Lee, Hongki; Lahooti, Mohsen; Kim, Daegyoum; Jung, Seyeong

2017-11-01

Hairy appendages of animals are used to capture particles, sense surrounding flow, and generate propulsive force. Due to the small size of the hairy structures, their hydrodynamics have been studied mostly in very low Reynolds number. In this work, in a broad range of Reynolds number, O(1) - O(100), flow structure and inertial particle dynamics around an array of two-dimensional cylinders are investigated numerically by using an immersed boundary method. Given flow fields, Maxey-Riley equation is adopted to examine particle dynamics. Here, we discuss the effects of Reynolds number, density ratio of inertial particles and fluid, and distance between cylinders on particle behaviors around a moving structure. In addition, drift volume of inertial particles is correlated with the model parameters.

A summary of the results from the UCLA OGO-5 fluxgate magnetometer

NASA Technical Reports Server (NTRS)

Coleman, P. J., Jr.; Russell, C. T.

1973-01-01

The OGO-5 fluxgate magnetometer experiment (E-14) was designed to measure the vector magnetic field over the full range of the OGO-5 orbit. Thus, it had a dynamic range of + or - 64,000 gamma yet it maintained a precision of + or - 1/16 gamma at all times. This enabled a broad spectrum of problems to be attached. Studies of the magnetospheric waves, currents, waves-particle interactions, pitch angle distributions and wave normal directions were made. The structure of the magnetopause, the magnetotail, and bow shock were probed, waves and discontinuities in the solar wind were examined and the various phases of substorms were examined in depth.

Electromagnetic behavior of spatial terahertz wave modulators based on reconfigurable micromirror gratings in Littrow configuration.

PubMed

Kappa, Jan; Schmitt, Klemens M; Rahm, Marco

2017-08-21

Efficient, high speed spatial modulators with predictable performance are a key element in any coded aperture terahertz imaging system. For spectroscopy, the modulators must also provide a broad modulation frequency range. In this study, we numerically analyze the electromagnetic behavior of a dynamically reconfigurable spatial terahertz wave modulator based on a micromirror grating in Littrow configuration. We show that such a modulator can modulate terahertz radiation over a wide frequency range from 1.7 THz to beyond 3 THz at a modulation depth of more than 0.6. As a specific example, we numerically simulated coded aperture imaging of an object with binary transmissive properties and successfully reconstructed the image.

Development of high sensitivity eight-element multiplexed fiber laser acoustic pressure hydrophone array and interrogation system

NASA Astrophysics Data System (ADS)

Li, Ming; Sun, Zhihui; Zhang, Xiaolei; Li, Shujuan; Song, Zhiqiang; Wang, Meng; Guo, Jian; Ni, Jiasheng; Wang, Chang; Peng, Gangding; Xu, Xiangang

2017-09-01

Fiber laser hydrophones have got widespread concerns due to the unique advantages and broad application prospects. In this paper, the research results of the eight-element multiplexed fiber laser acoustic pressure array and the interrogation system are introduced, containing low-noise distributed feedback fiber laser (DFB-FL) fabrication, sensitivity enhancement packaging, and interferometric signal demodulation. The frequency response range of the system is 10Hz-10kHz, the laser frequency acoustic pressure sensitivity reaches 115 dB re Hz/Pa, and the equivalent noise acoustic pressure is less than 60μPa/Hz1/2. The dynamic range of the system is greater than 120 dB.

Hierarchical classification with a competitive evolutionary neural tree.

PubMed

Adams, R G.; Butchart, K; Davey, N

1999-04-01

A new, dynamic, tree structured network, the Competitive Evolutionary Neural Tree (CENT) is introduced. The network is able to provide a hierarchical classification of unlabelled data sets. The main advantage that the CENT offers over other hierarchical competitive networks is its ability to self determine the number, and structure, of the competitive nodes in the network, without the need for externally set parameters. The network produces stable classificatory structures by halting its growth using locally calculated heuristics. The results of network simulations are presented over a range of data sets, including Anderson's IRIS data set. The CENT network demonstrates its ability to produce a representative hierarchical structure to classify a broad range of data sets.

Complex dynamics of memristive circuits: Analytical results and universal slow relaxation

NASA Astrophysics Data System (ADS)

Caravelli, F.; Traversa, F. L.; Di Ventra, M.

2017-02-01

Networks with memristive elements (resistors with memory) are being explored for a variety of applications ranging from unconventional computing to models of the brain. However, analytical results that highlight the role of the graph connectivity on the memory dynamics are still few, thus limiting our understanding of these important dynamical systems. In this paper, we derive an exact matrix equation of motion that takes into account all the network constraints of a purely memristive circuit, and we employ it to derive analytical results regarding its relaxation properties. We are able to describe the memory evolution in terms of orthogonal projection operators onto the subspace of fundamental loop space of the underlying circuit. This orthogonal projection explicitly reveals the coupling between the spatial and temporal sectors of the memristive circuits and compactly describes the circuit topology. For the case of disordered graphs, we are able to explain the emergence of a power-law relaxation as a superposition of exponential relaxation times with a broad range of scales using random matrices. This power law is also universal, namely independent of the topology of the underlying graph but dependent only on the density of loops. In the case of circuits subject to alternating voltage instead, we are able to obtain an approximate solution of the dynamics, which is tested against a specific network topology. These results suggest a much richer dynamics of memristive networks than previously considered.

Linear and nonlinear spectroscopy from quantum master equations.

PubMed

Fetherolf, Jonathan H; Berkelbach, Timothy C

2017-12-28

We investigate the accuracy of the second-order time-convolutionless (TCL2) quantum master equation for the calculation of linear and nonlinear spectroscopies of multichromophore systems. We show that even for systems with non-adiabatic coupling, the TCL2 master equation predicts linear absorption spectra that are accurate over an extremely broad range of parameters and well beyond what would be expected based on the perturbative nature of the approach; non-equilibrium population dynamics calculated with TCL2 for identical parameters are significantly less accurate. For third-order (two-dimensional) spectroscopy, the importance of population dynamics and the violation of the so-called quantum regression theorem degrade the accuracy of TCL2 dynamics. To correct these failures, we combine the TCL2 approach with a classical ensemble sampling of slow microscopic bath degrees of freedom, leading to an efficient hybrid quantum-classical scheme that displays excellent accuracy over a wide range of parameters. In the spectroscopic setting, the success of such a hybrid scheme can be understood through its separate treatment of homogeneous and inhomogeneous broadening. Importantly, the presented approach has the computational scaling of TCL2, with the modest addition of an embarrassingly parallel prefactor associated with ensemble sampling. The presented approach can be understood as a generalized inhomogeneous cumulant expansion technique, capable of treating multilevel systems with non-adiabatic dynamics.

Linear and nonlinear spectroscopy from quantum master equations

NASA Astrophysics Data System (ADS)

Fetherolf, Jonathan H.; Berkelbach, Timothy C.

2017-12-01

We investigate the accuracy of the second-order time-convolutionless (TCL2) quantum master equation for the calculation of linear and nonlinear spectroscopies of multichromophore systems. We show that even for systems with non-adiabatic coupling, the TCL2 master equation predicts linear absorption spectra that are accurate over an extremely broad range of parameters and well beyond what would be expected based on the perturbative nature of the approach; non-equilibrium population dynamics calculated with TCL2 for identical parameters are significantly less accurate. For third-order (two-dimensional) spectroscopy, the importance of population dynamics and the violation of the so-called quantum regression theorem degrade the accuracy of TCL2 dynamics. To correct these failures, we combine the TCL2 approach with a classical ensemble sampling of slow microscopic bath degrees of freedom, leading to an efficient hybrid quantum-classical scheme that displays excellent accuracy over a wide range of parameters. In the spectroscopic setting, the success of such a hybrid scheme can be understood through its separate treatment of homogeneous and inhomogeneous broadening. Importantly, the presented approach has the computational scaling of TCL2, with the modest addition of an embarrassingly parallel prefactor associated with ensemble sampling. The presented approach can be understood as a generalized inhomogeneous cumulant expansion technique, capable of treating multilevel systems with non-adiabatic dynamics.

Dynamic Covalent Chemistry within Biphenyl Scaffolds: Reversible Covalent Bonding, Control of Selectivity, and Chirality Sensing with a Single System.

PubMed

Ni, Cailing; Zha, Daijun; Ye, Hebo; Hai, Yu; Zhou, Yuntao; Anslyn, Eric V; You, Lei

2018-01-26

Axial chirality is a prevalent and important phenomenon in chemistry. Herein we report a combination of dynamic covalent chemistry and axial chirality for the development of a versatile platform for the binding and chirality sensing of multiple classes of mononucleophiles. An equilibrium between an open aldehyde and its cyclic hemiaminal within biphenyl derivatives enabled the dynamic incorporation of a broad range of alcohols, thiols, primary amines, and secondary amines with high efficiency. Selectivity toward different classes of nucleophiles was also achieved by regulating the distinct reactivity of the system with external stimuli. Through induced helicity as a result of central-to-axial chirality transfer, the handedness and ee values of chiral monoalcohol and monoamine analytes were reported by circular dichroism. The strategies introduced herein should find application in many contexts, including assembly, sensing, and labeling. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Imbibition of a textured surface decorated by short pillars with rounded edges.

PubMed

Obara, Noriko; Okumura, Ko

2012-08-01

Imbibition of micropatterned surfaces can have broad technological and fundamental implications for areas ranging from biomedical devices and fuel transport to writing with ink. Despite rapidly growing interests aimed at various applications, a fundamental physical understanding of the imbibition dynamics is still in its infancy. Recently, two simple scaling regimes for the dynamics have been established for a textured surface decorated with long pillars whose top and bottom edges are sharp. Here, we study the imbibition dynamics of textured surfaces decorated by short pillars with rounded edges, to find a different scaling regime. Interestingly, this regime originates not from the balance of two effects but from the hybrid balance of three effects. Furthermore, this scaling law can be universal or independent of the details of the texture geometry. We envision that this potentially universal scaling regime might be ubiquitous and will be useful in the handling and transportation of a small amount of liquid.

Frontiers in Chemical Physics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bowlan, Pamela Renee

2016-05-02

These are slides dealing with frontiers in chemical physics. The following topics are covered: Time resolving chemistry with ultrashort pulses in the 0.1-40 THz spectral range; Example: Mid-infrared absorption spectrum of the intermediate state CH 2OO; Tracking reaction dynamics through changes in the spectra; Single-shot measurement of the mid-IR absorption dynamics; Applying 2D coherent mid-IR spectroscopy to learn more about transition states; Time resolving chemical reactions at a catalysis using mid-IR and THz pulses; Studying topological insulators requires a surface sensitive probe; Nonlinear phonon dynamics in Bi 2Se 3; THz-pump, SHG-probe as a surface sensitive coherent 2D spectroscopy; Nanometer andmore » femtosecond spatiotemporal resolution mid-IR spectroscopy; Coherent two-dimensional THz/mid-IR spectroscopy with 10nm spatial resolution; Pervoskite oxides as catalysts; Functionalized graphene for catalysis; Single-shot spatiotemporal measurements; Spatiotemporal pulse measurement; Intense, broad-band THz/mid-IR generation with organic crystals.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Patankar, S.; Gumbrell, E. T.; Robinson, T. S.

Here we report a new method using high stability, laser-driven supercontinuum generation in a liquid cell to calibrate the absolute photon response of fast optical streak cameras as a function of wavelength when operating at fastest sweep speeds. A stable, pulsed white light source based around the use of self-phase modulation in a salt solution was developed to provide the required brightness on picosecond timescales, enabling streak camera calibration in fully dynamic operation. The measured spectral brightness allowed for absolute photon response calibration over a broad spectral range (425-650nm). Calibrations performed with two Axis Photonique streak cameras using the Photonismore » P820PSU streak tube demonstrated responses which qualitatively follow the photocathode response. Peak sensitivities were 1 photon/count above background. The absolute dynamic sensitivity is less than the static by up to an order of magnitude. We attribute this to the dynamic response of the phosphor being lower.« less

Team Learning: New Insights Through a Temporal Lens.

PubMed

Lehmann-Willenbrock, Nale

2017-04-01

Team learning is a complex social phenomenon that develops and changes over time. Hence, to promote understanding of the fine-grained dynamics of team learning, research should account for the temporal patterns of team learning behavior. Taking important steps in this direction, this special issue offers novel insights into the dynamics of team learning by advocating a temporal perspective. Based on a symposium presented at the 2016 Interdisciplinary Network for Group Research (INGRoup) Conference in Helsinki, the four empirical articles in this special issue showcase four different and innovative approaches to implementing a temporal perspective in team learning research. Specifically, the contributions highlight team learning dynamics in student teams, self-managing teams, teacher teams, and command and control teams. The articles cover a broad range of methods and designs, including both qualitative and quantitative methodologies, and longitudinal as well as micro-temporal approaches. The contributors represent four countries and five different disciplines in group research.

Evaluation of Dynamic Coastal Response to Sea-level Rise Modifies Inundation Likelihood

NASA Technical Reports Server (NTRS)

Lentz, Erika E.; Thieler, E. Robert; Plant, Nathaniel G.; Stippa, Sawyer R.; Horton, Radley M.; Gesch, Dean B.

2016-01-01

Sea-level rise (SLR) poses a range of threats to natural and built environments, making assessments of SLR-induced hazards essential for informed decision making. We develop a probabilistic model that evaluates the likelihood that an area will inundate (flood) or dynamically respond (adapt) to SLR. The broad-area applicability of the approach is demonstrated by producing 30x30m resolution predictions for more than 38,000 sq km of diverse coastal landscape in the northeastern United States. Probabilistic SLR projections, coastal elevation and vertical land movement are used to estimate likely future inundation levels. Then, conditioned on future inundation levels and the current land-cover type, we evaluate the likelihood of dynamic response versus inundation. We find that nearly 70% of this coastal landscape has some capacity to respond dynamically to SLR, and we show that inundation models over-predict land likely to submerge. This approach is well suited to guiding coastal resource management decisions that weigh future SLR impacts and uncertainty against ecological targets and economic constraints.

Dynamic response of a forward-swept-wing model at angles of attack up to 15 deg at a Mach number of 0.8. [Langley transonic dynamics tunnel tests

NASA Technical Reports Server (NTRS)

Doggett, R. V., Jr.; Ricketts, R. H.

1980-01-01

Root mean square (rms) bending moments for a dynamically scaled, aeroelastic wing of a proposed forward swept wing, flight demonstrator airplane are presented for angles of attack up to 15 deg at a Mach number of 0.8 The 0.6 size semispan model had a leading edge forward sweep of 44 deg and was constructed of composite material. In addition to broad band responses, individual rms responses and total damping ratios are presented for the first two natural modes. The results show that the rms response increases with angle of attack and has a peak value at an angle of attack near 13 deg. In general, the response was characteristic of buffeting and similar to results often observed for aft swept wings. At an angle of attack near 13 deg, however, the response had characteristics associated with approaching a dynamic instability, although no instability was observed over the range of parameters investigated.

Probing nanoscale ion dynamics in ultrathin films of polymerized ionic liquids by broadband dielectric spectroscopy

NASA Astrophysics Data System (ADS)

Sangoro, Joshua; Heres, Maximilian; Cosby, Tyler

Continuous progress in energy storage and conversion technologies necessitates novel experimental approaches that can provide fundamental insights regarding the impact of reduced dimensions on the functional properties of materials. In this talk, a nondestructive experimental approach to probe nanoscale ion dynamics in ultrathin films of polymerized ionic liquids over a broad frequency range spanning over six orders of magnitude by broadband dielectric spectroscopy will be presented. The approach involves using an electrode configuration with lithographically patterned silica nanostructures, which allow for an air gap between the confined ion conductor and one of the electrodes. It is observed that the characteristic ion dynamics rates significantly slow down with decreasing film thicknesses above the calorimetric glass transition of the bulk polymer. However, the mean rates remain bulk-like at lower temperatures. These results highlight the increasing influence of the polymer/substrate interactions with decreasing film thickness on ion dynamics. The authors gratefully acknowledge the National Science Foundation for financial support through the Polymers Program award DMR-1508394.

Evaluation of DNA extraction methods and their clinical application for direct detection of causative bacteria in continuous ambulatory peritoneal dialysis culture fluids from patients with peritonitis by using broad-range PCR.

PubMed

Kim, Si Hyun; Jeong, Haeng Soon; Kim, Yeong Hoon; Song, Sae Am; Lee, Ja Young; Oh, Seung Hwan; Kim, Hye Ran; Lee, Jeong Nyeo; Kho, Weon-Gyu; Shin, Jeong Hwan

2012-03-01

The aims of this study were to compare several DNA extraction methods and 16S rDNA primers and to evaluate the clinical utility of broad-range PCR in continuous ambulatory peritoneal dialysis (CAPD) culture fluids. Six type strains were used as model organisms in dilutions from 10(8) to 10(0) colony-forming units (CFU)/mL for the evaluation of 5 DNA extraction methods and 5 PCR primer pairs. Broad-range PCR was applied to 100 CAPD culture fluids, and the results were compared with conventional culture results. There were some differences between the various DNA extraction methods and primer sets with regard to the detection limits. The InstaGene Matrix (Bio-Rad Laboratories, USA) and Exgene Clinic SV kits (GeneAll Biotechnology Co. Ltd, Korea) seem to have higher sensitivities than the others. The results of broad-range PCR were concordant with the results from culture in 97% of all cases (97/100). Two culture-positive cases that were broad-range PCR-negative were identified as Candida albicans, and 1 PCR-positive but culture-negative sample was identified as Bacillus circulans by sequencing. Two samples among 54 broad-range PCR-positive products could not be sequenced. There were differences in the analytical sensitivity of various DNA extraction methods and primers for broad-range PCR. The broad-range PCR assay can be used to detect bacterial pathogens in CAPD culture fluid as a supplement to culture methods.

Nonlinear dielectric spectroscopy of propylene carbonate derivatives

NASA Astrophysics Data System (ADS)

Casalini, R.; Roland, C. M.

2018-04-01

Nonlinear dielectric measurements were carried out on two strongly polar liquids, 4-vinyl-1,3-dioxolan-2-one (VPC) and 4-ethyl-1,3-dioxolan-2-one (EPC), having chemical structures differing from propylene carbonate (PC) only by the presence of a pendant group. Despite their polarity, the compounds are all non-associated, "simple" liquids. From the linear component of the dielectric response, the α relaxation peak breadth was found to be invariant at a fixed value of the relaxation time, τα. From spectra from the nonlinear component, the number of dynamically correlated molecules was determined; it was also constant at fixed τα. Thus, two manifestations of dynamic heterogeneity depend only on the time constant for structural reorientation. More broadly, the cooperativity of molecular motions for non-associated glass-forming materials is connected to (i.e., reciprocally governs) the time scale. The equation of state for the two liquids was also obtained from density measurements made over a broad range of pressures and temperatures. Using these data, it was determined that the relaxation times of both liquids conform to density scaling. The effect of density, relative to thermal effects, on the α relaxation increases going from PC < VPC < EPC.

A novel approach to neutron scattering instrumentation for probing multiscale dynamics in soft and biological matter

DOE PAGES

Mamontov, Eugene

2016-06-29

We present a concept and ray-tracing simulation results of a mechanical device that will enable inelastic neutron scattering measurements where the data at energy transfers from a few eV to several hundred meV can be collected in a single, gapless spectrum. Besides covering 5 orders of magnitude on the energy (time) scale, the device provides data over 2 orders of magnitude on the scattering momentum (length) scale in a single measurement. Such capabilities are geared primarily toward soft and biological matter, where the broad dynamical features of relaxation origin largely overlap with vibration features, thus necessitating gapless spectral coverage overmore » several orders of magnitude in time and space. Furthermore, neutron scattering experiments with such a device are performed with a fixed neutron final energy, which enables measurements, with neutron energy loss in the sample, at arbitrarily low temperatures over the same broad spectral range. Lastly, this capability is also invaluable in biological and soft matter research, as the variable temperature dependence of different relaxation components allows their separation in the scattering spectra as a function of temperature.« less

Thermally-Driven Mantle Plumes Reconcile Hot-spot Observations

NASA Astrophysics Data System (ADS)

Davies, D.; Davies, J.

2008-12-01

Hot-spots are anomalous regions of magmatism that cannot be directly associated with plate tectonic processes (e.g. Morgan, 1972). They are widely regarded as the surface expression of upwelling mantle plumes. Hot-spots exhibit variable life-spans, magmatic productivity and fixity (e.g. Ito and van Keken, 2007). This suggests that a wide-range of upwelling structures coexist within Earth's mantle, a view supported by geochemical and seismic evidence, but, thus far, not reproduced by numerical models. Here, results from a new, global, 3-D spherical, mantle convection model are presented, which better reconcile hot-spot observations, the key modification from previous models being increased convective vigor. Model upwellings show broad-ranging dynamics; some drift slowly, while others are more mobile, displaying variable life-spans, intensities and migration velocities. Such behavior is consistent with hot-spot observations, indicating that the mantle must be simulated at the correct vigor and in the appropriate geometry to reproduce Earth-like dynamics. Thermally-driven mantle plumes can explain the principal features of hot-spot volcanism on Earth.

Origins of the anomalous stress behavior in charged colloidal suspensions under shear.

PubMed

Kumar, Amit; Higdon, Jonathan J L

2010-11-01

Numerical simulations are conducted to determine microstructure and rheology of sheared suspensions of charged colloidal particles at a volume fraction of ϕ=0.33. Over broad ranges of repulsive force strength F0 and Péclet number Pe, dynamic simulations show coexistence of ordered and disordered stable states with the state dependent on the initial condition. In contrast to the common view, at low shear rates, the disordered phase exhibits a lower viscosity (μ(r)) than the ordered phase, while this behavior is reversed at higher shear rates. Analysis shows the stress reversal is associated with different shear induced microstructural distortions in the ordered and disordered systems. Viscosity vs shear rate data over a wide range of F0 and Pe collapses well upon rescaling with the long-time self-diffusivity. Shear thinning viscosity in the ordered phase scaled as μ(r)∼Pe(-0.81) at low shear rates. The microstructural dynamics revealed in these studies explains the anomalous behavior and hysteresis loops in stress data reported in the literature.

78 FR 23826 - Information Collection Activities (Complaints, Petitions for Declaratory Orders, and Petitions...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-22

.... Under these statutory and regulatory sections, the Board provides procedures for persons to make a broad range of claims and to seek a broad range of remedies before the Board. The information collections... terminate a controversy or remove uncertainty. Because petitions for a declaratory order cover a broad range...

Broad-range PCR: past, present, or future of bacteriology?

PubMed

Renvoisé, A; Brossier, F; Sougakoff, W; Jarlier, V; Aubry, A

2013-08-01

PCR targeting the gene encoding 16S ribosomal RNA (commonly named broad-range PCR or 16S PCR) has been used for 20 years as a polyvalent tool to study prokaryotes. Broad-range PCR was first used as a taxonomic tool, then in clinical microbiology. We will describe the use of broad-range PCR in clinical microbiology. The first application was identification of bacterial strains obtained by culture but whose phenotypic or proteomic identification remained difficult or impossible. This changed bacterial taxonomy and allowed discovering many new species. The second application of broad-range PCR in clinical microbiology is the detection of bacterial DNA from clinical samples; we will review the clinical settings in which the technique proved useful (such as endocarditis) and those in which it did not (such as characterization of bacteria in ascites, in cirrhotic patients). This technique allowed identifying the etiological agents for several diseases, such as Whipple disease. This review is a synthesis of data concerning the applications, assets, and drawbacks of broad-range PCR in clinical microbiology. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Protocol for Landsat-Based Monitoring of Landscape Dynamics at North Coast and Cascades Network Parks

USGS Publications Warehouse

Kennedy, Robert E.; Cohen, Warren B.; Kirschbaum, Alan A.; Haunreiter, Erik

2007-01-01

Background and Objectives As part of the National Park Service's larger goal of developing long-term monitoring programs in response to the Natural Resource Challenge of 2000, the parks of the North Coast and Cascades Network (NCCN) have determined that monitoring of landscape dynamics is necessary to track ecosystem health (Weber and others, 2005). Landscape dynamics refer to a broad suite of ecological, geomorphological, and anthropogenic processes occurring across broad spatial scales. The NCCN has sought protocols that would leverage remote-sensing technologies to aid in monitoring landscape dynamics.

Three-Dimensional Multiscale, Multistable, and Geometrically Diverse Microstructures with Tunable Vibrational Dynamics Assembled by Compressive Buckling.

PubMed

Ning, Xin; Wang, Heling; Yu, Xinge; Soares, Julio A N T; Yan, Zheng; Nan, Kewang; Velarde, Gabriel; Xue, Yeguang; Sun, Rujie; Dong, Qiyi; Luan, Haiwen; Lee, Chan Mi; Chempakasseril, Aditya; Han, Mengdi; Wang, Yiqi; Li, Luming; Huang, Yonggang; Zhang, Yihui; Rogers, John

2017-04-11

Microelectromechanical systems remain an area of significant interest in fundamental and applied research due to their wide ranging applications. Most device designs, however, are largely two-dimensional and constrained to only a few simple geometries. Achieving tunable resonant frequencies or broad operational bandwidths requires complex components and/or fabrication processes. The work presented here reports unusual classes of three-dimensional (3D) micromechanical systems in the form of vibratory platforms assembled by controlled compressive buckling. Such 3D structures can be fabricated across a broad range of length scales and from various materials, including soft polymers, monocrystalline silicon, and their composites, resulting in a wide scope of achievable resonant frequencies and mechanical behaviors. Platforms designed with multistable mechanical responses and vibrationally de-coupled constituent elements offer improved bandwidth and frequency tunability. Furthermore, the resonant frequencies can be controlled through deformations of an underlying elastomeric substrate. Systematic experimental and computational studies include structures with diverse geometries, ranging from tables, cages, rings, ring-crosses, ring-disks, two-floor ribbons, flowers, umbrellas, triple-cantilever platforms, and asymmetric circular helices, to multilayer constructions. These ideas form the foundations for engineering designs that complement those supported by conventional, microelectromechanical systems, with capabilities that could be useful in systems for biosensing, energy harvesting and others.

Dynamical behavior of a single polymer chain under nanometric confinement

NASA Astrophysics Data System (ADS)

Lagrené, K.; Zanotti, J.-M.; Daoud, M.; Farago, B.; Judeinstein, P.

2010-10-01

We address the dynamical behavior of a single polymer chain under nanometric confinement. We consider a polymer melt made of a mixture of hydrogenated and deuterated high molecular mass Poly(Ethylene Oxide) (PEO). The confining material is a membrane of Anodic Aluminum Oxide (AAO), a macroscopically highly ordered confining system made of parallel cylindrical channels. We use Neutron Spin-Echo (NSE) under the Zero Average Contrast (ZAC) condition to, all at once, i) match the intense porous AAO detrimental elastic SANS (Small Angle Neutron Scattering) contribution to the total intermediate scattering function I(Q,t) and ii) measure the Q dependence of the dynamical modes of a single chain under confinement. The polymer dynamics is probed on an extremely broad spacial ([2.2 10-2 Å-1, 0.2 Å-1]) and temporal ([0.1 ns, 600 ns]) ranges. We do not detect any influence of confinement on the polymer dynamics. This result is discussed in the framework of the debate on the existence of a "corset effect" recently suggested by NMR relaxometry data.

Controlling laser-induced magnetization reversal dynamics in a rare-earth iron garnet across the magnetization compensation point

NASA Astrophysics Data System (ADS)

Deb, Marwan; Molho, Pierre; Barbara, Bernard; Bigot, Jean-Yves

2018-04-01

In this work we explore the ultrafast magnetization dynamics induced by femtosecond laser pulses in a doped film of gadolinium iron garnet over a broad temperature range including the magnetization compensation point TM. By exciting the phonon-assisted 6S→4G and 6S→4P electronic d -d transitions simultaneously by one- and two-photon absorption processes, we find out that the transfer of heat energy from the lattice to the spin has, at a temperature slightly below TM, a large influence on the magnetization dynamics. In particular, we show that the speed and the amplitude of the magnetization dynamics can be strongly increased when increasing either the external magnetic field or the laser energy density. The obtained results are explained by a magnetization reversal process across TM. Furthermore, we find that the dynamics has unusual characteristics which can be understood by considering the weak spin-phonon coupling in magnetic garnets. These results open new perspectives for controlling the magnetic state of magnetic dielectrics using an ultrashort optically induced heat pulse.

2-D and 3-D oscillating wing aerodynamics for a range of angles of attack including stall

NASA Technical Reports Server (NTRS)

Piziali, R. A.

1994-01-01

A comprehensive experimental investigation of the pressure distribution over a semispan wing undergoing pitching motions representative of a helicopter rotor blade was conducted. Testing the wing in the nonrotating condition isolates the three-dimensional (3-D) blade aerodynamic and dynamic stall characteristics from the complications of the rotor blade environment. The test has generated a very complete, detailed, and accurate body of data. These data include static and dynamic pressure distributions, surface flow visualizations, two-dimensional (2-D) airfoil data from the same model and installation, and important supporting blockage and wall pressure distributions. This body of data is sufficiently comprehensive and accurate that it can be used for the validation of rotor blade aerodynamic models over a broad range of the important parameters including 3-D dynamic stall. This data report presents all the cycle-averaged lift, drag, and pitching moment coefficient data versus angle of attack obtained from the instantaneous pressure data for the 3-D wing and the 2-D airfoil. Also presented are examples of the following: cycle-to-cycle variations occurring for incipient or lightly stalled conditions; 3-D surface flow visualizations; supporting blockage and wall pressure distributions; and underlying detailed pressure results.

Gait-force model and inertial measurement unit-based measurements: A new approach for gait analysis and balance monitoring.

PubMed

Li, Xinan; Xu, Hongyuan; Cheung, Jeffrey T

2016-12-01

This work describes a new approach for gait analysis and balance measurement. It uses an inertial measurement unit (IMU) that can either be embedded inside a dynamically unstable platform for balance measurement or mounted on the lower back of a human participant for gait analysis. The acceleration data along three Cartesian coordinates is analyzed by the gait-force model to extract bio-mechanics information in both the dynamic state as in the gait analyzer and the steady state as in the balance scale. For the gait analyzer, the simple, noninvasive and versatile approach makes it appealing to a broad range of applications in clinical diagnosis, rehabilitation monitoring, athletic training, sport-apparel design, and many other areas. For the balance scale, it provides a portable platform to measure the postural deviation and the balance index under visual or vestibular sensory input conditions. Despite its simple construction and operation, excellent agreement has been demonstrated between its performance and the high-cost commercial balance unit over a wide dynamic range. The portable balance scale is an ideal tool for routine monitoring of balance index, fall-risk assessment, and other balance-related health issues for both clinical and household use.

Understanding the role of spin-motion coupling in Ramsey spectroscopy

NASA Astrophysics Data System (ADS)

Koller, Andrew; Beverland, Michael; Mundinger, Joshua; Gorshkov, Alexey; Rey, Ana Maria

2014-05-01

Ramsey spectroscopy has become a powerful technique for probing non-equilibrium dynamics of internal (pseudospin) degrees of freedom of interacting systems. In many theoretical treatments, the key to understanding the dynamics has been to assume the external (motional) degrees of freedom are decoupled from the pseudospin degrees of freedom. Determining the validity of this approximation - known as the spin model approximation - has not been addressed in detail. We shed light in this direction by calculating Ramsey dynamics exactly for two interacting spin-1/2 particles in a harmonic trap. We find that in 1D the spin model assumption works well over a wide range of experimentally-relevant conditions, but can fail at time scales longer than those set by the mean interaction energy. Surprisingly, in 2D a modified version of the spin model is exact to first order in the interaction strength. This analysis is important for a correct interpretation of Ramsey spectroscopy and has broad applications ranging from precision measurements to quantum information and to fundamental probes of many-body systems. Supported by NSF, ARO-DARPA-OLE, AFOSR, NIST, the Lee A. DuBridge and Gordon and Betty Moore Foundations, and the NDSEG program.

How can present and future satellite missions support scientific studies that address ocean acidification?

USGS Publications Warehouse

Salisbury, Joseph; Vandemark, Douglas; Jonsson, Bror; Balch, William; Chakraborty, Sumit; Lohrenz, Steven; Chapron, Bertrand; Hales, Burke; Mannino, Antonio; Mathis, Jeremy T.; Reul, Nicolas; Signorini, Sergio; Wanninkhof, Rik; Yates, Kimberly K.

2016-01-01

Space-based observations offer unique capabilities for studying spatial and temporal dynamics of the upper ocean inorganic carbon cycle and, in turn, supporting research tied to ocean acidification (OA). Satellite sensors measuring sea surface temperature, color, salinity, wind, waves, currents, and sea level enable a fuller understanding of a range of physical, chemical, and biological phenomena that drive regional OA dynamics as well as the potentially varied impacts of carbon cycle change on a broad range of ecosystems. Here, we update and expand on previous work that addresses the benefits of space-based assets for OA and carbonate system studies. Carbonate chemistry and the key processes controlling surface ocean OA variability are reviewed. Synthesis of present satellite data streams and their utility in this arena are discussed, as are opportunities on the horizon for using new satellite sensors with increased spectral, temporal, and/or spatial resolution. We outline applications that include the ability to track the biochemically dynamic nature of water masses, to map coral reefs at higher resolution, to discern functional phytoplankton groups and their relationships to acid perturbations, and to track processes that contribute to acid variation near the land-ocean interface.

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

PubMed Central

2018-01-01

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA–ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field. PMID:29297679

Application of CFD in aeronautics at NASA Ames Research Center

NASA Astrophysics Data System (ADS)

Maksymiuk, Catherine M.; Enomoto, Francis Y.; Vandalsem, William R.

1995-03-01

The role of Computational Fluid Dynamics (CFD) at Ames Research Center has expanded to address a broad range of aeronautical problems, including wind tunnel support, flight test support, design, and analysis. Balancing the requirements of each new problem against the available resources - software, hardware, time, and expertise - is critical to the effective use of CFD. Several case studies of recent applications highlight the depth of CFD capability at Ames, the tradeoffs involved in various approaches, and lessons learned in the use of CFD as an engineering tool.

Dynamical Cooper pairing in nonequilibrium electron-phonon systems

DOE PAGES

Knap, Michael; Babadi, Mehrtash; Refael, Gil; ...

2016-12-08

In this paper, we analyze Cooper pairing instabilities in strongly driven electron-phonon systems. The light-induced nonequilibrium state of phonons results in a simultaneous increase of the superconducting coupling constant and the electron scattering. We demonstrate that the competition between these effects leads to an enhanced superconducting transition temperature in a broad range of parameters. Finally, our results may explain the observed transient enhancement of superconductivity in several classes of materials upon irradiation with high intensity pulses of terahertz light, and may pave new ways for engineering high-temperature light-induced superconducting states.

The ultra high resolution XUV spectroheliograph: An attached payload for the Space Station Freedom

NASA Technical Reports Server (NTRS)

Walker, Arthur B. C., Jr.; Hoover, Richard B.; Barbee, Troy W., Jr.; Tandberg-Hanssen, Einar; Timothy, J. Gethyn; Lindblom, Joakim F.

1990-01-01

The principle goal of the ultra high resolution XUV spectroheliograph (UHRXS) is to improve the ability to identify and understand the fundamental physical processes that shape the structure and dynamics of the solar chromosphere and corona. The ability of the UHRXS imaging telescope and spectrographs to resolve fine scale structures over a broad wavelength (and hence temperature) range is critical to this mission. The scientific objectives and instrumental capabilities of the UHRXS investigation are reviewed before proceeding to a discussion of the expected performance of the UHRXS observatory.

Energy consumption for shortcuts to adiabaticity

NASA Astrophysics Data System (ADS)

Torrontegui, E.; Lizuain, I.; González-Resines, S.; Tobalina, A.; Ruschhaupt, A.; Kosloff, R.; Muga, J. G.

2017-08-01

Shortcuts to adiabaticity let a system reach the results of a slow adiabatic process in a shorter time. We propose to quantify the "energy cost" of the shortcut by the energy consumption of the system enlarged by including the control device. A mechanical model where the dynamics of the system and control device can be explicitly described illustrates that a broad range of possible values for the consumption is possible, including zero (above the adiabatic energy increment) when friction is negligible and the energy given away as negative power is stored and reused by perfect regenerative braking.

The interplay of climate and land use change affects the distribution of EU bumblebees.

PubMed

Marshall, Leon; Biesmeijer, Jacobus C; Rasmont, Pierre; Vereecken, Nicolas J; Dvorak, Libor; Fitzpatrick, Una; Francis, Frédéric; Neumayer, Johann; Ødegaard, Frode; Paukkunen, Juho P T; Pawlikowski, Tadeusz; Reemer, Menno; Roberts, Stuart P M; Straka, Jakub; Vray, Sarah; Dendoncker, Nicolas

2018-01-01

Bumblebees in Europe have been in steady decline since the 1900s. This decline is expected to continue with climate change as the main driver. However, at the local scale, land use and land cover (LULC) change strongly affects the occurrence of bumblebees. At present, LULC change is rarely included in models of future distributions of species. This study's objective is to compare the roles of dynamic LULC change and climate change on the projected distribution patterns of 48 European bumblebee species for three change scenarios until 2100 at the scales of Europe, and Belgium, Netherlands and Luxembourg (BENELUX). We compared three types of models: (1) only climate covariates, (2) climate and static LULC covariates and (3) climate and dynamic LULC covariates. The climate and LULC change scenarios used in the models include, extreme growth applied strategy (GRAS), business as might be usual and sustainable European development goals. We analysed model performance, range gain/loss and the shift in range limits for all bumblebees. Overall, model performance improved with the introduction of LULC covariates. Dynamic models projected less range loss and gain than climate-only projections, and greater range loss and gain than static models. Overall, there is considerable variation in species responses and effects were most pronounced at the BENELUX scale. The majority of species were predicted to lose considerable range, particularly under the extreme growth scenario (GRAS; overall mean: 64% ± 34). Model simulations project a number of local extinctions and considerable range loss at the BENELUX scale (overall mean: 56% ± 39). Therefore, we recommend species-specific modelling to understand how LULC and climate interact in future modelling. The efficacy of dynamic LULC change should improve with higher thematic and spatial resolution. Nevertheless, current broad scale representations of change in major land use classes impact modelled future distribution patterns. © 2017 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

The Race To X-ray Microbeam and Nanobeam Science

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ice, Gene E; Budai, John D; Pang, Judy

2011-01-01

X-ray microbeams are an emerging characterization tool with transformational implications for broad areas of science ranging from materials structure and dynamics, geophysics and environmental science to biophysics and protein crystallography. In this review, we discuss the race toward sub-10 nm- x-ray beams with the ability to penetrate tens to hundreds of microns into most materials and with the ability to determine local (crystal) structure. Examples of science enabled by current micro/nanobeam technologies are presented and we provide a perspective on future directions. Applications highlighted are chosen to illustrate the important features of various submicron beam strategies and to highlight themore » directions of current and future research. While it is clear that x-ray microprobes will impact science broadly, the practical limit for hard x-ray beam size, the limit to trace element sensitivity, and the ultimate limitations associated with near-atomic structure determinations are the subject of ongoing research.« less

Experimental aerothermodynamic research of hypersonic aircraft

NASA Technical Reports Server (NTRS)

Cleary, Joseph W.

1987-01-01

The 2-D and 3-D advance computer codes being developed for use in the design of such hypersonic aircraft as the National Aero-Space Plane require comparison of the computational results with a broad spectrum of experimental data to fully assess the validity of the codes. This is particularly true for complex flow fields with control surfaces present and for flows with separation, such as leeside flow. Therefore, the objective is to provide a hypersonic experimental data base required for validation of advanced computational fluid dynamics (CFD) computer codes and for development of more thorough understanding of the flow physics necessary for these codes. This is being done by implementing a comprehensive test program for a generic all-body hypersonic aircraft model in the NASA/Ames 3.5 foot Hypersonic Wind Tunnel over a broad range of test conditions to obtain pertinent surface and flowfield data. Results from the flow visualization portion of the investigation are presented.

Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover

PubMed Central

Stegen, James C.; Fredrickson, James K.; Wilkins, Michael J.; Konopka, Allan E.; Nelson, William C.; Arntzen, Evan V.; Chrisler, William B.; Chu, Rosalie K.; Danczak, Robert E.; Fansler, Sarah J.; Kennedy, David W.; Resch, Charles T.; Tfaily, Malak

2016-01-01

Environmental transitions often result in resource mixtures that overcome limitations to microbial metabolism, resulting in biogeochemical hotspots and moments. Riverine systems, where groundwater mixes with surface water (the hyporheic zone), are spatially complex and temporally dynamic, making development of predictive models challenging. Spatial and temporal variations in hyporheic zone microbial communities are a key, but understudied, component of riverine biogeochemical function. Here, to investigate the coupling among groundwater–surface water mixing, microbial communities and biogeochemistry, we apply ecological theory, aqueous biogeochemistry, DNA sequencing and ultra-high-resolution organic carbon profiling to field samples collected across times and locations representing a broad range of mixing conditions. Our results indicate that groundwater–surface water mixing in the hyporheic zone stimulates heterotrophic respiration, alters organic carbon composition, causes ecological processes to shift from stochastic to deterministic and is associated with elevated abundances of microbial taxa that may degrade a broad suite of organic compounds. PMID:27052662

Groundwater-surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover.

PubMed

Stegen, James C; Fredrickson, James K; Wilkins, Michael J; Konopka, Allan E; Nelson, William C; Arntzen, Evan V; Chrisler, William B; Chu, Rosalie K; Danczak, Robert E; Fansler, Sarah J; Kennedy, David W; Resch, Charles T; Tfaily, Malak

2016-04-07

Environmental transitions often result in resource mixtures that overcome limitations to microbial metabolism, resulting in biogeochemical hotspots and moments. Riverine systems, where groundwater mixes with surface water (the hyporheic zone), are spatially complex and temporally dynamic, making development of predictive models challenging. Spatial and temporal variations in hyporheic zone microbial communities are a key, but understudied, component of riverine biogeochemical function. Here, to investigate the coupling among groundwater-surface water mixing, microbial communities and biogeochemistry, we apply ecological theory, aqueous biogeochemistry, DNA sequencing and ultra-high-resolution organic carbon profiling to field samples collected across times and locations representing a broad range of mixing conditions. Our results indicate that groundwater-surface water mixing in the hyporheic zone stimulates heterotrophic respiration, alters organic carbon composition, causes ecological processes to shift from stochastic to deterministic and is associated with elevated abundances of microbial taxa that may degrade a broad suite of organic compounds.

Mass spectrometry based proteomics: existing capabilities and future directions

PubMed Central

Angel, Thomas E.; Aryal, Uma K.; Hengel, Shawna M.; Baker, Erin S.; Kelly, Ryan T.; Robinson, Errol W.; Smith, Richard D.

2012-01-01

Mass spectrometry (MS)-based proteomics is emerging as a broadly effective means for identification, characterization, and quantification of proteins that are integral components of the processes essential for life. Characterization of proteins at the proteome and sub-proteome (e.g., the phosphoproteome, proteoglycome, or degradome/peptidome) levels provides a foundation for understanding fundamental aspects of biology. Emerging technologies such as ion mobility separations coupled with MS and microchip-based-proteome measurements combined with MS instrumentation and chromatographic separation techniques, such as nanoscale reversed phase liquid chromatography and capillary electrophoresis, show great promise for both broad undirected and targeted highly sensitive measurements. MS-based proteomics is increasingly contribute to our understanding of the dynamics, interactions, and roles that proteins and peptides play, advancing our understanding of biology on a systems wide level for a wide range of applications including investigations of microbial communities, bioremediation, and human health. PMID:22498958

A Fiber Bragg Grating Sensor Interrogation System Based on a Linearly Wavelength-Swept Thermo-Optic Laser Chip

PubMed Central

Lee, Hyung-Seok; Lee, Hwi Don; Kim, Hyo Jin; Cho, Jae Du; Jeong, Myung Yung; Kim, Chang-Seok

2014-01-01

A linearized wavelength-swept thermo-optic laser chip was applied to demonstrate a fiber Bragg grating (FBG) sensor interrogation system. A broad tuning range of 11.8 nm was periodically obtained from the laser chip for a sweep rate of 16 Hz. To measure the linear time response of the reflection signal from the FBG sensor, a programmed driving signal was directly applied to the wavelength-swept laser chip. The linear wavelength response of the applied strain was clearly extracted with an R-squared value of 0.99994. To test the feasibility of the system for dynamic measurements, the dynamic strain was successfully interrogated with a repetition rate of 0.2 Hz by using this FBG sensor interrogation system. PMID:25177803

Introduction to Focus Issue: Rhythms and Dynamic Transitions in Neurological Disease: Modeling, Computation, and Experiment

NASA Astrophysics Data System (ADS)

Kaper, Tasso J.; Kramer, Mark A.; Rotstein, Horacio G.

2013-12-01

Rhythmic neuronal oscillations across a broad range of frequencies, as well as spatiotemporal phenomena, such as waves and bumps, have been observed in various areas of the brain and proposed as critical to brain function. While there is a long and distinguished history of studying rhythms in nerve cells and neuronal networks in healthy organisms, the association and analysis of rhythms to diseases are more recent developments. Indeed, it is now thought that certain aspects of diseases of the nervous system, such as epilepsy, schizophrenia, Parkinson's, and sleep disorders, are associated with transitions or disruptions of neurological rhythms. This focus issue brings together articles presenting modeling, computational, analytical, and experimental perspectives about rhythms and dynamic transitions between them that are associated to various diseases.

Viscoinertial regime of immersed granular flows

NASA Astrophysics Data System (ADS)

Amarsid, L.; Delenne, J.-Y.; Mutabaruka, P.; Monerie, Y.; Perales, F.; Radjai, F.

2017-07-01

By means of extensive coupled molecular dynamics-lattice Boltzmann simulations, accounting for grain dynamics and subparticle resolution of the fluid phase, we analyze steady inertial granular flows sheared by a viscous fluid. We show that, for a broad range of system parameters (shear rate, confining stress, fluid viscosity, and relative fluid-grain density), the frictional strength and packing fraction can be described by a modified inertial number incorporating the fluid effect. In a dual viscous description, the effective viscosity diverges as the inverse square of the difference between the packing fraction and its jamming value, as observed in experiments. We also find that the fabric and force anisotropies extracted from the contact network are well described by the modified inertial number, thus providing clear evidence for the role of these key structural parameters in dense suspensions.

Sensing of single electrons using micro and nano technologies: a review

NASA Astrophysics Data System (ADS)

Jalil, Jubayer; Zhu, Yong; Ekanayake, Chandima; Ruan, Yong

2017-04-01

During the last three decades, the remarkable dynamic features of microelectromechanical systems (MEMS) and nanoelectromechanical systems (NEMS), and advances in solid-state electronics hold much potential for the fabrication of extremely sensitive charge sensors. These sensors have a broad range of applications, such as those involving the measurement of ionization radiation, detection of bio-analyte and aerosol particles, mass spectrometry, scanning tunneling microscopy, and quantum computation. Designing charge sensors (also known as charge electrometers) for electrometry is deemed significant because of the sensitivity and resolution issues in the range of micro- and nano-scales. This article reviews the development of state-of-the-art micro- and nano-charge sensors, and discusses their technological challenges for practical implementation.

Evaluation of the External RNA Controls Consortium (ERCC) reference material using a modified Latin square design.

PubMed

Pine, P Scott; Munro, Sarah A; Parsons, Jerod R; McDaniel, Jennifer; Lucas, Anne Bergstrom; Lozach, Jean; Myers, Timothy G; Su, Qin; Jacobs-Helber, Sarah M; Salit, Marc

2016-06-24

Highly multiplexed assays for quantitation of RNA transcripts are being used in many areas of biology and medicine. Using data generated by these transcriptomic assays requires measurement assurance with appropriate controls. Methods to prototype and evaluate multiple RNA controls were developed as part of the External RNA Controls Consortium (ERCC) assessment process. These approaches included a modified Latin square design to provide a broad dynamic range of relative abundance with known differences between four complex pools of ERCC RNA transcripts spiked into a human liver total RNA background. ERCC pools were analyzed on four different microarray platforms: Agilent 1- and 2-color, Illumina bead, and NIAID lab-made spotted microarrays; and two different second-generation sequencing platforms: the Life Technologies 5500xl and the Illumina HiSeq 2500. Individual ERCC controls were assessed for reproducible performance in signal response to concentration among the platforms. Most demonstrated linear behavior if they were not located near one of the extremes of the dynamic range. Performance issues with any individual ERCC transcript could be attributed to detection limitations, platform-specific target probe issues, or potential mixing errors. Collectively, these pools of spike-in RNA controls were evaluated for suitability as surrogates for endogenous transcripts to interrogate the performance of the RNA measurement process of each platform. The controls were useful for establishing the dynamic range of the assay, as well as delineating the useable region of that range where differential expression measurements, expressed as ratios, would be expected to be accurate. The modified Latin square design presented here uses a composite testing scheme for the evaluation of multiple performance characteristics: linear performance of individual controls, signal response within dynamic range pools of controls, and ratio detection between pairs of dynamic range pools. This compact design provides an economical sample format for the evaluation of multiple external RNA controls within a single experiment per platform. These results indicate that well-designed pools of RNA controls, spiked into samples, provide measurement assurance for endogenous gene expression studies.

Riverine habitat dynamics

USGS Publications Warehouse

Jacobson, R.B.

2013-01-01

The physical habitat template is a fundamental influence on riverine ecosystem structure and function. Habitat dynamics refers to the variation in habitat through space and time as the result of varying discharge and varying geomorphology. Habitat dynamics can be assessed at spatial scales ranging from the grain (the smallest resolution at which an organism relates to its environment) to the extent (the broadest resolution inclusive of all space occupied during its life cycle). In addition to a potentially broad range of spatial scales, assessments of habitat dynamics may include dynamics of both occupied and nonoccupied habitat patches because of process interactions among patches. Temporal aspects of riverine habitat dynamics can be categorized into hydrodynamics and morphodynamics. Hydrodynamics refers to habitat variation that results from changes in discharge in the absence of significant change of channel morphology and at generally low sediment-transport rates. Hydrodynamic assessments are useful in cases of relatively high flow exceedance (percent of time a flow is equaled or exceeded) or high critical shear stress, conditions that are applicable in many studies of instream flows. Morphodynamics refers to habitat variation resulting from changes to substrate conditions or channel/floodplain morphology. Morphodynamic assessments are necessary when channel and floodplain boundary conditions have been significantly changed, generally by relatively rare flood events or in rivers with low critical shear stress. Morphodynamic habitat variation can be particularly important as disturbance mechanisms that mediate population growth or for providing conditions needed for reproduction, such as channel-migration events that erode cutbanks and provide new pointbar surfaces for germination of riparian trees. Understanding of habitat dynamics is increasing in importance as societal goals shift toward restoration of riverine ecosystems. Effective investment in restoration strategies requires that the role of physical habitat is correctly diagnosed and that restoration activities address true habitat limitations, including the role of dynamic habitats.

Dynamic switching enables efficient bacterial colonization in flow.

PubMed

Kannan, Anerudh; Yang, Zhenbin; Kim, Minyoung Kevin; Stone, Howard A; Siryaporn, Albert

2018-05-22

Bacteria colonize environments that contain networks of moving fluids, including digestive pathways, blood vasculature in animals, and the xylem and phloem networks in plants. In these flow networks, bacteria form distinct biofilm structures that have an important role in pathogenesis. The physical mechanisms that determine the spatial organization of bacteria in flow are not understood. Here, we show that the bacterium P. aeruginosa colonizes flow networks using a cyclical process that consists of surface attachment, upstream movement, detachment, movement with the bulk flow, and surface reattachment. This process, which we have termed dynamic switching, distributes bacterial subpopulations upstream and downstream in flow through two phases: movement on surfaces and cellular movement via the bulk. The model equations that describe dynamic switching are identical to those that describe dynamic instability, a process that enables microtubules in eukaryotic cells to search space efficiently to capture chromosomes. Our results show that dynamic switching enables bacteria to explore flow networks efficiently, which maximizes dispersal and colonization and establishes the organizational structure of biofilms. A number of eukaryotic and mammalian cells also exhibit movement in two phases in flow, which suggests that dynamic switching is a modality that enables efficient dispersal for a broad range of cell types.

Vanishing amplitude of backbone dynamics causes a true protein dynamical transition: H2 NMR studies on perdeuterated C-phycocyanin

NASA Astrophysics Data System (ADS)

Kämpf, Kerstin; Kremmling, Beke; Vogel, Michael

2014-03-01

Using a combination of H2 nuclear magnetic resonance (NMR) methods, we study internal rotational dynamics of the perdeuterated protein C-phycocyanin (CPC) in dry and hydrated states over broad temperature and dynamic ranges with high angular resolution. Separating H2 NMR signals from methyl deuterons, we show that basically all backbone deuterons exhibit highly restricted motion occurring on time scales faster than microseconds. The amplitude of this motion increases when a hydration shell exists, while it decreases upon cooling and vanishes near 175 K. We conclude that the vanishing of the highly restricted motion marks a dynamical transition, which is independent of the time window and of a fundamental importance. This conclusion is supported by results from experimental and computational studies of the proteins myoglobin and elastin. In particular, we argue based on findings in molecular dynamics simulations that the behavior of the highly restricted motion of proteins at the dynamical transition resembles that of a characteristic secondary relaxation of liquids at the glass transition, namely the nearly constant loss. Furthermore, H2 NMR studies on perdeuterated CPC reveal that, in addition to highly restricted motion, small fractions of backbone segments exhibit weakly restricted dynamics when temperature and hydration are sufficiently high.

Neural Computations in a Dynamical System with Multiple Time Scales.

PubMed

Mi, Yuanyuan; Lin, Xiaohan; Wu, Si

2016-01-01

Neural systems display rich short-term dynamics at various levels, e.g., spike-frequency adaptation (SFA) at the single-neuron level, and short-term facilitation (STF) and depression (STD) at the synapse level. These dynamical features typically cover a broad range of time scales and exhibit large diversity in different brain regions. It remains unclear what is the computational benefit for the brain to have such variability in short-term dynamics. In this study, we propose that the brain can exploit such dynamical features to implement multiple seemingly contradictory computations in a single neural circuit. To demonstrate this idea, we use continuous attractor neural network (CANN) as a working model and include STF, SFA and STD with increasing time constants in its dynamics. Three computational tasks are considered, which are persistent activity, adaptation, and anticipative tracking. These tasks require conflicting neural mechanisms, and hence cannot be implemented by a single dynamical feature or any combination with similar time constants. However, with properly coordinated STF, SFA and STD, we show that the network is able to implement the three computational tasks concurrently. We hope this study will shed light on the understanding of how the brain orchestrates its rich dynamics at various levels to realize diverse cognitive functions.

Constitutive modeling of the mechanical behavior of high strength ferritic steels for static and dynamic applications

NASA Astrophysics Data System (ADS)

Abed, Farid H.

2010-11-01

A constitutive relation is presented in this paper to describe the plastic behavior of ferritic steel over a broad range of temperatures and strain rates. The thermo-mechanical behavior of high strength low alloy (HSLA-65) and DH-63 naval structural steels is considered in this study at strains over 40%. The temperatures and strain rates are considered in the range where dynamic strain aging is not effective. The concept of thermal activation analysis as well as the dislocation interaction mechanism is used in developing the flow model for both the isothermal and adiabatic viscoplastic deformation. The flow stresses of the two steels are very sensitive to temperature and strain rate, the yield stresses increase with decreasing temperatures and increasing strain rates. That is, the thermal flow stress is mainly captured by the yield stresses while the hardening stresses are totally pertained to the athermal component of the flow stress. The proposed constitutive model predicts results that compare very well with the measured ones at initial temperature range of 77 K to 1000 K and strain rates between 0.001 s-1 and 8500 s-1 for both steels.

Design of Broad-Spectrum Inhibitors of Influenza A Virus M2 Proton Channels: A Molecular Modeling Approach.

PubMed

Klimochkin, Yuri N; Shiryaev, Vadim A; Petrov, Pavel V; Radchenko, Eugene V; Palyulin, Vladimir A; Zefirov, Nikolay S

2016-01-01

The influenza A virus M2 proton channel plays a critical role in its life cycle. However, known M2 inhibitors have lost their clinical efficacy due to the spread of resistant mutant channels. Thus, the search for broad-spectrum M2 channel inhibitors is of great importance. The goal of the present work was to develop a general approach supporting the design of ligands interacting with multiple labile targets and to propose on its basis the potential broad-spectrum inhibitors of the M2 proton channel. The dynamic dimer-of-dimers structures of the three primary M2 target variants, wild-type, S31N and V27A, were modeled by molecular dynamics and thoroughly analyzed in order to define the inhibitor binding sites. The potential inhibitor structures were identified by molecular docking and their binding was verified by molecular dynamics simulation. The binding sites of the M2 proton channel inhibitors were analyzed, a number of potential broad-spectrum inhibitors were identified and the binding modes and probable mechanisms of action of one promising compound were clarified. Using the molecular dynamics and molecular docking techniques, we have refined the dynamic dimer-ofdimers structures of the WT, S31N and V27A variants of the M2 proton channel of the influenza A virus, analyzed the inhibitor binding sites, identified a number of potential broad-spectrum inhibitor structures targeting them, and clarified the binding modes and probable mechanisms of action of one promising compound. The proposed approach is also suitable for the design of ligands interacting with other multiple labile targets.

A Multi-Faceted Study of Three Forms of Galactic Formation in the Early Universe

NASA Astrophysics Data System (ADS)

Jones, Gareth Christopher

While observations of the early universe have focused on bright, highly starbursting galaxies, star formation activity in the early universe was dominated by main sequence galaxies. Observations of the former group have been accumulating for decades, but the latter are only recently observable using modern instruments. In this work, we apply the Very Large Array (VLA) and the Atacama Large Millimeter/submillimeter Array (ALMA) to observe specific examples of each galactic class, in order to explore three modes of galaxy formation: smooth accretion, satellite accretion, and massive mergers. Using the molecular gas tracer CO and a broad set of continuum measurements, we characterize the gas mass and distribution, star formation, and dust temperature of the two archetypal massively merging Hyper-Luminous IR Galaxies (HyLIRGs) BRI1202-0725 & BRI1335-0417. We then examine the [C II] emission of the Lyman-Break Galaxy (LBG) WMH5, which shows two infalling gas clouds, implying ongoing formation via filamentary accretion. Finally, we apply a classical suite of dynamical characterization tools to [C II] observations of three MS galaxies and three starbursts, resulting in rotation curves and dynamical masses for each. By examining each of these sources in detail, we find that galaxies in the early (i.e., z > 4) universe formed via a broad range of interactions, ranging from cold-mode accretion to major mergers. As these instruments continue observing, and with the future advent of JWST and perhaps the ngVLA, stronger constraints may be placed on the behavior of the galaxies in the epoch of initial galaxy formation.

Response Growth With Sound Level in Auditory-Nerve Fibers After Noise-Induced Hearing Loss

PubMed Central

Heinz, Michael G.; Young, Eric D.

2010-01-01

People with sensorineural hearing loss are often constrained by a reduced acoustic dynamic range associated with loudness recruitment; however, the neural correlates of loudness and recruitment are still not well understood. The growth of auditory-nerve (AN) activity with sound level was compared in normal-hearing cats and in cats with a noise-induced hearing loss to test the hypothesis that AN-fiber rate-level functions are steeper in impaired ears. Stimuli included best-frequency and fixed-frequency tones, broadband noise, and a brief speech token. Three types of impaired responses were observed. 1) Fibers with rate-level functions that were similar across all stimuli typically had broad tuning, consistent with outer-hair-cell (OHC) damage. 2) Fibers with a wide dynamic range and shallow slope above threshold often retained sharp tuning, consistent with primarily inner-hair-cell (IHC) damage. 3) Fibers with very steep rate-level functions for all stimuli had thresholds above approximately 80 dB SPL and very broad tuning, consistent with severe IHC and OHC damage. Impaired rate-level slopes were on average shallower than normal for tones, and were steeper in only limited conditions. There was less variation in rate-level slopes across stimuli in impaired fibers, presumably attributable to the lack of suppression-induced reductions in slopes for complex stimuli relative to BF-tone slopes. Sloping saturation was observed less often in impaired fibers. These results illustrate that AN fibers do not provide a simple representation of the basilar-membrane I/O function and suggest that both OHC and IHC damage can affect AN response growth. PMID:14534289

Short-range order of undercooled melts of PdZr2 intermetallic compound studied by X-ray and neutron scattering experiments

NASA Astrophysics Data System (ADS)

Klein, S.; Holland-Moritz, D.; Herlach, D. M.; Mauro, N. A.; Kelton, K. F.

2013-05-01

The short-range order in undercooled melts of the intermetallic Zr2Pd glass-forming alloy is investigated by combining electrostatic levitation (ESL) with high-energy X-ray diffraction and neutron diffraction. Experimentally determined structure factors are measured and analyzed with respect to various structures of short-range order. The comparative X-ray and neutron scattering experiments allow for investigations of topological and chemical short-range order. Based on these studies, no preference of a specific short-range order is found for the liquid Zr2Pd glass-forming alloy, even in the metastable state of the deeply undercooled melt. This is in agreement with an earlier report from X-ray diffraction and molecular-dynamics studies of a Zr75.5Pd24.5 liquid, which showed a broad distribution of cluster types. The results for the Zr2Pd liquid are discussed with respect to the glass-forming ability of this melt.

33 CFR 334.480 - Archers Creek, Ribbon Creek and Broad River, S.C.; U.S. Marine Corps Recruit Depot rifle and...

Code of Federal Regulations, 2011 CFR

2011-07-01

... Broad River, S.C.; U.S. Marine Corps Recruit Depot rifle and pistol ranges, Parris Island. 334.480... DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.480 Archers Creek, Ribbon Creek and Broad River... navigation: (1) At the rifle range. Archers Creek between Broad River and Beaufort River and Ribbon Creek...

33 CFR 334.480 - Archers Creek, Ribbon Creek and Broad River, S.C.; U.S. Marine Corps Recruit Depot rifle and...

Code of Federal Regulations, 2010 CFR

2010-07-01

... Broad River, S.C.; U.S. Marine Corps Recruit Depot rifle and pistol ranges, Parris Island. 334.480... DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.480 Archers Creek, Ribbon Creek and Broad River... navigation: (1) At the rifle range. Archers Creek between Broad River and Beaufort River and Ribbon Creek...

Lattice dynamics and broad-band dielectric properties of multiferroic Pb(Fe{sub 1/2}Nb{sub 1/2})O{sub 3} ceramics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mackeviciute, R.; Greicius, S.; Grigalaitis, R.

2015-02-28

Complex dielectric properties of Pb(Fe{sub 1/2}Nb{sub 1/2})O{sub 3} ceramics were investigated in a broad frequency range from 100 Hz up to 90 THz. A broad dielectric anomaly was observed near the temperature of the ferroelectric phase transition (T{sub C1} = 376 K). Below 1 MHz, the anomaly is strongly influenced by conductivity of the sample, but higher frequency data taken up to 81 MHz reveal a broad and frequency independent peak at T{sub C1} typical for a diffuse ferroelectric phase transition. Surprisingly, dielectric permittivity measured at 37 GHz exhibits a peak shifted by 25 K above T{sub C1}, which indicates polar nanoregions with dynamics in microwave frequencymore » region. A dielectric relaxation, which appears in THz region below 700 K, slows down towards T{sub C1} and again hardens below T{sub C2} = 356 K. This central mode drives both phase transitions, so they belong to order–disorder type, although the polar phonons exhibit anomalies near both phase transitions. In the paraelectric phase, infrared reflectivity spectra correspond to local Fm3{sup ¯}m structure due to short-range chemical ordering of Fe and Nb cations on the B perovskite sites. Moreover, each polar phonon is split due to two different cations on the B sites. Recently, Manley et al. [Nat. Commun. 5, 3683 (2014)] proposed a new mechanism of creation of polar nanoregions in relaxor ferroelectrics. They argued, based on their inelastic neutron scattering studies of PMN–PT, that the TO1 phonon is split and interaction of both components gives rise to so called Anderson phonon localization, which can produce regions of trapped standing waves and these waves induce polar nanoregions in relaxors. We cannot exclude or confirm this mechanism, but we show that the splitting of polar phonons is a common feature for all complex perovskites with relaxor ferroelectric behavior and it can be also observed in canonical ferroelectric BaTiO{sub 3}, where the soft mode is split in paraelectric phase due to a strong lattice anharmonicity.« less

ATMOSPHERIC DYNAMICS OF TERRESTRIAL EXOPLANETS OVER A WIDE RANGE OF ORBITAL AND ATMOSPHERIC PARAMETERS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaspi, Yohai; Showman, Adam P., E-mail: yohai.kaspi@weizmann.ac.il

The recent discoveries of terrestrial exoplanets and super-Earths extending over a broad range of orbital and physical parameters suggest that these planets will span a wide range of climatic regimes. Characterization of the atmospheres of warm super-Earths has already begun and will be extended to smaller and more distant planets over the coming decade. The habitability of these worlds may be strongly affected by their three-dimensional atmospheric circulation regimes, since the global climate feedbacks that control the inner and outer edges of the habitable zone—including transitions to Snowball-like states and runaway-greenhouse feedbacks—depend on the equator-to-pole temperature differences, patterns of relativemore » humidity, and other aspects of the dynamics. Here, using an idealized moist atmospheric general circulation model including a hydrological cycle, we study the dynamical principles governing the atmospheric dynamics on such planets. We show how the planetary rotation rate, stellar flux, atmospheric mass, surface gravity, optical thickness, and planetary radius affect the atmospheric circulation and temperature distribution on such planets. Our simulations demonstrate that equator-to-pole temperature differences, meridional heat transport rates, structure and strength of the winds, and the hydrological cycle vary strongly with these parameters, implying that the sensitivity of the planet to global climate feedbacks will depend significantly on the atmospheric circulation. We elucidate the possible climatic regimes and diagnose the mechanisms controlling the formation of atmospheric jet streams, Hadley and Ferrel cells, and latitudinal temperature differences. Finally, we discuss the implications for understanding how the atmospheric circulation influences the global climate.« less

Low-frequency vibrational properties of lysozyme in sugar aqueous solutions: A Raman scattering and molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Lerbret, A.; Affouard, F.; Bordat, P.; Hédoux, A.; Guinet, Y.; Descamps, M.

2009-12-01

The low-frequency (ω <400 cm-1) vibrational properties of lysozyme in aqueous solutions of three well-known protecting sugars, namely, trehalose, maltose, and sucrose, have been investigated by means of complementary Raman scattering experiments and molecular dynamics simulations. The comparison of the Raman susceptibility χ″(ω) of lysozyme/water and lysozyme/sugar/water solutions at a concentration of 40 wt % with the χ″ of dry lysozyme suggests that the protein dynamics mostly appears in the broad peak around 60-80 cm-1 that reflects the vibrations experienced by atoms within the cage formed by their neighbors, whereas the broad shoulder around 170 cm-1 mainly stems from the intermolecular O-H⋯O stretching vibrations of water. The addition of sugars essentially induces a significant high frequency shift and intensity reduction of this band that reveal a slowing down of water dynamics and a distortion of the tetrahedral hydrogen bond network of water, respectively. Furthermore, the lysozyme vibrational densities of states (VDOS) have been determined from simulations of lysozyme in 37-60 wt % disaccharide aqueous solutions. They exhibit an additional broad peak around 290 cm-1, in line with the VDOS of globular proteins obtained in neutron scattering experiments. The influence of sugars on the computed VDOS mostly appears on the first peak as a slight high-frequency shift and intensity reduction in the low-frequency range (ω <50 cm-1), which increase with the sugar concentration and with the exposition of protein residues to the solvent. These results suggest that sugars stiffen the environment experienced by lysozyme atoms, thereby counteracting the softening of protein vibrational modes upon denaturation, observed at high temperature in the Raman susceptibility of the lysozyme/water solution and in the computed VDOS of unfolded lysozyme in water. Finally, the Raman susceptibility of sugar/water solutions and the calculated VDOS of water in the different lysozyme solutions confirm that sugars induce a significant strengthening of the hydrogen bond network of water that may stabilize proteins at high temperatures.

Brief Exposure to Turbulence Permanently Alters Development of Sand Dollar Larvae

NASA Astrophysics Data System (ADS)

Ferner, M. C.; Hodin, J.; Ng, G.; Lowe, C. J.; Gaylord, B.

2016-02-01

Fluid motion underlies interactions between animals and their environment through effects on locomotion, food capture, respiration, information transfer, and other processes. Recent studies of marine invertebrates indicate that metamorphosis and settlement can be altered when swimming larvae experience a change in turbulence intensity, possibly increasing the likelihood that larvae will settle in appropriate habitat. For example, brief exposure to levels of turbulence characteristic of wave-swept coasts causes echinoderm larvae to quickly transition from a non-responsive "pre-competent" stage into a "competent" stage, thereby allowing the larvae to respond to local cues and settle. However, responding to one's entry into the nearshore environment isn't enough, as many such species live as adults in a narrower range of highly specific benthic habitat that is even more rarely encountered. Here we provide an account for this apparent mismatch between larval responses to broadly distributed cues and their need for more specialized settlement locations: turbulence exposure seems to cause larval sand dollars (Dendraster excentricus) to permanently shift from pre-competence to competence. This observation suggests a scenario where turbulence can activate a temporally extensive search image in larvae over a broad habitat range, a seemingly adaptive feature for larvae entering dynamic coastal environments.

The coupling between stability and ion pair formation in magnesium electrolytes from first-principles quantum mechanics and classical molecular dynamics

DOE PAGES

Rajput, Nav Nidhi; Qu, Xiaohuui; Sa, Niya; ...

2015-02-10

Here in this work we uncover a novel effect between concentration dependent ion pair formation and anion stability at reducing potentials, e.g., at the metal anode. Through comprehensive calculations using both first-principles as well as well-benchmarked classical molecular dynamics over a matrix of electrolytes, covering solvents and salt anions with a broad range in chemistry, we elucidate systematic correlations between molecular level interactions and composite electrolyte properties, such as electrochemical stability, solvation structure, and dynamics. We find that Mg electrolytes are highly prone to ion pair formation, even at modest concentrations, for a wide range of solvents with different dielectricmore » constants, which have implications for dynamics as well as charge transfer. Specifically, we observe that, at Mg metal potentials, the ion pair undergoes partial reduction at the Mg cation center (Mg 2+ -> Mg +), which competes with the charge transfer mechanism and can activate the anion to render it susceptible to decomposition. Specifically, TFSI exhibits a significant bond weakening while paired with the transient, partially reduced Mg +. In contrast, BH 4 $-$ and BF 4 $-$ are shown to be chemically stable in a reduced ion pair configuration. Furthermore, we observe that higher order glymes as well as DMSO improve the solubility of Mg salts, but only the longer glyme chains reduce the dynamics of the ions in solution. This information provides critical design metrics for future electrolytes as it elucidates a close connection between bulk solvation and cathodic stability as well as the dynamics of the salt.« less

Broad consent versus dynamic consent in biobank research: Is passive participation an ethical problem?

PubMed Central

Steinsbekk, Kristin Solum; Kåre Myskja, Bjørn; Solberg, Berge

2013-01-01

In the endeavour of biobank research there is dispute concerning what type of consent and which form of donor–biobank relationship meet high ethical standards. Up until now, a ‘broad consent' model has been used in many present-day biobank projects. However it has been, by some scholars, deemed as a pragmatic, and not an acceptable ethical solution. Calls for change have been made on the basis of avoidance of paternalism, intentions to fulfil the principle of autonomy, wish for increased user participation, a questioning of the role of experts and ideas advocating reduction of top–down governance. Recently, an approach termed ‘dynamic consent' has been proposed to meet such challenges. Dynamic consent uses modern communication strategies to inform, involve, offer choices and last but not the least obtain consent for every research projects based on biobank resources. At first glance dynamic consent seems appealing, and we have identified six claims of superiority of this model; claims pertaining to autonomy, information, increased engagement, control, social robustness and reciprocity. However, after closer examination, there seems to be several weaknesses with a dynamic consent approach; among others the risk of inviting people into the therapeutic misconception as well as individualizing the ethical review of research projects. When comparing the two models, broad consent still holds and can be deemed a good ethical solution for longitudinal biobank research. Nevertheless, there is potential for improvement in the broad model, and criticism can be met by adapting some of the modern communication strategies proposed in the dynamic consent approach. PMID:23299918

Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity.

PubMed

Papaleo, Elena

2015-01-01

In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.

The fresnel interferometric imager

NASA Astrophysics Data System (ADS)

Koechlin, Laurent; Serre, Denis; Deba, Paul; Pelló, Roser; Peillon, Christelle; Duchon, Paul; Gomez de Castro, Ana Ines; Karovska, Margarita; Désert, Jean-Michel; Ehrenreich, David; Hebrard, Guillaume; Lecavelier Des Etangs, Alain; Ferlet, Roger; Sing, David; Vidal-Madjar, Alfred

2009-03-01

The Fresnel Interferometric Imager has been proposed to the European Space Agency (ESA) Cosmic Vision plan as a class L mission. This mission addresses several themes of the CV Plan: Exoplanet study, Matter in extreme conditions, and The Universe taking shape. This paper is an abridged version of the original ESA proposal. We have removed most of the technical and financial issues, to concentrate on the instrumental design and astrophysical missions. The instrument proposed is an ultra-lightweight telescope, featuring a novel optical concept based on diffraction focussing. It yields high dynamic range images, while releasing constraints on positioning and manufacturing of the main optical elements. This concept should open the way to very large apertures in space. In this two spacecraft formation-flying instrument, one spacecraft holds the focussing element: the Fresnel interferometric array; the other spacecraft holds the field optics, focal instrumentation, and detectors. The Fresnel array proposed here is a 3.6 ×3.6 m square opaque foil punched with 105 to 106 void “subapertures”. Focusing is achieved with no other optical element: the shape and positioning of the subapertures (holes in the foil) is responsible for beam combining by diffraction, and 5% to 10% of the total incident light ends up into a sharp focus. The consequence of this high number of subapertures is high dynamic range images. In addition, as it uses only a combination of vacuum and opaque material, this focussing method is potentially efficient over a very broad wavelength domain. The focal length of such diffractive focussing devices is wavelength dependent. However, this can be corrected. We have tested optically the efficiency of the chromatism correction on artificial sources (500 < λ < 750 nm): the images are diffraction limited, and the dynamic range measured on an artificial double source reaches 6.2 10 - 6. We have also validated numerical simulation algorithms for larger Fresnel interferometric arrays. These simulations yield a dynamic range (rejection factor) close to 10 - 8 for arrays such as the 3.6 m one we propose. A dynamic range of 10 - 8 allows detection of objects at contrasts as high as than 10 - 9 in most of the field. The astrophysical applications cover many objects in the IR, visible an UV domains. Examples are presented, taking advantage of the high angular resolution and dynamic range capabilities of this concept.

Dynamic stiffness of chemically and physically ageing rubber vibration isolators in the audible frequency range. Part 1: constitutive equations

NASA Astrophysics Data System (ADS)

Kari, Leif

2017-09-01

The constitutive equations of chemically and physically ageing rubber in the audible frequency range are modelled as a function of ageing temperature, ageing time, actual temperature, time and frequency. The constitutive equations are derived by assuming nearly incompressible material with elastic spherical response and viscoelastic deviatoric response, using Mittag-Leffler relaxation function of fractional derivative type, the main advantage being the minimum material parameters needed to successfully fit experimental data over a broad frequency range. The material is furthermore assumed essentially entropic and thermo-mechanically simple while using a modified William-Landel-Ferry shift function to take into account temperature dependence and physical ageing, with fractional free volume evolution modelled by a nonlinear, fractional differential equation with relaxation time identical to that of the stress response and related to the fractional free volume by Doolittle equation. Physical ageing is a reversible ageing process, including trapping and freeing of polymer chain ends, polymer chain reorganizations and free volume changes. In contrast, chemical ageing is an irreversible process, mainly attributed to oxygen reaction with polymer network either damaging the network by scission or reformation of new polymer links. The chemical ageing is modelled by inner variables that are determined by inner fractional evolution equations. Finally, the model parameters are fitted to measurements results of natural rubber over a broad audible frequency range, and various parameter studies are performed including comparison with results obtained by ordinary, non-fractional ageing evolution differential equations.

Amyloid β (1-40) Toxicity Depends on the Molecular Contact between Phenylalanine 19 and Leucine 34.

PubMed

Korn, Alexander; McLennan, Steffane; Adler, Juliane; Krueger, Martin; Surendran, Dayana; Maiti, Sudipta; Huster, Daniel

2018-04-18

The formation of the hydrophobic contact between phenylalanine 19 (F19) and leucine 34 (L34) of amyloid β (1-40) (Aβ(1-40)) is known to be an important step in the fibrillation of Aβ(1-40) peptides. Mutations of this putatively early molecular contact were shown to strongly influence the toxicity of Aβ(1-40) ( Das et al. ( 2015 ) ACS Chem. Neurosci. 6 , 1290 - 1295 ). Any mutation of residue F19 completely abolished the toxicity of Aβ(1-40), suggesting that a proper F19-L34 contact is crucial also for the formation of transient oligomers. In this work, we investigate a series of isomeric substitutions of L34, namely, d-leucine, isoleucine, and valine, to study further details of this molecular contact. These replacements represent very minor alterations in the Aβ(1-40) structure posing the question how these alterations challenge the fibrillation kinetics, structure, dynamics, and toxicity of the Aβ(1-40) aggregates. Our work involves kinetic studies using thioflavin T, transmission electron microscopy, X-ray diffraction for the analysis of the fibril morphology, and nuclear magnetic resonance experiments for local structure and molecular dynamics investigations. Combined with cell toxicity assays of the mutated Aβ(1-40) peptides, the physicochemical and biological importance of the early folding contact between F19 and L34 in Aβ(1-40) is underlined. This implies that the F19-L34 contact influences a broad range of different processes including the initiation of fibrillation, oligomer stability, fibril elongation, local fibril structure, and dynamics and cellular toxicity. These processes do not only cover a broad range of diverse mechanisms, but also proved to be highly sensitive to minor modulations of this crucial contact. Furthermore, our work shows that the contact is not simply mediated by general hydrophobic interactions, but also depends on stereospecific mechanisms.

Digital Microarrays: Single-Molecule Readout with Interferometric Detection of Plasmonic Nanorod Labels.

PubMed

Sevenler, Derin; Daaboul, George G; Ekiz Kanik, Fulya; Ünlü, Neşe Lortlar; Ünlü, M Selim

2018-05-21

DNA and protein microarrays are a high-throughput technology that allow the simultaneous quantification of tens of thousands of different biomolecular species. The mediocre sensitivity and limited dynamic range of traditional fluorescence microarrays compared to other detection techniques have been the technology's Achilles' heel and prevented their adoption for many biomedical and clinical diagnostic applications. Previous work to enhance the sensitivity of microarray readout to the single-molecule ("digital") regime have either required signal amplifying chemistry or sacrificed throughput, nixing the platform's primary advantages. Here, we report the development of a digital microarray which extends both the sensitivity and dynamic range of microarrays by about 3 orders of magnitude. This technique uses functionalized gold nanorods as single-molecule labels and an interferometric scanner which can rapidly enumerate individual nanorods by imaging them with a 10× objective lens. This approach does not require any chemical signal enhancement such as silver deposition and scans arrays with a throughput similar to commercial fluorescence scanners. By combining single-nanoparticle enumeration and ensemble measurements of spots when the particles are very dense, this system achieves a dynamic range of about 6 orders of magnitude directly from a single scan. As a proof-of-concept digital protein microarray assay, we demonstrated detection of hepatitis B virus surface antigen in buffer with a limit of detection of 3.2 pg/mL. More broadly, the technique's simplicity and high-throughput nature make digital microarrays a flexible platform technology with a wide range of potential applications in biomedical research and clinical diagnostics.

Evaluation of dynamic coastal response to sea-level rise modifies inundation likelihood

USGS Publications Warehouse

Lentz, Erika E.; Thieler, E. Robert; Plant, Nathaniel G.; Stippa, Sawyer R.; Horton, Radley M.; Gesch, Dean B.

2016-01-01

Sea-level rise (SLR) poses a range of threats to natural and built environments1, 2, making assessments of SLR-induced hazards essential for informed decision making3. We develop a probabilistic model that evaluates the likelihood that an area will inundate (flood) or dynamically respond (adapt) to SLR. The broad-area applicability of the approach is demonstrated by producing 30 × 30 m resolution predictions for more than 38,000 km2 of diverse coastal landscape in the northeastern United States. Probabilistic SLR projections, coastal elevation and vertical land movement are used to estimate likely future inundation levels. Then, conditioned on future inundation levels and the current land-cover type, we evaluate the likelihood of dynamic response versus inundation. We find that nearly 70% of this coastal landscape has some capacity to respond dynamically to SLR, and we show that inundation models over-predict land likely to submerge. This approach is well suited to guiding coastal resource management decisions that weigh future SLR impacts and uncertainty against ecological targets and economic constraints.

Poisson's Ratio of a Hyperelastic Foam Under Quasi-static and Dynamic Loading

DOE PAGES

Sanborn, Brett; Song, Bo

2018-06-03

Poisson's ratio is a material constant representing compressibility of material volume. However, when soft, hyperelastic materials such as silicone foam are subjected to large deformation into densification, the Poisson's ratio may rather significantly change, which warrants careful consideration in modeling and simulation of impact/shock mitigation scenarios where foams are used as isolators. The evolution of Poisson's ratio of silicone foam materials has not yet been characterized, particularly under dynamic loading. In this study, radial and axial measurements of specimen strain are conducted simultaneously during quasi-static and dynamic compression tests to determine the Poisson's ratio of silicone foam. The Poisson's ratiomore » of silicone foam exhibited a transition from compressible to nearly incompressible at a threshold strain that coincided with the onset of densification in the material. Poisson's ratio as a function of engineering strain was different at quasi-static and dynamic rates. Here, the Poisson's ratio behavior is presented and can be used to improve constitutive modeling of silicone foams subjected to a broad range of mechanical loading.« less

Poisson's Ratio of a Hyperelastic Foam Under Quasi-static and Dynamic Loading

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanborn, Brett; Song, Bo

Poisson's ratio is a material constant representing compressibility of material volume. However, when soft, hyperelastic materials such as silicone foam are subjected to large deformation into densification, the Poisson's ratio may rather significantly change, which warrants careful consideration in modeling and simulation of impact/shock mitigation scenarios where foams are used as isolators. The evolution of Poisson's ratio of silicone foam materials has not yet been characterized, particularly under dynamic loading. In this study, radial and axial measurements of specimen strain are conducted simultaneously during quasi-static and dynamic compression tests to determine the Poisson's ratio of silicone foam. The Poisson's ratiomore » of silicone foam exhibited a transition from compressible to nearly incompressible at a threshold strain that coincided with the onset of densification in the material. Poisson's ratio as a function of engineering strain was different at quasi-static and dynamic rates. Here, the Poisson's ratio behavior is presented and can be used to improve constitutive modeling of silicone foams subjected to a broad range of mechanical loading.« less

Functional Dynamics of Hexameric Helicase Probed by Hydrogen Exchange and Simulation

PubMed Central

Radou, Gaël; Dreyer, Frauke N.; Tuma, Roman; Paci, Emanuele

2014-01-01

The biological function of large macromolecular assemblies depends on their structure and their dynamics over a broad range of timescales; for this reason, it is a significant challenge to investigate these assemblies using conventional experimental techniques. One of the most promising experimental techniques is hydrogen-deuterium exchange detected by mass spectrometry. Here, we describe to our knowledge a new computational method for quantitative interpretation of deuterium exchange kinetics and apply it to a hexameric viral helicase P4 that unwinds and translocates RNA into a virus capsid at the expense of ATP hydrolysis. Room-temperature dynamics probed by a hundred nanoseconds of all-atom molecular dynamics simulations is sufficient to predict the exchange kinetics of most sequence fragments and provide a residue-level interpretation of the low-resolution experimental results. The strategy presented here is also a valuable tool to validate experimental data, e.g., assignments, and to probe mechanisms that cannot be observed by x-ray crystallography, or that occur over timescales longer than those that can be realistically simulated, such as the opening of the hexameric ring. PMID:25140434

Active dynamics of colloidal particles in time-varying laser speckle patterns

PubMed Central

Bianchi, Silvio; Pruner, Riccardo; Vizsnyiczai, Gaszton; Maggi, Claudio; Di Leonardo, Roberto

2016-01-01

Colloidal particles immersed in a dynamic speckle pattern experience an optical force that fluctuates both in space and time. The resulting dynamics presents many interesting analogies with a broad class of non-equilibrium systems like: active colloids, self propelled microorganisms, transport in dynamical intracellular environments. Here we show that the use of a spatial light modulator allows to generate light fields that fluctuate with controllable space and time correlations and a prescribed average intensity profile. In particular we generate ring-shaped random patterns that can confine a colloidal particle over a quasi one-dimensional random energy landscape. We find a mean square displacement that is diffusive at both short and long times, while a superdiffusive or subdiffusive behavior is observed at intermediate times depending on the value of the speckles correlation time. We propose two alternative models for the mean square displacement in the two limiting cases of a short or long speckles correlation time. A simple interpolation formula is shown to account for the full phenomenology observed in the mean square displacement across the entire range from fast to slow fluctuating speckles. PMID:27279540

Markets on Networks

NASA Astrophysics Data System (ADS)

Toroczkai, Zoltan; Anghel, Marian; Bassler, Kevin; Korniss, Gyorgy

2003-03-01

The dynamics of human, and most biological populations is characterized by competition for resources. By its own nature, this dynamics creates the group of "elites", formed by those agents who have strategies that are the most successful in the given situation, and therefore the rest of the agents will tend to follow, imitate, or interact with them, creating a social structure of leadership in the agent society. These inter-agent communications generate a complex social network with small-world character which itself forms the substrate for a second network, the action network. The latter is a highly dynamic, adaptive, directed network, defined by those inter-agent communication links on the substrate along which the passed information /prediction is acted upon by the other agents. By using the minority game for competition dynamics, here we show that when the substrate network is highly connected, the action network spontaneously develops hubs with a broad distribution of out-degrees, defining a robust leadership structure that is scale-free. Furthermore, in certain, realistic parameter ranges, facilitated by information passing on the action network, agents can spontaneously generate a high degree of cooperation making the collective almost maximally efficient.

Dynamic Redox Regulation of IL-4 Signaling.

PubMed

Dwivedi, Gaurav; Gran, Margaret A; Bagchi, Pritha; Kemp, Melissa L

2015-11-01

Quantifying the magnitude and dynamics of protein oxidation during cell signaling is technically challenging. Computational modeling provides tractable, quantitative methods to test hypotheses of redox mechanisms that may be simultaneously operative during signal transduction. The interleukin-4 (IL-4) pathway, which has previously been reported to induce reactive oxygen species and oxidation of PTP1B, may be controlled by several other putative mechanisms of redox regulation; widespread proteomic thiol oxidation observed via 2D redox differential gel electrophoresis upon IL-4 treatment suggests more than one redox-sensitive protein implicated in this pathway. Through computational modeling and a model selection strategy that relied on characteristic STAT6 phosphorylation dynamics of IL-4 signaling, we identified reversible protein tyrosine phosphatase (PTP) oxidation as the primary redox regulatory mechanism in the pathway. A systems-level model of IL-4 signaling was developed that integrates synchronous pan-PTP oxidation with ROS-independent mechanisms. The model quantitatively predicts the dynamics of IL-4 signaling over a broad range of new redox conditions, offers novel hypotheses about regulation of JAK/STAT signaling, and provides a framework for interrogating putative mechanisms involving receptor-initiated oxidation.

Dynamic Redox Regulation of IL-4 Signaling

PubMed Central

Dwivedi, Gaurav; Gran, Margaret A.; Bagchi, Pritha; Kemp, Melissa L.

2015-01-01

Quantifying the magnitude and dynamics of protein oxidation during cell signaling is technically challenging. Computational modeling provides tractable, quantitative methods to test hypotheses of redox mechanisms that may be simultaneously operative during signal transduction. The interleukin-4 (IL-4) pathway, which has previously been reported to induce reactive oxygen species and oxidation of PTP1B, may be controlled by several other putative mechanisms of redox regulation; widespread proteomic thiol oxidation observed via 2D redox differential gel electrophoresis upon IL-4 treatment suggests more than one redox-sensitive protein implicated in this pathway. Through computational modeling and a model selection strategy that relied on characteristic STAT6 phosphorylation dynamics of IL-4 signaling, we identified reversible protein tyrosine phosphatase (PTP) oxidation as the primary redox regulatory mechanism in the pathway. A systems-level model of IL-4 signaling was developed that integrates synchronous pan-PTP oxidation with ROS-independent mechanisms. The model quantitatively predicts the dynamics of IL-4 signaling over a broad range of new redox conditions, offers novel hypotheses about regulation of JAK/STAT signaling, and provides a framework for interrogating putative mechanisms involving receptor-initiated oxidation. PMID:26562652

Development of structural health monitoring techniques using dynamics testing

DOE Office of Scientific and Technical Information (OSTI.GOV)

James, G.H. III

Today`s society depends upon many structures (such as aircraft, bridges, wind turbines, offshore platforms, buildings, and nuclear weapons) which are nearing the end of their design lifetime. Since these structures cannot be economically replaced, techniques for structural health monitoring must be developed and implemented. Modal and structural dynamics measurements hold promise for the global non-destructive inspection of a variety of structures since surface measurements of a vibrating structure can provide information about the health of the internal members without costly (or impossible) dismantling of the structure. In order to develop structural health monitoring for application to operational structures, developments inmore » four areas have been undertaken within this project: operational evaluation, diagnostic measurements, information condensation, and damage identification. The developments in each of these four aspects of structural health monitoring have been exercised on a broad range of experimental data. This experimental data has been extracted from structures from several application areas which include aging aircraft, wind energy, aging bridges, offshore structures, structural supports, and mechanical parts. As a result of these advances, Sandia National Laboratories is in a position to perform further advanced development, operational implementation, and technical consulting for a broad class of the nation`s aging infrastructure problems.« less

SQUID-detected FMR: Resonance in single crystalline and polycrystalline yttrium iron garnet

NASA Astrophysics Data System (ADS)

O'Reilly, J. M.; Stamenov, P.

2018-04-01

Here two new techniques for the detection of broadband (100 MHz-20 GHz) ferromagnetic resonance (FMR)/ferrimagnetic resonance in single and poly-crystalline materials, which rely on SQUID-based gradiometry detection of small changes in the magnetisation, are developed. In the first method, small changes in the along-the-applied-field projection of the coupled magnetic moment (Δmz) are detected as the material is driven into resonance. Absolute measurement of the longitudinal component of the magnetisation and the resonance induced lowering of this moment makes estimation of the precession cone angle accessible, which is typically difficult to extract using conventional cavity or stripline based detection methods. The second method invokes the change in Δmz with the resonance-induced thermal heating (d/mz d T ). Magnetisation dynamics in bulk Y3Fe5O12 are observed over a broad range of experimental temperatures (4 K-400 K) and fields (10-500 mT). The inhomogeneous microwave excitation allows for the observation of higher magnetostatic modes and the convenient tracking of very broad resonances. The two SQUID-detection techniques when combined with conventional broadband vector network analyser-FMR, low-frequency magnetic susceptibility, and DC magnetometry, all easily realised, essentially concurrently, using the same module, greatly expand the amount of static and dynamic information accessible.

[Microelement contents of litter, soil fauna and soil in Pinus koraiensis and broad-leaved mixed forest].

PubMed

Yin, Xiu-qin; Li, Jin-xia; Dong, Wei-hua

2007-02-01

The analysis on the Mn, Zn and Cu contents of litter, soil fauna and soil in Pinus korazenszis and broad-leaved mixed forest in Liangshui Natural Reserve of Xiaoxing' an Mountains showed that the test microelement contents in the litter, soil fauna and soil all followed the sequence of Mn > Zn > Cu, but varied with these environmental components, being in the sequence of soil > litter > soil fauna for Mn, soil fauna > litter and soil for Zn, and soil fauna > soil > litter for Cu. The change range of test microelement contents in litter was larger in broad-leaved forest than in coniferous forest. Different soil fauna differed in their microelement-enrichment capability, e. g. , earthworm, centipede, diplopod had the highest content of Mn, Zn and Cu, respectively. The contents of test microelements in soil fauna had significant correlations with their environmental background values, litter decomposition rate, food habit of soil fauna, and its absorbing selectivity and enrichment to microelements. The microelements contained in 5-20 cm soil layer were more than those in 0-5 cm soil layer, and their dynamics differed in various soil layers.

Scaling participation in payments for ecosystem services programs

PubMed Central

Donlan, C. Josh; Boyle, Kevin J.; Xu, Weibin; Gelcich, Stefan

2018-01-01

Payments for ecosystem services programs have become common tools but most have failed to achieve wide-ranging conservation outcomes. The capacity for scale and impact increases when PES programs are designed through the lens of the potential participants, yet this has received little attention in research or practice. Our work with small-scale marine fisheries integrates the social science of PES programs and provides a framework for designing programs that focus a priori on scaling. In addition to payments, desirable non-monetary program attributes and ecological feedbacks attract a wider range of potential participants into PES programs, including those who have more negative attitudes and lower trust. Designing programs that draw individuals into participating in PES programs is likely the most strategic path to reaching scale. Research should engage in new models of participatory research to understand these dynamics and to design programs that explicitly integrate a broad range of needs, values, and modes of implementation. PMID:29522554

Oceanic forcing of coral reefs.

PubMed

Lowe, Ryan J; Falter, James L

2015-01-01

Although the oceans play a fundamental role in shaping the distribution and function of coral reefs worldwide, a modern understanding of the complex interactions between ocean and reef processes is still only emerging. These dynamics are especially challenging owing to both the broad range of spatial scales (less than a meter to hundreds of kilometers) and the complex physical and biological feedbacks involved. Here, we review recent advances in our understanding of these processes, ranging from the small-scale mechanics of flow around coral communities and their influence on nutrient exchange to larger, reef-scale patterns of wave- and tide-driven circulation and their effects on reef water quality and perceived rates of metabolism. We also examine regional-scale drivers of reefs such as coastal upwelling, internal waves, and extreme disturbances such as cyclones. Our goal is to show how a wide range of ocean-driven processes ultimately shape the growth and metabolism of coral reefs.

A general strategy to construct small molecule biosensors in eukaryotes.

PubMed

Feng, Justin; Jester, Benjamin W; Tinberg, Christine E; Mandell, Daniel J; Antunes, Mauricio S; Chari, Raj; Morey, Kevin J; Rios, Xavier; Medford, June I; Church, George M; Fields, Stanley; Baker, David

2015-12-29

Biosensors for small molecules can be used in applications that range from metabolic engineering to orthogonal control of transcription. Here, we produce biosensors based on a ligand-binding domain (LBD) by using a method that, in principle, can be applied to any target molecule. The LBD is fused to either a fluorescent protein or a transcriptional activator and is destabilized by mutation such that the fusion accumulates only in cells containing the target ligand. We illustrate the power of this method by developing biosensors for digoxin and progesterone. Addition of ligand to yeast, mammalian, or plant cells expressing a biosensor activates transcription with a dynamic range of up to ~100-fold. We use the biosensors to improve the biotransformation of pregnenolone to progesterone in yeast and to regulate CRISPR activity in mammalian cells. This work provides a general methodology to develop biosensors for a broad range of molecules in eukaryotes.

Universality of the Peregrine Soliton in the Focusing Dynamics of the Cubic Nonlinear Schrödinger Equation

NASA Astrophysics Data System (ADS)

Tikan, Alexey; Billet, Cyril; El, Gennady; Tovbis, Alexander; Bertola, Marco; Sylvestre, Thibaut; Gustave, Francois; Randoux, Stephane; Genty, Goëry; Suret, Pierre; Dudley, John M.

2017-07-01

We report experimental confirmation of the universal emergence of the Peregrine soliton predicted to occur during pulse propagation in the semiclassical limit of the focusing nonlinear Schrödinger equation. Using an optical fiber based system, measurements of temporal focusing of high power pulses reveal both intensity and phase signatures of the Peregrine soliton during the initial nonlinear evolution stage. Experimental and numerical results are in very good agreement, and show that the universal mechanism that yields the Peregrine soliton structure is highly robust and can be observed over a broad range of parameters.

Ferroelectric or non-ferroelectric: Why so many materials exhibit “ferroelectricity” on the nanoscale

DOE PAGES

Vasudevan, Rama K.; Balke, Nina; Maksymovych, Peter; ...

2017-05-01

Here, ferroelectric materials have remained one of the major focal points of condensed matter physics and materials science for over 50 years. In the last 20 years, the development of voltage-modulated scanning probe microscopy techniques, exemplified by Piezoresponse force microscopy (PFM) and associated time- and voltage spectroscopies, opened a pathway to explore these materials on a single-digit nanometer level. Consequently, domain structures and walls and polarization dynamics can now be imaged in real space. More generally, PFM has allowed studying electromechanical coupling in a broad variety of materials ranging from ionics to biological systems.

Proceedings of the 8th Annual Conference on Manual Control

NASA Technical Reports Server (NTRS)

Pew, R. W.

1972-01-01

The volume presents recent developments in the field of manual control theory and applications. The papers give analytical methods as well as examples of the important interplay between man and machine, such as how man controls and stabilizes machine dynamics, and how machines extend man's capability. Included in the broad range of subjects are procedures to evaluate and identify display systems, controllers, manipulators, human operators, aircraft, and non-flying vehicles. Of particular interest is the continuing trend of applying control theory to problems in medicine and psychology, as well as to problems in vehicle control.

Identifying Structural Flow Defects in Disordered Solids Using Machine-Learning Methods

NASA Astrophysics Data System (ADS)

Cubuk, E. D.; Schoenholz, S. S.; Rieser, J. M.; Malone, B. D.; Rottler, J.; Durian, D. J.; Kaxiras, E.; Liu, A. J.

2015-03-01

We use machine-learning methods on local structure to identify flow defects—or particles susceptible to rearrangement—in jammed and glassy systems. We apply this method successfully to two very different systems: a two-dimensional experimental realization of a granular pillar under compression and a Lennard-Jones glass in both two and three dimensions above and below its glass transition temperature. We also identify characteristics of flow defects that differentiate them from the rest of the sample. Our results show it is possible to discern subtle structural features responsible for heterogeneous dynamics observed across a broad range of disordered materials.

Deciphering the physics and chemistry of perovskites with transmission electron microscopy.

PubMed

Polking, Mark J

2016-03-28

Perovskite oxides exhibit rich structural complexity and a broad range of functional properties, including ferroelectricity, ferromagnetism, and superconductivity. The development of aberration correction for the transmission electron microscope and concurrent progress in electron spectroscopy, electron holography, and other techniques has fueled rapid progress in the understanding of the physics and chemistry of these materials. New techniques based on the transmission electron microscope are first surveyed, and the applications of these techniques for the study of the structure, chemistry, electrostatics, and dynamics of perovskite oxides are then explored in detail, with a particular focus on ferroelectric materials.

Computing observables in curved multifield models of inflation—A guide (with code) to the transport method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dias, Mafalda; Seery, David; Frazer, Jonathan, E-mail: m.dias@sussex.ac.uk, E-mail: j.frazer@sussex.ac.uk, E-mail: a.liddle@sussex.ac.uk

We describe how to apply the transport method to compute inflationary observables in a broad range of multiple-field models. The method is efficient and encompasses scenarios with curved field-space metrics, violations of slow-roll conditions and turns of the trajectory in field space. It can be used for an arbitrary mass spectrum, including massive modes and models with quasi-single-field dynamics. In this note we focus on practical issues. It is accompanied by a Mathematica code which can be used to explore suitable models, or as a basis for further development.

Regional differences in the potential exposure of US minority populations to hazardous facilities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nieves, L.A.; Nieves, A.L.

1992-01-01

In the literature that examines the distribution of environmental disamenities of various types, there is considerable documentation that minority groups and lower income groups are more likely to be exposed. Such differential exposure has been attributed to environmental racism'' by some authors, but there has been no systematic investigation of the factors and dynamics underlying this exposure pattern. This study examines regional differences in the proximity of African-American, Hispanics, Asians, and non-Hispanic Whites to a broad range facility types and explores the degree to which this may be related to urban and income factors.

Broad-Band Pump-Probe Spectroscopy Quantifies Ultrafast Solvation Dynamics of Proteins and Molecules.

PubMed

Jumper, Chanelle C; Arpin, Paul C; Turner, Daniel B; McClure, Scott D; Rafiq, Shahnawaz; Dean, Jacob C; Cina, Jeffrey A; Kovac, Philip A; Mirkovic, Tihana; Scholes, Gregory D

2016-11-17

In this work, we demonstrate the use of broad-band pump-probe spectroscopy to measure femtosecond solvation dynamics. We report studies of a rhodamine dye in methanol and cryptophyte algae light-harvesting proteins in aqueous suspension. Broad-band impulsive excitation generates a vibrational wavepacket that oscillates on the excited-state potential energy surface, destructively interfering with itself at the minimum of the surface. This destructive interference gives rise to a node at a certain probe wavelength that varies with time. This reveals the Gibbs free-energy changes of the excited-state potential energy surface, which equates to the solvation time correlation function. This method captures the inertial solvent response of water (∼40 fs) and the bimodal inertial response of methanol (∼40 and ∼150 fs) and reveals how protein-buried chromophores are sensitive to the solvent dynamics inside and outside of the protein environment.

Absolute calibration of optical streak cameras on picosecond time scales using supercontinuum generation

DOE PAGES

Patankar, S.; Gumbrell, E. T.; Robinson, T. S.; ...

2017-08-17

Here we report a new method using high stability, laser-driven supercontinuum generation in a liquid cell to calibrate the absolute photon response of fast optical streak cameras as a function of wavelength when operating at fastest sweep speeds. A stable, pulsed white light source based around the use of self-phase modulation in a salt solution was developed to provide the required brightness on picosecond timescales, enabling streak camera calibration in fully dynamic operation. The measured spectral brightness allowed for absolute photon response calibration over a broad spectral range (425-650nm). Calibrations performed with two Axis Photonique streak cameras using the Photonismore » P820PSU streak tube demonstrated responses which qualitatively follow the photocathode response. Peak sensitivities were 1 photon/count above background. The absolute dynamic sensitivity is less than the static by up to an order of magnitude. We attribute this to the dynamic response of the phosphor being lower.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kostylev, M.

In this work, we derive the interface exchange boundary conditions for the classical linear dynamics of magnetization in ferromagnetic layers with the interface Dzyaloshinskii-Moriya interaction (IDMI). We show that IDMI leads to pinning of dynamic magnetization at the interface. An unusual peculiarity of the IDMI-based pinning is that its scales as the spin-wave wave number. We incorporate these boundary conditions into an existing numerical model for the dynamics of the Damon-Eshbach spin wave in ferromagnetic films. IDMI affects the dispersion and the frequency non-reciprocity of the travelling Damon-Eshbach spin wave. For a broad range of film thicknesses L and wavemore » numbers, the results of the numerical simulations of the spin wave dispersion are in a good agreement with a simple analytical expression, which shows that the contribution of IDMI to the dispersion scales as 1/L, similarly to the effect of other types of interfacial anisotropy. Suggestions to experimentalists how to detect the presence of IDMI in a spin wave experiment are given.« less

A Voyage through the Heliosphere (Invited)

NASA Astrophysics Data System (ADS)

Burlaga, L. F.

2009-12-01

Parker adopted the word “Heliosphere” to denote “the region of interstellar space swept out by the solar wind” His book “Interplanetary Dynamical Processes” (1963) provided “a comprehensive self-consistent dynamical picture of interplanetary activity” on spatial scales from the Larmor radius to the outermost limits of the heliosphere and over a broad range of temporal scales. The spacecraft Voyagers 1 and 2 have taken us on a journey through much of the heliosphere: from Earth, past the termination shock near 90 AU, and into the inner heliosheath. This talk will use magnetic field observations from V1 and V2 to illustrate how Parker’s dynamical picture has been largely confirmed by observations out to ~100 AU. It will also discuss some “complicating aspects of the dynamics…which will turn up in future observations…” that Parker envisaged. With continued funding, the Voyager spacecraft will allow us to explore the heliosheath, cross the boundary of the heliosphere, and sample the local interstellar medium, guided by still untested predictions of Parker.

Li-Diffusion in Spinel Li[Ni1/2Mn3/2]O4 Powder and Film Studied with μ+SR

NASA Astrophysics Data System (ADS)

Sugiyama, Jun; Nozaki, Hiroshi; Umegaki, Izumi; Mukai, Kazuhiko; Cottrell, Stephen P.; Shiraki, Susumu; Hitosugi, Taro; Sassa, Yasmine; Suter, Andreas; Salman, Zaher; Prokscha, Thomas; Månsson, Martin

A dynamic behavior in spinel Li[Ni1/2Mn3/2]O4 has been studied with μ+SR measurements in film and powder samples in the temperature range between 5 and 500 K. Both samples exhibited a broad ferromagnetic transition below 120 K, indicating the random distribution of Ni and Mn ions at the octahedral 16d site. Above 150 K, the ZF-μ+SR spectrum showed a dynamic behavior well explained by a dynamic Kubo-Toyabe function. Assuming a jump diffusion of Li+ at the tetrahedral 8a site to the vacant octahedral 16c site, a diffusion coefficient of Li+ is estimated as ˜5 × 10-11 cm2/s at 300 K and ˜8 × 10-11 cm2/s at 350 K and ˜14 × 10-11 cm2/s at 400 K, with thermal activation energy Ea ˜ 0.1 eV.

Cell fate determination dynamics in bacteria

NASA Astrophysics Data System (ADS)

Kuchina, Anna; Espinar, Lorena; Cagatay, Tolga; Garcia-Ojalvo, Jordi; Suel, Gurol

2010-03-01

The fitness of an organism depends on many processes that serve the purpose to adapt to changing environment in a robust and coordinated fashion. One example of such process is cellular fate determination. In the presence of a variety of alternative responses each cell adopting a particular fate represents a ``choice'' that must be tightly regulated to ensure the best survival strategy for the population taking into account the broad range of possible environmental challenges. We investigated this problem in the model organism B.Subtilis which under stress conditions differentiates terminally into highly resistant spores or initiates an alternative transient state of competence. The dynamics underlying cell fate choice remains largely unknown. We utilize quantitative fluorescent microscopy to track the activities of genes involved in these responses on a single-cell level. We explored the importance of temporal interactions between competing cell fates by re- engineering the differentiation programs. I will discuss how the precise dynamics of cellular ``decision-making'' governed by the corresponding biological circuits may enable cells to adjust to diverse environments and determine survival.

Autonomous Guidance of Agile Small-scale Rotorcraft

NASA Technical Reports Server (NTRS)

Mettler, Bernard; Feron, Eric

2004-01-01

This report describes a guidance system for agile vehicles based on a hybrid closed-loop model of the vehicle dynamics. The hybrid model represents the vehicle dynamics through a combination of linear-time-invariant control modes and pre-programmed, finite-duration maneuvers. This particular hybrid structure can be realized through a control system that combines trim controllers and a maneuvering control logic. The former enable precise trajectory tracking, and the latter enables trajectories at the edge of the vehicle capabilities. The closed-loop model is much simpler than the full vehicle equations of motion, yet it can capture a broad range of dynamic behaviors. It also supports a consistent link between the physical layer and the decision-making layer. The trajectory generation was formulated as an optimization problem using mixed-integer-linear-programming. The optimization is solved in a receding horizon fashion. Several techniques to improve the computational tractability were investigate. Simulation experiments using NASA Ames 'R-50 model show that this approach fully exploits the vehicle's agility.

Ultrasensitive dual phosphorylation dephosphorylation cycle kinetics exhibits canonical competition behavior

NASA Astrophysics Data System (ADS)

Huang, Qingdao; Qian, Hong

2009-09-01

We establish a mathematical model for a cellular biochemical signaling module in terms of a planar differential equation system. The signaling process is carried out by two phosphorylation-dephosphorylation reaction steps that share common kinase and phosphatase with saturated enzyme kinetics. The pair of equations is particularly simple in the present mathematical formulation, but they are singular. A complete mathematical analysis is developed based on an elementary perturbation theory. The dynamics exhibits the canonical competition behavior in addition to bistability. Although widely understood in ecological context, we are not aware of a full range of biochemical competition in a simple signaling network. The competition dynamics has broad implications to cellular processes such as cell differentiation and cancer immunoediting. The concepts of homogeneous and heterogeneous multisite phosphorylation are introduced and their corresponding dynamics are compared: there is no bistability in a heterogeneous dual phosphorylation system. A stochastic interpretation is also provided that further gives intuitive understanding of the bistable behavior inside the cells.

Detection of time delays and directional interactions based on time series from complex dynamical systems

NASA Astrophysics Data System (ADS)

Ma, Huanfei; Leng, Siyang; Tao, Chenyang; Ying, Xiong; Kurths, Jürgen; Lai, Ying-Cheng; Lin, Wei

2017-07-01

Data-based and model-free accurate identification of intrinsic time delays and directional interactions is an extremely challenging problem in complex dynamical systems and their networks reconstruction. A model-free method with new scores is proposed to be generally capable of detecting single, multiple, and distributed time delays. The method is applicable not only to mutually interacting dynamical variables but also to self-interacting variables in a time-delayed feedback loop. Validation of the method is carried out using physical, biological, and ecological models and real data sets. Especially, applying the method to air pollution data and hospital admission records of cardiovascular diseases in Hong Kong reveals the major air pollutants as a cause of the diseases and, more importantly, it uncovers a hidden time delay (about 30-40 days) in the causal influence that previous studies failed to detect. The proposed method is expected to be universally applicable to ascertaining and quantifying subtle interactions (e.g., causation) in complex systems arising from a broad range of disciplines.

Towards pump-probe experiments of defect dynamics with short ion beam pulses

NASA Astrophysics Data System (ADS)

Schenkel, T.; Lidia, S. M.; Weis, C. D.; Waldron, W. L.; Schwartz, J.; Minor, A. M.; Hosemann, P.; Kwan, J. W.

2013-11-01

A novel, induction type linear accelerator, the Neutralized Drift Compression eXperiment (NDCX-II), is currently being commissioned at Berkeley Lab. This accelerator is designed to deliver intense (up to 3 × 1011 ions/pulse), 0.6 to ∼600 ns duration pulses of 0.05-1.2 MeV lithium ions at a rate of about 2 pulses per minute onto 1-10 mm scale target areas. When focused to mm-diameter spots, the beam is predicted to volumetrically heat micrometer thick foils to temperatures of ∼30,000 °K. At lower beam power densities, the short excitation pulse with tunable intensity and time profile enables pump-probe type studies of defect dynamics in a broad range of materials. We briefly describe the accelerator concept and design, present results from beam pulse shaping experiments and discuss examples of pump-probe type studies of defect dynamics following irradiation of materials with intense, short ion beam pulses from NDCX-II.

Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover

DOE PAGES

Stegen, James C.; Fredrickson, James K.; Wilkins, Michael J.; ...

2016-04-07

Environmental transition zones are associated with geochemical gradients that overcome energy limitations to microbial metabolism, resulting in biogeochemical hot spots and moments. Riverine systems where groundwater mixes with surface water (the hyporheic zone) are spatially complex and temporally dynamic, making development of predictive models challenging. Spatial and temporal variations in hyporheic zone microbial communities are a key, but understudied, component of riverine biogeochemical function. To investigate the coupling among groundwater-surface water mixing, microbial communities, and biogeochemistry we applied ecological theory, aqueous biogeochemistry, DNA sequencing, and ultra-high resolution organic carbon profiling to field samples collected across times and locations representing amore » broad range of mixing conditions. Mixing of groundwater and surface water resulted in a shift from transport-driven stochastic dynamics to a deterministic microbial structure associated with elevated biogeochemical rates. While the dynamics of the hyporheic make predictive modeling a challenge, we provide new knowledge that can improve the tractability of such models.« less

TDM interrogation of intensity-modulated USFBGs network based on multichannel lasers.

PubMed

Rohollahnejad, Jalal; Xia, Li; Cheng, Rui; Ran, Yanli; Rahubadde, Udaya; Zhou, Jiaao; Zhu, Lin

2017-01-23

We report a large-scale multi-channel fiber sensing network, where ultra-short FBGs (USFBGs) instead of conventional narrow-band ultra-weak FBGs are used as the sensors. In the time division multiplexing scheme of the network, each grating response is resolved as three adjacent discrete peaks. The central wavelengths of USFBGs are tracked with the differential detection, which is achieved by calculating the peak-to-peak ratio of two maximum peaks. Compared with previous large-scale hybrid multiplexing sensing networks (e.g., WDM/TDM) which typically have relatively low interrogation speed and very high complexity, the proposed system can achieve interrogation of all channel sensors through very fast and simple intensity measurements with a broad dynamic range. A proof-of-concept experiment with twenty USFBGs, at two wavelength channels, was performed and a fast static strain measurements were demonstrated, with a high average sensitivity of ~0.54dB/µƐ and wide dynamic range of over ~3000µƐ. The channel to channel switching time was 10ms and total network interrogation time was 50ms.

Breakdown of Spin-Waves in Anisotropic Magnets: Spin Dynamics in α-RuCl3

NASA Astrophysics Data System (ADS)

Winter, Stephen; Riedl, Kira; Honecker, Andreas; Valenti, Roser

α -RuCl3 has recently emerged as a promising candidate for realizing the hexagonal Kitaev model in a real material. Similar to the related iridates (e.g. Na2IrO3), complex magnetic interactions arise from a competition between various similar energy scales, including spin-orbit coupling (SOC), Hund's coupling, and crystal-field splitting. Due to this complexity, the correct spin Hamiltonians for such systems remain hotly debated. For α-RuCl3, a combination of ab-initio calculations, microscopic considerations, and analysis of the static magnetic response have suggested off-diagonal couplings (Γ ,Γ') and long-range interactions in addition to the expected Kitaev exchange. However, the effect of such additional terms on the dynamic response remains unclear. In this contribution, we discuss the recently measured inelastic neutron scattering response in the context of realistic proposals for the microscopic spin Hamiltonian. We conclude that the observed scattering continuum, which has been taken as a signature of Kitaev spin liquid physics, likely persists over a broad range of parameters.

On the emergence of an ‘intention field’ for socially cohesive agents

NASA Astrophysics Data System (ADS)

Bouchaud, Jean-Philippe; Borghesi, Christian; Jensen, Pablo

2014-03-01

We argue that when a social convergence mechanism exists and is strong enough, one should expect the emergence of a well-defined ‘field’, i.e. a slowly evolving, local quantity around which individual attributes fluctuate in a finite range. This condensation phenomenon is well illustrated by the Deffuant-Weisbuch opinion model for which we provide a natural extension to allow for spatial heterogeneities. We show analytically and numerically that the resulting dynamics of the emergent field is a noisy diffusion equation that has a slow dynamics. This random diffusion equation reproduces the long-ranged, logarithmic decrease of the correlation of spatial voting patterns empirically found in Borghesi and Bouchaud (2010 Eur. Phys. J. B 75 395) and Borghesi et al (2012 PLoS One 7 e36289). Interestingly enough, we find that when the social cohesion mechanism becomes too weak, cultural cohesion breaks down completely, in the sense that the distribution of intentions/opinions becomes infinitely broad. No emerging field exists in this case. All these analytical findings are confirmed by numerical simulations of an agent-based model.

Ultrasensitive direct impedimetric immunosensor for detection of serum HER2.

PubMed

Sharma, Shikha; Zapatero-Rodríguez, Julia; Saxena, Rahul; O'Kennedy, Richard; Srivastava, Sudha

2018-05-30

Assesment of human epidermal growth factor receptor 2 status is a key factor prompting definitive treatment decisions that help in reducing mortality rates associated with breast cancer. In this article, highly sensitive and low-cost impedimetric immunosensor using single-chain fragment variable antibody fragments was developed for quantitative detection of human epidermal growth factor receptor 2 from serum employing gold nanoparticle-modified disposable screen-printed carbon electrodes. The gold nanoparticles facilitate fast electron transfer and offer a biocompatible surface for immobilization of small antibody fragments in an oriented manner, resulting in improved antigen binding efficiency. The single-chain fragment variable antibody fragment-modified screen printed immunosensor exhibits wide dynamic range of 0.01-100 ng mL -1 and detection limit of 0.01 ng mL -1 . The advantages offered by this platform in terms of high sensitivity, broad dynamic range and low-cost demonstrates great potential for improved monitoring of human epidermal growth factor receptor 2 levels for the management of breast and other cancers. Copyright © 2018 Elsevier B.V. All rights reserved.

Development of test methodology for dynamic mechanical analysis instrumentation

NASA Technical Reports Server (NTRS)

Allen, V. R.

1982-01-01

Dynamic mechanical analysis instrumentation was used for the development of specific test methodology in the determination of engineering parameters of selected materials, esp. plastics and elastomers, over a broad range of temperature with selected environment. The methodology for routine procedures was established with specific attention given to sample geometry, sample size, and mounting techniques. The basic software of the duPont 1090 thermal analyzer was used for data reduction which simplify the theoretical interpretation. Clamps were developed which allowed 'relative' damping during the cure cycle to be measured for the fiber-glass supported resin. The correlation of fracture energy 'toughness' (or impact strength) with the low temperature (glassy) relaxation responses for a 'rubber-modified' epoxy system was negative in result because the low-temperature dispersion mode (-80 C) of the modifier coincided with that of the epoxy matrix, making quantitative comparison unrealistic.

Generation and precise control of dynamic biochemical gradients for cellular assays

NASA Astrophysics Data System (ADS)

Saka, Yasushi; MacPherson, Murray; Giuraniuc, Claudiu V.

2017-03-01

Spatial gradients of diffusible signalling molecules play crucial roles in controlling diverse cellular behaviour such as cell differentiation, tissue patterning and chemotaxis. In this paper, we report the design and testing of a microfluidic device for diffusion-based gradient generation for cellular assays. A unique channel design of the device eliminates cross-flow between the source and sink channels, thereby stabilizing gradients by passive diffusion. The platform also enables quick and flexible control of chemical concentration that makes highly dynamic gradients in diffusion chambers. A model with the first approximation of diffusion and surface adsorption of molecules recapitulates the experimentally observed gradients. Budding yeast cells cultured in a gradient of a chemical inducer expressed a reporter fluorescence protein in a concentration-dependent manner. This microfluidic platform serves as a versatile prototype applicable to a broad range of biomedical investigations.

The Interstellar Medium in External Galaxies: Summaries of contributed papers

NASA Technical Reports Server (NTRS)

Hollenbach, David J. (Editor); Thronson, Harley A., Jr. (Editor)

1990-01-01

The Second Wyoming Conference entitled, The Interstellar Medium in External Galaxies, was held on July 3 to 7, 1989, to discuss the current understanding of the interstellar medium in external galaxies and to analyze the basic physical processes underlying interstellar phenomena. The papers covered a broad range of research on the gas and dust in external galaxies and focused on such topics as the distribution and morphology of the atomic, molecular, and dust components; the dynamics of the gas and the role of the magnetic field in the dynamics; elemental abundances and gas depletions in the atomic and ionized components; cooling flows; star formation; the correlation of the nonthermal radio continuum with the cool component of the interstellar medium; the origin and effect of hot galactic halos; the absorption line systems seen in distant quasars; and the effect of galactic collisions.

How to control chaotic behaviour and population size with proportional feedback

NASA Astrophysics Data System (ADS)

Liz, Eduardo

2010-01-01

We study the control of chaos in one-dimensional discrete maps as they often occur in modelling population dynamics. For managing the population, we seek to suppress any possible chaotic behavior, leading the system to a stable equilibrium. In this Letter, we make a rigorous analysis of the proportional feedback method under certain conditions fulfilled by a wide family of maps. We show that it is possible to stabilize the chaotic dynamics towards a globally stable positive equilibrium, that can be chosen among a broad range of possible values. In particular, the size of the population can be enhanced by control in form of population reduction. This paradoxical phenomenon is known as the hydra effect, and it has important implications in the design of strategies in such areas as fishing, pest management, and conservation biology.

Introduction to Focus Issue: Rhythms and Dynamic Transitions in Neurological Disease: Modeling, Computation, and Experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaper, Tasso J., E-mail: tasso@bu.edu; Kramer, Mark A., E-mail: mak@bu.edu; Rotstein, Horacio G., E-mail: horacio@njit.edu

Rhythmic neuronal oscillations across a broad range of frequencies, as well as spatiotemporal phenomena, such as waves and bumps, have been observed in various areas of the brain and proposed as critical to brain function. While there is a long and distinguished history of studying rhythms in nerve cells and neuronal networks in healthy organisms, the association and analysis of rhythms to diseases are more recent developments. Indeed, it is now thought that certain aspects of diseases of the nervous system, such as epilepsy, schizophrenia, Parkinson's, and sleep disorders, are associated with transitions or disruptions of neurological rhythms. This focusmore » issue brings together articles presenting modeling, computational, analytical, and experimental perspectives about rhythms and dynamic transitions between them that are associated to various diseases.« less

Topics in black holes and quantum cosmology

NASA Astrophysics Data System (ADS)

Campiglia, Miguel

2012-06-01

Black holes and the big bang beginning of the universe are among the most spectacular predictions of general relativity, having a broad impact that ranges from observational astronomy to quantum gravity. In this thesis we will focus on classical and quantum aspects of these subjects: In the first part we present a coordinate-free way of describing the approach to equilibrium of black holes within the framework of dynamical and isolated horizons. In the second part we focus on loop quantum cosmology. We present a uniqueness theorem of its kinematics, and explore the possible ways to implement its dynamics via path integrals.¹ ¹The topics presented here form part of the research done during my PhD studies. See the Vita at the end of the Thesis for a complete list of my work during this period.

Pseudoscaffolds and anchoring proteins: the difference is in the details

PubMed Central

Aggarwal-Howarth, Stacey; Scott, John D.

2017-01-01

Pseudokinases and pseudophosphatases possess the ability to bind substrates without catalyzing their modification, thereby providing a mechanism to recruit potential phosphotargets away from active enzymes. Since many of these pseudoenzymes possess other characteristics such as localization signals, separate catalytic sites, and protein–protein interaction domains, they have the capacity to influence signaling dynamics in local environments. In a similar manner, the targeting of signaling enzymes to subcellular locations by A-kinase-anchoring proteins (AKAPs) allows for precise and local control of second messenger signaling events. Here, we will discuss how pseudoenzymes form ‘pseudoscaffolds’ and compare and contrast this compartment-specific regulatory role with the signal organization properties of AKAPs. The mitochondria will be the focus of this review, as they are dynamic organelles that influence a broad range of cellular processes such as metabolism, ATP synthesis, and apoptosis. PMID:28408477

Beyond the Rayleigh instability limit for multicharged finite systems: From fission to Coulomb explosion

PubMed Central

Last, Isidore; Levy, Yaakov; Jortner, Joshua

2002-01-01

We address the stability of multicharged finite systems driven by Coulomb forces beyond the Rayleigh instability limit. Our exploration of the nuclear dynamics of heavily charged Morse clusters enabled us to vary the range of the pair potential and of the fissibility parameter, which results in distinct fragmentation patterns and in the angular distributions of the fragments. The Rayleigh instability limit separates between nearly binary (or tertiary) spatially unisotropic fission and spatially isotropic Coulomb explosion into a large number of small, ionic fragments. Implications are addressed for a broad spectrum of dynamics in chemical physics, radiation physics of ultracold gases, and biophysics, involving the fission of clusters and droplets, the realization of Coulomb explosion of molecular clusters, the isotropic expansion of optical molasses, and the Coulomb instability of “isolated” proteins. PMID:12093910

Universal Faraday Rotation in HgTe Wells with Critical Thickness.

PubMed

Shuvaev, A; Dziom, V; Kvon, Z D; Mikhailov, N N; Pimenov, A

2016-09-09

The universal value of the Faraday rotation angle close to the fine structure constant (α≈1/137) is experimentally observed in thin HgTe quantum wells with a thickness on the border between trivial insulating and the topologically nontrivial Dirac phases. The quantized value of the Faraday angle remains robust in the broad range of magnetic fields and gate voltages. Dynamic Hall conductivity of the holelike carriers extracted from the analysis of the transmission data shows a theoretically predicted universal value of σ_{xy}=e^{2}/h, which is consistent with the doubly degenerate Dirac state. On shifting the Fermi level by the gate voltage, the effective sign of the charge carriers changes from positive (holes) to negative (electrons). The electronlike part of the dynamic response does not show quantum plateaus and is well described within the classical Drude model.

oGNM: online computation of structural dynamics using the Gaussian Network Model

PubMed Central

Yang, Lee-Wei; Rader, A. J.; Liu, Xiong; Jursa, Cristopher Jon; Chen, Shann Ching; Karimi, Hassan A.; Bahar, Ivet

2006-01-01

An assessment of the equilibrium dynamics of biomolecular systems, and in particular their most cooperative fluctuations accessible under native state conditions, is a first step towards understanding molecular mechanisms relevant to biological function. We present a web-based system, oGNM that enables users to calculate online the shape and dispersion of normal modes of motion for proteins, oligonucleotides and their complexes, or associated biological units, using the Gaussian Network Model (GNM). Computations with the new engine are 5–6 orders of magnitude faster than those using conventional normal mode analyses. Two cases studies illustrate the utility of oGNM. The first shows that the thermal fluctuations predicted for 1250 non-homologous proteins correlate well with X-ray crystallographic data over a broad range [7.3–15 Å] of inter-residue interaction cutoff distances and the correlations improve with increasing observation temperatures. The second study, focused on 64 oligonucleotides and oligonucleotide–protein complexes, shows that good agreement with experiments is achieved by representing each nucleotide by three GNM nodes (as opposed to one-node-per-residue in proteins) along with uniform interaction ranges for all components of the complexes. These results open the way to a rapid assessment of the dynamics of DNA/RNA-containing complexes. The server can be accessed at . PMID:16845002

To react or not to react? Intrinsic stochasticity of human control in virtual stick balancing

PubMed Central

Zgonnikov, Arkady; Lubashevsky, Ihor; Kanemoto, Shigeru; Miyazawa, Toru; Suzuki, Takashi

2014-01-01

Understanding how humans control unstable systems is central to many research problems, with applications ranging from quiet standing to aircraft landing. Increasingly, much evidence appears in favour of event-driven control hypothesis: human operators only start actively controlling the system when the discrepancy between the current and desired system states becomes large enough. The event-driven models based on the concept of threshold can explain many features of the experimentally observed dynamics. However, much still remains unclear about the dynamics of human-controlled systems, which likely indicates that humans use more intricate control mechanisms. This paper argues that control activation in humans may be not threshold-driven, but instead intrinsically stochastic, noise-driven. Specifically, we suggest that control activation stems from stochastic interplay between the operator's need to keep the controlled system near the goal state, on the one hand, and the tendency to postpone interrupting the system dynamics, on the other hand. We propose a model capturing this interplay and show that it matches the experimental data on human balancing of virtual overdamped stick. Our results illuminate that the noise-driven activation mechanism plays a crucial role at least in the considered task, and, hypothetically, in a broad range of human-controlled processes. PMID:25056217

Density Functional Methods for Shock Physics and High Energy Density Science

NASA Astrophysics Data System (ADS)

Desjarlais, Michael

2017-06-01

Molecular dynamics with density functional theory has emerged over the last two decades as a powerful and accurate framework for calculating thermodynamic and transport properties with broad application to dynamic compression, high energy density science, and warm dense matter. These calculations have been extensively validated against shock and ramp wave experiments, are a principal component of high-fidelity equation of state generation, and are having wide-ranging impacts on inertial confinement fusion, planetary science, and shock physics research. In addition to thermodynamic properties, phase boundaries, and the equation of state, one also has access to electrical conductivity, thermal conductivity, and lower energy optical properties. Importantly, all these properties are obtained within the same theoretical framework and are manifestly consistent. In this talk I will give a brief history and overview of molecular dynamics with density functional theory and its use in calculating a wide variety of thermodynamic and transport properties for materials ranging from ambient to extreme conditions and with comparisons to experimental data. I will also discuss some of the limitations and difficulties, as well as active research areas. Sandia is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

The Holy See on sexual and reproductive health rights: conservative in position, dynamic in response.

PubMed

Coates, Amy L; Hill, Peter S; Rushton, Simon; Balen, Julie

2014-11-01

The Holy See has engaged extensively in United Nations negotiations on issues concerning sexual and reproductive health rights as they have emerged and evolved in a dynamic global agenda over the past two decades. A meta-narrative review of the mission's official statements was conducted to examine the positions, discourses and tensions across the broad range of agendas. The Holy See represents a fundamentally conservative and stable position on a range of sexual and reproductive health rights concerns. However, the mission has been dynamic in the ways in which it has forwarded its arguments, increasingly relying upon secularised technical claims and empirical evidence; strategically interpreting human rights norms in ways consistent with its own position; and framing sexuality and reproduction in the context of "the family". Seen in the broader context of a "religious resurgence" in international relations, and in light of the fact that the Holy See has frequently sought to form alliances with conservative State and non-State actors, these findings make an important contribution to understanding the slow progress as well as the potential obstacles that lie ahead in the battle to realise sexual and reproductive health rights in a changing global political environment. Copyright © 2014 Reproductive Health Matters. Published by Elsevier Ltd. All rights reserved.

Market-based demand forecasting promotes informed strategic financial planning.

PubMed

Beech, A J

2001-11-01

Market-based demand forecasting is a method of estimating future demand for a healthcare organization's services by using a broad range of data that describe the nature of demand within the organization's service area. Such data include the primary and secondary service areas, the service-area populations by various demographic groupings, discharge utilization rates, market size, and market share by service line and organizationwide. Based on observable market dynamics, strategic planners can make a variety of explicit assumptions about future trends regarding these data to develop scenarios describing potential future demand. Financial planners then can evaluate each scenario to determine its potential effect on selected financial and operational measures, such as operating margin, days cash on hand, and debt-service coverage, and develop a strategic financial plan that covers a range of contingencies.

High-order synchronization of hair cell bundles

NASA Astrophysics Data System (ADS)

Levy, Michael; Molzon, Adrian; Lee, Jae-Hyun; Kim, Ji-Wook; Cheon, Jinwoo; Bozovic, Dolores

2016-12-01

Auditory and vestibular hair cell bundles exhibit active mechanical oscillations at natural frequencies that are typically lower than the detection range of the corresponding end organs. We explore how these noisy nonlinear oscillators mode-lock to frequencies higher than their internal clocks. A nanomagnetic technique is used to stimulate the bundles without an imposed mechanical load. The evoked response shows regimes of high-order mode-locking. Exploring a broad range of stimulus frequencies and intensities, we observe regions of high-order synchronization, analogous to Arnold Tongues in dynamical systems literature. Significant areas of overlap occur between synchronization regimes, with the bundle intermittently flickering between different winding numbers. We demonstrate how an ensemble of these noisy spontaneous oscillators could be entrained to efficiently detect signals significantly above the characteristic frequencies of the individual cells.

Reynolds Number Effects on Leading Edge Radius Variations of a Supersonic Transport at Transonic Conditions

NASA Technical Reports Server (NTRS)

Rivers, S. M. B.; Wahls, R. A.; Owens, L. R.

2001-01-01

A computational study focused on leading-edge radius effects and associated Reynolds number sensitivity for a High Speed Civil Transport configuration at transonic conditions was conducted as part of NASA's High Speed Research Program. The primary purposes were to assess the capabilities of computational fluid dynamics to predict Reynolds number effects for a range of leading-edge radius distributions on a second-generation supersonic transport configuration, and to evaluate the potential performance benefits of each at the transonic cruise condition. Five leading-edge radius distributions are described, and the potential performance benefit including the Reynolds number sensitivity for each is presented. Computational results for two leading-edge radius distributions are compared with experimental results acquired in the National Transonic Facility over a broad Reynolds number range.

The clinical impact of recent advances in LC-MS for cancer biomarker discovery and verification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Hui; Shi, Tujin; Qian, Wei-Jun

2015-12-04

Mass spectrometry-based proteomics has become an indispensable tool in biomedical research with broad applications ranging from fundamental biology, systems biology, and biomarker discovery. Recent advances in LC-MS have made it become a major technology in clinical applications, especially in cancer biomarker discovery and verification. To overcome the challenges associated with the analysis of clinical samples, such as extremely wide dynamic range of protein concentrations in biofluids and the need to perform high throughput and accurate quantification, significant efforts have been devoted to improve the overall performance of LC-MS bases clinical proteomics. In this review, we summarize the recent advances inmore » LC-MS in the aspect of cancer biomarker discovery and quantification, and discuss its potentials, limitations, and future perspectives.« less

An introduction to electronic learning and its use to address challenges in surgical training.

PubMed

Baran, Szczepan W; Johnson, Elizabeth J; Kehler, James

2009-06-01

The animal research community faces a shortage of surgical training opportunities along with an increasing demand for expertise in surgical techniques. One possible means of overcoming this challenge is the use of computer-based or electronic learning (e-learning) to disseminate material to a broad range of animal users. E-learning platforms can take many different forms, ranging from simple text documents that are posted online to complex virtual courses that incorporate dynamic video or audio content and in which students and instructors can interact in real time. The authors present an overview of e-learning and discuss its potential benefits as a supplement to hands-on rodent surgical training. They also discuss a few basic considerations in developing and implementing electronic courses.

High-order synchronization of hair cell bundles

PubMed Central

Levy, Michael; Molzon, Adrian; Lee, Jae-Hyun; Kim, Ji-wook; Cheon, Jinwoo; Bozovic, Dolores

2016-01-01

Auditory and vestibular hair cell bundles exhibit active mechanical oscillations at natural frequencies that are typically lower than the detection range of the corresponding end organs. We explore how these noisy nonlinear oscillators mode-lock to frequencies higher than their internal clocks. A nanomagnetic technique is used to stimulate the bundles without an imposed mechanical load. The evoked response shows regimes of high-order mode-locking. Exploring a broad range of stimulus frequencies and intensities, we observe regions of high-order synchronization, analogous to Arnold Tongues in dynamical systems literature. Significant areas of overlap occur between synchronization regimes, with the bundle intermittently flickering between different winding numbers. We demonstrate how an ensemble of these noisy spontaneous oscillators could be entrained to efficiently detect signals significantly above the characteristic frequencies of the individual cells. PMID:27974743

Molecular dynamics study on the structural and dynamic properties of xanthan gum in a dilute solution under the effect of temperature

NASA Astrophysics Data System (ADS)

Ong, Ernest E. S.; O'Byrne, Sean; Liow, Jong-Leng

2018-04-01

Xanthan gum (XG) is considered one of the most industrially important polysaccharides, with applications ranging from food products such as ice creams and salad dressings to pharmaceuticals and oil well drilling fluids. The wide application of XG is due to its favourable rheological properties and its capability to resist degradation under a high shear or high temperature environment. It is generally accepted that both inter- and intramolecular interactions, including hydrogen bonding (HB), are responsible for its unique properties. To date, there is still a lack of comprehensive examination on the HB mechanism in polysaccharides. Therefore, the study proposed here was conducted using molecular dynamics (MD) simulations that are able to provide insights with an unparalleled temporal and spatial resolution. Since XG is used over a broad range of temperatures, the implications of thermal effect on the structure and molecular interactions of XG in an aqueous solution are discussed in this paper. MD simulations were run at an isobaric-isothermal condition with 1 atm target pressure and five temperatures ranging between 283K and 353K. From the simulation results, an increasingly extended conformation of XG is observed as the temperature rises, and this finding matches qualitatively with the results published in the literature. The radius of gyration, radial pair distribution functions and intramolecular HB of XG were also discussed. The outcomes of the present study may serve as a stepping stone for the future studies on polysaccharides using MD simulations.

SRG110 Stirling Generator Dynamic Simulator Vibration Test Results and Analysis Correlation

NASA Technical Reports Server (NTRS)

Suarez, Vicente J.; Lewandowski, Edward J.; Callahan, John

2006-01-01

The U.S. Department of Energy (DOE), Lockheed Martin (LM), and NASA Glenn Research Center (GRC) have been developing the Stirling Radioisotope Generator (SRG110) for use as a power system for space science missions. The launch environment enveloping potential missions results in a random input spectrum that is significantly higher than historical RPS launch levels and is a challenge for designers. Analysis presented in prior work predicted that tailoring the compliance at the generator-spacecraft interface reduced the dynamic response of the system thereby allowing higher launch load input levels and expanding the range of potential generator missions. To confirm analytical predictions, a dynamic simulator representing the generator structure, Stirling convertors and heat sources was designed and built for testing with and without a compliant interface. Finite element analysis was performed to guide the generator simulator and compliant interface design so that test modes and frequencies were representative of the SRG110 generator. This paper presents the dynamic simulator design, the test setup and methodology, test article modes and frequencies and dynamic responses, and post-test analysis results. With the compliant interface, component responses to an input environment exceeding the SRG110 qualification level spectrum were all within design allowables. Post-test analysis included finite element model tuning to match test frequencies and random response analysis using the test input spectrum. Analytical results were in good overall agreement with the test results and confirmed previous predictions that the SRG110 power system may be considered for a broad range of potential missions, including those with demanding launch environments.

SRG110 Stirling Generator Dynamic Simulator Vibration Test Results and Analysis Correlation

NASA Technical Reports Server (NTRS)

Lewandowski, Edward J.; Suarez, Vicente J.; Goodnight, Thomas W.; Callahan, John

2007-01-01

The U.S. Department of Energy (DOE), Lockheed Martin (LM), and NASA Glenn Research Center (GRC) have been developing the Stirling Radioisotope Generator (SRG110) for use as a power system for space science missions. The launch environment enveloping potential missions results in a random input spectrum that is significantly higher than historical radioisotope power system (RPS) launch levels and is a challenge for designers. Analysis presented in prior work predicted that tailoring the compliance at the generator-spacecraft interface reduced the dynamic response of the system thereby allowing higher launch load input levels and expanding the range of potential generator missions. To confirm analytical predictions, a dynamic simulator representing the generator structure, Stirling convertors and heat sources were designed and built for testing with and without a compliant interface. Finite element analysis was performed to guide the generator simulator and compliant interface design so that test modes and frequencies were representative of the SRG110 generator. This paper presents the dynamic simulator design, the test setup and methodology, test article modes and frequencies and dynamic responses, and post-test analysis results. With the compliant interface, component responses to an input environment exceeding the SRG110 qualification level spectrum were all within design allowables. Post-test analysis included finite element model tuning to match test frequencies and random response analysis using the test input spectrum. Analytical results were in good overall agreement with the test results and confirmed previous predictions that the SRG110 power system may be considered for a broad range of potential missions, including those with demanding launch environments.

Dynamic cross-correlations between entangled biofilaments as they diffuse

PubMed Central

Tsang, Boyce; Dell, Zachary E.; Jiang, Lingxiang; Schweizer, Kenneth S.; Granick, Steve

2017-01-01

Entanglement in polymer and biological physics involves a state in which linear interthreaded macromolecules in isotropic liquids diffuse in a spatially anisotropic manner beyond a characteristic mesoscopic time and length scale (tube diameter). The physical reason is that linear macromolecules become transiently localized in directions transverse to their backbone but diffuse with relative ease parallel to it. Within the resulting broad spectrum of relaxation times there is an extended period before the longest relaxation time when filaments occupy a time-averaged cylindrical space of near-constant density. Here we show its implication with experiments based on fluorescence tracking of dilutely labeled macromolecules. The entangled pairs of aqueous F-actin biofilaments diffuse with separation-dependent dynamic cross-correlations that exceed those expected from continuum hydrodynamics up to strikingly large spatial distances of ≈15 µm, which is more than 104 times the size of the solvent water molecules in which they are dissolved, and is more than 50 times the dynamic tube diameter, but is almost equal to the filament length. Modeling this entangled system as a collection of rigid rods, we present a statistical mechanical theory that predicts these long-range dynamic correlations as an emergent consequence of an effective long-range interpolymer repulsion due to the de Gennes correlation hole, which is a combined consequence of chain connectivity and uncrossability. The key physical assumption needed to make theory and experiment agree is that solutions of entangled biofilaments localized in tubes that are effectively dynamically incompressible over the relevant intermediate time and length scales. PMID:28283664

Biomechanics of the Peacock’s Display: How Feather Structure and Resonance Influence Multimodal Signaling

PubMed Central

Dakin, Roslyn; McCrossan, Owen; Hare, James F.; Montgomerie, Robert; Amador Kane, Suzanne

2016-01-01

Courtship displays may serve as signals of the quality of motor performance, but little is known about the underlying biomechanics that determines both their signal content and costs. Peacocks (Pavo cristatus) perform a complex, multimodal “train-rattling” display in which they court females by vibrating the iridescent feathers in their elaborate train ornament. Here we study how feather biomechanics influences the performance of this display using a combination of field recordings and laboratory experiments. Using high-speed video, we find that train-rattling peacocks stridulate their tail feathers against the train at 25.6 Hz, on average, generating a broadband, pulsating mechanical sound at that frequency. Laboratory measurements demonstrate that arrays of peacock tail and train feathers have a broad resonant peak in their vibrational spectra at the range of frequencies used for train-rattling during the display, and the motion of feathers is just as expected for feathers shaking near resonance. This indicates that peacocks are able to drive feather vibrations energetically efficiently over a relatively broad range of frequencies, enabling them to modulate the feather vibration frequency of their displays. Using our field data, we show that peacocks with longer trains use slightly higher vibration frequencies on average, even though longer train feathers are heavier and have lower resonant frequencies. Based on these results, we propose hypotheses for future studies of the function and energetics of this display that ask why its dynamic elements might attract and maintain female attention. Finally, we demonstrate how the mechanical structure of the train feathers affects the peacock’s visual display by allowing the colorful iridescent eyespots–which strongly influence female mate choice–to remain nearly stationary against a dynamic iridescent background. PMID:27119380

Biomechanics of the Peacock's Display: How Feather Structure and Resonance Influence Multimodal Signaling.

PubMed

Dakin, Roslyn; McCrossan, Owen; Hare, James F; Montgomerie, Robert; Amador Kane, Suzanne

2016-01-01

Courtship displays may serve as signals of the quality of motor performance, but little is known about the underlying biomechanics that determines both their signal content and costs. Peacocks (Pavo cristatus) perform a complex, multimodal "train-rattling" display in which they court females by vibrating the iridescent feathers in their elaborate train ornament. Here we study how feather biomechanics influences the performance of this display using a combination of field recordings and laboratory experiments. Using high-speed video, we find that train-rattling peacocks stridulate their tail feathers against the train at 25.6 Hz, on average, generating a broadband, pulsating mechanical sound at that frequency. Laboratory measurements demonstrate that arrays of peacock tail and train feathers have a broad resonant peak in their vibrational spectra at the range of frequencies used for train-rattling during the display, and the motion of feathers is just as expected for feathers shaking near resonance. This indicates that peacocks are able to drive feather vibrations energetically efficiently over a relatively broad range of frequencies, enabling them to modulate the feather vibration frequency of their displays. Using our field data, we show that peacocks with longer trains use slightly higher vibration frequencies on average, even though longer train feathers are heavier and have lower resonant frequencies. Based on these results, we propose hypotheses for future studies of the function and energetics of this display that ask why its dynamic elements might attract and maintain female attention. Finally, we demonstrate how the mechanical structure of the train feathers affects the peacock's visual display by allowing the colorful iridescent eyespots-which strongly influence female mate choice-to remain nearly stationary against a dynamic iridescent background.

Phase sensitive molecular dynamics of self-assembly glycolipid thin films: A dielectric spectroscopy investigation

NASA Astrophysics Data System (ADS)

Velayutham, T. S.; Ng, B. K.; Gan, W. C.; Majid, W. H. Abd.; Hashim, R.; Zahid, N. I.; Chaiprapa, Jitrin

2014-08-01

Glycolipid, found commonly in membranes, is also a liquid crystal material which can self-assemble without the presence of a solvent. Here, the dielectric and conductivity properties of three synthetic glycolipid thin films in different thermotropic liquid crystal phases were investigated over a frequency and temperature range of (10-2-106 Hz) and (303-463 K), respectively. The observed relaxation processes distinguish between the different phases (smectic A, columnar/hexagonal, and bicontinuous cubic Q) and the glycolipid molecular structures. Large dielectric responses were observed in the columnar and bicontinuous cubic phases of the longer branched alkyl chain glycolipids. Glycolipids with the shortest branched alkyl chain experience the most restricted self-assembly dynamic process over the broad temperature range studied compared to the longer ones. A high frequency dielectric absorption (Process I) was observed in all samples. This is related to the dynamics of the hydrogen bond network from the sugar group. An additional low-frequency mechanism (Process II) with a large dielectric strength was observed due to the internal dynamics of the self-assembly organization. Phase sensitive domain heterogeneity in the bicontinuous cubic phase was related to the diffusion of charge carriers. The microscopic features of charge hopping were modelled using the random walk scheme, and two charge carrier hopping lengths were estimated for two glycolipid systems. For Process I, the hopping length is comparable to the hydrogen bond and is related to the dynamics of the hydrogen bond network. Additionally, that for Process II is comparable to the bilayer spacing, hence confirming that this low-frequency mechanism is associated with the internal dynamics within the phase.

Batch-batch stable microbial community in the traditional fermentation process of huyumei broad bean pastes.

PubMed

Zhu, Linjiang; Fan, Zihao; Kuai, Hui; Li, Qi

2017-09-01

During natural fermentation processes, a characteristic microbial community structure (MCS) is naturally formed, and it is interesting to know about its batch-batch stability. This issue was explored in a traditional semi-solid-state fermentation process of huyumei, a Chinese broad bean paste product. The results showed that this MCS mainly contained four aerobic Bacillus species (8 log CFU per g), including B. subtilis, B. amyloliquefaciens, B. methylotrophicus, and B. tequilensis, and the facultative anaerobe B. cereus with a low concentration (4 log CFU per g), besides a very small amount of the yeast Zygosaccharomyces rouxii (2 log CFU per g). The dynamic change of the MCS in the brine fermentation process showed that the abundance of dominant species varied within a small range, and in the beginning of process the growth of lactic acid bacteria was inhibited and Staphylococcus spp. lost its viability. Also, the MCS and its dynamic change were proved to be highly reproducible among seven batches of fermentation. Therefore, the MCS naturally and stably forms between different batches of the traditional semi-solid-state fermentation of huyumei. Revealing microbial community structure and its batch-batch stability is helpful for understanding the mechanisms of community formation and flavour production in a traditional fermentation. This issue in a traditional semi-solid-state fermentation of huyumei broad bean paste was firstly explored. This fermentation process was revealed to be dominated by a high concentration of four aerobic species of Bacillus, a low concentration of B. cereus and a small amount of Zygosaccharomyces rouxii. Lactic acid bacteria and Staphylococcus spp. lost its viability at the beginning of fermentation. Such the community structure was proved to be highly reproducible among seven batches. © 2017 The Society for Applied Microbiology.

The First Mammalian Aldehyde Oxidase Crystal Structure

PubMed Central

Coelho, Catarina; Mahro, Martin; Trincão, José; Carvalho, Alexandra T. P.; Ramos, Maria João; Terao, Mineko; Garattini, Enrico; Leimkühler, Silke; Romão, Maria João

2012-01-01

Aldehyde oxidases (AOXs) are homodimeric proteins belonging to the xanthine oxidase family of molybdenum-containing enzymes. Each 150-kDa monomer contains a FAD redox cofactor, two spectroscopically distinct [2Fe-2S] clusters, and a molybdenum cofactor located within the protein active site. AOXs are characterized by broad range substrate specificity, oxidizing different aldehydes and aromatic N-heterocycles. Despite increasing recognition of its role in the metabolism of drugs and xenobiotics, the physiological function of the protein is still largely unknown. We have crystallized and solved the crystal structure of mouse liver aldehyde oxidase 3 to 2.9 Å. This is the first mammalian AOX whose structure has been solved. The structure provides important insights into the protein active center and further evidence on the catalytic differences characterizing AOX and xanthine oxidoreductase. The mouse liver aldehyde oxidase 3 three-dimensional structure combined with kinetic, mutagenesis data, molecular docking, and molecular dynamics studies make a decisive contribution to understand the molecular basis of its rather broad substrate specificity. PMID:23019336

Unified rheology of vibro-fluidized dry granular media: From slow dense flows to fast gas-like regimes

PubMed Central

Gnoli, Andrea; Lasanta, Antonio; Sarracino, Alessandro; Puglisi, Andrea

2016-01-01

Granular media take on great importance in industry and geophysics, posing a severe challenge to materials science. Their response properties elude known soft rheological models, even when the yield-stress discontinuity is blurred by vibro-fluidization. Here we propose a broad rheological scenario where average stress sums up a frictional contribution, generalizing conventional μ(I)-rheology, and a kinetic collisional term dominating at fast fluidization. Our conjecture fairly describes a wide series of experiments in a vibrofluidized vane setup, whose phenomenology includes velocity weakening, shear thinning, a discontinuous thinning transition, and gaseous shear thickening. The employed setup gives access to dynamic fluctuations, which exhibit a broad range of timescales. In the slow dense regime the frequency of cage-opening increases with stress and enhances, with respect to μ(I)-rheology, the decrease of viscosity. Diffusivity is exponential in the shear stress in both thinning and thickening regimes, with a huge growth near the transition. PMID:27924928

Dynamics of Reactive Microbial Hotspots in Concentration Gradient.

NASA Astrophysics Data System (ADS)

Hubert, A.; Farasin, J.; Tabuteau, H.; Dufresne, A.; Meheust, Y.; Le Borgne, T.

2017-12-01

In subsurface environments, bacteria play a major role in controlling the kinetics of a broad range of biogeochemical reactions. In such environments, nutrients fluxes and solute concentrations needed for bacteria metabolism may be highly variable in space and intermittent in time. This can lead to the formation of reactive hotspots where and when conditions are favorable to particular microorganisms, hence inducing biogeochemical reaction kinetics that differ significantly from those measured in homogeneous model environments. To investigate the impact of chemical gradients on the spatial structure and temporal dynamics of subsurface microorganism populations, we develop microfluidic cells allowing for a precise control of flow and chemical gradient conditions, as well as quantitative monitoring of the bacteria's spatial distribution and biofilm development. Using the non-motile Escherichia coli JW1908-1 strain and Gallionella capsiferriformans ES-2 as model organisms, we investigate the behavior and development of bacteria over a range of single and double concentration gradients in the concentrations of nutrients, electron donors and electron acceptors. We measure bacterial activity and population growth locally in precisely known hydrodynamic and chemical environments. This approach allows time-resolved monitoring of the location and intensity of reactive hotspots in micromodels as a function of the flow and chemical gradient conditions. We compare reactive microbial hotspot dynamics in our micromodels to classic growth laws and well-known growth parameters for the laboratory model bacteria Escherichia coli.We also discuss consequences for the formation and temporal dynamics of biofilms in the subsurface.

Asymmetric multiscale multifractal analysis of wind speed signals

NASA Astrophysics Data System (ADS)

Zhang, Xiaonei; Zeng, Ming; Meng, Qinghao

We develop a new method called asymmetric multiscale multifractal analysis (A-MMA) to explore the multifractality and asymmetric autocorrelations of the signals with a variable scale range. Three numerical experiments are provided to demonstrate the effectiveness of our approach. Then, the proposed method is applied to investigate multifractality and asymmetric autocorrelations of difference sequences between wind speed fluctuations with uptrends or downtrends. The results show that these sequences appear to be far more complex and contain abundant fractal dynamics information. Through analyzing the Hurst surfaces of nine difference sequences, we found that all series exhibit multifractal properties and multiscale structures. Meanwhile, the asymmetric autocorrelations are observed in all variable scale ranges and the asymmetry results are of good consistency within a certain spatial range. The sources of multifractality and asymmetry in nine difference series are further discussed using the corresponding shuffled series and surrogate series. We conclude that the multifractality of these series is due to both long-range autocorrelation and broad probability density function, but the major source of multifractality is long-range autocorrelation, and the source of asymmetry is affected by the spatial distance.

Maximum likelihood estimators for truncated and censored power-law distributions show how neuronal avalanches may be misevaluated

NASA Astrophysics Data System (ADS)

Langlois, Dominic; Cousineau, Denis; Thivierge, J. P.

2014-01-01

The coordination of activity amongst populations of neurons in the brain is critical to cognition and behavior. One form of coordinated activity that has been widely studied in recent years is the so-called neuronal avalanche, whereby ongoing bursts of activity follow a power-law distribution. Avalanches that follow a power law are not unique to neuroscience, but arise in a broad range of natural systems, including earthquakes, magnetic fields, biological extinctions, fluid dynamics, and superconductors. Here, we show that common techniques that estimate this distribution fail to take into account important characteristics of the data and may lead to a sizable misestimation of the slope of power laws. We develop an alternative series of maximum likelihood estimators for discrete, continuous, bounded, and censored data. Using numerical simulations, we show that these estimators lead to accurate evaluations of power-law distributions, improving on common approaches. Next, we apply these estimators to recordings of in vitro rat neocortical activity. We show that different estimators lead to marked discrepancies in the evaluation of power-law distributions. These results call into question a broad range of findings that may misestimate the slope of power laws by failing to take into account key aspects of the observed data.

Maximum likelihood estimators for truncated and censored power-law distributions show how neuronal avalanches may be misevaluated.

PubMed

Langlois, Dominic; Cousineau, Denis; Thivierge, J P

2014-01-01

The coordination of activity amongst populations of neurons in the brain is critical to cognition and behavior. One form of coordinated activity that has been widely studied in recent years is the so-called neuronal avalanche, whereby ongoing bursts of activity follow a power-law distribution. Avalanches that follow a power law are not unique to neuroscience, but arise in a broad range of natural systems, including earthquakes, magnetic fields, biological extinctions, fluid dynamics, and superconductors. Here, we show that common techniques that estimate this distribution fail to take into account important characteristics of the data and may lead to a sizable misestimation of the slope of power laws. We develop an alternative series of maximum likelihood estimators for discrete, continuous, bounded, and censored data. Using numerical simulations, we show that these estimators lead to accurate evaluations of power-law distributions, improving on common approaches. Next, we apply these estimators to recordings of in vitro rat neocortical activity. We show that different estimators lead to marked discrepancies in the evaluation of power-law distributions. These results call into question a broad range of findings that may misestimate the slope of power laws by failing to take into account key aspects of the observed data.

Prediction and validation of diffusion coefficients in a model drug delivery system using microsecond atomistic molecular dynamics simulation and vapour sorption analysis.

PubMed

Forrey, Christopher; Saylor, David M; Silverstein, Joshua S; Douglas, Jack F; Davis, Eric M; Elabd, Yossef A

2014-10-14

Diffusion of small to medium sized molecules in polymeric medical device materials underlies a broad range of public health concerns related to unintended leaching from or uptake into implantable medical devices. However, obtaining accurate diffusion coefficients for such systems at physiological temperature represents a formidable challenge, both experimentally and computationally. While molecular dynamics simulation has been used to accurately predict the diffusion coefficients, D, of a handful of gases in various polymers, this success has not been extended to molecules larger than gases, e.g., condensable vapours, liquids, and drugs. We present atomistic molecular dynamics simulation predictions of diffusion in a model drug eluting system that represent a dramatic improvement in accuracy compared to previous simulation predictions for comparable systems. We find that, for simulations of insufficient duration, sub-diffusive dynamics can lead to dramatic over-prediction of D. We present useful metrics for monitoring the extent of sub-diffusive dynamics and explore how these metrics correlate to error in D. We also identify a relationship between diffusion and fast dynamics in our system, which may serve as a means to more rapidly predict diffusion in slowly diffusing systems. Our work provides important precedent and essential insights for utilizing atomistic molecular dynamics simulations to predict diffusion coefficients of small to medium sized molecules in condensed soft matter systems.

Structure and dynamics of single hydrophobic/ionic heteropolymers at the vapor-liquid interface of water.

PubMed

Vembanur, Srivathsan; Venkateshwaran, Vasudevan; Garde, Shekhar

2014-04-29

We focus on the conformational stability, structure, and dynamics of hydrophobic/charged homopolymers and heteropolymers at the vapor-liquid interface of water using extensive molecular dynamics simulations. Hydrophobic polymers collapse into globular structures in bulk water but unfold and sample a broad range of conformations at the vapor-liquid interface of water. We show that adding a pair of charges to a hydrophobic polymer at the interface can dramatically change its conformations, stabilizing hairpinlike structures, with molecular details depending on the location of the charged pair in the sequence. The translational dynamics of homopolymers and heteropolymers are also different, whereas the homopolymers skate on the interface with low drag, the tendency of charged groups to remain hydrated pulls the heteropolymers toward the liquid side of the interface, thus pinning them, increasing drag, and slowing the translational dynamics. The conformational dynamics of heteropolymers are also slower than that of the homopolymer and depend on the location of the charged groups in the sequence. Conformational dynamics are most restricted for the end-charged heteropolymer and speed up as the charge pair is moved toward the center of the sequence. We rationalize these trends using the fundamental understanding of the effects of the interface on primitive pair-level interactions between two hydrophobic groups and between oppositely charged ions in its vicinity.

Efficient, Decentralized Detection of Qualitative Spatial Events in a Dynamic Scalar Field

PubMed Central

Jeong, Myeong-Hun; Duckham, Matt

2015-01-01

This paper describes an efficient, decentralized algorithm to monitor qualitative spatial events in a dynamic scalar field. The events of interest involve changes to the critical points (i.e., peak, pits and passes) and edges of the surface network derived from the field. Four fundamental types of event (appearance, disappearance, movement and switch) are defined. Our algorithm is designed to rely purely on qualitative information about the neighborhoods of nodes in the sensor network and does not require information about nodes’ coordinate positions. Experimental investigations confirm that our algorithm is efficient, with O(n) overall communication complexity (where n is the number of nodes in the sensor network), an even load balance and low operational latency. The accuracy of event detection is comparable to established centralized algorithms for the identification of critical points of a surface network. Our algorithm is relevant to a broad range of environmental monitoring applications of sensor networks. PMID:26343672

Imaging electric field dynamics with graphene optoelectronics.

PubMed

Horng, Jason; Balch, Halleh B; McGuire, Allister F; Tsai, Hsin-Zon; Forrester, Patrick R; Crommie, Michael F; Cui, Bianxiao; Wang, Feng

2016-12-16

The use of electric fields for signalling and control in liquids is widespread, spanning bioelectric activity in cells to electrical manipulation of microstructures in lab-on-a-chip devices. However, an appropriate tool to resolve the spatio-temporal distribution of electric fields over a large dynamic range has yet to be developed. Here we present a label-free method to image local electric fields in real time and under ambient conditions. Our technique combines the unique gate-variable optical transitions of graphene with a critically coupled planar waveguide platform that enables highly sensitive detection of local electric fields with a voltage sensitivity of a few microvolts, a spatial resolution of tens of micrometres and a frequency response over tens of kilohertz. Our imaging platform enables parallel detection of electric fields over a large field of view and can be tailored to broad applications spanning lab-on-a-chip device engineering to analysis of bioelectric phenomena.

Regge trajectories and Hagedorn behavior: Hadronic realizations of dynamical dark matter

NASA Astrophysics Data System (ADS)

Dienes, Keith R.; Huang, Fei; Su, Shufang; Thomas, Brooks

2017-11-01

Dynamical Dark Matter (DDM) is an alternative framework for dark-matter physics in which the dark sector comprises a vast ensemble of particle species whose Standard-Model decay widths are balanced against their cosmological abundances. In this talk, we study the properties of a hitherto-unexplored class of DDM ensembles in which the ensemble constituents are the "hadronic" resonances associated with the confining phase of a strongly-coupled dark sector. Such ensembles exhibit masses lying along Regge trajectories and Hagedorn-like densities of states that grow exponentially with mass. We investigate the applicable constraints on such dark-"hadronic" DDM ensembles and find that these constraints permit a broad range of mass and confinement scales for these ensembles. We also find that the distribution of the total present-day abundance across the ensemble is highly correlated with the values of these scales. This talk reports on research originally presented in Ref. [1].

Structure and information in spatial segregation

PubMed Central

2017-01-01

Ethnoracial residential segregation is a complex, multiscalar phenomenon with immense moral and economic costs. Modeling the structure and dynamics of segregation is a pressing problem for sociology and urban planning, but existing methods have limitations. In this paper, we develop a suite of methods, grounded in information theory, for studying the spatial structure of segregation. We first advance existing profile and decomposition methods by posing two related regionalization methods, which allow for profile curves with nonconstant spatial scale and decomposition analysis with nonarbitrary areal units. We then formulate a measure of local spatial scale, which may be used for both detailed, within-city analysis and intercity comparisons. These methods highlight detailed insights in the structure and dynamics of urban segregation that would be otherwise easy to miss or difficult to quantify. They are computationally efficient, applicable to a broad range of study questions, and freely available in open source software. PMID:29078323

Structure and information in spatial segregation.

PubMed

Chodrow, Philip S

2017-10-31

Ethnoracial residential segregation is a complex, multiscalar phenomenon with immense moral and economic costs. Modeling the structure and dynamics of segregation is a pressing problem for sociology and urban planning, but existing methods have limitations. In this paper, we develop a suite of methods, grounded in information theory, for studying the spatial structure of segregation. We first advance existing profile and decomposition methods by posing two related regionalization methods, which allow for profile curves with nonconstant spatial scale and decomposition analysis with nonarbitrary areal units. We then formulate a measure of local spatial scale, which may be used for both detailed, within-city analysis and intercity comparisons. These methods highlight detailed insights in the structure and dynamics of urban segregation that would be otherwise easy to miss or difficult to quantify. They are computationally efficient, applicable to a broad range of study questions, and freely available in open source software. Published under the PNAS license.

Aerodynamic performance of a small vertical axis wind turbine using an overset grid method

NASA Astrophysics Data System (ADS)

Bangga, Galih; Solichin, Mochammad; Daman, Aida; Sa'adiyah, Devy; Dessoky, Amgad; Lutz, Thorsten

2017-08-01

The present paper aims to asses the aerodynamic performance of a small vertical axis wind turbine operating at a small wind speed of 5 m/s for 6 different tip speed ratios (λ=2-7). The turbine consists of two blades constructed using the NACA 0015 airfoil. The study is carried out using computational fluid dynamics (CFD) methods employing an overset grid approach. The (URANS) SST k - ω is used as the turbulence model. For the preliminary study, simulations of the NACA 0015 under static conditions for a broad range of angle of attack and a rotating two-bladed VAWT are carried out. The results are compared with available measurement data and a good agreement is obtained. The simulations demonstrate that the maximum power coefficient attained is 0.45 for λ=4. The aerodynamic loads hysteresis are presented showing that the dynamic stall effect decreases with λ.

Efficient, Decentralized Detection of Qualitative Spatial Events in a Dynamic Scalar Field.

PubMed

Jeong, Myeong-Hun; Duckham, Matt

2015-08-28

This paper describes an efficient, decentralized algorithm to monitor qualitative spatial events in a dynamic scalar field. The events of interest involve changes to the critical points (i.e., peak, pits and passes) and edges of the surface network derived from the field. Four fundamental types of event (appearance, disappearance, movement and switch) are defined. Our algorithm is designed to rely purely on qualitative information about the neighborhoods of nodes in the sensor network and does not require information about nodes' coordinate positions. Experimental investigations confirm that our algorithm is efficient, with O(n) overall communication complexity (where n is the number of nodes in the sensor network), an even load balance and low operational latency. The accuracy of event detection is comparable to established centralized algorithms for the identification of critical points of a surface network. Our algorithm is relevant to a broad range of environmental monitoring applications of sensor networks.

Regional Level Influenza Study with Geo-Tagged Twitter Data.

PubMed

Wang, Feng; Wang, Haiyan; Xu, Kuai; Raymond, Ross; Chon, Jaime; Fuller, Shaun; Debruyn, Anton

2016-08-01

The rich data generated and read by millions of users on social media tells what is happening in the real world in a rapid and accurate fashion. In recent years many researchers have explored real-time streaming data from Twitter for a broad range of applications, including predicting stock markets and public health trend. In this paper we design, implement, and evaluate a prototype system to collect and analyze influenza statuses over different geographical locations with real-time tweet streams. We investigate the correlation between the Twitter flu counts and the official statistics from the Center for Disease Control and Prevention (CDC) and discover that real-time tweet streams capture the dynamics of influenza cases at both national and regional level and could potentially serve as an early warning system of influenza epidemics. Furthermore, we propose a dynamic mathematical model which can forecast Twitter flu counts with high accuracy.

Single-Molecule FRET Spectroscopy and the Polymer Physics of Unfolded and Intrinsically Disordered Proteins.

PubMed

Schuler, Benjamin; Soranno, Andrea; Hofmann, Hagen; Nettels, Daniel

2016-07-05

The properties of unfolded proteins have long been of interest because of their importance to the protein folding process. Recently, the surprising prevalence of unstructured regions or entirely disordered proteins under physiological conditions has led to the realization that such intrinsically disordered proteins can be functional even in the absence of a folded structure. However, owing to their broad conformational distributions, many of the properties of unstructured proteins are difficult to describe with the established concepts of structural biology. We have thus seen a reemergence of polymer physics as a versatile framework for understanding their structure and dynamics. An important driving force for these developments has been single-molecule spectroscopy, as it allows structural heterogeneity, intramolecular distance distributions, and dynamics to be quantified over a wide range of timescales and solution conditions. Polymer concepts provide an important basis for relating the physical properties of unstructured proteins to folding and function.

Molecular dynamics simulation of self-diffusion processes in titanium in bulk material, on grain junctions and on surface.

PubMed

Sushko, Gennady B; Verkhovtsev, Alexey V; Yakubovich, Alexander V; Schramm, Stefan; Solov'yov, Andrey V

2014-08-21

The process of self-diffusion of titanium atoms in a bulk material, on grain junctions and on surface is explored numerically in a broad temperature range by means of classical molecular dynamics simulation. The analysis is carried out for a nanoscale cylindrical sample consisting of three adjacent sectors and various junctions between nanocrystals. The calculated diffusion coefficient varies by several orders of magnitude for different regions of the sample. The calculated values of the bulk diffusion coefficient correspond reasonably well to the experimental data obtained for solid and molten states of titanium. Investigation of diffusion in the nanocrystalline titanium is of a significant importance because of its numerous technological applications. This paper aims to reduce the lack of data on diffusion in titanium and describe the processes occurring in bulk, at different interfaces and on surface of the crystalline titanium.

Universal Faraday Rotation in HgTe Wells with Critical Thickness

NASA Astrophysics Data System (ADS)

Shuvaev, A.; Dziom, V.; Kvon, Z. D.; Mikhailov, N. N.; Pimenov, A.

2016-09-01

The universal value of the Faraday rotation angle close to the fine structure constant (α ≈1 /137 ) is experimentally observed in thin HgTe quantum wells with a thickness on the border between trivial insulating and the topologically nontrivial Dirac phases. The quantized value of the Faraday angle remains robust in the broad range of magnetic fields and gate voltages. Dynamic Hall conductivity of the holelike carriers extracted from the analysis of the transmission data shows a theoretically predicted universal value of σx y=e2/h , which is consistent with the doubly degenerate Dirac state. On shifting the Fermi level by the gate voltage, the effective sign of the charge carriers changes from positive (holes) to negative (electrons). The electronlike part of the dynamic response does not show quantum plateaus and is well described within the classical Drude model.

Species abundance distribution and population dynamics in a two-community model of neutral ecology

NASA Astrophysics Data System (ADS)

Vallade, M.; Houchmandzadeh, B.

2006-11-01

Explicit formulas for the steady-state distribution of species in two interconnected communities of arbitrary sizes are derived in the framework of Hubbell’s neutral model of biodiversity. Migrations of seeds from both communities as well as mutations in both of them are taken into account. These results generalize those previously obtained for the “island-continent” model and they allow an analysis of the influence of the ratio of the sizes of the two communities on the dominance/diversity equilibrium. Exact expressions for species abundance distributions are deduced from a master equation for the joint probability distribution of species in the two communities. Moreover, an approximate self-consistent solution is derived. It corresponds to a generalization of previous results and it proves to be accurate over a broad range of parameters. The dynamical correlations between the abundances of a species in both communities are also discussed.

Ring polymer dynamics in curved spaces

NASA Astrophysics Data System (ADS)

Wolf, S.; Curotto, E.

2012-07-01

We formulate an extension of the ring polymer dynamics approach to curved spaces using stereographic projection coordinates. We test the theory by simulating the particle in a ring, {T}^1, mapped by a stereographic projection using three potentials. Two of these are quadratic, and one is a nonconfining sinusoidal model. We propose a new class of algorithms for the integration of the ring polymer Hamilton equations in curved spaces. These are designed to improve the energy conservation of symplectic integrators based on the split operator approach. For manifolds, the position-position autocorrelation function can be formulated in numerous ways. We find that the position-position autocorrelation function computed from configurations in the Euclidean space {R}^2 that contains {T}^1 as a submanifold has the best statistical properties. The agreement with exact results obtained with vector space methods is excellent for all three potentials, for all values of time in the interval simulated, and for a relatively broad range of temperatures.

Highly designable phenotypes and mutational buffers emerge from a systematic mapping between network topology and dynamic output.

PubMed

Nochomovitz, Yigal D; Li, Hao

2006-03-14

Deciphering the design principles for regulatory networks is fundamental to an understanding of biological systems. We have explored the mapping from the space of network topologies to the space of dynamical phenotypes for small networks. Using exhaustive enumeration of a simple model of three- and four-node networks, we demonstrate that certain dynamical phenotypes can be generated by an atypically broad spectrum of network topologies. Such dynamical outputs are highly designable, much like certain protein structures can be designed by an unusually broad spectrum of sequences. The network topologies that encode a highly designable dynamical phenotype possess two classes of connections: a fully conserved core of dedicated connections that encodes the stable dynamical phenotype and a partially conserved set of variable connections that controls the transient dynamical flow. By comparing the topologies and dynamics of the three- and four-node network ensembles, we observe a large number of instances of the phenomenon of "mutational buffering," whereby addition of a fourth node suppresses phenotypic variation amongst a set of three-node networks.

Fully "Eqwipped" to See the Heat

NASA Technical Reports Server (NTRS)

2002-01-01

Developed by NASA's Jet Propulsion Laboratory over the past decade with an excess of $15 million of government research and development investment, quantum well infrared photodetectors (QWIPs) are infrared imaging sensors that can operate in the long wavelength portion of the electromagnetic spectrum, where objects at an ambient temperature emit the most energy. QWIPTECH was formed in July 1998 to offer JPL's QWIPs in a commercial format. The company currently holds an exclusive worldwide license to manufacture and sell the infrared photodetector sensors as part of a focal plane array called a QWIP Chip(TM). The QWIP Chip provides high thermal sensitivity (0.001 C) and possesses a broad dynamic range, permitting precise observations over a wide range of temperatures. Since the technology uses heat rather than light, it can "see" in complete darkness and through conditions such as dust, smoke, and light fog.

Electrostatic fluctuations in collisional plasmas

NASA Astrophysics Data System (ADS)

Rozmus, W.; Brantov, A.; Fortmann-Grote, C.; Bychenkov, V. Yu.; Glenzer, S.

2017-10-01

We present a theory of electrostatic fluctuations in two-component plasmas where electrons and ions are described by Maxwellian distribution functions at unequal temperatures. Based on the exact solution of the Landau kinetic equation, that includes electron-electron, electron-ion, and ion-ion collision integrals, the dynamic form factor, S (k ⃗,ω ) , is derived for weakly coupled plasmas. The collective plasma responses at ion-acoustic, Langmuir, and entropy mode resonances are described for arbitrary wave numbers and frequencies in the entire range of plasma collisionality. The collisionless limit of S (k ⃗,ω ) and the strong-collision result based on the fluctuation-dissipation theorem and classical transport at Te=Ti are recovered and discussed. Results of several Thomson scattering experiments in the broad range of plasma parameters are described and discussed by means of our theory for S (k ⃗,ω ) .

Bistable Topological Insulator with Exciton-Polaritons

NASA Astrophysics Data System (ADS)

Kartashov, Yaroslav V.; Skryabin, Dmitry V.

2017-12-01

The functionality of many nonlinear and quantum optical devices relies on the effect of optical bistability. Using microcavity exciton-polaritons in a honeycomb arrangement of microcavity pillars, we report the resonance response and bistability of topological edge states. A balance between the pump, loss, and nonlinearity ensures a broad range of dynamical stability and controls the distribution of power between counterpropagating states on the opposite edges of the honeycomb lattice stripe. Tuning energy and polarization of the pump photons, while keeping their momentum constant, we demonstrate control of the propagation direction of the dominant edge state. Our results facilitate the development of practical applications of topological photonics.

Higher order temporal finite element methods through mixed formalisms.

PubMed

Kim, Jinkyu

2014-01-01

The extended framework of Hamilton's principle and the mixed convolved action principle provide new rigorous weak variational formalism for a broad range of initial boundary value problems in mathematical physics and mechanics. In this paper, their potential when adopting temporally higher order approximations is investigated. The classical single-degree-of-freedom dynamical systems are primarily considered to validate and to investigate the performance of the numerical algorithms developed from both formulations. For the undamped system, all the algorithms are symplectic and unconditionally stable with respect to the time step. For the damped system, they are shown to be accurate with good convergence characteristics.

On inconsistency in frictional granular systems

NASA Astrophysics Data System (ADS)

Alart, Pierre; Renouf, Mathieu

2018-04-01

Numerical simulation of granular systems is often based on a discrete element method. The nonsmooth contact dynamics approach can be used to solve a broad range of granular problems, especially involving rigid bodies. However, difficulties could be encountered and hamper successful completion of some simulations. The slow convergence of the nonsmooth solver may sometimes be attributed to an ill-conditioned system, but the convergence may also fail. The prime aim of the present study was to identify situations that hamper the consistency of the mathematical problem to solve. Some simple granular systems were investigated in detail while reviewing and applying the related theoretical results. A practical alternative is briefly analyzed and tested.

Notes on the 1978 summer study program on dynamo models of geomagnetism in geophysical fluid dynamics at the Woods Hole Oceanographic Institution. Technical report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Malkus, W.V.R.; Thayer, M.

1978-11-01

This volume contains the manuscripts of research lectures by the eleven fellows of the summer program. Five of the lectures overlap significantly with the central summer theme of geomagnetism. The other six lectures cover a broad range of current G.F.D. topics from collective instability to strange attractors. Several of these research efforts are quite polished and probably will appear in journals soon. The middle half represent reports of sound progress on studies of thesis calibre. A few of the lectures report on only the very first consequences of a novel idea.

Scientific and Operational Requirements for TOMS Data

NASA Technical Reports Server (NTRS)

Krueger, Arlin J. (Editor)

1987-01-01

Global total ozone and sulfur dioxide data from the Nimbus 7 Total Ozone Mapping Spectrometer (TOMS) instrument have applications in a broad range of disciplines. The presentations of 29 speakers who are using the data in research or who have operational needs for the data are summarized. Five sessions addressed topics in stratospheric processes, tropospheric dynamics and chemistry, remote sensing, volcanology, and future instrument requirements. Stratospheric and some volcanology requirements can be met by a continuation of polar orbit satellites using a slightly modified TOMS but weather related research, tropospheric sulfur budget studies, and most operational needs require the time resolution of a geostationary instrument.

TEMPEST: A three-dimensional time-dependent computer program for hydrothermal analysis: Volume 1, Numerical methods and input instructions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trent, D.S.; Eyler, L.L.; Budden, M.J.

This document describes the numerical methods, current capabilities, and the use of the TEMPEST (Version L, MOD 2) computer program. TEMPEST is a transient, three-dimensional, hydrothermal computer program that is designed to analyze a broad range of coupled fluid dynamic and heat transfer systems of particular interest to the Fast Breeder Reactor thermal-hydraulic design community. The full three-dimensional, time-dependent equations of motion, continuity, and heat transport are solved for either laminar or turbulent fluid flow, including heat diffusion and generation in both solid and liquid materials. 10 refs., 22 figs., 2 tabs.

Common spaceborne multicomputer operating system and development environment

NASA Technical Reports Server (NTRS)

Craymer, L. G.; Lewis, B. F.; Hayes, P. J.; Jones, R. L.

1994-01-01

A preliminary technical specification for a multicomputer operating system is developed. The operating system is targeted for spaceborne flight missions and provides a broad range of real-time functionality, dynamic remote code-patching capability, and system fault tolerance and long-term survivability features. Dataflow concepts are used for representing application algorithms. Functional features are included to ensure real-time predictability for a class of algorithms which require data-driven execution on an iterative steady state basis. The development environment supports the development of algorithm code, design of control parameters, performance analysis, simulation of real-time dataflow applications, and compiling and downloading of the resulting application.

Cascades on a class of clustered random networks

NASA Astrophysics Data System (ADS)

Hackett, Adam; Melnik, Sergey; Gleeson, James P.

2011-05-01

We present an analytical approach to determining the expected cascade size in a broad range of dynamical models on the class of random networks with arbitrary degree distribution and nonzero clustering introduced previously in [M. E. J. Newman, Phys. Rev. Lett. PRLTAO0031-900710.1103/PhysRevLett.103.058701103, 058701 (2009)]. A condition for the existence of global cascades is derived as well as a general criterion that determines whether increasing the level of clustering will increase, or decrease, the expected cascade size. Applications, examples of which are provided, include site percolation, bond percolation, and Watts’ threshold model; in all cases analytical results give excellent agreement with numerical simulations.

New parasitoid-predator associations: female parasitoids do not avoid competition with generalist predators when sharing invasive prey

NASA Astrophysics Data System (ADS)

Chailleux, Anaïs; Wajnberg, Eric; Zhou, Yuxiang; Amiens-Desneux, Edwige; Desneux, Nicolas

2014-12-01

Optimal habitat selection is essential for species survival in ecosystems, and interspecific competition is a key ecological mechanism for many observed species association patterns. Specialized animal species are commonly affected by resource and interference competition with generalist and/or omnivorous competitors, so avoidance behavior could be expected. We hypothesize that specialist species may exploit broad range cues from such potential resource competitors (i.e., cues possibly common to various generalist and/or omnivorous predators) to avoid costly competition regarding food or reproduction, even in new species associations. We tested this hypothesis by studying short-term interactions between a native larval parasitoid and a native generalist omnivorous predator recently sharing the same invasive host/prey, the leaf miner Tuta absoluta. We observed a strong negative effect of kleptoparasitism (food resource stealing) instead of classical intraguild predation on immature parasitoids. There was no evidence that parasitoid females avoided the omnivorous predator when searching for oviposition sites, although we studied both long- and short-range known detection mechanisms. Therefore, we conclude that broad range cue avoidance may not exist in our biological system, probably because it would lead to too much oviposition site avoidance which would not be an efficient and, thus, beneficial strategy. If confirmed in other parasitoids or specialist predators, our findings may have implications for population dynamics, especially in the current context of increasing invasive species and the resulting creation of many new species associations.

Assessment of the apparent bending stiffness and damping of multilayer plates; modelling and experiment

NASA Astrophysics Data System (ADS)

Ege, Kerem; Roozen, N. B.; Leclère, Quentin; Rinaldi, Renaud G.

2018-07-01

In the context of aeronautics, automotive and construction applications, the design of light multilayer plates with optimized vibroacoustical damping and isolation performances remains a major industrial challenge and a hot topic of research. This paper focuses on the vibrational behavior of three-layered sandwich composite plates in a broad-band frequency range. Several aspects are studied through measurement techniques and analytical modelling of a steel/polymer/steel plate sandwich system. A contactless measurement of the velocity field of plates using a scanning laser vibrometer is performed, from which the equivalent single layer complex rigidity (apparent bending stiffness and apparent damping) in the mid/high frequency ranges is estimated. The results are combined with low/mid frequency estimations obtained with a high-resolution modal analysis method so that the frequency dependent equivalent Young's modulus and equivalent loss factor of the composite plate are identified for the whole [40 Hz-20 kHz] frequency band. The results are in very good agreement with an equivalent single layer analytical modelling based on wave propagation analysis (model of Guyader). The comparison with this model allows identifying the frequency dependent complex modulus of the polymer core layer through inverse resolution. Dynamical mechanical analysis measurements are also performed on the polymer layer alone and compared with the values obtained through the inverse method. Again, a good agreement between these two estimations over the broad-band frequency range demonstrates the validity of the approach.

Optimal channel efficiency in a sensory network

NASA Astrophysics Data System (ADS)

Mosqueiro, Thiago S.; Maia, Leonardo P.

2013-07-01

Spontaneous neural activity has been increasingly recognized as a subject of key relevance in neuroscience. It exhibits nontrivial spatiotemporal structure reflecting the organization of the underlying neural network and has proved to be closely intertwined with stimulus-induced activity patterns. As an additional contribution in this regard, we report computational studies that strongly suggest that a stimulus-free feature rules the behavior of an important psychophysical measure of the sensibility of a sensory system to a stimulus, the so-called dynamic range. Indeed in this paper we show that the entropy of the distribution of avalanche lifetimes (information efficiency, since it can be interpreted as the efficiency of the network seen as a communication channel) always accompanies the dynamic range in the benchmark model for sensory systems. Specifically, by simulating the Kinouchi-Copelli (KC) model on two broad families of model networks, we generically observed that both quantities always increase or decrease together as functions of the average branching ratio (the control parameter of the KC model) and that the information efficiency typically exhibits critical optimization jointly with the dynamic range (i.e., both quantities are optimized at the same value of that control parameter, that turns out to be the critical point of a nonequilibrium phase transition). In contrast with the practice of taking power laws to identify critical points in most studies describing measured neuronal avalanches, we rely on data collapses as more robust signatures of criticality to claim that critical optimization may happen even when the distribution of avalanche lifetimes is not a power law, as suggested by a recent experiment. Finally, we note that the entropy of the size distribution of avalanches (information capacity) does not always follow the dynamic range and the information efficiency when they are critically optimized, despite being more widely used than the latter to describe the computational capabilities of a neural network. This strongly suggests that dynamical rules allowing a proper temporal matching of the states of the interacting neurons is the key for achieving good performance in information processing, rather than increasing the number of available units.

Feedback control by online learning an inverse model.

PubMed

Waegeman, Tim; Wyffels, Francis; Schrauwen, Francis

2012-10-01

A model, predictor, or error estimator is often used by a feedback controller to control a plant. Creating such a model is difficult when the plant exhibits nonlinear behavior. In this paper, a novel online learning control framework is proposed that does not require explicit knowledge about the plant. This framework uses two learning modules, one for creating an inverse model, and the other for actually controlling the plant. Except for their inputs, they are identical. The inverse model learns by the exploration performed by the not yet fully trained controller, while the actual controller is based on the currently learned model. The proposed framework allows fast online learning of an accurate controller. The controller can be applied on a broad range of tasks with different dynamic characteristics. We validate this claim by applying our control framework on several control tasks: 1) the heating tank problem (slow nonlinear dynamics); 2) flight pitch control (slow linear dynamics); and 3) the balancing problem of a double inverted pendulum (fast linear and nonlinear dynamics). The results of these experiments show that fast learning and accurate control can be achieved. Furthermore, a comparison is made with some classical control approaches, and observations concerning convergence and stability are made.

Multiscale Simulations of Dynamics of Ferroelectric Domains

NASA Astrophysics Data System (ADS)

Liu, Shi

Ferroelectrics with switchable polarization have many important technological applications, which heavily rely on the interactions between the polarization and external perturbations. Understanding the dynamical response of ferroelectric materials is crucial for the discovery and development of new design principles and engineering strategies for optimized and breakthrough applications of ferroelectrics. We developed a multiscale computational approach that combines methods at different length and time scales to elucidate the connection between local structures, domain dynamics, and macroscopic finite-temperature properties of ferroelectrics. We started from first-principles calculations of ferroelectrics to build a model interatomic potential, enabling large-scale molecular dynamics (MD) simulations. The atomistic insights of nucleation and growth at the domain wall obtained from MD were then incorporated into a continuum model within the framework of Landau-Ginzburg-Devonshire theory. This progressive theoretical framework allows for the first time an efficient and accurate estimation of macroscopic properties such as the coercive field for a broad range of ferroelectrics from first-principles. This multiscale approach has also been applied to explore the effect of dipolar defects on ferroelectric switching and to understand the origin of giant electro-strain coupling. ONR, NSF, Carnegie Institution for Science.

Dynamics of genetic and morphological variability within Neandertals.

PubMed

Hawks, John

2012-01-01

Paleogenomics may suggest changes to the way anthropologists have discussed the dynamics and morphological diversity among Neandertals. Genetic comparisons show that later Neandertals had relatively low autosomal genetic variation compared to recent humans. The known mitochondrial sample from Neandertals covers a broader geographic and temporal range, and shows greater diversity. This review addresses how genetic data compare to morphological and archaeological evidence about Neandertal variation and dynamics. Traditional views emphasized the morphological differences between western and eastern Neandertal populations, and between early and later Neandertals. Genomes broadly support these groupings, without resolving the outstanding question of the affinities of specimens from southwest Asia. However, the pattern of genetic variation appears to reject a long, in situ transformation of Neandertal groups over time, suggesting instead a more rapid process of regional dispersal and partial population replacement. Archaeological indicators sample dynamics on a much finer timescale than morphological or genetic evidence, and point to dispersal and turnover among Neandertals on a regional scale. In this way, genetic evidence may provide a bridge between the timescales relevant to morphological and archaeological comparisons. New ways of looking at the morphology of Neandertals may yield a better picture of their interactions and movements.

Ultrafast dynamics of photogenerated electrons in CdS nanocluster multilayers assembled on solid substrates: effects of assembly and electrode potential.

PubMed

Yagi, Ichizo; Mikami, Kensuke; Okamura, Masayuki; Uosaki, Kohei

2013-07-22

The ultrafast dynamics of photogenerated electrons in multilayer assemblies of CdS nanoparticles prepared on quartz and indium-tin oxide (ITO) substrates were followed by femtosecond (fs) visible-pump/mid-IR probe spectroscopy. Based on the observation of the photoinduced transient absorption spectra in the broad mid-IR range at the multilayer assembly of CdS nanoparticles, the occupation and fast relaxation of higher electronic states (1P(e)) were clarified. As compared with the electron dynamics of isolated (dispersed in solution) nanoparticles, the decay of photoexcited electrons in the multilayer assembly was clearly accelerated probably due to both electron hopping and scattering during interparticle electron tunneling. By using an ITO electrode as a substrate, the effect of the electric field on the photoelectron dynamics in the multilayer assembly was also investigated in situ. Both the amplitude and lifetime of photoexcited electrons gradually reduced as the potential became more positive. This result was explained by considering the reduction of the interparticle tunneling probability and the increase in the electron-transfer rate from the CdS nanoparticle assembly to the ITO electrode. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Broad ion energy distributions in helicon wave-coupled helium plasma

NASA Astrophysics Data System (ADS)

Woller, K. B.; Whyte, D. G.; Wright, G. M.

2017-05-01

Helium ion energy distributions were measured in helicon wave-coupled plasmas of the dynamics of ion implantation and sputtering of surface experiment using a retarding field energy analyzer. The shape of the energy distribution is a double-peak, characteristic of radiofrequency plasma potential modulation. The broad distribution is located within a radius of 0.8 cm, while the quartz tube of the plasma source has an inner radius of 2.2 cm. The ion energy distribution rapidly changes from a double-peak to a single peak in the radius range of 0.7-0.9 cm. The average ion energy is approximately uniform across the plasma column including the double-peak and single peak regions. The widths of the broad distribution, ΔE , in the wave-coupled mode are large compared to the time-averaged ion energy, ⟨E ⟩. On the axis (r = 0), ΔE / ⟨E ⟩ ≲ 3.4, and at a radius near the edge of the plasma column (r = 2.2 cm), ΔE / ⟨E ⟩ ˜ 1.2. The discharge parameter space is scanned to investigate the effects of the magnetic field, input power, and chamber fill pressure on the wave-coupled mode that exhibits the sharp radial variation in the ion energy distribution.

Better Broader Impacts through National Science Foundation Centers

NASA Astrophysics Data System (ADS)

Campbell, K. M.

2010-12-01

National Science Foundation Science and Technology Centers (STCs) play a leading role in developing and evaluating “Better Broader Impacts”; best practices for recruiting a broad spectrum of American students into STEM fields and for educating these future professionals, as well as their families, teachers and the general public. With staff devoted full time to Broader Impacts activities, over the ten year life of a Center, STCs are able to address both a broad range of audiences and a broad range of topics. Along with other NSF funded centers, such as Centers for Ocean Sciences Education Excellence, Engineering Research Centers and Materials Research Science and Engineering Centers, STCs develop both models and materials that individual researchers can adopt, as well as, in some cases, direct opportunities for individual researchers to offer their disciplinary research expertise to existing center Broader Impacts Programs. The National Center for Earth-surface Dynamics is an STC headquartered at the University of Minnesota. NCED’s disciplinary research spans the physical, biological and engineering issues associated with developing an integrative, quantitative and predictive understanding of rivers and river basins. Funded in 2002, we have had the opportunity to partner with individuals and institutions ranging from formal to informal education and from science museums to Tribal and women’s colleges. We have developed simple table top physical models, complete museum exhibitions, 3D paper maps and interactive computer based visualizations, all of which have helped us communicate with this wide variety of learners. Many of these materials themselves or plans to construct them are available online; in many cases they have also been formally evaluated. We have also listened to the formal and informal educators with whom we partner, from whom we have learned a great deal about how to design Broader Impacts activities and programs. Using NCED as a case study, this session showcases NCED’s materials, approaches and lessons learned. We will also introduce the work of our sister STCs, whose disciplines span the STEM fields.

A hybrid stochastic hierarchy equations of motion approach to treat the low temperature dynamics of non-Markovian open quantum systems

NASA Astrophysics Data System (ADS)

Moix, Jeremy M.; Cao, Jianshu

2013-10-01

The hierarchical equations of motion technique has found widespread success as a tool to generate the numerically exact dynamics of non-Markovian open quantum systems. However, its application to low temperature environments remains a serious challenge due to the need for a deep hierarchy that arises from the Matsubara expansion of the bath correlation function. Here we present a hybrid stochastic hierarchical equation of motion (sHEOM) approach that alleviates this bottleneck and leads to a numerical cost that is nearly independent of temperature. Additionally, the sHEOM method generally converges with fewer hierarchy tiers allowing for the treatment of larger systems. Benchmark calculations are presented on the dynamics of two level systems at both high and low temperatures to demonstrate the efficacy of the approach. Then the hybrid method is used to generate the exact dynamics of systems that are nearly impossible to treat by the standard hierarchy. First, exact energy transfer rates are calculated across a broad range of temperatures revealing the deviations from the Förster rates. This is followed by computations of the entanglement dynamics in a system of two qubits at low temperature spanning the weak to strong system-bath coupling regimes.

A hybrid stochastic hierarchy equations of motion approach to treat the low temperature dynamics of non-Markovian open quantum systems.

PubMed

Moix, Jeremy M; Cao, Jianshu

2013-10-07

The hierarchical equations of motion technique has found widespread success as a tool to generate the numerically exact dynamics of non-Markovian open quantum systems. However, its application to low temperature environments remains a serious challenge due to the need for a deep hierarchy that arises from the Matsubara expansion of the bath correlation function. Here we present a hybrid stochastic hierarchical equation of motion (sHEOM) approach that alleviates this bottleneck and leads to a numerical cost that is nearly independent of temperature. Additionally, the sHEOM method generally converges with fewer hierarchy tiers allowing for the treatment of larger systems. Benchmark calculations are presented on the dynamics of two level systems at both high and low temperatures to demonstrate the efficacy of the approach. Then the hybrid method is used to generate the exact dynamics of systems that are nearly impossible to treat by the standard hierarchy. First, exact energy transfer rates are calculated across a broad range of temperatures revealing the deviations from the Förster rates. This is followed by computations of the entanglement dynamics in a system of two qubits at low temperature spanning the weak to strong system-bath coupling regimes.

Hair-based sensors for micro-autonomous systems

NASA Astrophysics Data System (ADS)

Sadeghi, Mahdi M.; Peterson, Rebecca L.; Najafi, Khalil

2012-06-01

We seek to harness microelectromechanical systems (MEMS) technologies to build biomimetic devices for low-power, high-performance, robust sensors and actuators on micro-autonomous robot platforms. Hair is used abundantly in nature for a variety of functions including balance and inertial sensing, flow sensing and aerodynamic (air foil) control, tactile and touch sensing, insulation and temperature control, particle filtering, and gas/chemical sensing. Biological hairs, which are typically characterized by large surface/volume ratios and mechanical amplification of movement, can be distributed in large numbers over large areas providing unprecedented sensitivity, redundancy, and stability (robustness). Local neural transduction allows for space- and power-efficient signal processing. Moreover by varying the hair structure and transduction mechanism, the basic hair form can be used for a wide diversity of functions. In this paper, by exploiting a novel wafer-level, bubble-free liquid encapsulation technology, we make arrays of micro-hydraulic cells capable of electrostatic actuation and hydraulic amplification, which enables high force/high deflection actuation and extremely sensitive detection (sensing) at low power. By attachment of cilia (hair) to the micro-hydraulic cell, air flow sensors with excellent sensitivity (< few cm/s) and dynamic range (> 10 m/s) have been built. A second-generation design has significantly reduced the sensor response time while maintaining sensitivity of about 2 cm/s and dynamic range of more than 15 m/s. These sensors can be used for dynamic flight control of flying robots or for situational awareness in surveillance applications. The core biomimetic technologies developed are applicable to a broad range of sensors and actuators.

Identifying forest patterns from space to explore dynamics across the circumpolar boreal

NASA Astrophysics Data System (ADS)

Montesano, P. M.; Neigh, C. S. R.; Feng, M.; Channan, S.; Sexton, J. O.; Wagner, W.; Wooten, M.; Poulter, B.; Wang, L.

2017-12-01

A variety of forest patterns are the result of interactions between broad-scale climate and local-scale site factors and history across the northernmost portion of the circumpolar boreal. Patterns of forest extent, height, and cover help describe forest structure transitions that influence future and reflect past dynamics. Coarse spaceborne observations lack structural detail at forest transitions, which inhibits understanding of these dynamics. We highlight: (1) the use of sub-meter spaceborne stereogrammetry for deriving structure estimates in boreal forests; (2) its potential to complement other spaceborne estimates of forest structure at critical scales; and (3) the potential of these sub-meter and other Landsat-derived structure estimates for improving understanding of broad-scale boreal dynamics such as carbon flux and albedo, capturing the spatial variability of the boreal-tundra biome boundary, and assessing its potential for change.

Crystallization and dynamical arrest of attractive hard spheres.

PubMed

Babu, Sujin; Gimel, Jean-Christophe; Nicolai, Taco

2009-02-14

Crystallization of hard spheres interacting with a square well potential was investigated by numerical simulations using so-called Brownian cluster dynamics. The phase diagram was determined over a broad range of volume fractions. The crystallization rate was studied as a function of the interaction strength expressed in terms of the second virial coefficient. For volume fractions below about 0.3 the rate was found to increase abruptly with increasing attraction at the binodal of the metastable liquid-liquid phase separation. The rate increased until a maximum was reached after which it decreased with a power law dependence on the second virial coefficient. Above a critical percolation concentration, a transient system spanning network of connected particles was formed. Crystals were formed initially as part of the network, but eventually crystallization led to the breakup of the network. The lifetime of the transient gels increased very rapidly over a small range of interaction energies. Weak attraction destabilized the so-called repulsive crystals formed in pure hard sphere systems and shifted the coexistence line to higher volume fractions. Stronger attraction led to the formation of a denser, so-called attractive, crystalline phase. Nucleation of attractive crystals in the repulsive crystalline phase was observed close to the transition.

Achieving large dynamic range control of gene expression with a compact RNA transcription–translation regulator

PubMed Central

2017-01-01

Abstract RNA transcriptional regulators are emerging as versatile components for genetic network construction. However, these regulators suffer from incomplete repression in their OFF state, making their dynamic range less than that of their protein counterparts. This incomplete repression causes expression leak, which impedes the construction of larger synthetic regulatory networks as leak propagation can interfere with desired network function. To address this, we demonstrate how naturally derived antisense RNA-mediated transcriptional regulators can be configured to regulate both transcription and translation in a single compact RNA mechanism that functions in Escherichia coli. Using in vivo gene expression assays, we show that a combination of transcriptional termination and ribosome binding site sequestration increases repression from 85% to 98%, or activation from 10-fold to over 900-fold, in response to cognate antisense RNAs. We also show that orthogonal repressive versions of this mechanism can be created through engineering minimal antisense RNAs. Finally, to demonstrate the utility of this mechanism, we use it to reduce network leak in an RNA-only cascade. We anticipate these regulators will find broad use as synthetic biology moves beyond parts engineering to the design and construction of more sophisticated regulatory networks. PMID:28387839

Through-wafer optical probe characterization for microelectromechanical systems positional state monitoring and feedback control

NASA Astrophysics Data System (ADS)

Dawson, Jeremy M.; Chen, Jingdong; Brown, Kolin S.; Famouri, Parviz F.; Hornak, Lawrence A.

2000-12-01

Implementation of closed-loop microelectromechanical system (MEMS) control enables mechanical microsystems to adapt to the demands of the environment that they are actuating, opening a broad range of new opportunities for future MEMS applications. Integrated optical microsystems have the potential to enable continuous in situ optical interrogation of MEMS microstructure position fully decoupled from the means of mechanical actuation that is necessary for realization of feedback control. We present the results of initial research evaluating through-wafer optical microprobes for surface micromachined MEMS integrated optical position monitoring. Results from the through-wafer free-space optical probe of a lateral comb resonator fabricated using the multiuser MEMS process service (MUMPS) indicate significant positional information content with an achievable return probe signal dynamic range of up to 80% arising from film transmission contrast. Static and dynamic deflection analysis and experimental results indicate a through-wafer probe positional signal sensitivity of 40 mV/micrometers for the present setup or 10% signal change per micrometer. A simulation of the application of nonlinear sliding control is presented illustrating position control of the lateral comb resonator structure given the availability of positional state information.

Physics of the saturation of particle acceleration in relativistic magnetic reconnection

NASA Astrophysics Data System (ADS)

Kagan, Daniel; Nakar, Ehud; Piran, Tsvi

2018-05-01

We investigate the saturation of particle acceleration in relativistic reconnection using two-dimensional particle-in-cell simulations at various magnetizations σ. We find that the particle energy spectrum produced in reconnection quickly saturates as a hard power law that cuts off at γ ≈ 4σ, confirming previous work. Using particle tracing, we find that particle acceleration by the reconnection electric field in X-points determines the shape of the particle energy spectrum. By analysing the current sheet structure, we show that physical cause of saturation is the spontaneous formation of secondary magnetic islands that can disrupt particle acceleration. By comparing the size of acceleration regions to the typical distance between disruptive islands, we show that the maximum Lorentz factor produced in reconnection is γ ≈ 5σ, which is very close to what we find in our particle energy spectra. We also show that the dynamic range in Lorentz factor of the power-law spectrum in reconnection is ≤40. The hardness of the power law combined with its narrow dynamic range implies that relativistic reconnection is capable of producing the hard narrow-band flares observed in the Crab nebula but has difficulty producing the softer broad-band prompt gamma-ray burst emission.

Ultrahigh resolution photographic films for X-ray/EUV/FUV astronomy

NASA Technical Reports Server (NTRS)

Hoover, Richard B.; Walker, Arthur B. C., Jr.; Deforest, Craig E.; Watts, Richard; Tarrio, Charles

1993-01-01

The quest for ultrahigh resolution full-disk images of the sun at soft X-ray/EUV/FUV wavelengths has increased the demand for photographic films with broad spectral sensitivity, high spatial resolution, and wide dynamic range. These requirements were made more stringent by the recent development of multilayer telescopes and coronagraphs capable of operating at normal incidence at soft X-ray/EUV wavelengths. Photographic films are the only detectors now available with the information storage capacity and dynamic range such as is required for recording images of the solar disk and corona simultaneously with sub arc second spatial resolution. During the Stanford/MSFC/LLNL Rocket X-Ray Spectroheliograph and Multi-Spectral Solar Telescope Array (MSSTA) programs, we utilized photographic films to obtain high resolution full-disk images of the sun at selected soft X-ray/EUV/FUV wavelengths. In order to calibrate our instrumentation for quantitative analysis of our solar data and to select the best emulsions and processing conditions for the MSSTA reflight, we recently tested several photographic films. These studies were carried out at the NIST SURF II synchrotron and the Stanford Synchrotron Radiation Laboratory. In this paper, we provide the results of those investigations.

2009 MICROBIAL POPULATION BIOLOGY GORDON RESEARCH CONFERENCES JULY 19-24,2009

DOE Office of Scientific and Technical Information (OSTI.GOV)

ANTHONY DEAN

2009-07-24

The 2009 Gordon Conference on Microbial Population Biology will cover a diverse range of cutting edge issues in the microbial sciences and beyond. Firmly founded in evolutionary biology and with a strongly integrative approach, past Conferences have covered a range of topics from the dynamics and genetics of adaptation to the evolution of mutation rate, community ecology, evolutionary genomics, altruism, and epidemiology. The 2009 Conference is no exception, and will include sessions on the evolution of infectious diseases, social evolution, the evolution of symbioses, experimental evolution, adaptive landscapes, community dynamics, and the evolution of protein structure and function. While genomicmore » approaches continue to make inroads, broadening our knowledge and encompassing new questions, the conference will also emphasize the use of experimental approaches to test hypotheses decisively. As in the past, this Conference provides young scientists and graduate students opportunities to present their work in poster format and exchange ideas with leading investigators from a broad spectrum of disciplines. This meeting is never dull: some of the most significant and contentious issues in biology have been thrashed out here. The 2009 meeting will be no exception.« less

Phase diagram of the ultrafast photoinduced insulator-metal transition in vanadium dioxide

NASA Astrophysics Data System (ADS)

Cocker, T. L.; Titova, L. V.; Fourmaux, S.; Holloway, G.; Bandulet, H.-C.; Brassard, D.; Kieffer, J.-C.; El Khakani, M. A.; Hegmann, F. A.

2012-04-01

We use time-resolved terahertz spectroscopy to probe the ultrafast dynamics of the insulator-metal phase transition induced by femtosecond laser pulses in a nanogranular vanadium dioxide (VO2) film. Based on the observed thresholds for characteristic transient terahertz dynamics, a phase diagram of critical pump fluence versus temperature for the insulator-metal phase transition in VO2 is established for the first time over a broad range of temperatures down to 17 K. We find that both Mott and Peierls mechanisms are present in the insulating state and that the photoinduced transition is nonthermal. We propose a critical-threshold model for the ultrafast photoinduced transition based on a critical density of electrons and a critical density of coherently excited phonons necessary for the structural transition to the metallic state. As a result, evidence is found at low temperatures for an intermediate metallic state wherein the Mott state is melted but the Peierls distortion remains intact, consistent with recent theoretical predictions. Finally, the observed terahertz conductivity dynamics above the photoinduced transition threshold reveal nucleation and growth of metallic nanodomains over picosecond time scales.

How reproducible are methods to measure the dynamic viscoelastic properties of poroelastic media?

NASA Astrophysics Data System (ADS)

Bonfiglio, Paolo; Pompoli, Francesco; Horoshenkov, Kirill V.; Rahim, Mahmud Iskandar B. Seth A.; Jaouen, Luc; Rodenas, Julia; Bécot, François-Xavier; Gourdon, Emmanuel; Jaeger, Dirk; Kursch, Volker; Tarello, Maurizio; Roozen, Nicolaas Bernardus; Glorieux, Christ; Ferrian, Fabrizio; Leroy, Pierre; Vangosa, Francesco Briatico; Dauchez, Nicolas; Foucart, Félix; Lei, Lei; Carillo, Kevin; Doutres, Olivier; Sgard, Franck; Panneton, Raymond; Verdiere, Kévin; Bertolini, Claudio; Bär, Rolf; Groby, Jean-Philippe; Geslain, Alan; Poulain, Nicolas; Rouleau, Lucie; Guinault, Alain; Ahmadi, Hamid; Forge, Charlie

2018-08-01

There is a considerable number of research publications on the acoustical properties of porous media with an elastic frame. A simple search through the Web of Science™ (last accessed 21 March 2018) suggests that there are at least 819 publications which deal with the acoustics of poroelastic media. A majority of these researches require accurate knowledge of the elastic properties over a broad frequency range. However, the accuracy of the measurement of the dynamic elastic properties of poroelastic media has been a contentious issue. The novelty of this paper is that it studies the reproducibility of some popular experimental methods which are used routinely to measure the key elastic properties such as the dynamic Young's modulus, loss factor and Poisson ratio of poroelastic media. In this paper, fourteen independent sets of laboratory measurements were performed on specimens of the same porous materials. The results from these measurements suggest that the reproducibility of this type of experimental method is poor. This work can be helpful to suggest improvements which can be developed to harmonize the way the elastic properties of poroelastic media are measured worldwide.

Dynamic interrogator for elastic wave sensing using Fabry Perot filters based on fiber Bragg gratings.

PubMed

Harish, Achar V; Varghese, Bibin; Rao, Babu; Balasubramaniam, Krishnan; Srinivasan, Balaji

2015-07-01

Use of in-fiber Fabry-Perot (FP) filters based on fiber Bragg gratings as both sensor as well as an interrogator for enhancing the detection limit of elastic wave sensing is investigated in this paper. The sensitivity of such a demodulation scheme depends on the spectral discrimination of the sensor and interrogator gratings. Simulations have shown that the use of in-fiber FP filters with high finesse provide better performance in terms of sensitivity compared to the demodulation using fiber Bragg gratings. Based on these results, a dynamic interrogator capable of sensing acoustic waves with amplitude of less than 1 micro-strain over frequencies of 10 kHz to several 100 kHz has been implemented. Frequency response of the fiber Bragg gratings in the given experimental setup has been compared to that of the conventional piezo sensors demonstrating that fiber Bragg gratings can be used over a relatively broad frequency range. Dynamic interrogator has been packaged in a compact box without any degradation in its performance. Copyright © 2015 Elsevier B.V. All rights reserved.

Chaotic non-planar vibrations of the thin elastica. Part I: Experimental observation of planar instability

NASA Astrophysics Data System (ADS)

Cusumano, J. P.; Moon, F. C.

1995-01-01

In this two-part paper, the results of an investigation into the non-linear dynamics of a flexible cantilevered rod (the elastica) with a thin rectangular cross-section are presented. An experimental examination of the dynamics of the elastica over a broad parameter range forms the core of Part I. In Part II, the experimental work is related to a theoretical study of the mechanics of the elastica, and the study of a two-degree-of-freedom model obtained by modal projection. The experimental system used in this investigation is a rod with clamped-free boundary conditions, forced by sinusoidally displacing the clamped end. Planar periodic motions of the driven elastica are shown to lose stability at distinct resonant wedges, and the resulting motions are shown in general to be non-planar, chaotic, bending-torsion oscillations. Non-planar motions in all resonances exhibit energy cascading and dynamic two-well phenomena, and a family of asymmetric, bending-torsion non-linear modes is discovered. Correlation dimension calculations are used to estimate the number of active degrees of freedom in the system.

Dynamic Wavelength-Tunable Photodetector Using Subwavelength Graphene Field-Effect Transistors

DOE PAGES

Léonard, François; Spataru, Catalin D.; Goldflam, Michael; ...

2017-04-04

The holy grail of photodetector technology is dynamic wavelength tunability. Because of its atomic thickness and unique properties, graphene opens up new paradigms to realize this concept, but so far this has been elusive experimentally. We employ detailed quantum transport modeling of photocurrent in graphene field-effect transistors (including realistic electromagnetic fields) to show that wavelength tunability is possible by dynamically changing the gate voltage. We also reveal the phenomena that govern the behavior of this type of device and show significant departure from the simple expectations based on vertical transitions. We find strong focusing of the electromagnetic fields at themore » contact edges over the same length scale as the band-bending. Both of these spatially-varying potentials lead to an enhancement of non-vertical optical transitions, which dominate even in the absence of phonon or impurity scattering. Furthermore, we show that the vanishing density of states near the Dirac point leads to contact blocking and a gate-dependent modulation of the photocurrent. Several of the effects discussed here should be applicable to a broad range of one- and two-dimensional materials and devices.« less

On the accuracy of the LSC-IVR approach for excitation energy transfer in molecular aggregates

NASA Astrophysics Data System (ADS)

Teh, Hung-Hsuan; Cheng, Yuan-Chung

2017-04-01

We investigate the applicability of the linearized semiclassical initial value representation (LSC-IVR) method to excitation energy transfer (EET) problems in molecular aggregates by simulating the EET dynamics of a dimer model in a wide range of parameter regime and comparing the results to those obtained from a numerically exact method. It is found that the LSC-IVR approach yields accurate population relaxation rates and decoherence rates in a broad parameter regime. However, the classical approximation imposed by the LSC-IVR method does not satisfy the detailed balance condition, generally leading to incorrect equilibrium populations. Based on this observation, we propose a post-processing algorithm to solve the long time equilibrium problem and demonstrate that this long-time correction method successfully removed the deviations from exact results for the LSC-IVR method in all of the regimes studied in this work. Finally, we apply the LSC-IVR method to simulate EET dynamics in the photosynthetic Fenna-Matthews-Olson complex system, demonstrating that the LSC-IVR method with long-time correction provides excellent description of coherent EET dynamics in this typical photosynthetic pigment-protein complex.

Dynamic Wavelength-Tunable Photodetector Using Subwavelength Graphene Field-Effect Transistors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Léonard, François; Spataru, Catalin D.; Goldflam, Michael

The holy grail of photodetector technology is dynamic wavelength tunability. Because of its atomic thickness and unique properties, graphene opens up new paradigms to realize this concept, but so far this has been elusive experimentally. We employ detailed quantum transport modeling of photocurrent in graphene field-effect transistors (including realistic electromagnetic fields) to show that wavelength tunability is possible by dynamically changing the gate voltage. We also reveal the phenomena that govern the behavior of this type of device and show significant departure from the simple expectations based on vertical transitions. We find strong focusing of the electromagnetic fields at themore » contact edges over the same length scale as the band-bending. Both of these spatially-varying potentials lead to an enhancement of non-vertical optical transitions, which dominate even in the absence of phonon or impurity scattering. Furthermore, we show that the vanishing density of states near the Dirac point leads to contact blocking and a gate-dependent modulation of the photocurrent. Several of the effects discussed here should be applicable to a broad range of one- and two-dimensional materials and devices.« less

Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics.

PubMed

Farlik, Matthias; Sheffield, Nathan C; Nuzzo, Angelo; Datlinger, Paul; Schönegger, Andreas; Klughammer, Johanna; Bock, Christoph

2015-03-03

Methods for single-cell genome and transcriptome sequencing have contributed to our understanding of cellular heterogeneity, whereas methods for single-cell epigenomics are much less established. Here, we describe a whole-genome bisulfite sequencing (WGBS) assay that enables DNA methylation mapping in very small cell populations (μWGBS) and single cells (scWGBS). Our assay is optimized for profiling many samples at low coverage, and we describe a bioinformatic method that analyzes collections of single-cell methylomes to infer cell-state dynamics. Using these technological advances, we studied epigenomic cell-state dynamics in three in vitro models of cellular differentiation and pluripotency, where we observed characteristic patterns of epigenome remodeling and cell-to-cell heterogeneity. The described method enables single-cell analysis of DNA methylation in a broad range of biological systems, including embryonic development, stem cell differentiation, and cancer. It can also be used to establish composite methylomes that account for cell-to-cell heterogeneity in complex tissue samples. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Structures-propulsion interactions and requirements. [large space structures

NASA Technical Reports Server (NTRS)

Coyner, J. V.

1982-01-01

The effects of low-thrust primary propulsion system characteristics on the mass, area, and orbit transfer characteristics of large space systems (LSS) were determined. Three general structural classes of LSS were considered, each with a broad range of diameters and nonstructural surface densities. While transferring the deployed structure from LEO and to GEO, an acceleration range of 0.02 to 0.1 g's was found to maximize deliverable payload based on structural mass impact. After propulsion system parametric analyses considering four propellant combinations produced values for available payload mass, length and volume, a thrust level range which maximizes deliverable LSS diameter was determined corresponding to a structure and propulsion vehicle. The engine start and/or shutdown thrust transients on the last orbit transfer (apogee) burn can impose transient loads which would be greater than the steady-state loads at the burnout acceleration. The effect of the engine thrust transients on the LSS was determined from the dynamic models upon which various engine ramps were imposed.

A general strategy to construct small molecule biosensors in eukaryotes

DOE PAGES

Feng, Justin; Jester, Benjamin W.; Tinberg, Christine E.; ...

2015-12-29

Biosensors for small molecules can be used in applications that range from metabolic engineering to orthogonal control of transcription. Here, we produce biosensors based on a ligand-binding domain (LBD) by using a method that, in principle, can be applied to any target molecule. The LBD is fused to either a fluorescent protein or a transcriptional activator and is destabilized by mutation such that the fusion accumulates only in cells containing the target ligand. We illustrate the power of this method by developing biosensors for digoxin and progesterone. Addition of ligand to yeast, mammalian, or plant cells expressing a biosensor activatesmore » transcription with a dynamic range of up to ~100-fold. We use the biosensors to improve the biotransformation of pregnenolone to progesterone in yeast and to regulate CRISPR activity in mammalian cells. As a result, this work provides a general methodology to develop biosensors for a broad range of molecules in eukaryotes.« less

A general strategy to construct small molecule biosensors in eukaryotes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feng, Justin; Jester, Benjamin W.; Tinberg, Christine E.

Biosensors for small molecules can be used in applications that range from metabolic engineering to orthogonal control of transcription. Here, we produce biosensors based on a ligand-binding domain (LBD) by using a method that, in principle, can be applied to any target molecule. The LBD is fused to either a fluorescent protein or a transcriptional activator and is destabilized by mutation such that the fusion accumulates only in cells containing the target ligand. We illustrate the power of this method by developing biosensors for digoxin and progesterone. Addition of ligand to yeast, mammalian, or plant cells expressing a biosensor activatesmore » transcription with a dynamic range of up to ~100-fold. We use the biosensors to improve the biotransformation of pregnenolone to progesterone in yeast and to regulate CRISPR activity in mammalian cells. As a result, this work provides a general methodology to develop biosensors for a broad range of molecules in eukaryotes.« less

A general strategy to construct small molecule biosensors in eukaryotes

PubMed Central

Feng, Justin; Jester, Benjamin W; Tinberg, Christine E; Mandell, Daniel J; Antunes, Mauricio S; Chari, Raj; Morey, Kevin J; Rios, Xavier; Medford, June I; Church, George M; Fields, Stanley; Baker, David

2015-01-01

Biosensors for small molecules can be used in applications that range from metabolic engineering to orthogonal control of transcription. Here, we produce biosensors based on a ligand-binding domain (LBD) by using a method that, in principle, can be applied to any target molecule. The LBD is fused to either a fluorescent protein or a transcriptional activator and is destabilized by mutation such that the fusion accumulates only in cells containing the target ligand. We illustrate the power of this method by developing biosensors for digoxin and progesterone. Addition of ligand to yeast, mammalian, or plant cells expressing a biosensor activates transcription with a dynamic range of up to ~100-fold. We use the biosensors to improve the biotransformation of pregnenolone to progesterone in yeast and to regulate CRISPR activity in mammalian cells. This work provides a general methodology to develop biosensors for a broad range of molecules in eukaryotes. DOI: http://dx.doi.org/10.7554/eLife.10606.001 PMID:26714111

Photonic crystal fibre for industrial laser delivery

NASA Astrophysics Data System (ADS)

O'Driscoll, E. J.; McDonald, J.; Morgan, S.; Simpson, G.; Sidhu, J.; Baggett, J. C.; Hayes, J. R.; Petrovich, M. N.; Finazzi, V.; Polletti, F.; Richardson, D. J.; Horley, R.; Harker, A.; Grunewald, P.; Allott, R.; Judd, E.

2006-12-01

Fiber delivery of intense laser radiation is important for a broad range of application sectors, from medicine through to industrial laser processing of materials, and offers many practical system benefits relative to free space solutions. In recent years, photonic crystal fiber technology has revolutionized the dynamic field of optical fibers, bringing with them a wide range of novel optical properties that make them ideally suited to power delivery with unparalleled control over the beam properties. The DTI funded project: Photonic Fibers for Industrial beam DELivery (PFIDEL), aims to develop novel fiber geometries for use as a delivery system for high power industrial lasers and to assess their potential in a range of "real" industrial applications. In this paper we review, from an industrial laser user perspective, the advantages of each of the fibers studied under PFIDEL. We present results of application demonstrations and discuss how these fibers can positively impact the field of industrial laser systems and processes, in particular for direct write and micromachining applications.

Preferred gait and walk-run transition speeds in ostriches measured using GPS-IMU sensors.

PubMed

Daley, Monica A; Channon, Anthony J; Nolan, Grant S; Hall, Jade

2016-10-15

The ostrich (Struthio camelus) is widely appreciated as a fast and agile bipedal athlete, and is a useful comparative bipedal model for human locomotion. Here, we used GPS-IMU sensors to measure naturally selected gait dynamics of ostriches roaming freely over a wide range of speeds in an open field and developed a quantitative method for distinguishing walking and running using accelerometry. We compared freely selected gait-speed distributions with previous laboratory measures of gait dynamics and energetics. We also measured the walk-run and run-walk transition speeds and compared them with those reported for humans. We found that ostriches prefer to walk remarkably slowly, with a narrow walking speed distribution consistent with minimizing cost of transport (CoT) according to a rigid-legged walking model. The dimensionless speeds of the walk-run and run-walk transitions are slower than those observed in humans. Unlike humans, ostriches transition to a run well below the mechanical limit necessitating an aerial phase, as predicted by a compass-gait walking model. When running, ostriches use a broad speed distribution, consistent with previous observations that ostriches are relatively economical runners and have a flat curve for CoT against speed. In contrast, horses exhibit U-shaped curves for CoT against speed, with a narrow speed range within each gait for minimizing CoT. Overall, the gait dynamics of ostriches moving freely over natural terrain are consistent with previous lab-based measures of locomotion. Nonetheless, ostriches, like humans, exhibit a gait-transition hysteresis that is not explained by steady-state locomotor dynamics and energetics. Further study is required to understand the dynamics of gait transitions. © 2016. Published by The Company of Biologists Ltd.

Evaluation of slide based cytometry (SBC) for concentration measurements of fluorescent dyes in solution

NASA Astrophysics Data System (ADS)

Pierzchalski, Arkadiusz; Marecka, Monika; Müller, Hans-Willy; Bocsi, József; Tárnok, Attila

2009-02-01

Flow cytometers (FCM) are built for particle measurements. In principle, concentration measurement of a homogeneous solution is not possible with FCM due to the lack of a trigger signal. In contrast to FCM slide based cytometry systems could act as tools for the measurement of concentrations using volume defined cell counting chambers. These chambers enable to analyze a well defined volume. Sensovation AG (Stockach, Germany) introduced an automated imaging system that combines imaging with cytometric features analysis. Aim of this study was to apply this imaging system to quantify the fluorescent molecule concentrations. The Lumisens (Sensovation AG) slide-based technology based on fluorescence digital imaging microscopy was used. The instrument is equipped with an inverted microscope, blue and red LEDs, double band-pass filters and a high-resolution cooled 16-bit digital camera. The instrument was focussed on the bottom of 400μm deep 6 chamber slides (IBIDI GmbH, Martinsried, Germany) or flat bottom 96 well plates (Greiner Bio One GmbH, Frickenhausen, Germany). Fluorescent solutions were imaged under 90% pixel saturation in a broad concentration range (FITC: 0.0002-250 μg/ml, methylene blue (MethB): 0.0002-250 μg/ml). Exposition times were recorded. Images were analysed by the iCys (CompuCyte Corp., Cambridge, MA, USA) image analysis software with the phantom contour function. Relative fluorescence intensities were calculated from mean fluorescence intensities per phantom contours divided by the exposition time. Solution concentrations could be distinguished over a broad dynamic range of 3.5 to 5.5 decades log (range FITC: 0.0002-31.25μg/ml, MethB: 0.0076-31.25μg/ml) with a good linear relationship between dye concentration and relative fluorescence intensity. The minimal number of fluorescent molecules per pixel as determined by the mean fluorescence intensity and the molecular weight of the fluorochrome were about 800 molecules FITC and ~2.000 MethB. The novel slide-based imaging system is suitable for detection of fluorescence differences over a broad range of concentrations. This approach may lead to novel assays for measuring concentration differences in cell free solutions and cell cultures e.g. in secretion assays.

The response to selection for broad male response to female sex pheromone and its implications for divergence in close-range mating behavior in the European corn borer moth, Ostrinia nubilalis.

PubMed

Droney, David C; Musto, Callie J; Mancuso, Katie; Roelofs, Wendell L; Linn, Charles E

2012-12-01

Coordinated sexual communication systems, seen in many species of moths, are hypothesized to be under strong stabilizing natural selection. Stabilized communication systems should be resistant to change, but there are examples of species/populations that show great diversification. A possible solution is that it is directional sexual selection on variation in male response that drives evolution. We tested a component of this model by asking whether 'rare' males (ca. 5 % of all males in a population) of the European corn borer moth (ECB), Ostrinia nubilalis, that respond to the sex pheromones of both ECB and a different Ostrinia species (O. furnacalis, the Asian corn borer, ACB), might play an important role in diversification. We specifically tested, via artificial selection, whether this broad male response has an evolvable genetic component. We increased the frequency of broad male response from 5 to 70 % in 19 generations, showing that broad-responding males could be important for the evolution of novel communication systems in ECB. We did not find a broader range of mating acceptance of broad males by females of the base population, however, suggesting that broad response would be unlikely to increase in frequency without the involvement of other factors. However, we found that ECB selection-line females accepted a broader range of courting males, including those of ACB, than did females of the base population. Thus, a genetic correlation exists between broad, long-range response to female sex pheromone and the breadth of female acceptance of males at close range. These results are discussed in the context of evolution of novel communication systems in Ostrinia.

Delay-correlation landscape reveals characteristic time delays of brain rhythms and heart interactions

PubMed Central

Lin, Aijing; Liu, Kang K. L.; Bartsch, Ronny P.; Ivanov, Plamen Ch.

2016-01-01

Within the framework of ‘Network Physiology’, we ask a fundamental question of how modulations in cardiac dynamics emerge from networked brain–heart interactions. We propose a generalized time-delay approach to identify and quantify dynamical interactions between physiologically relevant brain rhythms and the heart rate. We perform empirical analysis of synchronized continuous EEG and ECG recordings from 34 healthy subjects during night-time sleep. For each pair of brain rhythm and heart interaction, we construct a delay-correlation landscape (DCL) that characterizes how individual brain rhythms are coupled to the heart rate, and how modulations in brain and cardiac dynamics are coordinated in time. We uncover characteristic time delays and an ensemble of specific profiles for the probability distribution of time delays that underly brain–heart interactions. These profiles are consistently observed in all subjects, indicating a universal pattern. Tracking the evolution of DCL across different sleep stages, we find that the ensemble of time-delay profiles changes from one physiologic state to another, indicating a strong association with physiologic state and function. The reported observations provide new insights on neurophysiological regulation of cardiac dynamics, with potential for broad clinical applications. The presented approach allows one to simultaneously capture key elements of dynamic interactions, including characteristic time delays and their time evolution, and can be applied to a range of coupled dynamical systems. PMID:27044991

Delay-correlation landscape reveals characteristic time delays of brain rhythms and heart interactions

NASA Astrophysics Data System (ADS)

Lin, Aijing; Liu, Kang K. L.; Bartsch, Ronny P.; Ivanov, Plamen Ch.

2016-05-01

Within the framework of `Network Physiology', we ask a fundamental question of how modulations in cardiac dynamics emerge from networked brain-heart interactions. We propose a generalized time-delay approach to identify and quantify dynamical interactions between physiologically relevant brain rhythms and the heart rate. We perform empirical analysis of synchronized continuous EEG and ECG recordings from 34 healthy subjects during night-time sleep. For each pair of brain rhythm and heart interaction, we construct a delay-correlation landscape (DCL) that characterizes how individual brain rhythms are coupled to the heart rate, and how modulations in brain and cardiac dynamics are coordinated in time. We uncover characteristic time delays and an ensemble of specific profiles for the probability distribution of time delays that underly brain-heart interactions. These profiles are consistently observed in all subjects, indicating a universal pattern. Tracking the evolution of DCL across different sleep stages, we find that the ensemble of time-delay profiles changes from one physiologic state to another, indicating a strong association with physiologic state and function. The reported observations provide new insights on neurophysiological regulation of cardiac dynamics, with potential for broad clinical applications. The presented approach allows one to simultaneously capture key elements of dynamic interactions, including characteristic time delays and their time evolution, and can be applied to a range of coupled dynamical systems.

Glasslike dynamical behavior of the plastocyanin hydration water

NASA Astrophysics Data System (ADS)

Bizzarri, Anna Rita; Paciaroni, Alessandro; Cannistraro, Salvatore

2000-09-01

The dynamical behavior of water around plastocyanin has been investigated in a wide temperature range by molecular dynamics simulation. The mean square displacements of water oxygen atoms show, at long times, a tα trend for all temperatures. Below 150 K, α is constant and equal to 1; at higher temperatures it drops to a value significantly smaller than 1, and thereafter decreases with increasing temperature. The occurrence of such an anomalous diffusion matches the onset of the dynamical transition observed in the protein. The intermediate scattering function of water is characterized, at high temperature, by a stretched exponential decay evolving, at low temperature, toward a two step relaxation behavior, which becomes more evident on increasing the exchanged wave vector q. Both the mean square displacements and the intermediate scattering functions show, beyond the ballistic regime, a plateau, which progressively extends for longer times as long as the temperature is lowered, such behavior reflecting trapping of water molecules within a cage formed by the nearest neighbors. At low temperature, a low frequency broad inelastic peak is observed in the dynamical structure factor of hydration water; such an excess of vibrational modes being reminiscent of the boson peak, characteristic of disordered, amorphous systems. All these features, which are typical of complex systems, can be traced back to the glassy character of the hydration water and suggest a dynamical coupling occurring at the macromolecule-solvent interface.

Dynamic Assessment in Educational Settings: Is Potential Ever Realised?

ERIC Educational Resources Information Center

Stringer, Phil

2018-01-01

This paper reports on what has happened since Elliott ("Dynamic Assessment in Educational Settings: Realising Potential," 2003) in those applications of dynamic assessment that he considered. There continues to be two broad applications, one, largely researcher led, and the other, largely practitioner led, although there are examples of…

Tenth Workshop for Computational Fluid Dynamic Applications in Rocket Propulsion, part 1

NASA Technical Reports Server (NTRS)

Williams, R. W. (Compiler)

1992-01-01

Experimental and computational fluid dynamic activities in rocket propulsion were discussed. The workshop was an open meeting of government, industry, and academia. A broad number of topics were discussed including computational fluid dynamic methodology, liquid and solid rocket propulsion, turbomachinery, combustion, heat transfer, and grid generation.

Functional groups show distinct differences in nitrogen cycling during early stand development: implications for forest management.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aubrey, Doug, P.; Coyle, David, R. Coleman, Mark, D.

2011-08-26

Nutrient acquisition of forest stands is controlled by soil resource availability and belowground production, but tree species are rarely compared in this regard. Here, we examine ecological and management implications of nitrogen (N) dynamics during early forest stand development in productive commercial tree species with narrow (Populus deltoides Bartr. and Platanus occidentalis L.) and broad (Liquidambar styraciflua L. and Pinus taeda L.) site requirements while grown with a range of nutrient and water resources. We constructed N budgets by measuring N concentration ([N]) and N content (N{sub C}) of above- and belowground perennial and ephemeral tissues, determined N uptake (N{submore » UP}), and calculated N use efficiency (NUE). Forest stands regulated [N] within species-specific operating ranges without clear temporal or treatment patterns, thus demonstrating equilibrium between tissue [N] and biomass accumulation. Forest stand N{sub C} and N{sub UP} increased with stand development and paralleled treatment patterns of biomass accumulation, suggesting productivity is tightly linked to N{sub UP}. Inclusion of above- and belowground ephemeral tissue turnover in N{sub UP} calculations demonstrated that maximum N demand for narrow-sites adapted species exceeded 200 kg N ha{sup -1} year{sup -1} while demand for broad-site adapted species was below this level. NUE was species dependent but not consistently influenced by N availability, suggesting relationships between NUE and resource availability were species dependent. Based on early stand development, species with broad site adaptability are favored for woody cropping systems because they maintain high above- and belowground productivity with minimal fertilization requirements due to higher NUE than narrow site adapted species.« less

Fresh broad (Vicia faba) tissue homogenate-based biosensor for determination of phenolic compounds.

PubMed

Ozcan, Hakki Mevlut; Sagiroglu, Ayten

2014-08-01

In this study, a novel fresh broad (Vicia faba) tissue homogenate-based biosensor for determination of phenolic compounds was developed. The biosensor was constructed by immobilizing tissue homogenate of fresh broad (Vicia faba) on to glassy carbon electrode. For the stability of the biosensor, general immobilization techniques were used to secure the fresh broad tissue homogenate in gelatin-glutaraldehyde cross-linking matrix. In the optimization and characterization studies, the amount of fresh broad tissue homogenate and gelatin, glutaraldehyde percentage, optimum pH, optimum temperature and optimum buffer concentration, thermal stability, interference effects, linear range, storage stability, repeatability and sample applications (Wine, beer, fruit juices) were also investigated. Besides, the detection ranges of thirteen phenolic compounds were obtained with the help of the calibration graphs. A typical calibration curve for the sensor revealed a linear range of 5-60 μM catechol. In reproducibility studies, variation coefficient (CV) and standard deviation (SD) were calculated as 1.59%, 0.64×10(-3) μM, respectively.

Design, calibration and application of broad-range optical nanosensors for determining intracellular pH.

PubMed

Søndergaard, Rikke V; Henriksen, Jonas R; Andresen, Thomas L

2014-12-01

Particle-based nanosensors offer a tool for determining the pH in the endosomal-lysosomal system of living cells. Measurements providing absolute values of pH have so far been restricted by the limited sensitivity range of nanosensors, calibration challenges and the complexity of image analysis. This protocol describes the design and application of a polyacrylamide-based nanosensor (∼60 nm) that covalently incorporates two pH-sensitive fluorophores, fluorescein (FS) and Oregon Green (OG), to broaden the sensitivity range of the sensor (pH 3.1-7.0), and uses the pH-insensitive fluorophore rhodamine as a reference fluorophore. The nanosensors are spontaneously taken up via endocytosis and directed to the lysosomes where dynamic changes in pH can be measured with live-cell confocal microscopy. The most important focus areas of the protocol are the choice of pH-sensitive fluorophores, the design of calibration buffers, the determination of the effective range and especially the description of how to critically evaluate results. The entire procedure typically takes 2-3 weeks.

Tertiary climates and floristic relationships at high latitudes in the northern hemisphere

USGS Publications Warehouse

Wolfe, J.A.

1980-01-01

During the Paleocene and Eocene, climates were characterized by a low mean annual range of temperature (a maximum of 10-15??C), a moderate to high mean annual temperature (10-20??C), and abundant precipitation; strong broad-leaved evergreen vegetation extended to almost lat. 60??N during the Paleocene and to well above 61??N during the Eocene. Poleward of the broad-leaved evergreen forests were forests that were broad-leaved deciduous; these deciduous forests, however, were unlike extant broad-leaved deciduous forests in general floristic composition and physiognomy. Coniferous forests probably occupied the northernmost latitudes. At the end of the Eocene, a major climatic deterioration resulted in a high (> 30??C) mean annual range of temperature and a low mean annual temperature (< 10??C). Vegetation represented temperate broad-leaved deciduous and coniferous forests. The Oligocene and Neogene climatic trends represent a decrease in both mean annual range of temperature and mean annual temperature. Tundra vegetation did not appear until late in the Neogene. The present distribution of broad-leaved evergreens concomitant with the principles of plant physiology indicates that present winter light conditions at high latitudes could not support broad-leaved evergreen forest. A possible solution to the problem is to increase winter light by lessening the inclination of the earth's rotational axis. ?? 1980.

Broad-Range 16S rDNA PCR on Heart Valves in Infective Endocarditis.

PubMed

Müller Premru, Manica; Lejko Zupanc, Tatjana; Klokočovnik, Tomislav; Ruzić Sabljić, Eva; Cerar, Tjaša

2016-03-01

Infective endocarditis (IE) is diagnosed by blood and/or resected valve cultivation and echocardiographic findings, as defined by the Duke criteria. Unfortunately, cultures may be negative due to prior antibiotic therapy or fastidious or slow-growing microorganisms. The study aim was to investigate the value of the broad-range polymerase chain reaction (PCR) in addition to blood and valve culture for the detection of causative microorganisms. Between February 2012 and March 2015, valve samples from 36 patients undergoing cardiac surgery were analyzed; of these patients, 26 had a preoperative diagnosis of IE and 10 served as controls. Multiple blood cultures were obtained from 34 patients before antibiotic therapy was commenced. Valve samples were inoculated on bacteriological media and underwent analysis using broad-range PCR (16S rDNA). IE was confirmed microbiologically in 21 of the 26 patients (80.7%); in 20 cases (76.9%) this was by positive blood cultures and in 16 (61.5%) by positive valves. Valves were positive in 15 blood culturepositive patients, and in one blood-culture negative patient. Broad-range PCR detected a microorganism in valves significantly more frequently (n = 14; 53.8%) compared to valve culture (n = 8; 30.7%) (chisquare 11.5, p <0.001). The predominant microorganisms were Staphylococcus aureus, Streptococcus of the viridans group, coagulasenegative staphylococci and Enterococcus faecalis. Blood, valve cultures and broad-range PCR were negative in five patients (19.3%) with IE, and in all 10 subjects of the control group. Broad-range PCR on valves was more sensitive than valve culture. However, blood culture, if taken before the start of antibiotic therapy, was the best method for detecting IE.

Distribution of Human papillomavirus load in clinical specimens.

PubMed

Lowe, Brian; O'Neil, Dominic; Loeffert, Dirk; Nazarenko, Irina

2011-04-01

The information about the range and distribution of Human papillomavirus load in clinical specimens is important for the design of accurate clinical tests. The amount of Human papillomavirus in cervical specimens was estimated using the digene HC2 HPV DNA Test(®) (QIAGEN). This semi-quantitative assay is based on linear signal amplification with an analytical limit-of-detection of approximately 2500 virus copies per assay and 3-4 log dynamic range. The dynamic range of the assay was extended by a serial dilution strategy. Two large sets of positive specimens (n=501 and 569) were analyzed and 9-11% of specimens was estimated to contain more than 7 × 10(7) copies of virus. The viral load was also assessed for an assortment of specimens with known cytology diagnoses (n=9435) and histological diagnoses (n=2056). The percentage of specimens with more than 7 × 10(7) copies of virus was estimated to be 0.89 for normal cells, 4.2 for atypical cells (unknown significance), 14.31 for cells of low-grade lesions and 22.24 for cells of high-grade lesions. The viral load increased with disease severity, but its broad distribution may not support its use as a disease biomarker. This information is important for assay design and automation, where cross-reactivity and sample-to-sample contamination must be addressed rigorously. Copyright © 2011 Elsevier B.V. All rights reserved.

Contemporary Business Administration Curricula

ERIC Educational Resources Information Center

Gleason, James R.

2006-01-01

The National Association of State Directors of Career Technical Education Consortium (NASDCTEc) career clusters initiative was designed to research and foster development of curicula and assessments for each of 16 broad occupational groupings known as career clusters. These clusters encompass a broad range of careers, ranging from agriculture to…

Electrostatic fluctuations in collisional plasmas

DOE PAGES

Rozmus, W.; Brantov, A.; Fortmann-Grote, C.; ...

2017-10-12

Here, we present a theory of electrostatic fluctuations in two-component plasmas where electrons and ions are described by Maxwellian distribution functions at unequal temperatures. Based on the exact solution of the Landau kinetic equation, that includes electron-electron, electron-ion, and ion-ion collision integrals, the dynamic form factor, S( →k,ω), is derived for weakly coupled plasmas. The collective plasma responses at ion-acoustic, Langmuir, and entropy mode resonances are described for arbitrary wave numbers and frequencies in the entire range of plasma collisionality. The collisionless limit of S( →k,ω) and the strong-collision result based on the fluctuation-dissipation theorem and classical transport at Tmore » e = T i are recovered and discussed. Results of several Thomson scattering experiments in the broad range of plasma parameters are described and discussed by means of our theory for S( →k,ω).« less

Electrostatic fluctuations in collisional plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rozmus, W.; Brantov, A.; Fortmann-Grote, C.

Here, we present a theory of electrostatic fluctuations in two-component plasmas where electrons and ions are described by Maxwellian distribution functions at unequal temperatures. Based on the exact solution of the Landau kinetic equation, that includes electron-electron, electron-ion, and ion-ion collision integrals, the dynamic form factor, S( →k,ω), is derived for weakly coupled plasmas. The collective plasma responses at ion-acoustic, Langmuir, and entropy mode resonances are described for arbitrary wave numbers and frequencies in the entire range of plasma collisionality. The collisionless limit of S( →k,ω) and the strong-collision result based on the fluctuation-dissipation theorem and classical transport at Tmore » e = T i are recovered and discussed. Results of several Thomson scattering experiments in the broad range of plasma parameters are described and discussed by means of our theory for S( →k,ω).« less

Electrostatic fluctuations in collisional plasmas.

PubMed

Rozmus, W; Brantov, A; Fortmann-Grote, C; Bychenkov, V Yu; Glenzer, S

2017-10-01

We present a theory of electrostatic fluctuations in two-component plasmas where electrons and ions are described by Maxwellian distribution functions at unequal temperatures. Based on the exact solution of the Landau kinetic equation, that includes electron-electron, electron-ion, and ion-ion collision integrals, the dynamic form factor, S(k[over ⃗],ω), is derived for weakly coupled plasmas. The collective plasma responses at ion-acoustic, Langmuir, and entropy mode resonances are described for arbitrary wave numbers and frequencies in the entire range of plasma collisionality. The collisionless limit of S(k[over ⃗],ω) and the strong-collision result based on the fluctuation-dissipation theorem and classical transport at T_{e}=T_{i} are recovered and discussed. Results of several Thomson scattering experiments in the broad range of plasma parameters are described and discussed by means of our theory for S(k[over ⃗],ω).

Information of Complex Systems and Applications in Agent Based Modeling.

PubMed

Bao, Lei; Fritchman, Joseph C

2018-04-18

Information about a system's internal interactions is important to modeling the system's dynamics. This study examines the finer categories of the information definition and explores the features of a type of local information that describes the internal interactions of a system. Based on the results, a dual-space agent and information modeling framework (AIM) is developed by explicitly distinguishing an information space from the material space. The two spaces can evolve both independently and interactively. The dual-space framework can provide new analytic methods for agent based models (ABMs). Three examples are presented including money distribution, individual's economic evolution, and artificial stock market. The results are analyzed in the dual-space, which more clearly shows the interactions and evolutions within and between the information and material spaces. The outcomes demonstrate the wide-ranging applicability of using the dual-space AIMs to model and analyze a broad range of interactive and intelligent systems.

Web-based resources for mass-spectrometry-based metabolomics: a user's guide.

PubMed

Tohge, Takayuki; Fernie, Alisdair R

2009-03-01

In recent years, a plethora of web-based tools aimed at supporting mass-spectrometry-based metabolite profiling and metabolomics applications have appeared. Given the huge hurdles presented by the chemical diversity and dynamic range of the metabolites present in the plant kingdom, profiling the levels of a broad range of metabolites is highly challenging. Given the scale and costs involved in defining the plant metabolome, it is imperative that data are effectively shared between laboratories pursuing this goal. However, ensuring accurate comparison of samples run on the same machine within the same laboratory, let alone cross-machine and cross-laboratory comparisons, requires both careful experimentation and data interpretation. In this review, we present an overview of currently available software that aids either in peak identification or in the related field of peak alignment as well as those with utility in defining structural information of compounds and metabolic pathways.

Calculations of rate constants for the three-body recombination of H2 in the presence of H2

NASA Technical Reports Server (NTRS)

Schwenke, David W.

1988-01-01

A new global potential energy hypersurface for H2 + H2 is constructed and quasiclassical trajectory calculations performed using the resonance complex theory and energy transfer mechanism to estimate the rate of three body recombination over the temperature range 100 to 5000 K. The new potential is a faithful representation of ab initio electron structure calculations, is unchanged under the operation of exchanging H atoms, and reproduces the accurate H3 potential as one H atom is pulled away. Included in the fitting procedure are geometries expected to be important when one H2 is near or above the dissociation limit. The dynamics calculations explicitly include the motion of all four atoms and are performed efficiently using a vectorized variable-stepsize integrator. The predicted rate constants are approximately a factor of two smaller than experimental estimates over a broad temperature range.

Development and testing of the EVS 2000 enhanced vision system

NASA Astrophysics Data System (ADS)

Way, Scott P.; Kerr, Richard; Imamura, Joe J.; Arnoldy, Dan; Zeylmaker, Richard; Zuro, Greg

2003-09-01

An effective enhanced vision system must operate over a broad spectral range in order to offer a pilot an optimized scene that includes runway background as well as airport lighting and aircraft operations. The large dynamic range of intensities of these images is best handled with separate imaging sensors. The EVS 2000 is a patented dual-band Infrared Enhanced Vision System (EVS) utilizing image fusion concepts to provide a single image from uncooled infrared imagers in both the LWIR and SWIR. The system is designed to provide commercial and corporate airline pilots with improved situational awareness at night and in degraded weather conditions. A prototype of this system was recently fabricated and flown on the Boeing Advanced Technology Demonstrator 737-900 aircraft. This paper will discuss the current EVS 2000 concept, show results taken from the Boeing Advanced Technology Demonstrator program, and discuss future plans for EVS systems.

Picosecond molecular motions in bacteriorhodopsin from neutron scattering.

PubMed Central

Fitter, J; Lechner, R E; Dencher, N A

1997-01-01

The characteristics of internal molecular motions of bacteriorhodopsin in the purple membrane have been studied by quasielastic incoherent neutron scattering. Because of the quasihomogeneous distribution of hydrogen atoms in biological molecules, this technique enables one to study a wide variety of intramolecular motions, especially those occurring in the picosecond to nanosecond time scale. We performed measurements at different energy resolutions with samples at various hydration levels within a temperature range of 10-300 K. The analysis of the data revealed a dynamical transition at temperatures Td between 180 K and 220 K for all motions resolved at time scales ranging from 0.1 to a few hundred picoseconds. Whereas below Td the motions are purely vibrational, they are predominantly diffusive above Td, characterized by an enormously broad distribution of correlation times. The variation of the hydration level, on the other hand, mainly affects motions slower than a few picoseconds. PMID:9336208

Rapid mapping of polarization switching through complete information acquisition

NASA Astrophysics Data System (ADS)

Somnath, Suhas; Belianinov, Alex; Kalinin, Sergei V.; Jesse, Stephen

2016-12-01

Polarization switching in ferroelectric and multiferroic materials underpins a broad range of current and emergent applications, ranging from random access memories to field-effect transistors, and tunnelling devices. Switching in these materials is exquisitely sensitive to local defects and microstructure on the nanometre scale, necessitating spatially resolved high-resolution studies of these phenomena. Classical piezoresponse force microscopy and spectroscopy, although providing necessary spatial resolution, are fundamentally limited in data acquisition rates and energy resolution. This limitation stems from their two-tiered measurement protocol that combines slow (~1 s) switching and fast (~10 kHz-1 MHz) detection waveforms. Here we develop an approach for rapid probing of ferroelectric switching using direct strain detection of material response to probe bias. This approach, facilitated by high-sensitivity electronics and adaptive filtering, enables spectroscopic imaging at a rate 3,504 times faster the current state of the art, achieving high-veracity imaging of polarization dynamics in complex microstructures.

Enhanced sampling techniques in molecular dynamics simulations of biological systems.

PubMed

Bernardi, Rafael C; Melo, Marcelo C R; Schulten, Klaus

2015-05-01

Molecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.

Somatic Hypermutation-Induced Changes in the Structure and Dynamics of HIV-1 Broadly Neutralizing Antibodies.

PubMed

Davenport, Thaddeus M; Gorman, Jason; Joyce, M Gordon; Zhou, Tongqing; Soto, Cinque; Guttman, Miklos; Moquin, Stephanie; Yang, Yongping; Zhang, Baoshan; Doria-Rose, Nicole A; Hu, Shiu-Lok; Mascola, John R; Kwong, Peter D; Lee, Kelly K

2016-08-02

Antibody somatic hypermutation (SHM) and affinity maturation enhance antigen recognition by modifying antibody paratope structure to improve its complementarity with the target epitope. SHM-induced changes in paratope dynamics may also contribute to antibody maturation, but direct evidence of this is limited. Here, we examine two classes of HIV-1 broadly neutralizing antibodies (bNAbs) for SHM-induced changes in structure and dynamics, and delineate the effects of these changes on interactions with the HIV-1 envelope glycoprotein (Env). In combination with new and existing structures of unmutated and affinity matured antibody Fab fragments, we used hydrogen/deuterium exchange with mass spectrometry to directly measure Fab structural dynamics. Changes in antibody structure and dynamics were positioned to improve complementarity with Env, with changes in dynamics primarily observed at the paratope peripheries. We conclude that SHM optimizes paratope complementarity to conserved HIV-1 epitopes and restricts the mobility of paratope-peripheral residues to minimize clashes with variable features on HIV-1 Env. Copyright © 2016 Elsevier Ltd. All rights reserved.

A visual water vapor photonic crystal sensor with PVA/SiO2 opal structure

NASA Astrophysics Data System (ADS)

Yang, Haowei; Pan, Lei; Han, Yingping; Ma, Lihua; Li, Yao; Xu, Hongbo; Zhao, Jiupeng

2017-11-01

In study, we proposed a simple yet fast optical sensing motif based on thimbleful of polyvinyl alcohol (PVA) infiltrated photonic crystal (PC), which allows for high efficiency in vapor sensing through changes in their inter-layer space. Linear response to a broad dynamic range of vapor concentration was realized. Ultrafast response time (<1 s) and excellent recyclability were also demonstrated. Selective response to a vapor was exhibited, reflecting well the characteristic sorption properties of PVA, with which colorimetric reporting was readily achieved. These substantial improvements in performance are attributed to the efficacy of signal transduction and the enhanced signal transduction because of thimbleful PVA infiltrated space between adjacent SiO2 nanospheres.

Contour detection improved by context-adaptive surround suppression.

PubMed

Sang, Qiang; Cai, Biao; Chen, Hao

2017-01-01

Recently, many image processing applications have taken advantage of a psychophysical and neurophysiological mechanism, called "surround suppression" to extract object contour from a natural scene. However, these traditional methods often adopt a single suppression model and a fixed input parameter called "inhibition level", which needs to be manually specified. To overcome these drawbacks, we propose a novel model, called "context-adaptive surround suppression", which can automatically control the effect of surround suppression according to image local contextual features measured by a surface estimator based on a local linear kernel. Moreover, a dynamic suppression method and its stopping mechanism are introduced to avoid manual intervention. The proposed algorithm is demonstrated and validated by a broad range of experimental results.

Microswimmers near surfaces

NASA Astrophysics Data System (ADS)

Elgeti, Jens; Gompper, Gerhard

2016-11-01

Both, in their natural environment and in a controlled experimental setup, microswimmers regularly interact with surfaces. These surfaces provide a steric boundary, both for the swimming motion and the hydrodynamic flow pattern. These effects typically imply a strong accumulation of microswimmers near surfaces. While some generic features can be derived, details of the swimmer shape and propulsion mechanism matter, which give rise to a broad range of adhesion phenomena and have to be taken into account to predict the surface accumulation for a given swimmer. We show in this minireview how numerical simulations and analytic theory can be used to predict the accumulation statistics for different systems, with an emphasis on swimmer shape, hydrodynamics interactions, and type of noisy dynamics.

Posttraumatic Stress Disorder: Five Vicious Cycles that Inhibit Effective Treatment.

PubMed

Ghaffarzadegan, Navid; Larson, Richard C

2015-01-01

Despite a wide range of studies and medical progress, it seems that we are far from significantly mitigating the problem of posttraumatic stress disorder (PTSD). The problem has major social and behavioral components. Developing innovative and effective policies requires a broad scope of analysis and consideration of the highly interconnected social, behavioral, and medical variables. In this article, we take a systems approach and offer an illustrative causal loop diagram which includes individual and social dynamics. Based on the map, we discuss 5 major barriers for effective interventions in PTSD. These barriers work as vicious cycles in the system, reduce effectiveness and therefore value of PTSD treatment. We also discuss policy implications of this perspective.

Characterization of FBG sensor interrogation based on a FDML wavelength swept laser

PubMed Central

Jung, Eun Joo; Kim, Chang-Seok; Jeong, Myung Yung; Kim, Moon Ki; Jeon, Min Yong; Jung, Woonggyu; Chen, Zhongping

2012-01-01

In this study, we develop an ultra-fast fiber Bragg grating sensor system that is based on the Fourier domain mode-locked (FDML) swept laser. A FDML wavelength swept laser has many advantages compared to the conventional wavelength swept laser source, such as high-speed interrogation, narrow spectral sensitivity, and high phase stability. The newly developed FDML wavelength swept laser shows a superior performance of a high scan rate of 31.3 kHz and a broad scan range of over 70 nm simultaneously. The performance of the grating sensor interrogating system using a FDML wavelength swept laser is characterized in both static and dynamic strain responses. PMID:18852764

A highly tunable system for the simultaneous expression of multiple enzymes in Saccharomyces cerevisiae.

PubMed

Ito, Yoichiro; Yamanishi, Mamoru; Ikeuchi, Akinori; Matsuyama, Takashi

2015-01-16

Control of the expression levels of multiple enzymes in transgenic yeasts is essential for the effective production of complex molecules through fermentation. Here, we propose a tunable strategy for the control of expression levels based on the design of terminator regions and other gene-expression control elements in Saccharomyces cerevisiae. Our genome-integrated system, which is capable of producing high expression levels over a wide dynamic range, will broadly enable metabolic engineering and synthetic biology. We demonstrated that the activities of multiple cellulases and the production of ethanol were doubled in a transgenic yeast constructed with our system compared with those achieved with a standard expression system.

Linking protein motion to enzyme catalysis.

PubMed

Singh, Priyanka; Abeysinghe, Thelma; Kohen, Amnon

2015-01-13

Enzyme motions on a broad range of time scales can play an important role in various intra- and intermolecular events, including substrate binding, catalysis of the chemical conversion, and product release. The relationship between protein motions and catalytic activity is of contemporary interest in enzymology. To understand the factors influencing the rates of enzyme-catalyzed reactions, the dynamics of the protein-solvent-ligand complex must be considered. The current review presents two case studies of enzymes-dihydrofolate reductase (DHFR) and thymidylate synthase (TSase)-and discusses the role of protein motions in their catalyzed reactions. Specifically, we will discuss the utility of kinetic isotope effects (KIEs) and their temperature dependence as tools in probing such phenomena.

The effect of gravity modulation on thermosolutal convection

NASA Technical Reports Server (NTRS)

Saunders, Bonita V.; Murray, Bruce T.; Mcfadden, G. B.; Coriell, S. R.; Wheeler, A. A.

1992-01-01

In a gravitational field, the opposing effects of components of different diffusivities, for example, temperature and solute, in the density profile in a fluid may produce convective instabilities that exhibit a broad range of dynamical behavior. The effect of time periodic vertical gravity modulation on the onset of these instabilities in an infinite horizontal layer with stress free boundaries is examined. This work is viewed as a first step in expanding previous results in solidification to the full problem of characterizing the effects of gravity modulation in thermosolutal convection during the directional solidification of binary alloys. Calculations carried out both with and without steady background acceleration are presented, the latter results being relevant to microgravity conditions.

High shrew diversity on Alaska's Seward Peninsula: Community assembly and environmental change

USGS Publications Warehouse

Hope, Andrew G.

2012-01-01

In September 2010, 6 species of shrews (genus: Sorex) were collected at a single locality on the Seward Peninsula of Alaska. Such high sympatric diversity within a single mammalian genus is seldom realized. This phenomenon at high latitudes highlights complex Arctic community dynamics that reflect significant turnover through time as a consequence of environmental change. Each of these shrew species occupies a broad geographic distribution collectively spanning the entire Holarctic, although the study site lies within Eastern Beringia, near the periphery of all individual ranges. A review of published genetic evidence reflects a depauperate shrew community within ice-free Beringia through the last glaciation, and recent assembly of current diversity during the Holocene.

Dynamic characteristics of organic bulk-heterojunction solar cells

NASA Astrophysics Data System (ADS)

Babenko, S. D.; Balakai, A. A.; Moskvin, Yu. L.; Simbirtseva, G. V.; Troshin, P. A.

2010-12-01

Transient characteristics of organic bulk-heterojunction solar cells have been studied using pulsed laser probing. An analysis of the photoresponse waveforms of a typical solar cell measured by varying load resistance within broad range at different values of the bias voltage provided detailed information on the photocell parameters that characterize electron-transport properties of active layers. It is established that the charge carrier mobility is sufficient to ensure high values of the fill factor (˜0.6) in the obtained photocells. On approaching the no-load voltage, the differential capacitance of the photocell exhibits a sixfold increase as compared to the geometric capacitance. A possible mechanism of recombination losses in the active medium is proposed.

Engineering Approaches to Illuminating Brain Structure and Dynamics

PubMed Central

Deisseroth, Karl; Schnitzer, Mark J.

2017-01-01

Historical milestones in neuroscience have come in diverse forms, ranging from the resolution of specific biological mysteries via creative experimentation to broad technological advances allowing neuroscientists to ask new kinds of questions. The continuous development of tools is driven with a special necessity by the complexity, fragility, and inaccessibility of intact nervous systems, such that inventive technique development and application drawing upon engineering and the applied sciences has long been essential to neuroscience. Here we highlight recent technological directions in neuroscience spurred by progress in optical, electrical, mechanical, chemical, and biological engineering. These research areas are poised for rapid growth and will likely be central to the practice of neuroscience well into the future. PMID:24183010

Describing the silent human virome with an emphasis on giant viruses.

PubMed

Popgeorgiev, Nikolay; Temmam, Sarah; Raoult, Didier; Desnues, Christelle

2013-01-01

Viruses are the most abundant obligate intracellular entities in our body. Until recently, they were only considered to be pathogens that caused a broad array of pathologies, ranging from mild disease to deaths in the most severe cases. However, recent advances in unbiased mass sequencing techniques as well as increasing epidemiological evidence have indicated that the human body is home to diverse viral species under non-pathological conditions. Despite these studies, the description of the presumably healthy viral flora, i.e. the normal human virome, is still in its infancy regarding viral composition and dynamics. This review summarizes our current knowledge of the human virome under non-pathological conditions.

The Solar Wind Ion Analyzer for MAVEN

NASA Astrophysics Data System (ADS)

Halekas, J. S.; Taylor, E. R.; Dalton, G.; Johnson, G.; Curtis, D. W.; McFadden, J. P.; Mitchell, D. L.; Lin, R. P.; Jakosky, B. M.

2015-12-01

The Solar Wind Ion Analyzer (SWIA) on the MAVEN mission will measure the solar wind ion flows around Mars, both in the upstream solar wind and in the magneto-sheath and tail regions inside the bow shock. The solar wind flux provides one of the key energy inputs that can drive atmospheric escape from the Martian system, as well as in part controlling the structure of the magnetosphere through which non-thermal ion escape must take place. SWIA measurements contribute to the top level MAVEN goals of characterizing the upper atmosphere and the processes that operate there, and parameterizing the escape of atmospheric gases to extrapolate the total loss to space throughout Mars' history. To accomplish these goals, SWIA utilizes a toroidal energy analyzer with electrostatic deflectors to provide a broad 360∘×90∘ field of view on a 3-axis spacecraft, with a mechanical attenuator to enable a very high dynamic range. SWIA provides high cadence measurements of ion velocity distributions with high energy resolution (14.5 %) and angular resolution (3.75∘×4.5∘ in the sunward direction, 22.5∘×22.5∘ elsewhere), and a broad energy range of 5 eV to 25 keV. Onboard computation of bulk moments and energy spectra enable measurements of the basic properties of the solar wind at 0.25 Hz.

Uncovering a new Uranus ring-moon connection in 25 years of occultation data

NASA Astrophysics Data System (ADS)

Chancia, R. O.; Hedman, M. M.; French, R. G.

2017-12-01

The Uranus ring-moon system consists of 10 narrow and dense main rings, 3 broad diffuse and dusty rings, and 13 small inner moons. Nine of these moons, dubbed the `Portia group', orbit within a radial range of less than 20,000 km, making them the most tightly packed system of moons in our solar system. For the first time, we have constrained the mass of one of the inner moons by measuring its gravitational influence on the η ring. The η ring is one of the narrow rings of Uranus, consisting of a dense core that is 1-2 km wide and a diffuse outer sheet spanning about 40 km. Its dense core lies just exterior to the 3:2 Inner Lindblad Resonance of the small moon Cressida. We fit the η ring radius residuals and longitudes from a complete set of both ground-based and Voyager stellar and radio occultations of the Uranian rings spanning 1977-2002. We find variations in the radial position of the η ring that are likely generated by this resonance, and take the form of a 3-lobed structure rotating at an angular rate equal to the mean motion of the moon Cressida. The amplitude of these radial oscillations is 0.667 ± 0.113 km, which is consistent with the expected shape due to the perturbations of Cressida. The magnitude of these variations provides the first measurement of the mass and density of the moon Cressida or, indeed, any of Uranus' small inner moons. The system has previously been simulated over a wide range of presumed masses and is found to be dynamically unstable, with the next collision most likely occurring in less than a few million years. Two of the broad dusty rings orbit in range of the moons and may be evidence of collisions in the recent past. A better grasp of inner Uranian satellite masses will provide another clue to the composition, dynamical stability, and history of this tightly packed system of moons.

A Plasmonic Mass Spectrometry Approach for Detection of Small Nutrients and Toxins

NASA Astrophysics Data System (ADS)

Wu, Shu; Qian, Linxi; Huang, Lin; Sun, Xuming; Su, Haiyang; Gurav, Deepanjali D.; Jiang, Mawei; Cai, Wei; Qian, Kun

2018-07-01

Nutriology relies on advanced analytical tools to study the molecular compositions of food and provide key information on sample quality/safety. Small nutrients detection is challenging due to the high diversity and broad dynamic range of molecules in food samples, and a further issue is to track low abundance toxins. Herein, we developed a novel plasmonic matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) approach to detect small nutrients and toxins in complex biological emulsion samples. Silver nanoshells (SiO2@Ag) with optimized structures were used as matrices and achieved direct analysis of 6 nL of human breast milk without any enrichment or separation. We performed identification and quantitation of small nutrients and toxins with limit-of-detection down to 0.4 pmol (for melamine) and reaction time shortened to minutes, which is superior to the conventional biochemical method currently in use. The developed approach contributes to the near-future application of MALDI MS in a broad field and personalized design of plasmonic materials for real-case bio-analysis.[Figure not available: see fulltext.

Centromere Transcription: Means and Motive.

PubMed

Duda, Zachary; Trusiak, Sarah; O'Neill, Rachel

2017-01-01

The chromosome biology field at large has benefited from studies of the cell cycle components, protein cascades and genomic landscape that are required for centromere identity, assembly and stable transgenerational inheritance. Research over the past 20 years has challenged the classical descriptions of a centromere as a stable, unmutable, and transcriptionally silent chromosome component. Instead, based on studies from a broad range of eukaryotic species, including yeast, fungi, plants, and animals, the centromere has been redefined as one of the more dynamic areas of the eukaryotic genome, requiring coordination of protein complex assembly, chromatin assembly, and transcriptional activity in a cell cycle specific manner. What has emerged from more recent studies is the realization that the transcription of specific types of nucleic acids is a key process in defining centromere integrity and function. To illustrate the transcriptional landscape of centromeres across eukaryotes, we focus this review on how transcripts interact with centromere proteins, when in the cell cycle centromeric transcription occurs, and what types of sequences are being transcribed. Utilizing data from broadly different organisms, a picture emerges that places centromeric transcription as an integral component of centromere function.

Machine Learning Biogeographic Processes from Biotic Patterns: A New Trait-Dependent Dispersal and Diversification Model with Model Choice By Simulation-Trained Discriminant Analysis.

PubMed

Sukumaran, Jeet; Economo, Evan P; Lacey Knowles, L

2016-05-01

Current statistical biogeographical analysis methods are limited in the ways ecology can be related to the processes of diversification and geographical range evolution, requiring conflation of geography and ecology, and/or assuming ecologies that are uniform across all lineages and invariant in time. This precludes the possibility of studying a broad class of macroevolutionary biogeographical theories that relate geographical and species histories through lineage-specific ecological and evolutionary dynamics, such as taxon cycle theory. Here we present a new model that generates phylogenies under a complex of superpositioned geographical range evolution, trait evolution, and diversification processes that can communicate with each other. We present a likelihood-free method of inference under our model using discriminant analysis of principal components of summary statistics calculated on phylogenies, with the discriminant functions trained on data generated by simulations under our model. This approach of model selection by classification of empirical data with respect to data generated under training models is shown to be efficient, robust, and performs well over a broad range of parameter space defined by the relative rates of dispersal, trait evolution, and diversification processes. We apply our method to a case study of the taxon cycle, that is testing for habitat and trophic level constraints in the dispersal regimes of the Wallacean avifaunal radiation. ©The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Broad-Spectrum Molecular Detection of Fungal Nucleic Acids by PCR-Based Amplification Techniques.

PubMed

Czurda, Stefan; Lion, Thomas

2017-01-01

Over the past decade, the incidence of life-threatening invasive fungal infections has dramatically increased. Infections caused by hitherto rare and emerging fungal pathogens are associated with significant morbidity and mortality among immunocompromised patients. These observations render the coverage of a broad range of clinically relevant fungal pathogens highly important. The so-called panfungal or, perhaps more correctly, broad-range nucleic acid amplification techniques do not only facilitate sensitive detection of all clinically relevant fungal species but are also rapid and can be applied to analyses of any patient specimens. They have therefore become valuable diagnostic tools for sensitive screening of patients at risk of invasive fungal infections. This chapter summarizes the currently available molecular technologies employed in testing of a wide range of fungal pathogens, and provides a detailed workflow for patient screening by broad-spectrum nucleic acid amplification techniques.

Influence of depth on sex-specific energy allocation patterns in a tropical reef fish

NASA Astrophysics Data System (ADS)

Hoey, J.; McCormick, M. I.; Hoey, A. S.

2007-09-01

The effect of depth on the distribution and sex-specific energy allocation patterns of a common coral reef fish, Chrysiptera rollandi (Pomacentridae), was investigated using depth-stratified collections over a broad depth range (5-39 m) and a translocation experiment. C. rollandi consistently selected rubble habitats at each depth, however abundance patterns did not reflect the availability of the preferred microhabitat suggesting a preference for depth as well as microhabitat. Reproductive investment (gonado-somatic index), energy stores (liver cell density and hepatocyte vacuolation), and overall body condition (hepato-somatic index and Fulton’s K) of female fish varied significantly among depths and among the three reefs sampled. Male conspecifics displayed no variation between depth or reef. Depth influenced growth dynamics, with faster initial growth rates and smaller mean asymptotic lengths with decreasing depth. In female fish, relative gonad weight and overall body condition (Fulton’s K and hepato-somatic index) were generally higher in shallower depths (≤10 m). Hepatic lipid storage was highest at the deepest sites sampled on each reef, whereas hepatic glycogen stores tended to decrease with depth. Depth was found to influence energy allocation dynamics in C. rollandi. While it is unclear what processes directly influenced the depth-related patterns in energy allocation, this study shows that individuals across a broad depth gradient are not all in the same physiological state and may contribute differentially to the population reproductive output.

Synchrony, waves and ripple in spatially coupled Kuramoto oscillators with Mexican hat connectivity.

PubMed

Heitmann, Stewart; Ermentrout, G Bard

2015-06-01

Spatiotemporal waves of synchronized activity are known to arise in oscillatory neural networks with lateral inhibitory coupling. How such patterns respond to dynamic changes in coupling strength is largely unexplored. The present study uses analysis and simulation to investigate the evolution of wave patterns when the strength of lateral inhibition is varied dynamically. Neural synchronization was modeled by a spatial ring of Kuramoto oscillators with Mexican hat lateral coupling. Broad bands of coexisting stable wave solutions were observed at all levels of inhibition. The stability of these waves was formally analyzed in both the infinite ring and the finite ring. The broad range of multi-stability predicted hysteresis in transitions between neighboring wave solutions when inhibition is slowly varied. Numerical simulation confirmed the predicted transitions when inhibition was ramped down from a high initial value. However, non-wave solutions emerged from the uniform solution when inhibition was ramped upward from zero. These solutions correspond to spatially periodic deviations of phase that we call ripple states. Numerical continuation showed that stable ripple states emerge from synchrony via a supercritical pitchfork bifurcation. The normal form of this bifurcation was derived analytically, and its predictions compared against the numerical results. Ripple states were also found to bifurcate from wave solutions, but these were locally unstable. Simulation also confirmed the existence of hysteresis and ripple states in two spatial dimensions. Our findings show that spatial synchronization patterns can remain structurally stable despite substantial changes in network connectivity.

Dynamic Evolution of Pathogenicity Revealed by Sequencing and Comparative Genomics of 19 Pseudomonas syringae Isolates

PubMed Central

Romanchuk, Artur; Chang, Jeff H.; Mukhtar, M. Shahid; Cherkis, Karen; Roach, Jeff; Grant, Sarah R.; Jones, Corbin D.; Dangl, Jeffery L.

2011-01-01

Closely related pathogens may differ dramatically in host range, but the molecular, genetic, and evolutionary basis for these differences remains unclear. In many Gram- negative bacteria, including the phytopathogen Pseudomonas syringae, type III effectors (TTEs) are essential for pathogenicity, instrumental in structuring host range, and exhibit wide diversity between strains. To capture the dynamic nature of virulence gene repertoires across P. syringae, we screened 11 diverse strains for novel TTE families and coupled this nearly saturating screen with the sequencing and assembly of 14 phylogenetically diverse isolates from a broad collection of diseased host plants. TTE repertoires vary dramatically in size and content across all P. syringae clades; surprisingly few TTEs are conserved and present in all strains. Those that are likely provide basal requirements for pathogenicity. We demonstrate that functional divergence within one conserved locus, hopM1, leads to dramatic differences in pathogenicity, and we demonstrate that phylogenetics-informed mutagenesis can be used to identify functionally critical residues of TTEs. The dynamism of the TTE repertoire is mirrored by diversity in pathways affecting the synthesis of secreted phytotoxins, highlighting the likely role of both types of virulence factors in determination of host range. We used these 14 draft genome sequences, plus five additional genome sequences previously reported, to identify the core genome for P. syringae and we compared this core to that of two closely related non-pathogenic pseudomonad species. These data revealed the recent acquisition of a 1 Mb megaplasmid by a sub-clade of cucumber pathogens. This megaplasmid encodes a type IV secretion system and a diverse set of unknown proteins, which dramatically increases both the genomic content of these strains and the pan-genome of the species. PMID:21799664

Microelectromechanical systems (MEMS) sensors based on lead zirconate titanate (PZT) films

NASA Astrophysics Data System (ADS)

Wang, Li-Peng

2001-12-01

In this thesis, modeling, fabrication and testing of microelectromechanical systems (MEMS) accelerometers based on piezoelectric lead zirconate titanate (PZT) films are investigated. Three different types of structures, cantilever beam, trampoline, and annular diaphragm, are studied. It demonstrates the high-performance, miniaturate, mass-production-compatible, and potentially circuitry-integratable piezoelectric-type PZT MEMS devices. Theoretical models of the cantilever-beam and trampoline accelerometers are derived via structural dynamics and the constitutive equations of piezoelectricity. The time-dependent transverse vibration equations, mode shapes, resonant frequencies, and sensitivities of the accelerometers are calculated through the models. Optimization of the silicon and PZT thickness is achieved with considering the effects of the structural dynamics, the material properties, and manufacturability for different accelerometer specifications. This work is the first demonstration of the fabrication of bulk-micromachined accelerometers combining a deep-trench reactive ion etching (DRIE) release strategy and thick piezoelectric PZT films deposited using a sol-gel method. Processing challenges which are overcome included materials compatibility, metallization, processing of thick layers, double-side processing, deep-trench silicon etching, post-etch cleaning and process integration. In addition, the processed PZT films are characterized by dielectric, ferroelectric (polarization electric-field hysteresis), and piezoelectric measurements and no adverse effects are found. Dynamic frequency response and impedance resonance measurements are performed to ascertain the performance of the MEMS accelerometers. The results show high sensitivities and broad frequency ranges of the piezoelectric-type PZT MEMS accelerometers; the sensitivities range from 0.1 to 7.6 pC/g for resonant frequencies ranging from 44.3 kHz to 3.7 kHz. The sensitivities were compared to theoretical values and a reasonable agreement (˜36% difference) is obtained.

Device and method for generating a beam of acoustic energy from a borehole, and applications thereof

DOEpatents

Vu, Cung Khac; Sinha, Dipen N; Pantea, Cristian; Nihei, Kurt T; Schmitt, Denis P; Skelt, Christopher

2013-10-01

In some aspects of the invention, a method of generating a beam of acoustic energy in a borehole is disclosed. The method includes generating a first broad-band acoustic pulse at a first broad-band frequency range having a first central frequency and a first bandwidth spread; generating a second broad-band acoustic pulse at a second broad-band frequency range different than the first frequency range having a second central frequency and a second bandwidth spread, wherein the first acoustic pulse and second acoustic pulse are generated by at least one transducer arranged on a tool located within the borehole; and transmitting the first and the second broad-band acoustic pulses into an acoustically non-linear medium, wherein the composition of the non-linear medium produces a collimated pulse by a non-linear mixing of the first and second acoustic pulses, wherein the collimated pulse has a frequency equal to the difference in frequencies between the first central frequency and the second central frequency and a bandwidth spread equal to the sum of the first bandwidth spread and the second bandwidth spread.

Enhanced Sensitivity to Rapid Input Fluctuations by Nonlinear Threshold Dynamics in Neocortical Pyramidal Neurons.

PubMed

Mensi, Skander; Hagens, Olivier; Gerstner, Wulfram; Pozzorini, Christian

2016-02-01

The way in which single neurons transform input into output spike trains has fundamental consequences for network coding. Theories and modeling studies based on standard Integrate-and-Fire models implicitly assume that, in response to increasingly strong inputs, neurons modify their coding strategy by progressively reducing their selective sensitivity to rapid input fluctuations. Combining mathematical modeling with in vitro experiments, we demonstrate that, in L5 pyramidal neurons, the firing threshold dynamics adaptively adjust the effective timescale of somatic integration in order to preserve sensitivity to rapid signals over a broad range of input statistics. For that, a new Generalized Integrate-and-Fire model featuring nonlinear firing threshold dynamics and conductance-based adaptation is introduced that outperforms state-of-the-art neuron models in predicting the spiking activity of neurons responding to a variety of in vivo-like fluctuating currents. Our model allows for efficient parameter extraction and can be analytically mapped to a Generalized Linear Model in which both the input filter--describing somatic integration--and the spike-history filter--accounting for spike-frequency adaptation--dynamically adapt to the input statistics, as experimentally observed. Overall, our results provide new insights on the computational role of different biophysical processes known to underlie adaptive coding in single neurons and support previous theoretical findings indicating that the nonlinear dynamics of the firing threshold due to Na+-channel inactivation regulate the sensitivity to rapid input fluctuations.

Transport and collision dynamics in periodic asymmetric obstacle arrays: Rational design of microfluidic rare-cell immunocapture devices

NASA Astrophysics Data System (ADS)

Gleghorn, Jason P.; Smith, James P.; Kirby, Brian J.

2013-09-01

Microfluidic obstacle arrays have been used in numerous applications, and their ability to sort particles or capture rare cells from complex samples has broad and impactful applications in biology and medicine. We have investigated the transport and collision dynamics of particles in periodic obstacle arrays to guide the design of convective, rather than diffusive, transport-based immunocapture microdevices. Ballistic and full computational fluid dynamics simulations are used to understand the collision modes that evolve in cylindrical obstacle arrays with various geometries. We identify previously unrecognized collision mode structures and differential size-based collision frequencies that emerge from these arrays. Previous descriptions of transverse displacements that assume unidirectional flow in these obstacle arrays cannot capture mode transitions properly as these descriptions fail to capture the dependence of the mode transitions on column spacing and the attendant change in the flow field. Using these analytical and computational simulations, we elucidate design parameters that induce high collision rates for all particles larger than a threshold size or selectively increase collision frequencies for a narrow range of particle sizes within a polydisperse population. Furthermore, we investigate how the particle Péclet number affects collision dynamics and mode transitions and demonstrate that experimental observations from various obstacle array geometries are well described by our computational model.

A general transfer-function approach to noise filtering in open-loop quantum control

NASA Astrophysics Data System (ADS)

Viola, Lorenza

2015-03-01

Hamiltonian engineering via unitary open-loop quantum control provides a versatile and experimentally validated framework for manipulating a broad class of non-Markovian open quantum systems of interest, with applications ranging from dynamical decoupling and dynamically corrected quantum gates, to noise spectroscopy and quantum simulation. In this context, transfer-function techniques directly motivated by control engineering have proved invaluable for obtaining a transparent picture of the controlled dynamics in the frequency domain and for quantitatively analyzing performance. In this talk, I will show how to identify a computationally tractable set of ``fundamental filter functions,'' out of which arbitrary filter functions may be assembled up to arbitrary high order in principle. Besides avoiding the infinite recursive hierarchy of filter functions that arises in general control scenarios, this fundamental set suffices to characterize the error suppression capabilities of the control protocol in both the time and frequency domain. I will show, in particular, how the resulting notion of ``filtering order'' reveals conceptually distinct, albeit complementary, features of the controlled dynamics as compared to the ``cancellation order,'' traditionally defined in the Magnus sense. Implications for current quantum control experiments will be discussed. Work supported by the U.S. Army Research Office under Contract No. W911NF-14-1-0682.

Linearly polarized GHz magnetization dynamics of spin helix modes in the ferrimagnetic insulator Cu2OSeO3.

PubMed

Stasinopoulos, I; Weichselbaumer, S; Bauer, A; Waizner, J; Berger, H; Garst, M; Pfleiderer, C; Grundler, D

2017-08-01

Linear dichroism - the polarization dependent absorption of electromagnetic waves- is routinely exploited in applications as diverse as structure determination of DNA or polarization filters in optical technologies. Here filamentary absorbers with a large length-to-width ratio are a prerequisite. For magnetization dynamics in the few GHz frequency regime strictly linear dichroism was not observed for more than eight decades. Here, we show that the bulk chiral magnet Cu 2 OSeO 3 exhibits linearly polarized magnetization dynamics at an unexpectedly small frequency of about 2 GHz at zero magnetic field. Unlike optical filters that are assembled from filamentary absorbers, the magnet is shown to provide linear polarization as a bulk material for an extremely wide range of length-to-width ratios. In addition, the polarization plane of a given mode can be switched by 90° via a small variation in width. Our findings shed a new light on magnetization dynamics in that ferrimagnetic ordering combined with antisymmetric exchange interaction offers strictly linear polarization and cross-polarized modes for a broad spectrum of sample shapes at zero field. The discovery allows for novel design rules and optimization of microwave-to-magnon transduction in emerging microwave technologies.

Effects of non-condensable gas on the dynamic oscillations of cavitation bubbles

NASA Astrophysics Data System (ADS)

Zhang, Yuning

2016-11-01

Cavitation is an essential topic of multiphase flow with a broad range of applications. Generally, there exists non-condensable gas in the liquid and a complex vapor/gas mixture bubble will be formed. A rigorous prediction of the dynamic behavior of the aforementioned mixture bubble is essential for the development of a complete cavitation model. In the present paper, effects of non-condensable gas on the dynamic oscillations of the vapor/gas mixture bubble are numerically investigated in great detail. For the completeness, a large parameter zone (e.g. bubble radius, frequency and ratio between gas and vapor) is investigated with many demonstrating examples. The mechanisms of mass diffusion are categorized into different groups with their characteristics and dominated regions given. Influences of non-condensable gas on the wave propagation (e.g. wave speed and attenuation) in the bubbly liquids are also briefly discussed. Specifically, the minimum wave speed is quantitatively predicted in order to close the pressure-density coupling relationship usually employed for the cavitation modelling. Finally, the application of the present finding on the development of cavitation model is demonstrated with a brief discussion of its influence on the cavitation dynamics. This work was financially supported by the National Natural Science Foundation of China (Project No.: 51506051).

Peptide kinetics from picoseconds to microseconds using boxed molecular dynamics: Power law rate coefficients in cyclisation reactions

NASA Astrophysics Data System (ADS)

Shalashilin, Dmitrii V.; Beddard, Godfrey S.; Paci, Emanuele; Glowacki, David R.

2012-10-01

Molecular dynamics (MD) methods are increasingly widespread, but simulation of rare events in complex molecular systems remains a challenge. We recently introduced the boxed molecular dynamics (BXD) method, which accelerates rare events, and simultaneously provides both kinetic and thermodynamic information. We illustrate how the BXD method may be used to obtain high-resolution kinetic data from explicit MD simulations, spanning picoseconds to microseconds. The method is applied to investigate the loop formation dynamics and kinetics of cyclisation for a range of polypeptides, and recovers a power law dependence of the instantaneous rate coefficient over six orders of magnitude in time, in good agreement with experimental observations. Analysis of our BXD results shows that this power law behaviour arises when there is a broad and nearly uniform spectrum of reaction rate coefficients. For the systems investigated in this work, where the free energy surfaces have relatively small barriers, the kinetics is very sensitive to the initial conditions: strongly non-equilibrium conditions give rise to power law kinetics, while equilibrium initial conditions result in a rate coefficient with only a weak dependence on time. These results suggest that BXD may offer us a powerful and general algorithm for describing kinetics and thermodynamics in chemical and biochemical systems.

Ultrafast rotation in an amphidynamic crystalline metal organic framework

DOE PAGES

Vogelsberg, Cortnie S.; Uribe-Romo, Fernando J.; Lipton, Andrew S.; ...

2017-12-26

Amphidynamic crystals are an emergent class of condensed phase matter designed with a combination of lattice-forming elements linked to components that display engineered dynamics in the solid state. Here, we address the design of a crystalline array of molecular rotors with inertial diffusional rotation at the nanoscale, characterized by the absence of steric or electronic barriers. We solved this challenge with 1,4-bicyclo[2.2.2]octane dicarboxylic acid (BODCA)-MOF, a metal-organic framework (MOF) built with a high-symmetry bicyclo[2.2.2]octane dicarboxylate linker in a Zn 4O cubic lattice. Using spin-lattice relaxation 1H solid-state NMR at 29.49 and 13.87 MHz in the temperature range of 2.3–80 K,more » we showed that internal rotation occurs in a potential with energy barriers of 0.185 kcal mol -1. These results were confirmed with 2H solid-state NMR line-shape analysis and spin-lattice relaxation at 76.78 MHz obtained between 6 and 298 K, which, combined with molecular dynamics simulations, indicate that inertial diffusional rotation is characterized by a broad range of angular displacements with no residence time at any given site. Furthermore, the ambient temperature rotation of the bicyclo[2.2.2]octane (BCO) group in BODCA-MOF constitutes an example where engineered rotational dynamics in the solid state are as fast as they would be in a high-density gas or in a low-density liquid phase.« less

Dynamics of reactive microbial hotspots in concentration gradients

NASA Astrophysics Data System (ADS)

Hubert, Antoine; Farasin, Julien; Tabuteau, Hervé; Méheust, Yves; Le Borgne, Tanguy

2017-04-01

In subsurface environments, bacteria play a major role in controlling the kinetics of a broad range of biogeochemical reactions. In such environments, nutrients fluxes and solute concentrations needed for bacteria metabolism may be highly variable in space and intermittent in time. This can lead to the formation of reactive hotspots where and when conditions are favorable to particular microorganisms, hence inducing biogeochemical reaction kinetics that differ significantly from those measured in homogeneous model environments. To investigate the impact of chemical gradients on the spatial structure and temporal dynamics of subsurface microorganism populations, we develop microfluidic cells allowing for a precise control of flow and chemical gradient conditions, as well as a quantitative monitoring of the bacteria's spatial distribution and biofilm development. Using the non-motile Escherichia coli JW1908-1 strain and Gallionella as model organisms, we investigate the behavior and development of bacteria over a range of single and double concentration gradients in the concentrations of nutrients, electron donors and electron acceptors. To quantify bacterial activity we use Fluorescein Diacetate (FDA) hydrolysis by bacterial enzymes which transforms FDA into Fluorescein, whose local concentration is measured optically. We thus measure bacterial activity locally from the time derivative of the measured fluorescence. This approach allows time-resolved monitoring of the location and intensity of reactive hotspots in micromodels as a function of the flow and chemical gradient conditions. We discuss consequences for the formation and temporal dynamics of biofilms in the subsurface.

Ultrafast rotation in an amphidynamic crystalline metal organic framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vogelsberg, Cortnie S.; Uribe-Romo, Fernando J.; Lipton, Andrew S.

Amphidynamic crystals are an emergent class of condensed phase matter designed with a combination of lattice-forming elements linked to components that display engineered dynamics in the solid state. Here, we address the design of a crystalline array of molecular rotors with inertial diffusional rotation at the nanoscale, characterized by the absence of steric or electronic barriers. We solved this challenge with 1,4-bicyclo[2.2.2]octane dicarboxylic acid (BODCA)-MOF, a metal-organic framework (MOF) built with a high-symmetry bicyclo[2.2.2]octane dicarboxylate linker in a Zn 4O cubic lattice. Using spin-lattice relaxation 1H solid-state NMR at 29.49 and 13.87 MHz in the temperature range of 2.3–80 K,more » we showed that internal rotation occurs in a potential with energy barriers of 0.185 kcal mol -1. These results were confirmed with 2H solid-state NMR line-shape analysis and spin-lattice relaxation at 76.78 MHz obtained between 6 and 298 K, which, combined with molecular dynamics simulations, indicate that inertial diffusional rotation is characterized by a broad range of angular displacements with no residence time at any given site. Furthermore, the ambient temperature rotation of the bicyclo[2.2.2]octane (BCO) group in BODCA-MOF constitutes an example where engineered rotational dynamics in the solid state are as fast as they would be in a high-density gas or in a low-density liquid phase.« less

Vertebral Osteomyelitis Caused by Helicobacter cinaedi Identified Using Broad-range Polymerase Chain Reaction with Sequencing of the Biopsied Specimen.

PubMed

Hase, Ryota; Hirooka, Takuya; Itabashi, Takashi; Endo, Yasunobu; Otsuka, Yoshihito

2018-05-15

A 65-year-old man presented with gradually exacerbating low back pain. Magnetic resonance imaging revealed vertebral osteomyelitis in the Th11-L2 vertebral bodies and discs. The patient showed negative findings on conventional cultures. Direct broad-range polymerase chain reaction (PCR) with sequencing of the biopsied specimen had the highest similarity to the 16S rRNA gene of Helicobacter cinaedi. This case suggests that direct broad-range PCR with sequencing should be considered when conventional cultures cannot identify the causative organism of vertebral osteomyelitis, and that this method may be particularly useful when the pathogen is a fastidious organism, such as H. cinaedi.

Binaural pitch fusion: Comparison of normal-hearing and hearing-impaired listenersa)

PubMed Central

Reiss, Lina A. J.; Shayman, Corey S.; Walker, Emily P.; Bennett, Keri O.; Fowler, Jennifer R.; Hartling, Curtis L.; Glickman, Bess; Lasarev, Michael R.; Oh, Yonghee

2017-01-01

Binaural pitch fusion is the fusion of dichotically presented tones that evoke different pitches between the ears. In normal-hearing (NH) listeners, the frequency range over which binaural pitch fusion occurs is usually <0.2 octaves. Recently, broad fusion ranges of 1–4 octaves were demonstrated in bimodal cochlear implant users. In the current study, it was hypothesized that hearing aid (HA) users would also exhibit broad fusion. Fusion ranges were measured in both NH and hearing-impaired (HI) listeners with hearing losses ranging from mild-moderate to severe-profound, and relationships of fusion range with demographic factors and with diplacusis were examined. Fusion ranges of NH and HI listeners averaged 0.17 ± 0.13 octaves and 1.7 ± 1.5 octaves, respectively. In HI listeners, fusion ranges were positively correlated with a principal component measure of the covarying factors of young age, early age of hearing loss onset, and long durations of hearing loss and HA use, but not with hearing threshold, amplification level, or diplacusis. In NH listeners, no correlations were observed with age, hearing threshold, or diplacusis. The association of broad fusion with early onset, long duration of hearing loss suggests a possible role of long-term experience with hearing loss and amplification in the development of broad fusion. PMID:28372056

The origin and dynamic evolution of chemical information transfer

PubMed Central

Steiger, Sandra; Schmitt, Thomas; Schaefer, H. Martin

2011-01-01

Although chemical communication is the most widespread form of communication, its evolution and diversity are not well understood. By integrating studies of a wide range of terrestrial plants and animals, we show that many chemicals are emitted, which can unintentionally provide information (cues) and, therefore, act as direct precursors for the evolution of intentional communication (signals). Depending on the content, design and the original function of the cue, there are predictable ways that selection can enhance the communicative function of chemicals. We review recent progress on how efficacy-based selection by receivers leads to distinct evolutionary trajectories of chemical communication. Because the original function of a cue may channel but also constrain the evolution of functional communication, we show that a broad perspective on multiple selective pressures acting upon chemicals provides important insights into the origin and dynamic evolution of chemical information transfer. Finally, we argue that integrating chemical ecology into communication theory may significantly enhance our understanding of the evolution, the design and the content of signals in general. PMID:21177681

Dynamic implicit 3D adaptive mesh refinement for non-equilibrium radiation diffusion

NASA Astrophysics Data System (ADS)

Philip, B.; Wang, Z.; Berrill, M. A.; Birke, M.; Pernice, M.

2014-04-01

The time dependent non-equilibrium radiation diffusion equations are important for solving the transport of energy through radiation in optically thick regimes and find applications in several fields including astrophysics and inertial confinement fusion. The associated initial boundary value problems that are encountered often exhibit a wide range of scales in space and time and are extremely challenging to solve. To efficiently and accurately simulate these systems we describe our research on combining techniques that will also find use more broadly for long term time integration of nonlinear multi-physics systems: implicit time integration for efficient long term time integration of stiff multi-physics systems, local control theory based step size control to minimize the required global number of time steps while controlling accuracy, dynamic 3D adaptive mesh refinement (AMR) to minimize memory and computational costs, Jacobian Free Newton-Krylov methods on AMR grids for efficient nonlinear solution, and optimal multilevel preconditioner components that provide level independent solver convergence.

A new course and textbook on Physical Models of Living Systems, for science and engineering undergraduates

NASA Astrophysics Data System (ADS)

Nelson, Philip

2015-03-01

I'll describe an intermediate-level course on ``Physical Models of Living Systems.'' The only prerequisite is first-year university physics and calculus. The course is a response to rapidly growing interest among undergraduates in a broad range of science and engineering majors. Students acquire several research skills that are often not addressed in traditional courses: Basic modeling skills Probabilistic modeling skills Data analysis methods Computer programming using a general-purpose platform like MATLAB or Python Dynamical systems, particularly feedback control. These basic skills, which are relevant to nearly any field of science or engineering, are presented in the context of case studies from living systems, including: Virus dynamics Bacterial genetics and evolution of drug resistance Statistical inference Superresolution microscopy Synthetic biology Naturally evolved cellular circuits. Work supported by NSF Grants EF-0928048 and DMR-0832802.

Evidence for ephemeral middle Eocene to early Oligocene Greenland glacial ice and pan-Arctic sea ice.

PubMed

Tripati, Aradhna; Darby, Dennis

2018-03-12

Earth's modern climate is defined by the presence of ice at both poles, but that ice is now disappearing. Therefore understanding the origin and causes of polar ice stability is more critical than ever. Here we provide novel geochemical data that constrain past dynamics of glacial ice on Greenland and Arctic sea ice. Based on accurate source determinations of individual ice-rafted Fe-oxide grains, we find evidence for episodic glaciation of distinct source regions on Greenland as far-ranging as ~68°N and ~80°N synchronous with ice-rafting from circum-Arctic sources, beginning in the middle Eocene. Glacial intervals broadly coincide with reduced CO 2 , with a potential threshold for glacial ice stability near ~500 p.p.m.v. The middle Eocene represents the Cenozoic onset of a dynamic cryosphere, with ice in both hemispheres during transient glacials and substantial regional climate heterogeneity. A more stable cryosphere developed at the Eocene-Oligocene transition, and is now threatened by anthropogenic emissions.

High bulk modulus of ionic liquid and effects on performance of hydraulic system.

PubMed

Kambic, Milan; Kalb, Roland; Tasner, Tadej; Lovrec, Darko

2014-01-01

Over recent years ionic liquids have gained in importance, causing a growing number of scientists and engineers to investigate possible applications for these liquids because of their unique physical and chemical properties. Their outstanding advantages such as nonflammable liquid within a broad liquid range, high thermal, mechanical, and chemical stabilities, low solubility for gases, attractive tribological properties (lubrication), and very low compressibility, and so forth, make them more interesting for applications in mechanical engineering, offering great potential for new innovative processes, and also as a novel hydraulic fluid. This paper focuses on the outstanding compressibility properties of ionic liquid EMIM-EtSO4, a very important physical chemically property when IL is used as a hydraulic fluid. This very low compressibility (respectively, very high Bulk modulus), compared to the classical hydraulic mineral oils or the non-flammable HFDU type of hydraulic fluids, opens up new possibilities regarding its usage within hydraulic systems with increased dynamics, respectively, systems' dynamic responses.

Exo-Milankovitch Cycles. I. Orbits and Rotation States

NASA Astrophysics Data System (ADS)

Deitrick, Russell; Barnes, Rory; Quinn, Thomas R.; Armstrong, John; Charnay, Benjamin; Wilhelm, Caitlyn

2018-02-01

The obliquity of the Earth, which controls our seasons, varies by only ∼2.°5 over ∼40,000 years, and its eccentricity varies by only ∼0.05 over 100,000 years. Nonetheless, these small variations influence Earth’s ice ages. For exoplanets, however, variations can be significantly larger. Previous studies of the habitability of moonless Earth-like exoplanets have found that high obliquities, high eccentricities, and dynamical variations can extend the outer edge of the habitable zone by preventing runaway glaciation (snowball states). We expand upon these studies by exploring the orbital dynamics with a semianalytic model that allows us to map broad regions of parameter space. We find that, in general, the largest drivers of obliquity variations are secular spin–orbit resonances. We show how the obliquity varies in several test cases, including Kepler-62 f, across a wide range of orbital and spin parameters. These obliquity variations, alongside orbital variations, will have a dramatic impact on the climates of such planets.

New Frontiers in Optical Science: Terahertz Spectroscopy ot Two Dimensional Systems

NASA Astrophysics Data System (ADS)

Lee, Yun-Shik

2011-10-01

Terahertz (THz) radiation is electromagnetic radiation whose frequency lies between the microwave and infrared regions of the spectrum. Naturally occurring THz radiation fills up the space of everyday life providing warmth, yet this part of the spectrum remains the least explored region mainly due to the technical difficulties. The technological gap, however, has been rapidly diminishing for the last two decades. The new and exciting frontier of the THz science and technology has encroached on many different disciplines producing a broad range of applications such as medical imaging, sensing of biochemical agents, and ultra-high speed communication. Furthermore, the unique and advanced techniques of the THz spectroscopy have been proved to be a powerful tool to investigate the material properties inaccessible until recently. For example, THz waves strongly interact with electrons and holes in two dimensional systems, in which their dynamics are governed mainly by many-body Coulomb interactions. I will present our experimental studies demonstrating remarkable quantum effects in semiconductor nanostructures and exotic charge carrier dynamics in graphene.

Towards Intelligent Control for Next Generation Aircraft

NASA Technical Reports Server (NTRS)

Acosta, Diana Michelle; KrishnaKumar, Kalmanje Srinvas; Frost, Susan Alane

2008-01-01

NASA Aeronautics Subsonic Fixed Wing Project is focused on mitigating the environmental and operation impacts expected as aviation operations triple by 2025. The approach is to extend technological capabilities and explore novel civil transport configurations that reduce noise, emissions, fuel consumption and field length. Two Next Generation (NextGen) aircraft have been identified to meet the Subsonic Fixed Wing Project goals - these are the Hybrid Wing-Body (HWB) and Cruise Efficient Short Take-Off and Landing (CESTOL) aircraft. The technologies and concepts developed for these aircraft complicate the vehicle s design and operation. In this paper, flight control challenges for NextGen aircraft are described. The objective of this paper is to examine the potential of state-of-the-art control architectures and algorithms to meet the challenges and needed performance metrics for NextGen flight control. A broad range of conventional and intelligent control approaches are considered, including dynamic inversion control, integrated flight-propulsion control, control allocation, adaptive dynamic inversion control, data-based predictive control and reinforcement learning control.

Imaging electric field dynamics with graphene optoelectronics

DOE PAGES

Horng, Jason; Balch, Halleh B.; McGuire, Allister F.; ...

2016-12-16

The use of electric fields for signalling and control in liquids is widespread, spanning bioelectric activity in cells to electrical manipulation of microstructures in lab-on-a-chip devices. However, an appropriate tool to resolve the spatio-temporal distribution of electric fields over a large dynamic range has yet to be developed. Here we present a label-free method to image local electric fields in real time and under ambient conditions. Our technique combines the unique gate-variable optical transitions of graphene with a critically coupled planar waveguide platform that enables highly sensitive detection of local electric fields with a voltage sensitivity of a few microvolts,more » a spatial resolution of tens of micrometres and a frequency response over tens of kilohertz. Our imaging platform enables parallel detection of electric fields over a large field of view and can be tailored to broad applications spanning lab-on-a-chip device engineering to analysis of bioelectric phenomena.« less

Microtubule assembly governed by tubulin allosteric gain in flexibility and lattice induced fit

PubMed Central

2018-01-01

Microtubules (MTs) are key components of the cytoskeleton and play a central role in cell division and development. MT assembly is known to be associated with a structural change in αβ-tubulin dimers from kinked to straight conformations. How GTP binding renders individual dimers polymerization-competent, however, is still unclear. Here, we have characterized the conformational dynamics and energetics of unassembled tubulin using atomistic molecular dynamics and free energy calculations. Contrary to existing allosteric and lattice models, we find that GTP-tubulin favors a broad range of almost isoenergetic curvatures, whereas GDP-tubulin has a much lower bending flexibility. Moreover, irrespective of the bound nucleotide and curvature, two conformational states exist differing in location of the anchor point connecting the monomers that affects tubulin bending, with one state being strongly favored in solution. Our findings suggest a new combined model in which MTs incorporate and stabilize flexible GTP-dimers with a specific anchor point state. PMID:29652248

Numerical and Experimental Investigations of Humping Phenomena in Laser Micro Welding

NASA Astrophysics Data System (ADS)

Otto, Andreas; Patschger, Andreas; Seiler, Michael

The Humping effect is a phenomenon which is observed approximately since 50 years in various welding procedures and is characterized by droplets due to a pile-up of the melt pool. It occurs within a broad range of process parameters. Particularly during micro welding, humping effect is critical due to typically high feed rates. In the past, essentially two approaches (fluid-dynamic approach of streaming melt within the molten pool and the Plateau-Rayleigh instability of a liquid jet) were discussed in order to explain the occurrence of the humping effect. But none of both can fully explain all observed effects. For this reason, experimental studies in micro welding of thin metal foils were performed in order to determine the influence of process parameters on the occurrence of humping effects. The experimental observations were compared with results from numerical multi-physical simulations (incorporating beam propagation, incoupling, heat transfer, fluid dynamics etc.) to provide a deeper understanding of the causes for hump formation.

Probing RNA Native Conformational Ensembles with Structural Constraints.

PubMed

Fonseca, Rasmus; van den Bedem, Henry; Bernauer, Julie

2016-05-01

Noncoding ribonucleic acids (RNA) play a critical role in a wide variety of cellular processes, ranging from regulating gene expression to post-translational modification and protein synthesis. Their activity is modulated by highly dynamic exchanges between three-dimensional conformational substates, which are difficult to characterize experimentally and computationally. Here, we present an innovative, entirely kinematic computational procedure to efficiently explore the native ensemble of RNA molecules. Our procedure projects degrees of freedom onto a subspace of conformation space defined by distance constraints in the tertiary structure. The dimensionality reduction enables efficient exploration of conformational space. We show that the conformational distributions obtained with our method broadly sample the conformational landscape observed in NMR experiments. Compared to normal mode analysis-based exploration, our procedure diffuses faster through the experimental ensemble while also accessing conformational substates to greater precision. Our results suggest that conformational sampling with a highly reduced but fully atomistic representation of noncoding RNA expresses key features of their dynamic nature.

Imaging electric field dynamics with graphene optoelectronics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Horng, Jason; Balch, Halleh B.; McGuire, Allister F.

The use of electric fields for signalling and control in liquids is widespread, spanning bioelectric activity in cells to electrical manipulation of microstructures in lab-on-a-chip devices. However, an appropriate tool to resolve the spatio-temporal distribution of electric fields over a large dynamic range has yet to be developed. Here we present a label-free method to image local electric fields in real time and under ambient conditions. Our technique combines the unique gate-variable optical transitions of graphene with a critically coupled planar waveguide platform that enables highly sensitive detection of local electric fields with a voltage sensitivity of a few microvolts,more » a spatial resolution of tens of micrometres and a frequency response over tens of kilohertz. Our imaging platform enables parallel detection of electric fields over a large field of view and can be tailored to broad applications spanning lab-on-a-chip device engineering to analysis of bioelectric phenomena.« less

Cooperativity in glassy dynamics investigated by higher-harmonic dielectric spectroscopy

NASA Astrophysics Data System (ADS)

Bauer, Thomas; Lunkenheimer, Peter; Loidl, Alois; Experimental Physics V Team

2014-03-01

In recent years, due to experimental advances initiated by hole burning experiments, nonlinear dielectric spectroscopy has gained increasing interest in the field of glass-forming matter. For example, refining the technique of high-field permittivity measurements, we found a surprising lack of nonlinearity in the so-called excess wing region, that could not be accessed by this method before. In the present contribution, we report new, detailed measurements of the third-order nonlinear dielectric susceptibility χ3 of four glass-forming liquids for a broad temperature range. We find a significant hump in χ3(ν) , from which we deduce the number of correlated molecules Ncorr. We detect a continuous increase of Ncorr on approaching the glass-transition temperature. Comparing these results with the temperature-dependent apparent energy barriers in these systems, our experiments finally prove the old notion that intermolecular correlations of glassy systems are responsible for the non-canonical temperature development of glassy dynamics. This work was supported by the Deutsche Forschungsgemeinschaft via Research Unit FOR1394.

Crossing Over from Attractive to Repulsive Interactions in a Tunneling Bosonic Josephson Junction.

PubMed

Spagnolli, G; Semeghini, G; Masi, L; Ferioli, G; Trenkwalder, A; Coop, S; Landini, M; Pezzè, L; Modugno, G; Inguscio, M; Smerzi, A; Fattori, M

2017-06-09

We explore the interplay between tunneling and interatomic interactions in the dynamics of a bosonic Josephson junction. We tune the scattering length of an atomic ^{39}K Bose-Einstein condensate confined in a double-well trap to investigate regimes inaccessible to other superconducting or superfluid systems. In the limit of small-amplitude oscillations, we study the transition from Rabi to plasma oscillations by crossing over from attractive to repulsive interatomic interactions. We observe a critical slowing down in the oscillation frequency by increasing the strength of an attractive interaction up to the point of a quantum phase transition. With sufficiently large initial oscillation amplitude and repulsive interactions, the system enters the macroscopic quantum self-trapping regime, where we observe coherent undamped oscillations with a self-sustained average imbalance of the relative well population. The exquisite agreement between theory and experiments enables the observation of a broad range of many body coherent dynamical regimes driven by tunable tunneling energy, interactions and external forces, with applications spanning from atomtronics to quantum metrology.

In-Vivo Real-Time X-ray μ-Imaging

NASA Astrophysics Data System (ADS)

Dammer, Jiri; Holy, Tomas; Jakubek, Jan; Jakubek, Martin; Pospisil, Stanislav; Vavrík, Daniel

2007-11-01

The technique of X-ray transmission imaging is available for more than 100 years and it is still one of the fastest and easiest ways how to study the internal structure of living biological samples. The advances in semiconductor technology in last years make possible to fabricate new types of X-ray detectors with direct conversion of interacting X-ray photon to an electric signal. Especially semiconductor pixel detectors seem to be very promising. Compared to the film technique they bring single-quantum and real-time digital information about the studied object with high resolution, high sensitivity and broad dynamic range. These pixel detector-based imaging stand promising as a new tool in the field of small animal imaging, for cancer research and for observation of dynamic processes inside organisms. These detectors open up for instance new possibilities for researchers to perform non-invasive studies of tissue for mutations or pathologies and to monitor disease progression or response to therapy.

Dynamics of the Random Field Ising Model

NASA Astrophysics Data System (ADS)

Xu, Jian

The Random Field Ising Model (RFIM) is a general tool to study disordered systems. Crackling noise is generated when disordered systems are driven by external forces, spanning a broad range of sizes. Systems with different microscopic structures such as disordered mag- nets and Earth's crust have been studied under the RFIM. In this thesis, we investigated the domain dynamics and critical behavior in two dipole-coupled Ising ferromagnets Nd2Fe14B and LiHoxY 1-xF4. With Tc well above room temperature, Nd2Fe14B has shown reversible disorder when exposed to an external transverse field and crosses between two universality classes in the strong and weak disorder limits. Besides tunable disorder, LiHoxY1-xF4 has shown quantum tunneling effects arising from quantum fluctuations, providing another mechanism for domain reversal. Universality within and beyond power law dependence on avalanche size and energy were studied in LiHo0.65Y0.35 F4.

Structure of Colloidal Quantum Dots from Dynamic Nuclear Polarization Surface Enhanced NMR Spectroscopy.

PubMed

Piveteau, Laura; Ong, Ta-Chung; Rossini, Aaron J; Emsley, Lyndon; Copéret, Christophe; Kovalenko, Maksym V

2015-11-04

Understanding the chemistry of colloidal quantum dots (QDs) is primarily hampered by the lack of analytical methods to selectively and discriminately probe the QD core, QD surface and capping ligands. Here, we present a general concept for studying a broad range of QDs such as CdSe, CdTe, InP, PbSe, PbTe, CsPbBr3, etc., capped with both organic and inorganic surface capping ligands, through dynamic nuclear polarization (DNP) surface enhanced NMR spectroscopy. DNP can enhance NMR signals by factors of 10-100, thereby reducing the measurement times by 2-4 orders of magnitude. 1D DNP enhanced spectra acquired in this way are shown to clearly distinguish QD surface atoms from those of the QD core, and environmental effects such as oxidation. Furthermore, 2D NMR correlation experiments, which were previously inconceivable for QD surfaces, are demonstrated to be readily performed with DNP and provide the bonding motifs between the QD surfaces and the capping ligands.

Computational Model of Population Dynamics Based on the Cell Cycle and Local Interactions

NASA Astrophysics Data System (ADS)

Oprisan, Sorinel Adrian; Oprisan, Ana

2005-03-01

Our study bridges cellular (mesoscopic) level interactions and global population (macroscopic) dynamics of carcinoma. The morphological differences and transitions between well and smooth defined benign tumors and tentacular malignat tumors suggest a theoretical analysis of tumor invasion based on the development of mathematical models exhibiting bifurcations of spatial patterns in the density of tumor cells. Our computational model views the most representative and clinically relevant features of oncogenesis as a fight between two distinct sub-systems: the immune system of the host and the neoplastic system. We implemented the neoplastic sub-system using a three-stage cell cycle: active, dormant, and necrosis. The second considered sub-system consists of cytotoxic active (effector) cells — EC, with a very broad phenotype ranging from NK cells to CTL cells, macrophages, etc. Based on extensive numerical simulations, we correlated the fractal dimensions for carcinoma, which could be obtained from tumor imaging, with the malignat stage. Our computational model was able to also simulate the effects of surgical, chemotherapeutical, and radiotherapeutical treatments.

An Update on NASA's Arctic Boreal Vulnerability Experiment

NASA Astrophysics Data System (ADS)

Goetz, S. J.; Miller, C. E.; Griffith, P. C.; Larson, E. K.; Kasischke, E. S.; Margolis, H. A.

2016-12-01

ABoVE is a NASA-led field campaign taking place in Alaska and western Canada over the next 8-10 years, with a wide range of interdisciplinary science objectives designed to address the extent to which ecosystems and society are vulnerable, or resilient, to environmental changes underway and expected. The first phase of ABoVE is underway, with a focus on ecosystem dynamics and ecosystem services objectives. Some 45 core and affiliated projects are currently included, and another 10-20 will be added in late 2016 with initiation of the airborne science component. The ABoVE leadership is fostering partnerships with several other major arctic and boreal research, management and policy initiatives. The Science Team is organized around science themes, with Working Groups (WGs) on vegetation, permafrost and hydrology, disturbance, carbon dynamics, wildlife and ecosystem services, and modeling. Despite the disciplinary science WGs, ABoVE research broadly focuses the complex interdependencies and feedbacks across disciplines. Additional WGs focus on airborne science, geospatial products, core variables and standards, and stakeholder engagement - all supplemented by a range of infrastructure activities such as data management, cloud computing, laboratory and field support. Ultimately ABoVE research will improve our understanding of the consequences of environmental changes occurring across the study domain, as well as increase our confidence in making projections of the ecosystem responses and vulnerability to changes taking place both within and outside the domain. ABoVE will also build a lasting legacy of research through an expanded knowledge base, the provision of key datasets archived for a broader network of researchers and resource managers, and the development of data products and knowledge designed to foster decision support and applied research partnerships with broad societal relevance. We will provide a brief status update of ABoVE activities and plans, including the upcoming airborne campaigns, science team meetings, and the potential for partnerships and engagement.

An empirical, hierarchical typology of tree species assemblages for assessing forest dynamics under global change scenarios

PubMed Central

Coulston, John W.; Wear, David N.

2017-01-01

The composition of tree species occurring in a forest is important and can be affected by global change drivers such as climate change. To inform assessment and projection of global change impacts at broad extents, we used hierarchical cluster analysis and over 120,000 recent forest inventory plots to empirically define forest tree assemblages across the U.S., and identified the indicator and dominant species associated with each. Cluster typologies in two levels of a hierarchy of forest assemblages, with 29 and 147 groups respectively, were supported by diagnostic criteria. Groups in these two levels of the hierarchy were labeled based on the top indicator species in each, and ranged widely in size. For example, in the 29-cluster typology, the sugar maple-red maple assemblage contained the largest number of plots (30,068), while the butternut-sweet birch and sourwood-scarlet oak assemblages were both smallest (6 plots each). We provide a case-study demonstration of the utility of the typology for informing forest climate change impact assessment. For five assemblages in the 29-cluster typology, we used existing projections of changes in importance value (IV) for the dominant species under one low and one high climate change scenario to assess impacts to the assemblages. Results ranged widely for each scenario by the end of the century, with each showing an average decrease in IV for dominant species in some assemblages, including the balsam fir-quaking aspen assemblage, and an average increase for others, like the green ash-American elm assemblage. Future work should assess adaptive capacity of these forest assemblages and investigate local population- and community-level dynamics in places where dominant species may be impacted. This typology will be ideal for monitoring, assessing, and projecting changes to forest communities within the emerging framework of macrosystems ecology, which emphasizes hierarchies and broad extents. PMID:28877258

Structure and Evolution of Kuiper Belt Objects: The Case for Compositional Classes

NASA Astrophysics Data System (ADS)

McKinnon, William B.; Prialnik, D.; Stern, S. A.

2007-10-01

Kuiper belt objects (KBOs) accreted from a mélange of ices, carbonaceous matter, and rock of mixed interstellar and solar nebular provenance. The transneptunian region, where this accretion took place, was likely more radially compact than today. This and the influence of gas drag during the solar nebula epoch argue for more rapid KBO accretion than usually considered. Early evolution of KBOs was largely the result of radiogenic heating, with both short-term and long-term contributions being potentially important. Depending on rock content and porous conductivity, KBO interiors may have reached relatively high temperatures. Models suggest that KBOs likely lost very volatile ices during early evolution, whereas less volatile ices should be retained in cold, less altered subsurface layers; initially amorphous ice may have crystallized in the interior as well, releasing trapped volatiles. Generally, KBOs should be stratified in terms of composition and porosity, albeit subject to impact disruption and collisional stripping. KBOs are thus unlikely to be "the most pristine objects in the Solar System.” Large (dwarf planet) KBOs may be fully differentiated. KBO surface color and compositional classes are usually discussed in terms of "nature vs. nurture,” i.e., a generic primordial composition vs. surface processing, but the true nature of KBOs also depends on how they have evolved. The broad range of albedos now found in the Kuiper belt, deep water-ice absorptions on some objects, evidence for differentiation of Pluto and 2003 EL61, and a range of densities incompatible with a single, primordial composition and variable porosity strongly imply significant, intrinsic compositional differences among KBOs. The interplay of formation zone (accretion rate), body size, and dynamical (collisional) history may yield KBO compositional classes (and their spectral correlates) that recall the different classes of asteroids in the inner Solar System, but whose members are broadly distributed among the KBO dynamical subpopulations.

Unravelling the Impacts of Climate and People on Vegetation Dynamics in the Sahel 1982- 2002

NASA Astrophysics Data System (ADS)

Seaquist, J. W.; Hickler, T.; Eklundh, L.; Ardö, J.; Heumann, B. W.

2009-05-01

Satellite sensors have recently shown that much of the Sahel belt of north Africa has experienced significant increases in photosynthetic activity since the early 1980s. This has reignited old debates about the role that people play in shaping land surface status at broad geographical extents. If the human 'footprint' on Sahel vegetation dynamics is measurable, then such impacts may be significant enough alter broad-scale both carbon budgets and climate via land surface atmosphere feedbacks. We test the hypothesis that people have had a measurable impact on vegetation dynamics in the Sahel for the period 1982-2002. We accomplish this by mapping the agreement between potential natural vegetation dynamics predicted by a process-based ecosystem model (Lund Potsdam Jena-Dynamic Global Vegetation Model) and satellite-derived greenness observations (Global Inventory Modelling and Mapping Studies data set) across a geographic grid at a spatial resolution of 0.5 degrees. We then relate this agreement metric to state-of-the-art data sets on demographics, pasture, and cropping. Demographic and agricultural pressures in the Sahel are unable to account for differences between simulated and observed vegetation dynamics, even for the most densely populated areas. But we do identify a weak, positive correlation between data-model agreement and pasture intensity at the Sahel-wide level. This indicates that herding or grazing does not appreciably affect vegetation dynamics in the region. Either people have not had a significant impact on vegetation dynamics in the Sahel or the identification of a human 'footprint' is precluded by inconsistent or subtle vegetation response to complex socio-environmental interactions, and/or limitations in the data used for this study. This research showcases untapped potential for combining ecosystem process models with remote sensing at broad spatial extents for examining the underlying causes of ecosystem change.

Bedform dynamics in a large sand-bedded river using multibeam echo sounding

NASA Astrophysics Data System (ADS)

Elliott, C. M.; Jacobson, R. B.; Erwin, S.; Eric, A. B.; DeLonay, A. J.

2014-12-01

High-resolution repeat multibeam Echo Sounder (MBES) surveys of the Lower Missouri River in Missouri, USA demonstrate sand bedform movement at a variety of scales over a range of discharges. Understanding dune transport rates and the temporal and spatial variability in sizes across the channel has implications for how sediment transport measurements are made and for understanding the dynamics of habitats utilized by benthic organisms over a range of life stages. Nearly 800 miles of the Lower Missouri River has been altered through channelization and bank stabilization that began in the early 1900's for navigation purposes. Channelization of the Lower Missouri River has created a self-scouring navigation channel with large dunes that migrate downstream over a wide range of discharges. Until the use of MBES surveys on the Missouri River the spatial variability of dune forms in the Missouri River navigation channel was poorly understood. MBES surveys allow for visualization of a range of sand bedforms and repeat measurements demonstrate that dunes are moving over a wide range of discharges on the river. Understanding the spatial variability of dunes and dune movement across the channel and in different channel settings (bends, channel cross-overs, near channel structures) will inform emerging methods in sediment transport measurement that use bedform differencing calculations and provide context for physical bedload sediment sampling on large sand-bedded rivers. Multiple benthic fish species of interest including the endangered pallid sturgeon utilize Missouri River dune fields and adjacent regions for migration, feeding, spawning, early development and dispersal. Surveys using MBES and other hydroacoustic tools provide fisheries biologists with broad new insights into the functionality of bedforms as habitat for critical life stages of large river fish species in the Missouri River, and similar sand-bedded systems.

Successes and challenges from formation to implementation of eleven broad-extent conservation programs.

PubMed

Beever, Erik A; Mattsson, Brady J; Germino, Matthew J; Burg, Max Post Van Der; Bradford, John B; Brunson, Mark W

2014-04-01

Integration of conservation partnerships across geographic, biological, and administrative boundaries is increasingly relevant because drivers of change, such as climate shifts, transcend these boundaries. We explored successes and challenges of established conservation programs that span multiple watersheds and consider both social and ecological concerns. We asked representatives from a diverse set of 11 broad-extent conservation partnerships in 29 countries 17 questions that pertained to launching and maintaining partnerships for broad-extent conservation, specifying ultimate management objectives, and implementation and learning. Partnerships invested more funds in implementing conservation actions than any other aspect of conservation, and a program's context (geographic extent, United States vs. other countries, developed vs. developing nation) appeared to substantially affect program approach. Despite early successes of these organizations and benefits of broad-extent conservation, specific challenges related to uncertainties in scaling up information and to coordination in the face of diverse partner governance structures, conflicting objectives, and vast uncertainties regarding future system dynamics hindered long-term success, as demonstrated by the focal organizations. Engaging stakeholders, developing conservation measures, and implementing adaptive management were dominant challenges. To inform future research on broad-extent conservation, we considered several challenges when we developed detailed questions, such as what qualities of broad-extent partnerships ensure they complement, integrate, and strengthen, rather than replace, local conservation efforts and which adaptive management processes yield actionable conservation strategies that account explicitly for dynamics and uncertainties regarding multiscale governance, environmental conditions, and knowledge of the system? © 2014 Society for Conservation Biology.

Highly Resolved Studies of Vacuum Ultraviolet Photoionization Dynamics

NASA Astrophysics Data System (ADS)

Kakar, Sandeep

We use measurements of dispersed fluorescence from electronically excited photoions to study fundamental aspects of intramolecular dynamics. Our experimental innovations make it possible to obtain highly resolved photoionization data that offer qualitative insights into molecular scattering. In particular, we obtain vibrationally resolved data to probe coupling between the electronic and nuclear degrees of freedom by studying the distribution of vibrational energy among photoions. Vibrationally resolved branching ratios are measured over a broad spectral range of excitation energy and their non-Franck-Condon behavior is used as a tool to investigate two diverse aspects of shape resonant photoionization. First, vibrational branching ratios are obtained for the SiF_4 5a _1^{-1} and CS_2 5sigma_{rm u} ^{-1} photoionization channels to help elucidate the microscopic aspects of shape resonant wavefunction for polyatomic molecules. It is shown that in such molecules the shape resonant wavefunction is not necessarily attributable to a specific bond in the molecule. Second, the multichannel aspect of shape resonant photoionization dynamics, reflected in continuum channel coupling, is investigated by obtaining vibrational branching ratios for the 2 sigma_{rm u}^{ -1} and 4sigma^{ -1} photoionization of the isoelectronic molecules N_2 and CO, respectively. These data indicate that effects of continuum coupling may be widespread. We also present the first set of rotationally resolved data over a wide energy range for the 2 sigma_{rm u}^{ -1} photoionization of N_2. These data probe the partitioning of the angular momentum between the photoelectron and photoion, and highlight the multicenter nature of the molecular potential. These case studies illustrate the utility of dispersed fluorescence measurements as a complement to photoelectron spectroscopy for obtaining highly resolved data for molecular photoionization. These measurements makes it possible to probe intrinsically molecular aspects, such as the vibration and rotation, of photoionization dynamics over an extended spectral range when used in conjunction with synchrotron radiation as the exciting source. Furthermore, the high resolution made possible by this technique provides high selectivity for accessing weaker ionization channels which are the ones strongly affected by resonant activity, and the present study repeatedly stresses the importance of this capability in discovering and deciphering new trends in resonant molecular ionization dynamics.

New insights into broad spectrum communities of the Early Holocene Near East: The birds of Hallan Çemi

NASA Astrophysics Data System (ADS)

Zeder, Melinda A.; Spitzer, Megan D.

2016-11-01

The Early Holocene in Near East was a pivotal transitional period that witnessed dramatic changes in climate and environment, human settlement, major changes in subsistence strategies focusing on a broad range of different plant and animal resources, and a radical restructuring of social relations. The remarkable corpus of avifauna from the Early Holocene site of Hallan Çemi in southeastern Turkey sheds new light on key issues about this dynamic period that has been termed the ;Broad Spectrum Revolution;. The avifauna from this important site demonstrate how Hallan Çemi occupants took advantage of the site's strategic location at the junction of multiple environmental zones by extracting a diverse range of seasonally available resources from both near-by and more distant eco-zones to cobble together a stable subsistence economy capable of supporting this small community throughout the year. They give testimony to the impacts of resource utilization over time, especially on species unable to rebound from sustained human hunting. At the same time, they show how Hallan Çemi residents mitigated these impacts by replacing depleted resources with alternative, more resilient ones that could be more sustainably harvested. They open a window onto the growing investment in feasting and ritual activity that helped bind this community together. In so doing they provide a means of empirically evaluating the efficacy of contrasting explanatory frameworks for the Broad Spectrum Revolution that gave rise to the subsequent domestication of plant and animals in the Near East. Contrary to frameworks that cast these developments as responses to resource depression, lessons learned from the Hallan Çemi avifauna lend support to frameworks that emphasize the human capacity to strategically target, capitalize, and improve upon circumscribed resource rich environments in a way that permits more permanent occupation of these niches. And they underscore the degree to which social and ritual activities work together with ecological and economic facets of the lives of these people to both perpetuate and reshape these communities on the threshold of domestication and the emergence of agriculture.

Galaxy Kinematics and Mass Calibration in Massive SZE Selected Galaxy Clusters to z=1.3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Capasso, R.; et al.

The galaxy phase-space distribution in galaxy clusters provides insights into the formation and evolution of cluster galaxies, and it can also be used to measure cluster mass profiles. We present a dynamical study based onmore » $$\\sim$$3000 passive, non-emission line cluster galaxies drawn from 110 galaxy clusters. The galaxy clusters were selected using the Sunyaev-Zel'dovich effect (SZE) in the 2500 deg$^2$ SPT-SZ survey and cover the redshift range $0.2 < z < 1.3$. We model the clusters using the Jeans equation, while adopting NFW mass profiles and a broad range of velocity dispersion anisotropy profiles. The data prefer velocity dispersion anisotropy profiles that are approximately isotropic near the center and increasingly radial toward the cluster virial radius, and this is true for all redshifts and masses we study. The pseudo-phase-space density profile of the passive galaxies is consistent with expectations for dark matter particles and subhalos from cosmological $N$-body simulations. The dynamical mass constraints are in good agreement with external mass estimates of the SPT cluster sample from either weak lensing, velocity dispersions, or X-ray $$Y_X$$ measurements. However, the dynamical masses are lower (at the 2.2$$\\sigma$$ level) when compared to the mass calibration favored when fitting the SPT cluster data to a LCDM model with external cosmological priors, including CMB anisotropy data from Planck. The tension grows with redshift, where in the highest redshift bin the ratio of dynamical to SPT+Planck masses is $$\\eta=0.63^{+0.13}_{-0.08}\\pm0.05$$ (statistical and systematic), corresponding to 2.6$$\\sigma$$ tension.« less

In situ observation of stishovite formation in shock-compressed fused silica

NASA Astrophysics Data System (ADS)

Tracy, Sally June; Turneaure, Stefan; Duffy, Thomas

2017-06-01

Silica, SiO2, has widespread applications ranging from optical components to refractory materials and is of geological importance as one of the major oxide components of the Earth's crust and mantle. The response of silica phases to dynamic loading has long been of interest for understanding the structural evolution of this fundamental oxide. Under shock compression both crystalline quartz and fused silica are characterized by the occurrence of a broad `mixed-phase region' (15-40 GPa) and a dense, high-pressure phase with much lower compressibility. Despite decades of study, the nature of this transformation and the identity of the high-pressure phase(s) remain poorly understood. In situ x-ray diffraction experiments on shock-compressed fused silica were conducted at the Dynamic Compression Sector of the Advanced Photon Source. The lattice-level structure was investigated through time-resolved x-ray diffraction measurements on samples reaching peak stress ranging from 12 to 47 GPa. Our results demonstrate that SiO2 adopts a dense amorphous structure in the `mixed-phase region' and abruptly transforms to stishovite above 34 GPa. These results provide clear evidence that high-pressure crystalline silicate phases can form from amorphous starting materials on the time-scale of laboratory shock experiments.

Evaluation of the performance of quantitative detection of the Listeria monocytogenes prfA locus with droplet digital PCR.

PubMed

Witte, Anna Kristina; Fister, Susanne; Mester, Patrick; Schoder, Dagmar; Rossmanith, Peter

2016-11-01

Fast and reliable pathogen detection is an important issue for human health. Since conventional microbiological methods are rather slow, there is growing interest in detection and quantification using molecular methods. The droplet digital polymerase chain reaction (ddPCR) is a relatively new PCR method for absolute and accurate quantification without external standards. Using the Listeria monocytogenes specific prfA assay, we focused on the questions of whether the assay was directly transferable to ddPCR and whether ddPCR was suitable for samples derived from heterogeneous matrices, such as foodstuffs that often included inhibitors and a non-target bacterial background flora. Although the prfA assay showed suboptimal cluster formation, use of ddPCR for quantification of L. monocytogenes from pure bacterial cultures, artificially contaminated cheese, and naturally contaminated foodstuff was satisfactory over a relatively broad dynamic range. Moreover, results demonstrated the outstanding detection limit of one copy. However, while poorer DNA quality, such as resulting from longer storage, can impair ddPCR, internal amplification control (IAC) of prfA by ddPCR, that is integrated in the genome of L. monocytogenes ΔprfA, showed even slightly better quantification over a broader dynamic range. Graphical Abstract Evaluating the absolute quantification potential of ddPCR targeting Listeria monocytogenes prfA.

Leadership Qualities Emerging in an Online Social Support Group Intervention.

PubMed

Kodatt, Stephanie A; Shenk, Jared E; Williams, Mark L; Horvath, Keith J

2014-11-01

Technology-delivered interventions addressing a broad range of problems for which clients present for therapy are proliferating. However, little is known of leadership dynamics that emerge in online group interventions. The purpose of this study was to assess the types of leadership qualities that would emerge in an online social support group intervention to improve medication adherence for men with HIV, and to characterize the demographic and psychosocial profiles of leaders. Written posts ( n =616) from 66 men were coded using an adapted version of the Full Range Model of Leadership. Results showed that 10% ( n =64) of posts reflected one of five leadership types, the most common of which was mentoring/providing feedback (40% of leadership posts). The next most common leadership style were instances in which encouragement was offered (30% of leadership posts). Leaders appeared to have lived with HIV longer and have higher Internet knowledge scores than non-leaders. Results indicate that online group interventions potentially may be useful to supplement traditional face-to-face treatment by providing an additional venue for group members to mentor and provide emotional support to each other. However, additional research is needed to more fully understand leadership qualities and group dynamics in other online group intervention settings.

Gradients, vegetation and climate: spatial and temporal dynamics in the Olympic Mountains, USA

USGS Publications Warehouse

Peterson, David L.; Schreiner, Edward G.; Buckingham, Nelsa M.

1997-01-01

The steep environmental gradients of mountains result in the juxtaposition of diverse vegetation associations with narrow ecotones because life zones are compressed. Variation in geologic substrate, landforms, and soils, in combination with steep environmental gradients, create habitat diversity across spatial scales from 106 ha to <10 m2. This leads to higher biodiversity in a smaller space than in landscapes with less topographic variation. Mountains are often considered to be refuges for biological diversity at the regional scale, although variation in landscape features creates refuges at a fine scale as well. Mountains should also be considered a source of biological diversity, because they provide the germplasm for migration into lowland areas following glacial recession. Many taxa are distributed over a broad range of elevations and habitats, which maximizes the potential to respond to environmental perturbations. Reorganization of species distribution and abundance as a result of climatic change may be impacted considerably by human-caused fragmentation of landscape features, especially at lower elevations. This paper uses palaeoecological and biogeographical data to investigate the spatial and temporal vegetation dynamics of a steep maritime range, the Olympic Mountains (USA). The role of resource management in protecting vegetation in a fragmented landscape is discussed, with emphasis on how to address uncertainties such as climatic change.

Can we use Earth Observations to improve monthly water level forecasts?

NASA Astrophysics Data System (ADS)

Slater, L. J.; Villarini, G.

2017-12-01

Dynamical-statistical hydrologic forecasting approaches benefit from different strengths in comparison with traditional hydrologic forecasting systems: they are computationally efficient, can integrate and `learn' from a broad selection of input data (e.g., General Circulation Model (GCM) forecasts, Earth Observation time series, teleconnection patterns), and can take advantage of recent progress in machine learning (e.g. multi-model blending, post-processing and ensembling techniques). Recent efforts to develop a dynamical-statistical ensemble approach for forecasting seasonal streamflow using both GCM forecasts and changing land cover have shown promising results over the U.S. Midwest. Here, we use climate forecasts from several GCMs of the North American Multi Model Ensemble (NMME) alongside 15-minute stage time series from the National River Flow Archive (NRFA) and land cover classes extracted from the European Space Agency's Climate Change Initiative 300 m annual Global Land Cover time series. With these data, we conduct systematic long-range probabilistic forecasting of monthly water levels in UK catchments over timescales ranging from one to twelve months ahead. We evaluate the improvement in model fit and model forecasting skill that comes from using land cover classes as predictors in the models. This work opens up new possibilities for combining Earth Observation time series with GCM forecasts to predict a variety of hazards from space using data science techniques.

Electromotile hearing: Acoustic tones mask psychophysical response to high-frequency electrical stimulation of intact guinea pig cochleaea)

PubMed Central

Le Prell, Colleen G.; Kawamoto, Kohei; Raphael, Yehoash; Dolan, David F.

2011-01-01

When sinusoidal electric stimulation is applied to the intact cochlea, a frequency-specific acoustic emission can be recorded in the ear canal. Acoustic emissions are produced by basilar membrane motion, and have been used to suggest a corresponding acoustic sensation termed “electromotile hearing.” Electromotile hearing has been specifically attributed to electric stimulation of outer hair cells in the intact organ of Corti. To determine the nature of the auditory perception produced by electric stimulation of a cochlea with intact outer hair cells, we tested guinea pigs in a psychophysical task. First, subjects were trained to report detection of sinusoidal acoustic stimuli and dynamic range was assessed using response latency. Subjects were then implanted with a ball electrode placed into scala tympani. Following the surgical implant procedure, subjects were transferred to a task in which acoustic signals were replaced by sinusoidal electric stimulation, and dynamic range was assessed again. Finally, the ability of acoustic pure-tone stimuli to mask the detection of the electric signals was assessed. Based on the masking effects, we conclude that sinusoidal electric stimulation of the intact cochlea results in perception of a tonal (rather than a broad-band or noisy) sound at a frequency of 8 kHz or above. PMID:17225416

Rapid evolution of regulatory element libraries for tunable transcriptional and translational control of gene expression.

PubMed

Jin, Erqing; Wong, Lynn; Jiao, Yun; Engel, Jake; Holdridge, Benjamin; Xu, Peng

2017-12-01

Engineering cell factories for producing biofuels and pharmaceuticals has spurred great interests to develop rapid and efficient synthetic biology tools customized for modular pathway engineering. Along the way, combinatorial gene expression control through modification of regulatory element offered tremendous opportunity for fine-tuning gene expression and generating digital-like genetic circuits. In this report, we present an efficient evolutionary approach to build a range of regulatory control elements. The reported method allows for rapid construction of promoter, 5'UTR, terminator and trans -activating RNA libraries. Synthetic overlapping oligos with high portion of degenerate nucleotides flanking the regulatory element could be efficiently assembled to a vector expressing fluorescence reporter. This approach combines high mutation rate of the synthetic DNA with the high assembly efficiency of Gibson Mix. Our constructed library demonstrates broad range of transcriptional or translational gene expression dynamics. Specifically, both the promoter library and 5'UTR library exhibits gene expression dynamics spanning across three order of magnitude. The terminator library and trans -activating RNA library displays relatively narrowed gene expression pattern. The reported study provides a versatile toolbox for rapidly constructing a large family of prokaryotic regulatory elements. These libraries also facilitate the implementation of combinatorial pathway engineering principles and the engineering of more efficient microbial cell factory for various biomanufacturing applications.

Circadian rhythms and fractal fluctuations in forearm motion

NASA Astrophysics Data System (ADS)

Hu, Kun; Hilton, Michael F.

2005-03-01

Recent studies have shown that the circadian pacemaker --- an internal body clock located in the brain which is normally synchronized with the sleep/wake behavioral cycles --- influences key physiologic functions such as the body temperature, hormone secretion and heart rate. Surprisingly, no previous studies have investigated whether the circadian pacemaker impacts human motor activity --- a fundamental physiologic function. We investigate high-frequency actigraph recordings of forearm motion from a group of young and healthy subjects during a forced desynchrony protocol which allows to decouple the sleep/wake cycles from the endogenous circadian cycle while controlling scheduled behaviors. We investigate both static properties (mean value, standard deviation), dynamical characteristics (long-range correlations), and nonlinear features (magnitude and Fourier-phase correlations) in the fluctuations of forearm acceleration across different circadian phases. We demonstrate that while the static properties exhibit significant circadian rhythms with a broad peak in the afternoon, the dynamical and nonlinear characteristics remain invariant with circadian phase. This finding suggests an intrinsic multi-scale dynamic regulation of forearm motion the mechanism of which is not influenced by the circadian pacemaker, thus suggesting that increased cardiac risk in the early morning hours is not related to circadian-mediated influences on motor activity.

Comparative Sensitivity Analysis of Muscle Activation Dynamics

PubMed Central

Günther, Michael; Götz, Thomas

2015-01-01

We mathematically compared two models of mammalian striated muscle activation dynamics proposed by Hatze and Zajac. Both models are representative for a broad variety of biomechanical models formulated as ordinary differential equations (ODEs). These models incorporate parameters that directly represent known physiological properties. Other parameters have been introduced to reproduce empirical observations. We used sensitivity analysis to investigate the influence of model parameters on the ODE solutions. In addition, we expanded an existing approach to treating initial conditions as parameters and to calculating second-order sensitivities. Furthermore, we used a global sensitivity analysis approach to include finite ranges of parameter values. Hence, a theoretician striving for model reduction could use the method for identifying particularly low sensitivities to detect superfluous parameters. An experimenter could use it for identifying particularly high sensitivities to improve parameter estimation. Hatze's nonlinear model incorporates some parameters to which activation dynamics is clearly more sensitive than to any parameter in Zajac's linear model. Other than Zajac's model, Hatze's model can, however, reproduce measured shifts in optimal muscle length with varied muscle activity. Accordingly we extracted a specific parameter set for Hatze's model that combines best with a particular muscle force-length relation. PMID:26417379

Artificial proteins as allosteric modulators of PDZ3 and SH3 in two-domain constructs: A computational characterization of novel chimeric proteins.

PubMed

Kirubakaran, Palani; Pfeiferová, Lucie; Boušová, Kristýna; Bednarova, Lucie; Obšilová, Veronika; Vondrášek, Jiří

2016-10-01

Artificial multidomain proteins with enhanced structural and functional properties can be utilized in a broad spectrum of applications. The design of chimeric fusion proteins utilizing protein domains or one-domain miniproteins as building blocks is an important advancement for the creation of new biomolecules for biotechnology and medical applications. However, computational studies to describe in detail the dynamics and geometry properties of two-domain constructs made from structurally and functionally different proteins are lacking. Here, we tested an in silico design strategy using all-atom explicit solvent molecular dynamics simulations. The well-characterized PDZ3 and SH3 domains of human zonula occludens (ZO-1) (3TSZ), along with 5 artificial domains and 2 types of molecular linkers, were selected to construct chimeric two-domain molecules. The influence of the artificial domains on the structure and dynamics of the PDZ3 and SH3 domains was determined using a range of analyses. We conclude that the artificial domains can function as allosteric modulators of the PDZ3 and SH3 domains. Proteins 2016; 84:1358-1374. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Importance of liquid fragility for energy applications of ionic liquids

NASA Astrophysics Data System (ADS)

Sippel, Pit; Lunkenheimer, Peter; Krohns, Stephan; Thoms, Erik; Loidl, Alois

Ionic liquids (ILs) are salts that are liquid at ambient temperatures. The strong electrostatic forces between their molecular ions result, e.g., in low volatility and high stability for many members of this huge material class. For this reason they bear a high potential for new advancements in applications, e.g., as electrolytes in energy-storage devices such as supercapacitors or batteries, where the ionic conductivity is an essential figure of merit. Most ILs show dynamic properties typical for glassy matter, which dominate many of their physical properties. An important method to study these dynamical glass-properties is dielectric spectroscopy that can access relaxation times of dynamic processes and the conductivity in a broad frequency and temperature range. In the present contribution, we present results on a large variety of ionic liquids showing that the conductivity of ILs depends in a systematic way not only on their glass temperature but also on the so-called fragility, characterizing the non-canonical super-Arrhenius temperature dependence of their ionic mobility. This work was supported by the Deutsche Forschungsgemeinschaft via Research Unit FOR1394 and by the BMBF via ENREKON 03EK3015.

Competing quantum effects in the free energy profiles and diffusion rates of hydrogen and deuterium molecules through clathrate hydrates.

PubMed

Cendagorta, Joseph R; Powers, Anna; Hele, Timothy J H; Marsalek, Ondrej; Bačić, Zlatko; Tuckerman, Mark E

2016-11-30

Clathrate hydrates hold considerable promise as safe and economical materials for hydrogen storage. Here we present a quantum mechanical study of H 2 and D 2 diffusion through a hexagonal face shared by two large cages of clathrate hydrates over a wide range of temperatures. Path integral molecular dynamics simulations are used to compute the free-energy profiles for the diffusion of H 2 and D 2 as a function of temperature. Ring polymer molecular dynamics rate theory, incorporating both exact quantum statistics and approximate quantum dynamical effects, is utilized in the calculations of the H 2 and D 2 diffusion rates in a broad temperature interval. We find that the shape of the quantum free-energy profiles and their height relative to the classical free energy barriers at a given temperature, as well as the rate of diffusion, are strongly affected by competing quantum effects: above 25 K, zero-point energy (ZPE) perpendicular to the reaction path for diffusion between cavities decreases the quantum rate compared to the classical rate, whereas at lower temperatures tunneling outcompetes the ZPE and as a result the quantum rate is greater than the classical rate.

Leishmania infection inhibits macrophage motility by altering F-actin dynamics and the expression of adhesion complex proteins

PubMed Central

de Menezes, Juliana Perrone Bezerra; Koushik, Amrita; Das, Satarupa; Guven, Can; Siegel, Ariel; Laranjeira-Silva, Maria Fernanda; Losert, Wolfgang; Andrews, Norma W.

2016-01-01

Leishmania is an intracellular protozoan parasite that causes a broad spectrum of clinical manifestations, ranging from self-healing skin lesions to fatal visceralizing disease. As the host cells of choice for all species of Leishmania, macrophages are critical for the establishment of infections. How macrophages contribute to parasite homing to specific tissues and how parasites modulate macrophage function is still poorly understood. In this study we show that L. amazonensis infection inhibits macrophage roaming motility. The reduction in macrophage speed is not dependent on particle load or on factors released by infected macrophages. L. amazonensis-infected macrophages also show reduced directional migration in response to the chemokine MCP-1. We found that infected macrophages have lower levels of total paxillin, phosphorylated paxillin and phosphorylated FAK when compared to non-infected macrophages, indicating abnormalities in the formation of signaling adhesion complexes that regulate motility. Analysis of the dynamics of actin polymerization at peripheral sites also revealed a markedly enhanced F-actin turnover frequency in L. amazonensis-infected macrophages. Thus, Leishmania infection inhibits macrophage motility by altering actin dynamics and impairing the expression of proteins that function in plasma membrane-extracellular matrix interactions. PMID:27641840

Dynamics of Entangled Polymers: Role of Attractive Interactions

NASA Astrophysics Data System (ADS)

Grest, Gary S.; Koski, Jason

The coupled dynamics of entangled polymers, which span broad time and length scales, govern their unique viscoelastic properties. Numerical simulations of highly coarse grained models are often used to follow chain mobility from the intermediate Rouse and reptation regimes to the late time diffusive regime. In these models, purely repulsive interactions between monomers are typically used because it is less computationally expensive than including attractive interactions. The effect of including the attractive interaction on the local and macroscopic properties of entangled polymer melts is explored over a wide temperature range using large scale molecular dynamics simulations. Attractive interactions are shown to have little effect on the local packing for all temperatures T and chain mobility for T higher than about twice the glass transition Tg. For lower T, the attractive interactions play a significant role, reducing the chain mobility compared to the repulsive case. As T approaches Tg breakdown of time-temperature superposition for the stress autocorrelation function is observed. Sandia National Labs is a multiprogram laboratory managed and operated by Sandia Corporation, a Lockheed-Martin Company, for the U.S. Dept of Energy under Contract No. DEAC04-94AL85000.

Pattern does not equal process: what does patch occupancy really tell us about metapopulation dynamics?

PubMed

Clinchy, Michael; Haydon, Daniel T; Smith, Andrew T

2002-04-01

Patch occupancy surveys are commonly used to parameterize metapopulation models. If isolation predicts patch occupancy, this is generally attributed to a balance between distance-dependent recolonization and spatially independent extinctions. We investigated whether similar patterns could also be generated by a process of spatially correlated extinctions following a unique colonization event (analogous to nonequilibrium processes in island biogeography). We simulated effects of spatially correlated extinctions on patterns of patch occupancy among pikas (Ochotona princeps) at Bodie, California, using randomly located extinction disks to represent the likely effects of predation. Our simulations produced similar patterns to those cited as evidence of balanced metapopulation dynamics. Simulations using a variety of disk sizes and patch configurations confirmed that our results are potentially applicable to a broad range of species and sites. Analyses of the observed patterns of patch occupancy at Bodie revealed little evidence of rescue effects and strong evidence that most recolonizations are ephemeral in nature. Persistence will be overestimated if static or declining patterns of patch occupancy are mistakenly attributed to dynamically stable metapopulation processes. Consequently, simple patch occupancy surveys should not be considered as substitutes for detailed experimental tests of hypothesized population processes, particularly when conservation concerns are involved.

Thirteenth Workshop for Computational Fluid Dynamic Applications in Rocket Propulsion and Launch Vehicle Technology. Volume 1

NASA Technical Reports Server (NTRS)

Williams, R. W. (Compiler)

1996-01-01

The purpose of the workshop was to discuss experimental and computational fluid dynamic activities in rocket propulsion and launch vehicles. The workshop was an open meeting for government, industry, and academia. A broad number of topics were discussed including computational fluid dynamic methodology, liquid and solid rocket propulsion, turbomachinery, combustion, heat transfer, and grid generation.

Research activities of the Geodynamics Branch

NASA Technical Reports Server (NTRS)

Kahn, W. D. (Editor); Cohen, S. C. (Editor)

1984-01-01

A broad spectrum of geoscience disciplines including space geodesy, geopotential field modeling, tectonophysics, and dynamic oceanography are discussed. The NASA programs, include the Geodynamics and Ocean Programs, the Crustal Dynamics Project, the proposed Ocean Topography Experiment (TOPEX), and the Geopotential Research Mission (GRM). The papers are grouped into chapters on Crustal Movements, Global Earth Dynamics, Gravity Field Model Development, Sea Surface Topography, and Advanced Studies.

Dynamic network expansion, contraction, and connectivity in the river corridor of mountain stream network

NASA Astrophysics Data System (ADS)

Ward, A. S.; Schmadel, N.; Wondzell, S. M.

2017-12-01

River networks are broadly recognized to expand and contract in response to hydrologic forcing. Additionally, the individual controls on river corridor dynamics of hydrologic forcing and geologic setting are well recognized. However, we currently lack tools to integrate our understanding of process dynamics in the river corridor and make predictions at the scale of river networks. In this study, we develop a perceptual model of the river corridor in mountain river networks, translate this into a reduced-complexity mechanistic model, and implement the model in a well-studied headwater catchment. We found that the river network was most sensitive to hydrologic dynamics under the lowest discharges (Qgauge < 1 L s-1). We also demonstrate a discharge-dependence on the dominant controls on network expansion, contraction, and river corridor exchange. Finally, we suggest this parsimonious model will be useful to managers of water resources who need to estimate connectivity and flow initiation location along the river corridor over broad, unstudied catchments.

Phosphorescent nanosensors for in vivo tracking of histamine levels.

PubMed

Cash, Kevin J; Clark, Heather A

2013-07-02

Continuously tracking bioanalytes in vivo will enable clinicians and researchers to profile normal physiology and monitor diseased states. Current in vivo monitoring system designs are limited by invasive implantation procedures and biofouling, limiting the utility of these tools for obtaining physiologic data. In this work, we demonstrate the first success in optically tracking histamine levels in vivo using a modular, injectable sensing platform based on diamine oxidase and a phosphorescent oxygen nanosensor. Our new approach increases the range of measurable analytes by combining an enzymatic recognition element with a reversible nanosensor capable of measuring the effects of enzymatic activity. We use these enzyme nanosensors (EnzNS) to monitor the in vivo histamine dynamics as the concentration rapidly increases and decreases due to administration and clearance. The EnzNS system measured kinetics that match those reported from ex vivo measurements. This work establishes a modular approach to in vivo nanosensor design for measuring a broad range of potential target analytes. Simply replacing the recognition enzyme, or both the enzyme and nanosensor, can produce a new sensor system capable of measuring a wide range of specific analytical targets in vivo.

Atmospheric simulator and calibration system for remote sensing radiometers

NASA Technical Reports Server (NTRS)

Holland, J. A.

1983-01-01

A system for calibrating the MAPS (measurement of air pollution from satellites) instruments was developed. The design of the system provides a capability for simulating a broad range of radiant energy source temperatures and a broad range of atmospheric pressures, temperatures, and pollutant concentrations for a single slab atmosphere. The system design and the system operation are described.

Long-range Li+ dynamics in the lithium argyrodite Li7PSe6 as probed by rotating-frame spin-lattice relaxation NMR.

PubMed

Epp, V; Gün, O; Deiseroth, H-J; Wilkening, M

2013-05-21

Lithium-rich argyrodites belong to a relatively new group of fast ion conducting solids. They might serve as powerful electrolytes in all-solid-state lithium-ion batteries being, from a medium-term point of view, the key technology when safe energy storage systems have to be developed. Spin-lattice relaxation (SLR) nuclear magnetic resonance (NMR) measurements carried out in the rotating frame of reference turned out to be the method of choice to study Li dynamics in argyrodites. When plotted as a function of the inverse temperature, the SLR rates log10(R1ρ) reveal an asymmetric diffusion-induced rate peak. The rate peak contains information on the Li jump rate, the activation energy of the hopping process as well as correlation effects. In particular, considering the high-temperature flank of the SLR NMR rate peak recorded in the rotating frame of reference, an activation energy of approximately 0.49 eV is found. This value represents long-range lithium jump diffusion in crystalline Li7PSe6. As an example, at 325 K the Li jump rate determined from SLR NMR is in the order of 1.4 × 10(5) s(-1). The pronounced asymmetry of the rate peak R1ρ(1/T) points to correlated Li motion. It is comparable to that which is typically found for structurally disordered materials showing a broad range of correlation times.

The Effective Dynamic Ranges for Glaucomatous Visual Field Progression With Standard Automated Perimetry and Stimulus Sizes III and V.

PubMed

Wall, Michael; Zamba, Gideon K D; Artes, Paul H

2018-01-01

It has been shown that threshold estimates below approximately 20 dB have little effect on the ability to detect visual field progression in glaucoma. We aimed to compare stimulus size V to stimulus size III, in areas of visual damage, to confirm these findings by using (1) a different dataset, (2) different techniques of progression analysis, and (3) an analysis to evaluate the effect of censoring on mean deviation (MD). In the Iowa Variability in Perimetry Study, 120 glaucoma subjects were tested every 6 months for 4 years with size III SITA Standard and size V Full Threshold. Progression was determined with three complementary techniques: pointwise linear regression (PLR), permutation of PLR, and linear regression of the MD index. All analyses were repeated on "censored'' datasets in which threshold estimates below a given criterion value were set to equal the criterion value. Our analyses confirmed previous observations that threshold estimates below 20 dB contribute much less to visual field progression than estimates above this range. These findings were broadly similar with stimulus sizes III and V. Censoring of threshold values < 20 dB has relatively little impact on the rates of visual field progression in patients with mild to moderate glaucoma. Size V, which has lower retest variability, performs at least as well as size III for longitudinal glaucoma progression analysis and appears to have a larger useful dynamic range owing to the upper sensitivity limit being higher.

Schottky Heterodyne Receivers With Full Waveguide Bandwidth

NASA Technical Reports Server (NTRS)

Hesler, Jeffrey; Crowe, Thomas

2011-01-01

Compact THz receivers with broad bandwidth and low noise have been developed for the frequency range from 100 GHz to 1 THz. These receivers meet the requirements for high-resolution spectroscopic studies of planetary atmospheres (including the Earth s) from spacecraft, as well as airborne and balloon platforms. The ongoing research is significant not only for the development of Schottky mixers, but also for the creation of a receiver system, including the LO chain. The new receivers meet the goals of high sensitivity, compact size, low total power requirement, and operation across complete waveguide bands. The exceptional performance makes these receivers ideal for the broader range of scientific and commercial applications. These include the extension of sophisticated test and measurement equipment to 1 THz and the development of low-cost imaging systems for security applications and industrial process monitoring. As a particular example, a WR-1.9SHM (400-600 GHz) has been developed (see Figure 1), with state-of-the-art noise temperature ranging from 1,000-1,800 K (DSB) over the full waveguide band. Also, a Vector Network Analyzer extender has been developed (see Figure 2) for the WR1.5 waveguide band (500 750 GHz) with 100-dB dynamic range.

Fitting stress relaxation experiments with fractional Zener model to predict high frequency moduli of polymeric acoustic foams

NASA Astrophysics Data System (ADS)

Guo, Xinxin; Yan, Guqi; Benyahia, Lazhar; Sahraoui, Sohbi

2016-11-01

This paper presents a time domain method to determine viscoelastic properties of open-cell foams on a wide frequency range. This method is based on the adjustment of the stress-time relationship, obtained from relaxation tests on polymeric foams' samples under static compression, with the four fractional derivatives Zener model. The experimental relaxation function, well described by the Mittag-Leffler function, allows for straightforward prediction of the frequency-dependence of complex modulus of polyurethane foams. To show the feasibility of this approach, complex shear moduli of the same foams were measured in the frequency range between 0.1 and 16 Hz and at different temperatures between -20 °C and 20 °C. A curve was reconstructed on the reduced frequency range (0.1 Hz-1 MHz) using the time-temperature superposition principle. Very good agreement was obtained between experimental complex moduli values and the fractional Zener model predictions. The proposed time domain method may constitute an improved alternative to resonant and non-resonant techniques often used for dynamic characterization of polymers for the determination of viscoelastic moduli on a broad frequency range.

Extending the Calibration of C IV-based Single-epoch Black Hole Mass Estimators for Active Galactic Nuclei

NASA Astrophysics Data System (ADS)

Park, Daeseong; Barth, Aaron J.; Woo, Jong-Hak; Malkan, Matthew A.; Treu, Tommaso; Bennert, Vardha N.; Assef, Roberto J.; Pancoast, Anna

2017-04-01

We provide an updated calibration of C IV λ 1549 broad emission line–based single-epoch (SE) black hole (BH) mass estimators for active galactic nuclei (AGNs) using new data for six reverberation-mapped AGNs at redshift z=0.005{--}0.028 with BH masses (bolometric luminosities) in the range {10}6.5{--}{10}7.5 {M}ȯ ({10}41.7{--}{10}43.8 erg s‑1). New rest-frame UV-to-optical spectra covering 1150–5700 Å for the six AGNs were obtained with the Hubble Space Telescope (HST). Multicomponent spectral decompositions of the HST spectra were used to measure SE emission-line widths for the C IV, Mg II, and Hβ lines, as well as continuum luminosities in the spectral region around each line. We combine the new data with similar measurements for a previous archival sample of 25 AGNs to derive the most consistent and accurate calibrations of the C IV-based SE BH mass estimators against the Hβ reverberation-based masses, using three different measures of broad-line width: full width at half maximum (FWHM), line dispersion ({σ }line}), and mean absolute deviation (MAD). The newly expanded sample at redshift z=0.005{--}0.234 covers a dynamic range in BH mass (bolometric luminosity) of {log}{M}BH}/{M}ȯ =6.5{--}9.1 ({log}{L}bol}/ erg s‑1 = 41.7{--}46.9), and we derive the new C IV-based mass estimators using a Bayesian linear regression analysis over this range. We generally recommend the use of {σ }line} or MAD rather than FWHM to obtain a less biased velocity measurement of the C IV emission line, because its narrow-line component contribution is difficult to decompose from the broad-line profile. Based on observations made with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. These observations are associated with program GO-12922.

Dynamics of Mass Transfer in Wide Symbiotic Systems

NASA Astrophysics Data System (ADS)

de Val-Borro, Miguel; Karovska, M.; Sasselov, D.

2010-01-01

We investigate the formation of accretion disks around the secondary in detached systems consisting of an Asymptotic Giant Branch (AGB) star and a compact accreting companion as a function of mass loss rate and orbital parameters. In particular, we study winds from late-type stars that are gravitationally focused by a companion in a wide binary system using hydrodynamical simulations. For a typical slow and massive wind from an evolved star there is a stream flow between the stars with accretion rates of a few percent of the mass loss from the primary. Mass transfer through a focused wind is an important mechanism for a broad range of interacting binary systems and can explain the formation of Barium stars and other chemically peculiar stars.

Frequency control of a spin-torque oscillator using magnetostrictive anisotropy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Min Gyu Albert; Lee, Seok-Hee, E-mail: bgpark@kaist.ac.kr, E-mail: shlee@kaist.edu; Baek, Seung-heon Chris

2016-01-11

We report the working principle of a spin-torque oscillator, of which the frequency is efficiently controlled by manipulating the magnetostrictive anisotropy. To justify the scheme, we simulate a conventional magnetic-tunnel junction-based oscillator which is fabricated on a piezoelectric material. By applying mechanical stress to a free layer using a piezoelectric material, the oscillation frequency can be controlled to ensure a broad tuning range without a significant reduction of the dynamic resistance variation. Such controllability, which appears in the absence of an external magnetic field, will not only enable the integration of spin-torque oscillators and conventional complimentary metal-oxide semiconductor technology butmore » will also broaden the applicability of spin-torque oscillators.« less

Angle-adjustable density field formulation for the modeling of crystalline microstructure

NASA Astrophysics Data System (ADS)

Wang, Zi-Le; Liu, Zhirong; Huang, Zhi-Feng

2018-05-01

A continuum density field formulation with particle-scale resolution is constructed to simultaneously incorporate the orientation dependence of interparticle interactions and the rotational invariance of the system, a fundamental but challenging issue in modeling the structure and dynamics of a broad range of material systems across variable scales. This generalized phase field crystal-type approach is based upon the complete expansion of particle direct correlation functions and the concept of isotropic tensors. Through applications to the modeling of various two- and three-dimensional crystalline structures, our study demonstrates the capability of bond-angle control in this continuum field theory and its effects on the emergence of ordered phases, and provides a systematic way of performing tunable angle analyses for crystalline microstructures.

Exciton Seebeck effect in molecular systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yan, Yun-An, E-mail: yunan@nano.gznc.edu.cn; Cai, Shaohong

2014-08-07

We investigate the exciton dynamics under temperature difference with the hierarchical equations of motion. Through a nonperturbative simulation of the transient absorption of a heterogeneous trimer model, we show that the temperature difference causes exciton population redistribution and affects the exciton transfer time. It is found that one can reproduce not only the exciton population redistribution but also the change of the exciton transfer time induced by the temperature difference with a proper tuning of the site energies of the aggregate. In this sense, there exists a site energy shift equivalence for any temperature difference in a broad range. Thismore » phenomenon is similar to the Seebeck effect as well as spin Seebeck effect and can be named as exciton Seebeck effect.« less