Porous electrode preparation method

DOEpatents

Arons, R.M.; Dusek, J.T.

1983-10-18

A porous sintered plaque is provided with a bimodal porosity that is especially well suited for use as an electrode within a molten carbonate fuel cell. The coarse porosity is sufficient for admitting gases into contact with the reaction surfaces while the fine porosity is wetted with and retains molten electrolyte on the reaction sites. The electrode structure is prepared by providing a very fine powder of such as nickel oxide and blending the powder with a suitable decomposable binder to form a solid mass. The mass is comminuted into agglomerate size particles substantially larger than the fine oxide particles and formed into a cohesive compact for subsequent sintering. Sintering is carried out at sufficient conditions to bind the agglomerates together into a porous structure having both coarse and fine porosity. Where lithiated nickel oxide cathodes are prepared, the sintering conditions can be moderate enough to retain substantial quantities of lithium within the electrode for adequate conductivity. 2 figs.

Weighted least squares phase unwrapping based on the wavelet transform

NASA Astrophysics Data System (ADS)

Chen, Jiafeng; Chen, Haiqin; Yang, Zhengang; Ren, Haixia

2007-01-01

The weighted least squares phase unwrapping algorithm is a robust and accurate method to solve phase unwrapping problem. This method usually leads to a large sparse linear equation system. Gauss-Seidel relaxation iterative method is usually used to solve this large linear equation. However, this method is not practical due to its extremely slow convergence. The multigrid method is an efficient algorithm to improve convergence rate. However, this method needs an additional weight restriction operator which is very complicated. For this reason, the multiresolution analysis method based on the wavelet transform is proposed. By applying the wavelet transform, the original system is decomposed into its coarse and fine resolution levels and an equivalent equation system with better convergence condition can be obtained. Fast convergence in separate coarse resolution levels speeds up the overall system convergence rate. The simulated experiment shows that the proposed method converges faster and provides better result than the multigrid method.

A Tale of Three Classes: Case Studies in Course Complexity

ERIC Educational Resources Information Center

Gill, T. Grandon; Jones, Joni

2010-01-01

This paper examines the question of decomposability versus complexity of teaching situations by presenting three case studies of MIS courses. Because all three courses were highly successful in their observed outcomes, the paper hypothesizes that if the attributes of effective course design are decomposable, one would expect to see a large number…

Fungal Traits That Drive Ecosystem Dynamics on Land

PubMed Central

Lennon, Jay T.

2015-01-01

SUMMARY Fungi contribute extensively to a wide range of ecosystem processes, including decomposition of organic carbon, deposition of recalcitrant carbon, and transformations of nitrogen and phosphorus. In this review, we discuss the current knowledge about physiological and morphological traits of fungi that directly influence these processes, and we describe the functional genes that encode these traits. In addition, we synthesize information from 157 whole fungal genomes in order to determine relationships among selected functional genes within fungal taxa. Ecosystem-related traits varied most at relatively coarse taxonomic levels. For example, we found that the maximum amount of variance for traits associated with carbon mineralization, nitrogen and phosphorus cycling, and stress tolerance could be explained at the levels of order to phylum. Moreover, suites of traits tended to co-occur within taxa. Specifically, the genetic capacities for traits that improve stress tolerance—β-glucan synthesis, trehalose production, and cold-induced RNA helicases—were positively related to one another, and they were more evident in yeasts. Traits that regulate the decomposition of complex organic matter—lignin peroxidases, cellobiohydrolases, and crystalline cellulases—were also positively related, but they were more strongly associated with free-living filamentous fungi. Altogether, these relationships provide evidence for two functional groups: stress tolerators, which may contribute to soil carbon accumulation via the production of recalcitrant compounds; and decomposers, which may reduce soil carbon stocks. It is possible that ecosystem functions, such as soil carbon storage, may be mediated by shifts in the fungal community between stress tolerators and decomposers in response to environmental changes, such as drought and warming. PMID:25971588

Coarse-grained simulations of polyelectrolyte complexes: MARTINI models for poly(styrene sulfonate) and poly(diallyldimethylammonium)

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

Vögele, Martin; Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt a. M.; Holm, Christian

2015-12-28

We present simulations of aqueous polyelectrolyte complexes with new MARTINI models for the charged polymers poly(styrene sulfonate) and poly(diallyldimethylammonium). Our coarse-grained polyelectrolyte models allow us to study large length and long time scales with regard to chemical details and thermodynamic properties. The results are compared to the outcomes of previous atomistic molecular dynamics simulations and verify that electrostatic properties are reproduced by our MARTINI coarse-grained approach with reasonable accuracy. Structural similarity between the atomistic and the coarse-grained results is indicated by a comparison between the pair radial distribution functions and the cumulative number of surrounding particles. Our coarse-grained models aremore » able to quantitatively reproduce previous findings like the correct charge compensation mechanism and a reduced dielectric constant of water. These results can be interpreted as the underlying reason for the stability of polyelectrolyte multilayers and complexes and validate the robustness of the proposed models.« less

Synthesis, Characterization, and Processing of Copper, Indium, and Gallium Dithiocarbamates for Energy Conversion Applications

NASA Technical Reports Server (NTRS)

Duraj, S. A.; Duffy, N. V.; Hepp, A. F.; Cowen, J. E.; Hoops, M. D.; Brothrs, S. M.; Baird, M. J.; Fanwick, P. E.; Harris, J. D.; Jin, M. H.-C.

2009-01-01

Ten dithiocarbamate complexes of indium(III) and gallium(III) have been prepared and characterized by elemental analysis, infrared spectra and melting point. Each complex was decomposed thermally and its decomposition products separated and identified with the combination of gas chromatography/mass spectrometry. Their potential utility as photovoltaic materials precursors was assessed. Bis(dibenzyldithiocarbamato)- and bis(diethyldithiocarbamato)copper(II), Cu(S2CN(CH2C6H5)2)2 and Cu(S2CN(C2H5)2)2 respectively, have also been examined for their suitability as precursors for copper sulfides for the fabrication of photovoltaic materials. Each complex was decomposed thermally and the products analyzed by GC/MS, TGA and FTIR. The dibenzyl derivative complex decomposed at a lower temperature (225-320 C) to yield CuS as the product. The diethyl derivative complex decomposed at a higher temperature (260-325 C) to yield Cu2S. No Cu containing fragments were noted in the mass spectra. Unusual recombination fragments were observed in the mass spectra of the diethyl derivative. Tris(bis(phenylmethyl)carbamodithioato-S,S'), commonly referred to as tris(N,N-dibenzyldithiocarbamato)indium(III), In(S2CNBz2)3, was synthesized and characterized by single crystal X-ray crystallography. The compound crystallizes in the triclinic space group P1(bar) with two molecules per unit cell. The material was further characterized using a novel analytical system employing the combined powers of thermogravimetric analysis, gas chromatography/mass spectrometry, and Fourier transform infrared (FT-IR) spectroscopy to investigate its potential use as a precursor for the chemical vapor deposition (CVD) of thin film materials for photovoltaic applications. Upon heating, the material thermally decomposes to release CS2 and benzyl moieties in to the gas phase, resulting in bulk In2S3. Preliminary spray CVD experiments indicate that In(S2CNBz2)3 decomposed on a Cu substrate reacts to produce stoichiometric CuInS2 films.

Experimentally simulated global warming and nitrogen enrichment effects on microbial litter decomposers in a marsh.

PubMed

Flury, Sabine; Gessner, Mark O

2011-02-01

Atmospheric warming and increased nitrogen deposition can lead to changes of microbial communities with possible consequences for biogeochemical processes. We used an enclosure facility in a freshwater marsh to assess the effects on microbes associated with decomposing plant litter under conditions of simulated climate warming and pulsed nitrogen supply. Standard batches of litter were placed in coarse-mesh and fine-mesh bags and submerged in a series of heated, nitrogen-enriched, and control enclosures. They were retrieved later and analyzed for a range of microbial parameters. Fingerprinting profiles obtained by denaturing gradient gel electrophoresis (DGGE) indicated that simulated global warming induced a shift in bacterial community structure. In addition, warming reduced fungal biomass, whereas bacterial biomass was unaffected. The mesh size of the litter bags and sampling date also had an influence on bacterial community structure, with the apparent number of dominant genotypes increasing from spring to summer. Microbial respiration was unaffected by any treatment, and nitrogen enrichment had no clear effect on any of the microbial parameters considered. Overall, these results suggest that microbes associated with decomposing plant litter in nutrient-rich freshwater marshes are resistant to extra nitrogen supplies but are likely to respond to temperature increases projected for this century.

Thermally Regenerative Battery with Intercalatable Electrodes and Selective Heating Means

NASA Technical Reports Server (NTRS)

Sharma, Pramod K. (Inventor); Narayanan, Sekharipuram R. (Inventor); Hickey, Gregory S. (Inventor)

2000-01-01

The battery contains at least one electrode such as graphite that intercalates a first species from the electrolyte disposed in a first compartment such as bromine to form a thermally decomposable complex during discharge. The other electrode can also be graphite which supplies another species such as lithium to the electrolyte in a second electrode compartment. The thermally decomposable complex is stable at room temperature but decomposes at elevated temperatures such as 50 C. to 150 C. The electrode compartments are separated by a selective ion permeable membrane that is impermeable to the first species. Charging is effected by selectively heating the first electrode.

Decay and nutrient dynamics of coarse woody debris in the Qinling Mountains, China

PubMed Central

Yuan, Jie; Hou, Lin; Wei, Xin; Shang, Zhengchun; Cheng, Fei; Zhang, Shuoxin

2017-01-01

As an ecological unit, coarse woody debris (CWD) plays an essential role in productivity, nutrient cycling, carbon sequestration, community regeneration and biodiversity. However, thus far, the information on quantification the decomposition and nutrient content of CWD in forest ecosystems remains considerably limited. In this study, we conducted a long-term (1996–2013) study on decay and nutrient dynamics of CWD for evaluating accurately the ecological value of CWD on the Huoditang Experimental Forest Farm in the Qinling Mountains, China. The results demonstrated that there was a strong correlation between forest biomass and CWD mass. The single exponential decay model well fit the CWD density loss at this site, and as the CWD decomposed, the CWD density decreased significantly. Annual temperature and precipitation were all significantly correlated with the annual mass decay rate. The K contents and the C/N ratio of the CWD decreased as the CWD decayed, but the C, N, P, Ca and Mg contents increased. We observed a significant CWD decay effect on the soil C, N and Mg contents, especially the soil C content. The soil N, P, K, Ca and Mg contents exhibited large fluctuations, but the variation had no obvious regularity and changed with different decay times. The results showed that CWD was a critical component of nutrient cycling in forest ecosystems. Further research is needed to determine the effect of diameter, plant tissue components, secondary wood compounds, and decomposer organisms on the CWD decay rates in the Qinling Mountains, which will be beneficial to clarifying the role of CWD in carbon cycles of forest ecosystems. PMID:28384317

An efficient and robust 3D mesh compression based on 3D watermarking and wavelet transform

NASA Astrophysics Data System (ADS)

Zagrouba, Ezzeddine; Ben Jabra, Saoussen; Didi, Yosra

2011-06-01

The compression and watermarking of 3D meshes are very important in many areas of activity including digital cinematography, virtual reality as well as CAD design. However, most studies on 3D watermarking and 3D compression are done independently. To verify a good trade-off between protection and a fast transfer of 3D meshes, this paper proposes a new approach which combines 3D mesh compression with mesh watermarking. This combination is based on a wavelet transformation. In fact, the used compression method is decomposed to two stages: geometric encoding and topologic encoding. The proposed approach consists to insert a signature between these two stages. First, the wavelet transformation is applied to the original mesh to obtain two components: wavelets coefficients and a coarse mesh. Then, the geometric encoding is done on these two components. The obtained coarse mesh will be marked using a robust mesh watermarking scheme. This insertion into coarse mesh allows obtaining high robustness to several attacks. Finally, the topologic encoding is applied to the marked coarse mesh to obtain the compressed mesh. The combination of compression and watermarking permits to detect the presence of signature after a compression of the marked mesh. In plus, it allows transferring protected 3D meshes with the minimum size. The experiments and evaluations show that the proposed approach presents efficient results in terms of compression gain, invisibility and robustness of the signature against of many attacks.

Coarse-graining and self-dissimilarity of complex networks

NASA Astrophysics Data System (ADS)

Itzkovitz, Shalev; Levitt, Reuven; Kashtan, Nadav; Milo, Ron; Itzkovitz, Michael; Alon, Uri

2005-01-01

Can complex engineered and biological networks be coarse-grained into smaller and more understandable versions in which each node represents an entire pattern in the original network? To address this, we define coarse-graining units as connectivity patterns which can serve as the nodes of a coarse-grained network and present algorithms to detect them. We use this approach to systematically reverse-engineer electronic circuits, forming understandable high-level maps from incomprehensible transistor wiring: first, a coarse-grained version in which each node is a gate made of several transistors is established. Then the coarse-grained network is itself coarse-grained, resulting in a high-level blueprint in which each node is a circuit module made of many gates. We apply our approach also to a mammalian protein signal-transduction network, to find a simplified coarse-grained network with three main signaling channels that resemble multi-layered perceptrons made of cross-interacting MAP-kinase cascades. We find that both biological and electronic networks are “self-dissimilar,” with different network motifs at each level. The present approach may be used to simplify a variety of directed and nondirected, natural and designed networks.

An efficient approach for pixel decomposition to increase the spatial resolution of land surface temperature images from MODIS thermal infrared band data.

PubMed

Wang, Fei; Qin, Zhihao; Li, Wenjuan; Song, Caiying; Karnieli, Arnon; Zhao, Shuhe

2014-12-25

Land surface temperature (LST) images retrieved from the thermal infrared (TIR) band data of Moderate Resolution Imaging Spectroradiometer (MODIS) have much lower spatial resolution than the MODIS visible and near-infrared (VNIR) band data. The coarse pixel scale of MODIS LST images (1000 m under nadir) have limited their capability in applying to many studies required high spatial resolution in comparison of the MODIS VNIR band data with pixel scale of 250-500 m. In this paper we intend to develop an efficient approach for pixel decomposition to increase the spatial resolution of MODIS LST image using the VNIR band data as assistance. The unique feature of this approach is to maintain the thermal radiance of parent pixels in the MODIS LST image unchanged after they are decomposed into the sub-pixels in the resulted image. There are two important steps in the decomposition: initial temperature estimation and final temperature determination. Therefore the approach can be termed double-step pixel decomposition (DSPD). Both steps involve a series of procedures to achieve the final result of decomposed LST image, including classification of the surface patterns, establishment of LST change with normalized difference of vegetation index (NDVI) and building index (NDBI), reversion of LST into thermal radiance through Planck equation, and computation of weights for the sub-pixels of the resulted image. Since the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) with much higher spatial resolution than MODIS data was on-board the same platform (Terra) as MODIS for Earth observation, an experiment had been done in the study to validate the accuracy and efficiency of our approach for pixel decomposition. The ASTER LST image was used as the reference to compare with the decomposed LST image. The result showed that the spatial distribution of the decomposed LST image was very similar to that of the ASTER LST image with a root mean square error (RMSE) of 2.7 K for entire image. Comparison with the evaluation DisTrad (E-DisTrad) and re-sampling methods for pixel decomposition also indicate that our DSPD has the lowest RMSE in all cases, including urban region, water bodies, and natural terrain. The obvious increase in spatial resolution remarkably uplifts the capability of the coarse MODIS LST images in highlighting the details of LST variation. Therefore it can be concluded that, in spite of complicated procedures, the proposed DSPD approach provides an alternative to improve the spatial resolution of MODIS LST image hence expand its applicability to the real world.

Theoretical study on interaction of cytochrome f and plastocyanin complex by a simple coarse-grained model with molecular crowding effect

NASA Astrophysics Data System (ADS)

Nakagawa, Satoshi; Kurniawan, Isman; Kodama, Koichi; Arwansyah, Muhammad Saleh; Kawaguchi, Kazutomo; Nagao, Hidemi

2018-03-01

We present a simple coarse-grained model with the molecular crowding effect in solvent to investigate the structure and dynamics of protein complexes including association and/or dissociation processes and investigate some physical properties such as the structure and the reaction rate from the viewpoint of the hydrophobic intermolecular interactions of protein complex. In the present coarse-grained model, a function depending upon the density of hydrophobic amino acid residues in a binding area of the complex is introduced, and the function involves the molecular crowding effect for the intermolecular interactions of hydrophobic amino acid residues between proteins. We propose a hydrophobic intermolecular potential energy between proteins by using the density-dependent function. The present coarse-grained model is applied to the complex of cytochrome f and plastocyanin by using the Langevin dynamics simulation to investigate some physical properties such as the complex structure, the electron transfer reaction rate constant from plastocyanin to cytochrome f and so on. We find that for proceeding the electron transfer reaction, the distance between metals in their active sites is necessary within about 18 Å. We discuss some typical complex structures formed in the present simulation in relation to the molecular crowding effect on hydrophobic interactions.

The total amounts of radioactively contaminated materials in forests in Fukushima, Japan

PubMed Central

Hashimoto, Shoji; Ugawa, Shin; Nanko, Kazuki; Shichi, Koji

2012-01-01

There has been leakage of radioactive materials from the Fukushima Daiichi Nuclear Power Plant. A heavily contaminated area (≥ 134, 137Cs 1000 kBq m−2) has been identified in the area northwest of the plant. The majority of the land in the contaminated area is forest. Here we report the amounts of biomass, litter (small organic matter on the surface of the soil), coarse woody litter, and soil in the contaminated forest area. The estimated overall volume and weight were 33 Mm3 (branches, leaves, litter, and coarse woody litter are not included) and 21 Tg (dry matter), respectively. Our results suggest that removing litter is an efficient method of decontamination. However, litter is being continuously decomposed, and contaminated leaves will continue to fall on the soil surface for several years; hence, the litter should be removed promptly but continuously before more radioactive elements are transferred into the soil. PMID:22639724

A boundary condition for layer to level ocean model interaction

NASA Astrophysics Data System (ADS)

Mask, A.; O'Brien, J.; Preller, R.

2003-04-01

A radiation boundary condition based on vertical normal modes is introduced to allow a physical transition between nested/coupled ocean models that are of differing vertical structure and/or differing physics. In this particular study, a fine resolution regional/coastal sigma-coordinate Naval Coastal Ocean Model (NCOM) has been successfully nested to a coarse resolution (in the horizontal and vertical) basin scale NCOM and a coarse resolution basin scale Navy Layered Ocean Model (NLOM). Both of these models were developed at the Naval Research Laboratory (NRL) at Stennis Space Center, Mississippi, USA. This new method, which decomposes the vertical structure of the models into barotropic and baroclinic modes, gives improved results in the coastal domain over Orlanski radiation boundary conditions for the test cases. The principle reason for the improvement is that each mode has the radiation boundary condition applied individually; therefore, the packet of information passing through the boundary is allowed to have multiple phase speeds instead of a single-phase speed. Allowing multiple phase speeds reduces boundary reflections, thus improving results.

AmeriFlux CA-SF1 Saskatchewan - Western Boreal, forest burned in 1977.

DOE Data Explorer

Amiro, Brian [University of Manitoba

2016-01-01

This is the AmeriFlux version of the carbon flux data for the site CA-SF1 Saskatchewan - Western Boreal, forest burned in 1977.. Site Description - Regenerated jack pine (Pinus banksiana) following fire in 1977; canopy height 6 m and LAI = 2.8. Some black spruce understory developing. Trees tend to be clumpy, with some clear spaces that can be easily walked thorugh, and other areas are thick. Fire killed coarse woody debris on the ground, that is soft and decomposing. Very few perched trunks. Understory are short shrubs such as Vaccinium and Arctostaphylus uva-ursi.

Relative entropy and optimization-driven coarse-graining methods in VOTCA

DOE PAGES

Mashayak, S. Y.; Jochum, Mara N.; Koschke, Konstantin; ...

2015-07-20

We discuss recent advances of the VOTCA package for systematic coarse-graining. Two methods have been implemented, namely the downhill simplex optimization and the relative entropy minimization. We illustrate the new methods by coarse-graining SPC/E bulk water and more complex water-methanol mixture systems. The CG potentials obtained from both methods are then evaluated by comparing the pair distributions from the coarse-grained to the reference atomistic simulations.We have also added a parallel analysis framework to improve the computational efficiency of the coarse-graining process.

A coarse-grained model of the effective interaction for charged amino acid residues and its application to formation of GCN4-pLI tetramer

NASA Astrophysics Data System (ADS)

Kawaguchi, Kazutomo; Nakagawa, Satoshi; Kurniawan, Isman; Kodama, Koichi; Arwansyah, Muhammad Saleh; Nagao, Hidemi

2018-03-01

We present a simple coarse-grained model of the effective interaction for charged amino acid residues, such as Glu and Lys, in a water solvent. The free-energy profile as a function of the distance between two charged amino acid side-chain analogues in an explicit water solvent is calculated with all-atom molecular dynamics simulation and thermodynamic integration method. The calculated free-energy profile is applied to the coarse-grained potential of the effective interaction between two amino acid residues. The Langevin dynamics simulations with our coarse-grained potential are performed for association of a small protein complex, GCN4-pLI tetramer. The tetramer conformation reproduced by our coarse-grained model is similar to the X-ray crystallographic structure. We show that the effective interaction between charged amino acid residues stabilises association and orientation of protein complex. We also investigate the association pathways of GCN4-pLI tetramer.

APPARATUS FOR CATALYTICALLY COMBINING GASES

DOEpatents

Busey, H.M.

1958-08-12

A convection type recombiner is described for catalytically recombining hydrogen and oxygen which have been radiolytically decomposed in an aqueous homogeneous nuclear reactor. The device is so designed that the energy of recombination is used to circulate the gas mixture over the catalyst. The device consists of a vertical cylinder having baffles at its lower enda above these coarse screens having platinum and alumina pellets cemented thereon, and an annular passage for the return of recombined, condensed water to the reactor moderator system. This devicea having no moving parts, provides a simple and efficient means of removing the danger of accumulated hot radioactive, explosive gases, and restoring them to the moderator system for reuse.

Coarse-grained molecular dynamics simulations for giant protein-DNA complexes

NASA Astrophysics Data System (ADS)

Takada, Shoji

Biomolecules are highly hierarchic and intrinsically flexible. Thus, computational modeling calls for multi-scale methodologies. We have been developing a coarse-grained biomolecular model where on-average 10-20 atoms are grouped into one coarse-grained (CG) particle. Interactions among CG particles are tuned based on atomistic interactions and the fluctuation matching algorithm. CG molecular dynamics methods enable us to simulate much longer time scale motions of much larger molecular systems than fully atomistic models. After broad sampling of structures with CG models, we can easily reconstruct atomistic models, from which one can continue conventional molecular dynamics simulations if desired. Here, we describe our CG modeling methodology for protein-DNA complexes, together with various biological applications, such as the DNA duplication initiation complex, model chromatins, and transcription factor dynamics on chromatin-like environment.

An Efficient Approach for Pixel Decomposition to Increase the Spatial Resolution of Land Surface Temperature Images from MODIS Thermal Infrared Band Data

PubMed Central

Wang, Fei; Qin, Zhihao; Li, Wenjuan; Song, Caiying; Karnieli, Arnon; Zhao, Shuhe

2015-01-01

Land surface temperature (LST) images retrieved from the thermal infrared (TIR) band data of Moderate Resolution Imaging Spectroradiometer (MODIS) have much lower spatial resolution than the MODIS visible and near-infrared (VNIR) band data. The coarse pixel scale of MODIS LST images (1000 m under nadir) have limited their capability in applying to many studies required high spatial resolution in comparison of the MODIS VNIR band data with pixel scale of 250–500 m. In this paper we intend to develop an efficient approach for pixel decomposition to increase the spatial resolution of MODIS LST image using the VNIR band data as assistance. The unique feature of this approach is to maintain the thermal radiance of parent pixels in the MODIS LST image unchanged after they are decomposed into the sub-pixels in the resulted image. There are two important steps in the decomposition: initial temperature estimation and final temperature determination. Therefore the approach can be termed double-step pixel decomposition (DSPD). Both steps involve a series of procedures to achieve the final result of decomposed LST image, including classification of the surface patterns, establishment of LST change with normalized difference of vegetation index (NDVI) and building index (NDBI), reversion of LST into thermal radiance through Planck equation, and computation of weights for the sub-pixels of the resulted image. Since the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) with much higher spatial resolution than MODIS data was on-board the same platform (Terra) as MODIS for Earth observation, an experiment had been done in the study to validate the accuracy and efficiency of our approach for pixel decomposition. The ASTER LST image was used as the reference to compare with the decomposed LST image. The result showed that the spatial distribution of the decomposed LST image was very similar to that of the ASTER LST image with a root mean square error (RMSE) of 2.7 K for entire image. Comparison with the evaluation DisTrad (E-DisTrad) and re-sampling methods for pixel decomposition also indicate that our DSPD has the lowest RMSE in all cases, including urban region, water bodies, and natural terrain. The obvious increase in spatial resolution remarkably uplifts the capability of the coarse MODIS LST images in highlighting the details of LST variation. Therefore it can be concluded that, in spite of complicated procedures, the proposed DSPD approach provides an alternative to improve the spatial resolution of MODIS LST image hence expand its applicability to the real world. PMID:25609048

Effects of flow scarcity on leaf-litter processing under oceanic climate conditions in calcareous streams.

PubMed

Martínez, Aingeru; Pérez, Javier; Molinero, Jon; Sagarduy, Mikel; Pozo, Jesús

2015-01-15

Although temporary streams represent a high proportion of the total number and length of running waters, historically the study of intermittent streams has received less attention than that of perennial ones. The goal of the present study was to assess the effects of flow cessation on litter decomposition in calcareous streams under oceanic climate conditions. For this, leaf litter of alder was incubated in four streams (S1, S2, S3 and S4) with different flow regimes (S3 and S4 with zero-flow periods) from northern Spain. To distinguish the relative importance and contribution of decomposers and detritivores, fine- and coarse-mesh litter bags were used. We determined processing rates, leaf-C, -N and -P concentrations, invertebrate colonization in coarse bags and benthic invertebrates. Decomposition rates in fine bags were similar among streams. In coarse bags, only one of the intermittent streams, S4, showed a lower rate than that in the other ones as a consequence of lower invertebrate colonization. The material incubated in fine bags presented higher leaf-N and -P concentrations than those in the coarse ones, except in S4, pointing out that the decomposition in this stream was driven mainly by microorganisms. Benthic macroinvertebrate and shredder density and biomass were lower in intermittent streams than those in perennial ones. However, the bags in S3 presented a greater amount of total macroinvertebrates and shredders comparing with the benthos. The most suitable explanation is that the fauna find a food substrate in bags less affected by calcite precipitation, which is common in the streambed at this site. Decomposition rate in coarse bags was positively related to associated shredder biomass. Thus, droughts in streams under oceanic climate conditions affect mainly the macroinvertebrate detritivore activity, although macroinvertebrates may show distinct behavior imposed by the physicochemical properties of water, mainly travertine precipitation, which can override the flow intermittence effects. Copyright © 2014. Published by Elsevier B.V.

Embrittlement of Intercritically Reheated Coarse Grain Heat-Affected Zone of ASTM4130 Steel

NASA Astrophysics Data System (ADS)

Li, Liying; Han, Tao; Han, Bin

2018-04-01

In this investigation, a thermal welding simulation technique was used to investigate the microstructures and mechanical properties of the intercritically reheated coarse grain heat-affected zone (IR CGHAZ) of ASTM4130 steel. The effect of post weld heat treatment (PWHT) on the toughness of IR CGHAZ was also analyzed. The toughness of IR CGHAZ was measured by means of Charpy impact, and it is found that IR CGHAZ has the lowest toughness which is much lower than that of the base metal regardless of whether PWHT is applied or not. The as-welded IR CGHAZ is mainly composed of ferrite, martensite, and many blocky M-A constituents distributing along grain boundaries and subgrain boundaries in a near-connected network. Also, the prior austenite grains are still as coarse as those in the coarse grain heat-affected zone (CGHAZ). The presence of the blocky M-A constituents and the coarsened austenite grains result in the toughness deterioration of the as-welded IR CGHAZ. Most of the blocky M-A constituents are decomposed to granular bainite due to the effect of the PWHT. However, PWHT cannot refine the prior austenite grains. Thus, the low toughness of IR CGHAZ after PWHT can be attributed to two factors, i.e., the coarsened austenite grains, and the presence of the remaining M-A constituents and granular bainite, which are located at grain boundaries and subgrain boundaries in a near-connected network. The absorbed energy of the IR CGHAZ was increased by about 3.75 times, which means that the PWHT can effectively improve the toughness but it cannot be recovered to the level of base metal.

Highly Coarse-Grained Representations of Transmembrane Proteins

PubMed Central

2017-01-01

Numerous biomolecules and biomolecular complexes, including transmembrane proteins (TMPs), are symmetric or at least have approximate symmetries. Highly coarse-grained models of such biomolecules, aiming at capturing the essential structural and dynamical properties on resolution levels coarser than the residue scale, must preserve the underlying symmetry. However, making these models obey the correct physics is in general not straightforward, especially at the highly coarse-grained resolution where multiple (∼3–30 in the current study) amino acid residues are represented by a single coarse-grained site. In this paper, we propose a simple and fast method of coarse-graining TMPs obeying this condition. The procedure involves partitioning transmembrane domains into contiguous segments of equal length along the primary sequence. For the coarsest (lowest-resolution) mappings, it turns out to be most important to satisfy the symmetry in a coarse-grained model. As the resolution is increased to capture more detail, however, it becomes gradually more important to match modular repeats in the secondary structure (such as helix-loop repeats) instead. A set of eight TMPs of various complexity, functionality, structural topology, and internal symmetry, representing different classes of TMPs (ion channels, transporters, receptors, adhesion, and invasion proteins), has been examined. The present approach can be generalized to other systems possessing exact or approximate symmetry, allowing for reliable and fast creation of multiscale, highly coarse-grained mappings of large biomolecular assemblies. PMID:28043122

Into the decomposed body-forensic digital autopsy using multislice-computed tomography.

PubMed

Thali, M J; Yen, K; Schweitzer, W; Vock, P; Ozdoba, C; Dirnhofer, R

2003-07-08

It is impossible to obtain a representative anatomical documentation of an entire body using classical X-ray methods, they subsume three-dimensional bodies into a two-dimensional level. We used the novel multislice-computed tomography (MSCT) technique in order to evaluate a case of homicide with putrefaction of the corpse before performing a classical forensic autopsy. This non-invasive method showed gaseous distension of the decomposing organs and tissues in detail as well as a complex fracture of the calvarium. MSCT also proved useful in screening for foreign matter in decomposing bodies, and full-body scanning took only a few minutes. In conclusion, we believe postmortem MSCT imaging is an excellent vizualisation tool with great potential for forensic documentation and evaluation of decomposed bodies.

Disentangling the drivers of coarse woody debris behavior and carbon gas emissions during fire

NASA Astrophysics Data System (ADS)

Zhao, Weiwei; van der Werf, Guido R.; van Logtestijn, Richard S. P.; van Hal, Jurgen R.; Cornelissen, Johannes H. C.

2016-04-01

The turnover of coarse woody debris, a key terrestrial carbon pool, plays fundamental roles in global carbon cycling. Biological decomposition and fire are two main fates for dead wood turnover. Compared to slow decomposition, fire rapidly transfers organic carbon from the earth surface to the atmosphere. Both a-biotic environmental factors and biotic wood properties determine coarse wood combustion and thereby its carbon gas emissions during fire. Moisture is a key inhibitory environmental factor for fire. The properties of dead wood strongly affect how it burns either directly or indirectly through interacting with moisture. Coarse wood properties vary between plant species and between various decay stages. Moreover, if we put a piece of dead wood in the context of a forest fuel bed, the soil and wood contact might also greatly affect their fire behavior. Using controlled laboratory burns, we disentangled the effects of all these driving factors: tree species (one gymnosperms needle-leaf species, three angiosperms broad-leaf species), wood decay stages (freshly dead, middle decayed, very strongly decayed), moisture content (air-dried, 30% moisture content in mass), and soil-wood contact (on versus 3cm above the ground surface) on dead wood flammability and carbon gas efflux (CO2 and CO released in grams) during fire. Wood density was measured for all coarse wood samples used in our experiment. We found that compared to other drivers, wood decay stages have predominant positive effects on coarse wood combustion (for wood mass burned, R2=0.72 when air-dried and R2=0.52 at 30% moisture content) and associated carbon gas emissions (for CO2andCO (g) released, R2=0.55 when air-dried and R2=0.42 at 30% moisture content) during fire. Thus, wood decay accelerates wood combustion and its CO2 and CO emissions during fire, which can be mainly attributed to the decreasing wood density (for wood mass burned, R2=0.91 when air-dried and R2=0.63 at 30% moisture content) as wood becomes more decomposed. Our results provide quantitative experimental evidence for how several key abiotic and biotic factors, especially moisture content and the key underlying trait wood density, as well as their interactions, together drive coarse wood carbon turnover through fire. Our experimental data on coarse wood behavior and gas efflux during fire will help to improve the predictive power of global vegetation climate models on dead wood turnover and its feedback to climate.

Coarse-graining using the relative entropy and simplex-based optimization methods in VOTCA

NASA Astrophysics Data System (ADS)

Rühle, Victor; Jochum, Mara; Koschke, Konstantin; Aluru, N. R.; Kremer, Kurt; Mashayak, S. Y.; Junghans, Christoph

2014-03-01

Coarse-grained (CG) simulations are an important tool to investigate systems on larger time and length scales. Several methods for systematic coarse-graining were developed, varying in complexity and the property of interest. Thus, the question arises which method best suits a specific class of system and desired application. The Versatile Object-oriented Toolkit for Coarse-graining Applications (VOTCA) provides a uniform platform for coarse-graining methods and allows for their direct comparison. We present recent advances of VOTCA, namely the implementation of the relative entropy method and downhill simplex optimization for coarse-graining. The methods are illustrated by coarse-graining SPC/E bulk water and a water-methanol mixture. Both CG models reproduce the pair distributions accurately. SYM is supported by AFOSR under grant 11157642 and by NSF under grant 1264282. CJ was supported in part by the NSF PHY11-25915 at KITP. K. Koschke acknowledges funding by the Nestle Research Center.

Liquidity spillover in international stock markets through distinct time scales.

PubMed

Righi, Marcelo Brutti; Vieira, Kelmara Mendes

2014-01-01

This paper identifies liquidity spillovers through different time scales based on a wavelet multiscaling method. We decompose daily data from U.S., British, Brazilian and Hong Kong stock markets indices in order to calculate the scale correlation between their illiquidities. The sample is divided in order to consider non-crisis, sub-prime crisis and Eurozone crisis. We find that there are changes in correlations of distinct scales and different periods. Association in finest scales is smaller than in coarse scales. There is a rise on associations in periods of crisis. In frequencies, there is predominance for significant distinctions involving the coarsest scale, while for crises periods there is predominance for distinctions on the finest scale.

Liquidity Spillover in International Stock Markets through Distinct Time Scales

PubMed Central

Righi, Marcelo Brutti; Vieira, Kelmara Mendes

2014-01-01

This paper identifies liquidity spillovers through different time scales based on a wavelet multiscaling method. We decompose daily data from U.S., British, Brazilian and Hong Kong stock markets indices in order to calculate the scale correlation between their illiquidities. The sample is divided in order to consider non-crisis, sub-prime crisis and Eurozone crisis. We find that there are changes in correlations of distinct scales and different periods. Association in finest scales is smaller than in coarse scales. There is a rise on associations in periods of crisis. In frequencies, there is predominance for significant distinctions involving the coarsest scale, while for crises periods there is predominance for distinctions on the finest scale. PMID:24465918

Systematic coarse-grained modeling of complexation between small interfering RNA and polycations

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

Wei, Zonghui; Luijten, Erik, E-mail: luijten@northwestern.edu; Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208

All-atom molecular dynamics simulations can provide insight into the properties of polymeric gene-delivery carriers by elucidating their interactions and detailed binding patterns with nucleic acids. However, to explore nanoparticle formation through complexation of these polymers and nucleic acids and study their behavior at experimentally relevant time and length scales, a reliable coarse-grained model is needed. Here, we systematically develop such a model for the complexation of small interfering RNA (siRNA) and grafted polyethyleneimine copolymers, a promising candidate for siRNA delivery. We compare the predictions of this model with all-atom simulations and demonstrate that it is capable of reproducing detailed bindingmore » patterns, charge characteristics, and water release kinetics. Since the coarse-grained model accelerates the simulations by one to two orders of magnitude, it will make it possible to quantitatively investigate nanoparticle formation involving multiple siRNA molecules and cationic copolymers.« less

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

Dongil Chun; Dohyeon Kim; Kwangyong Eun

TiC-Ni-Mo cermet specimens were prepared by using a mixture of fine (1.5 [mu]m) and coarse (30 [mu]m) TiC powders. When the fraction of fine TiC particles was 80%, a (Ti,Mo,Ni)C complex carbide phase was observed deposited on the coarse TiC particles and resulted in a typical cored structure. As the fraction of fine TiC particles decreased, the coarse TiC particles exhibited a unique microstructural evolution with the development of a concave interface. This microstructural change of the coarse TiC grains can be explained in terms of the coherency strain energy.

MO-G-BRF-01: BEST IN PHYSICS (JOINT IMAGING-THERAPY) - Sensitivity of PET-Based Texture Features to Respiratory Motion in Non-Small Cell Lung Cancer (NSCLC)

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

Yip, S; Aerts, H; Berbeco, R

2014-06-15

Purpose: PET-based texture features are used to quantify tumor heterogeneity due to their predictive power in treatment outcome. We investigated the sensitivity of texture features to tumor motion by comparing whole body (3D) and respiratory-gated (4D) PET imaging. Methods: Twenty-six patients (34 lesions) received 3D and 4D [F-18]FDG-PET scans before chemo-radiotherapy. The acquired 4D data were retrospectively binned into five breathing phases to create the 4D image sequence. Four texture features (Coarseness, Contrast, Busyness, and Complexity) were computed within the the physician-defined tumor volume. The relative difference (δ) in each measure between the 3D- and 4D-PET imaging was calculated. Wilcoxonmore » signed-rank test (p<0.01) was used to determine if δ was significantly different from zero. Coefficient of variation (CV) was used to determine the variability in the texture features between all 4D-PET phases. Pearson correlation coefficient was used to investigate the impact of tumor size and motion amplitude on δ. Results: Significant differences (p<<0.01) between 3D and 4D imaging were found for Coarseness, Busyness, and Complexity. The difference for Contrast was not significant (p>0.24). 4D-PET increased Busyness (∼20%) and Complexity (∼20%), and decreased Coarseness (∼10%) and Contrast (∼5%) compared to 3D-PET. Nearly negligible variability (CV=3.9%) was found between the 4D phase bins for Coarseness and Complexity. Moderate variability was found for Contrast and Busyness (CV∼10%). Poor correlation was found between the tumor volume and δ for the texture features (R=−0.34−0.34). Motion amplitude had moderate impact on δ for Contrast and Busyness (R=−0.64− 0.54) and no impact for Coarseness and Complexity (R=−0.29−0.17). Conclusion: Substantial differences in textures were found between 3D and 4D-PET imaging. Moreover, the variability between phase bins for Coarseness and Complexity was negligible, suggesting that similar quantification can be obtained from all phases. Texture features, blurred out by respiratory motion during 3D-PET acquisition, can be better resolved by 4D-PET imaging with any phase.« less

Correlations between the Signal Complexity of Cerebral and Cardiac Electrical Activity: A Multiscale Entropy Analysis

PubMed Central

Lin, Pei-Feng; Lo, Men-Tzung; Tsao, Jenho; Chang, Yi-Chung; Lin, Chen; Ho, Yi-Lwun

2014-01-01

The heart begins to beat before the brain is formed. Whether conventional hierarchical central commands sent by the brain to the heart alone explain all the interplay between these two organs should be reconsidered. Here, we demonstrate correlations between the signal complexity of brain and cardiac activity. Eighty-seven geriatric outpatients with healthy hearts and varied cognitive abilities each provided a 24-hour electrocardiography (ECG) and a 19-channel eye-closed routine electroencephalography (EEG). Multiscale entropy (MSE) analysis was applied to three epochs (resting-awake state, photic stimulation of fast frequencies (fast-PS), and photic stimulation of slow frequencies (slow-PS)) of EEG in the 1–58 Hz frequency range, and three RR interval (RRI) time series (awake-state, sleep and that concomitant with the EEG) for each subject. The low-to-high frequency power (LF/HF) ratio of RRI was calculated to represent sympatho-vagal balance. With statistics after Bonferroni corrections, we found that: (a) the summed MSE value on coarse scales of the awake RRI (scales 11–20, RRI-MSE-coarse) were inversely correlated with the summed MSE value on coarse scales of the resting-awake EEG (scales 6–20, EEG-MSE-coarse) at Fp2, C4, T6 and T4; (b) the awake RRI-MSE-coarse was inversely correlated with the fast-PS EEG-MSE-coarse at O1, O2 and C4; (c) the sleep RRI-MSE-coarse was inversely correlated with the slow-PS EEG-MSE-coarse at Fp2; (d) the RRI-MSE-coarse and LF/HF ratio of the awake RRI were correlated positively to each other; (e) the EEG-MSE-coarse at F8 was proportional to the cognitive test score; (f) the results conform to the cholinergic hypothesis which states that cognitive impairment causes reduction in vagal cardiac modulation; (g) fast-PS significantly lowered the EEG-MSE-coarse globally. Whether these heart-brain correlations could be fully explained by the central autonomic network is unknown and needs further exploration. PMID:24498375

Coarse-graining errors and numerical optimization using a relative entropy framework

NASA Astrophysics Data System (ADS)

Chaimovich, Aviel; Shell, M. Scott

2011-03-01

The ability to generate accurate coarse-grained models from reference fully atomic (or otherwise "first-principles") ones has become an important component in modeling the behavior of complex molecular systems with large length and time scales. We recently proposed a novel coarse-graining approach based upon variational minimization of a configuration-space functional called the relative entropy, Srel, that measures the information lost upon coarse-graining. Here, we develop a broad theoretical framework for this methodology and numerical strategies for its use in practical coarse-graining settings. In particular, we show that the relative entropy offers tight control over the errors due to coarse-graining in arbitrary microscopic properties, and suggests a systematic approach to reducing them. We also describe fundamental connections between this optimization methodology and other coarse-graining strategies like inverse Monte Carlo, force matching, energy matching, and variational mean-field theory. We suggest several new numerical approaches to its minimization that provide new coarse-graining strategies. Finally, we demonstrate the application of these theoretical considerations and algorithms to a simple, instructive system and characterize convergence and errors within the relative entropy framework.

Coarse-grained simulations of protein-protein association: an energy landscape perspective.

PubMed

Ravikumar, Krishnakumar M; Huang, Wei; Yang, Sichun

2012-08-22

Understanding protein-protein association is crucial in revealing the molecular basis of many biological processes. Here, we describe a theoretical simulation pipeline to study protein-protein association from an energy landscape perspective. First, a coarse-grained model is implemented and its applications are demonstrated via molecular dynamics simulations for several protein complexes. Second, an enhanced search method is used to efficiently sample a broad range of protein conformations. Third, multiple conformations are identified and clustered from simulation data and further projected on a three-dimensional globe specifying protein orientations and interacting energies. Results from several complexes indicate that the crystal-like conformation is favorable on the energy landscape even if the landscape is relatively rugged with metastable conformations. A closer examination on molecular forces shows that the formation of associated protein complexes can be primarily electrostatics-driven, hydrophobics-driven, or a combination of both in stabilizing specific binding interfaces. Taken together, these results suggest that the coarse-grained simulations and analyses provide an alternative toolset to study protein-protein association occurring in functional biomolecular complexes. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Coarse-Grained Simulations of Protein-Protein Association: An Energy Landscape Perspective

PubMed Central

Ravikumar, Krishnakumar M.; Huang, Wei; Yang, Sichun

2012-01-01

Understanding protein-protein association is crucial in revealing the molecular basis of many biological processes. Here, we describe a theoretical simulation pipeline to study protein-protein association from an energy landscape perspective. First, a coarse-grained model is implemented and its applications are demonstrated via molecular dynamics simulations for several protein complexes. Second, an enhanced search method is used to efficiently sample a broad range of protein conformations. Third, multiple conformations are identified and clustered from simulation data and further projected on a three-dimensional globe specifying protein orientations and interacting energies. Results from several complexes indicate that the crystal-like conformation is favorable on the energy landscape even if the landscape is relatively rugged with metastable conformations. A closer examination on molecular forces shows that the formation of associated protein complexes can be primarily electrostatics-driven, hydrophobics-driven, or a combination of both in stabilizing specific binding interfaces. Taken together, these results suggest that the coarse-grained simulations and analyses provide an alternative toolset to study protein-protein association occurring in functional biomolecular complexes. PMID:22947945

On coarse projective integration for atomic deposition in amorphous systems

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

Chuang, Claire Y., E-mail: yungc@seas.upenn.edu, E-mail: meister@unm.edu, E-mail: zepedaruiz1@llnl.gov; Sinno, Talid, E-mail: talid@seas.upenn.edu; Han, Sang M., E-mail: yungc@seas.upenn.edu, E-mail: meister@unm.edu, E-mail: zepedaruiz1@llnl.gov

2015-10-07

Direct molecular dynamics simulation of atomic deposition under realistic conditions is notoriously challenging because of the wide range of time scales that must be captured. Numerous simulation approaches have been proposed to address the problem, often requiring a compromise between model fidelity, algorithmic complexity, and computational efficiency. Coarse projective integration, an example application of the “equation-free” framework, offers an attractive balance between these constraints. Here, periodically applied, short atomistic simulations are employed to compute time derivatives of slowly evolving coarse variables that are then used to numerically integrate differential equations over relatively large time intervals. A key obstacle to themore » application of this technique in realistic settings is the “lifting” operation in which a valid atomistic configuration is recreated from knowledge of the coarse variables. Using Ge deposition on amorphous SiO{sub 2} substrates as an example application, we present a scheme for lifting realistic atomistic configurations comprised of collections of Ge islands on amorphous SiO{sub 2} using only a few measures of the island size distribution. The approach is shown to provide accurate initial configurations to restart molecular dynamics simulations at arbitrary points in time, enabling the application of coarse projective integration for this morphologically complex system.« less

On Coarse Projective Integration for Atomic Deposition in Amorphous Systems

DOE PAGES

Chuang, Claire Y.; Han, Sang M.; Zepeda-Ruiz, Luis A.; ...

2015-10-02

Direct molecular dynamics simulation of atomic deposition under realistic conditions is notoriously challenging because of the wide range of timescales that must be captured. Numerous simulation approaches have been proposed to address the problem, often requiring a compromise between model fidelity, algorithmic complexity and computational efficiency. Coarse projective integration, an example application of the ‘equation-free’ framework, offers an attractive balance between these constraints. Here, periodically applied, short atomistic simulations are employed to compute gradients of slowly-evolving coarse variables that are then used to numerically integrate differential equations over relatively large time intervals. A key obstacle to the application of thismore » technique in realistic settings is the ‘lifting’ operation in which a valid atomistic configuration is recreated from knowledge of the coarse variables. Using Ge deposition on amorphous SiO 2 substrates as an example application, we present a scheme for lifting realistic atomistic configurations comprised of collections of Ge islands on amorphous SiO 2 using only a few measures of the island size distribution. In conclusion, the approach is shown to provide accurate initial configurations to restart molecular dynamics simulations at arbitrary points in time, enabling the application of coarse projective integration for this morphologically complex system.« less

Coarse-graining errors and numerical optimization using a relative entropy framework.

PubMed

Chaimovich, Aviel; Shell, M Scott

2011-03-07

The ability to generate accurate coarse-grained models from reference fully atomic (or otherwise "first-principles") ones has become an important component in modeling the behavior of complex molecular systems with large length and time scales. We recently proposed a novel coarse-graining approach based upon variational minimization of a configuration-space functional called the relative entropy, S(rel), that measures the information lost upon coarse-graining. Here, we develop a broad theoretical framework for this methodology and numerical strategies for its use in practical coarse-graining settings. In particular, we show that the relative entropy offers tight control over the errors due to coarse-graining in arbitrary microscopic properties, and suggests a systematic approach to reducing them. We also describe fundamental connections between this optimization methodology and other coarse-graining strategies like inverse Monte Carlo, force matching, energy matching, and variational mean-field theory. We suggest several new numerical approaches to its minimization that provide new coarse-graining strategies. Finally, we demonstrate the application of these theoretical considerations and algorithms to a simple, instructive system and characterize convergence and errors within the relative entropy framework. © 2011 American Institute of Physics.

Numerical benchmarking of a Coarse-Mesh Transport (COMET) Method for medical physics applications

NASA Astrophysics Data System (ADS)

Blackburn, Megan Satterfield

2009-12-01

Radiation therapy has become a very import method for treating cancer patients. Thus, it is extremely important to accurately determine the location of energy deposition during these treatments, maximizing dose to the tumor region and minimizing it to healthy tissue. A Coarse-Mesh Transport Method (COMET) has been developed at the Georgia Institute of Technology in the Computational Reactor and Medical Physics Group for use very successfully with neutron transport to analyze whole-core criticality. COMET works by decomposing a large, heterogeneous system into a set of smaller fixed source problems. For each unique local problem that exists, a solution is obtained that we call a response function. These response functions are pre-computed and stored in a library for future use. The overall solution to the global problem can then be found by a linear superposition of these local problems. This method has now been extended to the transport of photons and electrons for use in medical physics problems to determine energy deposition from radiation therapy treatments. The main goal of this work was to develop benchmarks for testing in order to evaluate the COMET code to determine its strengths and weaknesses for these medical physics applications. For response function calculations, legendre polynomial expansions are necessary for space, angle, polar angle, and azimuthal angle. An initial sensitivity study was done to determine the best orders for future testing. After the expansion orders were found, three simple benchmarks were tested: a water phantom, a simplified lung phantom, and a non-clinical slab phantom. Each of these benchmarks was decomposed into 1cm x 1cm and 0.5cm x 0.5cm coarse meshes. Three more clinically relevant problems were developed from patient CT scans. These benchmarks modeled a lung patient, a prostate patient, and a beam re-entry situation. As before, the problems were divided into 1cm x 1cm, 0.5cm x 0.5cm, and 0.25cm x 0.25cm coarse mesh cases. Multiple beam energies were also tested for each case. The COMET solutions for each case were compared to a reference solution obtained by pure Monte Carlo results from EGSnrc. When comparing the COMET results to the reference cases, a pattern of differences appeared in each phantom case. It was found that better results were obtained for lower energy incident photon beams as well as for larger mesh sizes. Possible changes may need to be made with the expansion orders used for energy and angle to better model high energy secondary electrons. Heterogeneity also did not pose a problem for the COMET methodology. Heterogeneous results were found in a comparable amount of time to the homogeneous water phantom. The COMET results were typically found in minutes to hours of computational time, whereas the reference cases typically required hundreds or thousands of hours. A second sensitivity study was also performed on a more stringent problem and with smaller coarse meshes. Previously, the same expansion order was used for each incident photon beam energy so better comparisons could be made. From this second study, it was found that it is optimal to have different expansion orders based on the incident beam energy. Recommendations for future work with this method include more testing on higher expansion orders or possible code modification to better handle secondary electrons. The method also needs to handle more clinically relevant beam descriptions with an energy and angular distribution associated with it.

Entropy Production in Field Theories without Time-Reversal Symmetry: Quantifying the Non-Equilibrium Character of Active Matter

NASA Astrophysics Data System (ADS)

Nardini, Cesare; Fodor, Étienne; Tjhung, Elsen; van Wijland, Frédéric; Tailleur, Julien; Cates, Michael E.

2017-04-01

Active-matter systems operate far from equilibrium because of the continuous energy injection at the scale of constituent particles. At larger scales, described by coarse-grained models, the global entropy production rate S quantifies the probability ratio of forward and reversed dynamics and hence the importance of irreversibility at such scales: It vanishes whenever the coarse-grained dynamics of the active system reduces to that of an effective equilibrium model. We evaluate S for a class of scalar stochastic field theories describing the coarse-grained density of self-propelled particles without alignment interactions, capturing such key phenomena as motility-induced phase separation. We show how the entropy production can be decomposed locally (in real space) or spectrally (in Fourier space), allowing detailed examination of the spatial structure and correlations that underly departures from equilibrium. For phase-separated systems, the local entropy production is concentrated mainly on interfaces, with a bulk contribution that tends to zero in the weak-noise limit. In homogeneous states, we find a generalized Harada-Sasa relation that directly expresses the entropy production in terms of the wave-vector-dependent deviation from the fluctuation-dissipation relation between response functions and correlators. We discuss extensions to the case where the particle density is coupled to a momentum-conserving solvent and to situations where the particle current, rather than the density, should be chosen as the dynamical field. We expect the new conceptual tools developed here to be broadly useful in the context of active matter, allowing one to distinguish when and where activity plays an essential role in the dynamics.

Ecology of coarse wood decomposition by the saprotrophic fungus Fomes fomentarius.

PubMed

Větrovský, Tomáš; Voříšková, Jana; Snajdr, Jaroslav; Gabriel, Jiří; Baldrian, Petr

2011-07-01

Saprotrophic wood-inhabiting basidiomycetes are the most important decomposers of lignin and cellulose in dead wood and as such they attracted considerable attention. The aims of this work were to quantify the activity and spatial distribution of extracellular enzymes in coarse wood colonised by the white-rot basidiomycete Fomes fomentarius and in adjacent fruitbodies of the fungus and to analyse the diversity of the fungal and bacterial community in a fungus-colonised wood and its potential effect on enzyme production by F. fomentarius. Fungus-colonised wood and fruitbodies were collected in low management intensity forests in the Czech Republic. There were significant differences in enzyme production by F. fomentarius between Betula pendula and Fagus sylvatica wood, the activity of cellulose and xylan-degrading enzymes was significantly higher in beech wood than in birch wood. Spatial analysis of a sample B. pendula log segment proved that F. fomentarius was the single fungal representative found in the log. There was a high level of spatial variability in the amount of fungal biomass detected, but no effects on enzyme activities were observed. Samples from the fruiting body showed high β-glucosidase and chitinase activities compared to wood samples. Significantly higher levels of xylanase and cellobiohydrolase were found in samples located near the fruitbody (proximal), and higher laccase and Mn-peroxidase activities were found in the distal ones. The microbial community in wood was dominated by the fungus (fungal to bacterial DNA ratio of 62-111). Bacterial abundance composition was lower in proximal than distal parts of wood by a factor of 24. These results show a significant level of spatial heterogeneity in coarse wood. One of the explanations may be the successive colonization of wood by the fungus: due to differential enzyme production, the rates of biodegradation of coarse wood are also spatially inhomogeneous.

Decomposition of Rotor Hopfield Neural Networks Using Complex Numbers.

PubMed

Kobayashi, Masaki

2018-04-01

A complex-valued Hopfield neural network (CHNN) is a multistate model of a Hopfield neural network. It has the disadvantage of low noise tolerance. Meanwhile, a symmetric CHNN (SCHNN) is a modification of a CHNN that improves noise tolerance. Furthermore, a rotor Hopfield neural network (RHNN) is an extension of a CHNN. It has twice the storage capacity of CHNNs and SCHNNs, and much better noise tolerance than CHNNs, although it requires twice many connection parameters. In this brief, we investigate the relations between CHNN, SCHNN, and RHNN; an RHNN is uniquely decomposed into a CHNN and SCHNN. In addition, the Hebbian learning rule for RHNNs is decomposed into those for CHNNs and SCHNNs.

Protein-Protein Interactions of Azurin Complex by Coarse-Grained Simulations with a Gō-Like Model

NASA Astrophysics Data System (ADS)

Rusmerryani, Micke; Takasu, Masako; Kawaguchi, Kazutomo; Saito, Hiroaki; Nagao, Hidemi

Proteins usually perform their biological functions by forming a complex with other proteins. It is very important to study the protein-protein interactions since these interactions are crucial in many processes of a living organism. In this study, we develop a coarse grained model to simulate protein complex in liquid system. We carry out molecular dynamics simulations with topology-based potential interactions to simulate dynamical properties of Pseudomonas Aeruginosa azurin complex systems. Azurin is known to play an essential role as an anticancer agent and bind many important intracellular molecules. Some physical properties are monitored during simulation time to get a better understanding of the influence of protein-protein interactions to the azurin complex dynamics. These studies will provide valuable insights for further investigation on protein-protein interactions in more realistic system.

Variations in the microstructure and properties of Mn-Ti multiple-phase steel with high strength under different tempering temperatures

NASA Astrophysics Data System (ADS)

Li, Dazhao; Li, Xiaonan; Cui, Tianxie; Li, Jianmin; Wang, Yutian; Fu, Peimao

2015-03-01

There are few relevant researches on coils by tempering, and the variations of microstructure and properties of steel coil during the tempering process also remain unclear. By using thermo-mechanical control process(TMCP) technology, Mn-Ti typical HSLA steel coils with yield strength of 920 MPa are produced on the 2250 hot rolling production line. Then, the samples are taken from the coils and tempered at the temperatures of 220 °C, 350 °C, and 620 °C respectively. After tempering the strength, ductility and toughness of samples are tested, and meanwhile microstructures are investigated. Precipitates initially emerge inside the ferrite laths and the density of the dislocation drops. Then, the lath-shaped ferrites begin to gather, and the retained austenite films start to decompose. Finally, the retained austenite films are completely decomposed into coarse and short rod-shape precipitates composed of C and Ti compounds. The yield strength increases with increasing tempering temperature due to the pinning effect of the precipitates, and the dislocation density decreases. The yield strength is highest when the steel is tempered at 220 °C because of pinning of the precipitates to dislocations. The total elongation increases in all samples because of the development of ferrites during tempering. The tensile strength and impact absorbed energy decline because the effect of impeding crack propagation weakens as the retained austenite films completely decompose and the precipitates coarsen. This paper clarifies the influence of different tempering temperatures on phase transformation characteristics and process of Mn-Ti typical multiphase steels, as well as its resulting performance variation rules.

Star polymers as unit cells for coarse-graining cross-linked networks

NASA Astrophysics Data System (ADS)

Molotilin, Taras Y.; Maduar, Salim R.; Vinogradova, Olga I.

2018-03-01

Reducing the complexity of cross-linked polymer networks by preserving their main macroscale properties is key to understanding them, and a crucial issue is to relate individual properties of the polymer constituents to those of the reduced network. Here we study polymer networks in a good solvent, by considering star polymers as their unit elements, and first quantify the interaction between their centers of masses. We then reduce the complexity of a network by replacing sets of its bridged star polymers by equivalent effective soft particles with dense cores. Our coarse graining allows us to approximate complex polymer networks by much simpler ones, keeping their relevant mechanical properties, as illustrated in computer experiments.

Opaque for the Reader but Transparent for the Brain: Neural Signatures of Morphological Complexity

ERIC Educational Resources Information Center

Meinzer, Marcus; Lahiri, Aditi; Flaisch, Tobias; Hannemann, Ronny; Eulitz, Carsten

2009-01-01

Within linguistics, words with a complex internal structure are commonly assumed to be decomposed into their constituent morphemes (e.g., un-help-ful). Nevertheless, an ongoing debate concerns the brain structures that subserve this process. Using functional magnetic resonance imaging, the present study varied the internal complexity of derived…

Erosion and deposition by supercritical density flows during channel avulsion and backfilling: Field examples from coarse-grained deepwater channel-levée complexes (Sandino Forearc Basin, southern Central America)

NASA Astrophysics Data System (ADS)

Lang, Jörg; Brandes, Christian; Winsemann, Jutta

2017-03-01

Erosion and deposition by supercritical density flows can strongly impact the facies distribution and architecture of submarine fans. Field examples from coarse-grained channel-levée complexes from the Sandino Forearc Basin (southern Central America) show that cyclic-step and antidune deposits represent common sedimentary facies of these depositional systems and relate to the different stages of avulsion, bypass, levée construction and channel backfilling. During channel avulsion, large-scale scour-fill complexes (18 to 29 m deep, 18 to 25 m wide, 60 to > 120 m long) were incised by supercritical density flows. The multi-storey infill of the large-scale scour-fill complexes comprises amalgamated massive, normally coarse-tail graded or widely spaced subhorizontally stratified conglomerates and pebbly sandstones, interpreted as deposits of the hydraulic-jump zone of cyclic steps. The large-scale scour-fill complexes can be distinguished from small-scale channel fills based on the preservation of a steep upper margin and a coarse-grained infill comprising mainly amalgamated hydraulic-jump zone deposits. Channel fills include repeated successions deposited by cyclic steps with superimposed antidunes. The deposits of the hydraulic-jump zone of cyclic steps comprise regularly spaced scours (0.2 to 2.6 m deep, 0.8 to 23 m long) infilled by intraclast-rich conglomerates or pebbly sandstones, displaying normal coarse-tail grading or backsets. These deposits are laterally and vertically associated with subhorizontally stratified, low-angle cross-stratified or sinusoidally stratified sandstones and pebbly sandstones, which were deposited by antidunes on the stoss side of the cyclic steps during flow re-acceleration. The field examples indicate that so-called spaced stratified deposits may commonly represent antidune deposits with varying stratification styles controlled by the aggradation rate, grain-size distribution and amalgamation. The deposits of small-scale cyclic steps with superimposed antidunes form fining-upwards successions with decreasing antidune wavelengths, indicating waning flows. Such cyclic step-antidune successions form the characteristic basal infill of mid-fan channels, and are inferred to be related to successive supercritical high-density turbidity flows triggered by retrogressive slope failures.

Long-term dynamics of organic matter and elements exported as coarse particulates from two Caribbean montane watersheds

Treesearch

T. Heartsill Scalley; F.N. Scatena; S. Moya; A.E. Lugo

2012-01-01

In heterotrophic streams the retention and export of coarse particulate organic matter and associated elements are fundamental biogeochemical processes that influence water quality, food webs and the structural complexity of forested headwater streams. Nevertheless, few studies have documented the quantity and quality of exported organic matter over multiple years and...

Subsurface Optical Microscopy of Coarse Grain Spinels. Phase 1

DTIC Science & Technology

2013-12-01

A 456 nm LED line bar illuminated in figure 15 and a Xenon fiber optic bar illuminator is shown for figure 16. The optical in situ or subsurface ... imaging of coarse grain spinels and AlONs is optically more complex than expected. An overhead view of the side illumination field is shown in figure 20

Domain-averaged snow depth over complex terrain from flat field measurements

NASA Astrophysics Data System (ADS)

Helbig, Nora; van Herwijnen, Alec

2017-04-01

Snow depth is an important parameter for a variety of coarse-scale models and applications, such as hydrological forecasting. Since high-resolution snow cover models are computational expensive, simplified snow models are often used. Ground measured snow depth at single stations provide a chance for snow depth data assimilation to improve coarse-scale model forecasts. Snow depth is however commonly recorded at so-called flat fields, often in large measurement networks. While these ground measurement networks provide a wealth of information, various studies questioned the representativity of such flat field snow depth measurements for the surrounding topography. We developed two parameterizations to compute domain-averaged snow depth for coarse model grid cells over complex topography using easy to derive topographic parameters. To derive the two parameterizations we performed a scale dependent analysis for domain sizes ranging from 50m to 3km using highly-resolved snow depth maps at the peak of winter from two distinct climatic regions in Switzerland and in the Spanish Pyrenees. The first, simpler parameterization uses a commonly applied linear lapse rate. For the second parameterization, we first removed the obvious elevation gradient in mean snow depth, which revealed an additional correlation with the subgrid sky view factor. We evaluated domain-averaged snow depth derived with both parameterizations using flat field measurements nearby with the domain-averaged highly-resolved snow depth. This revealed an overall improved performance for the parameterization combining a power law elevation trend scaled with the subgrid parameterized sky view factor. We therefore suggest the parameterization could be used to assimilate flat field snow depth into coarse-scale snow model frameworks in order to improve coarse-scale snow depth estimates over complex topography.

Upscaling of Mixed Finite Element Discretization Problems by the Spectral AMGe Method

DOE PAGES

Kalchev, Delyan Z.; Lee, C. S.; Villa, U.; ...

2016-09-22

Here, we propose two multilevel spectral techniques for constructing coarse discretization spaces for saddle-point problems corresponding to PDEs involving a divergence constraint, with a focus on mixed finite element discretizations of scalar self-adjoint second order elliptic equations on general unstructured grids. We use element agglomeration algebraic multigrid (AMGe), which employs coarse elements that can have nonstandard shape since they are agglomerates of fine-grid elements. The coarse basis associated with each agglomerated coarse element is constructed by solving local eigenvalue problems and local mixed finite element problems. This construction leads to stable upscaled coarse spaces and guarantees the inf-sup compatibility ofmore » the upscaled discretization. Also, the approximation properties of these upscaled spaces improve by adding more local eigenfunctions to the coarse spaces. The higher accuracy comes at the cost of additional computational effort, as the sparsity of the resulting upscaled coarse discretization (referred to as operator complexity) deteriorates when we introduce additional functions in the coarse space. We also provide an efficient solver for the coarse (upscaled) saddle-point system by employing hybridization, which leads to a symmetric positive definite (s.p.d.) reduced system for the Lagrange multipliers, and to solve the latter s.p.d. system, we use our previously developed spectral AMGe solver. Numerical experiments, in both two and three dimensions, are provided to illustrate the efficiency of the proposed upscaling technique.« less

Upscaling of Mixed Finite Element Discretization Problems by the Spectral AMGe Method

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

Kalchev, Delyan Z.; Lee, C. S.; Villa, U.

Here, we propose two multilevel spectral techniques for constructing coarse discretization spaces for saddle-point problems corresponding to PDEs involving a divergence constraint, with a focus on mixed finite element discretizations of scalar self-adjoint second order elliptic equations on general unstructured grids. We use element agglomeration algebraic multigrid (AMGe), which employs coarse elements that can have nonstandard shape since they are agglomerates of fine-grid elements. The coarse basis associated with each agglomerated coarse element is constructed by solving local eigenvalue problems and local mixed finite element problems. This construction leads to stable upscaled coarse spaces and guarantees the inf-sup compatibility ofmore » the upscaled discretization. Also, the approximation properties of these upscaled spaces improve by adding more local eigenfunctions to the coarse spaces. The higher accuracy comes at the cost of additional computational effort, as the sparsity of the resulting upscaled coarse discretization (referred to as operator complexity) deteriorates when we introduce additional functions in the coarse space. We also provide an efficient solver for the coarse (upscaled) saddle-point system by employing hybridization, which leads to a symmetric positive definite (s.p.d.) reduced system for the Lagrange multipliers, and to solve the latter s.p.d. system, we use our previously developed spectral AMGe solver. Numerical experiments, in both two and three dimensions, are provided to illustrate the efficiency of the proposed upscaling technique.« less

Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

PubMed

Shen, Lin; Yang, Weitao

2016-04-12

We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.

Automated deconvolution of structured mixtures from heterogeneous tumor genomic data

PubMed Central

Roman, Theodore; Xie, Lu

2017-01-01

With increasing appreciation for the extent and importance of intratumor heterogeneity, much attention in cancer research has focused on profiling heterogeneity on a single patient level. Although true single-cell genomic technologies are rapidly improving, they remain too noisy and costly at present for population-level studies. Bulk sequencing remains the standard for population-scale tumor genomics, creating a need for computational tools to separate contributions of multiple tumor clones and assorted stromal and infiltrating cell populations to pooled genomic data. All such methods are limited to coarse approximations of only a few cell subpopulations, however. In prior work, we demonstrated the feasibility of improving cell type deconvolution by taking advantage of substructure in genomic mixtures via a strategy called simplicial complex unmixing. We improve on past work by introducing enhancements to automate learning of substructured genomic mixtures, with specific emphasis on genome-wide copy number variation (CNV) data, as well as the ability to process quantitative RNA expression data, and heterogeneous combinations of RNA and CNV data. We introduce methods for dimensionality estimation to better decompose mixture model substructure; fuzzy clustering to better identify substructure in sparse, noisy data; and automated model inference methods for other key model parameters. We further demonstrate their effectiveness in identifying mixture substructure in true breast cancer CNV data from the Cancer Genome Atlas (TCGA). Source code is available at https://github.com/tedroman/WSCUnmix PMID:29059177

A comparative study of the microstructures observed in statically cast and continuously cast Bi-In-Sn ternary eutectic alloy

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

Sengupta, S.; Soda, H.; McLean, A.

2000-01-01

A ternary eutectic alloy with a composition of 57.2 pct Bi, 24.8 pct In, and 18 pct Sn was continuously cast into wire of 2 mm diameter with casting speeds of 14 and 79 mm/min using the Ohno Continuous Casting (OCC) process. The microstructures obtained were compared with those of statically cast specimens. Extensive segregation of massive Bi blocks, Bi complex structures, and tin-rich dendrites was found in specimens that were statically cast. Decomposition of {radical}Sn by a eutectoid reaction was confirmed based on microstructural evidence. Ternary eutectic alloy with a cooling rate of approximately 1 C/min formed a doublemore » binary eutectic. The double binary eutectic consisted of regions of BiIn and decomposed {radical}Sn in the form of a dendrite cell structure and regions of Bi and decomposed {radical}Sn in the form of a complex-regular cell. The Bi complex-regular cells, which are a ternary eutectic constituent, existed either along the boundaries of the BiIn-decomposed {radical}Sn dendrite cells or at the front of elongated dendrite cell structures. In the continuously cast wires, primary Sn dendrites coupled with a small Bi phase were uniformly distributed within the Bi-In alloy matrix. Neither massive Bi phase, Bi complex-regular cells, no BiIn eutectic dendrite cells were observed, resulting in a more uniform microstructure in contrast to the heavily segregated structures of the statically cast specimens.« less

THE OPEP COARSE-GRAINED PROTEIN MODEL: FROM SINGLE MOLECULES, AMYLOID FORMATION, ROLE OF MACROMOLECULAR CROWDING AND HYDRODYNAMICS TO RNA/DNA COMPLEXES

PubMed Central

Sterpone, Fabio; Melchionna, Simone; Tuffery, Pierre; Pasquali, Samuela; Mousseau, Normand; Cragnolini, Tristan; Chebaro, Yassmine; Saint-Pierre, Jean-Francois; Kalimeri, Maria; Barducci, Alessandro; Laurin, Yohan; Tek, Alex; Baaden, Marc; Nguyen, Phuong Hoang; Derreumaux, Philippe

2015-01-01

The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows studying single protein properties, DNA/RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the on-going developments. PMID:24759934

Natural 13C abundance: a tool to trace the incorporation of dung-derived carbon into soil particle-size fractions.

PubMed

Amelung, W; Bol, R; Friedrich, C

1999-01-01

During the decay of 13C enriched dung patches, the; delta 13C signal of surface soil (1-5 cm) increased with a temporary maximum after 42 d. To understand the underlying processes, we investigated the incorporation of dung-derived C into soil particle-size fractions. Dung, collected from beef steers fed on maize (delta 13C = -15.36/1000) or ryegrass (delta 13C = -25.67/1000), was applied in circular patches to a C3 pasture at North Wyke, UK. Triplicates were sampled from surface soil (1-5 cm) at 14, 28, 42, and 70 d after application, pooled, separated into fine (< 0.2 micron) and coarse clay (0.2-2 microns), silt plus fine sand (2-250 microns), and coarse sand (250-2000 microns), and analyzed for total C, N, and delta 13C. As particle-size diameter decreased, the C/N ratios decreased and delta 13C values increased at all plots due to increasing microbial alteration of soil organic matter. After dung application, ca. 60% of dung-derived C in soil was recovered in the 0.2-250 microns fractions during the whole experiment. The proportion of dung-derived C in the fine clay peaked 42 d after dung application, coinciding with the delta 13C maximum in the bulk soil and the maximum leaching rate measured in lysimeters at this time in another study at the same sites. The percentage of dung-derived C as particulate C in the coarse sand fraction increased until the end of the experiment. We conclude that incorporation of C into soil from decomposing dung patches involved both temporary sorption of leached dung C to < 0.2 micron fractions and continuous accumulation of particulate C (> 250 microns).

Vertebrate Decomposition Is Accelerated by Soil Microbes

PubMed Central

Lauber, Christian L.; Metcalf, Jessica L.; Keepers, Kyle; Ackermann, Gail; Carter, David O.

2014-01-01

Carrion decomposition is an ecologically important natural phenomenon influenced by a complex set of factors, including temperature, moisture, and the activity of microorganisms, invertebrates, and scavengers. The role of soil microbes as decomposers in this process is essential but not well understood and represents a knowledge gap in carrion ecology. To better define the role and sources of microbes in carrion decomposition, lab-reared mice were decomposed on either (i) soil with an intact microbial community or (ii) soil that was sterilized. We characterized the microbial community (16S rRNA gene for bacteria and archaea, and the 18S rRNA gene for fungi and microbial eukaryotes) for three body sites along with the underlying soil (i.e., gravesoils) at time intervals coinciding with visible changes in carrion morphology. Our results indicate that mice placed on soil with intact microbial communities reach advanced stages of decomposition 2 to 3 times faster than those placed on sterile soil. Microbial communities associated with skin and gravesoils of carrion in stages of active and advanced decay were significantly different between soil types (sterile versus untreated), suggesting that substrates on which carrion decompose may partially determine the microbial decomposer community. However, the source of the decomposer community (soil- versus carcass-associated microbes) was not clear in our data set, suggesting that greater sequencing depth needs to be employed to identify the origin of the decomposer communities in carrion decomposition. Overall, our data show that soil microbial communities have a significant impact on the rate at which carrion decomposes and have important implications for understanding carrion ecology. PMID:24907317

Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method

PubMed Central

Ovchinnikov, Victor; Karplus, Martin

2014-01-01

A parallel implementation of the finite-temperature string method is described, which takes into account the invariance of coordinates with respect to rigid-body motions. The method is applied to the complex α-helix↔β-sheet transition in a β-hairpin miniprotein in implicit solvent, which exhibits much of the complexity of conformational changes in proteins. Two transition paths are considered, one derived from a linear interpolant between the endpoint structures and the other derived from a targeted dynamics simulation. Two methods for computing the conformational free energy (FE) along the string are compared, a restrained method, and a tessellation method introduced by E. Vanden-Eijnden and M. Venturoli [J. Chem. Phys. 130, 194103 (2009)]. It is found that obtaining meaningful free energy profiles using the present atom-based coordinates requires restricting sampling to a vicinity of the converged path, where the hyperplanar approximation to the isocommittor surface is sufficiently accurate. This sampling restriction can be easily achieved using restraints or constraints. The endpoint FE differences computed from the FE profiles are validated by comparison with previous calculations using a path-independent confinement method. The FE profiles are decomposed into the enthalpic and entropic contributions, and it is shown that the entropy difference contribution can be as large as 10 kcal/mol for intermediate regions along the path, compared to 15–20 kcal/mol for the enthalpy contribution. This result demonstrates that enthalpic barriers for transitions are offset by entropic contributions arising from the existence of different paths across a barrier. The possibility of using systematically coarse-grained representations of amino acids, in the spirit of multiple interaction site residue models, is proposed as a means to avoid ad hoc sampling restrictions to narrow transition tubes. PMID:24811667

Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method

NASA Astrophysics Data System (ADS)

Ovchinnikov, Victor; Karplus, Martin

2014-05-01

A parallel implementation of the finite-temperature string method is described, which takes into account the invariance of coordinates with respect to rigid-body motions. The method is applied to the complex α-helix↔β-sheet transition in a β-hairpin miniprotein in implicit solvent, which exhibits much of the complexity of conformational changes in proteins. Two transition paths are considered, one derived from a linear interpolant between the endpoint structures and the other derived from a targeted dynamics simulation. Two methods for computing the conformational free energy (FE) along the string are compared, a restrained method, and a tessellation method introduced by E. Vanden-Eijnden and M. Venturoli [J. Chem. Phys. 130, 194103 (2009)]. It is found that obtaining meaningful free energy profiles using the present atom-based coordinates requires restricting sampling to a vicinity of the converged path, where the hyperplanar approximation to the isocommittor surface is sufficiently accurate. This sampling restriction can be easily achieved using restraints or constraints. The endpoint FE differences computed from the FE profiles are validated by comparison with previous calculations using a path-independent confinement method. The FE profiles are decomposed into the enthalpic and entropic contributions, and it is shown that the entropy difference contribution can be as large as 10 kcal/mol for intermediate regions along the path, compared to 15-20 kcal/mol for the enthalpy contribution. This result demonstrates that enthalpic barriers for transitions are offset by entropic contributions arising from the existence of different paths across a barrier. The possibility of using systematically coarse-grained representations of amino acids, in the spirit of multiple interaction site residue models, is proposed as a means to avoid ad hoc sampling restrictions to narrow transition tubes.

Morphological Decomposition Based on the Analysis of Orthography

ERIC Educational Resources Information Center

Rastle, Kathleen; Davis, Matthew H.

2008-01-01

Recent theories of morphological processing have been dominated by the notion that morphologically complex words are decomposed into their constituents on the basis of their semantic properties. In this article we argue that the weight of evidence now suggests that the recognition of morphologically complex words begins with a rapid morphemic…

Can organic matter hide from decomposers in the labyrinth of soil aggregates? Micro-engineered Soil Chips challenging foraging fungi

NASA Astrophysics Data System (ADS)

Hammer, Edith C.; Aleklett, Kristin; Arellano Caicedo, Carlos G.; Bengtsson, Martin; Micaela Mafla Endara, Paola; Ohlsson, Pelle

2017-04-01

From the point of view of microorganisms, the soil environment is an enormously complex labyrinth with paths and dead-end streets, where resources and shelters are unevenly distributed. We study foraging strategies of soil organisms, especially fungi, and the possibility of physio-spatial stabilization of organic matter by "hiding" in occluded soil spaces. We manipulate growth habitat microstructure with lab-on-a-chip techniques, where we designed complex environments with channels and obstacle at dimensions of the size of hyphae, and construct them in the transparent, gas-permeable polymer PDMS. We fill those with different nutrient solutions or combine with mineral nutrient gradients, and inoculate them with soil organisms. We analyze organisms and substrates with microscopy, fluorescence microscopy and analytical chemistry. We compared different soil litter decomposers and an arbuscular mycorrhizal fungus for their ability to forage through complex air-gap structures and attempt to classify them into functional traits concerning their mycelium directionality, space-exploring approach and ability to grow through acute angles and narrow constrictions. We identified structures which are very difficult to penetrate for most species, and compounds located behind such features may thus be spatially unavailable for decomposers. We discuss our approach in comparison to soil pore space tomographic analyses and findings we made in the pore space of colonized wood biochar.

Does Learning a Complex Task Have To Be Complex?: A Study in Learning Decomposition.

ERIC Educational Resources Information Center

Lee, Frank J.; Anderson, John R.

2001-01-01

Decomposed the learning in the Kanfer-Ackerman Air-Traffic Controller Task (P. Ackerman, 1988) down to learning at the keyboard level. Reanalyzed the Ackerman data to show that learning in this complex task reflects learning at the keystroke level. Conducted an eye-tracking experiment with 10 adults that showed that learning at the key stroke…

Interplay between morphology and frequency in lexical access: The case of the base frequency effect

PubMed Central

Vannest, Jennifer; Newport, Elissa L.; Newman, Aaron J.; Bavelier, Daphne

2011-01-01

A major issue in lexical processing concerns storage and access of lexical items. Here we make use of the base frequency effect to examine this. Specifically, reaction time to morphologically complex words (words made up of base and suffix, e.g., agree+able) typically reflects frequency of the base element (i.e., total frequency of all words in which agree appears) rather than surface word frequency (i.e., frequency of agreeable itself). We term these complex words decomposable. However, a class of words termed whole-word do not show such sensitivity to base frequency (e.g., serenity). Using an event-related MRI design, we exploited the fact that processing low-frequency words increases BOLD activity relative to high frequency ones, and examined effects of base frequency on brain activity for decomposable and whole-word items. Morphologically complex words, half high and half low base frequency, were compared to matched high and low frequency simple monomorphemic words using a lexical decision task. Morphologically complex words increased activation in left inferior frontal and left superior temporal cortices versus simple words. The only area to mirror the behavioral distinction between decomposable and whole-word types was the thalamus. Surprisingly, most frequency-sensitive areas failed to show base frequency effects. This variety of responses to frequency and word type across brain areas supports an integrative view of multiple variables during lexical access, rather than a dichotomy between memory-based access and on-line computation. Lexical access appears best captured as interplay of several neural processes with different sensitivities to various linguistic factors including frequency and morphological complexity. PMID:21167136

MWIR imaging spectrometer with digital time delay integration for remote sensing and characterization of solar system objects

NASA Astrophysics Data System (ADS)

Kendrick, Stephen E.; Harwit, Alex; Kaplan, Michael; Smythe, William D.

2007-09-01

An MWIR TDI (Time Delay and Integration) Imager and Spectrometer (MTIS) instrument for characterizing from orbit the moons of Jupiter and Saturn is proposed. Novel to this instrument is the planned implementation of a digital TDI detector array and an innovative imaging/spectroscopic architecture. Digital TDI enables a higher SNR for high spatial resolution surface mapping of Titan and Enceladus and for improved spectral discrimination and resolution at Europa. The MTIS imaging/spectroscopic architecture combines a high spatial resolution coarse wavelength resolution imaging spectrometer with a hyperspectral sensor to spectrally decompose a portion of the data adjacent to the data sampled in the imaging spectrometer. The MTIS instrument thus maps with high spatial resolution a planetary object while spectrally decomposing enough of the data that identification of the constituent materials is highly likely. Additionally, digital TDI systems have the ability to enable the rejection of radiation induced spikes in high radiation environments (Europa) and the ability to image in low light levels (Titan and Enceladus). The ability to image moving objects that might be missed utilizing a conventional TDI system is an added advantage and is particularly important for characterizing atmospheric effects and separating atmospheric and surface components. This can be accomplished with on-orbit processing or collecting and returning individual non co-added frames.

Characterisation of silica derived from rice husk (Muar, Johor, Malaysia) decomposition at different temperatures

NASA Astrophysics Data System (ADS)

Azmi, M. A.; Ismail, N. A. A.; Rizamarhaiza, M.; W. M. Hasif. A. A., K.; Taib, H.

2016-07-01

Rice husk was thermally decomposed to yield powder composed of silica (SiO2). Temperatures of 700°C and 1000°C were chosen as the decomposition temperatures. X-Ray Diffraction (XRD), X-Ray Florescence (XRF), Fourier Transform Infrared (FTIR), and Field Emission Scanning Electron Microscope (FESEM) analyses were conducted on a synthetic silica powder (SS-SiO2) and the rice husk ash as for the comparative characterisation study. XRD analyses clearly indicated that the decomposed rice husk yielded silica of different nature which are Crystalline Rice Husk Silica (C-RHSiO2) and Amorphous Rice Husk Silica (A-RHSiO2). Moreover, it was found that SS-SiO2 was of Quartz phase, C-RHSiO2 was of Trydimite and Cristobalite. Through XRF detection, the highest SiO2 purity was detected in SS-SiO2 followed by C-RHSiO2 and A-RHSiO2 with purity percentages of 99.60%, 82.30% and 86.30% respectively. FTIR results clearly indicated silica (SiO2) bonding 1056, 1064, 1047, 777, 790 and 798 cm-1) increased as the crystallinity silica increased. The Cristobalite phase was detected in C-RH SiO2 at the wavelength of 620 cm-1. Morphological features as observed by FESEM analyses confirmed that, SS-SiO2 and C-RH SiO2 showed prominent coarse granular morphology.

Bryophyte species associations with coarse woody debris and stand ages in Oregon

USGS Publications Warehouse

Rambo, T.; Muir, Patricia S.

1998-01-01

We quantified the relationships of 93 forest floor bryophyte species, including epiphytes from incorporated litterfall, to substrate and stand age in Pseudotsuga menziesii-Tsuga heterophylla stands at two sites in western Oregon. We used the method of Dufrêne and Legendre that combines a species' relative abundance and relative frequency, to calculate that species' importance in relation to environmental variables. The resulting "indicator value" describes a species' reliability for indicating the given environmental parameter. Thirty-nine species were indicative of either humus, a decay class of coarse woody debris, or stand age. Bryophyte community composition changed along the continuum of coarse woody debris decomposition from recently fallen trees with intact bark to forest floor humus. Richness of forest floor bryophytes will be enhanced when a full range of coarse woody debris decay classes is present. A suite of bryophytes indicated old-growth forest. These were mainly either epiphytes associated with older conifers or liverworts associated with coarse woody debris. Hardwood-associated epiphytes mainly indicated young stands. Mature conifers, hardwoods, and coarse woody debris are biological legacies that can be protected when thinning managed stands to foster habitat complexity and biodiversity, consistent with an ecosystem approach to forest management.

The Application of High Energy Resolution Green's Functions to Threat Scenario Simulation

NASA Astrophysics Data System (ADS)

Thoreson, Gregory G.; Schneider, Erich A.

2012-04-01

Radiation detectors installed at key interdiction points provide defense against nuclear smuggling attempts by scanning vehicles and traffic for illicit nuclear material. These hypothetical threat scenarios may be modeled using radiation transport simulations. However, high-fidelity models are computationally intensive. Furthermore, the range of smuggler attributes and detector technologies create a large problem space not easily overcome by brute-force methods. Previous research has demonstrated that decomposing the scenario into independently simulated components using Green's functions can simulate photon detector signals with coarse energy resolution. This paper extends this methodology by presenting physics enhancements and numerical treatments which allow for an arbitrary level of energy resolution for photon transport. As a result, spectroscopic detector signals produced from full forward transport simulations can be replicated while requiring multiple orders of magnitude less computation time.

Systems approach to excitation-energy and electron transfer reaction networks in photosystem II complex: model studies for chlorophyll a fluorescence induction kinetics.

PubMed

Matsuoka, Takeshi; Tanaka, Shigenori; Ebina, Kuniyoshi

2015-09-07

Photosystem II (PS II) is a protein complex which evolves oxygen and drives charge separation for photosynthesis employing electron and excitation-energy transfer processes over a wide timescale range from picoseconds to milliseconds. While the fluorescence emitted by the antenna pigments of this complex is known as an important indicator of the activity of photosynthesis, its interpretation was difficult because of the complexity of PS II. In this study, an extensive kinetic model which describes the complex and multi-timescale characteristics of PS II is analyzed through the use of the hierarchical coarse-graining method proposed in the authors׳ earlier work. In this coarse-grained analysis, the reaction center (RC) is described by two states, open and closed RCs, both of which consist of oxidized and neutral special pairs being in quasi-equilibrium states. Besides, the PS II model at millisecond scale with three-state RC, which was studied previously, could be derived by suitably adjusting the kinetic parameters of electron transfer between tyrosine and RC. Our novel coarse-grained model of PS II can appropriately explain the light-intensity dependent change of the characteristic patterns of fluorescence induction kinetics from O-J-I-P, which shows two inflection points, J and I, between initial point O and peak point P, to O-J-D-I-P, which shows a dip D between J and I inflection points. Copyright © 2015 Elsevier Ltd. All rights reserved.

Predictive coarse-graining

NASA Astrophysics Data System (ADS)

Schöberl, Markus; Zabaras, Nicholas; Koutsourelakis, Phaedon-Stelios

2017-03-01

We propose a data-driven, coarse-graining formulation in the context of equilibrium statistical mechanics. In contrast to existing techniques which are based on a fine-to-coarse map, we adopt the opposite strategy by prescribing a probabilistic coarse-to-fine map. This corresponds to a directed probabilistic model where the coarse variables play the role of latent generators of the fine scale (all-atom) data. From an information-theoretic perspective, the framework proposed provides an improvement upon the relative entropy method [1] and is capable of quantifying the uncertainty due to the information loss that unavoidably takes place during the coarse-graining process. Furthermore, it can be readily extended to a fully Bayesian model where various sources of uncertainties are reflected in the posterior of the model parameters. The latter can be used to produce not only point estimates of fine-scale reconstructions or macroscopic observables, but more importantly, predictive posterior distributions on these quantities. Predictive posterior distributions reflect the confidence of the model as a function of the amount of data and the level of coarse-graining. The issues of model complexity and model selection are seamlessly addressed by employing a hierarchical prior that favors the discovery of sparse solutions, revealing the most prominent features in the coarse-grained model. A flexible and parallelizable Monte Carlo - Expectation-Maximization (MC-EM) scheme is proposed for carrying out inference and learning tasks. A comparative assessment of the proposed methodology is presented for a lattice spin system and the SPC/E water model.

Predictive coarse-graining

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

Schöberl, Markus, E-mail: m.schoeberl@tum.de; Zabaras, Nicholas; Department of Aerospace and Mechanical Engineering, University of Notre Dame, 365 Fitzpatrick Hall, Notre Dame, IN 46556

We propose a data-driven, coarse-graining formulation in the context of equilibrium statistical mechanics. In contrast to existing techniques which are based on a fine-to-coarse map, we adopt the opposite strategy by prescribing a probabilistic coarse-to-fine map. This corresponds to a directed probabilistic model where the coarse variables play the role of latent generators of the fine scale (all-atom) data. From an information-theoretic perspective, the framework proposed provides an improvement upon the relative entropy method and is capable of quantifying the uncertainty due to the information loss that unavoidably takes place during the coarse-graining process. Furthermore, it can be readily extendedmore » to a fully Bayesian model where various sources of uncertainties are reflected in the posterior of the model parameters. The latter can be used to produce not only point estimates of fine-scale reconstructions or macroscopic observables, but more importantly, predictive posterior distributions on these quantities. Predictive posterior distributions reflect the confidence of the model as a function of the amount of data and the level of coarse-graining. The issues of model complexity and model selection are seamlessly addressed by employing a hierarchical prior that favors the discovery of sparse solutions, revealing the most prominent features in the coarse-grained model. A flexible and parallelizable Monte Carlo – Expectation–Maximization (MC-EM) scheme is proposed for carrying out inference and learning tasks. A comparative assessment of the proposed methodology is presented for a lattice spin system and the SPC/E water model.« less

Highly Scalable Matching Pursuit Signal Decomposition Algorithm

NASA Technical Reports Server (NTRS)

Christensen, Daniel; Das, Santanu; Srivastava, Ashok N.

2009-01-01

Matching Pursuit Decomposition (MPD) is a powerful iterative algorithm for signal decomposition and feature extraction. MPD decomposes any signal into linear combinations of its dictionary elements or atoms . A best fit atom from an arbitrarily defined dictionary is determined through cross-correlation. The selected atom is subtracted from the signal and this procedure is repeated on the residual in the subsequent iterations until a stopping criterion is met. The reconstructed signal reveals the waveform structure of the original signal. However, a sufficiently large dictionary is required for an accurate reconstruction; this in return increases the computational burden of the algorithm, thus limiting its applicability and level of adoption. The purpose of this research is to improve the scalability and performance of the classical MPD algorithm. Correlation thresholds were defined to prune insignificant atoms from the dictionary. The Coarse-Fine Grids and Multiple Atom Extraction techniques were proposed to decrease the computational burden of the algorithm. The Coarse-Fine Grids method enabled the approximation and refinement of the parameters for the best fit atom. The ability to extract multiple atoms within a single iteration enhanced the effectiveness and efficiency of each iteration. These improvements were implemented to produce an improved Matching Pursuit Decomposition algorithm entitled MPD++. Disparate signal decomposition applications may require a particular emphasis of accuracy or computational efficiency. The prominence of the key signal features required for the proper signal classification dictates the level of accuracy necessary in the decomposition. The MPD++ algorithm may be easily adapted to accommodate the imposed requirements. Certain feature extraction applications may require rapid signal decomposition. The full potential of MPD++ may be utilized to produce incredible performance gains while extracting only slightly less energy than the standard algorithm. When the utmost accuracy must be achieved, the modified algorithm extracts atoms more conservatively but still exhibits computational gains over classical MPD. The MPD++ algorithm was demonstrated using an over-complete dictionary on real life data. Computational times were reduced by factors of 1.9 and 44 for the emphases of accuracy and performance, respectively. The modified algorithm extracted similar amounts of energy compared to classical MPD. The degree of the improvement in computational time depends on the complexity of the data, the initialization parameters, and the breadth of the dictionary. The results of the research confirm that the three modifications successfully improved the scalability and computational efficiency of the MPD algorithm. Correlation Thresholding decreased the time complexity by reducing the dictionary size. Multiple Atom Extraction also reduced the time complexity by decreasing the number of iterations required for a stopping criterion to be reached. The Course-Fine Grids technique enabled complicated atoms with numerous variable parameters to be effectively represented in the dictionary. Due to the nature of the three proposed modifications, they are capable of being stacked and have cumulative effects on the reduction of the time complexity.

Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations.

PubMed

Shen, Lin; Hu, Hao

2014-06-10

We develop here an adaptive multiresolution method for the simulation of complex heterogeneous systems such as the protein molecules. The target molecular system is described with the atomistic structure while maintaining concurrently a mapping to the coarse-grained models. The theoretical model, or force field, used to describe the interactions between two sites is automatically adjusted in the simulation processes according to the interaction distance/strength. Therefore, all-atomic, coarse-grained, or mixed all-atomic and coarse-grained models would be used together to describe the interactions between a group of atoms and its surroundings. Because the choice of theory is made on the force field level while the sampling is always carried out in the atomic space, the new adaptive method preserves naturally the atomic structure and thermodynamic properties of the entire system throughout the simulation processes. The new method will be very useful in many biomolecular simulations where atomistic details are critically needed.

Adiabatic coarse-graining and simulations of stochastic biochemical networks

PubMed Central

Sinitsyn, N. A.; Hengartner, Nicolas; Nemenman, Ilya

2009-01-01

We propose a universal approach for analysis and fast simulations of stiff stochastic biochemical networks, which rests on elimination of fast chemical species without a loss of information about mesoscopic, non-Poissonian fluctuations of the slow ones. Our approach is similar to the Born–Oppenheimer approximation in quantum mechanics and follows from the stochastic path integral representation of the cumulant generating function of reaction events. In applications with a small number of chemical reactions, it produces analytical expressions for cumulants of chemical fluxes between the slow variables. This allows for a low-dimensional, interpretable representation and can be used for high-accuracy, low-complexity coarse-grained numerical simulations. As an example, we derive the coarse-grained description for a chain of biochemical reactions and show that the coarse-grained and the microscopic simulations agree, but the former is 3 orders of magnitude faster. PMID:19525397

Initial Isotopic Heterogeneities in ZAGAMI: Evidence of a Complex Magmatic History

NASA Technical Reports Server (NTRS)

Nyquist, L. E.; Shih, C.-Y.; Reese, Y. D.

2006-01-01

Interpretations of Zagami s magmatic history range from complex [1,2] to relatively simple [3]. Discordant radiometric ages led to a suggestion that the ages had been reset [4]. In an attempt to identify the mechanism, Rb-Sr isochrons were individually determined for both fine-grained and coarse-grained Zagami [5]. Ages of approx.180 Ma were obtained from both lithologies, but the initial Sr-87/Sr-86 (ISr) of the fine-grained lithology was higher by 8.6+/-0.4 e-units. Recently, a much older age of approx.4 Ga has been advocated [6]. Here, we extend our earlier investigation [5]. Rb-Sr Data: In [5] we applied identical, simplified, procedures to both lithologies to test whether a grain-size dependent process such as thermally-driven subsolidus isotopic reequilibration had caused age-resetting. Minerals were separated only by density. In the present experiment, purer mineral separates were analysed with improved techniques. Combined Rb-Sr results give ages (T) = 166+/-12 Ma and 177+/-9 Ma and I(subSr) = 0.72174+/-9 and 0.72227+/-7 for the coarse-grained and fine-grained lithologies, respectively. ISr in the fine-grained sample is thus higher than in the coarse-grained sample by 7.3+/-1.6 e-units. The results for the coarse-grained lithology are in close agreement with T = 166+/-6 Ma, ISr = 0.72157+/-8 for an adjacent sample [7] and T = 178+/-4 Ma, ISr = 0.72151+/-5 [4, adjusted] for a separate sample. Thus, fine-grained Zagami appears on average to be less typical of the bulk than coarse-grained Zagami.

C–IBI: Targeting cumulative coordination within an iterative protocol to derive coarse-grained models of (multi-component) complex fluids

DOE PAGES

de Oliveira, Tiago E.; Netz, Paulo A.; Kremer, Kurt; ...

2016-05-03

We present a coarse-graining strategy that we test for aqueous mixtures. The method uses pair-wise cumulative coordination as a target function within an iterative Boltzmann inversion (IBI) like protocol. We name this method coordination iterative Boltzmann inversion (C–IBI). While the underlying coarse-grained model is still structure based and, thus, preserves pair-wise solution structure, our method also reproduces solvation thermodynamics of binary and/or ternary mixtures. In addition, we observe much faster convergence within C–IBI compared to IBI. To validate the robustness, we apply C–IBI to study test cases of solvation thermodynamics of aqueous urea and a triglycine solvation in aqueous urea.

Application of electromagnetic techniques in survey of contaminated groundwater at an abandoned mine complex in southwestern Indiana, U.S.A.

USGS Publications Warehouse

Brooks, G.A.; Olyphant, G.A.; Harper, D.

1991-01-01

In part of a large abandoned mining complex, electromagnetic geophysical surveys were used along with data derived from cores and monitoring wells to infer sources of contamination and subsurface hydrologic connections between acidic refuse deposits and adjacent undisturbed geologic materials. Electrical resistivity increases sharply along the boundary of an elevated deposit of pyritic coarse refuse, which is highly contaminated and electrically conductive, indicating poor subsurface hydrologic connections with surrounding deposits of fine refuse and undisturbed glacial material. Groundwater chemistry, as reflected in values of specific conductance, also differs markedly across the deposit's boundary, indicating that a widespread contaminant plume has not developed around the coarse refuse in more than 40 yr since the deposit was created. Most acidic drainage from the coarse refuse is by surface runoff and is concentrated around stream channels. Although most of the contaminated groundwater within the study area is concentrated within the surficial refuse deposits, transects of apparent resistivity and phase angle indicate the existence of an anomalous conductive layer at depth (>4 m) in thick alluvial sediments along the northern boundary of the mining complex. Based on knowledge of local geology, the anomaly is interpreted to represent a subsurface connection between the alluvium and a flooded abandoned underground mine. ?? 1991 Springer-Verlag New York Inc.

Application of electromagnetic techniques in survey of contaminated groundwater at an abandoned mine complex in southwestern Indiana, U.S.A.

NASA Astrophysics Data System (ADS)

Brooks, Glenn A.; Olyphant, Greg A.; Harper, Denver

1991-07-01

In part of a large abandoned mining complex, electromagnetic geophysical surveys were used along with data derived from cores and monitoring wells to infer sources of contamination and subsurface hydrologic connections between acidic refuse deposits and adjacent undisturbed geologic materials. Electrical resistivity increases sharply along the boundary of an elevated deposit of pyritic coarse refuse, which is highly contaminated and electrically conductive, indicating poor subsurface hydrologic connections with surrounding deposits of fine refuse and undisturbed glacial material. Groundwater chemistry, as reflected in values of specific conductance, also differs markedly across the deposit's boundary, indicating that a widespread contaminant plume has not developed around the coarse refuse in more than 40 yr since the deposit was created. Most acidic drainage from the coarse refuse is by surface runoff and is concentrated around stream channels. Although most of the contaminated groundwater within the study area is concentrated within the surficial refuse deposits, transects of apparent resistivity and phase angle indicate the existence of an anomalous conductive layer at depth (>4 m) in thick alluvial sediments along the northern boundary of the mining complex. Based on knowledge of local geology, the anomaly is interpreted to represent a subsurface connection between the alluvium and a flooded abandoned underground mine.

Lennard-Jones type pair-potential method for coarse-grained lipid bilayer membrane simulations in LAMMPS

NASA Astrophysics Data System (ADS)

Fu, S.-P.; Peng, Z.; Yuan, H.; Kfoury, R.; Young, Y.-N.

2017-01-01

Lipid bilayer membranes have been extensively studied by coarse-grained molecular dynamics simulations. Numerical efficiencies have been reported in the cases of aggressive coarse-graining, where several lipids are coarse-grained into a particle of size 4 ∼ 6 nm so that there is only one particle in the thickness direction. Yuan et al. proposed a pair-potential between these one-particle-thick coarse-grained lipid particles to capture the mechanical properties of a lipid bilayer membrane, such as gel-fluid-gas phase transitions of lipids, diffusion, and bending rigidity Yuan et al. (2010). In this work we implement such an interaction potential in LAMMPS to simulate large-scale lipid systems such as a giant unilamellar vesicle (GUV) and red blood cells (RBCs). We also consider the effect of cytoskeleton on the lipid membrane dynamics as a model for RBC dynamics, and incorporate coarse-grained water molecules to account for hydrodynamic interactions. The interaction between the coarse-grained water molecules (explicit solvent molecules) is modeled as a Lennard-Jones (L-J) potential. To demonstrate that the proposed methods do capture the observed dynamics of vesicles and RBCs, we focus on two sets of LAMMPS simulations: 1. Vesicle shape transitions with enclosed volume; 2. RBC shape transitions with different enclosed volume. Finally utilizing the parallel computing capability in LAMMPS, we provide some timing results for parallel coarse-grained simulations to illustrate that it is possible to use LAMMPS to simulate large-scale realistic complex biological membranes for more than 1 ms.

Eruption processes and deposit characteristics at the monogenetic Mt. Gambier Volcanic Complex, SE Australia: implications for alternating magmatic and phreatomagmatic activity

NASA Astrophysics Data System (ADS)

van Otterloo, Jozua; Cas, Raymond A. F.; Sheard, Malcolm J.

2013-08-01

The ˜5 ka Mt. Gambier Volcanic Complex in the Newer Volcanics Province, Australia is an extremely complex monogenetic, volcanic system that preserves at least 14 eruption points aligned along a fissure system. The complex stratigraphy can be subdivided into six main facies that record alternations between magmatic and phreatomagmatic eruption styles in a random manner. The facies are (1) coherent to vesicular fragmental alkali basalt (effusive/Hawaiian spatter and lava flows); (2) massive scoriaceous fine lapilli with coarse ash (Strombolian fallout); (3) bedded scoriaceous fine lapilli tuff (violent Strombolian fallout); (4) thin-medium bedded, undulating very fine lapilli in coarse ash (dry phreatomagmatic surge-modified fallout); (5) palagonite-altered, cross-bedded, medium lapilli to fine ash (wet phreatomagmatic base surges); and (6) massive, palagonite-altered, very poorly sorted tuff breccia and lapilli tuff (phreato-Vulcanian pyroclastic flows). Since most deposits are lithified, to quantify the grain size distributions (GSDs), image analysis was performed. The facies are distinct based on their GSDs and the fine ash to coarse+fine ash ratios. These provide insights into the fragmentation intensities and water-magma interaction efficiencies for each facies. The eruption chronology indicates a random spatial and temporal sequence of occurrence of eruption styles, except for a "magmatic horizon" of effusive activity occurring at both ends of the volcanic complex simultaneously. The eruption foci are located along NW-SE trending lineaments, indicating that the complex was fed by multiple dykes following the subsurface structures related to the Tartwaup Fault System. Possible factors causing vent migration along these dykes and changes in eruption styles include differences in magma ascent rates, viscosity, crystallinity, degassing and magma discharge rate, as well as hydrological parameters.

Reactions in trifluoroacetic acid (CF 3COOH) induced by low energy electron attachment

NASA Astrophysics Data System (ADS)

Langer, Judith; Stano, Michal; Gohlke, Sascha; Foltin, Victor; Matejcik, Stefan; Illenberger, Eugen

2006-02-01

Dissociative electron attachment to trifluoroacetic acid (CF 3COOH) is characterized by an intense low energy shape resonance located near 1 eV and a comparatively weaker core excited resonance located near 7 eV. The shape resonance decomposes into the fragment ions CF 3COO -, CF 2COO -, and CF2-. The underlying reactions include simple bond cleavage but also more complex sequences involving multiple bond cleavages, rearrangement in the precursor ion and formation of new molecules (HF, CO 2). The core excited resonance additionally decomposes into F -, CF3- and probably metastable CO2-.

Dynamics of Different Bacterial Communities Are Capable of Generating Sustainable Electricity from Microbial Fuel Cells with Organic Waste

PubMed Central

Yamamoto, Shuji; Suzuki, Kei; Araki, Yoko; Mochihara, Hiroki; Hosokawa, Tetsuya; Kubota, Hiroko; Chiba, Yusuke; Rubaba, Owen; Tashiro, Yosuke; Futamata, Hiroyuki

2014-01-01

The relationship between the bacterial communities in anolyte and anode biofilms and the electrochemical properties of microbial fuel cells (MFCs) was investigated when a complex organic waste-decomposing solution was continuously supplied to MFCs as an electron donor. The current density increased gradually and was maintained at approximately 100 to 150 mA m−2. Polarization curve analyses revealed that the maximum power density was 7.4 W m−3 with an internal resistance of 110 Ω. Bacterial community structures in the organic waste-decomposing solution and MFCs differed from each other. Clonal analyses targeting 16S rRNA genes indicated that bacterial communities in the biofilms on MFCs developed to specific communities dominated by novel Geobacter. Multidimensional scaling analyses based on DGGE profiles revealed that bacterial communities in the organic waste-decomposing solution fluctuated and had no dynamic equilibrium. Bacterial communities on the anolyte in MFCs had a dynamic equilibrium with fluctuations, while those of the biofilm converged to the Geobacter-dominated structure. These bacterial community dynamics of MFCs differed from those of control-MFCs under open circuit conditions. These results suggested that bacterial communities in the anolyte and biofilm have a gentle symbiotic system through electron flow, which resulted in the advance of current density from complex organic waste. PMID:24789988

Dynamics of different bacterial communities are capable of generating sustainable electricity from microbial fuel cells with organic waste.

PubMed

Yamamoto, Shuji; Suzuki, Kei; Araki, Yoko; Mochihara, Hiroki; Hosokawa, Tetsuya; Kubota, Hiroko; Chiba, Yusuke; Rubaba, Owen; Tashiro, Yosuke; Futamata, Hiroyuki

2014-01-01

The relationship between the bacterial communities in anolyte and anode biofilms and the electrochemical properties of microbial fuel cells (MFCs) was investigated when a complex organic waste-decomposing solution was continuously supplied to MFCs as an electron donor. The current density increased gradually and was maintained at approximately 100 to 150 mA m(-2). Polarization curve analyses revealed that the maximum power density was 7.4 W m(-3) with an internal resistance of 110 Ω. Bacterial community structures in the organic waste-decomposing solution and MFCs differed from each other. Clonal analyses targeting 16S rRNA genes indicated that bacterial communities in the biofilms on MFCs developed to specific communities dominated by novel Geobacter. Multidimensional scaling analyses based on DGGE profiles revealed that bacterial communities in the organic waste-decomposing solution fluctuated and had no dynamic equilibrium. Bacterial communities on the anolyte in MFCs had a dynamic equilibrium with fluctuations, while those of the biofilm converged to the Geobacter-dominated structure. These bacterial community dynamics of MFCs differed from those of control-MFCs under open circuit conditions. These results suggested that bacterial communities in the anolyte and biofilm have a gentle symbiotic system through electron flow, which resulted in the advance of current density from complex organic waste.

Coarse-grained simulation of polymer-filler blends

NASA Astrophysics Data System (ADS)

Legters, Gregg; Kuppa, Vikram; Beaucage, Gregory; Univ of Dayton Collaboration; Univ of Cincinnati Collaboration

The practical use of polymers often relies on additives that improve the property of the mixture. Examples of such complex blends include tires, pigments, blowing agents and other reactive additives in thermoplastics, and recycled polymers. Such systems usually exhibit a complex partitioning of the components. Most prior work has either focused on fine-grained details such as molecular modeling of chains at interfaces, or on coarse, heuristic, trial-and-error approaches to compounding (eg: tire industry). Thus, there is a significant gap in our understanding of how complex hierarchical structure (across several decades in length) develops in these multicomponent systems. This research employs dissipative particle thermodynamics in conjunction with a pseudo-thermodynamic parameter derived from scattering experiments to represent polymer-filler interactions. DPD simulations will probe how filler dispersion and hierarchical morphology develops in these complex blends, and are validated against experimental (scattering) data. The outcome of our approach is a practical solution to compounding issues, based on a mutually validating experimental and simulation methodology. Support from the NSF (CMMI-1636036/1635865) is gratefully acknowledged.

Calculations of the binding affinities of protein-protein complexes with the fast multipole method

NASA Astrophysics Data System (ADS)

Kim, Bongkeun; Song, Jiming; Song, Xueyu

2010-09-01

In this paper, we used a coarse-grained model at the residue level to calculate the binding free energies of three protein-protein complexes. General formulations to calculate the electrostatic binding free energy and the van der Waals free energy are presented by solving linearized Poisson-Boltzmann equations using the boundary element method in combination with the fast multipole method. The residue level model with the fast multipole method allows us to efficiently investigate how the mutations on the active site of the protein-protein interface affect the changes in binding affinities of protein complexes. Good correlations between the calculated results and the experimental ones indicate that our model can capture the dominant contributions to the protein-protein interactions. At the same time, additional effects on protein binding due to atomic details are also discussed in the context of the limitations of such a coarse-grained model.

PACSAB: Coarse-Grained Force Field for the Study of Protein-Protein Interactions and Conformational Sampling in Multiprotein Systems.

PubMed

Emperador, Agustí; Sfriso, Pedro; Villarreal, Marcos Ariel; Gelpí, Josep Lluis; Orozco, Modesto

2015-12-08

Molecular dynamics simulations of proteins are usually performed on a single molecule, and coarse-grained protein models are calibrated using single-molecule simulations, therefore ignoring intermolecular interactions. We present here a new coarse-grained force field for the study of many protein systems. The force field, which is implemented in the context of the discrete molecular dynamics algorithm, is able to reproduce the properties of folded and unfolded proteins, in both isolation, complexed forming well-defined quaternary structures, or aggregated, thanks to its proper evaluation of protein-protein interactions. The accuracy and computational efficiency of the method makes it a universal tool for the study of the structure, dynamics, and association/dissociation of proteins.

Computing the non-Markovian coarse-grained interactions derived from the Mori-Zwanzig formalism in molecular systems: Application to polymer melts

NASA Astrophysics Data System (ADS)

Li, Zhen; Lee, Hee Sun; Darve, Eric; Karniadakis, George Em

2017-01-01

Memory effects are often introduced during coarse-graining of a complex dynamical system. In particular, a generalized Langevin equation (GLE) for the coarse-grained (CG) system arises in the context of Mori-Zwanzig formalism. Upon a pairwise decomposition, GLE can be reformulated into its pairwise version, i.e., non-Markovian dissipative particle dynamics (DPD). GLE models the dynamics of a single coarse particle, while DPD considers the dynamics of many interacting CG particles, with both CG systems governed by non-Markovian interactions. We compare two different methods for the practical implementation of the non-Markovian interactions in GLE and DPD systems. More specifically, a direct evaluation of the non-Markovian (NM) terms is performed in LE-NM and DPD-NM models, which requires the storage of historical information that significantly increases computational complexity. Alternatively, we use a few auxiliary variables in LE-AUX and DPD-AUX models to replace the non-Markovian dynamics with a Markovian dynamics in a higher dimensional space, leading to a much reduced memory footprint and computational cost. In our numerical benchmarks, the GLE and non-Markovian DPD models are constructed from molecular dynamics (MD) simulations of star-polymer melts. Results show that a Markovian dynamics with auxiliary variables successfully generates equivalent non-Markovian dynamics consistent with the reference MD system, while maintaining a tractable computational cost. Also, transient subdiffusion of the star-polymers observed in the MD system can be reproduced by the coarse-grained models. The non-interacting particle models, LE-NM/AUX, are computationally much cheaper than the interacting particle models, DPD-NM/AUX. However, the pairwise models with momentum conservation are more appropriate for correctly reproducing the long-time hydrodynamics characterised by an algebraic decay in the velocity autocorrelation function.

Acquisition of HPLC-Mass Spectrometer

DTIC Science & Technology

2015-08-18

phenyl alanine. This dithiol is coordinated to the iron and all attempts to decompose the ionic coordination complex 56 to recover strictly the...sulfonation process of an asymmetric deprotonation providing a lithium complex with sparteine. This reaction scheme will also direct stereochemistry of...currently used in ointments for treatment of pain and inflammation. Capsaicin shows promise as an effective anti-cancer nutritional agent and

Diversity of Riparian Plants among and within Species Shapes River Communities

PubMed Central

Jackrel, Sara L.; Wootton, J. Timothy

2015-01-01

Organismal diversity among and within species may affect ecosystem function with effects transmitting across ecosystem boundaries. Whether recipient communities adjust their composition, in turn, to maximize their function in response to changes in donor composition at these two scales of diversity is unknown. We use small stream communities that rely on riparian subsidies as a model system. We used leaf pack experiments to ask how variation in plants growing beside streams in the Olympic Peninsula of Washington State, USA affects stream communities via leaf subsidies. Leaves from red alder (Alnus rubra), vine maple (Acer cinereus), bigleaf maple (Acer macrophyllum) and western hemlock (Tsuga heterophylla) were assembled in leaf packs to contrast low versus high diversity, and deployed in streams to compare local versus non-local leaf sources at the among and within species scales. Leaves from individuals within species decomposed at varying rates; most notably thin leaves decomposed rapidly. Among deciduous species, vine maple decomposed most rapidly, harbored the least algal abundance, and supported the greatest diversity of aquatic invertebrates, while bigleaf maple was at the opposite extreme for these three metrics. Recipient communities decomposed leaves from local species rapidly: leaves from early successional plants decomposed rapidly in stream reaches surrounded by early successional forest and leaves from later successional plants decomposed rapidly adjacent to later successional forest. The species diversity of leaves inconsistently affected decomposition, algal abundance and invertebrate metrics. Intraspecific diversity of leaf packs also did not affect decomposition or invertebrate diversity. However, locally sourced alder leaves decomposed more rapidly and harbored greater levels of algae than leaves sourced from conspecifics growing in other areas on the Olympic Peninsula, but did not harbor greater aquatic invertebrate diversity. In contrast to alder, local intraspecific differences via decomposition, algal or invertebrate metrics were not observed consistently among maples. These results emphasize that biodiversity of riparian subsidies at the within and across species scale have the potential to affect aquatic ecosystems, although there are complex species-specific effects. PMID:26539714

Diversity of Riparian Plants among and within Species Shapes River Communities.

PubMed

Jackrel, Sara L; Wootton, J Timothy

2015-01-01

Organismal diversity among and within species may affect ecosystem function with effects transmitting across ecosystem boundaries. Whether recipient communities adjust their composition, in turn, to maximize their function in response to changes in donor composition at these two scales of diversity is unknown. We use small stream communities that rely on riparian subsidies as a model system. We used leaf pack experiments to ask how variation in plants growing beside streams in the Olympic Peninsula of Washington State, USA affects stream communities via leaf subsidies. Leaves from red alder (Alnus rubra), vine maple (Acer cinereus), bigleaf maple (Acer macrophyllum) and western hemlock (Tsuga heterophylla) were assembled in leaf packs to contrast low versus high diversity, and deployed in streams to compare local versus non-local leaf sources at the among and within species scales. Leaves from individuals within species decomposed at varying rates; most notably thin leaves decomposed rapidly. Among deciduous species, vine maple decomposed most rapidly, harbored the least algal abundance, and supported the greatest diversity of aquatic invertebrates, while bigleaf maple was at the opposite extreme for these three metrics. Recipient communities decomposed leaves from local species rapidly: leaves from early successional plants decomposed rapidly in stream reaches surrounded by early successional forest and leaves from later successional plants decomposed rapidly adjacent to later successional forest. The species diversity of leaves inconsistently affected decomposition, algal abundance and invertebrate metrics. Intraspecific diversity of leaf packs also did not affect decomposition or invertebrate diversity. However, locally sourced alder leaves decomposed more rapidly and harbored greater levels of algae than leaves sourced from conspecifics growing in other areas on the Olympic Peninsula, but did not harbor greater aquatic invertebrate diversity. In contrast to alder, local intraspecific differences via decomposition, algal or invertebrate metrics were not observed consistently among maples. These results emphasize that biodiversity of riparian subsidies at the within and across species scale have the potential to affect aquatic ecosystems, although there are complex species-specific effects.

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

Azmi, M. A.; Ismail, N. A. A.; Rizamarhaiza, M.

Rice husk was thermally decomposed to yield powder composed of silica (SiO{sub 2}). Temperatures of 700°C and 1000°C were chosen as the decomposition temperatures. X-Ray Diffraction (XRD), X-Ray Florescence (XRF), Fourier Transform Infrared (FTIR), and Field Emission Scanning Electron Microscope (FESEM) analyses were conducted on a synthetic silica powder (SS-SiO{sub 2}) and the rice husk ash as for the comparative characterisation study. XRD analyses clearly indicated that the decomposed rice husk yielded silica of different nature which are Crystalline Rice Husk Silica (C-RHSiO{sub 2}) and Amorphous Rice Husk Silica (A-RHSiO{sub 2}). Moreover, it was found that SS-SiO{sub 2} was ofmore » Quartz phase, C-RHSiO{sub 2} was of Trydimite and Cristobalite. Through XRF detection, the highest SiO{sub 2} purity was detected in SS-SiO{sub 2} followed by C-RHSiO{sub 2} and A-RHSiO{sub 2} with purity percentages of 99.60%, 82.30% and 86.30% respectively. FTIR results clearly indicated silica (SiO{sub 2}) bonding 1056, 1064, 1047, 777, 790 and 798 cm{sup −1}) increased as the crystallinity silica increased. The Cristobalite phase was detected in C-RH SiO{sub 2} at the wavelength of 620 cm{sup −1}. Morphological features as observed by FESEM analyses confirmed that, SS-SiO{sub 2} and C-RH SiO{sub 2} showed prominent coarse granular morphology.« less

Stepping inside the niche: microclimate data are critical for accurate assessment of species' vulnerability to climate change

PubMed Central

Storlie, Collin; Merino-Viteri, Andres; Phillips, Ben; VanDerWal, Jeremy; Welbergen, Justin; Williams, Stephen

2014-01-01

To assess a species' vulnerability to climate change, we commonly use mapped environmental data that are coarsely resolved in time and space. Coarsely resolved temperature data are typically inaccurate at predicting temperatures in microhabitats used by an organism and may also exhibit spatial bias in topographically complex areas. One consequence of these inaccuracies is that coarsely resolved layers may predict thermal regimes at a site that exceed species' known thermal limits. In this study, we use statistical downscaling to account for environmental factors and develop high-resolution estimates of daily maximum temperatures for a 36 000 km2 study area over a 38-year period. We then demonstrate that this statistical downscaling provides temperature estimates that consistently place focal species within their fundamental thermal niche, whereas coarsely resolved layers do not. Our results highlight the need for incorporation of fine-scale weather data into species' vulnerability analyses and demonstrate that a statistical downscaling approach can yield biologically relevant estimates of thermal regimes. PMID:25252835

A unified data representation theory for network visualization, ordering and coarse-graining

PubMed Central

Kovács, István A.; Mizsei, Réka; Csermely, Péter

2015-01-01

Representation of large data sets became a key question of many scientific disciplines in the last decade. Several approaches for network visualization, data ordering and coarse-graining accomplished this goal. However, there was no underlying theoretical framework linking these problems. Here we show an elegant, information theoretic data representation approach as a unified solution of network visualization, data ordering and coarse-graining. The optimal representation is the hardest to distinguish from the original data matrix, measured by the relative entropy. The representation of network nodes as probability distributions provides an efficient visualization method and, in one dimension, an ordering of network nodes and edges. Coarse-grained representations of the input network enable both efficient data compression and hierarchical visualization to achieve high quality representations of larger data sets. Our unified data representation theory will help the analysis of extensive data sets, by revealing the large-scale structure of complex networks in a comprehensible form. PMID:26348923

A parallelized binary search tree

USDA-ARS?s Scientific Manuscript database

PTTRNFNDR is an unsupervised statistical learning algorithm that detects patterns in DNA sequences, protein sequences, or any natural language texts that can be decomposed into letters of a finite alphabet. PTTRNFNDR performs complex mathematical computations and its processing time increases when i...

Large photorefractive effect in a thermally decomposed polymer compared with that in molecularly doped systems

NASA Astrophysics Data System (ADS)

Yokoyama, Kenji; Arishima, Koichi; Sukegawa, Ken

1994-07-01

Photorefractive polymers with the same electro-optic effect were fabricated to investigate the photorefractive effects in different photoconductive systems. The photoconduction in the polymers was varied by the addition of squarylium dye to diethylaminobenzaldehyde-diphenylhydrazone (DEH), by the formation of a charge-transfer complex between tetracyanoquinodimethane and DEH, and by the thermal decomposition of DEH. The largest photorefractive effect was observed in the thermally decomposed polymer among these polymers. A diffraction efficiency of 1.1% and a beam-coupling gain coefficient of 10 cm-1 were achieved in a 34.9 V/μm dc electric field.

Detecting population-environmental interactions with mismatched time series data.

PubMed

Ferguson, Jake M; Reichert, Brian E; Fletcher, Robert J; Jager, Henriëtte I

2017-11-01

Time series analysis is an essential method for decomposing the influences of density and exogenous factors such as weather and climate on population regulation. However, there has been little work focused on understanding how well commonly collected data can reconstruct the effects of environmental factors on population dynamics. We show that, analogous to similar scale issues in spatial data analysis, coarsely sampled temporal data can fail to detect covariate effects when interactions occur on timescales that are fast relative to the survey period. We propose a method for modeling mismatched time series data that couples high-resolution environmental data to low-resolution abundance data. We illustrate our approach with simulations and by applying it to Florida's southern Snail kite population. Our simulation results show that our method can reliably detect linear environmental effects and that detecting nonlinear effects requires high-resolution covariate data even when the population turnover rate is slow. In the Snail kite analysis, our approach performed among the best in a suite of previously used environmental covariates explaining Snail kite dynamics and was able to detect a potential phenological shift in the environmental dependence of Snail kites. Our work provides a statistical framework for reliably detecting population-environment interactions from coarsely surveyed time series. An important implication of this work is that the low predictability of animal population growth by weather variables found in previous studies may be due, in part, to how these data are utilized as covariates. © 2017 by the Ecological Society of America.

Detecting population–environmental interactions with mismatched time series data

PubMed Central

Ferguson, Jake M.; Reichert, Brian E.; Fletcher, Robert J.; Jager, Henriëtte I.

2017-01-01

Time series analysis is an essential method for decomposing the influences of density and exogenous factors such as weather and climate on population regulation. However, there has been little work focused on understanding how well commonly collected data can reconstruct the effects of environmental factors on population dynamics. We show that, analogous to similar scale issues in spatial data analysis, coarsely sampled temporal data can fail to detect covariate effects when interactions occur on timescales that are fast relative to the survey period. We propose a method for modeling mismatched time series data that couples high-resolution environmental data to low-resolution abundance data. We illustrate our approach with simulations and by applying it to Florida’s southern Snail kite population. Our simulation results show that our method can reliably detect linear environmental effects and that detecting nonlinear effects requires high-resolution covariate data even when the population turnover rate is slow. In the Snail kite analysis, our approach performed among the best in a suite of previously used environmental covariates explaining Snail kite dynamics and was able to detect a potential phenological shift in the environmental dependence of Snail kites. Our work provides a statistical framework for reliably detecting population–environment interactions from coarsely surveyed time series. An important implication of this work is that the low predictability of animal population growth by weather variables found in previous studies may be due, in part, to how these data are utilized as covariates. PMID:28759123

Airflow and nanoparticle deposition in a 16-generation tracheobronchial airway model

EPA Science Inventory

In order to achieve both manageable simulation and local accuracy of airflow and nanoparticle deposition in a representative human tracheobronchial (TB) region, the complex airway network was decomposed into adjustable triple-bifurcation units, spreading axially and laterally. Gi...

Decomposer food web in a deciduous forest shows high share of generalist microorganisms and importance of microbial biomass recycling.

PubMed

López-Mondéjar, Ruben; Brabcová, Vendula; Štursová, Martina; Davidová, Anna; Jansa, Jan; Cajthaml, Tomaš; Baldrian, Petr

2018-06-01

Forest soils represent important terrestrial carbon (C) pools where C is primarily fixed in the plant-derived biomass but it flows further through the biomass of fungi and bacteria before it is lost from the ecosystem as CO 2 or immobilized in recalcitrant organic matter. Microorganisms are the main drivers of C flow in forests and play critical roles in the C balance through the decomposition of dead biomass of different origins. Here, we track the path of C that enters forest soil by following respiration, microbial biomass production, and C accumulation by individual microbial taxa in soil microcosms upon the addition of 13 C-labeled biomass of plant, fungal, and bacterial origin. We demonstrate that both fungi and bacteria are involved in the assimilation and mineralization of C from the major complex sources existing in soil. Decomposer fungi are, however, better suited to utilize plant biomass compounds, whereas the ability to utilize fungal and bacterial biomass is more frequent among bacteria. Due to the ability of microorganisms to recycle microbial biomass, we suggest that the decomposer food web in forest soil displays a network structure with loops between and within individual pools. These results question the present paradigms describing food webs as hierarchical structures with unidirectional flow of C and assumptions about the dominance of fungi in the decomposition of complex organic matter.

Successive mixing and mingling of magmas in a plutonic complex of Northeast Brazil

NASA Astrophysics Data System (ADS)

Neves, S. P.; Vauchez, A.

1995-02-01

Field and petrographic evidence together with major element geochemistry suggest that mixing and mingling of magmas of contrasting compositions were important petrogenetic processes in the Fazenda Nova/Serra da Japeganga plutonic complex of Northeast Brazil. The complex was emplaced at pressures of 300-500 MPa in amphibolite facies metamorphic rocks of Neoproterozoic age and consists of three main rock types: (1) coarse-grained granite; (2) porphyritic granite and (3) diorite to quartz-monzodiorite. The latter two make up the Fazenda Nova batholith which is located on the northwestern side of the sinistral, NE-trending, Fazenda Nova strike-slip shear zone. NE-plunging stretching lineations in the shear zone suggest that this batholith represents an uplifted, and therefore deeper, portion of the complex. The structure of the complex reflects the stratigraphy in a magma chamber, with the porphyritic granite above the diorite and below the coarse-grained granite. The porphyritic granite has a uniform composition, intermediate in mafic mineral content, quartz, and majorelements between the coarse-grained granite and the diorite. It is free of disequilibrium mineral assemblages, and locally displays gradational contacts with the overlain coarse-grained granite. Most elements display linear correlation with SiO 2 in Harker diagrams. These features are interpreted as resulting from mixing of almost crystal-free felsic and intermediate magmas. Fluid dynamic calculations using the coarse-grained granite and the silica-poorest diorite as end-members in the mixing process show that mechanical mixing was possible, and thermal modelling suggests that the formation of an homogeneous hybrid may have been achieved in less than 50,000 yr. The diorites contain corroded K-feldspar megacrysts, and range in composition from low to relatively high silica contents, partly overlapping with the porphyritic granite. This suggests that a new mixing event occurred during the crystallisation of the porphyritic granite, this time producing a heterogeneous, xenocryst-bearing, dioritic hybrid. Abundant enclaves of diorite in the porphyritic granite, despite their textural diversity, are typically devoid of chilled margins, and were therefore formed relatively early in the crystallisation history of the granite. They are interpreted as liquid droplets separated from the heterogeneous hybrid magma through convection currents and incorporated in the, crystallising granitic magma. Subsequently, during the crystallisation of the porphyritic granite, mafic magma supply to the batholith continued at a declining rate, probably assisted by the development of the Fazenda Nova shear zone. This leads to the production of stromatitic-like structures, with alternating bands of mutually contaminated granite and diorite, then to the intrusion of contorted synplutonic dykes, and, finally, of late-stage dykes, some of which with chilled finer-grained margins.

Ionic complexation of N 2O 4 by 18-crown-6

NASA Astrophysics Data System (ADS)

Ricard, S.; Audet, P.; Savoie, R.

1988-08-01

An ionic complex has been obtained from N 2O 4 in the presence of the macrocyclic ether 18-crown-6. This crystalline compound has been shown from its Raman spectrum to have the formula NO +·crown·H(NO 3) 2-, with the nitrosonium ion closely associated with the crown ether rather than with the hydrogen dinitrate accompanying ion. This adduct decomposes readily in moist air to give the known complex (HNO 3·H 2O) 2·crown.

"Martinizing" the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins.

PubMed

Ricci, Clarisse G; Li, Bo; Cheng, Li-Tien; Dzubiella, Joachim; McCammon, J Andrew

2017-07-13

Solvation is a fundamental driving force in many biological processes including biomolecular recognition and self-assembly, not to mention protein folding, dynamics, and function. The variational implicit solvent method (VISM) is a theoretical tool currently developed and optimized to estimate solvation free energies for systems of very complex topology, such as biomolecules. VISM's theoretical framework makes it unique because it couples hydrophobic, van der Waals, and electrostatic interactions as a functional of the solvation interface. By minimizing this functional, VISM produces the solvation interface as an output of the theory. In this work, we push VISM to larger scale applications by combining it with coarse-grained solute Hamiltonians adapted from the MARTINI framework, a well-established mesoscale force field for modeling large-scale biomolecule assemblies. We show how MARTINI-VISM ( M VISM) compares with atomistic VISM ( A VISM) for a small set of proteins differing in size, shape, and charge distribution. We also demonstrate M VISM's suitability to study the solvation properties of an interesting encounter complex, barnase-barstar. The promising results suggest that coarse-graining the protein with the MARTINI force field is indeed a valuable step to broaden VISM's and MARTINI's applications in the near future.

Physics-based statistical learning approach to mesoscopic model selection.

PubMed

Taverniers, Søren; Haut, Terry S; Barros, Kipton; Alexander, Francis J; Lookman, Turab

2015-11-01

In materials science and many other research areas, models are frequently inferred without considering their generalization to unseen data. We apply statistical learning using cross-validation to obtain an optimally predictive coarse-grained description of a two-dimensional kinetic nearest-neighbor Ising model with Glauber dynamics (GD) based on the stochastic Ginzburg-Landau equation (sGLE). The latter is learned from GD "training" data using a log-likelihood analysis, and its predictive ability for various complexities of the model is tested on GD "test" data independent of the data used to train the model on. Using two different error metrics, we perform a detailed analysis of the error between magnetization time trajectories simulated using the learned sGLE coarse-grained description and those obtained using the GD model. We show that both for equilibrium and out-of-equilibrium GD training trajectories, the standard phenomenological description using a quartic free energy does not always yield the most predictive coarse-grained model. Moreover, increasing the amount of training data can shift the optimal model complexity to higher values. Our results are promising in that they pave the way for the use of statistical learning as a general tool for materials modeling and discovery.

Variable-free exploration of stochastic models: a gene regulatory network example.

PubMed

Erban, Radek; Frewen, Thomas A; Wang, Xiao; Elston, Timothy C; Coifman, Ronald; Nadler, Boaz; Kevrekidis, Ioannis G

2007-04-21

Finding coarse-grained, low-dimensional descriptions is an important task in the analysis of complex, stochastic models of gene regulatory networks. This task involves (a) identifying observables that best describe the state of these complex systems and (b) characterizing the dynamics of the observables. In a previous paper [R. Erban et al., J. Chem. Phys. 124, 084106 (2006)] the authors assumed that good observables were known a priori, and presented an equation-free approach to approximate coarse-grained quantities (i.e., effective drift and diffusion coefficients) that characterize the long-time behavior of the observables. Here we use diffusion maps [R. Coifman et al., Proc. Natl. Acad. Sci. U.S.A. 102, 7426 (2005)] to extract appropriate observables ("reduction coordinates") in an automated fashion; these involve the leading eigenvectors of a weighted Laplacian on a graph constructed from network simulation data. We present lifting and restriction procedures for translating between physical variables and these data-based observables. These procedures allow us to perform equation-free, coarse-grained computations characterizing the long-term dynamics through the design and processing of short bursts of stochastic simulation initialized at appropriate values of the data-based observables.

Membrane extraction with thermodynamically unstable diphosphonic acid derivatives

DOEpatents

Horwitz, Earl Philip; Gatrone, Ralph Carl; Nash, Kenneth LaVerne

1997-01-01

Thermodynamically-unstable complexing agents which are diphosphonic acids and diphosphonic acid derivatives (or sulphur containing analogs), like carboxyhydroxymethanediphosphonic acid and vinylidene-1,1-diphosphonic acid, are capable of complexing with metal ions, and especially metal ions in the II, III, IV, V and VI oxidation states, to form stable, water-soluble metal ion complexes in moderately alkaline to highly-acidic media. However, the complexing agents can be decomposed, under mild conditions, into non-organic compounds which, for many purposes are environmentally-nondamaging compounds thereby degrading the complex and releasing the metal ion for disposal or recovery. Uses for such complexing agents as well as methods for their manufacture are also described.

Refined composite multivariate generalized multiscale fuzzy entropy: A tool for complexity analysis of multichannel signals

NASA Astrophysics Data System (ADS)

Azami, Hamed; Escudero, Javier

2017-01-01

Multiscale entropy (MSE) is an appealing tool to characterize the complexity of time series over multiple temporal scales. Recent developments in the field have tried to extend the MSE technique in different ways. Building on these trends, we propose the so-called refined composite multivariate multiscale fuzzy entropy (RCmvMFE) whose coarse-graining step uses variance (RCmvMFEσ2) or mean (RCmvMFEμ). We investigate the behavior of these multivariate methods on multichannel white Gaussian and 1/ f noise signals, and two publicly available biomedical recordings. Our simulations demonstrate that RCmvMFEσ2 and RCmvMFEμ lead to more stable results and are less sensitive to the signals' length in comparison with the other existing multivariate multiscale entropy-based methods. The classification results also show that using both the variance and mean in the coarse-graining step offers complexity profiles with complementary information for biomedical signal analysis. We also made freely available all the Matlab codes used in this paper.

Coarse-to-fine construction for high-resolution representation in visual working memory.

PubMed

Gao, Zaifeng; Ding, Xiaowei; Yang, Tong; Liang, Junying; Shui, Rende

2013-01-01

This study explored whether the high-resolution representations created by visual working memory (VWM) are constructed in a coarse-to-fine or all-or-none manner. The coarse-to-fine hypothesis suggests that coarse information precedes detailed information in entering VWM and that its resolution increases along with the processing time of the memory array, whereas the all-or-none hypothesis claims that either both enter into VWM simultaneously, or neither does. We tested the two hypotheses by asking participants to remember two or four complex objects. An ERP component, contralateral delay activity (CDA), was used as the neural marker. CDA is higher for four objects than for two objects when coarse information is primarily extracted; yet, this CDA difference vanishes when detailed information is encoded. Experiment 1 manipulated the comparison difficulty of the task under a 500-ms exposure time to determine a condition in which the detailed information was maintained. No CDA difference was found between two and four objects, even in an easy-comparison condition. Thus, Experiment 2 manipulated the memory array's exposure time under the easy-comparison condition and found a significant CDA difference at 100 ms while replicating Experiment 1's results at 500 ms. In Experiment 3, the 500-ms memory array was blurred to block the detailed information; this manipulation reestablished a significant CDA difference. These findings suggest that the creation of high-resolution representations in VWM is a coarse-to-fine process.

Decomposition of water-soluble mononitrosyl iron complexes with dithiocarbamates and of dinitrosyl iron complexes with thiol ligands in animal organisms.

PubMed

Serezhenkov, Vladimir A; Timoshin, Alexander A; Orlova, Tsvetina R; Mikoyan, Vasak D; Kubrina, Lioudmila N; Poltorakov, Alexander P; Ruuge, Enno K; Sanina, Natalia A; Vanin, Anatoly F

2008-05-01

EPR studies have shown that water-soluble mononitrosyl iron complexes with N-methyl-d-glucamine dithiocarbamate (MNIC-MGD) (3 micromol) injected to intact mice were decomposed virtually completely within 1h. The total content of MNIC-MGD in animal urine did not exceed 30 nmol/ml. In the liver, a small amount of MNIC-MGD were converted into dinitrosyl iron complexes (30 nmol/g of liver tissue). The same was observed in intact rabbits in which MNIC-MGD formation was induced by endogenous or exogenous NO binding to NO traps, viz., iron complexes with MGD. In mice, the content of MNIC-MGD in urine samples did not change after bacterial lipopolysaccharide-induced expression of iNOS. It was supposed that MNIC-MGD decomposition in intact animals was largely due to the release of NO from the complexes and its further transfer to other specific acceptors. In mice with iNOS expression, the main contribution to MNIC-MGD decomposition was made by superoxide ions whose destructive effect is mediated by an oxidative mechanism. This effect could fully compensate the augmented synthesis of MNIC-MGD involving endogenous NO whose production was supported by iNOS. Water-soluble dinitrosyl iron complexes (DNIC) with various thiol-containing ligands and thiosulfate injected to intact mice were also decomposed; however, in this case the effect was less pronounced than in the case of MNIC-MGD. It was concluded that DNIC decomposition was largely due to the oxidative effect of superoxide ions on these complexes.

Petri net model for analysis of concurrently processed complex algorithms

NASA Technical Reports Server (NTRS)

Stoughton, John W.; Mielke, Roland R.

1986-01-01

This paper presents a Petri-net model suitable for analyzing the concurrent processing of computationally complex algorithms. The decomposed operations are to be processed in a multiple processor, data driven architecture. Of particular interest is the application of the model to both the description of the data/control flow of a particular algorithm, and to the general specification of the data driven architecture. A candidate architecture is also presented.

Coarse-clast ridge complexes of the Caribbean: A preliminary basis for distinguishing tsunami and storm-wave origins

USGS Publications Warehouse

Morton, R.A.; Richmond, B.M.; Jaffe, B.E.; Gelfenbaum, G.

2008-01-01

Coastal gravel-ridge complexes deposited on islands in the Caribbean Sea are recorders of past extreme-wave events that could be associated with either tsunamis or hurricanes. The ridge complexes of Bonaire, Jamaica, Puerto Rico (Isla de Mona), and Guadeloupe consist of polymodal clasts ranging in size from sand to coarse boulders that are derived from the adjacent coral reefs or subjacent rock platforms. Ridge-complex morphologies and crest elevations are largely controlled by availability of sediments, clast sizes, and heights of wave runup. The ridge complexes are internally organized, display textural sorting and a broad range of ages including historical events. Some display seaward-dipping beds and ridge-and-swale topography, and some terminate in fans or steep avalanche slopes. Together, the morphologic, sedimentologic, lithostratigraphic, and chronostratigraphic evidence indicates that shore-parallet ridge complexes composed of gravel and sand that are tens of meters wide and several meters thick are primarily storm-constructed features that have accumulated for a few centuries or millennia as a result of multiple high-frequency intense-wave events. They are not entirely the result of one or a few tsunamis as recently reported. Tsunami deposition may account for some of the lateral ridge-complex accretion or boulder fields and isolated blocks that are associated with the ridge complexes. Copyright ?? 2008, SEPM (Society for Sedimentary Geology).

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

Sehgal, Ray M.; Maroudas, Dimitrios, E-mail: maroudas@ecs.umass.edu, E-mail: ford@ecs.umass.edu; Ford, David M., E-mail: maroudas@ecs.umass.edu, E-mail: ford@ecs.umass.edu

We have developed a coarse-grained description of the phase behavior of the isolated 38-atom Lennard-Jones cluster (LJ{sub 38}). The model captures both the solid-solid polymorphic transitions at low temperatures and the complex cluster breakup and melting transitions at higher temperatures. For this coarse model development, we employ the manifold learning technique of diffusion mapping. The outcome of the diffusion mapping analysis over a broad temperature range indicates that two order parameters are sufficient to describe the cluster's phase behavior; we have chosen two such appropriate order parameters that are metrics of condensation and overall crystallinity. In this well-justified coarse-variable space,more » we calculate the cluster's free energy landscape (FEL) as a function of temperature, employing Monte Carlo umbrella sampling. These FELs are used to quantify the phase behavior and onsets of phase transitions of the LJ{sub 38} cluster.« less

Stepping inside the niche: microclimate data are critical for accurate assessment of species' vulnerability to climate change.

PubMed

Storlie, Collin; Merino-Viteri, Andres; Phillips, Ben; VanDerWal, Jeremy; Welbergen, Justin; Williams, Stephen

2014-09-01

To assess a species' vulnerability to climate change, we commonly use mapped environmental data that are coarsely resolved in time and space. Coarsely resolved temperature data are typically inaccurate at predicting temperatures in microhabitats used by an organism and may also exhibit spatial bias in topographically complex areas. One consequence of these inaccuracies is that coarsely resolved layers may predict thermal regimes at a site that exceed species' known thermal limits. In this study, we use statistical downscaling to account for environmental factors and develop high-resolution estimates of daily maximum temperatures for a 36 000 km(2) study area over a 38-year period. We then demonstrate that this statistical downscaling provides temperature estimates that consistently place focal species within their fundamental thermal niche, whereas coarsely resolved layers do not. Our results highlight the need for incorporation of fine-scale weather data into species' vulnerability analyses and demonstrate that a statistical downscaling approach can yield biologically relevant estimates of thermal regimes. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Quantitative comparison of alternative methods for coarse-graining biological networks

PubMed Central

Bowman, Gregory R.; Meng, Luming; Huang, Xuhui

2013-01-01

Markov models and master equations are a powerful means of modeling dynamic processes like protein conformational changes. However, these models are often difficult to understand because of the enormous number of components and connections between them. Therefore, a variety of methods have been developed to facilitate understanding by coarse-graining these complex models. Here, we employ Bayesian model comparison to determine which of these coarse-graining methods provides the models that are most faithful to the original set of states. We find that the Bayesian agglomerative clustering engine and the hierarchical Nyström expansion graph (HNEG) typically provide the best performance. Surprisingly, the original Perron cluster cluster analysis (PCCA) method often provides the next best results, outperforming the newer PCCA+ method and the most probable paths algorithm. We also show that the differences between the models are qualitatively significant, rather than being minor shifts in the boundaries between states. The performance of the methods correlates well with the entropy of the resulting coarse-grainings, suggesting that finding states with more similar populations (i.e., avoiding low population states that may just be noise) gives better results. PMID:24089717

Electron attachment to trinitrotoluene (TNT) embedded in He droplets: complete freezing of dissociation intermediates in an extended range of electron energies.

PubMed

Mauracher, Andreas; Schöbel, Harald; Ferreira da Silva, Filipe; Edtbauer, Achim; Mitterdorfer, Christian; Denifl, Stephan; Märk, Tilmann D; Illenberger, Eugen; Scheier, Paul

2009-10-01

Electron attachment to the explosive trinitrotoluene (TNT) embedded in Helium droplets (TNT@He) generates the non-decomposed complexes (TNT)(n)(-), but no fragment ions in the entire energy range 0-12 eV. This strongly contrasts the behavior of single TNT molecules in the gas phase at ambient temperatures, where electron capture leads to a variety of different fragmentation products via different dissociative electron attachment (DEA) reactions. Single TNT molecules decompose by attachment of an electron at virtually no extra energy reflecting the explosive nature of the compound. The complete freezing of dissociation intermediates in TNT embedded in the droplet is explained by the particular mechanisms of DEA in nitrobenzenes, which is characterized by complex rearrangement processes in the transient negative ion (TNI) prior to decomposition. These mechanisms provide the condition for effective energy withdrawal from the TNI into the dissipative environment thereby completely suppressing its decomposition.

Coarse graining flow of spin foam intertwiners

NASA Astrophysics Data System (ADS)

Dittrich, Bianca; Schnetter, Erik; Seth, Cameron J.; Steinhaus, Sebastian

2016-12-01

Simplicity constraints play a crucial role in the construction of spin foam models, yet their effective behavior on larger scales is scarcely explored. In this article we introduce intertwiner and spin net models for the quantum group SU (2 )k×SU (2 )k, which implement the simplicity constraints analogous to four-dimensional Euclidean spin foam models, namely the Barrett-Crane (BC) and the Engle-Pereira-Rovelli-Livine/Freidel-Krasnov (EPRL/FK) model. These models are numerically coarse grained via tensor network renormalization, allowing us to trace the flow of simplicity constraints to larger scales. In order to perform these simulations we have substantially adapted tensor network algorithms, which we discuss in detail as they can be of use in other contexts. The BC and the EPRL/FK model behave very differently under coarse graining: While the unique BC intertwiner model is a fixed point and therefore constitutes a two-dimensional topological phase, BC spin net models flow away from the initial simplicity constraints and converge to several different topological phases. Most of these phases correspond to decoupling spin foam vertices; however we find also a new phase in which this is not the case, and in which a nontrivial version of the simplicity constraints holds. The coarse graining flow of the BC spin net models indicates furthermore that the transitions between these phases are not of second order. The EPRL/FK model by contrast reveals a far more intricate and complex dynamics. We observe an immediate flow away from the original simplicity constraints; however, with the truncation employed here, the models generically do not converge to a fixed point. The results show that the imposition of simplicity constraints can indeed lead to interesting and also very complex dynamics. Thus we need to further develop coarse graining tools to efficiently study the large scale behavior of spin foam models, in particular for the EPRL/FK model.

Self-reduction of a copper complex MOD ink for inkjet printing conductive patterns on plastics.

PubMed

Farraj, Yousef; Grouchko, Michael; Magdassi, Shlomo

2015-01-31

Highly conductive copper patterns on low-cost flexible substrates are obtained by inkjet printing a metal complex based ink. Upon heating the ink, the soluble complex, which is composed of copper formate and 2-amino-2-methyl-1-propanol, decomposes under nitrogen at 140 °C and is converted to pure metallic copper. The decomposition process of the complex is investigated and a suggested mechanism is presented. The ink is stable in air for prolonged periods, with no sedimentation or oxidation problems, which are usually encountered in copper nanoparticle based inks.

Grain refinement of a nickel and manganese free austenitic stainless steel produced by pressurized solution nitriding

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

Mohammadzadeh, Roghayeh, E-mail: r_mohammadzadeh@sut.ac.ir; Akbari, Alireza, E-mail: akbari@sut.ac.ir

2014-07-01

Prolonged exposure at high temperatures during solution nitriding induces grain coarsening which deteriorates the mechanical properties of high nitrogen austenitic stainless steels. In this study, grain refinement of nickel and manganese free Fe–22.75Cr–2.42Mo–1.17N high nitrogen austenitic stainless steel plates was investigated via a two-stage heat treatment procedure. Initially, the coarse-grained austenitic stainless steel samples were subjected to an isothermal heating at 700 °C to be decomposed into the ferrite + Cr{sub 2}N eutectoid structure and then re-austenitized at 1200 °C followed by water quenching. Microstructure and hardness of samples were characterized using X-ray diffraction, optical and scanning electron microscopy, andmore » micro-hardness testing. The results showed that the as-solution-nitrided steel decomposes non-uniformly to the colonies of ferrite and Cr{sub 2}N nitrides with strip like morphology after isothermal heat treatment at 700 °C. Additionally, the complete dissolution of the Cr{sub 2}N precipitates located in the sample edges during re-austenitizing requires longer times than 1 h. In order to avoid this problem an intermediate nitrogen homogenizing heat treatment cycle at 1200 °C for 10 h was applied before grain refinement process. As a result, the initial austenite was uniformly decomposed during the first stage, and a fine grained austenitic structure with average grain size of about 20 μm was successfully obtained by re-austenitizing for 10 min. - Highlights: • Successful grain refinement of Fe–22.75Cr–2.42Mo–1.17N steel by heat treatment • Using the γ → α + Cr{sub 2}N reaction for grain refinement of a Ni and Mn free HNASS • Obtaining a single phase austenitic structure with average grain size of ∼ 20 μm • Incomplete dissolution of Cr{sub 2}N during re-austenitizing at 1200 °C for long times • Reducing re-austenitizing time by homogenizing treatment before grain refinement.« less

Synthesis, structure and stability of a chiral imine-based Schiff-based ligand derived from L-glutamic acid and its [Cu4] complex

NASA Astrophysics Data System (ADS)

Muche, Simon; Levacheva, Irina; Samsonova, Olga; Biernasiuk, Anna; Malm, Anna; Lonsdale, Richard; Popiołek, Łukasz; Bakowsky, Udo; Hołyńska, Małgorzata

2017-01-01

Studies of the stability of a ligand derived from L-glutamic acid and ortho-vanillin and its new [Cu4] complex are presented. The [Cu4] complex contains a heterocubane [CuII4O4] core and pendant carboxylic groups increasing its solubility in water, also under basic conditions. The stability of the complex in different solvents is confirmed with ESI-MS studies and such experiments as successful recrystallization. The complex is stable also under physiological conditions whereas the ligand is partly decomposed to L-glutamic acid and ortho-vanillin.

Adaptive Skin Meshes Coarsening for Biomolecular Simulation

PubMed Central

Shi, Xinwei; Koehl, Patrice

2011-01-01

In this paper, we present efficient algorithms for generating hierarchical molecular skin meshes with decreasing size and guaranteed quality. Our algorithms generate a sequence of coarse meshes for both the surfaces and the bounded volumes. Each coarser surface mesh is adaptive to the surface curvature and maintains the topology of the skin surface with guaranteed mesh quality. The corresponding tetrahedral mesh is conforming to the interface surface mesh and contains high quality tetrahedral that decompose both the interior of the molecule and the surrounding region (enclosed in a sphere). Our hierarchical tetrahedral meshes have a number of advantages that will facilitate fast and accurate multigrid PDE solvers. Firstly, the quality of both the surface triangulations and tetrahedral meshes is guaranteed. Secondly, the interface in the tetrahedral mesh is an accurate approximation of the molecular boundary. In particular, all the boundary points lie on the skin surface. Thirdly, our meshes are Delaunay meshes. Finally, the meshes are adaptive to the geometry. PMID:21779137

Eigenvector decomposition of full-spectrum x-ray computed tomography.

PubMed

Gonzales, Brian J; Lalush, David S

2012-03-07

Energy-discriminated x-ray computed tomography (CT) data were projected onto a set of basis functions to suppress the noise in filtered back-projection (FBP) reconstructions. The x-ray CT data were acquired using a novel x-ray system which incorporated a single-pixel photon-counting x-ray detector to measure the x-ray spectrum for each projection ray. A matrix of the spectral response of different materials was decomposed using eigenvalue decomposition to form the basis functions. Projection of FBP onto basis functions created a de facto image segmentation of multiple contrast agents. Final reconstructions showed significant noise suppression while preserving important energy-axis data. The noise suppression was demonstrated by a marked improvement in the signal-to-noise ratio (SNR) along the energy axis for multiple regions of interest in the reconstructed images. Basis functions used on a more coarsely sampled energy axis still showed an improved SNR. We conclude that the noise-resolution trade off along the energy axis was significantly improved using the eigenvalue decomposition basis functions.

Spatio-temporal hierarchy in the dynamics of a minimalist protein model

NASA Astrophysics Data System (ADS)

Matsunaga, Yasuhiro; Baba, Akinori; Li, Chun-Biu; Straub, John E.; Toda, Mikito; Komatsuzaki, Tamiki; Berry, R. Stephen

2013-12-01

A method for time series analysis of molecular dynamics simulation of a protein is presented. In this approach, wavelet analysis and principal component analysis are combined to decompose the spatio-temporal protein dynamics into contributions from a hierarchy of different time and space scales. Unlike the conventional Fourier-based approaches, the time-localized wavelet basis captures the vibrational energy transfers among the collective motions of proteins. As an illustrative vehicle, we have applied our method to a coarse-grained minimalist protein model. During the folding and unfolding transitions of the protein, vibrational energy transfers between the fast and slow time scales were observed among the large-amplitude collective coordinates while the other small-amplitude motions are regarded as thermal noise. Analysis employing a Gaussian-based measure revealed that the time scales of the energy redistribution in the subspace spanned by such large-amplitude collective coordinates are slow compared to the other small-amplitude coordinates. Future prospects of the method are discussed in detail.

Momentum conserving Brownian dynamics propagator for complex soft matter fluids

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

Padding, J. T.; Briels, W. J.

2014-12-28

We present a Galilean invariant, momentum conserving first order Brownian dynamics scheme for coarse-grained simulations of highly frictional soft matter systems. Friction forces are taken to be with respect to moving background material. The motion of the background material is described by locally averaged velocities in the neighborhood of the dissolved coarse coordinates. The velocity variables are updated by a momentum conserving scheme. The properties of the stochastic updates are derived through the Chapman-Kolmogorov and Fokker-Planck equations for the evolution of the probability distribution of coarse-grained position and velocity variables, by requiring the equilibrium distribution to be a stationary solution.more » We test our new scheme on concentrated star polymer solutions and find that the transverse current and velocity time auto-correlation functions behave as expected from hydrodynamics. In particular, the velocity auto-correlation functions display a long time tail in complete agreement with hydrodynamics.« less

Segmenting human from photo images based on a coarse-to-fine scheme.

PubMed

Lu, Huchuan; Fang, Guoliang; Shao, Xinqing; Li, Xuelong

2012-06-01

Human segmentation in photo images is a challenging and important problem that finds numerous applications ranging from album making and photo classification to image retrieval. Previous works on human segmentation usually demand a time-consuming training phase for complex shape-matching processes. In this paper, we propose a straightforward framework to automatically recover human bodies from color photos. Employing a coarse-to-fine strategy, we first detect a coarse torso (CT) using the multicue CT detection algorithm and then extract the accurate region of the upper body. Then, an iterative multiple oblique histogram algorithm is presented to accurately recover the lower body based on human kinematics. The performance of our algorithm is evaluated on our own data set (contains 197 images with human body region ground truth data), VOC 2006, and the 2010 data set. Experimental results demonstrate the merits of the proposed method in segmenting a person with various poses.

Crowding with detection and coarse discrimination of simple visual features.

PubMed

Põder, Endel

2008-04-24

Some recent studies have suggested that there are actually no crowding effects with detection and coarse discrimination of simple visual features. The present study tests the generality of this idea. A target Gabor patch, surrounded by either 2 or 6 flanker Gabors, was presented briefly at 4 deg eccentricity of the visual field. Each Gabor patch was oriented either vertically or horizontally (selected randomly). Observers' task was either to detect the presence of the target (presented with probability 0.5) or to identify the orientation of the target. The target-flanker distance was varied. Results were similar for the two tasks but different for 2 and 6 flankers. The idea that feature detection and coarse discrimination are immune to crowding may be valid for the two-flanker condition only. With six flankers, a normal crowding effect was observed. It is suggested that the complexity of the full pattern (target plus flankers) could explain the difference.

Coarse-graining of proteins based on elastic network models

NASA Astrophysics Data System (ADS)

Sinitskiy, Anton V.; Voth, Gregory A.

2013-08-01

To simulate molecular processes on biologically relevant length- and timescales, coarse-grained (CG) models of biomolecular systems with tens to even hundreds of residues per CG site are required. One possible way to build such models is explored in this article: an elastic network model (ENM) is employed to define the CG variables. Free energy surfaces are approximated by Taylor series, with the coefficients found by force-matching. CG potentials are shown to undergo renormalization due to roughness of the energy landscape and smoothing of it under coarse-graining. In the case study of hen egg-white lysozyme, the entropy factor is shown to be of critical importance for maintaining the native structure, and a relationship between the proposed ENM-mode-based CG models and traditional CG-bead-based models is discussed. The proposed approach uncovers the renormalizable character of CG models and offers new opportunities for automated and computationally efficient studies of complex free energy surfaces.

Membrane extraction with thermodynamically unstable diphosphonic acid derivatives

DOEpatents

Horwitz, E.P.; Gatrone, R.C.; Nash, K.L.

1997-10-14

Thermodynamically-unstable complexing agents which are diphosphonic acids and diphosphonic acid derivatives (or sulphur containing analogs), like carboxyhydroxymethanediphosphonic acid and vinylidene-1,1-diphosphonic acid, are capable of complexing with metal ions, and especially metal ions in the II, III, IV, V and VI oxidation states, to form stable, water-soluble metal ion complexes in moderately alkaline to highly-acidic media. However, the complexing agents can be decomposed, under mild conditions, into non-organic compounds which, for many purposes are environmentally-nondamaging compounds thereby degrading the complex and releasing the metal ion for disposal or recovery. Uses for such complexing agents as well as methods for their manufacture are also described. 1 fig.

Extracting metal ions with diphosphonic acid, or derivative thereof

DOEpatents

Horwitz, Earl P.; Gatrone, Ralph C.; Nash, Kenneth L.

1994-01-01

Thermodynamically-unstable complexing agents which are diphosphonic acids and diphosphonic acid derivatives (or sulphur containing analogs), like carboxyhydroxymethanediphosphonic acid and vinylidene-1,1-diphosphonic acid, are capable of complexing with metal ions, and especially metal ions in the II, III, IV, V and VI oxidation states, to form stable, water-soluble metal ion complexes in moderately alkaline to highly-acidic media. However, the complexing agents can be decomposed, under mild conditions, into non-organic compounds which, for many purposes are environmentally-nondamaging compounds thereby degrading the complex and releasing the metal ion for disposal or recovery. Uses for such complexing agents as well as methods for their manufacture are also described.

Extracting metal ions with diphosphonic acid, or derivative thereof

DOEpatents

Horwitz, E.P.; Gatrone, R.C.; Nash, K.L.

1994-07-26

Thermodynamically-unstable complexing agents which are diphosphonic acids and diphosphonic acid derivatives (or sulfur containing analogs), like carboxyhydroxymethanediphosphonic acid and vinylidene-1,1-diphosphonic acid, are capable of complexing with metal ions, and especially metal ions in the II, III, IV, V and VI oxidation states, to form stable, water-soluble metal ion complexes in moderately alkaline to highly-acidic media. However, the complexing agents can be decomposed, under mild conditions, into non-organic compounds which, for many purposes are environmentally-nondamaging compounds thereby degrading the complex and releasing the metal ion for disposal or recovery. Uses for such complexing agents as well as methods for their manufacture are also described. 1 fig.

Coarse-grained Simulations of Sugar Transport and Conformational Changes of Lactose Permease

NASA Astrophysics Data System (ADS)

Liu, Jin; Jewel, S. M. Yead; Dutta, Prashanta

2016-11-01

Escherichia coli lactose permease (LacY) actively transports lactose and other galactosides across cell membranes through lactose/H+ symport process. Lactose/H+ symport is a highly complex process that involves sugar translocation, H+ transfer, as well as large-scale protein conformational changes. The complete picture of lactose/H+ symport is largely unclear due to the complexity and multiscale nature of the process. In this work, we develop the force field for sugar molecules compatible with PACE, a hybrid and coarse-grained force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid. After validation, we implement the new force field to investigate the transport of a β-D-galactopyranosyl-1-thio- β-D-galactopyranoside (TDG) molecule across a wild-type LacY during lactose/H+ symport process. Results show that the local interactions between TDG and LacY at the binding pocket are consistent with the X-ray experiment. Protonation of Glu325 stabilizes the TDG and inward-facing conformation of LacY. Protonation of Glu269 induces a dramatic protein structural reorganization and causes the expulsion of TDG from LacY to both sides of the membrane. The structural changes occur primarily in the N-terminal domain of LacY. This work is supported by NSF Grants: CBET-1250107 and CBET -1604211.

“Martinizing” the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins

PubMed Central

2017-01-01

Solvation is a fundamental driving force in many biological processes including biomolecular recognition and self-assembly, not to mention protein folding, dynamics, and function. The variational implicit solvent method (VISM) is a theoretical tool currently developed and optimized to estimate solvation free energies for systems of very complex topology, such as biomolecules. VISM’s theoretical framework makes it unique because it couples hydrophobic, van der Waals, and electrostatic interactions as a functional of the solvation interface. By minimizing this functional, VISM produces the solvation interface as an output of the theory. In this work, we push VISM to larger scale applications by combining it with coarse-grained solute Hamiltonians adapted from the MARTINI framework, a well-established mesoscale force field for modeling large-scale biomolecule assemblies. We show how MARTINI-VISM (MVISM) compares with atomistic VISM (AVISM) for a small set of proteins differing in size, shape, and charge distribution. We also demonstrate MVISM’s suitability to study the solvation properties of an interesting encounter complex, barnase–barstar. The promising results suggest that coarse-graining the protein with the MARTINI force field is indeed a valuable step to broaden VISM’s and MARTINI’s applications in the near future. PMID:28613904

Characterizing protein conformations by correlation analysis of coarse-grained contact matrices.

PubMed

Lindsay, Richard J; Siess, Jan; Lohry, David P; McGee, Trevor S; Ritchie, Jordan S; Johnson, Quentin R; Shen, Tongye

2018-01-14

We have developed a method to capture the essential conformational dynamics of folded biopolymers using statistical analysis of coarse-grained segment-segment contacts. Previously, the residue-residue contact analysis of simulation trajectories was successfully applied to the detection of conformational switching motions in biomolecular complexes. However, the application to large protein systems (larger than 1000 amino acid residues) is challenging using the description of residue contacts. Also, the residue-based method cannot be used to compare proteins with different sequences. To expand the scope of the method, we have tested several coarse-graining schemes that group a collection of consecutive residues into a segment. The definition of these segments may be derived from structural and sequence information, while the interaction strength of the coarse-grained segment-segment contacts is a function of the residue-residue contacts. We then perform covariance calculations on these coarse-grained contact matrices. We monitored how well the principal components of the contact matrices is preserved using various rendering functions. The new method was demonstrated to assist the reduction of the degrees of freedom for describing the conformation space, and it potentially allows for the analysis of a system that is approximately tenfold larger compared with the corresponding residue contact-based method. This method can also render a family of similar proteins into the same conformational space, and thus can be used to compare the structures of proteins with different sequences.

Large Contribution of Coarse Mode to Aerosol Microphysical and Optical Properties: Evidence from Ground-Based Observations of a Transpacific Dust Outbreak at a High-Elevation North American Site

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

Kassianov, E.; Pekour, M.; Flynn, C.

Our work is motivated by previous studies of the long-range trans-Atlantic transport of Saharan dust and the observed quasi-static nature of coarse mode aerosol with a volume median diameter (VMD) of approximately 3.5 µm. We examine coarse mode contributions from the trans-Pacific transport of Asian dust to North American aerosol microphysical and optical properties using a dataset collected at the high-elevation, mountain-top Storm Peak Laboratory (SPL, 3.22 km above sea level [ASL]) and the nearby Atmospheric Radiation Measurement (ARM) Mobile Facility (AMF, 2.76 km ASL). Data collected during the SPL Cloud Property Validation Experiment (STORMVEX, March 2011) are complemented bymore » quasi-global high-resolution model simulations coupled with aerosol chemistry. We identify dust event associated mostly with Asian plume (about 70% of dust mass) where the coarse mode with moderate (~4 µm) VMD is distinct and contributes substantially to aerosol microphysical (up to 70% for total volume) and optical (up to 45% for total scattering and aerosol optical depth) properties. Our results, when compared with previous Saharan dust studies, suggest a fairly invariant behavior of coarse mode dust aerosols. If confirmed in additional studies, this invariant behavior may simplify considerably model parameterizations for complex and size-dependent processes associated with dust transport and removal.« less

Characterizing protein conformations by correlation analysis of coarse-grained contact matrices

NASA Astrophysics Data System (ADS)

Lindsay, Richard J.; Siess, Jan; Lohry, David P.; McGee, Trevor S.; Ritchie, Jordan S.; Johnson, Quentin R.; Shen, Tongye

2018-01-01

We have developed a method to capture the essential conformational dynamics of folded biopolymers using statistical analysis of coarse-grained segment-segment contacts. Previously, the residue-residue contact analysis of simulation trajectories was successfully applied to the detection of conformational switching motions in biomolecular complexes. However, the application to large protein systems (larger than 1000 amino acid residues) is challenging using the description of residue contacts. Also, the residue-based method cannot be used to compare proteins with different sequences. To expand the scope of the method, we have tested several coarse-graining schemes that group a collection of consecutive residues into a segment. The definition of these segments may be derived from structural and sequence information, while the interaction strength of the coarse-grained segment-segment contacts is a function of the residue-residue contacts. We then perform covariance calculations on these coarse-grained contact matrices. We monitored how well the principal components of the contact matrices is preserved using various rendering functions. The new method was demonstrated to assist the reduction of the degrees of freedom for describing the conformation space, and it potentially allows for the analysis of a system that is approximately tenfold larger compared with the corresponding residue contact-based method. This method can also render a family of similar proteins into the same conformational space, and thus can be used to compare the structures of proteins with different sequences.

Insights into DNA-mediated interparticle interactions from a coarse-grained model

NASA Astrophysics Data System (ADS)

Ding, Yajun; Mittal, Jeetain

2014-11-01

DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system in metastable amorphous states. Therefore, it is vital to explore the molecular details of particle assembly processes in order to understand the underlying mechanisms. Molecular simulations based on coarse-grained models can provide a convenient route to explore these details. Most of the currently available coarse-grained models of DNA-functionalized particles ignore key chemical and structural details of DNA behavior. These models therefore are limited in scope for studying experimental phenomena. In this paper, we present a new coarse-grained model of DNA-functionalized particles which incorporates some of the desired features of DNA behavior. The coarse-grained DNA model used here provides explicit DNA representation (at the nucleotide level) and complementary interactions between Watson-Crick base pairs, which lead to the formation of single-stranded hairpin and double-stranded DNA. Aggregation between multiple complementary strands is also prevented in our model. We study interactions between two DNA-functionalized particles as a function of DNA grafting density, lengths of the hybridizing and non-hybridizing parts of DNA, and temperature. The calculated free energies as a function of pair distance between particles qualitatively resemble experimental measurements of DNA-mediated pair interactions.

Microbial Decomposers Not Constrained by Climate History Along a Mediterranean Climate Gradient

NASA Astrophysics Data System (ADS)

Baker, N. R.; Khalili, B.; Martiny, J. B. H.; Allison, S. D.

2017-12-01

The return of organic carbon to the atmosphere through terrestrial decomposition is mediated through the breakdown of complex organic polymers by extracellular enzymes produced by microbial decomposer communities. Determining if and how these decomposer communities are constrained in their ability to degrade plant litter is necessary for predicting how carbon cycling will be affected by future climate change. To address this question, we deployed fine-pore nylon mesh "microbial cage" litterbags containing grassland litter with and without local inoculum across five sites in southern California, spanning a gradient of 10.3-22.8° C in mean annual temperature and 100-400+ mm mean annual precipitation. Litterbags were deployed in October 2014 and collected four times over the course of 14 months. Recovered litter was assayed for mass loss, litter chemistry, microbial biomass, extracellular enzymes (Vmax and Km­), and enzyme temperature sensitivities. We hypothesized that grassland litter would decompose most rapidly in the grassland site, and that access to local microbial communities would enhance litter decomposition rates and microbial activity in the other sites along the gradient. We determined that temperature and precipitation likely interact to limit microbial decomposition in the extreme sites along our gradient. Despite their unique climate history, grassland microbes were not restricted in their ability to decompose litter under different climate conditions. Although we observed a strong correlation between bacterial biomass and mass loss across the gradient, litter that was inoculated with local microbial communities lost less mass despite having greater bacterial biomass and potentially accumulating more microbial residues. Our results suggest that microbial community composition may not constrain C-cycling rates under climate change in our system. However, there may be community constraints on decomposition if climate change alters litter chemistry, a mechanism only indirectly addressed by our design.

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

Maiolo, M., E-mail: massimo.maiolo@zhaw.ch; ZHAW, Institut für Angewandte Simulation, Grüental, CH-8820 Wädenswil; Vancheri, A., E-mail: alberto.vancheri@supsi.ch

In this paper, we apply Multiresolution Analysis (MRA) to develop sparse but accurate representations for the Multiscale Coarse-Graining (MSCG) approximation to the many-body potential of mean force. We rigorously framed the MSCG method into MRA so that all the instruments of this theory become available together with a multitude of new basis functions, namely the wavelets. The coarse-grained (CG) force field is hierarchically decomposed at different resolution levels enabling to choose the most appropriate wavelet family for each physical interaction without requiring an a priori knowledge of the details localization. The representation of the CG potential in this new efficientmore » orthonormal basis leads to a compression of the signal information in few large expansion coefficients. The multiresolution property of the wavelet transform allows to isolate and remove the noise from the CG force-field reconstruction by thresholding the basis function coefficients from each frequency band independently. We discuss the implementation of our wavelet-based MSCG approach and demonstrate its accuracy using two different condensed-phase systems, i.e. liquid water and methanol. Simulations of liquid argon have also been performed using a one-to-one mapping between atomistic and CG sites. The latter model allows to verify the accuracy of the method and to test different choices of wavelet families. Furthermore, the results of the computer simulations show that the efficiency and sparsity of the representation of the CG force field can be traced back to the mathematical properties of the chosen family of wavelets. This result is in agreement with what is known from the theory of multiresolution analysis of signals.« less

A combined emitter threat assessment method based on ICW-RCM

NASA Astrophysics Data System (ADS)

Zhang, Ying; Wang, Hongwei; Guo, Xiaotao; Wang, Yubing

2017-08-01

Considering that the tradition al emitter threat assessment methods are difficult to intuitively reflect the degree of target threaten and the deficiency of real-time and complexity, on the basis of radar chart method(RCM), an algorithm of emitter combined threat assessment based on ICW-RCM (improved combination weighting method, ICW) is proposed. The coarse sorting is integrated with fine sorting in emitter combined threat assessment, sequencing the emitter threat level roughly accordance to radar operation mode, and reducing task priority of the low-threat emitter; On the basis of ICW-RCM, sequencing the same radar operation mode emitter roughly, finally, obtain the results of emitter threat assessment through coarse and fine sorting. Simulation analyses show the correctness and effectiveness of this algorithm. Comparing with classical method of emitter threat assessment based on CW-RCM, the algorithm is visual in image and can work quickly with lower complexity.

Identification and location of catenary insulator in complex background based on machine vision

NASA Astrophysics Data System (ADS)

Yao, Xiaotong; Pan, Yingli; Liu, Li; Cheng, Xiao

2018-04-01

It is an important premise to locate insulator precisely for fault detection. Current location algorithms for insulator under catenary checking images are not accurate, a target recognition and localization method based on binocular vision combined with SURF features is proposed. First of all, because of the location of the insulator in complex environment, using SURF features to achieve the coarse positioning of target recognition; then Using binocular vision principle to calculate the 3D coordinates of the object which has been coarsely located, realization of target object recognition and fine location; Finally, Finally, the key is to preserve the 3D coordinate of the object's center of mass, transfer to the inspection robot to control the detection position of the robot. Experimental results demonstrate that the proposed method has better recognition efficiency and accuracy, can successfully identify the target and has a define application value.

SIRAH: a structurally unbiased coarse-grained force field for proteins with aqueous solvation and long-range electrostatics.

PubMed

Darré, Leonardo; Machado, Matías Rodrigo; Brandner, Astrid Febe; González, Humberto Carlos; Ferreira, Sebastián; Pantano, Sergio

2015-02-10

Modeling of macromolecular structures and interactions represents an important challenge for computational biology, involving different time and length scales. However, this task can be facilitated through the use of coarse-grained (CG) models, which reduce the number of degrees of freedom and allow efficient exploration of complex conformational spaces. This article presents a new CG protein model named SIRAH, developed to work with explicit solvent and to capture sequence, temperature, and ionic strength effects in a topologically unbiased manner. SIRAH is implemented in GROMACS, and interactions are calculated using a standard pairwise Hamiltonian for classical molecular dynamics simulations. We present a set of simulations that test the capability of SIRAH to produce a qualitatively correct solvation on different amino acids, hydrophilic/hydrophobic interactions, and long-range electrostatic recognition leading to spontaneous association of unstructured peptides and stable structures of single polypeptides and protein-protein complexes.

Isotropic stochastic rotation dynamics

NASA Astrophysics Data System (ADS)

Mühlbauer, Sebastian; Strobl, Severin; Pöschel, Thorsten

2017-12-01

Stochastic rotation dynamics (SRD) is a widely used method for the mesoscopic modeling of complex fluids, such as colloidal suspensions or multiphase flows. In this method, however, the underlying Cartesian grid defining the coarse-grained interaction volumes induces anisotropy. We propose an isotropic, lattice-free variant of stochastic rotation dynamics, termed iSRD. Instead of Cartesian grid cells, we employ randomly distributed spherical interaction volumes. This eliminates the requirement of a grid shift, which is essential in standard SRD to maintain Galilean invariance. We derive analytical expressions for the viscosity and the diffusion coefficient in relation to the model parameters, which show excellent agreement with the results obtained in iSRD simulations. The proposed algorithm is particularly suitable to model systems bound by walls of complex shape, where the domain cannot be meshed uniformly. The presented approach is not limited to SRD but is applicable to any other mesoscopic method, where particles interact within certain coarse-grained volumes.

Intramolecular Oxidative O-Demethylation of an Oxoferryl Porphyrin Complexed with a Per-O-methylated β-Cyclodextrin Dimer.

PubMed

Kitagishi, Hiroaki; Kurosawa, Shun; Kano, Koji

2016-11-22

The intramolecular oxidation of ROCH 3 to ROCH 2 OH, where the latter compound spontaneously decomposed to ROH and HCHO, was observed during the reaction of the supramolecular complex (met-hemoCD3) with cumene hydroperoxide in aqueous solution. Met-hemoCD3 is composed of meso-tetrakis(4-sulfonatophenyl)porphinatoiron(III) (Fe III TPPS) and a per-O-methylated β-cyclodextrin dimer having an -OCH 2 PyCH 2 O- linker (Py=pyridine-3,5-diyl). The O=Fe IV TPPS complex was formed by the reaction of met-hemoCD3 with cumene hydroperoxide, and isolated by gel-filtration chromatography. Although the isolated O=Fe IV TPPS complex in the cyclodextrin cage was stable in aqueous solution at 25 °C, it was gradually converted to Fe II TPPS (t 1/2 =7.6 h). This conversion was accompanied by oxidative O-demethylation of an OCH 3 group in the cyclodextrin dimer. The results indicated that hydrogen abstraction by O=Fe IV TPPS from ROCH 3 yields HO-Fe III TPPS and ROCH 2 . . This was followed by radical coupling to afford Fe II TPPS and ROCH 2 OH. The hemiacetal (ROCH 2 OH) immediately decomposed to ROH and HCHO. This study revealed the ability of oxoferryl porphyrin to induce two-electron oxidation. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Coarse gaining of molecular crystals: limitations imposed by molecular flexibility

NASA Astrophysics Data System (ADS)

Picu, Catalin; Pal, Anirban

Molecular crystals include molecular electronics, energetic materials, pharmaceuticals and some food components. In many of these applications the small scale mechanical behavior of the crystal is important such as for example in energetic materials where detonation is induced by the formation of hot spots which are induced thermomechanically, and in pharmaceuticals where phase stability is critical for the biochemical activity of the drug. Accurate modeling of these processes requires resolving the atomistic scale details of the material. However, the cost of these models is very large due to the complexity of the molecules forming the crystal, and some form of coarse graning is necessary. In this study we identify the limitations imposed by the need to accurately capture molecular flexibility on the development of coarse grained models for the energetic molecular crystal RDX. We define guidelines for the definition of coarse grained models that target elastic and plastic crystal scale properties such as elastic constants, thermal expansion, compressibility, the critical stress for the motion of dislocations (Peierls stress) and the stacking fault energy This work was supported by the ARO through Grant W911NF-09-1-0330 and AFRL through Grant FA8651-16-1-0004.

Coastal dune facies, Permian Cutler Formation (White Rim Sandstone), Capitol Reef National Park area, southern Utah

NASA Astrophysics Data System (ADS)

Kamola, Diane L.; Chan, Marjorie A.

1988-04-01

The Permian Cutler Formation (White Rim Sandstone) in the Capitol Reef National Park area in southern Utah is an excellent example of a coastal dune complex subjected to periodic flooding by marine waters. Wind-ripple, grainfall and grainflow laminae compose the cross-sets deposited by eolian dunes. However, wave-reworked structures such as oscillation ripples, the occurrence of the characteristically marine trace fossils Thalassinoides and Chondrites, and interfingering marine carbonate beds of the Kaibab Formation collectively indicate marine interaction with the eolian environment. Four facies are distinguished: cross-stratified sandstone, burrowed to bioturbated sandstone, brecciated and deformed sandstone, and ripple-laminated sandstone and thin carbonate beds. One unusual aspect of the cross-stratified sandstone facies is the abundance of coarse-grained sand. Coarse-grained sand is atypical in many ancient eolian slipface deposits, but occurs here in large slipface foresets as both grainflow and wind-ripple deposits. No water-laid structures are found in these slipface deposits. Coarse-grained sand was probably transported to the Cutler shoreline by fluvial systems draining the Uncompahgre Uplift to the east, and then concentrated as coarse-grained ripples in interdune areas. Some of these coarse-grained ripples migrated up the stoss side of the dunes and accumulations of coarse-grained sand avalanched down the crest to form grainflow deposits. An extensive amount of soft-sediment deformation is indicated by the presence of convolute bedding and brecciation. These features occur near the zone of interfingering with marine carbonate beds of the Kaibab Formation. The water-saturated and moist conditions required for extensive deformation may have been controlled by the proximity of these sandstones to the shoreline, and fluctuations in the associated groundwater table.

Temporal Fine Structure and Applications to Cochlear Implants

ERIC Educational Resources Information Center

Li, Xing

2013-01-01

Complex broadband sounds are decomposed by the auditory filters into a series of relatively narrowband signals, each of which conveys information about the sound by time-varying features. The slow changes in the overall amplitude constitute envelope, while the more rapid events, such as zero crossings, constitute temporal fine structure (TFS).…

Insect-mediated nitrogen dynamics in decomposing wood

Treesearch

Michael D. Ulyshen

2015-01-01

1.Wood decomposition is characterised by complex and poorly understood nitrogen (N) dynamics with unclear implications for forest nutrient cycling and productivity.Wood-dwelling microbes have developed unique strategies for coping with the N limitations imposed by their substrate, including the translocation of N into wood by cord-forming fungi and the fixation of...

Prospects and challenges for fungal metatranscriptomics of complex communities

Treesearch

Cheryl R. Kuske; Cedar N. Hesse; Jean F. Challacombe; Daniel Cullen; Joshua R. Herr; Rebecca C. Mueller; Adrian Tsang; Rytas Vilgalys

2015-01-01

The ability to extract and purify messenger RNA directly from plants, decomposing organic matter and soil, followed by highthroughput sequencing of the pool of expressed genes, has spawned the emerging research area of metatranscriptomics. Each metatranscriptome provides a snapshot of the composition and relative abundance of actively transcribed genes, and thus...

Effects of Temperature on Microstructure and Wear of Salt Bath Nitrided 17-4PH Stainless Steel

NASA Astrophysics Data System (ADS)

Wang, Jun; Lin, Yuanhua; Fan, Hongyuan; Zeng, Dezhi; Peng, Qian; Shen, Baoluo

2012-08-01

Salt bath nitriding of 17-4 PH martensitic precipitation hardening stainless steels was conducted at 610, 630, and 650 °C for 2 h using a complex salt bath heat-treatment, and the properties of the nitrided surface were systematically evaluated. Experimental results revealed that the microstructure and phase constituents of the nitrided surface alloy are highly process condition dependent. When 17-4PH stainless steel was subjected to complex salt bathing nitriding, the main phase of the nitrided layer was expanded martensite (α'), expanded austenite (γN), CrN, Fe4N, and (Fe,Cr) x O y . In the sample nitrided above 610 °C, the expanded martensite transformed into expanded austenite. But in the sample nitrided at 650 °C, the expanded austenite decomposed into αN and CrN. The decomposed αN then disassembled into CrN and alpha again. The nitrided layer depth thickened intensively with the increasing nitriding temperature. The activation energy of nitriding in this salt bath was 125 ± 5 kJ/mol.

Electrical, structural and thermal studies of carbon nanotubes from natural legume seeds: kala chana

NASA Astrophysics Data System (ADS)

Ranu, Rachana; Chauhan, Yatishwar; Singh, Pramod K.; Bhattacharya, B.; Tomar, S. K.

2016-12-01

Carbon nanotubes (CNTs) are the carbon materials measured at nanoscale level and they are defined in two types according to the number of concentric layers, i.e. single-layer tube is single-walled nanotubes, while multi-layer tube structure is called multi-walled nanotubes. The green method synthesis for the preparation of CNTs begins with the smashing of legume seeds kala chana, and then they form complex with cobalt salt. Desiccation of the complex compound forms cobalt salt and seed protein. The complex is then decomposed at 625 °C in muffle furnace for 20 min. Purification of the decomposed sample is done through acid wash treatment and dried in vacuum oven. The confirmations of CNTs are done by nuclear magnetic resonance and Fourier transform infrared, which analyzes the denatured protein, reacted to the metal salt. X-Ray diffraction determines the MWNTs with transmission electron microscope (TEM) reports the network structure of CNTs. thermal gravimetric analysis (TGA)-differential thermal analysis (DTA)-thermogravimetric analysis (DTG) tests the amount of sample under thermal treatment. Vibrating sample magnetometer determines the paramagnetic nature of CNTs. CNTs thus prepared can be used in mechanical fields, in solar cells, in electronics fields, etc. because of their multidisciplinary properties. The synthesized CNTs are eco-friendly in nature, prepared by the legume seed natural precursor.

Einstein Equations from Varying Complexity

NASA Astrophysics Data System (ADS)

Czech, Bartłomiej

2018-01-01

A recent proposal equates the circuit complexity of a quantum gravity state with the gravitational action of a certain patch of spacetime. Since Einstein's equations follow from varying the action, it should be possible to derive them by varying complexity. I present such a derivation for vacuum solutions of pure Einstein gravity in three-dimensional asymptotically anti-de Sitter space. The argument relies on known facts about holography and on properties of tensor network renormalization, an algorithm for coarse-graining (and optimizing) tensor networks.

Physical interpretation of isothermal remanent magnetization end-members: New insights into the environmental history of Lake Hovsgul, Mongolia

NASA Astrophysics Data System (ADS)

Fabian, Karl; Shcherbakov, Valeriy P.; Kosareva, Lina; Nourgaliev, Danis

2016-11-01

Acquisition curves of isothermal remanent magnetization for 1057 samples of core KDP-01 from Lake Hovsgul (Mongolia) are decomposed into three end-members using non-negative matrix factorization. The obtained mixing coefficients also decompose hysteresis loops, back-field, and strong-field thermomagnetic curves into their related end-member components. This proves that the end-members represent different mineralogical fractions of the Lake Hovsgul sedimentary environment. The method used for unmixing offers a new possibility to apply rock magnetism in paleoecological and paleoclimatic studies. For Lake Hovsgul, it indicates that a low-coercivity component with a covarying paramagnetic phase represents a coarse-grained magnetite fraction from terrigenous influx probably via fluvial transport. A second component with coercivities close to 50 mT is identified as a magnetite fraction related to magnetosomes of magnetotactic bacteria. The third component has coercivities near 85 mT and is identified as greigite of biotic or abiotic origin common in suboxic/anoxic sediments. Significant positive correlations between variations of intensity of all three mineralogical components along the core are found. A rapid drop in all end-member concentrations by more than one order of magnitude at about 20 m depth testifies to a major change of the environmental or geological conditions of Lake Hovsgul. It possibly is related to the onset of MIS 10 marking the termination of arid climate conditions. Short intervals of high productivity are characterized by an abundance of magnetite magnetosomes and may highlight glacial-interglacial transition intervals. For the rest of the core, greigite magnetization substantially exceeds that of magnetite, indicating a predominantly anoxic environment.

Are pretreatment 18F-FDG PET tumor textural features in non-small cell lung cancer associated with response and survival after chemoradiotherapy?

PubMed

Cook, Gary J R; Yip, Connie; Siddique, Muhammad; Goh, Vicky; Chicklore, Sugama; Roy, Arunabha; Marsden, Paul; Ahmad, Shahreen; Landau, David

2013-01-01

There is evidence in some solid tumors that textural features of tumoral uptake in (18)F-FDG PET images are associated with response to chemoradiotherapy and survival. We have investigated whether a similar relationship exists in non-small cell lung cancer (NSCLC). Fifty-three patients (mean age, 65.8 y; 31 men, 22 women) with NSCLC treated with chemoradiotherapy underwent pretreatment (18)F-FDG PET/CT scans. Response was assessed by CT Response Evaluation Criteria in Solid Tumors (RECIST) at 12 wk. Overall survival (OS), progression-free survival (PFS), and local PFS (LPFS) were recorded. Primary tumor texture was measured by the parameters coarseness, contrast, busyness, and complexity. The following parameters were also derived from the PET data: primary tumor standardized uptake values (SUVs) (mean SUV, maximum SUV, and peak SUV), metabolic tumor volume, and total lesion glycolysis. Compared with nonresponders, RECIST responders showed lower coarseness (mean, 0.012 vs. 0.027; P = 0.004) and higher contrast (mean, 0.11 vs. 0.044; P = 0.002) and busyness (mean, 0.76 vs. 0.37; P = 0.027). Neither complexity nor any of the SUV parameters predicted RECIST response. By Kaplan-Meier analysis, OS, PFS, and LPFS were lower in patients with high primary tumor coarseness (median, 21.1 mo vs. not reached, P = 0.003; 12.6 vs. 25.8 mo, P = 0.002; and 12.9 vs. 20.5 mo, P = 0.016, respectively). Tumor coarseness was an independent predictor of OS on multivariable analysis. Contrast and busyness did not show significant associations with OS (P = 0.075 and 0.059, respectively), but PFS and LPFS were longer in patients with high levels of each (for contrast: median of 20.5 vs. 12.6 mo, P = 0.015, and median not reached vs. 24 mo, P = 0.02; and for busyness: median of 20.5 vs. 12.6 mo, P = 0.01, and median not reached vs. 24 mo, P = 0.006). Neither complexity nor any of the SUV parameters showed significant associations with the survival parameters. In NSCLC, baseline (18)F-FDG PET scan uptake showing abnormal texture as measured by coarseness, contrast, and busyness is associated with nonresponse to chemoradiotherapy by RECIST and with poorer prognosis. Measurement of tumor metabolic heterogeneity with these parameters may provide indices that can be used to stratify patients in clinical trials for lung cancer chemoradiotherapy.

A constraint-logic based implementation of the coarse-grained approach to data acquisition scheduling of the International Ultraviolet Explorer orbiting observatory

NASA Technical Reports Server (NTRS)

Mccollum, Bruce; Graves, Mark

1994-01-01

The International Ultraviolet Explorer (IUE) satellite observatory has been in operation continuously since 1978. It typically carries out several thousand observations per year for over a hundred different science projects. These observations, which can occur in one of four different data-taking modes, fall under several satellite-related constraints and many other constraints which derive from the science goals of the projects being undertaken. One strategy which has made the scheduling problem tractable has been that of 'coarse-graining' the time into discrete blocks of equal size (8 hours), each of which is devoted to a single science program, and each of which is sufficiently long for several observations to be carried out. We call it 'coarse-graining' because the schedule is done at a 'coarse' level which ignores fine structure; i.e., no attempt is made to plan the sequence of observations occurring within each time block. We have incorporated the IUE's coarse-grained approach in new software which examines the science needs of the observations and produces a limited set of alternative schedules which meet all of the instrument and science-related constraints. With this algorithm, the IUE can still be scheduled by a single person using a standard workstation, as it has been. We believe that this software could could be adapted to a more complex mission while retaining the IUE's high flexibility and efficiency and scientific return of future satellite missions.

A general gridding, discretization, and coarsening methodology for modeling flow in porous formations with discrete geological features

NASA Astrophysics Data System (ADS)

Karimi-Fard, M.; Durlofsky, L. J.

2016-10-01

A comprehensive framework for modeling flow in porous media containing thin, discrete features, which could be high-permeability fractures or low-permeability deformation bands, is presented. The key steps of the methodology are mesh generation, fine-grid discretization, upscaling, and coarse-grid discretization. Our specialized gridding technique combines a set of intersecting triangulated surfaces by constructing approximate intersections using existing edges. This procedure creates a conforming mesh of all surfaces, which defines the internal boundaries for the volumetric mesh. The flow equations are discretized on this conforming fine mesh using an optimized two-point flux finite-volume approximation. The resulting discrete model is represented by a list of control-volumes with associated positions and pore-volumes, and a list of cell-to-cell connections with associated transmissibilities. Coarse models are then constructed by the aggregation of fine-grid cells, and the transmissibilities between adjacent coarse cells are obtained using flow-based upscaling procedures. Through appropriate computation of fracture-matrix transmissibilities, a dual-continuum representation is obtained on the coarse scale in regions with connected fracture networks. The fine and coarse discrete models generated within the framework are compatible with any connectivity-based simulator. The applicability of the methodology is illustrated for several two- and three-dimensional examples. In particular, we consider gas production from naturally fractured low-permeability formations, and transport through complex fracture networks. In all cases, highly accurate solutions are obtained with significant model reduction.

Cyclic steps and superimposed antidune deposits: important elements of coarse-grained deepwater channel-levée complexes

NASA Astrophysics Data System (ADS)

Lang, Joerg; Brandes, Christian; Winsemann, Jutta

2017-04-01

The facies distribution and architecture of submarine fans can be strongly impacted by erosion and deposition by supercritical density flows. We present field examples from the Sandino Forearc Basin (southern Central America), where cyclic-step and antidune deposits represent important sedimentary facies of coarse-grained channel-levée complexes. These bedforms occur in all sub-environments of the depositional systems and relate to the different stages of avulsion, bypass, levée construction and channel backfilling. Large-scale scours (18 to 29 m deep, 18 to 25 m wide, 60 to >120 m long) with an amalgamated infill, comprising massive, normally coarse-tail graded or spaced subhorizontally stratified conglomerates and pebbly sandstones, are interpreted as deposits of the hydraulic-jump zone of cyclic steps. These cyclic steps probably formed during avulsion, when high-density flows were routed into the evolving channel. The large-scale scour fills can be distinguished from small-scale channel fills based on the preservation of a steep upper margin and a coarse-grained infill comprising mainly amalgamated hydraulic-jump deposits. Channel fills include repetitive successions deposited by cyclic steps with superimposed antidunes. The hydraulic-jump zone of cyclic-step deposits comprises regularly spaced scours (0.2 to 2.6 m deep, 0.8 to 23 m wide), which are infilled by intraclast-rich conglomerates or pebbly sandstones and display normal coarse-tail grading or backsets. Laterally and vertically these deposits are associated with subhorizontally stratified, low-angle cross-stratified or sinusoidal stratified pebbly sandstones and sandstones (wavelength 0.5 to 18 m), interpreted as representing antidune deposits formed on the stoss-side of the cyclic steps during flow re-acceleration. The field examples indicate that so-called crudely or spaced stratified deposits may commonly represent antidune deposits with varying stratification styles controlled by the aggradation rate, grain-size distribution and amalgamation. The deposits of small-scale cyclic steps with superimposed antidunes form fining upwards successions with decreasing antidune wavelengths. Such cyclic step-antidune successions are the characteristic basal infill of channels, probably related to supercritical high-density turbidity flows triggered by retrogressive slope failures.

Leaf litter quality affects aquatic insect emergence: contrasting patterns from two foundation trees.

PubMed

Compson, Zacchaeus G; Adams, Kenneth J; Edwards, Joeseph A; Maestas, Jesse M; Whitham, Thomas G; Marks, Jane C

2013-10-01

Reciprocal subsidies between rivers and terrestrial habitats are common where terrestrial leaf litter provides energy to aquatic invertebrates while emerging aquatic insects provide energy to terrestrial predators (e.g., birds, lizards, spiders). We examined how aquatic insect emergence changed seasonally with litter from two foundation riparian trees, whose litter often dominates riparian streams of the southwestern United States: Fremont (Populus fremontii) and narrowleaf (Populus angustifolia) cottonwood. P. fremontii litter is fast-decomposing and lower in defensive phytochemicals (i.e., condensed tannins, lignin) relative to P. angustifolia. We experimentally manipulated leaf litter from these two species by placing them in leaf enclosures with emergence traps attached in order to determine how leaf type influenced insect emergence. Contrary to our initial predictions, we found that packs with slow-decomposing leaves tended to support more emergent insects relative to packs with fast-decomposing leaves. Three findings emerged. Firstly, abundance (number of emerging insects m(-2) day(-1)) was 25% higher on narrowleaf compared to Fremont leaves for the spring but did not differ in the fall, demonstrating that leaf quality from two dominant trees of the same genus yielded different emergence patterns and that these patterns changed seasonally. Secondly, functional feeding groups of emerging insects differed between treatments and seasons. Specifically, in the spring collector-gatherer abundance and biomass were higher on narrowleaf leaves, whereas collector-filterer abundance and biomass were higher on Fremont leaves. Shredder abundance and biomass were higher on narrowleaf leaves in the fall. Thirdly, diversity (Shannon's H') was higher on Fremont leaves in the spring, but no differences were found in the fall, showing that fast-decomposing leaves can support a more diverse, complex emergent insect assemblage during certain times of the year. Collectively, these results challenge the notion that leaf quality is a simple function of decomposition, suggesting instead that aquatic insects benefit differentially from different leaf types, such that some use slow-decomposing litter for habitat and its temporal longevity and others utilize fast-decomposing litter with more immediate nutrient release.

Path statistics, memory, and coarse-graining of continuous-time random walks on networks

PubMed Central

Kion-Crosby, Willow; Morozov, Alexandre V.

2015-01-01

Continuous-time random walks (CTRWs) on discrete state spaces, ranging from regular lattices to complex networks, are ubiquitous across physics, chemistry, and biology. Models with coarse-grained states (for example, those employed in studies of molecular kinetics) or spatial disorder can give rise to memory and non-exponential distributions of waiting times and first-passage statistics. However, existing methods for analyzing CTRWs on complex energy landscapes do not address these effects. Here we use statistical mechanics of the nonequilibrium path ensemble to characterize first-passage CTRWs on networks with arbitrary connectivity, energy landscape, and waiting time distributions. Our approach can be applied to calculating higher moments (beyond the mean) of path length, time, and action, as well as statistics of any conservative or non-conservative force along a path. For homogeneous networks, we derive exact relations between length and time moments, quantifying the validity of approximating a continuous-time process with its discrete-time projection. For more general models, we obtain recursion relations, reminiscent of transfer matrix and exact enumeration techniques, to efficiently calculate path statistics numerically. We have implemented our algorithm in PathMAN (Path Matrix Algorithm for Networks), a Python script that users can apply to their model of choice. We demonstrate the algorithm on a few representative examples which underscore the importance of non-exponential distributions, memory, and coarse-graining in CTRWs. PMID:26646868

Principal component analysis acceleration of rovibrational coarse-grain models for internal energy excitation and dissociation

NASA Astrophysics Data System (ADS)

Bellemans, Aurélie; Parente, Alessandro; Magin, Thierry

2018-04-01

The present work introduces a novel approach for obtaining reduced chemistry representations of large kinetic mechanisms in strong non-equilibrium conditions. The need for accurate reduced-order models arises from compression of large ab initio quantum chemistry databases for their use in fluid codes. The method presented in this paper builds on existing physics-based strategies and proposes a new approach based on the combination of a simple coarse grain model with Principal Component Analysis (PCA). The internal energy levels of the chemical species are regrouped in distinct energy groups with a uniform lumping technique. Following the philosophy of machine learning, PCA is applied on the training data provided by the coarse grain model to find an optimally reduced representation of the full kinetic mechanism. Compared to recently published complex lumping strategies, no expert judgment is required before the application of PCA. In this work, we will demonstrate the benefits of the combined approach, stressing its simplicity, reliability, and accuracy. The technique is demonstrated by reducing the complex quantum N2(g+1Σ) -N(S4u ) database for studying molecular dissociation and excitation in strong non-equilibrium. Starting from detailed kinetics, an accurate reduced model is developed and used to study non-equilibrium properties of the N2(g+1Σ) -N(S4u ) system in shock relaxation simulations.

MEMD-enhanced multivariate fuzzy entropy for the evaluation of complexity in biomedical signals.

PubMed

Azami, Hamed; Smith, Keith; Escudero, Javier

2016-08-01

Multivariate multiscale entropy (mvMSE) has been proposed as a combination of the coarse-graining process and multivariate sample entropy (mvSE) to quantify the irregularity of multivariate signals. However, both the coarse-graining process and mvSE may not be reliable for short signals. Although the coarse-graining process can be replaced with multivariate empirical mode decomposition (MEMD), the relative instability of mvSE for short signals remains a problem. Here, we address this issue by proposing the multivariate fuzzy entropy (mvFE) with a new fuzzy membership function. The results using white Gaussian noise show that the mvFE leads to more reliable and stable results, especially for short signals, in comparison with mvSE. Accordingly, we propose MEMD-enhanced mvFE to quantify the complexity of signals. The characteristics of brain regions influenced by partial epilepsy are investigated by focal and non-focal electroencephalogram (EEG) time series. In this sense, the proposed MEMD-enhanced mvFE and mvSE are employed to discriminate focal EEG signals from non-focal ones. The results demonstrate the MEMD-enhanced mvFE values have a smaller coefficient of variation in comparison with those obtained by the MEMD-enhanced mvSE, even for long signals. The results also show that the MEMD-enhanced mvFE has better performance to quantify focal and non-focal signals compared with multivariate multiscale permutation entropy.

Refined generalized multiscale entropy analysis for physiological signals

NASA Astrophysics Data System (ADS)

Liu, Yunxiao; Lin, Youfang; Wang, Jing; Shang, Pengjian

2018-01-01

Multiscale entropy analysis has become a prevalent complexity measurement and been successfully applied in various fields. However, it only takes into account the information of mean values (first moment) in coarse-graining procedure. Then generalized multiscale entropy (MSEn) considering higher moments to coarse-grain a time series was proposed and MSEσ2 has been implemented. However, the MSEσ2 sometimes may yield an imprecise estimation of entropy or undefined entropy, and reduce statistical reliability of sample entropy estimation as scale factor increases. For this purpose, we developed the refined model, RMSEσ2, to improve MSEσ2. Simulations on both white noise and 1 / f noise show that RMSEσ2 provides higher entropy reliability and reduces the occurrence of undefined entropy, especially suitable for short time series. Besides, we discuss the effect on RMSEσ2 analysis from outliers, data loss and other concepts in signal processing. We apply the proposed model to evaluate the complexity of heartbeat interval time series derived from healthy young and elderly subjects, patients with congestive heart failure and patients with atrial fibrillation respectively, compared to several popular complexity metrics. The results demonstrate that RMSEσ2 measured complexity (a) decreases with aging and diseases, and (b) gives significant discrimination between different physiological/pathological states, which may facilitate clinical application.

Braided fluvial sedimentation in the lower paleozoic cape basin, South Africa

NASA Astrophysics Data System (ADS)

Vos, Richard G.; Tankard, Anthony J.

1981-07-01

Lower Paleozoic braided stream deposits from the Piekenier Formation in the Cape Province, South Africa, provide information on lateral and vertical facies variability in an alluvial plain complex influenced by a moderate to high runoff. Four braided stream facies are recognized on the basis of distinct lithologies and assemblages of sedimentary structures. A lower facies, dominated by upward-fining conglomerate to sandstone and mudstone channel fill sequences, is interpreted as a middle to lower alluvial plain deposit with significant suspended load sedimentation in areas of moderate to low gradients. These deposits are succeeded by longitudinal conglomerate bars which are attributed to middle to upper alluvial plain sedimentation with steeper gradients. This facies is in turn overlain by braid bar complexes of large-scale transverse to linguoid dunes consisting of coarse-grained pebbly sandstones with conglomerate lenses. These bar complexes are compared with environments of the Recent Platte River. They represent a middle to lower alluvial plain facies with moderate gradients and no significant suspended load sedimentation or vegetation to stabilize channels. These bar complexes interfinger basinward with plane bedded medium to coarse-grained sandstones interpreted as sheet flood deposits over the distal portions of an alluvial plain with low gradients and lacking fine-grained detritus or vegetation.

Effect of bimodal harmonic structure design on the deformation behaviour and mechanical properties of Co-Cr-Mo alloy.

PubMed

Vajpai, Sanjay Kumar; Sawangrat, Choncharoen; Yamaguchi, Osamu; Ciuca, Octav Paul; Ameyama, Kei

2016-01-01

In the present work, Co-Cr-Mo alloy compacts with a unique bimodal microstructural design, harmonic structure design, were successfully prepared via a powder metallurgy route consisting of controlled mechanical milling of pre-alloyed powders followed by spark plasma sintering. The harmonic structured Co-Cr-Mo alloy with bimodal grain size distribution exhibited relatively higher strength together with higher ductility as compared to the coarse-grained specimens. The harmonic Co-Cr-Mo alloy exhibited a very complex deformation behavior wherein it was found that the higher strength and the high retained ductility are derived from fine-grained shell and coarse-grained core regions, respectively. Finally, it was observed that the peculiar spatial/topological arrangement of stronger fine-grained and ductile coarse-grained regions in the harmonic structure promotes uniformity of strain distribution, leading to improved mechanical properties by suppressing the localized plastic deformation during straining. Copyright © 2015 Elsevier B.V. All rights reserved.

The effect of liming on antibacterial and hormone levels in wastewater biosolids.

PubMed

Olszewski, Jennifer M; Lozano, Nuria; Haines, Christine; Rice, Clifford P; Ramirez, Mark; Torrents, Alba

2013-01-01

This study analyzes the effect of liming on levels of triclocarban (TCC), triclosan (TCS), estrone (E1), and progesterone (P), two antimicrobial agents and two natural hormones, respectively. Factors studied include lime particle size, mixing time, and overall lime contact time. The study results suggest that coarse lime may be more active than fine lime due to less interaction with surrounding air. Both TCS and TCC concentrations were lower in coarse limed samples versus unlimed samples and the decrease was a function of time. A similar, but statistically insignificant trend in TCC and TCS levels was observed in fine lime samples with respect to unlimed samples. Liming was also found to decrease apparent E1 levels, with more notable decreases in samples amended with coarse lime. P-levels significantly increased after 1-day of contact time, stabilizing over the next 14 days of the study period. This increase and stabilization of P-levels was attributed to the pH and moisture-driven conversion of more chemically complex steroids into P.

Holliday Junction Thermodynamics and Structure: Coarse-Grained Simulations and Experiments

NASA Astrophysics Data System (ADS)

Wang, Wujie; Nocka, Laura M.; Wiemann, Brianne Z.; Hinckley, Daniel M.; Mukerji, Ishita; Starr, Francis W.

2016-03-01

Holliday junctions play a central role in genetic recombination, DNA repair and other cellular processes. We combine simulations and experiments to evaluate the ability of the 3SPN.2 model, a coarse-grained representation designed to mimic B-DNA, to predict the properties of DNA Holliday junctions. The model reproduces many experimentally determined aspects of junction structure and stability, including the temperature dependence of melting on salt concentration, the bias between open and stacked conformations, the relative populations of conformers at high salt concentration, and the inter-duplex angle (IDA) between arms. We also obtain a close correspondence between the junction structure evaluated by all-atom and coarse-grained simulations. We predict that, for salt concentrations at physiological and higher levels, the populations of the stacked conformers are independent of salt concentration, and directly observe proposed tetrahedral intermediate sub-states implicated in conformational transitions. Our findings demonstrate that the 3SPN.2 model captures junction properties that are inaccessible to all-atom studies, opening the possibility to simulate complex aspects of junction behavior.

A large coaxial reflection cell for broadband dielectric characterization of coarse-grained materials

NASA Astrophysics Data System (ADS)

Bore, Thierry; Bhuyan, Habibullah; Bittner, Tilman; Murgan, Vignesh; Wagner, Norman; Scheuermann, Alexander

2018-01-01

Knowledge of the frequency-dependent electromagnetic properties of coarse-grained materials is imperative for the successful application of high frequency electromagnetic measurement techniques for near and subsurface monitoring. This paper reports the design, calibration and application of a novel one-port large coaxial cell for broadband complex permittivity measurements of civil engineering materials. It was designed to allow the characterization of heterogeneous material with large aggregate dimensions (up to 28 mm) over a frequency range from 1 MHz-860 MHz. In the first step, the system parameters were calibrated using the measured scattering function in a perfectly known dielectric material in an optimization scheme. In the second step, the method was validated with measurements made on standard liquids. Then the performance of the cell was evaluated on a compacted coarse-grained soil. The dielectric spectra were obtained by means of fitting the measured scattering function using a transverse electromagnetic mode propagation model considering the frequency-dependent complex permittivity. Two scenarios were systematically analyzed and compared. The first scenario consisted of a broadband generalized dielectric relaxation model with two Cole-Cole type relaxation processes related to the interaction of the aqueous phase and the solid phase, a constant high frequency contribution as well as an apparent direct current conductivity term. The second scenario relied on a three-phase theoretical mixture equation which was used in a forward approach in order to calibrate the model. Both scenarios provide almost identical results for the broadband effective complex relative permittivity. The combination of both scenarios suggests the simultaneous estimation of water content, density, bulk and pore water conductivity for road base materials for in situ applications.

Hybrid copper complex-derived conductive patterns printed on polyimide substrates

NASA Astrophysics Data System (ADS)

Lee, Byoungyoon; Jeong, Sooncheol; Kim, Yoonhyun; Jeong, Inbum; Woo, Kyoohee; Moon, Jooho

2012-06-01

We synthesized new copper complexes that can be readily converted into highly conductive Cu film. Mechanochemical milling of copper (I) oxide suspended in formic acid resulted in the submicron-sized Cu formate together Cu nanoparticles. The submicrometer-sized Cu formates are reactive toward inter-particle sintering and metallic Cu seeds present in the Cu complexes assist their decomposition and the nucleation of Cu. The hybrid copper complex film printed on polyimide substrate is decomposed into dense and uniform Cu layer after annealing at 250 °C for 30 min under nitrogen atmosphere. The resulting Cu film exhibited a low resistivity of 8.2 μΩ·cm and good adhesion characteristics.

RECOVERY OF PROTACTINIUM FROM AQUEOUS SOLUTIONS

DOEpatents

Elson, R.E.

1959-07-14

The recovery of fluoride complexed protactinium from aqueous acidic solutions by solvent extraction is described. Generally the prccess of the invention com rises mixing an aqueous solution containing protactinium in a complexed form with an organic solvent which is specific for protactinium, such as diisopropyl carbinol, then decomposing the protactinium complex by adjusting the acidity of the aqueous solution to between 0-3 to 0-9 M in hydrogen ion concentration, and introducing a source of aluminum ions in sufficient quantity to establish a concentration of 0.5 to 1.2 M aluminum ion, whereupon decomposition of the protactinium fluoride complex takes place and the protactinium ion is taken up by the organic solvent phase.

Predicting Vulnerability of the Integrity and Connectivity Associated with Culverts in Low Order Streams of Northern Michigan

NASA Astrophysics Data System (ADS)

King, C. H.; Wagenbrenner, J.; Fedora, M.; Watkins, D.; Watkins, M. K.; Huckins, C.

2017-12-01

The Great Lakes Region of North America has experienced more frequent extreme precipitation events in recent decades, resulting in a large number of stream crossing failures. While there are accepted methods for designing stream crossings to accommodate peak storm discharges, less attention has been paid to assessing the risk of failure. To evaluate failure risk and potential impacts, coarse-resolution stream crossing surveys were completed on 51 stream crossings and dams in the North Branch Paint River watershed in Michigan's Upper Peninsula. These inventories determined stream crossing dimensions along with stream and watershed characteristics. Eleven culverts were selected from the coarse surveys for high resolution hydraulic analysis to estimate discharge conditions expected at crossing failure. Watershed attributes upstream of the crossing, including area, slope, and storage, were acquired. Sediment discharge and the economic impact associated with a failure event were also estimated for each stream crossing. Impacts to stream connectivity and fish passability were assessed from the coarse-level surveys. Using information from both the coarse and high-resolution surveys, we also developed indicators to predict failure risk without the need for complex hydraulic modeling. These passability scores and failure risk indicators will help to prioritize infrastructure replacement and improve the overall connectivity of river systems throughout the upper Great Lakes Region.

Coarse-Scale Biases for Spirals and Orientation in Human Visual Cortex

PubMed Central

Heeger, David J.

2013-01-01

Multivariate decoding analyses are widely applied to functional magnetic resonance imaging (fMRI) data, but there is controversy over their interpretation. Orientation decoding in primary visual cortex (V1) reflects coarse-scale biases, including an over-representation of radial orientations. But fMRI responses to clockwise and counter-clockwise spirals can also be decoded. Because these stimuli are matched for radial orientation, while differing in local orientation, it has been argued that fine-scale columnar selectivity for orientation contributes to orientation decoding. We measured fMRI responses in human V1 to both oriented gratings and spirals. Responses to oriented gratings exhibited a complex topography, including a radial bias that was most pronounced in the peripheral representation, and a near-vertical bias that was most pronounced near the foveal representation. Responses to clockwise and counter-clockwise spirals also exhibited coarse-scale organization, at the scale of entire visual quadrants. The preference of each voxel for clockwise or counter-clockwise spirals was predicted from the preferences of that voxel for orientation and spatial position (i.e., within the retinotopic map). Our results demonstrate a bias for local stimulus orientation that has a coarse spatial scale, is robust across stimulus classes (spirals and gratings), and suffices to explain decoding from fMRI responses in V1. PMID:24336733

Disentangling Stability, Variability and Adaptability in Human Performance: Focus on the Interplay between Local Variance and Serial Correlation

ERIC Educational Resources Information Center

Torre, Kjerstin; Balasubramaniam, Ramesh

2011-01-01

We address the complex relationship between the stability, variability, and adaptability of psychological systems by decomposing the global variance of serial performance into two independent parts: the local variance (LV) and the serial correlation structure. For two time series with equal LV, the presence of persistent long-range correlations…

Recursive restriction estimation: an alternative to post-stratification in surveys of land and forest cover

Treesearch

Raymond L. Czaplewski

2010-01-01

Numerous government surveys of natural resources use Post-Stratification to improve statistical efficiency, where strata are defined by full-coverage, remotely sensed data and geopolitical boundaries. Recursive Restriction Estimation, which may be considered a special case of the static Kalman filter, is an attractive alternative. It decomposes a complex estimation...

Are CORNER and BROTHER Morphologically Complex? Not in the Long Term

ERIC Educational Resources Information Center

Rueckl, Jay G.; Aicher, Karen A.

2008-01-01

Previous studies haves shown that under masked priming conditions, CORNER primes CORN as strongly as TEACHER primes TEACH and more strongly than BROTHEL primes BROTH. This result has been taken as evidence of a purely structural level of representation at which words are decomposed into morphological constituents in a manner that is independent of…

Promoting habitat complexity in second-growth forests.

Treesearch

Annette Bristol; Andrew B. Carey

2002-01-01

The following management tools can help meet multiple values—environmental, economic, and aesthetic—when used collectively and according to a well-devised plan.Cavity Tree CreationCoarse Woody Debris AugmentationUnderplantingConservation of Biological legaciesVariable-Density ThinningExtended...

Proteolytic regulation of metabolic enzymes by E3 ubiquitin ligase complexes: lessons from yeast.

PubMed

Nakatsukasa, Kunio; Okumura, Fumihiko; Kamura, Takumi

2015-01-01

Eukaryotic organisms use diverse mechanisms to control metabolic rates in response to changes in the internal and/or external environment. Fine metabolic control is a highly responsive, energy-saving process that is mediated by allosteric inhibition/activation and/or reversible modification of preexisting metabolic enzymes. In contrast, coarse metabolic control is a relatively long-term and expensive process that involves modulating the level of metabolic enzymes. Coarse metabolic control can be achieved through the degradation of metabolic enzymes by the ubiquitin-proteasome system (UPS), in which substrates are specifically ubiquitinated by an E3 ubiquitin ligase and targeted for proteasomal degradation. Here, we review select multi-protein E3 ligase complexes that directly regulate metabolic enzymes in Saccharomyces cerevisiae. The first part of the review focuses on the endoplasmic reticulum (ER) membrane-associated Hrd1 and Doa10 E3 ligase complexes. In addition to their primary roles in the ER-associated degradation pathway that eliminates misfolded proteins, recent quantitative proteomic analyses identified native substrates of Hrd1 and Doa10 in the sterol synthesis pathway. The second part focuses on the SCF (Skp1-Cul1-F-box protein) complex, an abundant prototypical multi-protein E3 ligase complex. While the best-known roles of the SCF complex are in the regulation of the cell cycle and transcription, accumulating evidence indicates that the SCF complex also modulates carbon metabolism pathways. The increasing number of metabolic enzymes whose stability is directly regulated by the UPS underscores the importance of the proteolytic regulation of metabolic processes for the acclimation of cells to environmental changes.

[Physico-chemical features of dinitrosyl iron complexes with natural thiol-containing ligands underlying biological activities of these complexes].

PubMed

Vanin, A F; Borodulin, R R; Kubrina, L N; Mikoian, V D; Burbaev, D Sh

2013-01-01

Current notions and new experimental data of the authors on physico-chemical features of dinitrosyl iron complexes with natural thiol-containing ligands (glutathione or cysteine), underlying the ability of the complexes to act as NO molecule and nitrosonium ion donors, are considered. This ability determines various biological activities of dinitrosyl iron complexes--inducing long-lasting vasodilation and thereby long-lasting hypotension in human and animals, inhibiting pellet aggregation, increasing red blood cell elasticity, thereby stimulating microcirculation, and reducing necrotic zone in animals with myocardial infarction. Moreover, dinitrosyl iron complexes are capable of accelerating skin wound healing, improving the function of penile cavernous tissue, blocking apoptosis development in cell cultures. When decomposed dinitrosyl iron complexes can exert cytotoxic effect that can be used for curing infectious and carcinogenic pathologies.

Bounds on Block Error Probability for Multilevel Concatenated Codes

NASA Technical Reports Server (NTRS)

Lin, Shu; Moorthy, Hari T.; Stojanovic, Diana

1996-01-01

Maximum likelihood decoding of long block codes is not feasable due to large complexity. Some classes of codes are shown to be decomposable into multilevel concatenated codes (MLCC). For these codes, multistage decoding provides good trade-off between performance and complexity. In this paper, we derive an upper bound on the probability of block error for MLCC. We use this bound to evaluate difference in performance for different decompositions of some codes. Examples given show that a significant reduction in complexity can be achieved when increasing number of stages of decoding. Resulting performance degradation varies for different decompositions. A guideline is given for finding good m-level decompositions.

A Kohonen-like decomposition method for the Euclidean traveling salesman problem-KNIES/spl I.bar/DECOMPOSE.

PubMed

Aras, N; Altinel, I K; Oommen, J

2003-01-01

In addition to the classical heuristic algorithms of operations research, there have also been several approaches based on artificial neural networks for solving the traveling salesman problem. Their efficiency, however, decreases as the problem size (number of cities) increases. A technique to reduce the complexity of a large-scale traveling salesman problem (TSP) instance is to decompose or partition it into smaller subproblems. We introduce an all-neural decomposition heuristic that is based on a recent self-organizing map called KNIES, which has been successfully implemented for solving both the Euclidean traveling salesman problem and the Euclidean Hamiltonian path problem. Our solution for the Euclidean TSP proceeds by solving the Euclidean HPP for the subproblems, and then patching these solutions together. No such all-neural solution has ever been reported.

Microbial decomposers not constrained by climate history along a Mediterranean climate gradient in southern California.

PubMed

Baker, Nameer R; Khalili, Banafshe; Martiny, Jennifer B H; Allison, Steven D

2018-06-01

Microbial decomposers mediate the return of CO 2 to the atmosphere by producing extracellular enzymes to degrade complex plant polymers, making plant carbon available for metabolism. Determining if and how these decomposer communities are constrained in their ability to degrade plant litter is necessary for predicting how carbon cycling will be affected by future climate change. We analyzed mass loss, litter chemistry, microbial biomass, extracellular enzyme activities, and enzyme temperature sensitivities in grassland litter transplanted along a Mediterranean climate gradient in southern California. Microbial community composition was manipulated by caging litter within bags made of nylon membrane that prevent microbial immigration. To test whether grassland microbes were constrained by climate history, half of the bags were inoculated with local microbial communities native to each gradient site. We determined that temperature and precipitation likely interact to limit microbial decomposition in the extreme sites along our gradient. Despite their unique climate history, grassland microbial communities were not restricted in their ability to decompose litter under different climate conditions across the gradient, although microbial communities across our gradient may be restricted in their ability to degrade different types of litter. We did find some evidence that local microbial communities were optimized based on climate, but local microbial taxa that proliferated after inoculation into litterbags did not enhance litter decomposition. Our results suggest that microbial community composition does not constrain C-cycling rates under climate change in our system, but optimization to particular resource environments may act as more general constraints on microbial communities. © 2018 by the Ecological Society of America.

Evaluating oxidation-reduction properties of dissolved organic matter from Chinese milk vetch (Astragalus sinicus L.): a comprehensive multi-parametric study.

PubMed

Liu, Yong; Lou, Jun; Li, Fang-Bai; Xu, Jian-Ming; Yu, Xiong-Sheng; Zhu, Li-An; Wang, Feng

2014-08-01

Green manuring is a common practice in replenishment of soil organic matter and nutrients in rice paddy field. Owing to the complex interplay of multiple factors, the oxidation--reduction (redox) properties of dissolved organic matter (DOM) from green manure crops are presently not fully understood. In this study, a variety of surrogate parameters were used to evaluate the redox capacity and redox state of DOM derived from Chinese milk vetch (CMV, Astragalus sinicus L.) via microbial decomposition under continuously flooded (CF) and non-flooded (NF) conditions. Additionally, the correlation between the surrogate parameters of CMV-DOM and the kinetic parameters of relevant redox reactions was evaluated in a soil-water system containing CMV-DOM. Results showed that the redox properties of CMV-DOM were substantially different between the fresh and decomposed CMV-DOM treatments. Determination of the surrogate parameters via ultraviolet-visible/Fourier transform infrared absorption spectroscopy and gel permeation chromatography generally provided high-quality data for predicting the redox capacity of CMV-DOM, while the surrogate parameters determined by elemental analysis were suitable for predicting the redox state of CMV-DOM. Depending on the redox capacity and redox state of various moieties/components, NF-decomposed CMV-DOM could easily accelerate soil reduction by shuttling electrons to iron oxides, because it contained more reversible redox-active functional groups (e.g. quinone and hydroquinone pairs) than CF-decomposed CMV-DOM. This work demonstrates that a single index cannot interpret complex changes in multiple factors that jointly determine the redox reactivity of CMV-DOM. Thus, a multi-parametric study is needed for providing comprehensive information on the redox properties of green manure DOM.

Mechanical properties of drug loaded diblock copolymer bilayers: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Grillo, Damián A.; Albano, Juan M. R.; Mocskos, Esteban E.; Facelli, Julio C.; Pickholz, Mónica; Ferraro, Marta B.

2018-06-01

In this work, we present results of coarse-grained simulations to study the encapsulation of prilocaine (PLC), both neutral and protonated, on copolymer bilayers through molecular dynamics simulations. Using a previously validated membrane model, we have simulated loaded bilayers at different drug concentrations and at low (protonated PLC) and high (neutral PLC) pH levels. We have characterized key structural parameters of the loaded bilayers in order to understand the effects of encapsulation of PLC on the bilayer structure and mechanical properties. Neutral PLC was encapsulated in the hydrophobic region leading to a thickness increase, while the protonated species partitioned between the water phase and the poly(ethylene oxide)-poly(butadiene) (PBD) interface, relaxing the PBD region and leading to a decrease in the thickness. The tangential pressures of the studied systems were calculated, and their components were decomposed in order to gain insights on their compensation. In all cases, it is observed that the loading of the membrane does not significantly decrease the stability of the bilayer, indicating that the system could be used for drug delivery.

Sodium fertilization increases termites and enhances decomposition in an Amazonian forest.

PubMed

Kaspari, Michael; Clay, Natalie A; Donoso, David A; Yanoviak, Steven P

2014-04-01

Added Na was used to determine whether litter decomposition and associated fungal biomass and termites are limited by Na availability in a lowland tropical rainforest at Yasuni, Ecuador. This is a partial test of the "sodium ecosystem respiration" (SER) hypothesis that posits Na is critical for consumers but not plants, that Na shortfall is more likely on highly weathered soils inland from oceanic aerosols, and that this shortfall results in decreased decomposer activity. We fertilized 4 x 4 m plots twice a month for a year with quantities of Na comparable to those falling on a coastal tropical rainforest. Decomposition rates of four substrates were consistently higher on +NaCl plots by up to 70% for cellulose, and 78%, 68%, and 29% for three woods of increasing percentage lignin. The density of termite workers averaged 17-fold higher on +NaCl plots; fungal biomass failed to differ. After controlling for temperature and precipitation, which co-limit gross primay productivity (GPP) and ecosystem respiration (ER), these results suggest that Na shortfall is an agent enhancing the storage of coarse woody debris in inland tropical forests.

Effect of Macrosegregation on the Microstructure and Mechanical Properties of a Pressure-Vessel Steel

NASA Astrophysics Data System (ADS)

Yan, Guanghua; Han, Lizhan; Li, Chuanwei; Luo, Xiaomeng; Gu, Jianfeng

2017-07-01

Macrosegregation refers to the chemical segregation, which occurs quite commonly in the large forgings such as nuclear reactor pressure vessel. This work assesses the effect of macrosegregation and homogenization treatment on the mechanical properties of a pressure-vessel steel (SA508 Gr.3). It was found that the primary reason for the inhomogeneity of the microstructure was the segregation of Mn, Mo, and Ni. Martensite, and coarse upper bainite with M-A (martensite-austenite) islands have been obtained, respectively, in the positive and negative segregation zone during a simulated quenching process. During tempering, the carbon-rich M-A islands decomposed into a mixture of ferrite and numerous carbides which deteriorated the toughness of the material. The segregation has been substantially minimized by a homogenizing treatment. The results indicate that the material homogenized has a higher impact toughness than the material with segregation, due to the reduction in M-A island in the negative segregation zone. It can be concluded that the microstructure and mechanical properties have been improved remarkably by means of homogenization treatment.

Mechanical properties of drug loaded diblock copolymer bilayers: A molecular dynamics study.

PubMed

Grillo, Damián A; Albano, Juan M R; Mocskos, Esteban E; Facelli, Julio C; Pickholz, Mónica; Ferraro, Marta B

2018-06-07

In this work, we present results of coarse-grained simulations to study the encapsulation of prilocaine (PLC), both neutral and protonated, on copolymer bilayers through molecular dynamics simulations. Using a previously validated membrane model, we have simulated loaded bilayers at different drug concentrations and at low (protonated PLC) and high (neutral PLC) pH levels. We have characterized key structural parameters of the loaded bilayers in order to understand the effects of encapsulation of PLC on the bilayer structure and mechanical properties. Neutral PLC was encapsulated in the hydrophobic region leading to a thickness increase, while the protonated species partitioned between the water phase and the poly(ethylene oxide)-poly(butadiene) (PBD) interface, relaxing the PBD region and leading to a decrease in the thickness. The tangential pressures of the studied systems were calculated, and their components were decomposed in order to gain insights on their compensation. In all cases, it is observed that the loading of the membrane does not significantly decrease the stability of the bilayer, indicating that the system could be used for drug delivery.

Prediction of S-wave velocity using complete ensemble empirical mode decomposition and neural networks

NASA Astrophysics Data System (ADS)

Gaci, Said; Hachay, Olga; Zaourar, Naima

2017-04-01

One of the key elements in hydrocarbon reservoirs characterization is the S-wave velocity (Vs). Since the traditional estimating methods often fail to accurately predict this physical parameter, a new approach that takes into account its non-stationary and non-linear properties is needed. In this view, a prediction model based on complete ensemble empirical mode decomposition (CEEMD) and a multiple layer perceptron artificial neural network (MLP ANN) is suggested to compute Vs from P-wave velocity (Vp). Using a fine-to-coarse reconstruction algorithm based on CEEMD, the Vp log data is decomposed into a high frequency (HF) component, a low frequency (LF) component and a trend component. Then, different combinations of these components are used as inputs of the MLP ANN algorithm for estimating Vs log. Applications on well logs taken from different geological settings illustrate that the predicted Vs values using MLP ANN with the combinations of HF, LF and trend in inputs are more accurate than those obtained with the traditional estimating methods. Keywords: S-wave velocity, CEEMD, multilayer perceptron neural networks.

Selection and preference of benthic habitat by small and large ammocoetes of the least brook lamprey (Lampetra aepyptera)

USGS Publications Warehouse

Smith, D.M.; Welsh, S.A.; Turk, P.J.

2011-01-01

In this laboratory study, we quantified substrate selection by small (<50 mm) and large (100-150 mm) ammocoetes of the least brook lamprey (Lampetra aepyptera). In aquaria, ammocoetes were given a choice to burrow into six equally-available substrate types: small gravel (2.360-4.750 mm), coarse sand (0.500-1.400 mm), fine sand (0.125-0.500 mm), organic substrate (approximately 70% decomposing leaves/stems and organic sediment particles, and 30% silt and fine sand), an even mixture of silt, clay, and fine sand, and silt/clay (<0.063 mm). Fine sand was selected with a significantly higher probability than any other substrate. Fine sand habitat is limited in many streams, in part owing to geology, but also as a result of channelization and excessive silt/clay sedimentation, which is a conservation concern. Our results indicate that ammocoetes of least brook lampreys are habitat specialists that prefer fine sand habitat. Hence, availability of fine sand habitat may limit distributions and population sizes. ?? 2011 Springer Science+Business Media B.V.

[The dinitrosyl-iron complexes with cysteine block the development of experimental endometriosis in rats].

PubMed

Burgova, E N; Tkachev, N A; Vanin, A F

2012-01-01

It has been shown that the administration of 0,5 ml of 5 mM aqueous solution of dinitrosyl-iron complexes (DNIC) with cysteine alleviated the development of experimental endometriosis in rats induced by surgical way: the size of endometriomes decreased 1.85 times when the DNIC was added every day during 10 days. The effect was suggested to be due to cytotoxic action of NO molecules and nitrosonium ions (NO+) released from rapidly decomposed DNIC in animal organism on endometriome tissues.

Development of a structured approach for decomposition of complex systems on a functional basis

NASA Astrophysics Data System (ADS)

Yildirim, Unal; Felician Campean, I.

2014-07-01

The purpose of this paper is to present the System State Flow Diagram (SSFD) as a structured and coherent methodology to decompose a complex system on a solution- independent functional basis. The paper starts by reviewing common function modelling frameworks in literature and discusses practical requirements of the SSFD in the context of the current literature and current approaches in industry. The proposed methodology is illustrated through the analysis of a case study: design analysis of a generic Bread Toasting System (BTS).

Examining Big-Fish-Little-Pond-Effects across 49 Countries: A Multilevel Latent Variable Modelling Approach

ERIC Educational Resources Information Center

Wang, Ze

2015-01-01

Using data from the Trends in International Mathematics and Science Study (TIMSS) 2007, this study examined the big-fish-little-pond-effects (BFLPEs) in 49 countries. In this study, the effect of math ability on math self-concept was decomposed into a within- and a between-level components using implicit mean centring and the complex data…

Acid sorption regeneration process using carbon dioxide

DOEpatents

King, C. Judson; Husson, Scott M.

2001-01-01

Carboxylic acids are sorbed from aqueous feedstocks onto a solid adsorbent in the presence of carbon dioxide under pressure. The acids are freed from the sorbent phase by a suitable regeneration method, one of which is treating them with an organic alkylamine solution thus forming an alkylamine-carboxylic acid complex which thermally decomposes to the desired carboxylic acid and the alkylamine.

Improving engineering system design by formal decomposition, sensitivity analysis, and optimization

NASA Technical Reports Server (NTRS)

Sobieski, J.; Barthelemy, J. F. M.

1985-01-01

A method for use in the design of a complex engineering system by decomposing the problem into a set of smaller subproblems is presented. Coupling of the subproblems is preserved by means of the sensitivity derivatives of the subproblem solution to the inputs received from the system. The method allows for the division of work among many people and computers.

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

Holm, Christian; Gompper, Gerhard; Dill, Ken A.

This special issue highlights new developments in theory and coarse-graining in biological and synthetic macromolecules and membranes. Such approaches give unique insights into the principles and design of the structures, dynamics, and assembly processes of these complex fluids and soft materials, where the length and time scales are often prohibitively long for fully atomistic modeling.

First Principles Dynamics and Coarse-Grained Characterization of Photoisomerization in Complex Environments

ERIC Educational Resources Information Center

Virshup, Aaron Michael

2009-01-01

Photoisomerization of conjugated systems is a common pathway for photomechanical energy conversion in biological chromophores. Such reactions are mediated by conical intersections (CIs)--points of degeneracy between different potential energy surfaces, which efficiently funnel population between electronic states. There are many examples of a…

EVALUATION OF COARSE, FINE, AND ULTRAFINE PARTICLES AS PART OF A HEALTH EFFECTS EXPOSURE STUDY

EPA Science Inventory

Ambient PM is a complex mixture that includes bioactive and toxic compounds of natural and anthropogenic origin, several of which have been theorized to be causative or contributory to the adverse effects of PM inhalation. Numerous epidemiological studies have reported associ...

Educational Opportunity and Immigration in México: Exploring the Individual and Systemic Relationships

ERIC Educational Resources Information Center

Martínez, José Felipe; Santibanez, Lucrecia; Serván Mori, Edson E.

2013-01-01

Background/Context: Much research has investigated the complex interplay between education and migration. Education has been alternatively conceptualized as playing an important role as motivator or deterrent of future migration. This relationship, however, is often investigated in terms of coarse indicators of educational attainment. Purpose: In…

Molecular determinants of the interactions between proteins and ssDNA.

PubMed

Mishra, Garima; Levy, Yaakov

2015-04-21

ssDNA binding proteins (SSBs) protect ssDNA from chemical and enzymatic assault that can derail DNA processing machinery. Complexes between SSBs and ssDNA are often highly stable, but predicting their structures is challenging, mostly because of the inherent flexibility of ssDNA and the geometric and energetic complexity of the interfaces that it forms. Here, we report a newly developed coarse-grained model to predict the structure of SSB-ssDNA complexes. The model is successfully applied to predict the binding modes of six SSBs with ssDNA strands of lengths of 6-65 nt. In addition to charge-charge interactions (which are often central to governing protein interactions with nucleic acids by means of electrostatic complementarity), an essential energetic term to predict SSB-ssDNA complexes is the interactions between aromatic residues and DNA bases. For some systems, flexibility is required from not only the ssDNA but also, the SSB to allow it to undergo conformational changes and the penetration of the ssDNA into its binding pocket. The association mechanisms can be quite varied, and in several cases, they involve the ssDNA sliding along the protein surface. The binding mechanism suggests that coarse-grained models are appropriate to study the motion of SSBs along ssDNA, which is expected to be central to the function carried out by the SSBs.

Monte Carlo simulations of flexible polyanions complexing with whey proteins at their isoelectric point

NASA Astrophysics Data System (ADS)

de Vries, R.

2004-02-01

Electrostatic complexation of flexible polyanions with the whey proteins α-lactalbumin and β-lactoglobulin is studied using Monte Carlo simulations. The proteins are considered at their respective isoelectric points. Discrete charges on the model polyelectrolytes and proteins interact through Debye-Hückel potentials. Protein excluded volume is taken into account through a coarse-grained model of the protein shape. Consistent with experimental results, it is found that α-lactalbumin complexes much more strongly than β-lactoglobulin. For α-lactalbumin, strong complexation is due to localized binding to a single large positive "charge patch," whereas for β-lactoglobulin, weak complexation is due to diffuse binding to multiple smaller charge patches.

On the Effect of Sphere-Overlap on Super Coarse-Grained Models of Protein Assemblies

NASA Astrophysics Data System (ADS)

Degiacomi, Matteo T.

2018-05-01

Ion mobility mass spectrometry (IM/MS) can provide structural information on intact protein complexes. Such data, including connectivity and collision cross sections (CCS) of assemblies' subunits, can in turn be used as a guide to produce representative super coarse-grained models. These models are constituted by ensembles of overlapping spheres, each representing a protein subunit. A model is considered plausible if the CCS and sphere-overlap levels of its subunits fall within predetermined confidence intervals. While the first is determined by experimental error, the latter is based on a statistical analysis on a range of protein dimers. Here, we first propose a new expression to describe the overlap between two spheres. Then we analyze the effect of specific overlap cutoff choices on the precision and accuracy of super coarse-grained models. Finally, we propose a method to determine overlap cutoff levels on a per-case scenario, based on collected CCS data, and show that it can be applied to the characterization of the assembly topology of symmetrical homo-multimers. [Figure not available: see fulltext.

Gene regulatory networks: a coarse-grained, equation-free approach to multiscale computation.

PubMed

Erban, Radek; Kevrekidis, Ioannis G; Adalsteinsson, David; Elston, Timothy C

2006-02-28

We present computer-assisted methods for analyzing stochastic models of gene regulatory networks. The main idea that underlies this equation-free analysis is the design and execution of appropriately initialized short bursts of stochastic simulations; the results of these are processed to estimate coarse-grained quantities of interest, such as mesoscopic transport coefficients. In particular, using a simple model of a genetic toggle switch, we illustrate the computation of an effective free energy Phi and of a state-dependent effective diffusion coefficient D that characterize an unavailable effective Fokker-Planck equation. Additionally we illustrate the linking of equation-free techniques with continuation methods for performing a form of stochastic "bifurcation analysis"; estimation of mean switching times in the case of a bistable switch is also implemented in this equation-free context. The accuracy of our methods is tested by direct comparison with long-time stochastic simulations. This type of equation-free analysis appears to be a promising approach to computing features of the long-time, coarse-grained behavior of certain classes of complex stochastic models of gene regulatory networks, circumventing the need for long Monte Carlo simulations.

Electrochemical alkaline Fe(VI) water purification and remediation.

PubMed

Licht, Stuart; Yu, Xingwen

2005-10-15

Fe(VI) is an unusual and strongly oxidizing form of iron, which provides a potentially less hazardous water-purifying agent than chlorine. A novel on-line electrochemical Fe(VI) water purification methodology is introduced. Fe(VI) addition had been a barrier to its effective use in water remediation, because solid Fe(VI) salts require complex (costly) syntheses steps and solutions of Fe(VI) decompose. Online electrochemical Fe(VI) water purification avoids these limitations, in which Fe(VI) is directly prepared in solution from an iron anode as the FeO42- ion, and is added to the contaminant stream. Added FeO42- decomposes, by oxidizing a wide range of water contaminants including sulfides (demonstrated in this study) and other sulfur-containing compounds, cyanides (demonstrated in this study), arsenic (demonstrated in this study), ammonia and other nitrogen-containing compounds (previously demonstrated), a wide range of organics (phenol demonstrated in this study), algae, and viruses (each previously demonstrated).

[Spectral characteristics of decomposition of incorporated straw in compound polluted arid loess].

PubMed

Fan, Chun-Hui; Zhang, Ying-Chao; Xu, Ji-Ting; Wang, Jia-Hong

2014-04-01

The original loess from western China was used as soil sample, the spectral methods of scanning electron microscope-energy dispersive X-ray spectroscopy (SEM-EDS), elemental analysis, Fourier transform infrared spectroscopy (FT-IR) and 13C nuclear magnetic resonance (13C NMR) were used to investigate the characteristics of decomposed straw and formed humic acids in compound polluted arid loess. The SEM micrographs show the variation from dense to decomposed surface, and finally to damaged structure, and the EDS data reveal the phenomenon of element transfer. The newly-formed humic acids are of low aromaticity, helpful for increasing the activity of organic matters in loess. The FTIR spectra in the whole process are similar, indicating the complexity of transformation dynamics of humic acids. The molecular structure of humic acids becomes simpler, shown from 13C NMR spectra. The spectral methods are useful for humic acids identification in loess region in straw incorporation process.

Spontaneous adsorption of coiled-coil model peptides K and E to a mixed lipid bilayer.

PubMed

Pluhackova, Kristyna; Wassenaar, Tsjerk A; Kirsch, Sonja; Böckmann, Rainer A

2015-03-26

A molecular description of the lipid-protein interactions underlying the adsorption of proteins to membranes is crucial for understanding, for example, the specificity of adsorption or the binding strength of a protein to a bilayer, or for characterizing protein-induced changes of membrane properties. In this paper, we extend an automated in silico assay (DAFT) for binding studies and apply it to characterize the adsorption of the model fusion peptides E and K to a mixed phospholipid/cholesterol membrane using coarse-grained molecular dynamics simulations. In addition, we couple the coarse-grained protocol to reverse transformation to atomistic resolution, thereby allowing to study molecular interactions with high detail. The experimentally observed differential binding of the peptides E and K to membranes, as well as the increased binding affinity of helical over unstructered peptides, could be well reproduced using the polarizable Martini coarse-grained (CG) force field. Binding to neutral membranes is shown to be dominated by initial binding of the positively charged N-terminus to the phospholipid headgroup region, followed by membrane surface-aligned insertion of the peptide at the interface between the hydrophobic core of the membrane and its polar headgroup region. Both coarse-grained and atomistic simulations confirm a before hypothesized snorkeling of lysine side chains for the membrane-bound state of the peptide K. Cholesterol was found to be enriched in peptide vicinity, which is probably of importance for the mechanism of membrane fusion. The applied sequential multiscale method, using coarse-grained simulations for the slow adsorption process of peptides to membranes followed by backward transformation to atomistic detail and subsequent atomistic simulations of the preformed peptide-lipid complexes, is shown to be a versatile approach to study the interactions of peptides or proteins with biomembranes.

meso-Octamethylcalix[4]pyrrole as an effective macrocyclic receptor for the univalent thallium cation in the gas phase: Experimental and theoretical study

NASA Astrophysics Data System (ADS)

Polášek, Miroslav; Makrlík, Emanuel; Kvíčala, Jaroslav; Křížová, Věra; Vaňura, Petr

2018-02-01

By using electrospray ionization mass spectrometry (ESI-MS), it was proven experimentally that the univalent thallium cation (Tl+) forms with meso-octamethylcalix[4]pyrrole (1) the cationic complex species 1 Tl+. When this kinetically stable cation-π complex 1 Tl+ is collisionally activated, it decomposes by elimination of the whole ligand 1 or small meso-octamethylcalix[4]pyrrole fragments. Further, applying quantum chemical DFT calculations, four different conformations of the resulting complex 1 Tl+ were derived. It means that under the present experimental conditions, this ligand 1 can be considered as a very effective macrocyclic receptor for the thallium cation.

Fine-scale variability of forest soil fungal communities in two contrasting habitat series in northern Idaho, USA identified with microbial metagenomics

Treesearch

Amy Ross-Davis; Jane E. Stewart; Matt Settles; John W. Hanna; John D. Shaw; Andrew T. Hudak; Deborah S. Page-Dumroese; Ned B. Klopfenstein

2016-01-01

Forests are home to some of the most complex microbial communities (Fierer et al. 2012) which drive biogeochemical cycles (Clemmensen et al. 2013; van der Heijden et al. 2008) and account for substantial terrestrial biomass (Nielsen et al. 2011). Fungi, through their ecological roles as decomposers, mutualists, or pathogens, are particularly important in...

Program Helps Decompose Complex Design Systems

NASA Technical Reports Server (NTRS)

Rogers, James L., Jr.; Hall, Laura E.

1994-01-01

DeMAID (A Design Manager's Aid for Intelligent Decomposition) computer program is knowledge-based software system for ordering sequence of modules and identifying possible multilevel structure for design problem. Groups modular subsystems on basis of interactions among them. Saves considerable money and time in total design process, particularly in new design problem in which order of modules has not been defined. Available in two machine versions: Macintosh and Sun.

Interaction of chemokine receptor CXCR4 in monomeric and dimeric state with its endogenous ligand CXCL12: coarse-grained simulations identify differences.

PubMed

Cutolo, Pasquale; Basdevant, Nathalie; Bernadat, Guillaume; Bachelerie, Françoise; Ha-Duong, Tâp

2017-02-01

Despite the recent resolutions of the crystal structure of the chemokine receptor CXCR4 in complex with small antagonists or viral chemokine, a description at the molecular level of the interactions between the full-length CXCR4 and its endogenous ligand, the chemokine CXCL12, in relationship with the receptor recognition and activation, is not yet completely elucidated. Moreover, since CXCR4 is able to form dimers, the question of whether the CXCR4-CXCL12 complex has a 1:1 or 2:1 preferential stoichiometry is still an open question. We present here results of coarse-grained protein-protein docking and molecular dynamics simulations of CXCL12 in association with CXCR4 in monomeric and dimeric states. Our proposed models for the 1:1 and 2:1 CXCR4-CXCL12 quaternary structures are consistent with recognition and activation motifs of both partners provided by the available site-directed mutagenesis data. Notably, we observed that in the 2:1 complex, the chemokine N-terminus makes more steady contacts with the receptor residues critical for binding and activation than in the 1:1 structure, suggesting that the 2:1 stoichiometry would favor the receptor signaling activity with respect to the 1:1 association.

75 FR 77961 - Endangered and Threatened Wildlife and Plants; Revised Critical Habitat for Santa Ana Sucker

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-14

... integrated water system that contains and provides the appropriate quantity of coarse substrates such as... reduces water temperature during summer and fall months. Therefore, a complex and integrated stream system... water velocities to support successful spawning. Swift (2001, p. 26) considered that only the Rialto...

A Software Architecture for the Construction and Management of Real-Time Virtual Worlds

DTIC Science & Technology

1993-06-01

University of California, Berkeley [FUNK921. The second improvement was the addition of a radiosity light model. The use of radiosity and its use of diffuse...the viewpoint is stationary, the coarse polygon model is replaced by progressively more complex radiosity lit scenes. The area of molecular modeling

Near-road enhancement and solubility of fine and coarse particulate matter trace elements near a major interstate in Detroit, Michigan

EPA Science Inventory

Communities near major roadways are disproportionately affected by traffic-related air pollution which can contribute to adverse health outcomes. The specific role of particulate matter (PM) from traffic sources is not fully understood due to complex emissions processes and physi...

Adaptation to wildfire: A fish story

Treesearch

John Kirkland; Rebecca Flitcroft; Gordon Reeves; Paul Hessburg

2017-01-01

In the Pacific Northwest, native salmon and trout are some of the toughest survivors on the block. Over time, these fish have evolved behavioral adaptations to natural disturbances, and they rely on these disturbances to deliver coarse sediment and wood that become complex stream habitat. Powerful disturbances such as wildfire, postfire landslides, and debris flows may...

Hysteresis of liquid adsorption in porous media by coarse-grained Monte Carlo with direct experimental validation

NASA Astrophysics Data System (ADS)

Zeidman, Benjamin D.; Lu, Ning; Wu, David T.

2016-05-01

The effects of path-dependent wetting and drying manifest themselves in many types of physical systems, including nanomaterials, biological systems, and porous media such as soil. It is desirable to better understand how these hysteretic macroscopic properties result from a complex interplay between gasses, liquids, and solids at the pore scale. Coarse-Grained Monte Carlo (CGMC) is an appealing approach to model these phenomena in complex pore spaces, including ones determined experimentally. We present two-dimensional CGMC simulations of wetting and drying in two systems with pore spaces determined by sections from micro X-ray computed tomography: a system of randomly distributed spheres and a system of Ottawa sand. Results for the phase distribution, water uptake, and matric suction when corrected for extending to three dimensions show excellent agreement with experimental measurements on the same systems. This supports the hypothesis that CGMC can generate metastable configurations representative of experimental hysteresis and can also be used to predict hysteretic constitutive properties of particular experimental systems, given pore space images.

Stream Processors

NASA Astrophysics Data System (ADS)

Erez, Mattan; Dally, William J.

Stream processors, like other multi core architectures partition their functional units and storage into multiple processing elements. In contrast to typical architectures, which contain symmetric general-purpose cores and a cache hierarchy, stream processors have a significantly leaner design. Stream processors are specifically designed for the stream execution model, in which applications have large amounts of explicit parallel computation, structured and predictable control, and memory accesses that can be performed at a coarse granularity. Applications in the streaming model are expressed in a gather-compute-scatter form, yielding programs with explicit control over transferring data to and from on-chip memory. Relying on these characteristics, which are common to many media processing and scientific computing applications, stream architectures redefine the boundary between software and hardware responsibilities with software bearing much of the complexity required to manage concurrency, locality, and latency tolerance. Thus, stream processors have minimal control consisting of fetching medium- and coarse-grained instructions and executing them directly on the many ALUs. Moreover, the on-chip storage hierarchy of stream processors is under explicit software control, as is all communication, eliminating the need for complex reactive hardware mechanisms.

Hysteresis of liquid adsorption in porous media by coarse-grained Monte Carlo with direct experimental validation

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

Zeidman, Benjamin D.; Lu, Ning; Wu, David T., E-mail: dwu@mines.edu

2016-05-07

The effects of path-dependent wetting and drying manifest themselves in many types of physical systems, including nanomaterials, biological systems, and porous media such as soil. It is desirable to better understand how these hysteretic macroscopic properties result from a complex interplay between gasses, liquids, and solids at the pore scale. Coarse-Grained Monte Carlo (CGMC) is an appealing approach to model these phenomena in complex pore spaces, including ones determined experimentally. We present two-dimensional CGMC simulations of wetting and drying in two systems with pore spaces determined by sections from micro X-ray computed tomography: a system of randomly distributed spheres andmore » a system of Ottawa sand. Results for the phase distribution, water uptake, and matric suction when corrected for extending to three dimensions show excellent agreement with experimental measurements on the same systems. This supports the hypothesis that CGMC can generate metastable configurations representative of experimental hysteresis and can also be used to predict hysteretic constitutive properties of particular experimental systems, given pore space images.« less

An Integrated Constraint Programming Approach to Scheduling Sports Leagues with Divisional and Round-robin Tournaments

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

Carlsson, Mats; Johansson, Mikael; Larson, Jeffrey

Previous approaches for scheduling a league with round-robin and divisional tournaments involved decomposing the problem into easier subproblems. This approach, used to schedule the top Swedish handball league Elitserien, reduces the problem complexity but can result in suboptimal schedules. This paper presents an integrated constraint programming model that allows to perform the scheduling in a single step. Particular attention is given to identifying implied and symmetry-breaking constraints that reduce the computational complexity significantly. The experimental evaluation of the integrated approach takes considerably less computational effort than the previous approach.

Carbene complexes of rhodium and iridium from tripodal N-heterocyclic carbene ligands: synthesis and catalytic properties.

PubMed

Mas-Marzá, Elena; Poyatos, Macarena; Sanaú, Mercedes; Peris, Eduardo

2004-03-22

Two tripodal trisimidazolium ligand precursors have been tested in the synthesis of new N-heterocyclic carbene rhodium and iridium complexes. [Tris(3-methylbenzimidazolium-1-yl)]methane sulfate gave products with coordination of the decomposed precursor. [1,1,1-Tris(3-butylimidazolium-1-yl)methyl]ethane trichloride (TIMEH(3)(Bu)) coordinated to the metal in a chelate and bridged-chelate form, depending on the reaction conditions. The crystal structures of two of the products are described. The compounds resulting from the coordination with TIME(Bu) were tested in the catalytic hydrosilylation of terminal alkynes.

An optical Fourier transform coprocessor with direct phase determination.

PubMed

Macfaden, Alexander J; Gordon, George S D; Wilkinson, Timothy D

2017-10-20

The Fourier transform is a ubiquitous mathematical operation which arises naturally in optics. We propose and demonstrate a practical method to optically evaluate a complex-to-complex discrete Fourier transform. By implementing the Fourier transform optically we can overcome the limiting O(nlogn) complexity of fast Fourier transform algorithms. Efficiently extracting the phase from the well-known optical Fourier transform is challenging. By appropriately decomposing the input and exploiting symmetries of the Fourier transform we are able to determine the phase directly from straightforward intensity measurements, creating an optical Fourier transform with O(n) apparent complexity. Performing larger optical Fourier transforms requires higher resolution spatial light modulators, but the execution time remains unchanged. This method could unlock the potential of the optical Fourier transform to permit 2D complex-to-complex discrete Fourier transforms with a performance that is currently untenable, with applications across information processing and computational physics.

Parameterizations of Dry Deposition for the Industrial Source Complex Model

NASA Astrophysics Data System (ADS)

Wesely, M. L.; Doskey, P. V.; Touma, J. S.

2002-05-01

Improved algorithms have been developed to simulate the dry deposition of hazardous air pollutants (HAPs) with the Industrial Source Complex model system. The dry deposition velocities are described in conventional resistance schemes, for which micrometeorological formulas are applied to describe the aerodynamic resistances above the surface. Pathways to uptake of gases at the ground and in vegetative canopies are depicted with several resistances that are affected by variations in air temperature, humidity, solar irradiance, and soil moisture. Standardized land use types and seasonal categories provide sets of resistances to uptake by various components of the surface. To describe the dry deposition of the large number of gaseous organic HAPS, a new technique based on laboratory study results and theoretical considerations has been developed to provide a means to evaluate the role of lipid solubility on uptake by the waxy outer cuticle of vegetative plant leaves. The dry deposition velocities of particulate HAPs are simulated with a resistance scheme in which deposition velocity is described for two size modes: a fine mode with particles less than about 2.5 microns in diameter and a coarse mode with larger particles but excluding very coarse particles larger than about 10 microns in diameter. For the fine mode, the deposition velocity is calculated with a parameterization based on observations of sulfate dry deposition. For the coarse mode, a representative settling velocity is assumed. Then the total deposition velocity is estimated as the sum of the two deposition velocities weighted according to the amount of mass expected in the two modes.

Monte Carlo simulations of flexible polyanions complexing with whey proteins at their isoelectric point.

PubMed

de Vries, R

2004-02-15

Electrostatic complexation of flexible polyanions with the whey proteins alpha-lactalbumin and beta-lactoglobulin is studied using Monte Carlo simulations. The proteins are considered at their respective isoelectric points. Discrete charges on the model polyelectrolytes and proteins interact through Debye-Huckel potentials. Protein excluded volume is taken into account through a coarse-grained model of the protein shape. Consistent with experimental results, it is found that alpha-lactalbumin complexes much more strongly than beta-lactoglobulin. For alpha-lactalbumin, strong complexation is due to localized binding to a single large positive "charge patch," whereas for beta-lactoglobulin, weak complexation is due to diffuse binding to multiple smaller charge patches. Copyright 2004 American Institute of Physics

Distinguishing Active Site Characteristics of Chlorite Dismutases with Their Cyanide Complexes.

PubMed

Geeraerts, Zachary; Celis, Arianna I; Mayfield, Jeffery A; Lorenz, Megan; Rodgers, Kenton R; DuBois, Jennifer L; Lukat-Rodgers, Gudrun S

2018-03-06

O 2 -evolving chlorite dismutases (Clds) efficiently convert chlorite (ClO 2 - ) to O 2 and Cl - . Dechloromonas aromatica Cld ( DaCld) is a highly active chlorite-decomposing homopentameric enzyme, typical of Clds found in perchlorate- and chlorate-respiring bacteria. The Gram-negative, human pathogen Klebsiella pneumoniae contains a homodimeric Cld ( KpCld) that also decomposes ClO 2 - , albeit with an activity 10-fold lower and a turnover number lower than those of DaCld. The interactions between the distal pocket and heme ligand of the DaCld and KpCld active sites have been probed via kinetic, thermodynamic, and spectroscopic behaviors of their cyanide complexes for insight into active site characteristics that are deterministic for chlorite decomposition. At 4.7 × 10 -9 M, the K D for the KpCld-CN - complex is 2 orders of magnitude smaller than that of DaCld-CN - and indicates an affinity for CN - that is greater than that of most heme proteins. The difference in CN - affinity between Kp- and DaClds is predominantly due to differences in k off . The kinetics of binding of cyanide to DaCld, DaCld(R183Q), and KpCld between pH 4 and 8.5 corroborate the importance of distal Arg183 and a p K a of ∼7 in stabilizing complexes of anionic ligands, including the substrate. The Fe-C stretching and FeCN bending modes of the DaCld-CN - (ν Fe-C , 441 cm -1 ; δ FeCN , 396 cm -1 ) and KpCld-CN - (ν Fe-C , 441 cm -1 ; δ FeCN , 356 cm -1 ) complexes reveal differences in their FeCN angle, which suggest different distal pocket interactions with their bound cyanide. Conformational differences in their catalytic sites are also reported by the single ferrous KpCld carbonyl complex, which is in contrast to the two conformers observed for DaCld-CO.

Brownian Dynamics Simulation of Nucleocytoplasmic Transport: A Coarse-Grained Model for the Functional State of the Nuclear Pore Complex

PubMed Central

Moussavi-Baygi, Ruhollah; Jamali, Yousef; Karimi, Reza; Mofrad, Mohammad R. K.

2011-01-01

The nuclear pore complex (NPC) regulates molecular traffic across the nuclear envelope (NE). Selective transport happens on the order of milliseconds and the length scale of tens of nanometers; however, the transport mechanism remains elusive. Central to the transport process is the hydrophobic interactions between karyopherins (kaps) and Phe-Gly (FG) repeat domains. Taking into account the polymeric nature of FG-repeats grafted on the elastic structure of the NPC, and the kap-FG hydrophobic affinity, we have established a coarse-grained model of the NPC structure that mimics nucleocytoplasmic transport. To establish a foundation for future works, the methodology and biophysical rationale behind the model is explained in details. The model predicts that the first-passage time of a 15 nm cargo-complex is about 2.6±0.13 ms with an inverse Gaussian distribution for statistically adequate number of independent Brownian dynamics simulations. Moreover, the cargo-complex is primarily attached to the channel wall where it interacts with the FG-layer as it passes through the central channel. The kap-FG hydrophobic interaction is highly dynamic and fast, which ensures an efficient translocation through the NPC. Further, almost all eight hydrophobic binding spots on kap-β are occupied simultaneously during transport. Finally, as opposed to intact NPCs, cytoplasmic filaments-deficient NPCs show a high degree of permeability to inert cargos, implying the defining role of cytoplasmic filaments in the selectivity barrier. PMID:21673865

Short-term Music Training Enhances Complex, Distributed Neural Communication during Music and Linguistic Tasks

PubMed Central

Carpentier, Sarah M.; Moreno, Sylvain; McIntosh, Anthony R.

2016-01-01

Musical training is frequently associated with benefits to linguistic abilities, and recent focus has been placed on possible benefits of bilingualism to lifelong executive functions; however, the neural mechanisms for such effects are unclear. The aim of this study was to gain better understanding of the whole-brain functional effects of music and second-language training that could support such previously observed cognitive transfer effects. We conducted a 28-day longitudinal study of monolingual English-speaking 4- to 6-year-old children randomly selected to receive daily music or French language training, excluding weekends. Children completed passive EEG music note and French vowel auditory oddball detection tasks before and after training. Brain signal complexity was measured on source waveforms at multiple temporal scales as an index of neural information processing and network communication load. Comparing pretraining with posttraining, musical training was associated with increased EEG complexity at coarse temporal scales during the music and French vowel tasks in widely distributed cortical regions. Conversely, very minimal decreases in complexity at fine scales and trends toward coarse-scale increases were displayed after French training during the tasks. Spectral analysis failed to distinguish between training types and found overall theta (3.5–7.5 Hz) power increases after all training forms, with spatially fewer decreases in power at higher frequencies (>10 Hz). These findings demonstrate that musical training increased diversity of brain network states to support domain-specific music skill acquisition and music-to-language transfer effects. PMID:27243611

Short-term Music Training Enhances Complex, Distributed Neural Communication during Music and Linguistic Tasks.

PubMed

Carpentier, Sarah M; Moreno, Sylvain; McIntosh, Anthony R

2016-10-01

Musical training is frequently associated with benefits to linguistic abilities, and recent focus has been placed on possible benefits of bilingualism to lifelong executive functions; however, the neural mechanisms for such effects are unclear. The aim of this study was to gain better understanding of the whole-brain functional effects of music and second-language training that could support such previously observed cognitive transfer effects. We conducted a 28-day longitudinal study of monolingual English-speaking 4- to 6-year-old children randomly selected to receive daily music or French language training, excluding weekends. Children completed passive EEG music note and French vowel auditory oddball detection tasks before and after training. Brain signal complexity was measured on source waveforms at multiple temporal scales as an index of neural information processing and network communication load. Comparing pretraining with posttraining, musical training was associated with increased EEG complexity at coarse temporal scales during the music and French vowel tasks in widely distributed cortical regions. Conversely, very minimal decreases in complexity at fine scales and trends toward coarse-scale increases were displayed after French training during the tasks. Spectral analysis failed to distinguish between training types and found overall theta (3.5-7.5 Hz) power increases after all training forms, with spatially fewer decreases in power at higher frequencies (>10 Hz). These findings demonstrate that musical training increased diversity of brain network states to support domain-specific music skill acquisition and music-to-language transfer effects.

Group Decision Support System to Aid the Process of Design and Maintenance of Large Scale Systems

DTIC Science & Technology

1992-03-23

from a fuzzy set of user requirements. The overall objective of the project is to develop a system combining the characteristics of a compact computer... AHP ) for hierarchical prioritization. 4) Individual Evaluation and Selection of Alternatives - Allows the decision maker to individually evaluate...its concept of outranking relations. The AHP method supports complex decision problems by successively decomposing and synthesizing various elements

Optimization of Analytical Potentials for Coarse-Grained Biopolymer Models.

PubMed

Mereghetti, Paolo; Maccari, Giuseppe; Spampinato, Giulia Lia Beatrice; Tozzini, Valentina

2016-08-25

The increasing trend in the recent literature on coarse grained (CG) models testifies their impact in the study of complex systems. However, the CG model landscape is variegated: even considering a given resolution level, the force fields are very heterogeneous and optimized with very different parametrization procedures. Along the road for standardization of CG models for biopolymers, here we describe a strategy to aid building and optimization of statistics based analytical force fields and its implementation in the software package AsParaGS (Assisted Parameterization platform for coarse Grained modelS). Our method is based on the use and optimization of analytical potentials, optimized by targeting internal variables statistical distributions by means of the combination of different algorithms (i.e., relative entropy driven stochastic exploration of the parameter space and iterative Boltzmann inversion). This allows designing a custom model that endows the force field terms with a physically sound meaning. Furthermore, the level of transferability and accuracy can be tuned through the choice of statistical data set composition. The method-illustrated by means of applications to helical polypeptides-also involves the analysis of two and three variable distributions, and allows handling issues related to the FF term correlations. AsParaGS is interfaced with general-purpose molecular dynamics codes and currently implements the "minimalist" subclass of CG models (i.e., one bead per amino acid, Cα based). Extensions to nucleic acids and different levels of coarse graining are in the course.

Removal of methylmercury and tributyltin (TBT) using marine microorganisms.

PubMed

Lee, Seong Eon; Chung, Jin Wook; Won, Ho Shik; Lee, Dong Sup; Lee, Yong-Woo

2012-02-01

Two marine species of bacteria were isolated that are capable of degrading organometallic contaminants: Pseudomonas balearica, which decomposes methylmercury; and Shewanella putrefaciens, which decomposes tributyltin. P. balearica decomposed 97% of methylmercury (20.0 μg/L) into inorganic mercury after 3 h, while S. putrefaciens decomposed 88% of tributyltin (55.3 μg Sn/L) in real wastewater after 36 h. These data indicate that the two bacteria efficiently decomposed the targeted substances and may be applied to real wastewater.

An Assembly Funnel Makes Biomolecular Complex Assembly Efficient

PubMed Central

Zenk, John; Schulman, Rebecca

2014-01-01

Like protein folding and crystallization, the self-assembly of complexes is a fundamental form of biomolecular organization. While the number of methods for creating synthetic complexes is growing rapidly, most require empirical tuning of assembly conditions and/or produce low yields. We use coarse-grained simulations of the assembly kinetics of complexes to identify generic limitations on yields that arise because of the many simultaneous interactions allowed between the components and intermediates of a complex. Efficient assembly occurs when nucleation is fast and growth pathways are few, i.e. when there is an assembly “funnel”. For typical complexes, an assembly funnel occurs in a narrow window of conditions whose location is highly complex specific. However, by redesigning the components this window can be drastically broadened, so that complexes can form quickly across many conditions. The generality of this approach suggests assembly funnel design as a foundational strategy for robust biomolecular complex synthesis. PMID:25360818

Multi-segmental movement patterns reflect juggling complexity and skill level.

PubMed

Zago, Matteo; Pacifici, Ilaria; Lovecchio, Nicola; Galli, Manuela; Federolf, Peter Andreas; Sforza, Chiarella

2017-08-01

The juggling action of six experts and six intermediates jugglers was recorded with a motion capture system and decomposed into its fundamental components through Principal Component Analysis. The aim was to quantify trends in movement dimensionality, multi-segmental patterns and rhythmicity as a function of proficiency level and task complexity. Dimensionality was quantified in terms of Residual Variance, while the Relative Amplitude was introduced to account for individual differences in movement components. We observed that: experience-related modifications in multi-segmental actions exist, such as the progressive reduction of error-correction movements, especially in complex task condition. The systematic identification of motor patterns sensitive to the acquisition of specific experience could accelerate the learning process. Copyright © 2017 Elsevier B.V. All rights reserved.

Thermal regeneration of an electrochemical concentration cell

DOEpatents

Krumpelt, Michael; Bates, John K.

1981-01-01

A system and method for thermally regenerating an electrochemical concentration cell having first and second aluminum electrodes respectively positioned in contact with first and second electrolytes separated by an ion exchange member, the first and second electrolytes being composed of different concentrations of an ionic solvent and a salt, preferably an aluminum halide. The ionic solvent may be either organic or inorganic with a relatively low melting point, the ionic solvent and the salt form a complex wherein the free energy of formation of said complex is less than about -5 Kcal/mole. A distillation column using solar heat or low grade industrial waste heat receives the first and second electrolytes and thermally decomposes the salt-solvent complex to provide feed material for the two half cells.

Relationships between rare plants of the White Mountains and the late Cenozoic geology of the Colorado Plateau

Treesearch

Jonathan W. Long

2007-01-01

A complex geologic history has shaped the distribution of Arizona willow (Salix arizonica Dorn) and the Mogollon paintbrush (Castilleja mogollonica Pennell). These subalpine plants do not appear to be strict substrate specialists, but they do seem to favor coarse-textured and well-watered soils. Most of their occupied habitats were...

Development and Application of Agglomerated Multigrid Methods for Complex Geometries

NASA Technical Reports Server (NTRS)

Nishikawa, Hiroaki; Diskin, Boris; Thomas, James L.

2010-01-01

We report progress in the development of agglomerated multigrid techniques for fully un- structured grids in three dimensions, building upon two previous studies focused on efficiently solving a model diffusion equation. We demonstrate a robust fully-coarsened agglomerated multigrid technique for 3D complex geometries, incorporating the following key developments: consistent and stable coarse-grid discretizations, a hierarchical agglomeration scheme, and line-agglomeration/relaxation using prismatic-cell discretizations in the highly-stretched grid regions. A signi cant speed-up in computer time is demonstrated for a model diffusion problem, the Euler equations, and the Reynolds-averaged Navier-Stokes equations for 3D realistic complex geometries.

Decomposed bodies--still an unrewarding autopsy?

PubMed

Ambade, Vipul Namdeorao; Keoliya, Ajay Narmadaprasad; Deokar, Ravindra Baliram; Dixit, Pradip Gangadhar

2011-04-01

One of the classic mistakes in forensic pathology is to regard the autopsy of decomposed body as unrewarding. The present study was undertaken with a view to debunk this myth and to determine the characteristic pattern in decomposed bodies brought for medicolegal autopsy. From a total of 4997 medicolegal deaths reported at an Apex Medical Centre, Yeotmal, a rural district of Maharashtra over seven year study period, only 180 cases were decomposed, representing 3.6% of the total medicolegal autopsies with the rate of 1.5 decomposed body/100,000 population per year. Male (79.4%) predominance was seen in decomposed bodies with male female ratio of 3.9:1. Most of the victims were between the ages of 31 and 60 years with peak at 31-40 years (26.7%) followed by 41-50 years (19.4%). Older age above 60 years was found in 8.6% cases. Married (64.4%) outnumbered unmarried ones in decomposition. Most of the decomposed bodies were complete (83.9%) and identified (75%). But when the body was incomplete/mutilated or skeletonised then 57.7% of the deceased remains unidentified. The cause and manner of death was ascertained in 85.6% and 81.1% cases respectively. Drowning (35.6%) was the commonest cause of death in decomposed bodies with suicide (52.8%) as the commonest manner of death. Decomposed bodies were commonly recovered from open places (43.9%), followed by water sources (43.3%) and enclosed place (12.2%). Most of the decomposed bodies were retrieved from well (49 cases) followed by barren land (27 cases) and forest (17 cases). 83.8% of the decomposed bodies were recovered before 72 h and only in 16.2% cases the time since death was more than 72 h, mostly recovered from barren land, forest and river. Most of the decomposed bodies were found in summer season (42.8%) with peak in the month of May. Despite technical difficulties in handling the body and artefactual alteration of the tissue, the decomposed body may still reveal cause and manner of death in significant number of cases. Copyright © 2011 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

A Coarse-to-Fine Geometric Scale-Invariant Feature Transform for Large Size High Resolution Satellite Image Registration

PubMed Central

Chang, Xueli; Du, Siliang; Li, Yingying; Fang, Shenghui

2018-01-01

Large size high resolution (HR) satellite image matching is a challenging task due to local distortion, repetitive structures, intensity changes and low efficiency. In this paper, a novel matching approach is proposed for the large size HR satellite image registration, which is based on coarse-to-fine strategy and geometric scale-invariant feature transform (SIFT). In the coarse matching step, a robust matching method scale restrict (SR) SIFT is implemented at low resolution level. The matching results provide geometric constraints which are then used to guide block division and geometric SIFT in the fine matching step. The block matching method can overcome the memory problem. In geometric SIFT, with area constraints, it is beneficial for validating the candidate matches and decreasing searching complexity. To further improve the matching efficiency, the proposed matching method is parallelized using OpenMP. Finally, the sensing image is rectified to the coordinate of reference image via Triangulated Irregular Network (TIN) transformation. Experiments are designed to test the performance of the proposed matching method. The experimental results show that the proposed method can decrease the matching time and increase the number of matching points while maintaining high registration accuracy. PMID:29702589

TMFF-A Two-Bead Multipole Force Field for Coarse-Grained Molecular Dynamics Simulation of Protein.

PubMed

Li, Min; Liu, Fengjiao; Zhang, John Z H

2016-12-13

Coarse-grained (CG) models are desirable for studying large and complex biological systems. In this paper, we propose a new two-bead multipole force field (TMFF) in which electric multipoles up to the quadrupole are included in the CG force field. The inclusion of electric multipoles in the proposed CG force field enables a more realistic description of the anisotropic electrostatic interactions in the protein system and, thus, provides an improvement over the standard isotropic two-bead CG models. In order to test the accuracy of the new CG force field model, extensive molecular dynamics simulations were carried out for a series of benchmark protein systems. These simulation studies showed that the TMFF model can realistically reproduce the structural and dynamical properties of proteins, as demonstrated by the close agreement of the CG results with those from the corresponding all-atom simulations in terms of root-mean-square deviations (RMSDs) and root-mean-square fluctuations (RMSFs) of the protein backbones. The current two-bead model is highly coarse-grained and is 50-fold more efficient than all-atom method in MD simulation of proteins in explicit water.

Parameterizing the Morse Potential for Coarse-Grained Modeling of Blood Plasma

PubMed Central

Zhang, Na; Zhang, Peng; Kang, Wei; Bluestein, Danny; Deng, Yuefan

2014-01-01

Multiscale simulations of fluids such as blood represent a major computational challenge of coupling the disparate spatiotemporal scales between molecular and macroscopic transport phenomena characterizing such complex fluids. In this paper, a coarse-grained (CG) particle model is developed for simulating blood flow by modifying the Morse potential, traditionally used in Molecular Dynamics for modeling vibrating structures. The modified Morse potential is parameterized with effective mass scales for reproducing blood viscous flow properties, including density, pressure, viscosity, compressibility and characteristic flow dynamics of human blood plasma fluid. The parameterization follows a standard inverse-problem approach in which the optimal micro parameters are systematically searched, by gradually decoupling loosely correlated parameter spaces, to match the macro physical quantities of viscous blood flow. The predictions of this particle based multiscale model compare favorably to classic viscous flow solutions such as Counter-Poiseuille and Couette flows. It demonstrates that such coarse grained particle model can be applied to replicate the dynamics of viscous blood flow, with the advantage of bridging the gap between macroscopic flow scales and the cellular scales characterizing blood flow that continuum based models fail to handle adequately. PMID:24910470

A coarse-grained model to study calcium activation of the cardiac thin filament

NASA Astrophysics Data System (ADS)

Zhang, Jing; Schwartz, Steven

2015-03-01

Familial hypertrophic cardiomyopathy (FHC) is one of the most common heart disease caused by genetic mutations. Cardiac muscle contraction and relaxation involve regulation of crossbridge binding to the cardiac thin filament, which regulates actomyosin interactions through calcium-dependent alterations in the dynamics of cardiac troponin (cTn) and tropomyosin (Tm). An atomistic model of cTn complex interacting with Tm has been studied by our group. A more realistic model requires the inclusion of the dynamics of actin filament, which is almost 6 times larger than cTn and Tm in terms of atom numbers, and extensive sampling of the model becomes very resource-demanding. By using physics-based protein united-residue force field, we introduce a coarse-grained model to study the calcium activation of the thin filament resulting from cTn's allosteric regulation of Tm dynamics on actin. The time scale is much longer than that of all-atom molecular dynamics simulation because of the reduction of the degrees of freedom. The coarse-grained model is a good template for studying cardiac thin filament mutations that cause FHC, and reduces the cost of computational resources.

Locating landmarks on high-dimensional free energy surfaces

PubMed Central

Chen, Ming; Yu, Tang-Qing; Tuckerman, Mark E.

2015-01-01

Coarse graining of complex systems possessing many degrees of freedom can often be a useful approach for analyzing and understanding key features of these systems in terms of just a few variables. The relevant energy landscape in a coarse-grained description is the free energy surface as a function of the coarse-grained variables, which, despite the dimensional reduction, can still be an object of high dimension. Consequently, navigating and exploring this high-dimensional free energy surface is a nontrivial task. In this paper, we use techniques from multiscale modeling, stochastic optimization, and machine learning to devise a strategy for locating minima and saddle points (termed “landmarks”) on a high-dimensional free energy surface “on the fly” and without requiring prior knowledge of or an explicit form for the surface. In addition, we propose a compact graph representation of the landmarks and connections between them, and we show that the graph nodes can be subsequently analyzed and clustered based on key attributes that elucidate important properties of the system. Finally, we show that knowledge of landmark locations allows for the efficient determination of their relative free energies via enhanced sampling techniques. PMID:25737545

Coarse-grained representation of the quasi adiabatic propagator path integral for the treatment of non-Markovian long-time bath memory

NASA Astrophysics Data System (ADS)

Richter, Martin; Fingerhut, Benjamin P.

2017-06-01

The description of non-Markovian effects imposed by low frequency bath modes poses a persistent challenge for path integral based approaches like the iterative quasi-adiabatic propagator path integral (iQUAPI) method. We present a novel approximate method, termed mask assisted coarse graining of influence coefficients (MACGIC)-iQUAPI, that offers appealing computational savings due to substantial reduction of considered path segments for propagation. The method relies on an efficient path segment merging procedure via an intermediate coarse grained representation of Feynman-Vernon influence coefficients that exploits physical properties of system decoherence. The MACGIC-iQUAPI method allows us to access the regime of biological significant long-time bath memory on the order of hundred propagation time steps while retaining convergence to iQUAPI results. Numerical performance is demonstrated for a set of benchmark problems that cover bath assisted long range electron transfer, the transition from coherent to incoherent dynamics in a prototypical molecular dimer and excitation energy transfer in a 24-state model of the Fenna-Matthews-Olson trimer complex where in all cases excellent agreement with numerically exact reference data is obtained.

Sedimentary and petrofacies analyses of the Amasiri Sandstone, southern Benue Trough, Nigeria: Implications for depositional environment and tectonic provenance

NASA Astrophysics Data System (ADS)

Okoro, A. U.; Igwe, E. O.; Nwajide, C. S.

2016-11-01

This study was undertaken to determine the depositional environment, provenance and tectonic setting for the Turonian Amasiri Sandstone, southern Benue Trough, Nigeria, using lithofacies analysis and re-appraisal of petrography of the sandstones. Local stratigraphy and field relationships show a thick succession of shales alternating with elongate/parallel sandstone ridges extending eastwards from Akpoha to Amasiri through Itigidi and Ugep to Apiapum areas. Lithofacies analysis reveals 9 lithofacies suggestive of storm (mass flow) and tidal shelf processes. These include dark grey to black laminated shale/silty mudstones, bioturbated mudstones, coquinoid limestones, very fine-grained bioturbated sandstones with shell hash/debris in places and limestone rip-up clasts, massive and chaotic sandy conglomerate with rip - up clasts, fine to medium-grained, parallel laminated sandstone, hummocky cross-stratified, massive, medium to coarse-grained sandstones, medium to very coarse-grained, planar cross-bedded sandstone, with clay-draped foresets and Ophiomorpha burrows, and coarse-grained trough cross-bedded sandstone. Petrofacies analysis identifies the sandstones as feldspathic and arkosic arenites. Ternary plot of framework mineralogy indicates derivation from an uplifted continental block related to the nearby Oban Massif and Cameroon Basement Complex.

Evaluation of the stability of uranyl peroxo-carbonato complex ions in carbonate media at different temperatures.

PubMed

Kim, Kwang-Wook; Lee, Keun-Young; Chung, Dong-Yong; Lee, Eil-Hee; Moon, Jei-Kwon; Shin, Dong-Woo

2012-09-30

This work studied the stability of peroxide in uranyl peroxo carbonato complex ions in a carbonate solution with hydrogen peroxide using absorption and Raman spectroscopies, and evaluated the temperature dependence of the decomposition characteristics of uranyl peroxo carbonato complex ions in the solution. The uranyl peroxo carbonato complex ions self-decomposed more rapidly into uranyl tris-carbonato complex ions in higher temperature carbonate solutions. The concentration of peroxide in the solution without free hydrogen peroxide represents the concentration of uranyl peroxo carbonato complex ions in a mixture of uranyl peroxo carbonato complex and uranyl tris-carbonato complex ions. The self-decomposition of the uranyl peroxo carbonato complex ions was a first order reaction, and its activation energy was evaluated to be 7.144×10(3) J mol(-1). The precipitation of sodium uranium oxide hydroxide occurred when the amount of uranyl tris-carbonato complex ions generated from the decomposition of the uranyl peroxo carbonato complex ions exceeded the solubility of uranyl tris-carbonato ions in the solution at the solution temperature. Copyright © 2012 Elsevier B.V. All rights reserved.

Changes in mass and nutrient content of wood during decomposition in a south Florida mangrove forest

USGS Publications Warehouse

Romero, L.M.; Smith, T. J.; Fourqurean, J.W.

2005-01-01

1 Large pools of dead wood in mangrove forests following disturbances such as hurricanes may influence nutrient fluxes. We hypothesized that decomposition of wood of mangroves from Florida, USA (Avicennia germinans, Laguncularia racemosa and Rhizophora mangle), and the consequent nutrient dynamics, would depend on species, location in the forest relative to freshwater and marine influences and whether the wood was standing, lying on the sediment surface or buried. 2 Wood disks (8-10 cm diameter, 1 cm thick) from each species were set to decompose at sites along the Shark River, either buried in the sediment, on the soil surface or in the air (above both the soil surface and high tide elevation). 3 A simple exponential model described the decay of wood in the air, and neither species nor site had any effect on the decay coefficient during the first 13 months of decomposition. 4 Over 28 months of decomposition, buried and surface disks decomposed following a two-component model, with labile and refractory components. Avicennia germinans had the largest labile component (18 ?? 2% of dry weight), while Laguncularia racemosa had the lowest (10 ?? 2%). Labile components decayed at rates of 0.37-23.71% month -1, while refractory components decayed at rates of 0.001-0.033% month-1. Disks decomposing on the soil surface had higher decay rates than buried disks, but both were higher than disks in the air. All species had similar decay rates of the labile and refractory components, but A. germinans exhibited faster overall decay because of a higher proportion of labile components. 5 Nitrogen content generally increased in buried and surface disks, but there was little change in N content of disks in the air over the 2-year study. Between 17% and 68% of total phosphorus in wood leached out during the first 2 months of decomposition, with buried disks having the greater losses, P remaining constant or increasing slightly thereafter. 6 Newly deposited wood from living trees was a short-term source of N for the ecosystem but, by the end of 2 years, had become a net sink. Wood, however, remained a source of P for the ecosystem. 7 As in other forested ecosystems, coarse woody debris can have a significant impact on carbon and nutrient dynamics in mangrove forests. The prevalence of disturbances, such as hurricanes, that can deposit large amounts of wood on the forest floor accentuates the importance of downed wood in these forests. ?? 2005 British Ecological Society.

Fungal-to-bacterial dominance of soil detrital food-webs: Consequences for biogeochemistry

NASA Astrophysics Data System (ADS)

Rousk, Johannes; Frey, Serita

2015-04-01

Resolving fungal and bacterial groups within the microbial decomposer community is thought to capture disparate microbial life strategies, associating bacteria with an r-selected strategy for carbon (C) and nutrient use, and fungi with a K-selected strategy. Additionally, food-web models have established a widely held belief that the bacterial decomposer pathway in soil supports high turnover rates of easily available substrates, while the slower fungal pathway supports the decomposition of more complex organic material, thus characterising the biogeochemistry of the ecosystem. Three field-experiments to generate gradients of SOC-quality were assessed. (1) the Detritus Input, Removal, and Trenching - DIRT - experiment in a temperate forest in mixed hardwood stands at Harvard Forest LTER, US. There, experimentally adjusted litter input and root input had affected the SOC quality during 23 years. (2) field-application of 14-C labelled glucose to grassland soils, sampled over the course of 13 months to generate an age-gradient of SOM (1 day - 13 months). (3) The Park Grass Experiment at Rothamsted, UK, where 150-years continuous N-fertilisation (0, 50, 100, 150 kg N ha-1 y-1) has affected the quality of SOM in grassland soils. A combination of carbon stable and radio isotope studies, fungal and bacterial growth and biomass measurements, and C and N mineralisation (15N pool dilution) assays were used to investigate how SOC-quality influenced fungal and bacterial food-web pathways and the implications this had for C and nutrient turnover. There was no support that decomposer food-webs dominated by bacteria support high turnover rates of easily available substrates, while slower fungal-dominated decomposition pathways support the decomposition of more complex organic material. Rather, an association between high quality SOC and fungi emerges from the results. This suggests that we need to revise our basic understanding for soil microbial communities and the processes they regulate in soil.

Luminescence of europium (III) complexes for visualization

NASA Astrophysics Data System (ADS)

Kolontaeva, Olga A.; Pozharov, Mikhail V.; Korolovich, Vladimir F.; Khokhlova, Anastasia R.; Kirdyanova, Anna N.; Burmistrova, Natalia A.; Zakharova, Tamara V.; Goryacheva, Irina Y.

2016-04-01

With the purpose to develop bright non-toxic luminescent label for theranostic application we have studied complexation of lanthanide dipicolinates (2,6-pyridinedicarboxylates) by sodium alginate and effect of thermal exposure of synthesized micro-capsules on their luminescent properties. Synthesized micro-capsules are stable in acidic medium but dissolve at pH ~ 4 due to transformation of cationic europium dipicolinate complex to anionic. Luminescence studies have shown that emission spectra of europium(III)-alginate complexes (both chloride and dipicolinate) contain two intensive bands characteristic to Eu3+ ion (5D0 --> 7F1 (590 nm) and 5D0 --> 7F1 (612 nm)). We have also found that at 160ºC europium(III)- alginate micro-capsules decompose to black, soot-like substance, therefore, their thermal treatment must be performed in closed environment (i.e., sealed ampoules).

Testing MODFLOW-LGR for simulating flow around buried Quaternary valleys - synthetic test cases

NASA Astrophysics Data System (ADS)

Vilhelmsen, T. N.; Christensen, S.

2009-12-01

In this study the Local Grid Refinement (LGR) method developed for MODFLOW-2005 (Mehl and Hill, 2005) is utilized to describe groundwater flow in areas containing buried Quaternary valley structures. The tests are conducted as comparative analysis between simulations run with a globally refined model, a locally refined model, and a globally coarse model, respectively. The models vary from simple one layer models to more complex ones with up to 25 model layers. The comparisons of accuracy are conducted within the locally refined area and focus on water budgets, simulated heads, and simulated particle traces. Simulations made with the globally refined model are used as reference (regarded as “true” values). As expected, for all test cases the application of local grid refinement resulted in more accurate results than when using the globally coarse model. A significant advantage of utilizing MODFLOW-LGR was that it allows increased numbers of model layers to better resolve complex geology within local areas. This resulted in more accurate simulations than when using either a globally coarse model grid or a locally refined model with lower geological resolution. Improved accuracy in the latter case could not be expected beforehand because difference in geological resolution between the coarse parent model and the refined child model contradicts the assumptions of the Darcy weighted interpolation used in MODFLOW-LGR. With respect to model runtimes, it was sometimes found that the runtime for the locally refined model is much longer than for the globally refined model. This was the case even when the closure criteria were relaxed compared to the globally refined model. These results are contradictory to those presented by Mehl and Hill (2005). Furthermore, in the complex cases it took some testing (model runs) to identify the closure criteria and the damping factor that secured convergence, accurate solutions, and reasonable runtimes. For our cases this is judged to be a serious disadvantage of applying MODFLOW-LGR. Another disadvantage in the studied cases was that the MODFLOW-LGR results proved to be somewhat dependent on the correction method used at the parent-child model interface. This indicates that when applying MODFLOW-LGR there is a need for thorough and case-specific considerations regarding choice of correction method. References: Mehl, S. and M. C. Hill (2005). "MODFLOW-2005, THE U.S. GEOLOGICAL SURVEY MODULAR GROUND-WATER MODEL - DOCUMENTATION OF SHARED NODE LOCAL GRID REFINEMENT (LGR) AND THE BOUNDARY FLOW AND HEAD (BFH) PACKAGE " U.S. Geological Survey Techniques and Methods 6-A12

Investigation of atmospheric oxidation of propyl gallate in an anionic surfactant system in the absence and presence of ascorbic acid.

PubMed

Szymula, M

2004-01-01

The antioxidant efficiency of two hydrophilic species, ascorbic acid (AA) and propyl gallate (PG), in an anionic surfactant system are studied. Ascorbic acid and propyl gallate are dissolved/solubilized in a microemulsion formed by water, pentanol, and sodium dodecyl sulfate. The determination of propyl gallate decomposition/oxidation kinetics shows enhanced oxidation of PG with increasing pentanol concentration in the system. When ascorbic acid and propyl gallate are both present in water, in surfactant aqueous solution, and in the studied microemulsion systems, the molecular complex AAPG is formed. After some time the complex decomposes.

Localized motion in random matrix decomposition of complex financial systems

NASA Astrophysics Data System (ADS)

Jiang, Xiong-Fei; Zheng, Bo; Ren, Fei; Qiu, Tian

2017-04-01

With the random matrix theory, we decompose the multi-dimensional time series of complex financial systems into a set of orthogonal eigenmode functions, which are classified into the market mode, sector mode, and random mode. In particular, the localized motion generated by the business sectors, plays an important role in financial systems. Both the business sectors and their impact on the stock market are identified from the localized motion. We clarify that the localized motion induces different characteristics of the time correlations for the stock-market index and individual stocks. With a variation of a two-factor model, we reproduce the return-volatility correlations of the eigenmodes.

Polymethacrylic acid as a new precursor of CuO nanoparticles

NASA Astrophysics Data System (ADS)

Hosny, Nasser Mohammed; Zoromba, Mohamed Shafick

2012-11-01

Polymethacrylic acid and its copper complexes have been synthesized and characterized. These complexes have been used as precursors to produce CuO nanoparticles by thermal decomposition in air. The stages of decompositions and the calcination temperature of the precursors have been determined from thermal analyses (TGA). The obtained CuO nanoparticles have been characterized by X-ray diffraction (XRD), scanning tunneling microscopy (STM) and transmission electron microscopy (TEM). XRD showed a monoclinic structure with particle size 8-20 nm for the synthesized copper oxide nanoparticles. These nanoparticles are catalytically active in decomposing hydrogen peroxide and a mechanism of decomposition has been suggested.

How salt lakes affect atmospheric new particle formation: A case study in Western Australia.

PubMed

Kamilli, K A; Ofner, J; Krause, T; Sattler, T; Schmitt-Kopplin, P; Eitenberger, E; Friedbacher, G; Lendl, B; Lohninger, H; Schöler, H F; Held, A

2016-12-15

New particle formation was studied above salt lakes in-situ using a mobile aerosol chamber set up above the salt crust and organic-enriched layers of seven different salt lakes in Western Australia. This unique setup made it possible to explore the influence of salt lake emissions on atmospheric new particle formation, and to identify interactions of aqueous-phase and gas-phase chemistry. New particle formation was typically observed at enhanced air temperatures and enhanced solar irradiance. Volatile organic compounds were released from the salt lake surfaces, probably from a soil layer enriched in organic compounds from decomposed leaf litter, and accumulated in the chamber air. After oxidation of these organic precursor gases, the reaction products contributed to new particle formation with observed growth rates from 2.7 to 25.4nmh -1 . The presence of ferrous and ferric iron and a drop of pH values in the salt lake water just before new particle formation events indicated that organic compounds were also oxidized in the aqueous phase, affecting the new particle formation process in the atmosphere. The contribution of aqueous-phase chemistry to new particle formation is assumed, as a mixture of hundreds of oxidized organic compounds was characterized with several analytical techniques. This chemically diverse composition of the organic aerosol fraction contained sulfur- and nitrogen-containing organic compounds, and halogenated organic compounds. Coarse mode particles were analyzed using electron microscopy, energy dispersive X-ray spectroscopy and Raman spectroscopy. Ultra-high resolution mass spectrometry was applied to analyze filter samples. A targeted mass spectral analysis revealed the formation of organosulfates from monoterpene precursors and two known tracers for secondary organic aerosol formation from atmospheric oxidation of 1,8-cineole, which indicates that a complex interplay of aqueous-phase and gas-phase oxidation of monoterpenes contributes to new particle formation in the investigated salt lake environment. Copyright © 2016. Published by Elsevier B.V.

Improvements in Operational Readiness by Distributing Manufacturing Capability in the Supply Chain through Additive Manufacturing

DTIC Science & Technology

2017-12-01

inefficiencies of a more complex system. Additional time may also be due to the longer distances traveled . The fulfillment time for a requisition to...Approved OMB No. 0704-0188 Public reporting burden for this collection of information is estimated to average 1 hour per response, including the time ...advanced manufacturing methods with additive manufacturing. This work decomposes the additive manufacturing processes into 11 primary functions. The time

Synthesis and characterization of silver nanoparticles from (bis)alkylamine silver carboxylate precursors.

PubMed

Uznanski, Pawel; Zakrzewska, Joanna; Favier, Frederic; Kazmierski, Slawomir; Bryszewska, Ewa

2017-01-01

A comparative study of amine and silver carboxylate adducts [R 1 COOAg-2(R 2 NH 2 )] (R 1  = 1, 7, 11; R 2  = 8, 12) as a key intermediate in NPs synthesis is carried out via differential scanning calorimetry, solid-state FT-infrared spectroscopy, 13 C CP MAS NMR, powder X-ray diffraction and X-ray photoelectron spectroscopy, and various solution NMR spectroscopies ( 1 H and 13 C NMR, pulsed field gradient spin-echo NMR, and ROESY). It is proposed that carboxyl moieties in the presence of amine ligands are bound to silver ions via chelating bidentate type of coordination as opposed to bridging bidentate coordination of pure silver carboxylates resulting from the formation of dimeric units. All complexes are packed as lamellar bilayer structures. Silver carboxylate/amine complexes show one first-order melting transition. The evidence presented in this study shows that phase behavior of monovalent metal carboxylates are controlled, mainly, by head group bonding. In solution, insoluble silver salt is stabilized by amine molecules which exist in dynamic equilibrium. Using (bis)amine-silver carboxylate complex as precursor, silver nanoparticles were fabricated. During high-temperature thermolysis, the (bis)amine-carboxylate adduct decomposes to produce silver nanoparticles of small size. NPs are stabilized by strongly interacting carboxylate and trace amounts of amine derived from the silver precursor interacting with carboxylic acid. A corresponding aliphatic amide obtained from silver precursor at high-temperature reaction conditions is not taking part in the stabilization. Combining NMR techniques with FTIR, it was possible to follow an original stabilization mechanism. Graphical abstractThe synthesis of a series (bis)alkylamine silver(I) carboxylate complexes in nonpolar solvents were carried out and fully characterized both in the solid and solution. Carboxyl moieties in the presence of amine ligands are bound to silver ions via chelating bidentate type of coordination. The complexes form layered structures which thermally decompose forming nanoparticles stabilized only by aliphatic carboxylates.

Reconnaissance investigation of Caribbean extreme wave deposits--Preliminary observations, interpretations, and research directions

USGS Publications Warehouse

Morton, Robert A.; Richmond, Bruce M.; Jaffe, Bruce E.; Gelfenbaum, Guy

2006-01-01

 This report presents an overview of preliminary geological investigations and recommended future research activities in the Caribbean region pertaining to coastal hazards with an emphasis on establishing tsunami risk for U.S. territories. Fieldwork was conducted in March 2006 on the islands of Bonaire, Puerto Rico, and Guadeloupe to evaluate the stratigraphic records of extreme wave deposits as possible indicators of paleotsunami recurrence. Morphological, sedimentological, and stratigraphic evidence indicate that shore-parallel coral rubble deposits composed of coarse clasts and sand that are 10s of meters wide and several meters thick are depositional complexes that have accumulated for a few centuries or millennia, and are not entirely the result of one or a few tsunamis as previously reported. The origins of boulder fields on elevated rock platforms of the Caribbean islands are more complicated than the origins of ridge complexes because boulder fields can be constructed by either storm waves or tsunamis. What is needed now for more conclusive interpretations is a systematic sedimentological approach to deposit analysis and a set of criteria for distinguishing between coarse clast storm and tsunami deposits. Assembling more field data from other Caribbean islands, analyzing stratigraphic deposits on Puerto Rico and Bonaire, and investigating boulder field deposits resulting from a historical tsunami can accomplish this. Also needed are improved sediment transport models for coarse clasts that can be used to estimate the competence and capacity of tsunamis and storms waves and to determine whether a deposit likely was created by a tsunami or extreme storm. Improved models may also be useful for reconstructing the magnitude of extreme wave events.

Bottled SAFT: A Web App Providing SAFT-γ Mie Force Field Parameters for Thousands of Molecular Fluids.

PubMed

Ervik, Åsmund; Mejía, Andrés; Müller, Erich A

2016-09-26

Coarse-grained molecular simulation has become a popular tool for modeling simple and complex fluids alike. The defining aspects of a coarse grained model are the force field parameters, which must be determined for each particular fluid. Because the number of molecular fluids of interest in nature and in engineering processes is immense, constructing force field parameter tables by individually fitting to experimental data is a futile task. A step toward solving this challenge was taken recently by Mejía et al., who proposed a correlation that provides SAFT-γ Mie force field parameters for a fluid provided one knows the critical temperature, the acentric factor and a liquid density, all relatively accessible properties. Building on this, we have applied the correlation to more than 6000 fluids, and constructed a web application, called "Bottled SAFT", which makes this data set easily searchable by CAS number, name or chemical formula. Alternatively, the application allows the user to calculate parameters for components not present in the database. Once the intermolecular potential has been found through Bottled SAFT, code snippets are provided for simulating the desired substance using the "raaSAFT" framework, which leverages established molecular dynamics codes to run the simulations. The code underlying the web application is written in Python using the Flask microframework; this allows us to provide a modern high-performance web app while also making use of the scientific libraries available in Python. Bottled SAFT aims at taking the complexity out of obtaining force field parameters for a wide range of molecular fluids, and facilitates setting up and running coarse-grained molecular simulations. The web application is freely available at http://www.bottledsaft.org . The underlying source code is available on Bitbucket under a permissive license.

Effects of moisture content on coarse woody debris respiration in a tropical rainforest of Brunei Darussalam

NASA Astrophysics Data System (ADS)

Roh, Y.; Li, G.; Han, S. H.; Abu Salim, K.; Son, Y.

2017-12-01

Since coarse woody debris (CWD) respiration (Rcwd) has an important role in carbon (C) cycling in forest ecosystems, it is a significant parameter in an investigation of CWD decomposition rate. Rcwd is known as to be influenced not only by environmental factors but also by CWD properties (e.g., moisture content). This study investigated the effects of CWD moisture content on Rcwd in a lowland mixed Dipterocarp tropical rainforest of Brunei Darussalam. CWDs in the forest were selected and categorized into two decay classes (sound and partially decomposed), and three diameter classes (10-20 cm, 20-30 cm, more than 30 cm). Samplings of CWDs were conducted in February and October, 2016. The fresh weight and Rcwd of the samples were measured within 24 h of sampling. Rcwd measurements were conducted using a closed chamber system with a diffusion-type, non-dispersive infrared (NDIR) sensor. In February, the fresh weight and Rcwd of the samples were remeasured, after submerging them in the fresh water for 24, 48, and 72 h. The Rcwd increased significantly with moisture content in February (r2=0.25, p<0.01). During the study period from February to October, 2016, the mean value of Rcwd (±SE) decreased from 18.26 (3.45) to 14.92 (2.67) mg C kg-1 h-1 (p<0.05), although the moisture content did not change significantly (p>0.05). Rcwd was lowest in the largest diameter class (p<0.01), and not significantly different between the decay classes (p>0.05). On the basis of these results, the Rcwd in this site was in the range of Rcwd in previous studies conducted in other tropical rainforests. Rcwd increased with moisture content, however, the contribution of moisture content to changes in Rcwd might not be influential during the eight months study period.*Supported by research grants from the Korea Forest Service (2017044B10-1719-BB01).

Time-marching multi-grid seismic tomography

NASA Astrophysics Data System (ADS)

Tong, P.; Yang, D.; Liu, Q.

2016-12-01

From the classic ray-based traveltime tomography to the state-of-the-art full waveform inversion, because of the nonlinearity of seismic inverse problems, a good starting model is essential for preventing the convergence of the objective function toward local minima. With a focus on building high-accuracy starting models, we propose the so-called time-marching multi-grid seismic tomography method in this study. The new seismic tomography scheme consists of a temporal time-marching approach and a spatial multi-grid strategy. We first divide the recording period of seismic data into a series of time windows. Sequentially, the subsurface properties in each time window are iteratively updated starting from the final model of the previous time window. There are at least two advantages of the time-marching approach: (1) the information included in the seismic data of previous time windows has been explored to build the starting models of later time windows; (2) seismic data of later time windows could provide extra information to refine the subsurface images. Within each time window, we use a multi-grid method to decompose the scale of the inverse problem. Specifically, the unknowns of the inverse problem are sampled on a coarse mesh to capture the macro-scale structure of the subsurface at the beginning. Because of the low dimensionality, it is much easier to reach the global minimum on a coarse mesh. After that, finer meshes are introduced to recover the micro-scale properties. That is to say, the subsurface model is iteratively updated on multi-grid in every time window. We expect that high-accuracy starting models should be generated for the second and later time windows. We will test this time-marching multi-grid method by using our newly developed eikonal-based traveltime tomography software package tomoQuake. Real application results in the 2016 Kumamoto earthquake (Mw 7.0) region in Japan will be demonstrated.

Rigid-Cluster Models of Conformational Transitions in Macromolecular Machines and Assemblies

PubMed Central

Kim, Moon K.; Jernigan, Robert L.; Chirikjian, Gregory S.

2005-01-01

We present a rigid-body-based technique (called rigid-cluster elastic network interpolation) to generate feasible transition pathways between two distinct conformations of a macromolecular assembly. Many biological molecules and assemblies consist of domains which act more or less as rigid bodies during large conformational changes. These collective motions are thought to be strongly related with the functions of a system. This fact encourages us to simply model a macromolecule or assembly as a set of rigid bodies which are interconnected with distance constraints. In previous articles, we developed coarse-grained elastic network interpolation (ENI) in which, for example, only Cα atoms are selected as representatives in each residue of a protein. We interpolate distance differences of two conformations in ENI by using a simple quadratic cost function, and the feasible conformations are generated without steric conflicts. Rigid-cluster interpolation is an extension of the ENI method with rigid-clusters replacing point masses. Now the intermediate conformations in an anharmonic pathway can be determined by the translational and rotational displacements of large clusters in such a way that distance constraints are observed. We present the derivation of the rigid-cluster model and apply it to a variety of macromolecular assemblies. Rigid-cluster ENI is then modified for a hybrid model represented by a mixture of rigid clusters and point masses. Simulation results show that both rigid-cluster and hybrid ENI methods generate sterically feasible pathways of large systems in a very short time. For example, the HK97 virus capsid is an icosahedral symmetric assembly composed of 60 identical asymmetric units. Its original Hessian matrix size for a Cα coarse-grained model is >(300,000)2. However, it reduces to (84)2 when we apply the rigid-cluster model with icosahedral symmetry constraints. The computational cost of the interpolation no longer scales heavily with the size of structures; instead, it depends strongly on the minimal number of rigid clusters into which the system can be decomposed. PMID:15833998

A robust cloud registration method based on redundant data reduction using backpropagation neural network and shift window

NASA Astrophysics Data System (ADS)

Xin, Meiting; Li, Bing; Yan, Xiao; Chen, Lei; Wei, Xiang

2018-02-01

A robust coarse-to-fine registration method based on the backpropagation (BP) neural network and shift window technology is proposed in this study. Specifically, there are three steps: coarse alignment between the model data and measured data, data simplification based on the BP neural network and point reservation in the contour region of point clouds, and fine registration with the reweighted iterative closest point algorithm. In the process of rough alignment, the initial rotation matrix and the translation vector between the two datasets are obtained. After performing subsequent simplification operations, the number of points can be reduced greatly. Therefore, the time and space complexity of the accurate registration can be significantly reduced. The experimental results show that the proposed method improves the computational efficiency without loss of accuracy.

Optimal reconstruction of the states in qutrit systems

NASA Astrophysics Data System (ADS)

Yan, Fei; Yang, Ming; Cao, Zhuo-Liang

2010-10-01

Based on mutually unbiased measurements, an optimal tomographic scheme for the multiqutrit states is presented explicitly. Because the reconstruction process of states based on mutually unbiased states is free of information waste, we refer to our scheme as the optimal scheme. By optimal we mean that the number of the required conditional operations reaches the minimum in this tomographic scheme for the states of qutrit systems. Special attention will be paid to how those different mutually unbiased measurements are realized; that is, how to decompose each transformation that connects each mutually unbiased basis with the standard computational basis. It is found that all those transformations can be decomposed into several basic implementable single- and two-qutrit unitary operations. For the three-qutrit system, there exist five different mutually unbiased-bases structures with different entanglement properties, so we introduce the concept of physical complexity to minimize the number of nonlocal operations needed over the five different structures. This scheme is helpful for experimental scientists to realize the most economical reconstruction of quantum states in qutrit systems.

An integrated condition-monitoring method for a milling process using reduced decomposition features

NASA Astrophysics Data System (ADS)

Liu, Jie; Wu, Bo; Wang, Yan; Hu, Youmin

2017-08-01

Complex and non-stationary cutting chatter affects productivity and quality in the milling process. Developing an effective condition-monitoring approach is critical to accurately identify cutting chatter. In this paper, an integrated condition-monitoring method is proposed, where reduced features are used to efficiently recognize and classify machine states in the milling process. In the proposed method, vibration signals are decomposed into multiple modes with variational mode decomposition, and Shannon power spectral entropy is calculated to extract features from the decomposed signals. Principal component analysis is adopted to reduce feature size and computational cost. With the extracted feature information, the probabilistic neural network model is used to recognize and classify the machine states, including stable, transition, and chatter states. Experimental studies are conducted, and results show that the proposed method can effectively detect cutting chatter during different milling operation conditions. This monitoring method is also efficient enough to satisfy fast machine state recognition and classification.

Augmenting the decomposition of EMG signals using supervised feature extraction techniques.

PubMed

Parsaei, Hossein; Gangeh, Mehrdad J; Stashuk, Daniel W; Kamel, Mohamed S

2012-01-01

Electromyographic (EMG) signal decomposition is the process of resolving an EMG signal into its constituent motor unit potential trains (MUPTs). In this work, the possibility of improving the decomposing results using two supervised feature extraction methods, i.e., Fisher discriminant analysis (FDA) and supervised principal component analysis (SPCA), is explored. Using the MUP labels provided by a decomposition-based quantitative EMG system as a training data for FDA and SPCA, the MUPs are transformed into a new feature space such that the MUPs of a single MU become as close as possible to each other while those created by different MUs become as far as possible. The MUPs are then reclassified using a certainty-based classification algorithm. Evaluation results using 10 simulated EMG signals comprised of 3-11 MUPTs demonstrate that FDA and SPCA on average improve the decomposition accuracy by 6%. The improvement for the most difficult-to-decompose signal is about 12%, which shows the proposed approach is most beneficial in the decomposition of more complex signals.

Using "big data" to optimally model hydrology and water quality across expansive regions

USGS Publications Warehouse

Roehl, E.A.; Cook, J.B.; Conrads, P.A.

2009-01-01

This paper describes a new divide and conquer approach that leverages big environmental data, utilizing all available categorical and time-series data without subjectivity, to empirically model hydrologic and water-quality behaviors across expansive regions. The approach decomposes large, intractable problems into smaller ones that are optimally solved; decomposes complex signals into behavioral components that are easier to model with "sub- models"; and employs a sequence of numerically optimizing algorithms that include time-series clustering, nonlinear, multivariate sensitivity analysis and predictive modeling using multi-layer perceptron artificial neural networks, and classification for selecting the best sub-models to make predictions at new sites. This approach has many advantages over traditional modeling approaches, including being faster and less expensive, more comprehensive in its use of available data, and more accurate in representing a system's physical processes. This paper describes the application of the approach to model groundwater levels in Florida, stream temperatures across Western Oregon and Wisconsin, and water depths in the Florida Everglades. ?? 2009 ASCE.

Multiscale structure of time series revealed by the monotony spectrum.

PubMed

Vamoş, Călin

2017-03-01

Observation of complex systems produces time series with specific dynamics at different time scales. The majority of the existing numerical methods for multiscale analysis first decompose the time series into several simpler components and the multiscale structure is given by the properties of their components. We present a numerical method which describes the multiscale structure of arbitrary time series without decomposing them. It is based on the monotony spectrum defined as the variation of the mean amplitude of the monotonic segments with respect to the mean local time scale during successive averagings of the time series, the local time scales being the durations of the monotonic segments. The maxima of the monotony spectrum indicate the time scales which dominate the variations of the time series. We show that the monotony spectrum can correctly analyze a diversity of artificial time series and can discriminate the existence of deterministic variations at large time scales from the random fluctuations. As an application we analyze the multifractal structure of some hydrological time series.

Multicriteria hierarchical iterative interactive algorithm for organizing operational modes of large heat supply systems

NASA Astrophysics Data System (ADS)

Korotkova, T. I.; Popova, V. I.

2017-11-01

The generalized mathematical model of decision-making in the problem of planning and mode selection providing required heat loads in a large heat supply system is considered. The system is multilevel, decomposed into levels of main and distribution heating networks with intermediate control stages. Evaluation of the effectiveness, reliability and safety of such a complex system is carried out immediately according to several indicators, in particular pressure, flow, temperature. This global multicriteria optimization problem with constraints is decomposed into a number of local optimization problems and the coordination problem. An agreed solution of local problems provides a solution to the global multicriterion problem of decision making in a complex system. The choice of the optimum operational mode of operation of a complex heat supply system is made on the basis of the iterative coordination process, which converges to the coordinated solution of local optimization tasks. The interactive principle of multicriteria task decision-making includes, in particular, periodic adjustment adjustments, if necessary, guaranteeing optimal safety, reliability and efficiency of the system as a whole in the process of operation. The degree of accuracy of the solution, for example, the degree of deviation of the internal air temperature from the required value, can also be changed interactively. This allows to carry out adjustment activities in the best way and to improve the quality of heat supply to consumers. At the same time, an energy-saving task is being solved to determine the minimum required values of heads at sources and pumping stations.

Geomorphology, hydrology, and ecology of Great Basin meadow complexes - implications for management and restoration

Treesearch

Jeanne C. Chambers; Jerry R. Miller

2011-01-01

This report contains the results of a 6-year project conducted by the U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station and U.S. Environmental Protection Agency, Office of Research and Development on stream incision and meadow ecosystem degradation in the central Great Basin. The project included a coarse-scale assessment of 56 different...

Comparative trends in log populations in northern Arizona mixed-conifer and ponderosa pine forests following severe drought

Treesearch

Joseph L. Ganey; Scott C. Vojta

2017-01-01

Logs provide an important form of coarse woody debris in forest systems, contributing to numerous ecological processes and affecting wildlife habitat and fuel complexes. Despite this, little information is available on the dynamics of log populations in southwestern ponderosa pine (Pinus ponderosa) and especially mixed-conifer forests. A recent episode of elevated tree...

SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.

PubMed

Boniecki, Michal J; Lach, Grzegorz; Dawson, Wayne K; Tomala, Konrad; Lukasz, Pawel; Soltysinski, Tomasz; Rother, Kristian M; Bujnicki, Janusz M

2016-04-20

RNA molecules play fundamental roles in cellular processes. Their function and interactions with other biomolecules are dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is laborious and challenging, and therefore, the majority of known RNAs remain structurally uncharacterized. Here, we present SimRNA: a new method for computational RNA 3D structure prediction, which uses a coarse-grained representation, relies on the Monte Carlo method for sampling the conformational space, and employs a statistical potential to approximate the energy and identify conformations that correspond to biologically relevant structures. SimRNA can fold RNA molecules using only sequence information, and, on established test sequences, it recapitulates secondary structure with high accuracy, including correct prediction of pseudoknots. For modeling of complex 3D structures, it can use additional restraints, derived from experimental or computational analyses, including information about secondary structure and/or long-range contacts. SimRNA also can be used to analyze conformational landscapes and identify potential alternative structures. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Systematic methods for defining coarse-grained maps in large biomolecules.

PubMed

Zhang, Zhiyong

2015-01-01

Large biomolecules are involved in many important biological processes. It would be difficult to use large-scale atomistic molecular dynamics (MD) simulations to study the functional motions of these systems because of the computational expense. Therefore various coarse-grained (CG) approaches have attracted rapidly growing interest, which enable simulations of large biomolecules over longer effective timescales than all-atom MD simulations. The first issue in CG modeling is to construct CG maps from atomic structures. In this chapter, we review the recent development of a novel and systematic method for constructing CG representations of arbitrarily complex biomolecules, in order to preserve large-scale and functionally relevant essential dynamics (ED) at the CG level. In this ED-CG scheme, the essential dynamics can be characterized by principal component analysis (PCA) on a structural ensemble, or elastic network model (ENM) of a single atomic structure. Validation and applications of the method cover various biological systems, such as multi-domain proteins, protein complexes, and even biomolecular machines. The results demonstrate that the ED-CG method may serve as a very useful tool for identifying functional dynamics of large biomolecules at the CG level.

Challenges for modeling global gene regulatory networks during development: insights from Drosophila.

PubMed

Wilczynski, Bartek; Furlong, Eileen E M

2010-04-15

Development is regulated by dynamic patterns of gene expression, which are orchestrated through the action of complex gene regulatory networks (GRNs). Substantial progress has been made in modeling transcriptional regulation in recent years, including qualitative "coarse-grain" models operating at the gene level to very "fine-grain" quantitative models operating at the biophysical "transcription factor-DNA level". Recent advances in genome-wide studies have revealed an enormous increase in the size and complexity or GRNs. Even relatively simple developmental processes can involve hundreds of regulatory molecules, with extensive interconnectivity and cooperative regulation. This leads to an explosion in the number of regulatory functions, effectively impeding Boolean-based qualitative modeling approaches. At the same time, the lack of information on the biophysical properties for the majority of transcription factors within a global network restricts quantitative approaches. In this review, we explore the current challenges in moving from modeling medium scale well-characterized networks to more poorly characterized global networks. We suggest to integrate coarse- and find-grain approaches to model gene regulatory networks in cis. We focus on two very well-studied examples from Drosophila, which likely represent typical developmental regulatory modules across metazoans. Copyright (c) 2009 Elsevier Inc. All rights reserved.

Deltaic sedimentation and stratigraphic sequences in post-orogenic basins, Western Greece

NASA Astrophysics Data System (ADS)

Piper, David J. W.; Kontopoulos, N.; Panagos, A. G.

1988-03-01

Post-orogenic basin sediments in the gulfs of Corinth, Patras and Amvrakia, on the western coast of Greece, occur in four tectonic settings: (1) true graben; (2) simple and complex half graben; (3) shallow half graben associated with the high-angel surface traces of thrust faults; and (4) marginal depressions adjacent to graben in which sediment loading has occurred. Late Quaternary facies distribution has been mapped in all three basins. Sea level changes, interacting with the apparently fortuitous elevation of horsts at basin margins, result in a complex alternation of well-mixed marine, stratified marine, brackish and lacustrine facies. Organic carbon contents of muds are high in all but the well-mixed marine facies. Basin margin slope is the most important determinant of facies distribution. The steep slopes of the Gulf of Corinth half graben result in fan-deltas which deliver coarse sediments in turbidity currents to the deep basin floor. Where gradients are reduced by marginal downwarping (Gulf of Patras) or on the gentle slopes of thrust-related half graben (Gulf of Amvrakia) coarse sediments are trapped on the subaerial delta or the coastal zone, and the fine sediment reaching the basin floor appears derived mainly from muddy plumes during winter floods.

Optimizing DNA nanotechnology through coarse-grained modeling: a two-footed DNA walker.

PubMed

Ouldridge, Thomas E; Hoare, Rollo L; Louis, Ard A; Doye, Jonathan P K; Bath, Jonathan; Turberfield, Andrew J

2013-03-26

DNA has enormous potential as a programmable material for creating artificial nanoscale structures and devices. For more complex systems, however, rational design and optimization can become difficult. We have recently proposed a coarse-grained model of DNA that captures the basic thermodynamic, structural, and mechanical changes associated with the fundamental process in much of DNA nanotechnology, the formation of duplexes from single strands. In this article, we demonstrate that the model can provide powerful insight into the operation of complex nanotechnological systems through a detailed investigation of a two-footed DNA walker that is designed to step along a reusable track, thereby offering the possibility of optimizing the design of such systems. We find that applying moderate tension to the track can have a large influence on the operation of the walker, providing a bias for stepping forward and helping the walker to recover from undesirable overstepped states. Further, we show that the process by which spent fuel detaches from the walker can have a significant impact on the rebinding of the walker to the track, strongly influencing walker efficiency and speed. Finally, using the results of the simulations, we propose a number of modifications to the walker to improve its operation.

Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models

PubMed Central

Lezon, Timothy R.; Sali, Andrej; Bahar, Ivet

2009-01-01

The nuclear pore complex (NPC) is the gate to the nucleus. Recent determination of the configuration of proteins in the yeast NPC at ∼5 nm resolution permits us to study the NPC global dynamics using coarse-grained structural models. We investigate these large-scale motions by using an extended elastic network model (ENM) formalism applied to several coarse-grained representations of the NPC. Two types of collective motions (global modes) are predicted by the ENMs to be intrinsically favored by the NPC architecture: global bending and extension/contraction from circular to elliptical shapes. These motions are shown to be robust against tested variations in the representation of the NPC, and are largely captured by a simple model of a toroid with axially varying mass density. We demonstrate that spoke multiplicity significantly affects the accessible number of symmetric low-energy modes of motion; the NPC-like toroidal structures composed of 8 spokes have access to highly cooperative symmetric motions that are inaccessible to toroids composed of 7 or 9 spokes. The analysis reveals modes of motion that may facilitate macromolecular transport through the NPC, consistent with previous experimental observations. PMID:19730674

Global motions of the nuclear pore complex: insights from elastic network models.

PubMed

Lezon, Timothy R; Sali, Andrej; Bahar, Ivet

2009-09-01

The nuclear pore complex (NPC) is the gate to the nucleus. Recent determination of the configuration of proteins in the yeast NPC at approximately 5 nm resolution permits us to study the NPC global dynamics using coarse-grained structural models. We investigate these large-scale motions by using an extended elastic network model (ENM) formalism applied to several coarse-grained representations of the NPC. Two types of collective motions (global modes) are predicted by the ENMs to be intrinsically favored by the NPC architecture: global bending and extension/contraction from circular to elliptical shapes. These motions are shown to be robust against tested variations in the representation of the NPC, and are largely captured by a simple model of a toroid with axially varying mass density. We demonstrate that spoke multiplicity significantly affects the accessible number of symmetric low-energy modes of motion; the NPC-like toroidal structures composed of 8 spokes have access to highly cooperative symmetric motions that are inaccessible to toroids composed of 7 or 9 spokes. The analysis reveals modes of motion that may facilitate macromolecular transport through the NPC, consistent with previous experimental observations.

Transpacific Transport of Dust to North American High-Elevation Sites: Integrated Dataset and Model Outputs

NASA Astrophysics Data System (ADS)

Kassianov, E.; Pekour, M. S.; Flynn, C. J.; Berg, L. K.; Beranek, J.; Zelenyuk, A.; Zhao, C.; Leung, L. R.; Ma, P. L.; Riihimaki, L.; Fast, J. D.; Barnard, J.; Hallar, G. G.; McCubbin, I.; Eloranta, E. W.; McComiskey, A. C.; Rasch, P. J.

2017-12-01

Understanding the effects of dust on the regional and global climate requires detailed information on particle size distributions and their changes with distance from the source. Awareness is now growing about the tendency of the dust coarse mode with moderate ( 3.5 µm) volume median diameter (VMD) to be rather insensitive to complex removal processes associated with long-range transport of dust from the main sources. Our study, with a focus on the transpacific transport of dust, demonstrates that the impact of coarse mode aerosol (VMD 3µm) is well defined at the high-elevation mountain-top Storm Peak Laboratory (SPL, about 3.2 km MSL) and nearby Atmospheric Radiation Measurement (ARM) Climate Research Facility Mobile Facility (AMF) during March 2011. Significant amounts of coarse mode aerosol are also found at the nearest Aerosol Robotic Network (AERONET) site. Outputs from the high-resolution Weather Research and Forecasting (WRF) Model coupled with chemistry (WRF-Chem) show that the major dust event is likely associated with transpacific transport of Asian and African plumes. Satellite data, including the Moderate Resolution Imaging Spectroradiometer (MODIS) and Multiangle Imaging SpectroRadiometer (MISR) aerosol optical depth (AOD) and plume height from the Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) lidar data provide the observational support of the WRF-Chem simulations. Our study complements previous findings by indicating that the quasi-static nature of the coarse mode appears to be a reasonable approximation for Asian and African dust despite expected frequent orographic precipitation over mountainous regions in the western United States.

Reduced Toxicity Fuel Satellite Propulsion System

NASA Technical Reports Server (NTRS)

Schneider, Steven J. (Inventor)

2001-01-01

A reduced toxicity fuel satellite propulsion system including a reduced toxicity propellant supply for consumption in an axial class thruster and an ACS class thruster. The system includes suitable valves and conduits for supplying the reduced toxicity propellant to the ACS decomposing element of an ACS thruster. The ACS decomposing element is operative to decompose the reduced toxicity propellant into hot propulsive gases. In addition the system includes suitable valves and conduits for supplying the reduced toxicity propellant to an axial decomposing element of the axial thruster. The axial decomposing element is operative to decompose the reduced toxicity propellant into hot gases. The system further includes suitable valves and conduits for supplying a second propellant to a combustion chamber of the axial thruster, whereby the hot gases and the second propellant auto-ignite and begin the combustion process for producing thrust.

Reduced Toxicity Fuel Satellite Propulsion System Including Plasmatron

NASA Technical Reports Server (NTRS)

Schneider, Steven J. (Inventor)

2003-01-01

A reduced toxicity fuel satellite propulsion system including a reduced toxicity propellant supply for consumption in an axial class thruster and an ACS class thruster. The system includes suitable valves and conduits for supplying the reduced toxicity propellant to the ACS decomposing element of an ACS thruster. The ACS decomposing element is operative to decompose the reduced toxicity propellant into hot propulsive gases. In addition the system includes suitable valves and conduits for supplying the reduced toxicity propellant to an axial decomposing element of the axial thruster. The axial decomposing element is operative to decompose the reduced toxicity propellant into hot gases. The system further includes suitable valves and conduits for supplying a second propellant to a combustion chamber of the axial thruster. whereby the hot gases and the second propellant auto-ignite and begin the combustion process for producing thrust.

Experimental evidence that the Ornstein-Uhlenbeck model best describes the evolution of leaf litter decomposability.

PubMed

Pan, Xu; Cornelissen, Johannes H C; Zhao, Wei-Wei; Liu, Guo-Fang; Hu, Yu-Kun; Prinzing, Andreas; Dong, Ming; Cornwell, William K

2014-09-01

Leaf litter decomposability is an important effect trait for ecosystem functioning. However, it is unknown how this effect trait evolved through plant history as a leaf 'afterlife' integrator of the evolution of multiple underlying traits upon which adaptive selection must have acted. Did decomposability evolve in a Brownian fashion without any constraints? Was evolution rapid at first and then slowed? Or was there an underlying mean-reverting process that makes the evolution of extreme trait values unlikely? Here, we test the hypothesis that the evolution of decomposability has undergone certain mean-reverting forces due to strong constraints and trade-offs in the leaf traits that have afterlife effects on litter quality to decomposers. In order to test this, we examined the leaf litter decomposability and seven key leaf traits of 48 tree species in the temperate area of China and fitted them to three evolutionary models: Brownian motion model (BM), Early burst model (EB), and Ornstein-Uhlenbeck model (OU). The OU model, which does not allow unlimited trait divergence through time, was the best fit model for leaf litter decomposability and all seven leaf traits. These results support the hypothesis that neither decomposability nor the underlying traits has been able to diverge toward progressively extreme values through evolutionary time. These results have reinforced our understanding of the relationships between leaf litter decomposability and leaf traits in an evolutionary perspective and may be a helpful step toward reconstructing deep-time carbon cycling based on taxonomic composition with more confidence.

Thermal regeneration of an electrochemical concentration cell

DOEpatents

Krumpelt, M.; Bates, J.K.

1980-05-09

A system and method are described for thermally regenerating an electrochemical concentration cell having first and second aluminum electrodes respectively positioned in contact with first and second electrolytes separated by an ion exchange member, the first and second electrolytes being composed of different concentrations of an ionic solvent and a salt, preferably an aluminum halide. The ionic solvent may be either organic or inorganic with a relatively low melting point, the ionic solvent and the salt form a complex wherein the free energy of formation of said complex is less than about -5 kcal/mole. A distillation column using solar heat or low grade industrial waste heat receives the first and second electrolytes and thermally decomposes the salt-solvent complex to provide feed material for the two half cells.

Overset grid applications on distributed memory MIMD computers

NASA Technical Reports Server (NTRS)

Chawla, Kalpana; Weeratunga, Sisira

1994-01-01

Analysis of modern aerospace vehicles requires the computation of flowfields about complex three dimensional geometries composed of regions with varying spatial resolution requirements. Overset grid methods allow the use of proven structured grid flow solvers to address the twin issues of geometrical complexity and the resolution variation by decomposing the complex physical domain into a collection of overlapping subdomains. This flexibility is accompanied by the need for irregular intergrid boundary communication among the overlapping component grids. This study investigates a strategy for implementing such a static overset grid implicit flow solver on distributed memory, MIMD computers; i.e., the 128 node Intel iPSC/860 and the 208 node Intel Paragon. Performance data for two composite grid configurations characteristic of those encountered in present day aerodynamic analysis are also presented.

A Global Approach to the Optimal Trajectory Based on an Improved Ant Colony Algorithm for Cold Spray

NASA Astrophysics Data System (ADS)

Cai, Zhenhua; Chen, Tingyang; Zeng, Chunnian; Guo, Xueping; Lian, Huijuan; Zheng, You; Wei, Xiaoxu

2016-12-01

This paper is concerned with finding a global approach to obtain the shortest complete coverage trajectory on complex surfaces for cold spray applications. A slicing algorithm is employed to decompose the free-form complex surface into several small pieces of simple topological type. The problem of finding the optimal arrangement of the pieces is translated into a generalized traveling salesman problem (GTSP). Owing to its high searching capability and convergence performance, an improved ant colony algorithm is then used to solve the GTSP. Through off-line simulation, a robot trajectory is generated based on the optimized result. The approach is applied to coat real components with a complex surface by using the cold spray system with copper as the spraying material.

Peculiar Traits of Coarse AP (Briefing Charts)

DTIC Science & Technology

2014-12-01

coarse AP Bircumshaw, Newman Active centers are sources of AP decomposition gases AP low temperature decomposition (LTD) Most unstable AP particles ...delay before coarse AP ejection *Coarse AP particle flame retardancy 19 Air Force Research Laboratory Distribution A: Approved for public release...distribution unlimited. PA clearance #. Combustion bomb trials 2 AP phase change may enable coarse particle breakage Fractured coarse AP ejection agrees

Megavoltage cargo radiography with dual energy material decomposition

NASA Astrophysics Data System (ADS)

Shikhaliev, Polad M.

2018-02-01

Megavoltage (MV) radiography has important applications in imaging large cargos for detecting illicit materials. A useful feature of MV radiography is the possibility of decomposing and quantifying materials with different atomic numbers. This can be achieved by imaging cargo at two different X-ray energies, or dual energy (DE) radiography. The performance of both single energy and DE radiography depends on beam energy, beam filtration, radiation dose, object size, and object content. The purpose of this work was to perform comprehensive qualitative and quantitative investigations of the image quality in MV radiography depending on the above parameters. A digital phantom was designed including Fe background with thicknesses of 2cm, 6cm, and 18cm, and materials samples of Polyethylene, Fe, Pb, and U. The single energy images were generated at x-ray beam energies 3.5MV, 6MV, and 9MV. The DE material decomposed images were generated using interlaced low and high energy beams 3.5/6MV and 6/9MV. The X-ray beams were filtered by low-Z (Polyethylene) and high-Z (Pb) filters with variable thicknesses. The radiation output of the accelerator was kept constant for all beam energies. The image quality metrics was signal-to-noise ratio (SNR) of the particular sample over a particular background. It was found that the SNR depends on the above parameters in a complex way, but can be optimized by selecting a particular set of parameters. For some imaging setups increased filter thicknesses, while strongly absorbing the beams, increased the SNR of material decomposed images. Beam hardening due to polyenergetic x-ray spectra resulted in material decomposition errors, but this could be addressed using region of interest decomposition. It was shown that it is not feasible to separate the materials with close atomic numbers using the DE method. Particularly, Pb and U were difficult to decompose, at least at the dose levels allowed by radiation source and safety requirements.

A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions

PubMed Central

Khalil, Ahmad S.; Lu, Timothy K.; Bashor, Caleb J.; Ramirez, Cherie L.; Pyenson, Nora C.; Joung, J. Keith; Collins, James J.

2013-01-01

SUMMARY Eukaryotic transcription factors (TFs) perform complex and combinatorial functions within transcriptional networks. Here, we present a synthetic framework for systematically constructing eukaryotic transcription functions using artificial zinc fingers, modular DNA-binding domains found within many eukaryotic TFs. Utilizing this platform, we construct a library of orthogonal synthetic transcription factors (sTFs) and use these to wire synthetic transcriptional circuits in yeast. We engineer complex functions, such as tunable output strength and transcriptional cooperativity, by rationally adjusting a decomposed set of key component properties, e.g., DNA specificity, affinity, promoter design, protein-protein interactions. We show that subtle perturbations to these properties can transform an individual sTF between distinct roles (activator, cooperative factor, inhibitory factor) within a transcriptional complex, thus drastically altering the signal processing behavior of multi-input systems. This platform provides new genetic components for synthetic biology and enables bottom-up approaches to understanding the design principles of eukaryotic transcriptional complexes and networks. PMID:22863014

The topological requirements for robust perfect adaptation in networks of any size.

PubMed

Araujo, Robyn P; Liotta, Lance A

2018-05-01

Robustness, and the ability to function and thrive amid changing and unfavorable environments, is a fundamental requirement for living systems. Until now it has been an open question how large and complex biological networks can exhibit robust behaviors, such as perfect adaptation to a variable stimulus, since complexity is generally associated with fragility. Here we report that all networks that exhibit robust perfect adaptation (RPA) to a persistent change in stimulus are decomposable into well-defined modules, of which there exist two distinct classes. These two modular classes represent a topological basis for all RPA-capable networks, and generate the full set of topological realizations of the internal model principle for RPA in complex, self-organizing, evolvable bionetworks. This unexpected result supports the notion that evolutionary processes are empowered by simple and scalable modular design principles that promote robust performance no matter how large or complex the underlying networks become.

Regeneration of carboxylic acid-laden basic sorbents by leaching with a volatile base in an organic solvent

DOEpatents

King, C. Judson; Husson, Scott M.

1999-01-01

Carboxylic acids are sorbed from aqueous feedstocks onto a solid adsorbent. The acids are freed from the sorbent phase by treating it with an organic solution of alkylamine thus forming an alkylamine/carboxylic acid complex which is decomposed with improved efficiency to the desired carboxylic acid and the alkylamine. Carbon dioxide addition can be used to improve the adsorption or the carboxylic acids by the solid phase sorbent.

Mission planning for autonomous systems

NASA Technical Reports Server (NTRS)

Pearson, G.

1987-01-01

Planning is a necessary task for intelligent, adaptive systems operating independently of human controllers. A mission planning system that performs task planning by decomposing a high-level mission objective into subtasks and synthesizing a plan for those tasks at varying levels of abstraction is discussed. Researchers use a blackboard architecture to partition the search space and direct the focus of attention of the planner. Using advanced planning techniques, they can control plan synthesis for the complex planning tasks involved in mission planning.

The Design, Synthesis and Screening of Potential Pyridinium Oxime Prodrugs.

DTIC Science & Technology

1985-07-31

copper sulfate pentahydrate , and 15 g (87 mol) of the mixture of bromo- picolines 13c and 131. The combined reactions produced 27 g (96%) of a brown...extracted with ethyl ether. The ether extracts were washed with brine, dried with sodium sulfate , filtered and flashed. The residue was then purified by...stirring to the reaction mix. The addition was exothermic as the copper complexes decomposed. The cooled mixture was extracted with several 20 ml

Nonlinear complexity behaviors of agent-based 3D Potts financial dynamics with random environments

NASA Astrophysics Data System (ADS)

Xing, Yani; Wang, Jun

2018-02-01

A new microscopic 3D Potts interaction financial price model is established in this work, to investigate the nonlinear complexity behaviors of stock markets. 3D Potts model, which extends the 2D Potts model to three-dimensional, is a cubic lattice model to explain the interaction behavior among the agents. In order to explore the complexity of real financial markets and the 3D Potts financial model, a new random coarse-grained Lempel-Ziv complexity is proposed to certain series, such as the price returns, the price volatilities, and the random time d-returns. Then the composite multiscale entropy (CMSE) method is applied to the intrinsic mode functions (IMFs) and the corresponding shuffled data to study the complexity behaviors. The empirical results indicate that the 3D financial model is feasible.

Reduced Toxicity Fuel Satellite Propulsion System Including Fuel Cell Reformer with Alcohols Such as Methanol

NASA Technical Reports Server (NTRS)

Schneider, Steven J. (Inventor)

2001-01-01

A reduced toxicity fuel satellite propulsion system including a reduced toxicity propellant supply for consumption in an axial class thruster and an ACS class thruster. The system includes suitable valves and conduits for supplying the reduced toxicity propellant to the ACS decomposing element of an ACS thruster. The ACS decomposing element is operative to decompose the reduced toxicity propellant into hot propulsive gases. In addition the system includes suitable valves and conduits for supplying the reduced toxicity propellant to an axial decomposing element of the axial thruster. The axial decomposing element is operative to decompose the reduced toxicity propellant into hot gases. The system further includes suitable valves and conduits for supplying a second propellant to a combustion chamber of the axial thruster, whereby the hot gases and the second propellant auto-ignite and begin the combustion process for producing thrust.

Simulated nitrogen deposition affects wood decomposition by cord-forming fungi.

PubMed

Bebber, Daniel P; Watkinson, Sarah C; Boddy, Lynne; Darrah, Peter R

2011-12-01

Anthropogenic nitrogen (N) deposition affects many natural processes, including forest litter decomposition. Saprotrophic fungi are the only organisms capable of completely decomposing lignocellulosic (woody) litter in temperate ecosystems, and therefore the responses of fungi to N deposition are critical in understanding the effects of global change on the forest carbon cycle. Plant litter decomposition under elevated N has been intensively studied, with varying results. The complexity of forest floor biota and variability in litter quality have obscured N-elevation effects on decomposers. Field experiments often utilize standardized substrates and N-levels, but few studies have controlled the decay organisms. Decomposition of beech (Fagus sylvatica) blocks inoculated with two cord-forming basidiomycete fungi, Hypholoma fasciculare and Phanerochaete velutina, was compared experimentally under realistic levels of simulated N deposition at Wytham Wood, Oxfordshire, UK. Mass loss was greater with P. velutina than with H. fasciculare, and with N treatment than in the control. Decomposition was accompanied by growth of the fungal mycelium and increasing N concentration in the remaining wood. We attribute the N effect on wood decay to the response of cord-forming wood decay fungi to N availability. Previous studies demonstrated the capacity of these fungi to scavenge and import N to decaying wood via a translocating network of mycelium. This study shows that small increases in N availability can increase wood decomposition by these organisms. Dead wood is an important carbon store and habitat. The responses of wood decomposers to anthropogenic N deposition should be considered in models of forest carbon dynamics.

Experimental evidence that the Ornstein-Uhlenbeck model best describes the evolution of leaf litter decomposability

PubMed Central

Pan, Xu; Cornelissen, Johannes H C; Zhao, Wei-Wei; Liu, Guo-Fang; Hu, Yu-Kun; Prinzing, Andreas; Dong, Ming; Cornwell, William K

2014-01-01

Leaf litter decomposability is an important effect trait for ecosystem functioning. However, it is unknown how this effect trait evolved through plant history as a leaf ‘afterlife’ integrator of the evolution of multiple underlying traits upon which adaptive selection must have acted. Did decomposability evolve in a Brownian fashion without any constraints? Was evolution rapid at first and then slowed? Or was there an underlying mean-reverting process that makes the evolution of extreme trait values unlikely? Here, we test the hypothesis that the evolution of decomposability has undergone certain mean-reverting forces due to strong constraints and trade-offs in the leaf traits that have afterlife effects on litter quality to decomposers. In order to test this, we examined the leaf litter decomposability and seven key leaf traits of 48 tree species in the temperate area of China and fitted them to three evolutionary models: Brownian motion model (BM), Early burst model (EB), and Ornstein-Uhlenbeck model (OU). The OU model, which does not allow unlimited trait divergence through time, was the best fit model for leaf litter decomposability and all seven leaf traits. These results support the hypothesis that neither decomposability nor the underlying traits has been able to diverge toward progressively extreme values through evolutionary time. These results have reinforced our understanding of the relationships between leaf litter decomposability and leaf traits in an evolutionary perspective and may be a helpful step toward reconstructing deep-time carbon cycling based on taxonomic composition with more confidence. PMID:25535551

A variational principle for compressible fluid mechanics: Discussion of the multi-dimensional theory

NASA Technical Reports Server (NTRS)

Prozan, R. J.

1982-01-01

The variational principle for compressible fluid mechanics previously introduced is extended to two dimensional flow. The analysis is stable, exactly conservative, adaptable to coarse or fine grids, and very fast. Solutions for two dimensional problems are included. The excellent behavior and results lend further credence to the variational concept and its applicability to the numerical analysis of complex flow fields.

Simultaneous Strength-Ductility Enhancement of a Nano-Lamellar AlCoCrFeNi2.1 Eutectic High Entropy Alloy by Cryo-Rolling and Annealing.

PubMed

Bhattacharjee, T; Wani, I S; Sheikh, S; Clark, I T; Okawa, T; Guo, S; Bhattacharjee, P P; Tsuji, N

2018-02-19

Nano-lamellar (L1 2  + B2) AlCoCrFeNi 2.1 eutectic high entropy alloy (EHEA) was processed by cryo-rolling and annealing. The EHEA developed a novel hierarchical microstructure featured by fine lamellar regions consisting of FCC lamellae filled with ultrafine FCC grains (average size ~200-250 nm) and B2 lamellae, and coarse non-lamellar regions consisting of ultrafine FCC (average size ~200-250 nm), few coarse recrystallized FCC grains and rather coarse unrecrystallized B2 phase (~2.5 µm). This complex and hierarchical microstructure originated from differences in strain-partitioning amongst the constituent phases, affecting the driving force for recrystallization. The hierarchical microstructure of the cryo-rolled and annealed material resulted in simultaneous enhancement in strength (Yield Strength/YS: 1437 ± 26 MPa, Ultimate Tensile Strength/UTS: 1562 ± 33 MPa) and ductility (elongation to failure/e f  ~ 14 ± 1%) as compared to the as-cast as well as cold-rolled and annealed materials. The present study for the first time demonstrated that cryo-deformation and annealing could be a novel microstructural design strategy for overcoming strength-ductility trade off in multiphase high entropy alloys.

Coarse-Grained Molecular Monte Carlo Simulations of Liquid Crystal-Nanoparticle Mixtures

NASA Astrophysics Data System (ADS)

Neufeld, Ryan; Kimaev, Grigoriy; Fu, Fred; Abukhdeir, Nasser M.

Coarse-grained intermolecular potentials have proven capable of capturing essential details of interactions between complex molecules, while substantially reducing the number of degrees of freedom of the system under study. In the domain of liquid crystals, the Gay-Berne (GB) potential has been successfully used to model the behavior of rod-like and disk-like mesogens. However, only ellipsoid-like interaction potentials can be described with GB, making it a poor fit for many real-world mesogens. In this work, the results of Monte Carlo simulations of liquid crystal domains using the Zewdie-Corner (ZC) potential are presented. The ZC potential is constructed from an orthogonal series of basis functions, allowing for potentials of essentially arbitrary shapes to be modeled. We also present simulations of mixtures of liquid crystalline mesogens with nanoparticles. Experimentally these mixtures have been observed to exhibit microphase separation and formation of long-range networks under some conditions. This highlights the need for a coarse-grained approach which can capture salient details on the molecular scale while simulating sufficiently large domains to observe these phenomena. We compare the phase behavior of our simulations with that of a recently presented continuum theory. This work was made possible by the Natural Sciences and Engineering Research Council of Canada and Compute Ontario.

Investigation of the relative fine and coarse mode aerosol loadings and properties in the Southern Arabian Gulf region

NASA Astrophysics Data System (ADS)

Kaku, Kathleen C.; Reid, Jeffrey S.; Reid, Elizabeth A.; Ross-Langerman, Kristy; Piketh, Stuart; Cliff, Steven; Al Mandoos, Abdulla; Broccardo, Stephen; Zhao, Yongjing; Zhang, Jianglong; Perry, Kevin D.

2016-03-01

The aerosol chemistry environment of the Arabian Gulf region is extraordinarily complex, with high concentrations of dust aerosols from surrounding deserts mixed with anthropogenic aerosols originating from a large petrochemical industry and pockets of highly urbanized areas. Despite the high levels of aerosols experienced by this region, little research has been done to explore the chemical composition of both the anthropogenic and mineral dust portion of the aerosol burden. The intensive portion of the United Arab Emirates Unified Aerosol Experiment (UAE2), conducted during August and September 2004 was designed in part to resolve the aerosol chemistry through the use of multiple size-segregated aerosol samplers. The coarse mode mass (derived by subtracting the PM2.5 aerosol mass from the PM10 mass) is largely dust at 76% ± 7% of the total coarse mode mass, but is significantly impacted by anthropogenic pollution, primarily sulfate and nitrate. The PM2.5 aerosol mass also contains a large dust burden, at 38% ± 26%, but the anthropogenic component dominates. The total aerosol burden has significant impact not only on the atmosphere, but also the local population, as the air quality levels for both the PM10 and PM2.5 aerosol masses reached unhealthy levels for 24% of the days sampled.

Coarse-grained Simulations of Substrate Export through Multidrug Efflux Transporter AcrB

NASA Astrophysics Data System (ADS)

Jewel, Yead; Dutta, Prashanta; Liu, Jin

2017-11-01

The treatment of bacterial infectious diseases hampered by the overexpression of multidrug resistance (MDR) systems. The MDR system actively pumps the antibiotic drugs as well as other toxic compounds out of the cells. During the pumping, AcrB (one of the key MDR components) undergoes a series of large-scale proton/substrate dependent conformational changes. In this work, we implement a hybrid coarse-grained PACE force field that couples the united-atom protein model with the coarse-grained MARTINI water/lipid, to investigate the conformational changes of AcrB. We first develop the substrate force field which is compatible with PACE, then we implement the force field to explore large scale structural changes of AcrB in microsecond simulations. The effects of the substrate and the protonation states of two key residues: Asp407 and Asp408, are investigated. Our results show that the drug export through AcrB is proton as well as substrate dependent. Our simulations explain molecular mechanisms of substrate transport through AcrB complex, as well as provide valuable insights for designing proper antibiotic drugs. Research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R01GM122081.

Multiple time-scales and the developmental dynamics of social systems.

PubMed

Flack, Jessica C

2012-07-05

To build a theory of social complexity, we need to understand how aggregate social properties arise from individual interaction rules. Here, I review a body of work on the developmental dynamics of pigtailed macaque social organization and conflict management that provides insight into the mechanistic causes of multi-scale social systems. In this model system coarse-grained, statistical representations of collective dynamics are more predictive of the future state of the system than the constantly in-flux behavioural patterns at the individual level. The data suggest that individuals can perceive and use these representations for strategical decision-making. As an interaction history accumulates the coarse-grained representations consolidate. This constrains individual behaviour and provides the foundations for new levels of organization. The time-scales on which these representations change impact whether the consolidating higher-levels can be modified by individuals and collectively. The time-scales appear to be a function of the 'coarseness' of the representations and the character of the collective dynamics over which they are averages. The data suggest that an advantage of multiple timescales is that they allow social systems to balance tradeoffs between predictability and adaptability. I briefly discuss the implications of these findings for cognition, social niche construction and the evolution of new levels of organization in biological systems.

Weak Galilean invariance as a selection principle for coarse-grained diffusive models.

PubMed

Cairoli, Andrea; Klages, Rainer; Baule, Adrian

2018-05-29

How does the mathematical description of a system change in different reference frames? Galilei first addressed this fundamental question by formulating the famous principle of Galilean invariance. It prescribes that the equations of motion of closed systems remain the same in different inertial frames related by Galilean transformations, thus imposing strong constraints on the dynamical rules. However, real world systems are often described by coarse-grained models integrating complex internal and external interactions indistinguishably as friction and stochastic forces. Since Galilean invariance is then violated, there is seemingly no alternative principle to assess a priori the physical consistency of a given stochastic model in different inertial frames. Here, starting from the Kac-Zwanzig Hamiltonian model generating Brownian motion, we show how Galilean invariance is broken during the coarse-graining procedure when deriving stochastic equations. Our analysis leads to a set of rules characterizing systems in different inertial frames that have to be satisfied by general stochastic models, which we call "weak Galilean invariance." Several well-known stochastic processes are invariant in these terms, except the continuous-time random walk for which we derive the correct invariant description. Our results are particularly relevant for the modeling of biological systems, as they provide a theoretical principle to select physically consistent stochastic models before a validation against experimental data.

Seafloor geology of the Monterey Bay area continental shelf

USGS Publications Warehouse

Eittreim, S.L.; Anima, R.J.; Stevenson, A.J.

2002-01-01

Acoustic swath-mapping of the greater Monterey Bay area continental shelf from Point An??o Nuevo to Point Sur reveals complex patterns of rock outcrops on the shelf, and coarse-sand bodies that occur in distinct depressions on the inner and mid-shelves. Most of the rock outcrops are erosional cuestas of dipping Tertiary rocks that make up the bedrock of the surrounding lands. A mid-shelf mud belt of Holocene sediment buries the Tertiary rocks in a continuous, 6-km-wide zone on the northern Monterey Bay shelf. Rock exposures occur on the inner shelf, near tectonically uplifting highlands, and on the outer shelf, beyond the reach of the mud depositing on the mid-shelf since the Holocene sea-level rise. The sediment-starved shelf off the Monterey Peninsula and south to Point Sur has a very thin cover of Holocene sediment, and bedrock outcrops occur across the whole shelf, with Salinian granite outcrops surrounding the Monterey Peninsula. Coarse-sand deposits occur both bounded within low-relief rippled scour depressions, and in broad sheets in areas like the Sur Platform where fine sediment sources are limited. The greatest concentrations of coarse-sand deposits occur on the southern Monterey Bay shelf and the Sur shelf. ?? 2002 Elsevier Science B.V. All rights reserved.

Provenance of Conglomerates within a Late Cretaceous Turbidite Channel System on the North American Margin: the Rosario Formation, Baja California, Mexico

NASA Astrophysics Data System (ADS)

Dos Santos, Thisiane; Kneller, Benjamin; Morton, Andrew; Armelenti, Garibaldi; Pantopoulos, George; De Ros, Luiz Fernando

2017-04-01

The Rosario Formation forms part of the Peninsular Ranges forearc basin complex, which crops out discontinuously along the Pacific coast of the Baja California Peninsula, Mexico. This study concerns the upper, deep marine part of the Rosario Formation , which includes several slope channel systems, one of these, the San Fernando channel systems consists of five channel complex sets (CCS1 to CCS5), each characterized by three filling stages. Stage I consists of predominantly clast­ and matrix-supported conglomerates, with subordinate medium to coarse grained sandstones. Stage II consists of units of clast-supported conglomerates with subordinate medium to coarse-grained sandstones, separated by mainly thinly-bedded turbidites (intercalation of thin beds of fine-grained sandstones and mudstones). Stage III consists mainly of hemipelagic mudstones. The main objective of this research is to determine source area and to compare the coarse fraction and finer fraction (fragments <2 cm) from conglomerates of each channel set, combining provenance methodology such as heavy minerals, clast counting, geochemistry, bulk petrography and U/Pb in detrital zircons by LA-ICPMS and SHRIMP. The heavy minerals assembly identified were Ca amphibole, epidote, clinozoisite, titanite, garnet, tourmaline, apatite, rutile and zircon, among them amphiboles are by far the most abundant detrital mineral. Clast counting and petrographic characterization showed that the pebble fraction of the conglomerates is constituted at least 18 different, and the majority being composed by pyroclastic, porphyritic volcanic and sandstone rocks. Bulk quantification indicates that the main provenance tectonic mode of the fine fraction of the conglomerates can be interpreted as dissected magmatic arc, with subordinate uplifted basement and recycled orogenic contributions. The preliminary conclusion is that the sedimentary supply to the Rosario Formation was mostly derived from volcanic and plutonic rocks of the Upper Peninsular Ranges Arc complex known as the Alisitos Arc, which follows the western margin of the Peninsular Ranges batholith, as well as from older magmatic arc, and from recycling of sedimentary/metasedimentary terrains.

Vertical Subsurface Flow Mixing and Horizontal Anisotropy in Coarse Fluvial Aquifers: Structural Aspects

NASA Astrophysics Data System (ADS)

Huggenberger, P.; Huber, E.

2014-12-01

Detailed descriptions of the subsurface heterogeneities in coarse fluvial aquifer gravel often lack in concepts to distinguish between the essence and the noise of a permeability structure and the ability to extrapolate site specific hydraulic information at the tens to several hundred meters scale. At this scale the heterogeneity strongly influences the anisotropies of the flow field and the mixing processes in groundwater. However, in many hydrogeological models the complexity of natural systems is oversimplified. Understanding the link between the dynamics of the surface processes of braided-river systems and the resulting subsurface sedimentary structures is the key to characterizing the complexity of horizontal and vertical mixing processes in groundwater. From the different depositional elements of coarse braided-river systems, the largest permeability contrasts can be observed in the scour-fills. Other elements (e.g. different types of gravel sheets) show much smaller variabilities and could be considered as a kind of matrix. Field experiments on the river Tagliamento (Northeast Italy) based on morphological observation and ground-penetrating radar (GPR) surveys, as well as outcrop analyses of gravel pit exposures (Switzerland) allowed us to define the shape, sizes, spatial distribution and preservation potential of scour-fills. In vertical sections (e.g. 2D GPR data, vertical outcrop), the spatial density of remnant erosional bounding surfaces of scours is an indicator for the dynamics of the braided-river system (lateral mobility of the active floodplain, rate of sediment net deposition and spatial distribution of the confluence scours). In case of combined low aggradation rate and low lateral mobility the deposits may be dominated by a complex overprinting of scour-fills. The delineation of the erosional bounding surfaces, that are coherent over the survey area, is based on the identification of angular discontinuities of the reflectors. Fence diagrams and horizontal time-slices from GPR data are used to construct simplified 3D hydraulic properties distribution models and to derive anisotropy patterns. On the basis of this work, conceptual models could be designed and implemented into numerical models to simulate the flow field and mixing in heterogeneous braided-river deposits.

Equation-free and variable free modeling for complex/multiscale systems. Coarse-grained computation in science and engineering using fine-grained models

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

Kevrekidis, Ioannis G.

The work explored the linking of modern developing machine learning techniques (manifold learning and in particular diffusion maps) with traditional PDE modeling/discretization/scientific computation techniques via the equation-free methodology developed by the PI. The result (in addition to several PhD degrees, two of them by CSGF Fellows) was a sequence of strong developments - in part on the algorithmic side, linking data mining with scientific computing, and in part on applications, ranging from PDE discretizations to molecular dynamics and complex network dynamics.

Simple and complex chimera states in a nonlinearly coupled oscillatory medium

NASA Astrophysics Data System (ADS)

Bolotov, Maxim; Smirnov, Lev; Osipov, Grigory; Pikovsky, Arkady

2018-04-01

We consider chimera states in a one-dimensional medium of nonlinear nonlocally coupled phase oscillators. In terms of a local coarse-grained complex order parameter, the problem of finding stationary rotating nonhomogeneous solutions reduces to a third-order ordinary differential equation. This allows finding chimera-type and other inhomogeneous states as periodic orbits of this equation. Stability calculations reveal that only some of these states are stable. We demonstrate that an oscillatory instability leads to a breathing chimera, for which the synchronous domain splits into subdomains with different mean frequencies. Further development of instability leads to turbulent chimeras.

Accurate Segmentation of Cervical Cytoplasm and Nuclei Based on Multiscale Convolutional Network and Graph Partitioning.

PubMed

Song, Youyi; Zhang, Ling; Chen, Siping; Ni, Dong; Lei, Baiying; Wang, Tianfu

2015-10-01

In this paper, a multiscale convolutional network (MSCN) and graph-partitioning-based method is proposed for accurate segmentation of cervical cytoplasm and nuclei. Specifically, deep learning via the MSCN is explored to extract scale invariant features, and then, segment regions centered at each pixel. The coarse segmentation is refined by an automated graph partitioning method based on the pretrained feature. The texture, shape, and contextual information of the target objects are learned to localize the appearance of distinctive boundary, which is also explored to generate markers to split the touching nuclei. For further refinement of the segmentation, a coarse-to-fine nucleus segmentation framework is developed. The computational complexity of the segmentation is reduced by using superpixel instead of raw pixels. Extensive experimental results demonstrate that the proposed cervical nucleus cell segmentation delivers promising results and outperforms existing methods.

Early stages of clathrin aggregation at a membrane in coarse-grained simulations

NASA Astrophysics Data System (ADS)

Giani, M.; den Otter, W. K.; Briels, W. J.

2017-04-01

The self-assembly process of clathrin coated pits during endocytosis has been simulated by combining and extending coarse grained models of the clathrin triskelion, the adaptor protein AP2, and a flexible network membrane. The AP2's core, upon binding to membrane and cargo, releases a motif that can bind clathrin. In conditions where the core-membrane-cargo binding is weak, the binding of this motif to clathrin can result in a stable complex. We characterize the conditions and mechanisms resulting in the formation of clathrin lattices that curve the membrane, i.e., clathrin coated pits. The mechanical properties of the AP2 β linker appear crucial to the orientation of the curved clathrin lattice relative to the membrane, with wild-type short linkers giving rise to the inward curving buds enabling endocytosis while long linkers produce upside-down cages and outward curving bulges.

A fast and accurate frequency estimation algorithm for sinusoidal signal with harmonic components

NASA Astrophysics Data System (ADS)

Hu, Jinghua; Pan, Mengchun; Zeng, Zhidun; Hu, Jiafei; Chen, Dixiang; Tian, Wugang; Zhao, Jianqiang; Du, Qingfa

2016-10-01

Frequency estimation is a fundamental problem in many applications, such as traditional vibration measurement, power system supervision, and microelectromechanical system sensors control. In this paper, a fast and accurate frequency estimation algorithm is proposed to deal with low efficiency problem in traditional methods. The proposed algorithm consists of coarse and fine frequency estimation steps, and we demonstrate that it is more efficient than conventional searching methods to achieve coarse frequency estimation (location peak of FFT amplitude) by applying modified zero-crossing technique. Thus, the proposed estimation algorithm requires less hardware and software sources and can achieve even higher efficiency when the experimental data increase. Experimental results with modulated magnetic signal show that the root mean square error of frequency estimation is below 0.032 Hz with the proposed algorithm, which has lower computational complexity and better global performance than conventional frequency estimation methods.

Coarse graining of NN inelastic interactions up to 3 GeV: Repulsive versus structural core

NASA Astrophysics Data System (ADS)

Fernández-Soler, P.; Ruiz Arriola, E.

2017-07-01

The repulsive short-distance core is one of the main paradigms of nuclear physics which even seems confirmed by QCD lattice calculations. On the other hand nuclear potentials at short distances are motivated by high energy behavior where inelasticities play an important role. We analyze NN interactions up to 3 GeV in terms of simple coarse grained complex and energy dependent interactions. We discuss two possible and conflicting scenarios which share the common feature of a vanishing wave function at the core location in the particular case of S waves. We find that the optical potential with a repulsive core exhibits a strong energy dependence whereas the optical potential with the structural core is characterized by a rather adiabatic energy dependence which allows one to treat inelasticity perturbatively. We discuss the possible implications for nuclear structure calculations of both alternatives.

Mixed sediment beach processes: Kachemak Bay, Alaska

USGS Publications Warehouse

Ruggiero, P.; Adams, P.N.; Warrick, J.A.

2007-01-01

Mixed sediment beaches are morphologically distinct from and more complex than either sand or gravel only beaches. Three digital imaging techniques are employed to quantify surficial grain size and bedload sediment transport rates along the mixed sediment beaches of Kachemak Bay, Alaska. Applying digital imaging procedures originally developed for quickly and efficiently quantifying grain sizes of sand to coarse sediment classes gives promising results. Hundreds of grain size estimates lead to a quantitative characterization of the region's sediment at a significant reduction in cost and time as compared to traditional techniques. Both the sand and coarse fractions on this megatidal beach mobilize into self-organized bedforms that migrate alongshore with a seasonally reflecting the temporal pattern of the alongshore component of wave power. In contrast, the gravel bedforms also migrate in the cross-shore without significant seasonally suggesting that swash asymmetry is sufficient to mobilize the gravel even during low energy summer conditions. ?? 2007 ASCE.

Coarse-Grained Structural Modeling of Molecular Motors Using Multibody Dynamics

PubMed Central

Parker, David; Bryant, Zev; Delp, Scott L.

2010-01-01

Experimental and computational approaches are needed to uncover the mechanisms by which molecular motors convert chemical energy into mechanical work. In this article, we describe methods and software to generate structurally realistic models of molecular motor conformations compatible with experimental data from different sources. Coarse-grained models of molecular structures are constructed by combining groups of atoms into a system of rigid bodies connected by joints. Contacts between rigid bodies enforce excluded volume constraints, and spring potentials model system elasticity. This simplified representation allows the conformations of complex molecular motors to be simulated interactively, providing a tool for hypothesis building and quantitative comparisons between models and experiments. In an example calculation, we have used the software to construct atomically detailed models of the myosin V molecular motor bound to its actin track. The software is available at www.simtk.org. PMID:20428469

Liposome encapsulation of chelating agents

DOEpatents

Rahman, Yueh Erh

1976-01-13

A method for transferring a chelating agent across a cellular membrane by encapsulating the charged chelating agent within liposomes and carrying the liposome-encapsulated chelating agent to the cellular membrane where the liposomes containing the chelating agent will be taken up by the cells, thereby transferring the chelating agent across the cellular membrane. A chelating agent can be introduced into the interior of a cell of a living organism wherein the liposomes will be decomposed, releasing the chelating agent to the interior of the cell. The released chelating agent will complex intracellularly deposited toxic heavy metals, permitting the more soluble metal complex to transfer across the cellular membrane from the cell and subsequently be removed from the living organism.

Signal enhancement based on complex curvelet transform and complementary ensemble empirical mode decomposition

NASA Astrophysics Data System (ADS)

Dong, Lieqian; Wang, Deying; Zhang, Yimeng; Zhou, Datong

2017-09-01

Signal enhancement is a necessary step in seismic data processing. In this paper we utilize the complementary ensemble empirical mode decomposition (CEEMD) and complex curvelet transform (CCT) methods to separate signal from random noise further to improve the signal to noise (S/N) ratio. Firstly, the original data with noise is decomposed into a series of intrinsic mode function (IMF) profiles with the aid of CEEMD. Then the IMFs with noise are transformed into CCT domain. By choosing different thresholds which are based on the noise level difference of each IMF profile, the noise in original data can be suppressed. Finally, we illustrate the effectiveness of the approach by simulated and field datasets.

Preparation and characterization of ligand types intermediate in the metal catalyzed conversion of coal to methane, methanol, and higher alkanes and alcohols. Second technical progress report, September 1, 1979-February 28, 1981

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

Gladysz, J. A.

1980-11-10

Mechanistic studies of anionic formyl complexes were made. The rate of decomposition of the formyl (CO)/sub 4/Mn(COC/sub 6/H/sub 5/)(CHO)/sup -/ anion as a function of counter-ion and trialkylborane present was examined. The deuterated formyl (CO)/sub 4/Mn(COC/sub 6/H/sub 5/)(CDO)/sup -/ was prepared and its decomposition was monitored by H/sup 2/ NMR. The data obtained indicate that the formyl decomposes by a disproportionative pathway not by initial CO loss, as commonly noted for formyl complexes.

Three-dimensional scene encryption and display based on computer-generated holograms.

PubMed

Kong, Dezhao; Cao, Liangcai; Jin, Guofan; Javidi, Bahram

2016-10-10

An optical encryption and display method for a three-dimensional (3D) scene is proposed based on computer-generated holograms (CGHs) using a single phase-only spatial light modulator. The 3D scene is encoded as one complex Fourier CGH. The Fourier CGH is then decomposed into two phase-only CGHs with random distributions by the vector stochastic decomposition algorithm. Two CGHs are interleaved as one final phase-only CGH for optical encryption and reconstruction. The proposed method can support high-level nonlinear optical 3D scene security and complex amplitude modulation of the optical field. The exclusive phase key offers strong resistances of decryption attacks. Experimental results demonstrate the validity of the novel method.

Soil actinomycetes in the National Forest Park in northeastern China

NASA Astrophysics Data System (ADS)

Shirokikh, I. G.; Shirokikh, A. A.

2017-01-01

The taxonomic and functional structure of actinomycete complexes in the litters and upper horizons of the soils under an artificial coniferous-broad-leaved forest located around the town of Chanchun (Tszilin province, PRC). The complex of actinomycetes included representatives of the Streptomyces, Micromonospora, Streptosporangium, and Streptoverticillium genera and oligosporous forms. In the actinomycete complexes, streptomycetes prevailed in the abundance (61-95%) and frequency of occurrence (100%). In the parcels of Korean pine ( Pinus koraiensis) and Mongolian oak ( Quercus mongolica), streptomycetes of 19 species from 8 series and 4 sections were isolated. The most representative, as in European forest biomes, was the Cinereus Achromogenes series. A distinguishing feature of the streptomycete complex in the biomes studied was the high participation of species from the Imperfectus series. The verification of the functional activity of natural isolates made it possible to reveal strains with high antagonistic and cellulolytic abilities. A high similarity of actinomycete complexes was found in Eurasian forest ecosystems remote from each other, probably due to the similarity of plant polymers decomposable by actinomycetes.

Sedimentology of rocky shorelines: 1. A review of the problem, with analytical methods, and insights gained from the Hulopoe Gravel and the modern rocky shoreline of Lanai, Hawaii

NASA Astrophysics Data System (ADS)

Felton, E. Anne

2002-10-01

Hypotheses advanced concerning the origin of the Pleistocene Hulopoe Gravel on Lanai include mega-tsunami, abandoned beach, 'multiple event,' rocky shoreline, and for parts of the deposit, Native Hawaiian constructions and degraded lava flow fronts. Uplift of Lanai shorelines has been suggested for deposits occurring up to at least 190 m. These conflicting hypotheses highlight problems with the interpretation of coarse gravel deposits containing marine biotic remains. The geological records of the processes implied by these hypotheses should look very different. Discrimination among these or any other hypotheses for the origins of the Hulopoe Gravel will require careful study of vertical and lateral variations in litho- and biofacies, facies architecture, contact relationships and stratal geometries of this deposit. Observations of modern rocky shorelines, particularly on Lanai adjacent to Hulopoe Gravel outcrops, have shown that distinctive coarse gravel facies are present, several of which occur in specific geomorphic settings. Tectonic, isostatic and eustatic changes which cause rapid shoreline translations on steep slopes favour preservation of former rocky shorelines and associated sedimentary deposits both above and below sea level. The sedimentary record of those shorelines is likely to be complex. The modern rocky shoreline sedimentary environment is a hostile one, largely neglected by sedimentologists. A range of high-energy processes characterize these shorelines. Long-period swell, tsunami and storm waves can erode hard bedrock and generate coarse gravel. They also erode older deposits, depositing fresh ones containing mixtures of materials of different ages. Additional gravelly material may be contributed by rivers draining steep hinterlands. To fully evaluate rocky shoreline deposition in the broadest sense, for both the Hulopoe Gravel and other deposits, sedimentary facies models are needed for rocky shorelines occurring in a range of settings. Recognition and description of rocky shoreline deposits are crucial for correctly interpreting the geological history of oceanic and volcanic arc islands, for distinguishing between ancient tsunami and storm deposits, and for interpreting coarse-grained deposits preserved on high energy coasts of continents. Problems include not only the absence of appropriate sedimentary facies models linking rocky shoreline deposits and environments but also, until recently, lack of a systematic descriptive scheme applicable to coarse gravel deposits generally. Two complementary methods serve to integrate the wide range of bed and clast attributes and parameters which characterize complex coarse gravel deposits. The composition and fabric (CAF) method has a materials focus, providing detailed description of attributes of the constituent clasts, petrology, the proportions of gravel, sand and mud, and the ways in which these materials are organized. The sedimentary facies model building (FMB) method emphasizes the organization of a deposit on a bed-by-bed basis to identify facies and infer depositional processes. The systematic use of a comprehensive gravel fabric and petrography log (GFPL), in conjunction with detailed vertical profiles, provides visual representations of a range of deposit characteristics. Criteria useful for distinguishing sedimentary facies in the Hulopoe Gravel are: grain-size modes, amount of matrix, bed geometry, sedimentary structures, bed fabric and clast roundness.

Seismo-acoustic imaging of marine hard substrate habitats: a case study from the German Bight (SE North Sea)

NASA Astrophysics Data System (ADS)

Papenmeier, Svenja; Hass, H. Christian

2016-04-01

The detection of hard substrate habitats in sublittoral environments is a considerable challenge in spite of modern high resolution hydroacoustic techniques. In offshore areas those habitats are mainly represented by either cobbles and boulders (stones) often located in wide areas of soft sediments or by glacial relict sediments (heterogeneous mixture of medium sand to gravel size with cobbles and boulders). Sediment classification and object detection is commonly done on the basis of hydroacoustic backscatter intensities recorded with e.g. sidescan sonar (SSS) and multibeam echo sounder (MBES). Single objects lying on the sediment such as stones can generally be recognized by the acoustic shadow behind the object. However, objects close to the sonar's nadir may remain undetected because their shadows are below the data resolution. Further limitation in the detection of objects is caused by sessile communities that thrive on the objects. The bio-cover tends to absorb most of the acoustic signal. Automated identification based on the backscatter signal is often not satisfactory, especially when stones are present in a setting with glacial deposits. Areas characterized by glacial relict sediments are hardly differentiable in their backscatter characteristics from rippled coarse sand and fine gravel (rippled coarse sediments) without an intensive ground-truthing program. From the ecological point of view the relict and rippled coarse sediments are completely different habitats and need to be distinguished. The case study represents a seismo-acoustic approach in which SSS and nonlinear sediment echo sounder (SES) data are combined to enable a reliable and reproducible differentiation between relict sediments (with stones and coarse gravels) and rippled coarse sediments. Elevated objects produce hyperbola signatures at the sediment surface in the echo data which can be used to complement the SSS data. The nonlinear acoustic propagation of the SES sound pulses produces a comparably small foot print which results in high spatial resolution (decimeter in the xyz directions) and hence allows a more precise demarcation of hard substrate areas. Data for this study were recorded in the "Sylt Outer Reef" (German Bight, North Sea) in May 2013 and March 2015. The investigated area is characterized by heterogeneously distributed moraine deposits and rippled coarse sediments partly draped with Holocene fine sands. The relict sediments and the rippled coarse sediments indicate both high backscatter intensities but can be distinguished by means of the hyperbola locations. The northeast of the study area is dominated by rippled coarse sediments (without hyperbolas) and the southwestern part by relict sediments with a high amount of stones represented by hyperbolas which is also proven by extensive ground-truthing (grab sampling and high quality underwater videos). An automated procedure to identify and export the hyperbola positions makes the demarcation of hard substrate grounds (here: relict sediments) reproducible, faster and less complex in comparison to the visual-manual identification on the basis of sidescan sonar data.

The Design, Development and Testing of Complex Avionics Systems: Conference Proceedings Held at the Avionics Panel Symposium in Las Vegas, Nevada on 27 April-1 May 1987

DTIC Science & Technology

1987-12-01

Normally, the system is decomposed into manageable parts with accurately defined interfaces. By rigidly controlling this process, aerospace companies have...Reference A CHANGE IN SYSTEM DESIGN EMPHASIS: FROM MACHINE TO MAN by M.L.Metersky and J.L.Ryder 16 SESSION I1 - MANAGING THE FUl URE SYSTEM DESIGN...PROCESS MANAGING ADVANCED AVIONIC SYSTEM DESIGN by P.Simons 17 ERGONOMIE PSYCHOSENSORIELLE DES COCKPITS, INTERET DES SYSTEMES INFORMATIQUES INTELLIGENTS

Super-resolution with an SLM and two intensity images

NASA Astrophysics Data System (ADS)

Alcalá Ochoa, Noé; de León, Y. Ponce

2018-06-01

It is reported a method which may simplify the optical setups used to achieve super-resolution through the amplitude multiplication of two waves. For this end we decompose a super-resolving pupil into two complex masks and with the aid of a Spatial Light Modulator (LCoS) we obtain two intensity images that are subtracted. With this proposal, the traditional experimental optical setups are considerably simplified, with the additional benefit that different masks can be utilized without needing to perform the setup alignment each time.

Forensic entomology of decomposing humans and their decomposing pets.

PubMed

Sanford, Michelle R

2015-02-01

Domestic pets are commonly found in the homes of decedents whose deaths are investigated by a medical examiner or coroner. When these pets become trapped with a decomposing decedent they may resort to feeding on the body or succumb to starvation and/or dehydration and begin to decompose as well. In this case report photographic documentation of cases involving pets and decedents were examined from 2009 through the beginning of 2014. This photo review indicated that in many cases the pets were cats and dogs that were trapped with the decedent, died and were discovered in a moderate (bloat to active decay) state of decomposition. In addition three cases involving decomposing humans and their decomposing pets are described as they were processed for time of insect colonization by forensic entomological approach. Differences in timing and species colonizing the human and animal bodies were noted as was the potential for the human or animal derived specimens to contaminate one another at the scene. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Submarine fan facies of Upper Cretaceous Strata, Southern San Rafael Mountains, Santa Barbara County, California

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

Toyne, C.D.

1986-04-01

A 2900-m thick Campanian-Maestrichtian(.) turbidite sequence in Upper Mono Creek Canyon is interpreted to be a progradational submarine fan complex comprised of outer fan, middle fan, inner fan, and slope facies. The basal 600 m of the section consists of thinly bedded, laterally continuous fine sandstones, siltstones, and mudstones (mainly Mutti and Ricci Lucci facies D), interpreted to be outer fan interlobe and lobe-fringe deposits. These are punctuated by infrequent medium to very thickly bedded, flat-based, fine to coarse sandstones (facies C and B), which commonly coarsen and thicken upward, and are interpreted to be depositional lobes. Overlying these depositsmore » are approximately 1400 m of middle fan deposits composed of frequent lenticular, commonly channelized and amalgamated, thickly bedded, fine to very coarse sandstones (facies C and B) organized in fining- and thinning-upward sequences, interpreted to be braided-channel deposits. These alternate with less common nonchannelized coarsening- and thickening-upward sequences suggestive of lobe-apical cycles. These multistory sand deposits are nested within thick intervals of fine sandstones, siltstones, and mudstones (facies C and D), interpreted to be levee, crevasse-splay, and interchannel deposits. Interfingered with and overlying these deposits are approximately 500 m of fining- and thinning-upward or noncyclic, erosionally based, commonly amalgamated, very thickly bedded, medium to very coarse sandstones, pebbly sandstones, and conglomerates (facies A and B), interpreted to be inner fan deposits. Intercalated within this facies, infrequent, laterally discontinuous, thin to thickly bedded, fine to coarse sandstones, siltstones, and mudstones exist, interpreted to be interchannel, levee, and possibly channel-fill deposits.« less

Spatial heterogeneity in ecologically important climate variables at coarse and fine scales in a high-snow mountain landscape.

PubMed

Ford, Kevin R; Ettinger, Ailene K; Lundquist, Jessica D; Raleigh, Mark S; Hille Ris Lambers, Janneke

2013-01-01

Climate plays an important role in determining the geographic ranges of species. With rapid climate change expected in the coming decades, ecologists have predicted that species ranges will shift large distances in elevation and latitude. However, most range shift assessments are based on coarse-scale climate models that ignore fine-scale heterogeneity and could fail to capture important range shift dynamics. Moreover, if climate varies dramatically over short distances, some populations of certain species may only need to migrate tens of meters between microhabitats to track their climate as opposed to hundreds of meters upward or hundreds of kilometers poleward. To address these issues, we measured climate variables that are likely important determinants of plant species distributions and abundances (snow disappearance date and soil temperature) at coarse and fine scales at Mount Rainier National Park in Washington State, USA. Coarse-scale differences across the landscape such as large changes in elevation had expected effects on climatic variables, with later snow disappearance dates and lower temperatures at higher elevations. However, locations separated by small distances (∼20 m), but differing by vegetation structure or topographic position, often experienced differences in snow disappearance date and soil temperature as great as locations separated by large distances (>1 km). Tree canopy gaps and topographic depressions experienced later snow disappearance dates than corresponding locations under intact canopy and on ridges. Additionally, locations under vegetation and on topographic ridges experienced lower maximum and higher minimum soil temperatures. The large differences in climate we observed over small distances will likely lead to complex range shift dynamics and could buffer species from the negative effects of climate change.

Coarse Grid Modeling of Turbine Film Cooling Flows Using Volumetric Source Terms

NASA Technical Reports Server (NTRS)

Heidmann, James D.; Hunter, Scott D.

2001-01-01

The recent trend in numerical modeling of turbine film cooling flows has been toward higher fidelity grids and more complex geometries. This trend has been enabled by the rapid increase in computing power available to researchers. However, the turbine design community requires fast turnaround time in its design computations, rendering these comprehensive simulations ineffective in the design cycle. The present study describes a methodology for implementing a volumetric source term distribution in a coarse grid calculation that can model the small-scale and three-dimensional effects present in turbine film cooling flows. This model could be implemented in turbine design codes or in multistage turbomachinery codes such as APNASA, where the computational grid size may be larger than the film hole size. Detailed computations of a single row of 35 deg round holes on a flat plate have been obtained for blowing ratios of 0.5, 0.8, and 1.0, and density ratios of 1.0 and 2.0 using a multiblock grid system to resolve the flows on both sides of the plate as well as inside the hole itself. These detailed flow fields were spatially averaged to generate a field of volumetric source terms for each conservative flow variable. Solutions were also obtained using three coarse grids having streamwise and spanwise grid spacings of 3d, 1d, and d/3. These coarse grid solutions used the integrated hole exit mass, momentum, energy, and turbulence quantities from the detailed solutions as volumetric source terms. It is shown that a uniform source term addition over a distance from the wall on the order of the hole diameter is able to predict adiabatic film effectiveness better than a near-wall source term model, while strictly enforcing correct values of integrated boundary layer quantities.

Spatial Heterogeneity in Ecologically Important Climate Variables at Coarse and Fine Scales in a High-Snow Mountain Landscape

PubMed Central

Ford, Kevin R.; Ettinger, Ailene K.; Lundquist, Jessica D.; Raleigh, Mark S.; Hille Ris Lambers, Janneke

2013-01-01

Climate plays an important role in determining the geographic ranges of species. With rapid climate change expected in the coming decades, ecologists have predicted that species ranges will shift large distances in elevation and latitude. However, most range shift assessments are based on coarse-scale climate models that ignore fine-scale heterogeneity and could fail to capture important range shift dynamics. Moreover, if climate varies dramatically over short distances, some populations of certain species may only need to migrate tens of meters between microhabitats to track their climate as opposed to hundreds of meters upward or hundreds of kilometers poleward. To address these issues, we measured climate variables that are likely important determinants of plant species distributions and abundances (snow disappearance date and soil temperature) at coarse and fine scales at Mount Rainier National Park in Washington State, USA. Coarse-scale differences across the landscape such as large changes in elevation had expected effects on climatic variables, with later snow disappearance dates and lower temperatures at higher elevations. However, locations separated by small distances (∼20 m), but differing by vegetation structure or topographic position, often experienced differences in snow disappearance date and soil temperature as great as locations separated by large distances (>1 km). Tree canopy gaps and topographic depressions experienced later snow disappearance dates than corresponding locations under intact canopy and on ridges. Additionally, locations under vegetation and on topographic ridges experienced lower maximum and higher minimum soil temperatures. The large differences in climate we observed over small distances will likely lead to complex range shift dynamics and could buffer species from the negative effects of climate change. PMID:23762277

3D Microstructure Effects in Ni-YSZ Anodes: Influence of TPB Lengths on the Electrochemical Performance.

PubMed

Pecho, Omar M; Mai, Andreas; Münch, Beat; Hocker, Thomas; Flatt, Robert J; Holzer, Lorenz

2015-10-21

3D microstructure-performance relationships in Ni-YSZ anodes for electrolyte-supported cells are investigated in terms of the correlation between the triple phase boundary (TPB) length and polarization resistance ( R pol ). Three different Ni-YSZ anodes of varying microstructure are subjected to eight reduction-oxidation (redox) cycles at 950 °C. In general the TPB lengths correlate with anode performance . However, the quantitative results also show that there is no simplistic relationship between TPB and R pol . The degradation mechanism strongly depends on the initial microstructure. Finer microstructures exhibit lower degradation rates of TPB and R pol . In fine microstructures, TPB loss is found to be due to Ni coarsening, while in coarse microstructures reduction of active TPB results mainly from loss of YSZ percolation. The latter is attributed to weak bottlenecks associated with lower sintering activity of the coarse YSZ. The coarse anode suffers from complete loss of YSZ connectivity and associated drop of TPB active by 93%. Surprisingly, this severe microstructure degradation did not lead to electrochemical failure. Mechanistic scenarios are discussed for different anode microstructures. These scenarios are based on a model for coupled charge transfer and transport, which allows using TPB and effective properties as input. The mechanistic scenarios describe the microstructure influence on current distributions, which explains the observed complex relationship between TPB lengths and anode performances. The observed loss of YSZ percolation in the coarse anode is not detrimental because the electrochemical activity is concentrated in a narrow active layer. The anode performance can be predicted reliably if the volume-averaged properties (TPB active , effective ionic conductivity) are corrected for the so-called short-range effect, which is particularly important in cases with a narrow active layer.

Thermodynamic and structural signatures of water-driven methane-methane attraction in coarse-grained mW water.

PubMed

Song, Bin; Molinero, Valeria

2013-08-07

Hydrophobic interactions are responsible for water-driven processes such as protein folding and self-assembly of biomolecules. Microscopic theories and molecular simulations have been used to study association of a pair of methanes in water, the paradigmatic example of hydrophobic attraction, and determined that entropy is the driving force for the association of the methane pair, while the enthalpy disfavors it. An open question is to which extent coarse-grained water models can still produce correct thermodynamic and structural signatures of hydrophobic interaction. In this work, we investigate the hydrophobic interaction between a methane pair in water at temperatures from 260 to 340 K through molecular dynamics simulations with the coarse-grained monatomic water model mW. We find that the coarse-grained model correctly represents the free energy of association of the methane pair, the temperature dependence of free energy, and the positive change in entropy and enthalpy upon association. We investigate the relationship between thermodynamic signatures and structural order of water through the analysis of the spatial distribution of the density, energy, and tetrahedral order parameter Qt of water. The simulations reveal an enhancement of tetrahedral order in the region between the first and second hydration shells of the methane molecules. The increase in tetrahedral order, however, is far from what would be expected for a clathrate-like or ice-like shell around the solutes. This work shows that the mW water model reproduces the key signatures of hydrophobic interaction without long ranged electrostatics or the need to be re-parameterized for different thermodynamic states. These characteristics, and its hundred-fold increase in efficiency with respect to atomistic models, make mW a promising water model for studying water-driven hydrophobic processes in more complex systems.

Effects of Coarse Legacy Sediment on Rivers of the Ozark Plateaus and Implications for Native Mussel Fauna

NASA Astrophysics Data System (ADS)

Erwin, S. O.; Jacobson, R. B.; Eric, A. B.; Jones, J. C.; Anderson, B. W.

2015-12-01

Perturbations to sediment regimes due to anthropogenic activities may have long lasting effects, especially in systems dominated by coarse sediment where travel times are relatively long. Effectively evaluating management alternatives requires understanding the future trajectory of river response at both the river network and reach scales. The Ozark Plateaus physiographic province is a montane region in the interior US composed primarily of Paleozoic sedimentary rock. Historic land-use practices around the turn of the last century accelerated delivery of coarse sediment to river channels. Effects of this legacy sediment persist in two national parks, Ozark National Scenic Riverways, MO and Buffalo National River, AR, and are of special concern for management of native mussel fauna. These species require stable habitat, yet they occupy inherently dynamic environments: alluvial rivers. At the river-network scale, analysis of historical data reveals the signature of sediment waves moving through river networks in the Ozarks. Channel planform alternates between relatively stable, straight reaches, and wider, multithread reaches which have been more dynamic over the past several decades. These alternate planform configurations route and store sediment differently, and translate into different patterns of bed stability at the reach scale, which in turn affects the distribution and availability of habitat for native biota. Geomorphic mapping and hydrodynamic modeling reveal the complex relations between planform (in)stability, flow dynamics, bed mobility, and aquatic habitat in systems responding to increased sediment supply. Reaches that have a more dynamic planform may provide more hydraulic refugia and habitat heterogeneity compared to stable, homogeneous reaches. This research provides new insights that may inform management of sediment and mussel habitat in rivers subject to coarse legacy sediment.

3D Microstructure Effects in Ni-YSZ Anodes: Influence of TPB Lengths on the Electrochemical Performance

PubMed Central

Pecho, Omar M.; Mai, Andreas; Münch, Beat; Hocker, Thomas; Flatt, Robert J.; Holzer, Lorenz

2015-01-01

3D microstructure-performance relationships in Ni-YSZ anodes for electrolyte-supported cells are investigated in terms of the correlation between the triple phase boundary (TPB) length and polarization resistance (Rpol). Three different Ni-YSZ anodes of varying microstructure are subjected to eight reduction-oxidation (redox) cycles at 950 °C. In general the TPB lengths correlate with anode performance. However, the quantitative results also show that there is no simplistic relationship between TPB and Rpol. The degradation mechanism strongly depends on the initial microstructure. Finer microstructures exhibit lower degradation rates of TPB and Rpol. In fine microstructures, TPB loss is found to be due to Ni coarsening, while in coarse microstructures reduction of active TPB results mainly from loss of YSZ percolation. The latter is attributed to weak bottlenecks associated with lower sintering activity of the coarse YSZ. The coarse anode suffers from complete loss of YSZ connectivity and associated drop of TPBactive by 93%. Surprisingly, this severe microstructure degradation did not lead to electrochemical failure. Mechanistic scenarios are discussed for different anode microstructures. These scenarios are based on a model for coupled charge transfer and transport, which allows using TPB and effective properties as input. The mechanistic scenarios describe the microstructure influence on current distributions, which explains the observed complex relationship between TPB lengths and anode performances. The observed loss of YSZ percolation in the coarse anode is not detrimental because the electrochemical activity is concentrated in a narrow active layer. The anode performance can be predicted reliably if the volume-averaged properties (TPBactive, effective ionic conductivity) are corrected for the so-called short-range effect, which is particularly important in cases with a narrow active layer. PMID:28793624

Attention theory and training research

NASA Technical Reports Server (NTRS)

Connelly, James G., Jr.; Wickens, Christopher D.; Lintern, Gavan; Harwood, Kelly

1987-01-01

This study used elements of attention theory as a methodological basis to decompose a complex training task in order to improve training efficiency. The complex task was a microcomputer flight simulation where subjects were required to control the stability of their own helicopter while acquiring and engaging enemy helicopers in a threat enviroment. Subjects were divided into whole-task, part-task, and part/open loop adaptive task groups in a transfer of training paradigm. The effect of reducing mental workload at the early stages of learning was examined with respect to the degree that subordinate elements of the complex task could be automated through practice of consistent, learnable stimulus-response relationships. Results revealed trends suggesting the benefit of isolating consistently mapped sub-tasks for part-task training and the presence of a time-sharing skill over and above the skill required for the separate subtasks.

Limited Effects of Variable-Retention Harvesting on Fungal Communities Decomposing Fine Roots in Coastal Temperate Rainforests.

PubMed

Philpott, Timothy J; Barker, Jason S; Prescott, Cindy E; Grayston, Sue J

2018-02-01

Fine root litter is the principal source of carbon stored in forest soils and a dominant source of carbon for fungal decomposers. Differences in decomposer capacity between fungal species may be important determinants of fine-root decomposition rates. Variable-retention harvesting (VRH) provides refuge for ectomycorrhizal fungi, but its influence on fine-root decomposers is unknown, as are the effects of functional shifts in these fungal communities on carbon cycling. We compared fungal communities decomposing fine roots (in litter bags) under VRH, clear-cut, and uncut stands at two sites (6 and 13 years postharvest) and two decay stages (43 days and 1 year after burial) in Douglas fir forests in coastal British Columbia, Canada. Fungal species and guilds were identified from decomposed fine roots using high-throughput sequencing. Variable retention had short-term effects on β-diversity; harvest treatment modified the fungal community composition at the 6-year-postharvest site, but not at the 13-year-postharvest site. Ericoid and ectomycorrhizal guilds were not more abundant under VRH, but stand age significantly structured species composition. Guild composition varied by decay stage, with ruderal species later replaced by saprotrophs and ectomycorrhizae. Ectomycorrhizal abundance on decomposing fine roots may partially explain why fine roots typically decompose more slowly than surface litter. Our results indicate that stand age structures fine-root decomposers but that decay stage is more important in structuring the fungal community than shifts caused by harvesting. The rapid postharvest recovery of fungal communities decomposing fine roots suggests resiliency within this community, at least in these young regenerating stands in coastal British Columbia. IMPORTANCE Globally, fine roots are a dominant source of carbon in forest soils, yet the fungi that decompose this material and that drive the sequestration or respiration of this carbon remain largely uncharacterized. Fungi vary in their capacity to decompose plant litter, suggesting that fungal community composition is an important determinant of decomposition rates. Variable-retention harvesting is a forestry practice that modifies fungal communities by providing refuge for ectomycorrhizal fungi. We evaluated the effects of variable retention and clear-cut harvesting on fungal communities decomposing fine roots at two sites (6 and 13 years postharvest), at two decay stages (43 days and 1 year), and in uncut stands in temperate rainforests. Harvesting impacts on fungal community composition were detected only after 6 years after harvest. We suggest that fungal community composition may be an important factor that reduces fine-root decomposition rates relative to those of above-ground plant litter, which has important consequences for forest carbon cycling. Copyright © 2018 American Society for Microbiology.

Studying the dynamics of interbeat interval time series of healthy and congestive heart failure subjects using scale based symbolic entropy analysis

PubMed Central

Awan, Imtiaz; Aziz, Wajid; Habib, Nazneen; Alowibdi, Jalal S.; Saeed, Sharjil; Nadeem, Malik Sajjad Ahmed; Shah, Syed Ahsin Ali

2018-01-01

Considerable interest has been devoted for developing a deeper understanding of the dynamics of healthy biological systems and how these dynamics are affected due to aging and disease. Entropy based complexity measures have widely been used for quantifying the dynamics of physical and biological systems. These techniques have provided valuable information leading to a fuller understanding of the dynamics of these systems and underlying stimuli that are responsible for anomalous behavior. The single scale based traditional entropy measures yielded contradictory results about the dynamics of real world time series data of healthy and pathological subjects. Recently the multiscale entropy (MSE) algorithm was introduced for precise description of the complexity of biological signals, which was used in numerous fields since its inception. The original MSE quantified the complexity of coarse-grained time series using sample entropy. The original MSE may be unreliable for short signals because the length of the coarse-grained time series decreases with increasing scaling factor τ, however, MSE works well for long signals. To overcome the drawback of original MSE, various variants of this method have been proposed for evaluating complexity efficiently. In this study, we have proposed multiscale normalized corrected Shannon entropy (MNCSE), in which instead of using sample entropy, symbolic entropy measure NCSE has been used as an entropy estimate. The results of the study are compared with traditional MSE. The effectiveness of the proposed approach is demonstrated using noise signals as well as interbeat interval signals from healthy and pathological subjects. The preliminary results of the study indicate that MNCSE values are more stable and reliable than original MSE values. The results show that MNCSE based features lead to higher classification accuracies in comparison with the MSE based features. PMID:29771977

Towards the understanding of network information processing in biology

NASA Astrophysics Data System (ADS)

Singh, Vijay

Living organisms perform incredibly well in detecting a signal present in the environment. This information processing is achieved near optimally and quite reliably, even though the sources of signals are highly variable and complex. The work in the last few decades has given us a fair understanding of how individual signal processing units like neurons and cell receptors process signals, but the principles of collective information processing on biological networks are far from clear. Information processing in biological networks, like the brain, metabolic circuits, cellular-signaling circuits, etc., involves complex interactions among a large number of units (neurons, receptors). The combinatorially large number of states such a system can exist in makes it impossible to study these systems from the first principles, starting from the interactions between the basic units. The principles of collective information processing on such complex networks can be identified using coarse graining approaches. This could provide insights into the organization and function of complex biological networks. Here I study models of biological networks using continuum dynamics, renormalization, maximum likelihood estimation and information theory. Such coarse graining approaches identify features that are essential for certain processes performed by underlying biological networks. We find that long-range connections in the brain allow for global scale feature detection in a signal. These also suppress the noise and remove any gaps present in the signal. Hierarchical organization with long-range connections leads to large-scale connectivity at low synapse numbers. Time delays can be utilized to separate a mixture of signals with temporal scales. Our observations indicate that the rules in multivariate signal processing are quite different from traditional single unit signal processing.

A coarse grained molecular dynamics simulation study on the structural properties of carbon nanotube-dendrimer composites.

PubMed

Kavyani, Sajjad; Dadvar, Mitra; Modarress, Hamid; Amjad-Iranagh, Sepideh

2018-04-25

By employing coarse grained (CG) molecular dynamics (MD) simulation, the effect of the size and hydrophilic/hydrophobic properties of the interior/exterior structures of the dendrimers in carbon nanotube (CNT)-dendrimer composites has been studied, to find a stable composite with high solubility in water and the capability to be used in drug delivery applications. For this purpose, composites consisting of core-shell dendrimer complexes including: [PPI{core}-PAMAM{shell}], [PAMAM{core}-polyethyleneglycol (PEG){shell}] and [PAMAM{core}-fattyacid (FTA){shell}] were constructed. A new CG model for the fatty acid (FTA) molecules as functionalized to the dendrimer was developed, which, unlike the previous models, could generate the structural conformations of the FTA properly. The obtained results indicated that the dendrimer complexes with short FTA chains can form stable composites with the CNT. Also, it was found that the pristine PAMAM and PPI-PAMAM with small PPI, and PAMAM-PEG dendrimers with short PEG chains, can distribute their chains into the water medium and interact with the CNT efficiently, to form a stable water-soluble CNT-dendrimer composite. The results demonstrated that the structural difference between the interior and exterior of a core-shell dendrimer complex can prevent the core and the interior layers of the dendrimer complex from interacting with the CNT. An overall analysis of the results manifested that the CNT-PAMAM:4-PEG:4 is the most stable composite, due to strong binding of the dendrimer with the CNT while also having high solubility in water, and its core retains its structure properly and unchanged, suitable for encapsulating drugs in the targeted delivery applications.

Studying the dynamics of interbeat interval time series of healthy and congestive heart failure subjects using scale based symbolic entropy analysis.

PubMed

Awan, Imtiaz; Aziz, Wajid; Shah, Imran Hussain; Habib, Nazneen; Alowibdi, Jalal S; Saeed, Sharjil; Nadeem, Malik Sajjad Ahmed; Shah, Syed Ahsin Ali

2018-01-01

Considerable interest has been devoted for developing a deeper understanding of the dynamics of healthy biological systems and how these dynamics are affected due to aging and disease. Entropy based complexity measures have widely been used for quantifying the dynamics of physical and biological systems. These techniques have provided valuable information leading to a fuller understanding of the dynamics of these systems and underlying stimuli that are responsible for anomalous behavior. The single scale based traditional entropy measures yielded contradictory results about the dynamics of real world time series data of healthy and pathological subjects. Recently the multiscale entropy (MSE) algorithm was introduced for precise description of the complexity of biological signals, which was used in numerous fields since its inception. The original MSE quantified the complexity of coarse-grained time series using sample entropy. The original MSE may be unreliable for short signals because the length of the coarse-grained time series decreases with increasing scaling factor τ, however, MSE works well for long signals. To overcome the drawback of original MSE, various variants of this method have been proposed for evaluating complexity efficiently. In this study, we have proposed multiscale normalized corrected Shannon entropy (MNCSE), in which instead of using sample entropy, symbolic entropy measure NCSE has been used as an entropy estimate. The results of the study are compared with traditional MSE. The effectiveness of the proposed approach is demonstrated using noise signals as well as interbeat interval signals from healthy and pathological subjects. The preliminary results of the study indicate that MNCSE values are more stable and reliable than original MSE values. The results show that MNCSE based features lead to higher classification accuracies in comparison with the MSE based features.

Rule-based spatial modeling with diffusing, geometrically constrained molecules.

PubMed

Gruenert, Gerd; Ibrahim, Bashar; Lenser, Thorsten; Lohel, Maiko; Hinze, Thomas; Dittrich, Peter

2010-06-07

We suggest a new type of modeling approach for the coarse grained, particle-based spatial simulation of combinatorially complex chemical reaction systems. In our approach molecules possess a location in the reactor as well as an orientation and geometry, while the reactions are carried out according to a list of implicitly specified reaction rules. Because the reaction rules can contain patterns for molecules, a combinatorially complex or even infinitely sized reaction network can be defined. For our implementation (based on LAMMPS), we have chosen an already existing formalism (BioNetGen) for the implicit specification of the reaction network. This compatibility allows to import existing models easily, i.e., only additional geometry data files have to be provided. Our simulations show that the obtained dynamics can be fundamentally different from those simulations that use classical reaction-diffusion approaches like Partial Differential Equations or Gillespie-type spatial stochastic simulation. We show, for example, that the combination of combinatorial complexity and geometric effects leads to the emergence of complex self-assemblies and transportation phenomena happening faster than diffusion (using a model of molecular walkers on microtubules). When the mentioned classical simulation approaches are applied, these aspects of modeled systems cannot be observed without very special treatment. Further more, we show that the geometric information can even change the organizational structure of the reaction system. That is, a set of chemical species that can in principle form a stationary state in a Differential Equation formalism, is potentially unstable when geometry is considered, and vice versa. We conclude that our approach provides a new general framework filling a gap in between approaches with no or rigid spatial representation like Partial Differential Equations and specialized coarse-grained spatial simulation systems like those for DNA or virus capsid self-assembly.

Rule-based spatial modeling with diffusing, geometrically constrained molecules

PubMed Central

2010-01-01

Background We suggest a new type of modeling approach for the coarse grained, particle-based spatial simulation of combinatorially complex chemical reaction systems. In our approach molecules possess a location in the reactor as well as an orientation and geometry, while the reactions are carried out according to a list of implicitly specified reaction rules. Because the reaction rules can contain patterns for molecules, a combinatorially complex or even infinitely sized reaction network can be defined. For our implementation (based on LAMMPS), we have chosen an already existing formalism (BioNetGen) for the implicit specification of the reaction network. This compatibility allows to import existing models easily, i.e., only additional geometry data files have to be provided. Results Our simulations show that the obtained dynamics can be fundamentally different from those simulations that use classical reaction-diffusion approaches like Partial Differential Equations or Gillespie-type spatial stochastic simulation. We show, for example, that the combination of combinatorial complexity and geometric effects leads to the emergence of complex self-assemblies and transportation phenomena happening faster than diffusion (using a model of molecular walkers on microtubules). When the mentioned classical simulation approaches are applied, these aspects of modeled systems cannot be observed without very special treatment. Further more, we show that the geometric information can even change the organizational structure of the reaction system. That is, a set of chemical species that can in principle form a stationary state in a Differential Equation formalism, is potentially unstable when geometry is considered, and vice versa. Conclusions We conclude that our approach provides a new general framework filling a gap in between approaches with no or rigid spatial representation like Partial Differential Equations and specialized coarse-grained spatial simulation systems like those for DNA or virus capsid self-assembly. PMID:20529264

The Cobalt cyclo‐P4 Sandwich Complex and Its Role in the Formation of Polyphosphorus Compounds

PubMed Central

Dielmann, Fabian; Timoshkin, Alexey; Piesch, Martin; Balázs, Gábor

2017-01-01

Abstract A synthetic approach to the sandwich complex [Cp′′′Co(η4‐P4)] (2) containing a cyclo‐P4 ligand as an end‐deck was developed. Complex 2 is the missing homologue in the series of first‐row cyclo‐Pn sandwich complexes, and shows a unique tendency to dimerize in solution to form two isomeric P8 complexes [(Cp′′′Co)2(μ,η4:η2:η1‐P8)] (3 and 4). Reactivity studies indicate that 2 and 3 react with further [Cp′′′Co] fragments to give [(Cp′′′Co)2(μ,η2:η2‐P2)2] (5) and [(Cp′′′Co)3P8] (6), respectively. Furthermore, complexes 2, 3, and 4 thermally decompose forming 5, 6, and the P12 complex [(Cp′′′Co)3P12] (7). DFT calculations on the P4 activation process suggest a η3‐P4 Co complex as the key intermediate in the synthesis of 2 as well as in the formation of larger polyphosphorus complexes via a unique oligomerization pathway. PMID:28078794

KOSMOS: a universal morph server for nucleic acids, proteins and their complexes.

PubMed

Seo, Sangjae; Kim, Moon Ki

2012-07-01

KOSMOS is the first online morph server to be able to address the structural dynamics of DNA/RNA, proteins and even their complexes, such as ribosomes. The key functions of KOSMOS are the harmonic and anharmonic analyses of macromolecules. In the harmonic analysis, normal mode analysis (NMA) based on an elastic network model (ENM) is performed, yielding vibrational modes and B-factor calculations, which provide insight into the potential biological functions of macromolecules based on their structural features. Anharmonic analysis involving elastic network interpolation (ENI) is used to generate plausible transition pathways between two given conformations by optimizing a topology-oriented cost function that guarantees a smooth transition without steric clashes. The quality of the computed pathways is evaluated based on their various facets, including topology, energy cost and compatibility with the NMA results. There are also two unique features of KOSMOS that distinguish it from other morph servers: (i) the versatility in the coarse-graining methods and (ii) the various connection rules in the ENM. The models enable us to analyze macromolecular dynamics with the maximum degrees of freedom by combining a variety of ENMs from full-atom to coarse-grained, backbone and hybrid models with one connection rule, such as distance-cutoff, number-cutoff or chemical-cutoff. KOSMOS is available at http://bioengineering.skku.ac.kr/kosmos.

Fast and reliable prediction of domain-peptide binding affinity using coarse-grained structure models.

PubMed

Tian, Feifei; Tan, Rui; Guo, Tailin; Zhou, Peng; Yang, Li

2013-07-01

Domain-peptide recognition and interaction are fundamentally important for eukaryotic signaling and regulatory networks. It is thus essential to quantitatively infer the binding stability and specificity of such interaction based upon large-scale but low-accurate complex structure models which could be readily obtained from sophisticated molecular modeling procedure. In the present study, a new method is described for the fast and reliable prediction of domain-peptide binding affinity with coarse-grained structure models. This method is designed to tolerate strong random noises involved in domain-peptide complex structures and uses statistical modeling approach to eliminate systematic bias associated with a group of investigated samples. As a paradigm, this method was employed to model and predict the binding behavior of various peptides to four evolutionarily unrelated peptide-recognition domains (PRDs), i.e. human amph SH3, human nherf PDZ, yeast syh GYF and yeast bmh 14-3-3, and moreover, we explored the molecular mechanism and biological implication underlying the binding of cognate and noncognate peptide ligands to their domain receptors. It is expected that the newly proposed method could be further used to perform genome-wide inference of domain-peptide binding at three-dimensional structure level. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Coarse Grained Model for Biological Simulations: Recent Refinements and Validation

PubMed Central

Vicatos, Spyridon; Rychkova, Anna; Mukherjee, Shayantani; Warshel, Arieh

2014-01-01

Exploring the free energy landscape of proteins and modeling the corresponding functional aspects presents a major challenge for computer simulation approaches. This challenge is due to the complexity of the landscape and the enormous computer time needed for converging simulations. The use of various simplified coarse grained (CG) models offers an effective way of sampling the landscape, but most current models are not expected to give a reliable description of protein stability and functional aspects. The main problem is associated with insufficient focus on the electrostatic features of the model. In this respect our recent CG model offers significant advantage as it has been refined while focusing on its electrostatic free energy. Here we review the current state of our model, describing recent refinement, extensions and validation studies while focusing on demonstrating key applications. These include studies of protein stability, extending the model to include membranes and electrolytes and electrodes as well as studies of voltage activated proteins, protein insertion trough the translocon, the action of molecular motors and even the coupling of the stalled ribosome and the translocon. Our example illustrates the general potential of our approach in overcoming major challenges in studies of structure function correlation in proteins and large macromolecular complexes. PMID:25050439

Our World without Decomposers: How Scary!

ERIC Educational Resources Information Center

Spring, Patty; Harr, Natalie

2014-01-01

Bugs, slugs, bacteria, and fungi are decomposers at the heart of every ecosystem. Fifth graders at Dodge Intermediate School in Twinsburg, Ohio, ventured outdoors to learn about the necessity of these amazing organisms. With the help of a naturalist, students explored their local park and discovered the wonder of decomposers and their…

Characterizing and contrasting instream and riparian coarse wood in western Montana basins

Treesearch

Michael K. Young; Ethan A. Mace; Eric T. Ziegler; Elaine K. Sutherland

2006-01-01

The importance of coarse wood to aquatic biota and stream channel structure is widely recognized, yet characterizations of large-scale patterns in coarse wood dimensions and loads are rare. To address these issues, we censused instream coarse wood ( 2 m long and 10 cm minimum diameter) and sampled riparian coarse wood and channel characteristics in and along 13 streams...

Changes in Moisture Flux over the Tibetan Plateau during 1979-2011: Insights from a High Resolution Simulation

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

Gao, Yanhong; Leung, Lai-Yung R.; Zhang, Yongxin

2015-05-15

Net precipitation (precipitation minus evapotranspiration, P-E) changes between 1979 and 2011 from a high resolution regional climate simulation and its reanalysis forcing are analyzed over the Tibet Plateau (TP) and compared to the global land data assimilation system (GLDAS) product. The high resolution simulation better resolves precipitation changes than its coarse resolution forcing, which contributes dominantly to the improved P-E change in the regional simulation compared to the global reanalysis. Hence, the former may provide better insights about the drivers of P-E changes. The mechanism behind the P-E changes is explored by decomposing the column integrated moisture flux convergence intomore » thermodynamic, dynamic, and transient eddy components. High-resolution climate simulation improves the spatial pattern of P-E changes over the best available global reanalysis. High-resolution climate simulation also facilitates new and substantial findings regarding the role of thermodynamics and transient eddies in P-E changes reflected in observed changes in major river basins fed by runoff from the TP. The analysis revealed the contrasting convergence/divergence changes between the northwestern and southeastern TP and feedback through latent heat release as an important mechanism leading to the mean P-E changes in the TP.« less

Factors controlling bark decomposition and its role in wood decomposition in five tropical tree species

PubMed Central

Dossa, Gbadamassi G. O.; Paudel, Ekananda; Cao, Kunfang; Schaefer, Douglas; Harrison, Rhett D.

2016-01-01

Organic matter decomposition represents a vital ecosystem process by which nutrients are made available for plant uptake and is a major flux in the global carbon cycle. Previous studies have investigated decomposition of different plant parts, but few considered bark decomposition or its role in decomposition of wood. However, bark can comprise a large fraction of tree biomass. We used a common litter-bed approach to investigate factors affecting bark decomposition and its role in wood decomposition for five tree species in a secondary seasonal tropical rain forest in SW China. For bark, we implemented a litter bag experiment over 12 mo, using different mesh sizes to investigate effects of litter meso- and macro-fauna. For wood, we compared the decomposition of branches with and without bark over 24 mo. Bark in coarse mesh bags decomposed 1.11–1.76 times faster than bark in fine mesh bags. For wood decomposition, responses to bark removal were species dependent. Three species with slow wood decomposition rates showed significant negative effects of bark-removal, but there was no significant effect in the other two species. Future research should also separately examine bark and wood decomposition, and consider bark-removal experiments to better understand roles of bark in wood decomposition. PMID:27698461

The Utility of Decomposition and Associated Microbial Parameters to Assess Changes in Stream Ecosystems due to Eutrophication

NASA Astrophysics Data System (ADS)

Gulis, V.; Ferreira, V. J.; Graca, M. A.

2005-05-01

Traditional approaches to assess stream ecosystem health rely on structural parameters, e.g. a variety of biotic indices. The goal of the Europe-wide RivFunction project is to develop methodology that uses functional parameters (e.g. plant litter decomposition) to this end. Here we report on decomposition experiments carried out in Portugal in five pairs of streams that differed in dissolved inorganic nutrients. On average, decomposition rates of alder and oak leaves were 2.8 and 1.4 times higher in high nutrient streams in coarse and fine mesh bags, respectively, than in corresponding reference streams. Breakdown rate correlated better with stream water SRP concentration rather than TIN. Fungal biomass and sporulation rates of aquatic hyphomycetes associated with decomposing leaves were stimulated by higher nutrient levels. Both fungal parameters measured at very early stages of decomposition (e.g. days 7-13) correlated well with overall decomposition rates. Eutrophication had no significant effect on shredder abundances in leaf bags but species richness was higher in disturbed streams. Decomposition is a key functional parameter in streams integrating many other variables and can be useful in assessing stream ecosystem health. We also argue that because decomposition is often controlled by fungal activity, microbial parameters can also be useful in bioassessment.

Angular-Rate Estimation Using Delayed Quaternion Measurements

NASA Technical Reports Server (NTRS)

Azor, R.; Bar-Itzhack, I. Y.; Harman, R. R.

1999-01-01

This paper presents algorithms for estimating the angular-rate vector of satellites using quaternion measurements. Two approaches are compared one that uses differentiated quaternion measurements to yield coarse rate measurements, which are then fed into two different estimators. In the other approach the raw quaternion measurements themselves are fed directly into the two estimators. The two estimators rely on the ability to decompose the non-linear part of the rotas rotational dynamics equation of a body into a product of an angular-rate dependent matrix and the angular-rate vector itself. This non unique decomposition, enables the treatment of the nonlinear spacecraft (SC) dynamics model as a linear one and, thus, the application of a PseudoLinear Kalman Filter (PSELIKA). It also enables the application of a special Kalman filter which is based on the use of the solution of the State Dependent Algebraic Riccati Equation (SDARE) in order to compute the gain matrix and thus eliminates the need to compute recursively the filter covariance matrix. The replacement of the rotational dynamics by a simple Markov model is also examined. In this paper special consideration is given to the problem of delayed quaternion measurements. Two solutions to this problem are suggested and tested. Real Rossi X-Ray Timing Explorer (RXTE) data is used to test these algorithms, and results are presented.

A stochastic approach to noise modeling for barometric altimeters.

PubMed

Sabatini, Angelo Maria; Genovese, Vincenzo

2013-11-18

The question whether barometric altimeters can be applied to accurately track human motions is still debated, since their measurement performance are rather poor due to either coarse resolution or drifting behavior problems. As a step toward accurate short-time tracking of changes in height (up to few minutes), we develop a stochastic model that attempts to capture some statistical properties of the barometric altimeter noise. The barometric altimeter noise is decomposed in three components with different physical origin and properties: a deterministic time-varying mean, mainly correlated with global environment changes, and a first-order Gauss-Markov (GM) random process, mainly accounting for short-term, local environment changes, the effects of which are prominent, respectively, for long-time and short-time motion tracking; an uncorrelated random process, mainly due to wideband electronic noise, including quantization noise. Autoregressive-moving average (ARMA) system identification techniques are used to capture the correlation structure of the piecewise stationary GM component, and to estimate its standard deviation, together with the standard deviation of the uncorrelated component. M-point moving average filters used alone or in combination with whitening filters learnt from ARMA model parameters are further tested in few dynamic motion experiments and discussed for their capability of short-time tracking small-amplitude, low-frequency motions.

Sources of organic compounds in fine soil and sand particles during winter in the metropolitan area of Riyadh, Saudi Arabia.

PubMed

Rushdi, Ahmed I; Al-Mutlaq, Khalid; Simoneit, Bernd R T

2005-11-01

Major advances have been made in molecular marker analysis to distinguish between natural and anthropogenic organic matter inputs to the atmosphere. Resuspension of soil and sand by wind is one of the major mechanisms that produces particle dusts in the atmosphere. Soil and sand samples from the Riyadh area were collected in winter 2002, sieved to remove coarse particles and extracted with a mixture of dichloromethane and methanol (3:1, v:v). The total extracts were analyzed by gas chromatography-mass spectrometry in order to characterize the contents and identify the potential sources of the organic components. The major organic compounds of these extracts were derived from natural biogenic and anthropogenic sources. Organic compounds from natural sources, mainly vegetation, were major in samples from outside the city of Riyadh and included n-alkanes, n-alkanoic acids, n- alkanols, methyl alkanoates, and sterols. Anthropogenic inputs were significant in the fine particles of soil and sand samples collected from populated areas of the city. They consisted mainly of n-alkanes, hopanes, UCM (from vehicular emissions), and plasticizers (from discarded plastics, e.g., shopping bags). Carbohydrates had high concentrations in all samples and indicate sources from decomposed cellulose fibers and/or the presence of viable microbiota such as bacteria and fungi.

Fast Detection of Material Deformation through Structural Dissimilarity

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

Ushizima, Daniela; Perciano, Talita; Parkinson, Dilworth

2015-10-29

Designing materials that are resistant to extreme temperatures and brittleness relies on assessing structural dynamics of samples. Algorithms are critically important to characterize material deformation under stress conditions. Here, we report on our design of coarse-grain parallel algorithms for image quality assessment based on structural information and on crack detection of gigabyte-scale experimental datasets. We show how key steps can be decomposed into distinct processing flows, one based on structural similarity (SSIM) quality measure, and another on spectral content. These algorithms act upon image blocks that fit into memory, and can execute independently. We discuss the scientific relevance of themore » problem, key developments, and decomposition of complementary tasks into separate executions. We show how to apply SSIM to detect material degradation, and illustrate how this metric can be allied to spectral analysis for structure probing, while using tiled multi-resolution pyramids stored in HDF5 chunked multi-dimensional arrays. Results show that the proposed experimental data representation supports an average compression rate of 10X, and data compression scales linearly with the data size. We also illustrate how to correlate SSIM to crack formation, and how to use our numerical schemes to enable fast detection of deformation from 3D datasets evolving in time.« less

Factors controlling bark decomposition and its role in wood decomposition in five tropical tree species.

PubMed

Dossa, Gbadamassi G O; Paudel, Ekananda; Cao, Kunfang; Schaefer, Douglas; Harrison, Rhett D

2016-10-04

Organic matter decomposition represents a vital ecosystem process by which nutrients are made available for plant uptake and is a major flux in the global carbon cycle. Previous studies have investigated decomposition of different plant parts, but few considered bark decomposition or its role in decomposition of wood. However, bark can comprise a large fraction of tree biomass. We used a common litter-bed approach to investigate factors affecting bark decomposition and its role in wood decomposition for five tree species in a secondary seasonal tropical rain forest in SW China. For bark, we implemented a litter bag experiment over 12 mo, using different mesh sizes to investigate effects of litter meso- and macro-fauna. For wood, we compared the decomposition of branches with and without bark over 24 mo. Bark in coarse mesh bags decomposed 1.11-1.76 times faster than bark in fine mesh bags. For wood decomposition, responses to bark removal were species dependent. Three species with slow wood decomposition rates showed significant negative effects of bark-removal, but there was no significant effect in the other two species. Future research should also separately examine bark and wood decomposition, and consider bark-removal experiments to better understand roles of bark in wood decomposition.

Plant stimulation of soil microbial community succession: how sequential expression mediates soil carbon stabilization and turnover

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

Firestone, Mary

2015-03-31

It is now understood that most plant C is utilized or transformed by soil microorganisms en route to stabilization. Hence the composition of microbial communities that mediate decomposition and transformation of root C is critical, as are the metabolic capabilities of these communities. The change in composition and function of the C-transforming microbial communities over time in effect defines the biological component of soil C stabilization. Our research was designed to test 2 general hypotheses; the first two hypotheses are discussed first; H1: Root-exudate interactions with soil microbial populations results in the expression of enzymatic capacities for macromolecular, complex carbonmore » decomposition; and H2: Microbial communities surrounding roots undergo taxonomic succession linked to functional gene activities as roots grow, mature, and decompose in soil. Over the term of the project we made significant progress in 1) quantifying the temporal pattern of root interactions with the soil decomposing community and 2) characterizing the role of root exudates in mediating these interactions.« less

Biological decomposition efficiency in different woodland soils.

PubMed

Herlitzius, H

1983-03-01

The decomposition (meaning disappearance) of different leaf types and artificial leaves made from cellulose hydrate foil was studied in three forests - an alluvial forest (Ulmetum), a beech forest on limestone soil (Melico-Fagetum), and a spruce forest in soil overlying limestone bedrock.Fine, medium, and coarse mesh litter bags of special design were used to investigate the roles of abiotic factors, microorganisms, and meso- and macrofauna in effecting decomposition in the three habitats. Additionally, the experimental design was carefully arranged so as to provide information about the effects on decomposition processes of the duration of exposure and the date or moment of exposure. 1. Exposure of litter samples oor 12 months showed: a) Litter enclosed in fine mesh bags decomposed to some 40-44% of the initial amount placed in each of the three forests. Most of this decomposition can be attributed to abiotic factors and microoganisms. b) Litter placed in medium mesh litter bags reduced by ca. 60% in alluvial forest, ca. 50% in beech forest and ca. 44% in spruce forest. c) Litter enclosed in coarse mesh litter bags was reduced by 71% of the initial weights exposed in alluvial and beech forests; in the spruce forest decomposition was no greater than observed with fine and medium mesh litter bags. Clearly, in spruce forest the macrofauna has little or no part to play in effecting decomposition. 2. Sequential month by month exposure of hazel leaves and cellulose hydrate foil in coarse mesh litter bags in all three forests showed that one month of exposure led to only slight material losses, they did occur smallest between March and May, and largest between June and October/November. 3. Coarse mesh litter bags containing either hazel or artificial leaves of cellulose hydrate foil were exposed to natural decomposition processes in December 1977 and subsampled monthly over a period of one year, this series constituted the From-sequence of experiments. Each of the From-sequence samples removed was immediately replaced by a fresh litter bag which was left in place until December 1978, this series constituted the To-sequence of experiments. The results arising from the designated From- and To-sequences showed: a) During the course of one year hazel leaves decomposed completely in alluvial forest, almost completely in beech forest but to only 50% of the initial value in spruce forest. b) Duration of exposure and not the date of exposure is the major controlling influence on decomposition in alluvial forest, a characteristic reflected in the mirror-image courses of the From- and To-sequences curves with respect to the abscissa or time axis. Conversely the date of exposure and not the duration of exposure is the major controlling influence on decomposition in the spruce forest, a characteristic reflected in the mirror-image courses of the From-and To-sequences with respect to the ordinate or axis of percentage decomposition. c) Leaf powder amendment increased the decomposition rate of the hazel and cellulose hydrate leaves in the spruce forest but had no significant effect on their decomposition rate in alluvial and beech forests. It is concluded from this, and other evidence, that litter amendment by leaf fragments of phytophage frass in sites of low biological decomposition activity (eg. spruce) enhances decomposition processes. d) The time course of hazel leaf decomposition in both alluvial and beech forest is sigmoidal. Three s-phases are distinguished and correspond to the activity of microflora/microfauna, mesofauna/macrofauna, and then microflora/microfauna again. In general, the sigmoidal pattern of the curve can be considered valid for all decomposition processes occurring in terrestrial situations. It is contended that no decomposition (=disappearance) curve actually follows an e-type exponential function. A logarithmic linear regression can be constructed from the sigmoid curve data and although this facilitates inter-system comparisons it does not clearly express the dynamics of decomposition. 4. The course of the curve constructed from information about the standard deviations of means derived from the From- and To-sequence data does reflect the dynamics of litter decomposition. The three s-phases can be recognised and by comparing the actual From-sequence deviation curve with a mirror inversion representation of the To-sequence curve it is possible to determine whether decomposition is primarily controlled by the duration of exposure or the date of exposure. As is the case for hazel leaf decomposition in beech forest intermediate conditions can be readily recognised.

Effect of the ortho-Hydroxyl Groups on a Bipyridine Ligand of Iridium Complexes for the High-Pressure Gas Generation from the Catalytic Decomposition of Formic Acid.

PubMed

Iguchi, Masayuki; Zhong, Heng; Himeda, Yuichiro; Kawanami, Hajime

2017-12-14

The hydroxyl groups of a 2,2'-bipyridine (bpy) ligand near the metal center activated the catalytic performance of the Ir complex for the dehydrogenation of formic acid at high pressure. The position of the hydroxyl groups on the ligand affected the catalytic durability for the high-pressure H 2 generation through the decomposition of formic acid. The Ir complex with a bipyridine ligand functionalized with para-hydroxyl groups shows a good durability with a constant catalytic activity during the reaction even under high-pressure conditions, whereas deactivation was observed for an Ir complex with a bipyridine ligand with ortho-hydroxyl groups (2). In the presence of high-pressure H 2 , complex 2 decomposed into the ligand and an Ir trihydride complex through the isomerization of the bpy ligand. This work provides the development of a durable catalyst for the high-pressure H 2 production from formic acid. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Technetium and rhenium pentacarbonyl complexes with C₂ and C₁₁ ω-isocyanocarboxylic acid esters.

PubMed

Miroslavov, Alexander E; Polotskii, Yuriy S; Gurzhiy, Vladislav V; Ivanov, Alexander Yu; Lumpov, Alexander A; Tyupina, Margarita Yu; Sidorenko, Georgy V; Tolstoy, Peter M; Maltsev, Daniil A; Suglobov, Dmitry N

2014-08-04

Technetium(I) and rhenium(I) pentacarbonyl complexes with ethyl 2-isocyanoacetate and methyl 11-isocyanoundecanoate, [M(CO)5(CNCH2COOEt)]ClO4 (M = Tc (1) and Re (2)) and [M(CO)5(CN(CH2)10COOMe)]ClO4 (M = Tc (3) and Re (4)), were prepared and characterized by IR, (1)H NMR, and (13)C{(1)H} NMR spectroscopy. The crystal structures of 1 and 2 were determined using single-crystal X-ray diffraction. The kinetics of thermal decarbonylation of technetium complexes 1 and 3 in ethylene glycol was studied by IR spectroscopy. The rate constants and activation parameters of this reaction were determined and compared with those for [Tc(CO)6](+). It was found that rhenium complexes 2 and 4 were stable with respect to thermal decarbonylation. Histidine challenge reaction of complexes 1 and 2 in phosphate buffer was examined by IR spectroscopy. In the presence of histidine, the rhenium pentacarbonyl isocyanide complex partially decomposes to form an unidentified yellow precipitate. Technetium analogue 1 is more stable under these conditions.

Traits determining the digestibility-decomposability relationships in species from Mediterranean rangelands.

PubMed

Bumb, Iris; Garnier, Eric; Coq, Sylvain; Nahmani, Johanne; Del Rey Granado, Maria; Gimenez, Olivier; Kazakou, Elena

2018-03-05

Forage quality for herbivores and litter quality for decomposers are two key plant properties affecting ecosystem carbon and nutrient cycling. Although there is a positive relationship between palatability and decomposition, very few studies have focused on larger vertebrate herbivores while considering links between the digestibility of living leaves and stems and the decomposability of litter and associated traits. The hypothesis tested is that some defences of living organs would reduce their digestibility and, as a consequence, their litter decomposability, through 'afterlife' effects. Additionally in high-fertility conditions the presence of intense herbivory would select for communities dominated by fast-growing plants, which are able to compensate for tissue loss by herbivory, producing both highly digestible organs and easily decomposable litter. Relationships between dry matter digestibility and decomposability were quantified in 16 dominant species from Mediterranean rangelands, which are subject to management regimes that differ in grazing intensity and fertilization. The digestibility and decomposability of leaves and stems were estimated at peak standing biomass, in plots that were either fertilized and intensively grazed or unfertilized and moderately grazed. Several traits were measured on living and senesced organs: fibre content, dry matter content and nitrogen, phosphorus and tannin concentrations. Digestibility was positively related to decomposability, both properties being influenced in the same direction by management regime, organ and growth forms. Digestibility of leaves and stems was negatively related to their fibre concentrations, and positively related to their nitrogen concentration. Decomposability was more strongly related to traits measured on living organs than on litter. Digestibility and decomposition were governed by similar structural traits, in particular fibre concentration, affecting both herbivores and micro-organisms through the afterlife effects. This study contributes to a better understanding of the interspecific relationships between forage quality and litter decomposition in leaves and stems and demonstrates the key role these traits play in the link between plant and soil via herbivory and decomposition. Fibre concentration and dry matter content can be considered as good predictors of both digestibility and decomposability. © The Author(s) 2018. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Systematic and simulation-free coarse graining of homopolymer melts: a relative-entropy-based study.

PubMed

Yang, Delian; Wang, Qiang

2015-09-28

We applied the systematic and simulation-free strategy proposed in our previous work (D. Yang and Q. Wang, J. Chem. Phys., 2015, 142, 054905) to the relative-entropy-based (RE-based) coarse graining of homopolymer melts. RE-based coarse graining provides a quantitative measure of the coarse-graining performance and can be used to select the appropriate analytic functional forms of the pair potentials between coarse-grained (CG) segments, which are more convenient to use than the tabulated (numerical) CG potentials obtained from structure-based coarse graining. In our general coarse-graining strategy for homopolymer melts using the RE framework proposed here, the bonding and non-bonded CG potentials are coupled and need to be solved simultaneously. Taking the hard-core Gaussian thread model (K. S. Schweizer and J. G. Curro, Chem. Phys., 1990, 149, 105) as the original system, we performed RE-based coarse graining using the polymer reference interaction site model theory under the assumption that the intrachain segment pair correlation functions of CG systems are the same as those in the original system, which de-couples the bonding and non-bonded CG potentials and simplifies our calculations (that is, we only calculated the latter). We compared the performance of various analytic functional forms of non-bonded CG pair potential and closures for CG systems in RE-based coarse graining, as well as the structural and thermodynamic properties of original and CG systems at various coarse-graining levels. Our results obtained from RE-based coarse graining are also compared with those from structure-based coarse graining.

Integrated boiler, superheater, and decomposer for sulfuric acid decomposition

DOEpatents

Moore, Robert [Edgewood, NM; Pickard, Paul S [Albuquerque, NM; Parma, Jr., Edward J.; Vernon, Milton E [Albuquerque, NM; Gelbard, Fred [Albuquerque, NM; Lenard, Roger X [Edgewood, NM

2010-01-12

A method and apparatus, constructed of ceramics and other corrosion resistant materials, for decomposing sulfuric acid into sulfur dioxide, oxygen and water using an integrated boiler, superheater, and decomposer unit comprising a bayonet-type, dual-tube, counter-flow heat exchanger with a catalytic insert and a central baffle to increase recuperation efficiency.

Procedures for Decomposing a Redox Reaction into Half-Reaction

ERIC Educational Resources Information Center

Fishtik, Ilie; Berka, Ladislav H.

2005-01-01

A simple algorithm for a complete enumeration of the possible ways a redox reaction (RR) might be uniquely decomposed into half-reactions (HRs) using the response reactions (RERs) formalism is presented. A complete enumeration of the possible ways a RR may be decomposed into HRs is equivalent to a complete enumeration of stoichiometrically…

Adaptive selection and validation of models of complex systems in the presence of uncertainty

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

Farrell-Maupin, Kathryn; Oden, J. T.

This study describes versions of OPAL, the Occam-Plausibility Algorithm in which the use of Bayesian model plausibilities is replaced with information theoretic methods, such as the Akaike Information Criterion and the Bayes Information Criterion. Applications to complex systems of coarse-grained molecular models approximating atomistic models of polyethylene materials are described. All of these model selection methods take into account uncertainties in the model, the observational data, the model parameters, and the predicted quantities of interest. A comparison of the models chosen by Bayesian model selection criteria and those chosen by the information-theoretic criteria is given.

Adaptive selection and validation of models of complex systems in the presence of uncertainty

DOE PAGES

Farrell-Maupin, Kathryn; Oden, J. T.

2017-08-01

This study describes versions of OPAL, the Occam-Plausibility Algorithm in which the use of Bayesian model plausibilities is replaced with information theoretic methods, such as the Akaike Information Criterion and the Bayes Information Criterion. Applications to complex systems of coarse-grained molecular models approximating atomistic models of polyethylene materials are described. All of these model selection methods take into account uncertainties in the model, the observational data, the model parameters, and the predicted quantities of interest. A comparison of the models chosen by Bayesian model selection criteria and those chosen by the information-theoretic criteria is given.

On Design Mining: Coevolution and Surrogate Models.

PubMed

Preen, Richard J; Bull, Larry

2017-01-01

Design mining is the use of computational intelligence techniques to iteratively search and model the attribute space of physical objects evaluated directly through rapid prototyping to meet given objectives. It enables the exploitation of novel materials and processes without formal models or complex simulation. In this article, we focus upon the coevolutionary nature of the design process when it is decomposed into concurrent sub-design-threads due to the overall complexity of the task. Using an abstract, tunable model of coevolution, we consider strategies to sample subthread designs for whole-system testing and how best to construct and use surrogate models within the coevolutionary scenario. Drawing on our findings, we then describe the effective design of an array of six heterogeneous vertical-axis wind turbines.

Segmental Refinement: A Multigrid Technique for Data Locality

DOE PAGES

Adams, Mark F.; Brown, Jed; Knepley, Matt; ...

2016-08-04

In this paper, we investigate a domain decomposed multigrid technique, termed segmental refinement, for solving general nonlinear elliptic boundary value problems. We extend the method first proposed in 1994 by analytically and experimentally investigating its complexity. We confirm that communication of traditional parallel multigrid is eliminated on fine grids, with modest amounts of extra work and storage, while maintaining the asymptotic exactness of full multigrid. We observe an accuracy dependence on the segmental refinement subdomain size, which was not considered in the original analysis. Finally, we present a communication complexity analysis that quantifies the communication costs ameliorated by segmental refinementmore » and report performance results with up to 64K cores on a Cray XC30.« less

[2+2] cycloaddition of 1,3-dienes by visible light photocatalysis.

PubMed

Hurtley, Anna E; Lu, Zhan; Yoon, Tehshik P

2014-08-18

[2+2] photocycloadditions of 1,3-dienes represent a powerful yet synthetically underutilized class of reactions. We report that visible light absorbing transition metal complexes enable the [2+2] cycloaddition of a diverse range of 1,3-dienes. The ability to use long-wavelength visible light is attractive because these reaction conditions tolerate the presence of sensitive functional groups that might be readily decomposed by the high-energy UVC radiation required for direct photoexcitation of 1,3-dienes. The resulting vinylcyclobutane products are poised for a variety of further diversification reactions, and this method is consequently expected to be powerfully enabling in the synthesis of complex organic targets. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Probing the structural dynamics of the CRISPR-Cas9 RNA-guided DNA-cleavage system by coarse-grained modeling.

PubMed

Zheng, Wenjun

2017-02-01

In the adaptive immune systems of many bacteria and archaea, the Cas9 endonuclease forms a complex with specific guide/scaffold RNA to identify and cleave complementary target sequences in foreign DNA. This DNA targeting machinery has been exploited in numerous applications of genome editing and transcription control. However, the molecular mechanism of the Cas9 system is still obscure. Recently, high-resolution structures have been solved for Cas9 in different structural forms (e.g., unbound forms, RNA-bound binary complexes, and RNA-DNA-bound tertiary complexes, corresponding to an inactive state, a pre-target-bound state, and a cleavage-competent or product state), which offered key structural insights to the Cas9 mechanism. To further probe the structural dynamics of Cas9 interacting with RNA and DNA at the amino-acid level of details, we have performed systematic coarse-grained modeling using an elastic network model and related analyses. Our normal mode analysis predicted a few key modes of collective motions that capture the observed conformational changes featuring large domain motions triggered by binding of RNA and DNA. Our flexibility analysis identified specific regions with high or low flexibility that coincide with key functional sites (such as DNA/RNA-binding sites, nuclease cleavage sites, and key hinges). We also identified a small set of hotspot residues that control the energetics of functional motions, which overlap with known functional sites and offer promising targets for future mutagenesis efforts to improve the specificity of Cas9. Finally, we modeled the conformational transitions of Cas9 from the unbound form to the binary complex and then the tertiary complex, and predicted a distinct sequence of domain motions. In sum, our findings have offered rich structural and dynamic details relevant to the Cas9 machinery, and will guide future investigation and engineering of the Cas9 systems. Proteins 2017; 85:342-353. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

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

Lamichhane, N; Johnson, P; Chinea, F

Purpose: To evaluate the correlation between image features and the accuracy of manually drawn target contours on synthetic PET images Methods: A digital PET phantom was used in combination with Monte Carlo simulation to create a set of 26 simulated PET images featuring a variety of tumor shapes and activity heterogeneity. These tumor volumes were used as a gold standard in comparisons with manual contours delineated by 10 radiation oncologist on the simulated PET images. Metrics used to evaluate segmentation accuracy included the dice coefficient, false positive dice, false negative dice, symmetric mean absolute surface distance, and absolute volumetric difference.more » Image features extracted from the simulated tumors consisted of volume, shape complexity, mean curvature, and intensity contrast along with five texture features derived from the gray-level neighborhood difference matrices including contrast, coarseness, busyness, strength, and complexity. Correlation between these features and contouring accuracy were examined. Results: Contour accuracy was reasonably well correlated with a variety of image features. Dice coefficient ranged from 0.7 to 0.90 and was correlated closely with contrast (r=0.43, p=0.02) and complexity (r=0.5, p<0.001). False negative dice ranged from 0.10 to 0.50 and was correlated closely with contrast (r=0.68, p<0.001) and complexity (r=0.66, p<0.001). Absolute volumetric difference ranged from 0.0002 to 0.67 and was correlated closely with coarseness (r=0.46, p=0.02) and complexity (r=0.49, p=0.008). Symmetric mean absolute difference ranged from 0.02 to 1 and was correlated closely with mean curvature (r=0.57, p=0.02) and contrast (r=0.6, p=0.001). Conclusion: The long term goal of this study is to assess whether contouring variability can be reduced by providing feedback to the practitioner based on image feature analysis. The results are encouraging and will be used to develop a statistical model which will enable a prediction of contour accuracy based purely on image feature analysis.« less

System for thermochemical hydrogen production

DOEpatents

Werner, R.W.; Galloway, T.R.; Krikorian, O.H.

1981-05-22

Method and apparatus are described for joule boosting a SO/sub 3/ decomposer using electrical instead of thermal energy to heat the reactants of the high temperature SO/sub 3/ decomposition step of a thermochemical hydrogen production process driven by a tandem mirror reactor. Joule boosting the decomposer to a sufficiently high temperature from a lower temperature heat source eliminates the need for expensive catalysts and reduces the temperature and consequent materials requirements for the reactor blanket. A particular decomposer design utilizes electrically heated silicon carbide rods, at a temperature of 1250/sup 0/K, to decompose a cross flow of SO/sub 3/ gas.

Bioavailable Carbon and the Relative Degradation State of Organic Matter in Active Layer and Permafrost Soils

NASA Astrophysics Data System (ADS)

Jastrow, J. D.; Burke, V. J.; Vugteveen, T. W.; Fan, Z.; Hofmann, S. M.; Lederhouse, J. S.; Matamala, R.; Michaelson, G. J.; Mishra, U.; Ping, C. L.

2015-12-01

The decomposability of soil organic carbon (SOC) in permafrost regions is a key uncertainty in efforts to predict carbon release from thawing permafrost and its impacts. The cold and often wet environment is the dominant factor limiting decomposer activity, and soil organic matter is often preserved in a relatively undecomposed and uncomplexed state. Thus, the impacts of soil warming and permafrost thaw are likely to depend at least initially on the genesis and past history of organic matter degradation before its stabilization in permafrost. We compared the bioavailability and relative degradation state of SOC in active layer and permafrost soils from Arctic tundra in Alaska. To assess readily bioavailable SOC, we quantified salt (0.5 M K2SO4) extractable organic matter (SEOM), which correlates well with carbon mineralization rates in short-term soil incubations. To assess the relative degradation state of SOC, we used particle size fractionation to isolate fibric (coarse) from more degraded (fine) particulate organic matter (POM) and separated mineral-associated organic matter into silt- and clay-sized fractions. On average, bulk SOC concentrations in permafrost were lower than in comparable active layer horizons. Although SEOM represented a very small proportion of the bulk SOC, this proportion was greater in permafrost than in comparable active layer soils. A large proportion of bulk SOC was found in POM for all horizons. Even for mineral soils, about 40% of bulk SOC was in POM pools, indicating that organic matter in both active layer and permafrost mineral soils was relatively undecomposed compared to typical temperate soils. Not surprisingly, organic soils had a greater proportion of POM and mineral soils had greater silt- and clay-sized carbon pools, while cryoturbated soils were intermediate. For organic horizons, permafrost organic matter was generally more degraded than in comparable active layer horizons. However, in mineral and cryoturbated horizons, the presence of permafrost appeared to have little effect on SOC distribution among size fractions. Future studies will investigate the utility of using organic matter pools defined by SEOM and particle size to predict the bioavailable pools characterized through more time-consuming long-term incubation studies of permafrost region soils.

Microbial Activity in Peat Soil Treated With Ordinary Portland Cement (OPC) and Coal Ashes

NASA Astrophysics Data System (ADS)

Rahman, J. A.; Mohamed, R. M. S. R.; Al-Gheethi, A. A.

2018-04-01

Peat soil is a cumulative of decayed plant fragment which developed as a result of microbial activity. The microbes degrade the organic matter in the peat soils by the production of hydrolysis enzyme. The least decomposed peat, known as fibric peat has big particles and retain lots of water. This made peat having high moisture content, up to 1500 %. The most decomposed peat known as sapric peat having fines particles and less void ratio. The present study aimed to understand the effects of solidification process on the bacterial growth and cellulase (CMCase) enzyme activity. Two types of mixing were designed for fibric, hemic and sapric peats; (i) Ordinary Portland cement (OPC) at an equal amount of dry peat, with 25 % of fly ash (FA) and total of coarse particle, a combination of bottom ash and fibre of 22 – 34 %, (ii) fibric peat was using water-to-binder ratio (w/b) = 1, 50% OPC, 25 % bottom ash (BA) and 25 % FA. For hemic and sapric peat, w/b=3 with 50 % OPC and 50 % BA were used. All samples were prepared triplicates, and were cured for 7, 14, 28 and 56 days in a closed container at room temperature. The results revealed that the first mix design giving a continuous strength development. However, the second mix design shows a decreased in strength pattern after day 28. The influence of the environment factors such as alkaline pH, reduction of the water content and peat temperature has no significant on the reduction amount of native microbes in the peat. The microbes survived in the solidified peat but the amount of microbes were found reduced for all types of mixing Fibric Mixed 1 (FM1), Hemic Mixed 1(HM1) and Sapric Mixed 1 (SM1) were having good strength increment for about 330 – 1427 % with enzymatic activity recorded even after D56. Nevertheless, with increase in the strength development through curing days, the enzymatic activities were reduced. For the time being, it can be concluded that the microbes have the ability to adapt with new environment. The reactivity of the microbes relates with the strength of solidified peat.

Quantum mechanics/coarse-grained molecular mechanics (QM/CG-MM)

NASA Astrophysics Data System (ADS)

Sinitskiy, Anton V.; Voth, Gregory A.

2018-01-01

Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used. However, the QM/MM approach often faces a number of challenges, including the high cost of repetitive QM computations, the slow sampling even for the MM part in those cases where a system under investigation has a complex dynamics, and a difficulty in providing a simple, qualitative interpretation of numerical results in terms of the influence of the molecular environment upon the active QM region. In this paper, we address these issues by combining QM/MM modeling with the methodology of "bottom-up" coarse-graining (CG) to provide the theoretical basis for a systematic quantum-mechanical/coarse-grained molecular mechanics (QM/CG-MM) mixed resolution approach. A derivation of the method is presented based on a combination of statistical mechanics and quantum mechanics, leading to an equation for the effective Hamiltonian of the QM part, a central concept in the QM/CG-MM theory. A detailed analysis of different contributions to the effective Hamiltonian from electrostatic, induction, dispersion, and exchange interactions between the QM part and the surroundings is provided, serving as a foundation for a potential hierarchy of QM/CG-MM methods varying in their accuracy and computational cost. A relationship of the QM/CG-MM methodology to other mixed resolution approaches is also discussed.

Nutrient concentrations in coarse and fine woody debris of Populus tremuloides Michx.-dominated forests, northern Minnesota, USA

USGS Publications Warehouse

Klockow, Paul A.; D'Amato, Anthony W.; Bradford, John B.; Fraver, Shawn

2014-01-01

Contemporary forest harvesting practices, specifically harvesting woody biomass as a source of bioenergy feedstock, may remove more woody debris from a site than conventional harvesting. Woody debris, particularly smaller diameter woody debris, plays a key role in maintaining ecosystem nutrient stores following disturbance. Understanding nutrient concentrations within woody debris is necessary for assessing the long-term nutrient balance consequences of altered woody debris retention, particularly in forests slated for use as bioenergy feedstocks. Nutrient concentrations in downed woody debris of various sizes, decay classes, and species were characterized within one such forest type, Populus tremuloides Michx.-dominated forests of northern Minnesota, USA. Nutrient concentrations differed significantly between size and decay classes and generally increased as decay progressed. Fine woody debris (≤ 7.5 cm diameter) had higher nutrient concentrations than coarse woody debris (> 7.5 cm diameter) for all nutrients examined except Na and Mn, and nutrient concentrations varied among species. Concentrations of N, Mn, Al, Fe, and Zn in coarse woody debris increased between one and three orders of magnitude, while K decreased by an order of magnitude with progressing decay. The variations in nutrient concentrations observed here underscore the complexity of woody debris nutrient stores in forested ecosystems and suggest that retaining fine woody debris at harvest may provide a potentially important source of nutrients following intensive removals of bioenergy feedstocks.

Coarse-to-fine wavelet-based airport detection

NASA Astrophysics Data System (ADS)

Li, Cheng; Wang, Shuigen; Pang, Zhaofeng; Zhao, Baojun

2015-10-01

Airport detection on optical remote sensing images has attracted great interest in the applications of military optics scout and traffic control. However, most of the popular techniques for airport detection from optical remote sensing images have three weaknesses: 1) Due to the characteristics of optical images, the detection results are often affected by imaging conditions, like weather situation and imaging distortion; and 2) optical images contain comprehensive information of targets, so that it is difficult for extracting robust features (e.g., intensity and textural information) to represent airport area; 3) the high resolution results in large data volume, which makes real-time processing limited. Most of the previous works mainly focus on solving one of those problems, and thus, the previous methods cannot achieve the balance of performance and complexity. In this paper, we propose a novel coarse-to-fine airport detection framework to solve aforementioned three issues using wavelet coefficients. The framework includes two stages: 1) an efficient wavelet-based feature extraction is adopted for multi-scale textural feature representation, and support vector machine(SVM) is exploited for classifying and coarsely deciding airport candidate region; and then 2) refined line segment detection is used to obtain runway and landing field of airport. Finally, airport recognition is achieved by applying the fine runway positioning to the candidate regions. Experimental results show that the proposed approach outperforms the existing algorithms in terms of detection accuracy and processing efficiency.

Quantum mechanics/coarse-grained molecular mechanics (QM/CG-MM).

PubMed

Sinitskiy, Anton V; Voth, Gregory A

2018-01-07

Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used. However, the QM/MM approach often faces a number of challenges, including the high cost of repetitive QM computations, the slow sampling even for the MM part in those cases where a system under investigation has a complex dynamics, and a difficulty in providing a simple, qualitative interpretation of numerical results in terms of the influence of the molecular environment upon the active QM region. In this paper, we address these issues by combining QM/MM modeling with the methodology of "bottom-up" coarse-graining (CG) to provide the theoretical basis for a systematic quantum-mechanical/coarse-grained molecular mechanics (QM/CG-MM) mixed resolution approach. A derivation of the method is presented based on a combination of statistical mechanics and quantum mechanics, leading to an equation for the effective Hamiltonian of the QM part, a central concept in the QM/CG-MM theory. A detailed analysis of different contributions to the effective Hamiltonian from electrostatic, induction, dispersion, and exchange interactions between the QM part and the surroundings is provided, serving as a foundation for a potential hierarchy of QM/CG-MM methods varying in their accuracy and computational cost. A relationship of the QM/CG-MM methodology to other mixed resolution approaches is also discussed.

Atomistic and Coarse-Grained Modeling of the Adsorption of Graphene Nanoflakes at the Oil-Water Interface.

PubMed

Ardham, Vikram Reddy; Leroy, Frédéric

2018-03-01

The high interfacial tension between two immiscible liquids can provide the necessary driving force for the self-assembly of nanoparticles at the interface. Particularly, the interface between water and oily liquids (hydrocarbon chains) has been exploited to prepare networks of highly interconnected graphene sheets of only a few layers thickness, which are well suited for industrial applications. Studying such complex systems through particle-based simulations could greatly enhance the understanding of the various driving forces in action and could possibly give more control over the self-assembly process. However, the interaction potentials used in particle-based simulations are typically derived by reproducing bulk properties and are therefore not suitable for describing systems dominated by interfaces. To address this issue, we introduce a methodology to derive solid-liquid interaction potentials that yield an accurate representation of the balance between interfacial interactions at atomistic and coarse-grained resolutions. Our approach is validated through its ability to lead to the adsorption of graphene nanoflakes at the interface between water and n-hexane. The development of accurate coarse-grained potentials that our approach enables will allow us to perform large-scale simulations to study the assembly of graphene nanoparticles at the interface between immiscible liquids. Our methodology is illustrated through a simulation of many graphene nanoflakes adsorbing at the interface.

Post-Disturbance Stability of Fish Assemblages Measured at Coarse Taxonomic Resolution Masks Change at Finer Scales.

PubMed

Ceccarelli, Daniela M; Emslie, Michael J; Richards, Zoe T

2016-01-01

Quantifying changes to coral reef fish assemblages in the wake of cyclonic disturbances is challenging due to spatial variability of damage inherent in such events. Often, fish abundance appears stable at one spatial scale (e.g. reef-wide), but exhibits substantial change at finer scales (e.g. site-specific decline or increase). Taxonomic resolution also plays a role; overall stability at coarse taxonomic levels (e.g. family) may mask species-level turnover. Here we document changes to reef fish communities after severe Tropical Cyclone Ita crossed Lizard Island, Great Barrier Reef. Coral and reef fish surveys were conducted concurrently before and after the cyclone at four levels of exposure to the prevailing weather. Coral cover declined across all exposures except sheltered sites, with the largest decline at exposed sites. There was no significant overall reduction in the total density, biomass and species richness of reef fishes between 2011 and 2015, but individual fish taxa (families and species) changed in complex and unpredictable ways. For example, more families increased in density and biomass than decreased following Cyclone Ita, particularly at exposed sites whilst more fish families declined at lagoon sites even though coral cover did not decline. All sites lost biomass of several damselfish species, and at most sites there was an increase in macroinvertivores and grazers. Overall, these results suggest that the degree of change measured at coarse taxonomic levels masked high species-level turnover, although other potential explanations include that there was no impact of the storm, fish assemblages were impacted but underwent rapid recovery or that there is a time lag before the full impacts become apparent. This study confirms that in high-complexity, high diversity ecosystems such as coral reefs, species level analyses are essential to adequately capture the consequences of disturbance events.

Post-Disturbance Stability of Fish Assemblages Measured at Coarse Taxonomic Resolution Masks Change at Finer Scales

PubMed Central

Ceccarelli, Daniela M.

2016-01-01

Quantifying changes to coral reef fish assemblages in the wake of cyclonic disturbances is challenging due to spatial variability of damage inherent in such events. Often, fish abundance appears stable at one spatial scale (e.g. reef-wide), but exhibits substantial change at finer scales (e.g. site-specific decline or increase). Taxonomic resolution also plays a role; overall stability at coarse taxonomic levels (e.g. family) may mask species-level turnover. Here we document changes to reef fish communities after severe Tropical Cyclone Ita crossed Lizard Island, Great Barrier Reef. Coral and reef fish surveys were conducted concurrently before and after the cyclone at four levels of exposure to the prevailing weather. Coral cover declined across all exposures except sheltered sites, with the largest decline at exposed sites. There was no significant overall reduction in the total density, biomass and species richness of reef fishes between 2011 and 2015, but individual fish taxa (families and species) changed in complex and unpredictable ways. For example, more families increased in density and biomass than decreased following Cyclone Ita, particularly at exposed sites whilst more fish families declined at lagoon sites even though coral cover did not decline. All sites lost biomass of several damselfish species, and at most sites there was an increase in macroinvertivores and grazers. Overall, these results suggest that the degree of change measured at coarse taxonomic levels masked high species-level turnover, although other potential explanations include that there was no impact of the storm, fish assemblages were impacted but underwent rapid recovery or that there is a time lag before the full impacts become apparent. This study confirms that in high-complexity, high diversity ecosystems such as coral reefs, species level analyses are essential to adequately capture the consequences of disturbance events. PMID:27285160

Eustatic and far-field tectonic control on the development of an intra-platform carbonate-shoal complex: upper tongue of the Tanglewood Member, Upper Ordovician Lexington Limestone, central Kentucky, U.S.A.

NASA Astrophysics Data System (ADS)

Koirala, Dibya Raj; Ettensohn, Frank R.; Clepper, Marta L.

2016-11-01

The Lexington or Trenton Limestone is an Upper Ordovician (Chatfieldian-Edenian; upper Sandbian-lower Katian), temperate-water unit, averaging about 60-m thick, that was deposited in relatively shallow waters across the Lexington Platform in east-central United States during the Taconian Orogeny. Lexington/Trenton shallow-water deposition ended across most of the platform in late Chatfieldian time and from that point deepened upward into the more shale-rich Clays Ferry, Point Pleasant and Kope formations due to apparent sea-level rise. In central Kentucky, however, deposition of the Lexington Limestone continued into early Edenian time and includes up to 50 m of additional coarse calcarenites and calcirudites at the top, which form the Tanglewood buildup and reflect locally regressive conditions, apparently related to local structural uplift. Consequently, in central Kentucky, the Lexington is more than 100-m thick, and Lexington deposition on the buildup continued into early Edenian time as an intra-platform shoal complex that tongues out into deeper-water units in all directions. In an attempt to understand how this shoal complex developed, we examined the last major body of coarse skeletal sands in the central Kentucky Lexington Limestone, the upper tongue of the Tanglewood Member, a 12-m-thick succession of fossiliferous calcarenite and calcirudite that occurs across an area of 5200 km2 near the center of the Lexington Platform. Although relatively homogeneous, the upper Tanglewood is divisible into five, small-scale, fining-upward, sequence-like cycles, which contain prominent, widespread deformed horizons. Facies analysis indicates that four lithofacies, which reflect distinct depositional environments, comprise the sequences across the shoal complex. Lithofacies were correlated across the shoal complex by integrating cyclicity and widespread deformed horizons in order to delineate the locations of major depositional environments. Facies analysis shows that the thickest and coarsest parts of each sequence, and the shallowest depositional environments, coincide with basement fault blocks, which are known to have experienced uplift during earlier Lexington Limestone deposition. The occurrence of thick, coarse facies on the same blocks suggests that the blocks continued to experience uplift into shallow water, where tides and waves redistributed sediments during upper Tanglewood deposition. Although eustasy apparently controlled cyclicity, Taconian far-field forces generated by orogeny in the east seem to have influenced facies distribution in each cycle through reactivation of basement fault zones as synsedimentary growth faults. The example of the upper Tanglewood Member shows that tectonic far-field forces can exert important influences on the development of carbonate depositional environments, even in distal intracratonic settings like the Lexington Platform.

Aridity and decomposition processes in complex landscapes

NASA Astrophysics Data System (ADS)

Ossola, Alessandro; Nyman, Petter

2015-04-01

Decomposition of organic matter is a key biogeochemical process contributing to nutrient cycles, carbon fluxes and soil development. The activity of decomposers depends on microclimate, with temperature and rainfall being major drivers. In complex terrain the fine-scale variation in microclimate (and hence water availability) as a result of slope orientation is caused by differences in incoming radiation and surface temperature. Aridity, measured as the long-term balance between net radiation and rainfall, is a metric that can be used to represent variations in water availability within the landscape. Since aridity metrics can be obtained at fine spatial scales, they could theoretically be used to investigate how decomposition processes vary across complex landscapes. In this study, four research sites were selected in tall open sclerophyll forest along a aridity gradient (Budyko dryness index ranging from 1.56 -2.22) where microclimate, litter moisture and soil moisture were monitored continuously for one year. Litter bags were packed to estimate decomposition rates (k) using leaves of a tree species not present in the study area (Eucalyptus globulus) in order to avoid home-field advantage effects. Litter mass loss was measured to assess the activity of macro-decomposers (6mm litter bag mesh size), meso-decomposers (1 mm mesh), microbes above-ground (0.2 mm mesh) and microbes below-ground (2 cm depth, 0.2 mm mesh). Four replicates for each set of bags were installed at each site and bags were collected at 1, 2, 4, 7 and 12 months since installation. We first tested whether differences in microclimate due to slope orientation have significant effects on decomposition processes. Then the dryness index was related to decomposition rates to evaluate if small-scale variation in decomposition can be predicted using readily available information on rainfall and radiation. Decomposition rates (k), calculated fitting single pool negative exponential models, generally decreased with increasing aridity with k going from 0.0025 day-1 on equatorial (dry) facing slopes to 0.0040 day-1 on polar (wet) facing slopes. However, differences in temperature as a result of morning vs afternoon sun on east and west aspects, respectively, (not captured in the aridity metric) resulted in poor prediction of decomposition for the sites located in the intermediate aridity range. Overall the results highlight that relatively small differences in microclimate due to slope orientation can have large effects on decomposition. Future research will aim to refine the aridity metric to better resolve small scale variation in surface temperature which is important when up-scaling decomposition processes to landscapes.

Reducing the complexity of the software design process with object-oriented design

NASA Technical Reports Server (NTRS)

Schuler, M. P.

1991-01-01

Designing software is a complex process. How object-oriented design (OOD), coupled with formalized documentation and tailored object diagraming techniques, can reduce the complexity of the software design process is described and illustrated. The described OOD methodology uses a hierarchical decomposition approach in which parent objects are decomposed into layers of lower level child objects. A method of tracking the assignment of requirements to design components is also included. Increases in the reusability, portability, and maintainability of the resulting products are also discussed. This method was built on a combination of existing technology, teaching experience, consulting experience, and feedback from design method users. The discussed concepts are applicable to hierarchal OOD processes in general. Emphasis is placed on improving the design process by documenting the details of the procedures involved and incorporating improvements into those procedures as they are developed.

Strategies for concurrent processing of complex algorithms in data driven architectures

NASA Technical Reports Server (NTRS)

Stoughton, John W.; Mielke, Roland R.

1988-01-01

The purpose is to document research to develop strategies for concurrent processing of complex algorithms in data driven architectures. The problem domain consists of decision-free algorithms having large-grained, computationally complex primitive operations. Such are often found in signal processing and control applications. The anticipated multiprocessor environment is a data flow architecture containing between two and twenty computing elements. Each computing element is a processor having local program memory, and which communicates with a common global data memory. A new graph theoretic model called ATAMM which establishes rules for relating a decomposed algorithm to its execution in a data flow architecture is presented. The ATAMM model is used to determine strategies to achieve optimum time performance and to develop a system diagnostic software tool. In addition, preliminary work on a new multiprocessor operating system based on the ATAMM specifications is described.

In situ transmission electron microscopy He + implantation and thermal aging of nanocrystalline iron

DOE PAGES

Muntifering, Brittany R.; Fang, Youwu; Leff, Asher C.; ...

2016-10-04

Due to their high density of interfaces, nanostructured material are hypothesized to show a higher tolerance to radiation damage compared to conventional coarse-grained materials and are on interest for use in future nuclear reactors. In order to investigate the roles of vacancies, self-interstitials, and helium during defect accumulation, and the thermal evolution of such defects, a complex set of in situ TEM experiments were performed in nanocrystalline iron.

The Aerosol Coarse Mode Initiative

NASA Astrophysics Data System (ADS)

Arnott, W. P.; Adhikari, N.; Air, D.; Kassianov, E.; Barnard, J.

2014-12-01

Many areas of the world show an aerosol volume distribution with a significant coarse mode and sometimes a dominant coarse mode. The large coarse mode is usually due to dust, but sea salt aerosol can also play an important role. However, in many field campaigns, the coarse mode tends to be ignored, because it is difficult to measure. This lack of measurements leads directly to a concomitant "lack of analysis" of this mode. Because, coarse mode aerosols can have significant effects on radiative forcing, both in the shortwave and longwave spectrum, the coarse mode -- and these forcings -- should be accounted for in atmospheric models. Forcings based only on fine mode aerosols have the potential to be misleading. In this paper we describe examples of large coarse modes that occur in areas of large aerosol loading (Mexico City, Barnard et al., 2010) as well as small loadings (Sacramento, CA; Kassianov et al., 2012; and Reno, NV). We then demonstrate that: (1) the coarse mode can contribute significantly to radiative forcing, relative to the fine mode, and (2) neglecting the coarse mode may result in poor comparisons between measurements and models. Next we describe -- in general terms -- the limitations of instrumentation to measure the coarse mode. Finally, we suggest a new initiative aimed at examining coarse mode aerosol generation mechanisms; transport and deposition; chemical composition; visible and thermal IR refractive indices; morphology; microphysical behavior when deposited on snow and ice; and specific instrumentation needs. Barnard, J. C., J. D. Fast, G. Paredes-Miranda, W. P. Arnott, and A. Laskin, 2010: Technical Note: Evaluation of the WRF-Chem "Aerosol Chemical to Aerosol Optical Properties" Module using data from the MILAGRO campaign, Atmospheric Chemistry and Physics, 10, 7325-7340. Kassianov, E. I., M. S. Pekour, and J. C. Barnard, 2012: Aerosols in Central California: Unexpectedly large contribution of coarse mode to aerosol radiative forcing, Geophys. Res. Lett., 39, L20806, doi:10.1029/2012GL053469.

Texture coarseness responsive neurons and their mapping in layer 2–3 of the rat barrel cortex in vivo

PubMed Central

Garion, Liora; Dubin, Uri; Rubin, Yoav; Khateb, Mohamed; Schiller, Yitzhak; Azouz, Rony; Schiller, Jackie

2014-01-01

Texture discrimination is a fundamental function of somatosensory systems, yet the manner by which texture is coded and spatially represented in the barrel cortex are largely unknown. Using in vivo two-photon calcium imaging in the rat barrel cortex during artificial whisking against different surface coarseness or controlled passive whisker vibrations simulating different coarseness, we show that layer 2–3 neurons within barrel boundaries differentially respond to specific texture coarsenesses, while only a minority of neurons responded monotonically with increased or decreased surface coarseness. Neurons with similar preferred texture coarseness were spatially clustered. Multi-contact single unit recordings showed a vertical columnar organization of texture coarseness preference in layer 2–3. These findings indicate that layer 2–3 neurons perform high hierarchical processing of tactile information, with surface coarseness embodied by distinct neuronal subpopulations that are spatially mapped onto the barrel cortex. DOI: http://dx.doi.org/10.7554/eLife.03405.001 PMID:25233151

[Intervention of coarse cereals on lipid metabolism in rats].

PubMed

Guo, Yanbo; Zhai, Chengkai; Wang, Yanli; Zhang, Qun; Ding, Zhoubo; Jin, Xin

2010-03-01

To observe the effect of coarse cereals on improving the disorder of lipid metabolism and the expression of PPARgamma mRNA in white adipose tissue in rats to investigate the mechanism of coarse cereals on lipid metabolism disorder. Forty four SPF rats were randomly divided into 4 groups: the negative control group was fed with normal diet and 3 experimental groups were fed with high-fat modeling diet for 6 weeks for model building. The 3 experimental groups, the coarse cereals group,rice-flour group and the hyperlipemia model group, were then fed with coarse cereals high-fat diet,rice-flour high-diet and high-fat modeling diet respectively for another 15 weeks. Compared with the hyperlipemia modeling group, serum TG, TC, IL-6 and TNF-alpha in the coarse cereals group were declined significantly (P < 0.05), serum HDL-C in coarse cereals group was higher than that in rice-flour group and hyperlipemia model group (P < 0.05), LPL, HL and TNF-alpha in coarse cereal group were close to the negative control group. Moreover, the expression of PPAR-gamma mRNA in white adipose tissue of the coarse cereals group was higher than other groups. The coarse cereals could activate PPARgamma and enhance the activity of key enzymes in lipids metabolism, so as to reduce the level of TG relieve inflammation and improve lipid dysmetabolism eventually.

Do Nonnative Language Speakers "Chew the Fat" and "Spill the Beans" with Different Brain Hemispheres? Investigating Idiom Decomposability with the Divided Visual Field Paradigm

ERIC Educational Resources Information Center

Cieslicka, Anna B.

2013-01-01

The purpose of this study was to explore possible cerebral asymmetries in the processing of decomposable and nondecomposable idioms by fluent nonnative speakers of English. In the study, native language (Polish) and foreign language (English) decomposable and nondecomposable idioms were embedded in ambiguous (neutral) and unambiguous (biasing…

Modeling and optimum time performance for concurrent processing

NASA Technical Reports Server (NTRS)

Mielke, Roland R.; Stoughton, John W.; Som, Sukhamoy

1988-01-01

The development of a new graph theoretic model for describing the relation between a decomposed algorithm and its execution in a data flow environment is presented. Called ATAMM, the model consists of a set of Petri net marked graphs useful for representing decision-free algorithms having large-grained, computationally complex primitive operations. Performance time measures which determine computing speed and throughput capacity are defined, and the ATAMM model is used to develop lower bounds for these times. A concurrent processing operating strategy for achieving optimum time performance is presented and illustrated by example.

Crossing symmetry in alpha space

NASA Astrophysics Data System (ADS)

Hogervorst, Matthijs; van Rees, Balt C.

2017-11-01

We initiate the study of the conformal bootstrap using Sturm-Liouville theory, specializing to four-point functions in one-dimensional CFTs. We do so by decomposing conformal correlators using a basis of eigenfunctions of the Casimir which are labeled by a complex number α. This leads to a systematic method for computing conformal block decompositions. Analyzing bootstrap equations in alpha space turns crossing symmetry into an eigenvalue problem for an integral operator K. The operator K is closely related to the Wilson transform, and some of its eigenfunctions can be found in closed form.

Graph-based analysis of kinetics on multidimensional potential-energy surfaces.

PubMed

Okushima, T; Niiyama, T; Ikeda, K S; Shimizu, Y

2009-09-01

The aim of this paper is twofold: one is to give a detailed description of an alternative graph-based analysis method, which we call saddle connectivity graph, for analyzing the global topography and the dynamical properties of many-dimensional potential-energy landscapes and the other is to give examples of applications of this method in the analysis of the kinetics of realistic systems. A Dijkstra-type shortest path algorithm is proposed to extract dynamically dominant transition pathways by kinetically defining transition costs. The applicability of this approach is first confirmed by an illustrative example of a low-dimensional random potential. We then show that a coarse-graining procedure tailored for saddle connectivity graphs can be used to obtain the kinetic properties of 13- and 38-atom Lennard-Jones clusters. The coarse-graining method not only reduces the complexity of the graphs, but also, with iterative use, reveals a self-similar hierarchical structure in these clusters. We also propose that the self-similarity is common to many-atom Lennard-Jones clusters.

Time irreversibility of financial time series based on higher moments and multiscale Kullback-Leibler divergence

NASA Astrophysics Data System (ADS)

Li, Jinyang; Shang, Pengjian

2018-07-01

Irreversibility is an important property of time series. In this paper, we propose the higher moments and multiscale Kullback-Leibler divergence to analyze time series irreversibility. The higher moments Kullback-Leibler divergence (HMKLD) can amplify irreversibility and make the irreversibility variation more obvious. Therefore, many time series whose irreversibility is hard to be found are also able to show the variations. We employ simulated data and financial stock data to test and verify this method, and find that HMKLD of stock data is growing in the form of fluctuations. As for multiscale Kullback-Leibler divergence (MKLD), it is very complex in the dynamic system, so that exploring the law of simulation and stock system is difficult. In conventional multiscale entropy method, the coarse-graining process is non-overlapping, however we apply a different coarse-graining process and obtain a surprising discovery. The result shows when the scales are 4 and 5, their entropy is nearly similar, which demonstrates MKLD is efficient to display characteristics of time series irreversibility.

Multiscale Mathematics for Biomass Conversion to Renewable Hydrogen

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

Katsoulakis, Markos

2014-08-09

Our two key accomplishments in the first three years were towards the development of, (1) a mathematically rigorous and at the same time computationally flexible framework for parallelization of Kinetic Monte Carlo methods, and its implementation on GPUs, and (2) spatial multilevel coarse-graining methods for Monte Carlo sampling and molecular simulation. A common underlying theme in both these lines of our work is the development of numerical methods which are at the same time both computationally efficient and reliable, the latter in the sense that they provide controlled-error approximations for coarse observables of the simulated molecular systems. Finally, our keymore » accomplishment in the last year of the grant is that we started developing (3) pathwise information theory-based and goal-oriented sensitivity analysis and parameter identification methods for complex high-dimensional dynamics and in particular of nonequilibrium extended (high-dimensional) systems. We discuss these three research directions in some detail below, along with the related publications.« less

Industrial Application Study on New-Type Mixed-Flow Fluidized Bed Bottom Ash Cooler

NASA Astrophysics Data System (ADS)

Zeng, B.; Lu, X. F.; Liu, H. Z.

As a key auxiliary device of CFB boiler, the bottom ash cooler (BAC) has a direct influence on secure and economic operation of the boiler. The operating situation of domestic CFB power plant is complex and changeable with a bad coal-fired condition. The principle for designing BAC suitable for the bad coal-fired condition and high parameter CFB boilers was summarized in this paper. Meanwhile, a new-type mixed-flow fluidized bed bottom ash cooler was successfully designed on the basis of the comprehensive investigation on the existing BAC s merits and drawbacks. Using coarse/fine slag separation technology and micro-bubbling fluidization are the significant characteristics of this new BAC. This paper also puts great emphasis on its industrial test in a 460t/h CFB boiler. The results indicate that it achieves significant separation of the coarse/fine slag, an obvious cooling effect, no slag block and coking phenomenon, and continuous stable operation. Figs 7, Tabs 4 and Refs 11.

Mineralogical, Chemical, and Isotopic Heterogeneity in Zagami: Evidence for a Complex Petrogenesis

NASA Technical Reports Server (NTRS)

Nyquist, L. E.; Misawa, K.; Shih, C-Y.; Niihara, T.; Park, J.

2013-01-01

Textural variations in the shergottite Zagami were initially interpreted as evidence that it formed in a heterogeneous lava flow. Variations in initial Sr-87/Sr-86 ratios between a Coarse Grained (CG) and a Fine Grained (FG) lithology and evidence for more extensive fractionation of the Rb/Sr ratio in a Dark Mottled Lithology (DML) are consistent with such an interpretation. More recently, Niihara et al. and Misawa et al. have reported the mineralogy and Sr-isotopic systematics of an Olivine Rich Lithology (ORL) found in association with the coarse-grained DML lithology in the Kanagawa Zagami specimen [6,7]. Here we call this lithology DML(Ka) to maintain a distinction with DML(USNM) as studied. An Ar-Ar study by Park et al. of a late stage K-rich melt enriched in K2O to approx 7% and intruded into ORL yielded an Ar-Ar age of 202+/0 7 Ma. The present work extends the study of Kanagawa Zagami to Nd-isotopes.

Electrodeposition of Rhodium Nanowires Arrays and Their Morphology-Dependent Hydrogen Evolution Activity

PubMed Central

Zhang, Liqiu; Liu, Lichun; Wang, Hongdan; Shen, Hongxia; Cheng, Qiong; Yan, Chao; Park, Sungho

2017-01-01

This work reports on the electrodeposition of rhodium (Rh) nanowires with a controlled surface morphology synthesized using an anodic aluminum oxide (AAO) template. Vertically aligned Rh nanowires with a smooth and coarse morphology were successfully deposited by adjusting the electrode potential and the concentration of precursor ions and by involving a complexing reagent in the electrolyte solution. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) analyses were used to follow the morphological evolution of Rh nanowires. As a heterogeneous electrocatalyst for hydrogen evolution reactions (HER), the coarse Rh nanowire array exhibited an enhanced catalytic performance respect to smooth ones due to the larger surface area to mass ratio and the higher density of catalytically active defects, as evidenced by voltammetric measurements and TEM. Results suggest that the morphology of metallic nanomaterials could be readily engineered by electrodeposition. The controlled electrodeposition offers great potential for the development of an effective synthesis tool for heterogeneous catalysts with a superior performance for wide applications. PMID:28467375

Skin Color Segmentation Using Coarse-to-Fine Region on Normalized RGB Chromaticity Diagram for Face Detection

NASA Astrophysics Data System (ADS)

Soetedjo, Aryuanto; Yamada, Koichi

This paper describes a new color segmentation based on a normalized RGB chromaticity diagram for face detection. Face skin is extracted from color images using a coarse skin region with fixed boundaries followed by a fine skin region with variable boundaries. Two newly developed histograms that have prominent peaks of skin color and non-skin colors are employed to adjust the boundaries of the skin region. The proposed approach does not need a skin color model, which depends on a specific camera parameter and is usually limited to a particular environment condition, and no sample images are required. The experimental results using color face images of various races under varying lighting conditions and complex backgrounds, obtained from four different resources on the Internet, show a high detection rate of 87%. The results of the detection rate and computation time are comparable to the well known real-time face detection method proposed by Viola-Jones [11], [12].

Coarse cluster enhancing collaborative recommendation for social network systems

NASA Astrophysics Data System (ADS)

Zhao, Yao-Dong; Cai, Shi-Min; Tang, Ming; Shang, Min-Sheng

2017-10-01

Traditional collaborative filtering based recommender systems for social network systems bring very high demands on time complexity due to computing similarities of all pairs of users via resource usages and annotation actions, which thus strongly suppresses recommending speed. In this paper, to overcome this drawback, we propose a novel approach, namely coarse cluster that partitions similar users and associated items at a high speed to enhance user-based collaborative filtering, and then develop a fast collaborative user model for the social tagging systems. The experimental results based on Delicious dataset show that the proposed model is able to dramatically reduce the processing time cost greater than 90 % and relatively improve the accuracy in comparison with the ordinary user-based collaborative filtering, and is robust for the initial parameter. Most importantly, the proposed model can be conveniently extended by introducing more users' information (e.g., profiles) and practically applied for the large-scale social network systems to enhance the recommending speed without accuracy loss.

Fast single image dehazing based on image fusion

NASA Astrophysics Data System (ADS)

Liu, Haibo; Yang, Jie; Wu, Zhengping; Zhang, Qingnian

2015-01-01

Images captured in foggy weather conditions often fade the colors and reduce the contrast of the observed objects. An efficient image fusion method is proposed to remove haze from a single input image. First, the initial medium transmission is estimated based on the dark channel prior. Second, the method adopts an assumption that the degradation level affected by haze of each region is the same, which is similar to the Retinex theory, and uses a simple Gaussian filter to get the coarse medium transmission. Then, pixel-level fusion is achieved between the initial medium transmission and coarse medium transmission. The proposed method can recover a high-quality haze-free image based on the physical model, and the complexity of the proposed method is only a linear function of the number of input image pixels. Experimental results demonstrate that the proposed method can allow a very fast implementation and achieve better restoration for visibility and color fidelity compared to some state-of-the-art methods.

Fractal dimension analysis for robust ultrasonic non-destructive evaluation (NDE) of coarse grained materials

NASA Astrophysics Data System (ADS)

Li, Minghui; Hayward, Gordon

2018-04-01

Over the recent decades, there has been a growing demand on reliable and robust non-destructive evaluation (NDE) of structures and components made from coarse grained materials such as alloys, stainless steels, carbon-reinforced composites and concrete; however, when inspected using ultrasound, the flaw echoes are usually contaminated by high-level, time-invariant, and correlated grain noise originating from the microstructure and grain boundaries, leading to pretty low signal-to-noise ratio (SNR) and the flaw information being obscured or completely hidden by the grain noise. In this paper, the fractal dimension analysis of the A-scan echoes is investigated as a measure of complexity of the time series to distinguish the echoes originating from the real defects and the grain noise, and then the normalized fractal dimension coefficients are applied to the amplitudes as the weighting factor to enhance the SNR and defect detection. Experiments on industrial samples of the mild steel and the stainless steel are conducted and the results confirm the great benefits of the method.

RACER a Coarse-Grained RNA Model for Capturing Folding Free Energy in Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Cheng, Sara; Bell, David; Ren, Pengyu

RACER is a coarse-grained RNA model that can be used in molecular dynamics simulations to predict native structures and sequence-specific variation of free energy of various RNA structures. RACER is capable of accurate prediction of native structures of duplexes and hairpins (average RMSD of 4.15 angstroms), and RACER can capture sequence-specific variation of free energy in excellent agreement with experimentally measured stabilities (r-squared =0.98). The RACER model implements a new effective non-bonded potential and re-parameterization of hydrogen bond and Debye-Huckel potentials. Insights from the RACER model include the importance of treating pairing and stacking interactions separately in order to distinguish folded an unfolded states and identification of hydrogen-bonding, base stacking, and electrostatic interactions as essential driving forces for RNA folding. Future applications of the RACER model include predicting free energy landscapes of more complex RNA structures and use of RACER for multiscale simulations.

Combination of Complex-Based and Magnitude-Based Multiecho Water-Fat Separation for Accurate Quantification of Fat-Fraction

PubMed Central

Yu, Huanzhou; Shimakawa, Ann; Hines, Catherine D. G.; McKenzie, Charles A.; Hamilton, Gavin; Sirlin, Claude B.; Brittain, Jean H.; Reeder, Scott B.

2011-01-01

Multipoint water–fat separation techniques rely on different water–fat phase shifts generated at multiple echo times to decompose water and fat. Therefore, these methods require complex source images and allow unambiguous separation of water and fat signals. However, complex-based water–fat separation methods are sensitive to phase errors in the source images, which may lead to clinically important errors. An alternative approach to quantify fat is through “magnitude-based” methods that acquire multiecho magnitude images. Magnitude-based methods are insensitive to phase errors, but cannot estimate fat-fraction greater than 50%. In this work, we introduce a water–fat separation approach that combines the strengths of both complex and magnitude reconstruction algorithms. A magnitude-based reconstruction is applied after complex-based water–fat separation to removes the effect of phase errors. The results from the two reconstructions are then combined. We demonstrate that using this hybrid method, 0–100% fat-fraction can be estimated with improved accuracy at low fat-fractions. PMID:21695724

A study on axial and torsional resonant mode matching for a mechanical system with complex nonlinear geometries

NASA Astrophysics Data System (ADS)

Watson, Brett; Yeo, Leslie; Friend, James

2010-06-01

Making use of mechanical resonance has many benefits for the design of microscale devices. A key to successfully incorporating this phenomenon in the design of a device is to understand how the resonant frequencies of interest are affected by changes to the geometric parameters of the design. For simple geometric shapes, this is quite easy, but for complex nonlinear designs, it becomes significantly more complex. In this paper, two novel modeling techniques are demonstrated to extract the axial and torsional resonant frequencies of a complex nonlinear geometry. The first decomposes the complex geometry into easy to model components, while the second uses scaling techniques combined with the finite element method. Both models overcome problems associated with using current analytical methods as design tools, and enable a full investigation of how changes in the geometric parameters affect the resonant frequencies of interest. The benefit of such models is then demonstrated through their use in the design of a prototype piezoelectric ultrasonic resonant micromotor which has improved performance characteristics over previous prototypes.

Decomposing potassium peroxychromate produces hydroxyl radical (.OH) that can peroxidize the unsaturated fatty acids of phospholipid dispersions.

PubMed

Edwards, J C; Quinn, P J

1982-09-01

The unsaturated fatty acyl residues of egg yolk lecithin are selectively removed when bilayer dispersions of the lipid are exposed to decomposing peroxychromate at pH 7.6 or pH 9.0. Mannitol (50 mM or 100 mM)partially prevents the oxidation of the phospholipid due to decomposing peroxychromate at pH 7.6 and the amount of lipid lost is inversely proportional to the concentration of mannitol. N,N-Dimethyl-p-nitrosoaniline, mixed with the lipid in a molar ratio of 1.3:1, completely prevents the oxidation of lipid due to decomposing peroxychromate at pH 9.0, but some linoleic acid is lost if the incubation is done at pH 7.6. If the concentration of this quench reagent is reduced tenfold, oxidation of linoleic acid by decomposing peroxychromate at pH 9.0 is observed. Hydrogen peroxide is capable of oxidizing the unsaturated fatty acids of lecithin dispersions. Catalase or boiled catalase (2 mg/ml) protects the lipid from oxidation due to decomposing peroxychromate at pH 7.6 to approximately the same extent, but their protective effect is believed to be due to the non-specific removal of .OH. It is concluded that .OH is the species responsible for the lipid oxidation caused by decomposing peroxychromate. This is consistent with the observed bleaching of N,N-dimethyl-p-nitrosoanaline and the formation of a characteristic paramagnetic .OH adduct of the spin trap, 5,5-dimethylpyrroline-1-oxide.

Emissions from prescribed fires in temperate forest in south-east Australia: implications for carbon accounting

NASA Astrophysics Data System (ADS)

Possell, M.; Jenkins, M.; Bell, T. L.; Adams, M. A.

2015-01-01

We estimated emissions of carbon, as equivalent CO2 (CO2e), from planned fires in four sites in a south-eastern Australian forest. Emission estimates were calculated using measurements of fuel load and carbon content of different fuel types, before and after burning, and determination of fuel-specific emission factors. Median estimates of emissions for the four sites ranged from 20 to 139 Mg CO2e ha-1. Variability in estimates was a consequence of different burning efficiencies of each fuel type from the four sites. Higher emissions resulted from more fine fuel (twigs, decomposing matter, near-surface live and leaf litter) or coarse woody debris (CWD; > 25 mm diameter) being consumed. In order to assess the effect of declining information quantity and the inclusion of coarse woody debris when estimating emissions, Monte Carlo simulations were used to create seven scenarios where input parameters values were replaced by probability density functions. Calculation methods were (1) all measured data were constrained between measured maximum and minimum values for each variable; (2) as in (1) except the proportion of carbon within a fuel type was constrained between 0 and 1; (3) as in (2) but losses of mass caused by fire were replaced with burning efficiency factors constrained between 0 and 1; and (4) emissions were calculated using default values in the Australian National Greenhouse Accounts (NGA), National Inventory Report 2011, as appropriate for our sites. Effects of including CWD in calculations were assessed for calculation Method 1, 2 and 3 but not for Method 4 as the NGA does not consider this fuel type. Simulations demonstrate that the probability of estimating true median emissions declines strongly as the amount of information available declines. Including CWD in scenarios increased uncertainty in calculations because CWD is the most variable contributor to fuel load. Inclusion of CWD in scenarios generally increased the amount of carbon lost. We discuss implications of these simulations and how emissions from prescribed burns in temperate Australian forests could be improved.

Input-decomposition balance of heterotrophic processes in a warm-temperate mixed forest in Japan

NASA Astrophysics Data System (ADS)

Jomura, M.; Kominami, Y.; Ataka, M.; Makita, N.; Dannoura, M.; Miyama, T.; Tamai, K.; Goto, Y.; Sakurai, S.

2010-12-01

Carbon accumulation in forest ecosystem has been evaluated using three approaches. One is net ecosystem exchange (NEE) estimated by tower flux measurement. The second is net ecosystem production (NEP) estimated by biometric measurements. NEP can be expressed as the difference between net primary production and heterotrophic respiration. NEP can also be expressed as the annual increment in the plant biomass (ΔW) plus soil (ΔS) carbon pools defined as follows; NEP = ΔW+ΔS The third approach needs to evaluate annual carbon increment in soil compartment. Soil carbon accumulation rate could not be measured directly in a short term because of the small amount of annual accumulation. Soil carbon accumulation rate can be estimated by a model calculation. Rothamsted carbon model is a soil organic carbon turnover model and a useful tool to estimate the rate of soil carbon accumulation. However, the model has not sufficiently included variations in decomposition processes of organic matters in forest ecosystems. Organic matter in forest ecosystems have a different turnover rate that creates temporal variations in input-decomposition balance and also have a large variation in spatial distribution. Thus, in order to estimate the rate of soil carbon accumulation, temporal and spatial variation in input-decomposition balance of heterotrophic processes should be incorporated in the model. In this study, we estimated input-decomposition balance and the rate of soil carbon accumulation using the modified Roth-C model. We measured respiration rate of many types of organic matters, such as leaf litter, fine root litter, twigs and coarse woody debris using a chamber method. We can illustrate the relation of respiration rate to diameter of organic matters. Leaf and fine root litters have no diameter, so assumed to be zero in diameter. Organic matters in small size, such as leaf and fine root litter, have high decomposition respiration. It could be caused by the difference in structure of organic matter. Because coarse woody debris has shape of cylinder, microbes decompose from the surface of it. Thus, respiration rate of coarse woody debris is lower than that of leaf and fine root litter. Based on this result, we modified Roth-C model and estimate soil carbon accumulation rate in recent years. Based on the results from a soil survey, the forest soil stored 30tC ha-1 in O and A horizon. We can evaluate the modified model using this result. NEP can be expressed as the annual increment in the plant biomass plus soil carbon pools. So if we can estimate NEP using this approach, then we can evaluate NEP estimated by micrometeorological and ecological approaches and reduce uncertainty of NEP estimation.

Coarse woody debris: Managing benefits and fire hazard in the recovering forest

Treesearch

James K. Brown; Elizabeth D. Reinhardt; Kylie A. Kramer

2003-01-01

Management of coarse woody debris following fire requires consideration of its positive and negative values. The ecological benefits of coarse woody debris and fire hazard considerations are summarized. This paper presents recommendations for desired ranges of coarse woody debris. Example simulations illustrate changes in debris over time and with varying management....

Coarse-sediment bands on the inner shelf of southern Monterey Bay, California

USGS Publications Warehouse

Hunter, R.E.; Dingler, J.R.; Anima, R.J.; Richmond, B.M.

1988-01-01

Bands of coarse sand that trend parallel to the shore, unlike the approximately shore-normal bands found in many inner shelf areas, occur in southern Monterey Bay at water depths of 10-20 m, less than 1 km from the shore. The bands are 20-100 m wide and alternate with bands of fine sand that are of similar width. The coarse-sand bands are as much as 1 m lower than the adjacent fine-sand bands, which have margins inclined at angles of about 20??. The mean grain sizes of the coarse and fine sand are in the range of 0.354-1.0 mm and 0.125-0.354 mm, respectively. Wave ripples that average about 1 m in spacing always occur in the coarse-sand bands. Over a period of 3 yrs, the individual bands moved irregularly and changed in shape, as demonstrated by repeated sidescan sonar surveys and by the monitoring of rods jetted into the sea floor. However, the overall pattern and distribution of the bands remained essentially unchanged. Cores, 0.5-1.0 m long, taken in coarse-sand bands contain 0.2-0.5 m of coarse sand overlying fine sand or interbedded fine and coarse sand. Cores from fine-sand bands have at least one thin coarse sand layer at about the depth of the adjacent coarse-sand band. None of the cores revealed a thick deposit of coarse sand. The shore-parallel bands are of unknown origin. Their origin is especially puzzling because approximately shore-normal bands are present in parts of the study area and immediately to the north. ?? 1988.

Seeing through the Canopy: Relationship between Coarse Woody Debris and Forest Structure measured by Airborne Lidar in the Brazilian Amazon

NASA Astrophysics Data System (ADS)

Scaranello, M. A., Sr.; Keller, M. M.; dos-Santos, M. N.; Longo, M.; Pinagé, E. R.; Leitold, V.

2016-12-01

Coarse woody debris is an important but infrequently quantified carbon pool in tropical forests. Based on studies at 12 sites spread across the Brazilian Amazon, we quantified coarse woody debris stocks in intact forests and forests affected by different intensities of degradation by logging and/or fire. Measurement were made in-situ and for the first time field measurements of coarse woody debris were related to structural metrics derived from airborne lidar. Using the line-intercept method we established 84 transects for sampling fallen coarse woody debris and associated inventory plots for sampling standing dead wood in intact, conventional logging, reduced impact logging, burned and burned after logging forests. Overall mean and standard deviation of total coarse woody debris were 50.0 Mg ha-1 and 26.4 Mg ha-1 respectively. Forest degradation increased coarse woody debris stocks compared to intact forests by a factor of 1.7 in reduced impact logging forests and up to 3-fold in burned forests, in a side-by-side comparison of nearby areas. The ratio between coarse woody debris and biomass increased linearly with number of degradation events (R²: 0.67, p<0.01). Individual lidar-derived structural variables strongly correlated with coarse woody debris in intact and reduced impact logging forests: the 5th percentile of last returns for in intact forests (R²: 0.78, p<0.01) and forest gap area, mapped using lidar-derived canopy height model, for reduced impact logging forests (R²: 0.63, p<0.01). Individual gap area also played a weak but significant role in determining coarse woody debris in burned forests (R2: 0.21, p<0.05), but with contrasting trend. Both degradation-specific and general multiple models using lidar-derived variables were good predictor of coarse woody debris stocks in different degradation levels in the Brazilian Amazon. The strong relation of coarse woody debris with lidar derived structural variables suggests an approach for quantifying infrequently measured coarse woody debris over large areas.

Computational Methods for Complex Flowfields

DTIC Science & Technology

1989-07-05

This treatment is easily every ohrgi ie(i.9.Telclyfns el a extedd fo a-D knds pinerfces. Ths reuatemen rost e belong to either an unembedded or an...leading edge region is embedded in both directions. The downstream region between the two shear layers remains unembedded . Comparison of the grid and...A2 are unembedded coarse cells with vertical dimensions twice those of cells As, A4. It is clear that an evaluation for example, of the viscous

An Efficient Multiscale Finite-Element Method for Frequency-Domain Seismic Wave Propagation

DOE PAGES

Gao, Kai; Fu, Shubin; Chung, Eric T.

2018-02-13

The frequency-domain seismic-wave equation, that is, the Helmholtz equation, has many important applications in seismological studies, yet is very challenging to solve, particularly for large geological models. Iterative solvers, domain decomposition, or parallel strategies can partially alleviate the computational burden, but these approaches may still encounter nontrivial difficulties in complex geological models where a sufficiently fine mesh is required to represent the fine-scale heterogeneities. We develop a novel numerical method to solve the frequency-domain acoustic wave equation on the basis of the multiscale finite-element theory. We discretize a heterogeneous model with a coarse mesh and employ carefully constructed high-order multiscalemore » basis functions to form the basis space for the coarse mesh. Solved from medium- and frequency-dependent local problems, these multiscale basis functions can effectively capture themedium’s fine-scale heterogeneity and the source’s frequency information, leading to a discrete system matrix with a much smaller dimension compared with those from conventional methods.We then obtain an accurate solution to the acoustic Helmholtz equation by solving only a small linear system instead of a large linear system constructed on the fine mesh in conventional methods.We verify our new method using several models of complicated heterogeneities, and the results show that our new multiscale method can solve the Helmholtz equation in complex models with high accuracy and extremely low computational costs.« less

An Efficient Multiscale Finite-Element Method for Frequency-Domain Seismic Wave Propagation

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

Gao, Kai; Fu, Shubin; Chung, Eric T.

The frequency-domain seismic-wave equation, that is, the Helmholtz equation, has many important applications in seismological studies, yet is very challenging to solve, particularly for large geological models. Iterative solvers, domain decomposition, or parallel strategies can partially alleviate the computational burden, but these approaches may still encounter nontrivial difficulties in complex geological models where a sufficiently fine mesh is required to represent the fine-scale heterogeneities. We develop a novel numerical method to solve the frequency-domain acoustic wave equation on the basis of the multiscale finite-element theory. We discretize a heterogeneous model with a coarse mesh and employ carefully constructed high-order multiscalemore » basis functions to form the basis space for the coarse mesh. Solved from medium- and frequency-dependent local problems, these multiscale basis functions can effectively capture themedium’s fine-scale heterogeneity and the source’s frequency information, leading to a discrete system matrix with a much smaller dimension compared with those from conventional methods.We then obtain an accurate solution to the acoustic Helmholtz equation by solving only a small linear system instead of a large linear system constructed on the fine mesh in conventional methods.We verify our new method using several models of complicated heterogeneities, and the results show that our new multiscale method can solve the Helmholtz equation in complex models with high accuracy and extremely low computational costs.« less

Spatio-temporal conditional inference and hypothesis tests for neural ensemble spiking precision

PubMed Central

Harrison, Matthew T.; Amarasingham, Asohan; Truccolo, Wilson

2014-01-01

The collective dynamics of neural ensembles create complex spike patterns with many spatial and temporal scales. Understanding the statistical structure of these patterns can help resolve fundamental questions about neural computation and neural dynamics. Spatio-temporal conditional inference (STCI) is introduced here as a semiparametric statistical framework for investigating the nature of precise spiking patterns from collections of neurons that is robust to arbitrarily complex and nonstationary coarse spiking dynamics. The main idea is to focus statistical modeling and inference, not on the full distribution of the data, but rather on families of conditional distributions of precise spiking given different types of coarse spiking. The framework is then used to develop families of hypothesis tests for probing the spatio-temporal precision of spiking patterns. Relationships among different conditional distributions are used to improve multiple hypothesis testing adjustments and to design novel Monte Carlo spike resampling algorithms. Of special note are algorithms that can locally jitter spike times while still preserving the instantaneous peri-stimulus time histogram (PSTH) or the instantaneous total spike count from a group of recorded neurons. The framework can also be used to test whether first-order maximum entropy models with possibly random and time-varying parameters can account for observed patterns of spiking. STCI provides a detailed example of the generic principle of conditional inference, which may be applicable in other areas of neurostatistical analysis. PMID:25380339

Technical note: Application of geophysical tools for tree root studies in forest ecosystems in complex soils

NASA Astrophysics Data System (ADS)

Rodríguez-Robles, Ulises; Arredondo, Tulio; Huber-Sannwald, Elisabeth; Alfredo Ramos-Leal, José; Yépez, Enrico A.

2017-11-01

While semiarid forests frequently colonize rocky substrates, knowledge is scarce on how roots garner resources in these extreme habitats. The Sierra San Miguelito Volcanic Complex in central Mexico exhibits shallow soils and impermeable rhyolitic-rock outcrops, which impede water movement and root placement beyond the soil matrix. However, rock fractures, exfoliated rocks and soil pockets potentially permit downward water percolation and root growth. With ground-penetrating radar (GPR) and electrical resistivity tomography (ERT), two geophysical methods advocated by Jayawickreme et al. (2014) to advance root ecology, we advanced in the method development studying root and water distribution in shallow rocky soils and rock fractures in a semiarid forest. We calibrated geophysical images with in situ root measurements, and then extrapolated root distribution over larger areas. Using GPR shielded antennas, we identified both fine and coarse pine and oak roots from 0.6 to 7.5 cm diameter at different depths into either soil or rock fractures. We also detected, trees anchoring their trunks using coarse roots underneath rock outcroppings. With ERT, we tracked monthly changes in humidity at the soil-bedrock interface, which clearly explained spatial root distribution of both tree species. Geophysical methods have enormous potential in elucidating root ecology. More interdisciplinary research could advance our understanding in belowground ecological niche functions and their role in forest ecohydrology and productivity.

A coarse grained protein model with internal degrees of freedom. Application to α-synuclein aggregation

NASA Astrophysics Data System (ADS)

Ilie, Ioana M.; den Otter, Wouter K.; Briels, Wim J.

2016-02-01

Particles in simulations are traditionally endowed with fixed interactions. While this is appropriate for particles representing atoms or molecules, objects with significant internal dynamics—like sequences of amino acids or even an entire protein—are poorly modelled by invariable particles. We develop a highly coarse grained polymorph patchy particle with the ultimate aim of simulating proteins as chains of particles at the secondary structure level. Conformational changes, e.g., a transition between disordered and β-sheet states, are accommodated by internal coordinates that determine the shape and interaction characteristics of the particles. The internal coordinates, as well as the particle positions and orientations, are propagated by Brownian Dynamics in response to their local environment. As an example of the potential offered by polymorph particles, we model the amyloidogenic intrinsically disordered protein α-synuclein, involved in Parkinson's disease, as a single particle with two internal states. The simulations yield oligomers of particles in the disordered state and fibrils of particles in the "misfolded" cross-β-sheet state. The aggregation dynamics is complex, as aggregates can form by a direct nucleation-and-growth mechanism and by two-step-nucleation through conversions between the two cluster types. The aggregation dynamics is complex, with fibrils formed by direct nucleation-and-growth, by two-step-nucleation through the conversion of an oligomer and by auto-catalysis of this conversion.

Finite Dimensional Approximations for Continuum Multiscale Problems

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

Berlyand, Leonid

2017-01-24

The completed research project concerns the development of novel computational techniques for modeling nonlinear multiscale physical and biological phenomena. Specifically, it addresses the theoretical development and applications of the homogenization theory (coarse graining) approach to calculation of the effective properties of highly heterogenous biological and bio-inspired materials with many spatial scales and nonlinear behavior. This theory studies properties of strongly heterogeneous media in problems arising in materials science, geoscience, biology, etc. Modeling of such media raises fundamental mathematical questions, primarily in partial differential equations (PDEs) and calculus of variations, the subject of the PI’s research. The focus of completed researchmore » was on mathematical models of biological and bio-inspired materials with the common theme of multiscale analysis and coarse grain computational techniques. Biological and bio-inspired materials offer the unique ability to create environmentally clean functional materials used for energy conversion and storage. These materials are intrinsically complex, with hierarchical organization occurring on many nested length and time scales. The potential to rationally design and tailor the properties of these materials for broad energy applications has been hampered by the lack of computational techniques, which are able to bridge from the molecular to the macroscopic scale. The project addressed the challenge of computational treatments of such complex materials by the development of a synergistic approach that combines innovative multiscale modeling/analysis techniques with high performance computing.« less

Fusion-based multi-target tracking and localization for intelligent surveillance systems

NASA Astrophysics Data System (ADS)

Rababaah, Haroun; Shirkhodaie, Amir

2008-04-01

In this paper, we have presented two approaches addressing visual target tracking and localization in complex urban environment. The two techniques presented in this paper are: fusion-based multi-target visual tracking, and multi-target localization via camera calibration. For multi-target tracking, the data fusion concepts of hypothesis generation/evaluation/selection, target-to-target registration, and association are employed. An association matrix is implemented using RGB histograms for associated tracking of multi-targets of interests. Motion segmentation of targets of interest (TOI) from the background was achieved by a Gaussian Mixture Model. Foreground segmentation, on other hand, was achieved by the Connected Components Analysis (CCA) technique. The tracking of individual targets was estimated by fusing two sources of information, the centroid with the spatial gating, and the RGB histogram association matrix. The localization problem is addressed through an effective camera calibration technique using edge modeling for grid mapping (EMGM). A two-stage image pixel to world coordinates mapping technique is introduced that performs coarse and fine location estimation of moving TOIs. In coarse estimation, an approximate neighborhood of the target position is estimated based on nearest 4-neighbor method, and in fine estimation, we use Euclidean interpolation to localize the position within the estimated four neighbors. Both techniques were tested and shown reliable results for tracking and localization of Targets of interests in complex urban environment.

KOSMOS: a universal morph server for nucleic acids, proteins and their complexes

PubMed Central

Seo, Sangjae; Kim, Moon Ki

2012-01-01

KOSMOS is the first online morph server to be able to address the structural dynamics of DNA/RNA, proteins and even their complexes, such as ribosomes. The key functions of KOSMOS are the harmonic and anharmonic analyses of macromolecules. In the harmonic analysis, normal mode analysis (NMA) based on an elastic network model (ENM) is performed, yielding vibrational modes and B-factor calculations, which provide insight into the potential biological functions of macromolecules based on their structural features. Anharmonic analysis involving elastic network interpolation (ENI) is used to generate plausible transition pathways between two given conformations by optimizing a topology-oriented cost function that guarantees a smooth transition without steric clashes. The quality of the computed pathways is evaluated based on their various facets, including topology, energy cost and compatibility with the NMA results. There are also two unique features of KOSMOS that distinguish it from other morph servers: (i) the versatility in the coarse-graining methods and (ii) the various connection rules in the ENM. The models enable us to analyze macromolecular dynamics with the maximum degrees of freedom by combining a variety of ENMs from full-atom to coarse-grained, backbone and hybrid models with one connection rule, such as distance-cutoff, number-cutoff or chemical-cutoff. KOSMOS is available at http://bioengineering.skku.ac.kr/kosmos. PMID:22669912

Undecidability and Irreducibility Conditions for Open-Ended Evolution and Emergence.

PubMed

Hernández-Orozco, Santiago; Hernández-Quiroz, Francisco; Zenil, Hector

2018-01-01

Is undecidability a requirement for open-ended evolution (OEE)? Using methods derived from algorithmic complexity theory, we propose robust computational definitions of open-ended evolution and the adaptability of computable dynamical systems. Within this framework, we show that decidability imposes absolute limits on the stable growth of complexity in computable dynamical systems. Conversely, systems that exhibit (strong) open-ended evolution must be undecidable, establishing undecidability as a requirement for such systems. Complexity is assessed in terms of three measures: sophistication, coarse sophistication, and busy beaver logical depth. These three complexity measures assign low complexity values to random (incompressible) objects. As time grows, the stated complexity measures allow for the existence of complex states during the evolution of a computable dynamical system. We show, however, that finding these states involves undecidable computations. We conjecture that for similar complexity measures that assign low complexity values, decidability imposes comparable limits on the stable growth of complexity, and that such behavior is necessary for nontrivial evolutionary systems. We show that the undecidability of adapted states imposes novel and unpredictable behavior on the individuals or populations being modeled. Such behavior is irreducible. Finally, we offer an example of a system, first proposed by Chaitin, that exhibits strong OEE.

Synthesis of In2O3nanoparticles by thermal decomposition of a citrate gel precursor

NASA Astrophysics Data System (ADS)

Rey, J. F. Q.; Plivelic, T. S.; Rocha, R. A.; Tadokoro, S. K.; Torriani, I.; Muccillo, E. N. S.

2005-06-01

This paper describes the synthesis of indium oxide by a modified sol-gel method, and the study of thermal decomposition of the metal complex in air. The characterization of the intermediate as well as the final compounds was carried out by thermogravimetry, differential thermal analysis, Fourier transform infrared spectroscopy, X-ray diffraction, transmission electron microscopy, and small angle X-ray scattering. The results show that the indium complex decomposes to In2O3 with the formation of an intermediate compound. Nanoparticles of cubic In2O3 with crystallite sizes in the nanosize range were formed after calcination at temperatures up to 900°C. Calcined materials are characterized by a polydisperse distribution of spherical particles with sharp and smooth surfaces.

Employing the Hilbert-Huang Transform to analyze observed natural complex signals: Calm wind meandering cases

NASA Astrophysics Data System (ADS)

Martins, Luis Gustavo Nogueira; Stefanello, Michel Baptistella; Degrazia, Gervásio Annes; Acevedo, Otávio Costa; Puhales, Franciano Scremin; Demarco, Giuliano; Mortarini, Luca; Anfossi, Domenico; Roberti, Débora Regina; Costa, Felipe Denardin; Maldaner, Silvana

2016-11-01

In this study we analyze natural complex signals employing the Hilbert-Huang spectral analysis. Specifically, low wind meandering meteorological data are decomposed into turbulent and non turbulent components. These non turbulent movements, responsible for the absence of a preferential direction of the horizontal wind, provoke negative lobes in the meandering autocorrelation functions. The meandering characteristic time scales (meandering periods) are determined from the spectral peak provided by the Hilbert-Huang marginal spectrum. The magnitudes of the temperature and horizontal wind meandering period obtained agree with the results found from the best fit of the heuristic meandering autocorrelation functions. Therefore, the new method represents a new procedure to evaluate meandering periods that does not employ mathematical expressions to represent observed meandering autocorrelation functions.

Decomposition rates and residue-colonizing microbial communities of Bacillus thuringiensis insecticidal protein Cry3Bb-expressing (Bt) and non-Bt corn hybrids in the field.

PubMed

Xue, Kai; Serohijos, Raquel C; Devare, Medha; Thies, Janice E

2011-02-01

Despite the rapid adoption of crops expressing the insecticidal Cry protein(s) from Bacillus thuringiensis (Bt), public concern continues to mount over the potential environmental impacts. Reduced residue decomposition rates and increased tissue lignin concentrations reported for some Bt corn hybrids have been highlighted recently as they may influence soil carbon dynamics. We assessed the effects of MON863 Bt corn, producing the Cry3Bb protein against the corn rootworm complex, on these aspects and associated decomposer communities by terminal restriction fragment length polymorphism (T-RFLP) analysis. Litterbags containing cobs, roots, or stalks plus leaves from Bt and unmodified corn with (non-Bt+I) or without (non-Bt) insecticide applied were placed on the soil surface and at a 10-cm depth in field plots planted with these crop treatments. The litterbags were recovered and analyzed after 3.5, 15.5, and 25 months. No significant effect of treatment (Bt, non-Bt, and non-Bt+I) was observed on initial tissue lignin concentrations, litter decomposition rate, or bacterial decomposer communities. The effect of treatment on fungal decomposer communities was minor, with only 1 of 16 comparisons yielding separation by treatment. Environmental factors (litterbag recovery year, litterbag placement, and plot history) led to significant differences for most measured variables. Combined, these results indicate that the differences detected were driven primarily by environmental factors rather than by any differences between the corn hybrids or the use of tefluthrin. We conclude that the Cry3Bb corn tested in this study is unlikely to affect carbon residence time or turnover in soils receiving these crop residues.

Meteors do not break exogenous organic molecules into high yields of diatomics

NASA Technical Reports Server (NTRS)

Jenniskens, Peter; Schaller, Emily L.; Laux, Christophe O.; Wilson, Michael A.; Schmidt, Greg; Rairden, Rick L.

2004-01-01

Meteoroids that dominate the Earth's extraterrestrial mass influx (50-300 microm size range) may have contributed a unique blend of exogenous organic molecules at the time of the origin of life. Such meteoroids are so large that most of their mass is ablated in the Earth's atmosphere. In the process, organic molecules are decomposed and chemically altered to molecules differently from those delivered to the Earth's surface by smaller (<50 microm) micrometeorites and larger (>10 cm) meteorites. The question addressed here is whether the organic matter in these meteoroids is fully decomposed into atoms or diatomic compounds during ablation. If not, then the ablation products made available for prebiotic organic chemistry, and perhaps early biology, might have retained some memory of their astrophysical nature. To test this hypothesis we searched for CN emission in meteor spectra in an airborne experiment during the 2001 Leonid meteor storm. We found that the meteor's light-emitting air plasma, which included products of meteor ablation, contained less than 1 CN molecule for every 30 meteoric iron atoms. This contrasts sharply with the nitrogen/iron ratio of 1:1.2 in the solid matter of comet 1P/Halley. Unless the nitrogen content or the abundance of complex organic matter in the Leonid parent body, comet 55P/Tempel-Tuttle, differs from that in comet 1P/Halley, it appears that very little of that organic nitrogen decomposes into CN molecules during meteor ablation in the rarefied flow conditions that characterize the atmospheric entry of meteoroids approximately 50 microm-10 cm in size. We propose that the organics of such meteoroids survive instead as larger compounds.

Role of translational entropy in spatially inhomogeneous, coarse-grained models

NASA Astrophysics Data System (ADS)

Langenberg, Marcel; Jackson, Nicholas E.; de Pablo, Juan J.; Müller, Marcus

2018-03-01

Coarse-grained models of polymer and biomolecular systems have enabled the computational study of cooperative phenomena, e.g., self-assembly, by lumping multiple atomistic degrees of freedom along the backbone of a polymer, lipid, or DNA molecule into one effective coarse-grained interaction center. Such a coarse-graining strategy leaves the number of molecules unaltered. In order to treat the surrounding solvent or counterions on the same coarse-grained level of description, one can also stochastically group several of those small molecules into an effective, coarse-grained solvent bead or "fluid element." Such a procedure reduces the number of molecules, and we discuss how to compensate the concomitant loss of translational entropy by density-dependent interactions in spatially inhomogeneous systems.

Coarse graining for synchronization in directed networks

NASA Astrophysics Data System (ADS)

Zeng, An; Lü, Linyuan

2011-05-01

Coarse-graining model is a promising way to analyze and visualize large-scale networks. The coarse-grained networks are required to preserve statistical properties as well as the dynamic behaviors of the initial networks. Some methods have been proposed and found effective in undirected networks, while the study on coarse-graining directed networks lacks of consideration. In this paper we proposed a path-based coarse-graining (PCG) method to coarse grain the directed networks. Performing the linear stability analysis of synchronization and numerical simulation of the Kuramoto model on four kinds of directed networks, including tree networks and variants of Barabási-Albert networks, Watts-Strogatz networks, and Erdös-Rényi networks, we find our method can effectively preserve the network synchronizability.

Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions

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

Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K.

Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for coarse grained models of electrolyte solution. Here, we provide rigorous definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation (DFT-MD) and isolate the effects of charge and cavitation,more » comparing to the Born (linear response) model. We show that using uncorrected Ewald summation leads to highly unphysical values for the solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry (CHA) for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. This suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation. We would like to thank Thomas Beck, Shawn Kathmann, Richard Remsing and John Weeks for helpful discussions. Computing resources were generously allocated by PNNL's Institutional Computing program. This research also used resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. TTD, GKS, and CJM were supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. MDB was supported by MS3 (Materials Synthesis and Simulation Across Scales) Initiative, a Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory (PNNL). PNNL is a multi-program national laboratory operated by Battelle for the U.S. Department of Energy.« less

Acute toxicity of live and decomposing green alga Ulva ( Enteromorpha) prolifera to abalone Haliotis discus hannai

NASA Astrophysics Data System (ADS)

Wang, Chao; Yu, Rencheng; Zhou, Mingjiang

2011-05-01

From 2007 to 2009, large-scale blooms of green algae (the so-called "green tides") occurred every summer in the Yellow Sea, China. In June 2008, huge amounts of floating green algae accumulated along the coast of Qingdao and led to mass mortality of cultured abalone and sea cucumber. However, the mechanism for the mass mortality of cultured animals remains undetermined. This study examined the toxic effects of Ulva ( Enteromorpha) prolifera, the causative species of green tides in the Yellow Sea during the last three years. The acute toxicity of fresh culture medium and decomposing algal effluent of U. prolifera to the cultured abalone Haliotis discus hannai were tested. It was found that both fresh culture medium and decomposing algal effluent had toxic effects to abalone, and decomposing algal effluent was more toxic than fresh culture medium. The acute toxicity of decomposing algal effluent could be attributed to the ammonia and sulfide presented in the effluent, as well as the hypoxia caused by the decomposition process.

Plant–herbivore–decomposer stoichiometric mismatches and nutrient cycling in ecosystems

PubMed Central

Cherif, Mehdi; Loreau, Michel

2013-01-01

Plant stoichiometry is thought to have a major influence on how herbivores affect nutrient availability in ecosystems. Most conceptual models predict that plants with high nutrient contents increase nutrient excretion by herbivores, in turn raising nutrient availability. To test this hypothesis, we built a stoichiometrically explicit model that includes a simple but thorough description of the processes of herbivory and decomposition. Our results challenge traditional views of herbivore impacts on nutrient availability in many ways. They show that the relationship between plant nutrient content and the impact of herbivores predicted by conceptual models holds only at high plant nutrient contents. At low plant nutrient contents, the impact of herbivores is mediated by the mineralization/immobilization of nutrients by decomposers and by the type of resource limiting the growth of decomposers. Both parameters are functions of the mismatch between plant and decomposer stoichiometries. Our work provides new predictions about the impacts of herbivores on ecosystem fertility that depend on critical interactions between plant, herbivore and decomposer stoichiometries in ecosystems. PMID:23303537

Gas Sensitivity and Sensing Mechanism Studies on Au-Doped TiO2 Nanotube Arrays for Detecting SF6 Decomposed Components

PubMed Central

Zhang, Xiaoxing; Yu, Lei; Tie, Jing; Dong, Xingchen

2014-01-01

The analysis to SF6 decomposed component gases is an efficient diagnostic approach to detect the partial discharge in gas-insulated switchgear (GIS) for the purpose of accessing the operating state of power equipment. This paper applied the Au-doped TiO2 nanotube array sensor (Au-TiO2 NTAs) to detect SF6 decomposed components. The electrochemical constant potential method was adopted in the Au-TiO2 NTAs' fabrication, and a series of experiments were conducted to test the characteristic SF6 decomposed gases for a thorough investigation of sensing performances. The sensing characteristic curves of intrinsic and Au-doped TiO2 NTAs were compared to study the mechanism of the gas sensing response. The results indicated that the doped Au could change the TiO2 nanotube arrays' performances of gas sensing selectivity in SF6 decomposed components, as well as reducing the working temperature of TiO2 NTAs. PMID:25330053

Effects of conformational ordering on protein/polyelectrolyte electrostatic complexation: ionic binding and chain stiffening

PubMed Central

Cao, Yiping; Fang, Yapeng; Nishinari, Katsuyoshi; Phillips, Glyn O.

2016-01-01

Coupling of electrostatic complexation with conformational transition is rather general in protein/polyelectrolyte interaction and has important implications in many biological processes and practical applications. This work studied the electrostatic complexation between κ-carrageenan (κ-car) and type B gelatin, and analyzed the effects of the conformational ordering of κ-car induced upon cooling in the presence of potassium chloride (KCl) or tetramethylammonium iodide (Me4NI). Experimental results showed that the effects of conformational ordering on protein/polyelectrolyte electrostatic complexation can be decomposed into ionic binding and chain stiffening. At the initial stage of conformational ordering, electrostatic complexation can be either suppressed or enhanced due to the ionic bindings of K+ and I− ions, which significantly alter the charge density of κ-car or occupy the binding sites of gelatin. Beyond a certain stage of conformational ordering, i.e., helix content θ > 0.30, the effect of chain stiffening, accompanied with a rapid increase in helix length ζ, becomes dominant and tends to dissociate the electrostatic complexation. The effect of chain stiffening can be theoretically interpreted in terms of double helix association. PMID:27030165

An experimental study of postmortem decomposition of methomyl in blood.

PubMed

Kawakami, Yuka; Fuke, Chiaki; Fukasawa, Maki; Ninomiya, Kenji; Ihama, Yoko; Miyazaki, Tetsuji

2017-03-01

Methomyl (S-methyl-1-N-[(methylcarbamoyl)oxy]thioacetimidate) is a carbamate pesticide. It has been noted that in some cases of methomyl poisoning, methomyl is either not detected or detected only in low concentrations in the blood of the victims. However, in such cases, methomyl is detected at higher concentrations in the vitreous humor than in the blood. This indicates that methomyl in the blood is possibly decomposed after death. However, the reasons for this phenomenon have been unclear. We have previously reported that methomyl is decomposed to dimethyl disulfide (DMDS) in the livers and kidneys of pigs but not in their blood. In addition, in the field of forensic toxicology, it is known that some compounds are decomposed or produced by internal bacteria in biological samples after death. This indicates that there is a possibility that methomyl in blood may be decomposed by bacteria after death. The aim of this study was therefore to investigate whether methomyl in blood is decomposed by bacteria isolated from human stool. Our findings demonstrated that methomyl was decomposed in human stool homogenates, resulting in the generation of DMDS. In addition, it was observed that three bacterial species isolated from the stool homogenates, Bacillus cereus, Pseudomonas aeruginosa, and Bacillus sp., showed methomyl-decomposing activity. The results therefore indicated that one reason for the difficulty in detecting methomyl in postmortem blood from methomyl-poisoning victims is the decomposition of methomyl by internal bacteria such as B. cereus, P. aeruginosa, and Bacillus sp. Copyright © 2017 Elsevier B.V. All rights reserved.

Effects of coarse chalk dust particles (2.5-10 μm) on respiratory burst and oxidative stress in alveolar macrophages.

PubMed

Zhang, Yuexia; Yang, Zhenhua; Feng, Yan; Li, Ruijin; Zhang, Quanxi; Geng, Hong; Dong, Chuan

2015-08-01

The main aim of the present study was to examine in vitro responses of rat alveolar macrophages (AMs) exposed to coarse chalk dust particles (particulate matter in the size range 2.5-10 μm, PM(coarse)) by respiratory burst and oxidative stress. Chalk PM(coarse)-induced respiratory burst in AMs was measured by using a luminol-dependent chemiluminescence (CL) method. Also, the cell viability; lactate dehydrogenase (LDH) release; levels of cellular superoxide dismutase (SOD), catalase (CAT), glutathione (GSH), malondialdehyde (MDA), and acid phosphatase (ACP); plasma membrane ATPase; and extracellular nitric oxide (NO) level were determined 4 h following the treatment with the different dosages of chalk PM(coarse). The results showed that chalk PM(coarse) initiated the respiratory burst of AMs as indicated by strong CL, which was inhibited by diphenyleneiodonium chloride and L-N-nitro-L-arginine methyl ester hydrochloride. It suggested that chalk PM(coarse) induced the production of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in AMs. This hypothesis was confirmed by the fact that chalk PM(coarse) resulted in a significant decrease of intracellular SOD, GSH, ACP, and ATPase levels and a notable increase of intracellular CAT, MDA content, and extracellular NO level, consequently leading to a decrease of the cell viability and a increase of LDH release. It was concluded that AMs exposed to chalk PM(coarse) can suffer from cytotoxicity which may be mediated by generation of excessive ROS/RNS. Graphical Abstract The possible mechanism of coarse chalk particles-induced adverse effects in AMs.

Assessment of bedload equations using data obtained with tracers in two coarse-bed mountain streams (Narcea River basin, NW Spain)

NASA Astrophysics Data System (ADS)

Vázquez-Tarrío, Daniel; Menéndez-Duarte, Rosana

2015-06-01

This paper evaluates the predictive power of nine bedload equations, comparing the results provided by the equations with the bedload rates obtained in a previous field-based tracer experiment accomplished in River Pigüeña and River Coto, two coarse bed streams from NW Spain. Rivers from NW Spain draining the northern watershed of the Cantabrian Mountain range flow into the Bay of Biscay in a short path (50-60 km). In this region, they are developed forested catchments featured by fluvial networks with relatively steep slopes, single-thread sinuous channels, and where bed sediment is typically coarse (cobble and gravel). Tagged stones were used to trace bed sediment movement during flood events in River Pigüeña and River Coto, the two main tributaries of the Narcea River basin. With the tracer results, bedload transport rates between 0.2 and 4.0 kg/s were estimated for six flood episodes. The tracer-based bedload discharges were compared with the bedload rates estimated with the bedload formulae (DuBoys-Straub, Schoklitsch, Meyer Peter-Müller, Bagbold, Einstein, Parker-Klingeman-McLean, Parker-Klingeman, Parker and Wilcock-Crowe). Our assessment shows that all of the bedload equations tend to overestimate when compared with the tracer-based results, with the Wilcock and Crowe (2003) equation the only exception in River Pigüeña. We linked these results to the particular geomorphology of coarse-bed rivers in humid and forested mountain environments. Within these rivers, armored textures and structural arrangements in the bed are ubiquitous; these features, together with a low sediment supply coming from upstream forested reaches, define a supply-limited condition for these channels limiting the potential use of bedload equations. The Wilcock and Crowe (2003) equation introduces complex corrections into the 'hiding function', and this could explain why it performs better.

Quantifying the coarse-root biomass of intensively managed loblolly pine plantations

Treesearch

Ashley T. Miller; H. Lee Allen; Chris A. Maier

2006-01-01

Most of the carbon accumulation during a forest rotation is in plant biomass and the forest floor. Most of the belowground biomass in older loblolly pine (Pinus taeda L.) forests is in coarse roots, and coarse roots persist longer after harvest than aboveground biomass and fine roots. The main objective was to assess the carbon accumulation in coarse...

Quantifying the coarse-root biomass of intensively managed loblolly pine plantations

Treesearch

Ashley T. Miller; H. Lee Allen; Chris A. Maier

2006-01-01

Most of the carbon accumulation during a forest rotation is in plant biomass and the forest floor. Most of the belowground biomass in older loblolly pine (Pinus taeda L.) forests is in coarse roots, and coarse roots ersist longer after harvest than aboveground biomass and fine oots. The main objective was to assess the carbon accumulation in coarse...

STOCK: Structure mapper and online coarse-graining kit for molecular simulations

DOE PAGES

Bevc, Staš; Junghans, Christoph; Praprotnik, Matej

2015-03-15

We present a web toolkit STructure mapper and Online Coarse-graining Kit for setting up coarse-grained molecular simulations. The kit consists of two tools: structure mapping and Boltzmann inversion tools. The aim of the first tool is to define a molecular mapping from high, e.g. all-atom, to low, i.e. coarse-grained, resolution. Using a graphical user interface it generates input files, which are compatible with standard coarse-graining packages, e.g. VOTCA and DL_CGMAP. Our second tool generates effective potentials for coarse-grained simulations preserving the structural properties, e.g. radial distribution functions, of the underlying higher resolution model. The required distribution functions can be providedmore » by any simulation package. Simulations are performed on a local machine and only the distributions are uploaded to the server. The applicability of the toolkit is validated by mapping atomistic pentane and polyalanine molecules to a coarse-grained representation. Effective potentials are derived for systems of TIP3P (transferable intermolecular potential 3 point) water molecules and salt solution. The presented coarse-graining web toolkit is available at http://stock.cmm.ki.si.« less

On system behaviour using complex networks of a compression algorithm

NASA Astrophysics Data System (ADS)

Walker, David M.; Correa, Debora C.; Small, Michael

2018-01-01

We construct complex networks of scalar time series using a data compression algorithm. The structure and statistics of the resulting networks can be used to help characterize complex systems, and one property, in particular, appears to be a useful discriminating statistic in surrogate data hypothesis tests. We demonstrate these ideas on systems with known dynamical behaviour and also show that our approach is capable of identifying behavioural transitions within electroencephalogram recordings as well as changes due to a bifurcation parameter of a chaotic system. The technique we propose is dependent on a coarse grained quantization of the original time series and therefore provides potential for a spatial scale-dependent characterization of the data. Finally the method is as computationally efficient as the underlying compression algorithm and provides a compression of the salient features of long time series.

Comprehensive evaluation of liver resection procedures: surgical mind development through cognitive task analysis.

PubMed

Ho, Cheng-Maw; Wakabayashi, Go; Yeh, Chi-Chuan; Hu, Rey-Heng; Sakaguchi, Takanori; Hasegawa, Yasushi; Takahara, Takeshi; Nitta, Hiroyuki; Sasaki, Akira; Lee, Po-Huang

2018-01-01

Liver resection is a complex procedure for trainee surgeons. Cognitive task analysis (CTA) facilitates understanding and decomposing tasks that require a great proportion of mental activity from experts. Using CTA and video-based coaching to compare liver resection by open and laparoscopic approaches, we decomposed the task of liver resection into exposure (visual field building), adequate tension made at the working plane (which may change three-dimensionally during the resection process), and target processing (intervention strategy) that can bridge the gap from the basic surgical principle. The key steps of highly-specialized techniques, including hanging maneuvers and looping of extra-hepatic hepatic veins, were shown on video by open and laparoscopic approaches. Familiarization with laparoscopic anatomical orientation may help surgeons already skilled at open liver resection transit to perform laparoscopic liver resection smoothly. Facilities at hand (such as patient tolerability, advanced instruments, and trained teams of personnel) can influence surgical decision making. Application of the rationale and realizing the interplay between the surgical principles and the other paramedical factors may help surgeons in training to understand the mental abstractions of experienced surgeons, to choose the most appropriate surgical strategy effectively at will, and to minimize the gap.

Parallel algorithms for placement and routing in VLSI design. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Brouwer, Randall Jay

1991-01-01

The computational requirements for high quality synthesis, analysis, and verification of very large scale integration (VLSI) designs have rapidly increased with the fast growing complexity of these designs. Research in the past has focused on the development of heuristic algorithms, special purpose hardware accelerators, or parallel algorithms for the numerous design tasks to decrease the time required for solution. Two new parallel algorithms are proposed for two VLSI synthesis tasks, standard cell placement and global routing. The first algorithm, a parallel algorithm for global routing, uses hierarchical techniques to decompose the routing problem into independent routing subproblems that are solved in parallel. Results are then presented which compare the routing quality to the results of other published global routers and which evaluate the speedups attained. The second algorithm, a parallel algorithm for cell placement and global routing, hierarchically integrates a quadrisection placement algorithm, a bisection placement algorithm, and the previous global routing algorithm. Unique partitioning techniques are used to decompose the various stages of the algorithm into independent tasks which can be evaluated in parallel. Finally, results are presented which evaluate the various algorithm alternatives and compare the algorithm performance to other placement programs. Measurements are presented on the parallel speedups available.

The Prediction of Students' Academic Performance With Fluid Intelligence in Giving Special Consideration to the Contribution of Learning.

PubMed

Ren, Xuezhu; Schweizer, Karl; Wang, Tengfei; Xu, Fen

2015-01-01

The present study provides a new account of how fluid intelligence influences academic performance. In this account a complex learning component of fluid intelligence tests is proposed to play a major role in predicting academic performance. A sample of 2, 277 secondary school students completed two reasoning tests that were assumed to represent fluid intelligence and standardized math and verbal tests assessing academic performance. The fluid intelligence data were decomposed into a learning component that was associated with the position effect of intelligence items and a constant component that was independent of the position effect. Results showed that the learning component contributed significantly more to the prediction of math and verbal performance than the constant component. The link from the learning component to math performance was especially strong. These results indicated that fluid intelligence, which has so far been considered as homogeneous, could be decomposed in such a way that the resulting components showed different properties and contributed differently to the prediction of academic performance. Furthermore, the results were in line with the expectation that learning was a predictor of performance in school.

Improved Cook-off Modeling of Multi-component Cast Explosives

NASA Astrophysics Data System (ADS)

Nichols, Albert

2017-06-01

In order to understand the hazards associated with energetic materials, it is important to understand their behavior in adverse thermal environments. These processes have been relatively well understood for solid explosives, however, the same cannot be said for multi-component melt-cast explosives. Here we describe the continued development of ALE3D, a coupled thermal/chemical/mechanical code, to improve its description of fluid explosives. The improved physics models include: 1) Chemical potential driven species segregation. This model allows us to model the complex flow fields associated with the melting and decomposing Comp-B, where the denser RDX tends to settle and the decomposing gasses rise, 2) Automatically scaled stream-wise diffusion model for thermal, species, and momentum diffusion. These models add sufficient numerical diffusion in the direction of flow to maintain numerical stability when the system is under resolved, as occurs for large systems. And 3) a slurry viscosity model, required to properly define the flow characteristics of the multi-component fluidized system. These models will be demonstrated on a simple Comp-B system. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under contract DE-AC52-07NA27344.

Learning and diagnosing faults using neural networks

NASA Technical Reports Server (NTRS)

Whitehead, Bruce A.; Kiech, Earl L.; Ali, Moonis

1990-01-01

Neural networks have been employed for learning fault behavior from rocket engine simulator parameters and for diagnosing faults on the basis of the learned behavior. Two problems in applying neural networks to learning and diagnosing faults are (1) the complexity of the sensor data to fault mapping to be modeled by the neural network, which implies difficult and lengthy training procedures; and (2) the lack of sufficient training data to adequately represent the very large number of different types of faults which might occur. Methods are derived and tested in an architecture which addresses these two problems. First, the sensor data to fault mapping is decomposed into three simpler mappings which perform sensor data compression, hypothesis generation, and sensor fusion. Efficient training is performed for each mapping separately. Secondly, the neural network which performs sensor fusion is structured to detect new unknown faults for which training examples were not presented during training. These methods were tested on a task of fault diagnosis by employing rocket engine simulator data. Results indicate that the decomposed neural network architecture can be trained efficiently, can identify faults for which it has been trained, and can detect the occurrence of faults for which it has not been trained.

The Prediction of Students’ Academic Performance With Fluid Intelligence in Giving Special Consideration to the Contribution of Learning

PubMed Central

Ren, Xuezhu; Schweizer, Karl; Wang, Tengfei; Xu, Fen

2015-01-01

The present study provides a new account of how fluid intelligence influences academic performance. In this account a complex learning component of fluid intelligence tests is proposed to play a major role in predicting academic performance. A sample of 2, 277 secondary school students completed two reasoning tests that were assumed to represent fluid intelligence and standardized math and verbal tests assessing academic performance. The fluid intelligence data were decomposed into a learning component that was associated with the position effect of intelligence items and a constant component that was independent of the position effect. Results showed that the learning component contributed significantly more to the prediction of math and verbal performance than the constant component. The link from the learning component to math performance was especially strong. These results indicated that fluid intelligence, which has so far been considered as homogeneous, could be decomposed in such a way that the resulting components showed different properties and contributed differently to the prediction of academic performance. Furthermore, the results were in line with the expectation that learning was a predictor of performance in school. PMID:26435760

The structure and functions of bacterial communities in an agrocenosis

NASA Astrophysics Data System (ADS)

Dobrovol'skaya, T. G.; Khusnetdinova, K. A.; Manucharova, N. A.; Balabko, P. N.

2016-01-01

The most significant factor responsible for the specific taxonomic composition of the bacterial communities in the agrocenosis studied was found to be a part or organ of plants (leaves, flowers, roots, fruits). A stage of plant ontogeny also determines changes of taxa. In the course of the plant growth, eccrisotrophic bacteria are replaced by hydrolytic ones that belong to the group of cellulose-decomposing bacteria. Representatives of the proteobacteria genera that are difficult to identify by phenotypic methods were determined using molecular-biological methods. They were revealed only on oat leaves in the moist period. As the vetch-oat mixture was fertilized with BIOUD-1 (foliar application) in the phyllosphere of both oats and vetch, on all the plant organs, representatives of the Rhodococcus genus as dominants were isolated. This fact was related to the capability of bacteria to decompose the complex aromatic compounds that are ingredients of the fertilizers applied. Another positive effect for plants of the bacterial communities forming in agrocenoses is the presence of bacteria that are antagonists of phytopathogenic bacteria. Thus, in agrocenoses, some interrelationships promoting the growth and reproduction of plants are formed in crop plants and bacteria.

Nonequilibrium forces between atoms and dielectrics mediated by a quantum field

NASA Astrophysics Data System (ADS)

Behunin, Ryan O.; Hu, Bei-Lok

2011-07-01

In this paper we give a first principles microphysics derivation of the nonequilibrium forces between an atom, treated as a three-dimensional harmonic oscillator, and a bulk dielectric medium modeled as a continuous lattice of oscillators coupled to a reservoir. We assume no direct interaction between the atom and the medium but there exist mutual influences transmitted via a common electromagnetic field. By employing concepts and techniques of open quantum systems we introduce coarse-graining to the physical variables—the medium, the quantum field, and the atom’s internal degrees of freedom, in that order—to extract their averaged effects from the lowest tier progressively to the top tier. The first tier of coarse-graining provides the averaged effect of the medium upon the field, quantified by a complex permittivity (in the frequency domain) describing the response of the dielectric to the field in addition to its back action on the field through a stochastic forcing term. The last tier of coarse-graining over the atom’s internal degrees of freedom results in an equation of motion for the atom’s center of mass from which we can derive the force on the atom. Our nonequilibrium formulation provides a fully dynamical description of the atom’s motion including back-action effects from all other relevant variables concerned. In the long-time limit we recover the known results for the atom-dielectric force when the combined system is in equilibrium or in a nonequilibrium stationary state.

Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism

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

Li, Zhen; Bian, Xin; Karniadakis, George Em, E-mail: george-karniadakis@brown.edu

2015-12-28

The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables, and the memory kernel is evaluated directly from microscopic dynamics. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while themore » corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons between the CG models with Markovian and non-Markovian approximations indicate that including the memory effects using NM-DPD yields similar results as the Markovian-based DPD if the system has clear time scale separation. However, for systems with small separation of time scales, NM-DPD can reproduce correct short-time properties that are related to how the system responds to high-frequency disturbances, which cannot be captured by the Markovian-based DPD model.« less

New Coarse-Grained Model and Its Implementation in Simulations of Graphene Assemblies.

PubMed

Shang, Jun-Jun; Yang, Qing-Sheng; Liu, Xia

2017-08-08

Graphene is a one-atom thick layer of carbon atoms arranged in a hexagonal pattern, which makes it the strongest material in the world. The Tersoff potential is a suitable potential for simulating the mechanical behavior of the complex covalently bonded system of graphene. In this paper, we describe a new coarse-grained (CG) potential, TersoffCG, which is based on the function form of the Tersoff potential. The TersoffCG applies to a CG model of graphene that uses the same hexagonal pattern as the atomistic model. The parameters of the TersoffCG potential are determined using structural feature and potential-energy fitting between the CG model and the atomic model. The modeling process of graphene is highly simplified using the present CG model as it avoids the necessity to define bonds/angles/dihedrals connectivity. What is more, the present CG model provides a new perspective of coarse-graining scheme for crystal structures of nanomaterials. The structural changes and mechanical properties of multilayer graphene were calculated using the new potential. Furthermore, a CG model of a graphene aerogel was built in a specific form of assembly. The chemical bonding in the joints of graphene-aerogel forms automatically during the energy relaxation process. The compressive and recover test of the graphene aerogel was reproduced to study its high elasticity. Our computational examples show that the TersoffCG potential can be used for simulations of graphene and its assemblies, which have many applications in areas of environmental protection, aerospace engineering, and others.

Direct measurements of mean Reynolds stress and ripple roughness in the presence of energetic forcing by surface waves

USGS Publications Warehouse

Scully, Malcolm; Trowbridge, John; Sherwood, Christopher R.; Jones, Katie R.; Traykovski, Peter A.

2018-01-01

Direct covariance observations of the mean flow Reynolds stress and sonar images of the seafloor collected on a wave‐exposed inner continental shelf demonstrate that the drag exerted by the seabed on the overlying flow is consistent with boundary layer models for wave‐current interaction, provided that the orientation and anisotropy of the bed roughness are appropriately quantified. Large spatial and temporal variations in drag result from nonequilibrium ripple dynamics, ripple anisotropy, and the orientation of the ripples relative to the current. At a location in coarse sand characterized by large two‐dimensional orbital ripples, the observed drag shows a strong dependence on the relative orientation of the mean current to the ripple crests. At a contrasting location in fine sand, where more isotropic sub‐orbital ripples are observed, the sensitivity of the current to the orientation of the ripples is reduced. Further, at the coarse site under conditions when the currents are parallel to the ripple crests and the wave orbital diameter is smaller than the wavelength of the relic orbital ripples, the flow becomes hydraulically smooth. This transition is not observed at the fine site, where the observed wave orbital diameter is always greater than the wavelength of the observed sub‐orbital ripples. Paradoxically, the dominant along‐shelf flows often experience lower drag at the coarse site than at the fine site, despite the larger ripples, highlighting the complex dynamics controlling drag in wave‐exposed environments with heterogeneous roughness.

Direct Measurements of Mean Reynolds Stress and Ripple Roughness in the Presence of Energetic Forcing by Surface Waves

NASA Astrophysics Data System (ADS)

Scully, Malcolm E.; Trowbridge, John H.; Sherwood, Christopher R.; Jones, Katie R.; Traykovski, Peter

2018-04-01

Direct covariance observations of the mean flow Reynolds stress and sonar images of the seafloor collected on a wave-exposed inner continental shelf demonstrate that the drag exerted by the seabed on the overlying flow is consistent with boundary layer models for wave-current interaction, provided that the orientation and anisotropy of the bed roughness are appropriately quantified. Large spatial and temporal variations in drag result from nonequilibrium ripple dynamics, ripple anisotropy, and the orientation of the ripples relative to the current. At a location in coarse sand characterized by large two-dimensional orbital ripples, the observed drag shows a strong dependence on the relative orientation of the mean current to the ripple crests. At a contrasting location in fine sand, where more isotropic sub-orbital ripples are observed, the sensitivity of the current to the orientation of the ripples is reduced. Further, at the coarse site under conditions when the currents are parallel to the ripple crests and the wave orbital diameter is smaller than the wavelength of the relic orbital ripples, the flow becomes hydraulically smooth. This transition is not observed at the fine site, where the observed wave orbital diameter is always greater than the wavelength of the observed sub-orbital ripples. Paradoxically, the dominant along-shelf flows often experience lower drag at the coarse site than at the fine site, despite the larger ripples, highlighting the complex dynamics controlling drag in wave-exposed environments with heterogeneous roughness.

The Renormalization Group and Its Applications to Generating Coarse-Grained Models of Large Biological Molecular Systems.

PubMed

Koehl, Patrice; Poitevin, Frédéric; Navaza, Rafael; Delarue, Marc

2017-03-14

Understanding the dynamics of biomolecules is the key to understanding their biological activities. Computational methods ranging from all-atom molecular dynamics simulations to coarse-grained normal-mode analyses based on simplified elastic networks provide a general framework to studying these dynamics. Despite recent successes in studying very large systems with up to a 100,000,000 atoms, those methods are currently limited to studying small- to medium-sized molecular systems due to computational limitations. One solution to circumvent these limitations is to reduce the size of the system under study. In this paper, we argue that coarse-graining, the standard approach to such size reduction, must define a hierarchy of models of decreasing sizes that are consistent with each other, i.e., that each model contains the information of the dynamics of its predecessor. We propose a new method, Decimate, for generating such a hierarchy within the context of elastic networks for normal-mode analysis. This method is based on the concept of the renormalization group developed in statistical physics. We highlight the details of its implementation, with a special focus on its scalability to large systems of up to millions of atoms. We illustrate its application on two large systems, the capsid of a virus and the ribosome translation complex. We show that highly decimated representations of those systems, containing down to 1% of their original number of atoms, still capture qualitatively and quantitatively their dynamics. Decimate is available as an OpenSource resource.

Source identification of coarse particles in the Desert ...

EPA Pesticide Factsheets

The Desert Southwest Coarse Particulate Matter Study was undertaken to further our understanding of the spatial and temporal variability and sources of fine and coarse particulate matter (PM) in rural, arid, desert environments. Sampling was conducted between February 2009 and February 2010 in Pinal County, AZ near the town of Casa Grande where PM concentrations routinely exceed the U.S. National Ambient Air Quality Standards (NAAQS) for both PM10 and PM2.5. In this desert region, exceedances of the PM10 NAAQS are dominated by high coarse particle concentrations, a common occurrence in this region of the United States. This work expands on previously published measurements of PM mass and chemistry by examining the sources of fine and coarse particles and the relative contribution of each to ambient PM mass concentrations using the Positive Matrix Factorization receptor model (Clements et al., 2014). Highlights • Isolation of coarse particles from fine particle sources. • Unique chemical composition of coarse particles. • Role of primary biological particles on aerosol loadings.

Effect of fly ash on the strength of porous concrete using recycled coarse aggregate to replace low-quality natural coarse aggregate

NASA Astrophysics Data System (ADS)

Arifi, Eva; Cahya, Evi Nur; Christin Remayanti, N.

2017-09-01

The performance of porous concrete made of recycled coarse aggregate was investigated. Fly ash was used as cement partial replacement. In this study, the strength of recycled aggregate was coMPared to low quality natural coarse aggregate which has high water absorption. Compression strength and tensile splitting strength test were conducted to evaluate the performance of porous concrete using fly ash as cement replacement. Results have shown that the utilization of recycled coarse aggregate up to 75% to replace low quality natural coarse aggregate with high water absorption increases compressive strength and splitting tensile strength of porous concrete. Using fly ash up to 25% as cement replacement improves compressive strength and splitting tensile strength of porous concrete.

Simulation study of entropy production in the one-dimensional Vlasov system

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

Dai, Zongliang, E-mail: liangliang1223@gmail.com; Wang, Shaojie

2016-07-15

The coarse-grain averaged distribution function of the one-dimensional Vlasov system is obtained by numerical simulation. The entropy productions in cases of the random field, the linear Landau damping, and the bump-on-tail instability are computed with the coarse-grain averaged distribution function. The computed entropy production is converged with increasing length of coarse-grain average. When the distribution function differs slightly from a Maxwellian distribution, the converged value agrees with the result computed by using the definition of thermodynamic entropy. The length of the coarse-grain average to compute the coarse-grain averaged distribution function is discussed.

Developing a complex independent component analysis technique to extract non-stationary patterns from geophysical time-series

NASA Astrophysics Data System (ADS)

Forootan, Ehsan; Kusche, Jürgen

2016-04-01

Geodetic/geophysical observations, such as the time series of global terrestrial water storage change or sea level and temperature change, represent samples of physical processes and therefore contain information about complex physical interactionswith many inherent time scales. Extracting relevant information from these samples, for example quantifying the seasonality of a physical process or its variability due to large-scale ocean-atmosphere interactions, is not possible by rendering simple time series approaches. In the last decades, decomposition techniques have found increasing interest for extracting patterns from geophysical observations. Traditionally, principal component analysis (PCA) and more recently independent component analysis (ICA) are common techniques to extract statistical orthogonal (uncorrelated) and independent modes that represent the maximum variance of observations, respectively. PCA and ICA can be classified as stationary signal decomposition techniques since they are based on decomposing the auto-covariance matrix or diagonalizing higher (than two)-order statistical tensors from centered time series. However, the stationary assumption is obviously not justifiable for many geophysical and climate variables even after removing cyclic components e.g., the seasonal cycles. In this paper, we present a new decomposition method, the complex independent component analysis (CICA, Forootan, PhD-2014), which can be applied to extract to non-stationary (changing in space and time) patterns from geophysical time series. Here, CICA is derived as an extension of real-valued ICA (Forootan and Kusche, JoG-2012), where we (i) define a new complex data set using a Hilbert transformation. The complex time series contain the observed values in their real part, and the temporal rate of variability in their imaginary part. (ii) An ICA algorithm based on diagonalization of fourth-order cumulants is then applied to decompose the new complex data set in (i). (iii) Dominant non-stationary patterns are recognized as independent complex patterns that can be used to represent the space and time amplitude and phase propagations. We present the results of CICA on simulated and real cases e.g., for quantifying the impact of large-scale ocean-atmosphere interaction on global mass changes. Forootan (PhD-2014) Statistical signal decomposition techniques for analyzing time-variable satellite gravimetry data, PhD Thesis, University of Bonn, http://hss.ulb.uni-bonn.de/2014/3766/3766.htm Forootan and Kusche (JoG-2012) Separation of global time-variable gravity signals into maximally independent components, Journal of Geodesy 86 (7), 477-497, doi: 10.1007/s00190-011-0532-5

Design and implementation of low complexity wake-up receiver for underwater acoustic sensor networks

NASA Astrophysics Data System (ADS)

Yue, Ming

This thesis designs a low-complexity dual Pseudorandom Noise (PN) scheme for identity (ID) detection and coarse frame synchronization. The two PN sequences for a node are identical and are separated by a specified length of gap which serves as the ID of different sensor nodes. The dual PN sequences are short in length but are capable of combating severe underwater acoustic (UWA) multipath fading channels that exhibit time varying impulse responses up to 100 taps. The receiver ID detection is implemented on a microcontroller MSP430F5529 by calculating the correlation between the two segments of the PN sequence with the specified separation gap. When the gap length is matched, the correlator outputs a peak which triggers the wake-up enable. The time index of the correlator peak is used as the coarse synchronization of the data frame. The correlator is implemented by an iterative algorithm that uses only one multiplication and two additions for each sample input regardless of the length of the PN sequence, thus achieving low computational complexity. The real-time processing requirement is also met via direct memory access (DMA) and two circular buffers to accelerate data transfer between the peripherals and the memory. The proposed dual PN detection scheme has been successfully tested by simulated fading channels and real-world measured channels. The results show that, in long multipath channels with more than 60 taps, the proposed scheme achieves high detection rate and low false alarm rate using maximal-length sequences as short as 31 bits to 127 bits, therefore it is suitable as a low-power wake-up receiver. The future research will integrate the wake-up receiver with Digital Signal Processors (DSP) for payload detection.

Arbuscular mycorrhizal fungi make a complex contribution to soil aggregation

NASA Astrophysics Data System (ADS)

McGee, Peter; Daynes, Cathal; Damien, Field

2013-04-01

Soil aggregates contain solid and fluid components. Aggregates develop as a consequence of the organic materials, plants and hyphae of arbuscular mycorrhizal (AM) fungi acting on the solid phase. Various correlative studies indicate hyphae of AM fungi enmesh soil particles, but their impact on the pore space is poorly understood. Hyphae may penetrate between particles, remove water from interstitial spaces, and otherwise re-arrange the solid phase. Thus we might predict that AM fungi also change the pore architecture of aggregates. Direct observations of pore architecture of soil, such as by computer-aided tomography (CT), is difficult. The refractive natures of solid and biological material are similar. The plant-available water in various treatments allows us to infer changes in pore architecture. Our experimental studies indicate AM fungi have a complex role in the formation and development of aggregates. Soils formed from compost and coarse subsoil materials were planted with mycorrhizal or non-mycorrhizal seedlings and the resultant soils compared after 6 or 14 months in separate experiments. As well as enmeshing particles, AM fungi were associated with the development of a complex pore space and greater pore volume. Even though AM fungi add organic matter to soil, the modification of pore space is not correlated with organic carbon. In a separate study, we visualised hyphae of AM fungi in a coarse material using CT. In this study, hyphae appeared to grow close to the surfaces of particles with limited ramification across the pore spaces. Hyphae of AM fungi appear to utilise soil moisture for their growth and development of mycelium. The strong correlation between moisture and hyphae has profound implications for soil aggregation, plant utilisation of soil water, and the distribution of water as water availability declines.

Coarse sediment transport dynamics at three spatial scales of bedrock channel bed complexity

NASA Astrophysics Data System (ADS)

Goode, J. R.; Wohl, E.

2007-12-01

Rivers incised into bedrock in fold-dominated terrain display a complex bed topography that strongly interacts with local hydraulics to produce spatial differences in bed sediment flux. We used painted tracer clasts to investigate how this complex bed topography influences coarse sediment transport at three spatial scales (reach, cross- section and grain). The study was conducted along the Ocoee River gorge, Tennessee between the TVA Ocoee #3 dam and the 1996 Olympic whitewater course. The bed topography consists of undulating bedrock ribs, which are formed at a consistent strike to the bedding and cleavage of the metagreywake and phyllite substrate. Ribs vary in their orientation to flow (from parallel to oblique) and amplitude among three study reaches. These bedrock ribs create a rough bed topography that substantially alters the local flow field and influences reach- scale roughness. In each reach, 300 tracer clasts were randomly selected from the existing bed material. Tracer clasts were surveyed and transport distances were calculated after five scheduled summer releases and a suite of slightly larger but sporadic winter releases. Transport distances were examined as a function of rib orientation and amplitude (reach scale), spatial proximity to bedrock ribs and standard deviation of the bed elevation (cross- section scale), and whether clasts were hydraulically shielded by surrounding clasts, incorporated in the armour layer, imbricated, and/or existed in a pothole, in addition to size and angularity. At the reach scale, where ribs are parallel to flow, lower reach-scale roughness leads to greater sediment transport capacity, sediment flux and transport distances because transport is uninhibited in the downstream direction. Preliminary results indicate that cross section scale characteristics of bed topography exert a greater control on transport distances than grain size.

Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins.

PubMed

May, Ali; Pool, René; van Dijk, Erik; Bijlard, Jochem; Abeln, Sanne; Heringa, Jaap; Feenstra, K Anton

2014-02-01

To assess whether two proteins will interact under physiological conditions, information on the interaction free energy is needed. Statistical learning techniques and docking methods for predicting protein-protein interactions cannot quantitatively estimate binding free energies. Full atomistic molecular simulation methods do have this potential, but are completely unfeasible for large-scale applications in terms of computational cost required. Here we investigate whether applying coarse-grained (CG) molecular dynamics simulations is a viable alternative for complexes of known structure. We calculate the free energy barrier with respect to the bound state based on molecular dynamics simulations using both a full atomistic and a CG force field for the TCR-pMHC complex and the MP1-p14 scaffolding complex. We find that the free energy barriers from the CG simulations are of similar accuracy as those from the full atomistic ones, while achieving a speedup of >500-fold. We also observe that extensive sampling is extremely important to obtain accurate free energy barriers, which is only within reach for the CG models. Finally, we show that the CG model preserves biological relevance of the interactions: (i) we observe a strong correlation between evolutionary likelihood of mutations and the impact on the free energy barrier with respect to the bound state; and (ii) we confirm the dominant role of the interface core in these interactions. Therefore, our results suggest that CG molecular simulations can realistically be used for the accurate prediction of protein-protein interaction strength. The python analysis framework and data files are available for download at http://www.ibi.vu.nl/downloads/bioinformatics-2013-btt675.tgz.

Rolling bearing fault detection and diagnosis based on composite multiscale fuzzy entropy and ensemble support vector machines

NASA Astrophysics Data System (ADS)

Zheng, Jinde; Pan, Haiyang; Cheng, Junsheng

2017-02-01

To timely detect the incipient failure of rolling bearing and find out the accurate fault location, a novel rolling bearing fault diagnosis method is proposed based on the composite multiscale fuzzy entropy (CMFE) and ensemble support vector machines (ESVMs). Fuzzy entropy (FuzzyEn), as an improvement of sample entropy (SampEn), is a new nonlinear method for measuring the complexity of time series. Since FuzzyEn (or SampEn) in single scale can not reflect the complexity effectively, multiscale fuzzy entropy (MFE) is developed by defining the FuzzyEns of coarse-grained time series, which represents the system dynamics in different scales. However, the MFE values will be affected by the data length, especially when the data are not long enough. By combining information of multiple coarse-grained time series in the same scale, the CMFE algorithm is proposed in this paper to enhance MFE, as well as FuzzyEn. Compared with MFE, with the increasing of scale factor, CMFE obtains much more stable and consistent values for a short-term time series. In this paper CMFE is employed to measure the complexity of vibration signals of rolling bearings and is applied to extract the nonlinear features hidden in the vibration signals. Also the physically meanings of CMFE being suitable for rolling bearing fault diagnosis are explored. Based on these, to fulfill an automatic fault diagnosis, the ensemble SVMs based multi-classifier is constructed for the intelligent classification of fault features. Finally, the proposed fault diagnosis method of rolling bearing is applied to experimental data analysis and the results indicate that the proposed method could effectively distinguish different fault categories and severities of rolling bearings.

Drilling into Rhyolitic Magma at Shallow depth at Krafla Volcanic Complex, NE-Iceland

NASA Astrophysics Data System (ADS)

Mortensen, A. K.; Markússon, S. H.; Gudmundsson, Á.; Pálsson, B.

2017-12-01

Krafla volcanic complex in NE-Iceland is an active volcano but the latest eruption was the Krafla Fires in 1975-1984. Though recent volcanic activity has consisted of basaltic fissure eruptions, then it is rhyolitic magma that has been intercepted on at least two occasions while drilling geothermal production wells in the geothermal field suggesting a layered magma plumbing system beneath the Krafla volcanic complex. In 2008 quenched rhyolitic glass was retrieved from the bottom of well KJ-39, which is 2865 m deep ( 2571 m true vertical depth). In 2009 magma was again encountered at an even shallower depth and in more than 2,5 km distance from the bottom of well KJ-39, but in 2009 well IDDP-1 was drilled into magma three times just below 2100 m depth. Only on the last occasion was quenched glass retrieved to confirm that magma had been encountered. In well KJ-39 the quenched glass was rhyolitic in composition. The glass contained resorbed minerals of plagioclase, clinopyroxene and titanomagnetite, but the composition of the glass resembles magma that has formed by partial melting of hydrated basalt. The melt was encountered among cuttings from impermeable, coarse basaltic intrusives at a depth, where the well was anticipated to penetrate the Hólseldar volcanic fissure. In IDDP-1 the quenched glass was also rhyolitic in composition. The glass contained less than 5% of phenocrysts, but the phenocryst assemblage included andesine plagioclase, augite, pigeonite, and titanomagnetite. At IDDP-1 the melt was encountered below a permeable zone composed of fine to coarse grained felsite and granophyre. The disclosure of magma in two wells at Krafla volcanic complex verify that rhyolitic magma can be encountered at shallow depth across a larger area within the caldera. The encounter of magma at shallow depth conforms with that superheated conditions have been found at >2000 m depth in large parts of Krafla geothermal field.

Multi-element least square HDMR methods and their applications for stochastic multiscale model reduction

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

Jiang, Lijian, E-mail: ljjiang@hnu.edu.cn; Li, Xinping, E-mail: exping@126.com

Stochastic multiscale modeling has become a necessary approach to quantify uncertainty and characterize multiscale phenomena for many practical problems such as flows in stochastic porous media. The numerical treatment of the stochastic multiscale models can be very challengeable as the existence of complex uncertainty and multiple physical scales in the models. To efficiently take care of the difficulty, we construct a computational reduced model. To this end, we propose a multi-element least square high-dimensional model representation (HDMR) method, through which the random domain is adaptively decomposed into a few subdomains, and a local least square HDMR is constructed in eachmore » subdomain. These local HDMRs are represented by a finite number of orthogonal basis functions defined in low-dimensional random spaces. The coefficients in the local HDMRs are determined using least square methods. We paste all the local HDMR approximations together to form a global HDMR approximation. To further reduce computational cost, we present a multi-element reduced least-square HDMR, which improves both efficiency and approximation accuracy in certain conditions. To effectively treat heterogeneity properties and multiscale features in the models, we integrate multiscale finite element methods with multi-element least-square HDMR for stochastic multiscale model reduction. This approach significantly reduces the original model's complexity in both the resolution of the physical space and the high-dimensional stochastic space. We analyze the proposed approach, and provide a set of numerical experiments to demonstrate the performance of the presented model reduction techniques. - Highlights: • Multi-element least square HDMR is proposed to treat stochastic models. • Random domain is adaptively decomposed into some subdomains to obtain adaptive multi-element HDMR. • Least-square reduced HDMR is proposed to enhance computation efficiency and approximation accuracy in certain conditions. • Integrating MsFEM and multi-element least square HDMR can significantly reduce computation complexity.« less

Outlier-resilient complexity analysis of heartbeat dynamics

NASA Astrophysics Data System (ADS)

Lo, Men-Tzung; Chang, Yi-Chung; Lin, Chen; Young, Hsu-Wen Vincent; Lin, Yen-Hung; Ho, Yi-Lwun; Peng, Chung-Kang; Hu, Kun

2015-03-01

Complexity in physiological outputs is believed to be a hallmark of healthy physiological control. How to accurately quantify the degree of complexity in physiological signals with outliers remains a major barrier for translating this novel concept of nonlinear dynamic theory to clinical practice. Here we propose a new approach to estimate the complexity in a signal by analyzing the irregularity of the sign time series of its coarse-grained time series at different time scales. Using surrogate data, we show that the method can reliably assess the complexity in noisy data while being highly resilient to outliers. We further apply this method to the analysis of human heartbeat recordings. Without removing any outliers due to ectopic beats, the method is able to detect a degradation of cardiac control in patients with congestive heart failure and a more degradation in critically ill patients whose life continuation relies on extracorporeal membrane oxygenator (ECMO). Moreover, the derived complexity measures can predict the mortality of ECMO patients. These results indicate that the proposed method may serve as a promising tool for monitoring cardiac function of patients in clinical settings.

Angular-Rate Estimation Using Star Tracker Measurements

NASA Technical Reports Server (NTRS)

Azor, R.; Bar-Itzhack, I.; Deutschmann, Julie K.; Harman, Richard R.

1999-01-01

This paper presents algorithms for estimating the angular-rate vector of satellites using quaternion measurements. Two approaches are compared, one that uses differentiated quatemion measurements to yield coarse rate measurements which are then fed into two different estimators. In the other approach the raw quatemion measurements themselves are fed directly into the two estimators. The two estimators rely on the ability to decompose the non-linear rate dependent part of the rotational dynamics equation of a rigid body into a product of an angular-rate dependent matrix and the angular-rate vector itself This decomposition, which is not unique, enables the treatment of the nonlinear spacecraft dynamics model as a linear one and, consequently, the application of a Pseudo-Linear Kalman Filter (PSELIKA). It also enables the application of a special Kalman filter which is based on the use of the solution of the State Dependent Algebraic Riccati Equation (SDARE) in order to compute the Kalman gain matrix and thus eliminates the need to propagate and update the filter covariance matrix. The replacement of the elaborate rotational dynamics by a simple first order Markov model is also examined. In this paper a special consideration is given to the problem of delayed quatemion measurements. Two solutions to this problem are suggested and tested. Real Rossi X-Ray Timing Explorer (RXTE) data is used to test these algorithms, and results of these tests are presented.

Angular-Rate Estimation using Star Tracker Measurements

NASA Technical Reports Server (NTRS)

Azor, R.; Bar-Itzhack, Itzhack Y.; Deutschmann, Julie K.; Harman, Richard R.

1999-01-01

This paper presents algorithms for estimating the angular-rate vector of satellites using quaternion measurements. Two approaches are compared, one that uses differentiated quaternion measurements to yield coarse rate measurements which are then fed into two different estimators. In the other approach the raw quaternion measurements themselves are fed directly into the two estimators. The two estimators rely on the ability to decompose the non-linear rate dependent part of the rotational dynamics equation of a rigid body into a product of an angular-rate dependent matrix and the angular-rate vector itself. This decomposition, which is not unique, enables the treatment of the nonlinear spacecraft dynamics model as a linear one and, consequently, the application of a Pseudo-Linear Kalman Filter (PSELIKA). It also enables the application of a special Kalman filter which is based on the use of the solution of the State Dependent Algebraic Riccati Equation (SDARE) in order to compute the Kalman gain matrix and thus eliminates the need to propagate and update the filter covariance matrix. The replacement of the elaborate rotational dynamics by a simple first order Markov model is also examined. In this paper a special consideration is given to the problem of delayed quaternion measurements. Two solutions to this problem are suggested and tested. Real Rossi X-Ray Timing Explorer (RXTE) data is used to test these algorithms, and results of these tests are presented.

Mass size distribution and source identification of particulate matter metal components at four urban sites and a background site of Istanbul.

PubMed

Şahin, Ülkü Alver; Polat, Gülfem; Onat, Burcu

2016-06-01

In this study, the size distribution characteristics and metal contents of particulate matter (PM) have been determined. In this scope, PM sampling has been done at five stations in Istanbul. PM filter samples were collected for eight different sizes using the Anderson cascade impactor. PM filters were decomposed and analyzed for 20 metals. The highest median concentration for Fe, Ca, K, and Mg, known as soil metals, were observed as follows: Fe and Ca were observed at Goztepe station (1.20 and 8.28 μg/m(3)), K was observed at Kilyos station (0.33 μg/m(3)), and Mg was observed at Avcilar station (0.37 μg/m(3)). The highest median concentrations for Zn, Cu, Pb, Ni, Cr, V, As, Se, Co, and Cd, known as anthropogenic metals, were observed at Avcilar, Goztepe, and Besiktas stations. Although the lowest metal concentrations was determined at Kilyos stations that was selected as the urban background. The enrichment factors (EFs) of most metals in the fine PM is higher than those in the coarse mode. According to the factor analyses, the most important emission source was observed to be industrial facilities at Avcilar; traffic at Besiktas; traffic and domestic heating at Goztepe; and domestic heating, sea salt aerosols, and ship traffic (in the Bosphorus Channel of Istanbul) at Rasathane.

A stochastic-geometric model of soil variation in Pleistocene patterned ground

NASA Astrophysics Data System (ADS)

Lark, Murray; Meerschman, Eef; Van Meirvenne, Marc

2013-04-01

In this paper we examine the spatial variability of soil in parent material with complex spatial structure which arises from complex non-linear geomorphic processes. We show that this variability can be better-modelled by a stochastic-geometric model than by a standard Gaussian random field. The benefits of the new model are seen in the reproduction of features of the target variable which influence processes like water movement and pollutant dispersal. Complex non-linear processes in the soil give rise to properties with non-Gaussian distributions. Even under a transformation to approximate marginal normality, such variables may have a more complex spatial structure than the Gaussian random field model of geostatistics can accommodate. In particular the extent to which extreme values of the variable are connected in spatially coherent regions may be misrepresented. As a result, for example, geostatistical simulation generally fails to reproduce the pathways for preferential flow in an environment where coarse infill of former fluvial channels or coarse alluvium of braided streams creates pathways for rapid movement of water. Multiple point geostatistics has been developed to deal with this problem. Multiple point methods proceed by sampling from a set of training images which can be assumed to reproduce the non-Gaussian behaviour of the target variable. The challenge is to identify appropriate sources of such images. In this paper we consider a mode of soil variation in which the soil varies continuously, exhibiting short-range lateral trends induced by local effects of the factors of soil formation which vary across the region of interest in an unpredictable way. The trends in soil variation are therefore only apparent locally, and the soil variation at regional scale appears random. We propose a stochastic-geometric model for this mode of soil variation called the Continuous Local Trend (CLT) model. We consider a case study of soil formed in relict patterned ground with pronounced lateral textural variations arising from the presence of infilled ice-wedges of Pleistocene origin. We show how knowledge of the pedogenetic processes in this environment, along with some simple descriptive statistics, can be used to select and fit a CLT model for the apparent electrical conductivity (ECa) of the soil. We use the model to simulate realizations of the CLT process, and compare these with realizations of a fitted Gaussian random field. We show how statistics that summarize the spatial coherence of regions with small values of ECa, which are expected to have coarse texture and so larger saturated hydraulic conductivity, are better reproduced by the CLT model than by the Gaussian random field. This suggests that the CLT model could be used to generate an unlimited supply of training images to allow multiple point geostatistical simulation or prediction of this or similar variables.

Integrated control/structure optimization by multilevel decomposition

NASA Technical Reports Server (NTRS)

Zeiler, Thomas A.; Gilbert, Michael G.

1990-01-01

A method for integrated control/structure optimization by multilevel decomposition is presented. It is shown that several previously reported methods were actually partial decompositions wherein only the control was decomposed into a subsystem design. One of these partially decomposed problems was selected as a benchmark example for comparison. The system is fully decomposed into structural and control subsystem designs and an improved design is produced. Theory, implementation, and results for the method are presented and compared with the benchmark example.

The influence of body position and microclimate on ketamine and metabolite distribution in decomposed skeletal remains.

PubMed

Cornthwaite, H M; Watterson, J H

2014-10-01

The influence of body position and microclimate on ketamine (KET) and metabolite distribution in decomposed bone tissue was examined. Rats received 75 mg/kg (i.p.) KET (n = 30) or remained drug-free (controls, n = 4). Following euthanasia, rats were divided into two groups and placed outdoors to decompose in one of the three positions: supine (SUP), prone (PRO) or upright (UPR). One group decomposed in a shaded, wooded microclimate (Site 1) while the other decomposed in an exposed sunlit microclimate with gravel substrate (Site 2), roughly 500 m from Site 1. Following decomposition, bones (lumbar vertebrae, thoracic vertebra, cervical vertebrae, rib, pelvis, femora, tibiae, humeri and scapulae) were collected and sorted for analysis. Clean, ground bones underwent microwave-assisted extraction using acetone : hexane mixture (1 : 1, v/v), followed by solid-phase extraction and analysis using GC-MS. Drug levels, expressed as mass normalized response ratios, were compared across all bone types between body position and microclimates. Bone type was a main effect (P < 0.05) for drug level and drug/metabolite level ratio for all body positions and microclimates examined. Microclimate and body position significantly influenced observed drug levels: higher levels were observed in carcasses decomposing in direct sunlight, where reduced entomological activity led to slowed decomposition. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Mimicking coarse-grained simulations without coarse-graining: enhanced sampling by damping short-range interactions.

PubMed

Wei, Dongshan; Wang, Feng

2010-08-28

The damped-short-range-interaction (DSRI) method is proposed to mimic coarse-grained simulations by propagating an atomistic scale system on a smoothed potential energy surface. The DSRI method has the benefit of enhanced sampling provided by a typical coarse-grained simulation without the need to perform coarse-graining. Our method was used to simulate liquid water, alanine dipeptide folding, and the self-assembly of dimyristoylphosphatidylcholine lipid. In each case, our method appreciably accelerated the dynamics without significantly changing the free energy surface. Additional insights from DSRI simulations and the promise of coupling our DSRI method with Hamiltonian replica-exchange molecular dynamics are discussed.

Mimicking coarse-grained simulations without coarse-graining: Enhanced sampling by damping short-range interactions

NASA Astrophysics Data System (ADS)

Wei, Dongshan; Wang, Feng

2010-08-01

The damped-short-range-interaction (DSRI) method is proposed to mimic coarse-grained simulations by propagating an atomistic scale system on a smoothed potential energy surface. The DSRI method has the benefit of enhanced sampling provided by a typical coarse-grained simulation without the need to perform coarse-graining. Our method was used to simulate liquid water, alanine dipeptide folding, and the self-assembly of dimyristoylphosphatidylcholine lipid. In each case, our method appreciably accelerated the dynamics without significantly changing the free energy surface. Additional insights from DSRI simulations and the promise of coupling our DSRI method with Hamiltonian replica-exchange molecular dynamics are discussed.

Sensitivity of aerosol radiative forcing efficiency to the coarse mode contributions across aerosol regimes

NASA Astrophysics Data System (ADS)

McComiskey, A. C.; Telg, H.; Sheridan, P. J.; Kassianov, E.

2017-12-01

The coarse mode contribution to the aerosol radiative effect in a range of clean and turbid aerosol regimes has not been well quantified. While the coarse-mode radiative effect in turbid conditions is generally assumed to be consequential, the effect in clean conditions has likely been underestimated. We survey ground-based in situ measurements of the coarse mode fraction of aerosol optical properties measured around the globe over the past 20 years by the DOE Atmospheric Radiation Measurement Facility and the NOAA Global Monitoring Division. The aerosol forcing efficiency is presented, allowing an evaluation of where the aerosol coarse mode might be climatologically significant.

Removal of Cu(II) in water by polymer enhanced ultrafiltration: Influence of polymer nature and pH.

PubMed

Kochkodan, Olga D; Kochkodan, Viktor M; Sharma, Virender K

2018-01-02

This study presents an efficient removal of Cu(II) in water using the polymer enhanced ultrafiltration (PEUF) method. Polymer of different molecular weight (MW) (polyethyleneimine (PEI), sodium lignosulfonates (SLS) and dextrans) were investigated to evaluate efficiency in removal of Cu(II) in water by the PEUF method. The decomposition of Cu(II)-polymer complex was also evaluated in order to reuse polymers. Cu(II) complexation depends on the MW of chelating polymer and the pH of feed solution. It was found that the Cu(II) rejection increased with the polymer dosage with high removal of Cu(II) when using PEI and SLS at a 10:20 (mg/mg) ratio ([Cu(II)]:[polymer]). It was found that the maximum chelating capacity was 15 mg of Cu(II) per 20 mg of PEI. The Cu(II)-PEI complex could be decomposed by acid addition and the polymer could be efficiently reused with multiple complexation-decomplexation cycles. A conceptual flow chart of the integrated process of efficient removal of Cu(II) by PEUF method is suggested.

Ferrate(VI) oxidation of cyanide in water.

PubMed

Costarramone, N; Kneip, A; Castetbon, A

2004-08-01

Experiments were conducted to test removal of cyanide (free cyanide and several cyanide complexes) in water, under alkaline medium (pH > or = 11), by a new potassium ferrate salt. The removal rate of free cyanide by oxidation with Fe(VI) was greater at pH 11.0 than at pH 12.0. A complete oxidation was obtained with a 2.67 Fe(VI)/CN ratio at pH 11.0. In these conditions, the rate of cyanide oxidation by Fe(VI) was slow, with a reaction rate constant estimated at 0.95 +/- 0.10 s(-1) l mol(-1) at pH 11.0 and 19.6 degrees C in this study. This study revealed that Fe(VI) did not decompose all cyanide complexes. Copper, cadmium and zinc complexes were removed efficiently by Fe(VI). Moreover, these metals were also removed from the solution by coagulation effect of Fe(OH)3, the Fe(VI) product of reaction. A particular behaviour was reported with copper, as a rapid oxidation of cyanide was observed in the presence of this metal. On the contrary, oxidation of nickel and silver complexes was incomplete.

Process for making surfactant capped metal oxide nanocrystals, and products produced by the process

DOEpatents

Alivisatos, A. Paul; Rockenberger, Joerg

2006-01-10

Disclosed is a process for making surfactant capped nanocrystals of metal oxides which are dispersable in organic solvents. The process comprises decomposing a metal cupferron complex of the formula M^XCup_X, wherein M is a metal, and Cup is a N-substituted N-Nitroso hydroxylamine, in the presence of a coordinating surfactant, the reaction being conducted at a temperature ranging from about 150 to about 400.degree. C., for a period of time sufficient to complete the reaction. Also disclosed are compounds made by the process.

Micro-Eukaryotic Diversity in Hypolithons from Miers Valley, Antarctica

PubMed Central

Gokul, Jarishma K.; Valverde, Angel; Tuffin, Marla; Cary, Stephen Craig; Cowan, Don A.

2013-01-01

The discovery of extensive and complex hypolithic communities in both cold and hot deserts has raised many questions regarding their ecology, biodiversity and relevance in terms of regional productivity. However, most hypolithic research has focused on the bacterial elements of the community. This study represents the first investigation of micro-eukaryotic communities in all three hypolith types. Here we show that Antarctic hypoliths support extensive populations of novel uncharacterized bryophyta, fungi and protists and suggest that well known producer-decomposer-predator interactions may create the necessary conditions for hypolithic productivity in Antarctic deserts. PMID:24832664

Implementing the sine transform of fermionic modes as a tensor network

NASA Astrophysics Data System (ADS)

Epple, Hannes; Fries, Pascal; Hinrichsen, Haye

2017-09-01

Based on the algebraic theory of signal processing, we recursively decompose the discrete sine transform of the first kind (DST-I) into small orthogonal block operations. Using a diagrammatic language, we then second-quantize this decomposition to construct a tensor network implementing the DST-I for fermionic modes on a lattice. The complexity of the resulting network is shown to scale as 5/4 n logn (not considering swap gates), where n is the number of lattice sites. Our method provides a systematic approach of generalizing Ferris' spectral tensor network for nontrivial boundary conditions.

Toxicity to woodlice of zinc and lead oxides added to soil litter

USGS Publications Warehouse

Beyer, W.N.; Anderson, A.

1985-01-01

Previous studies have shown that high concentrations of metals in soil are associated with reductions in decomposer populations. We have here determined the relation between the concentrations of lead and zinc added as oxides to soil litter and the survival and reproduction of a decomposer population under controlled conditions. Laboratory populations of woodlice (Porcellio scaber Latr) were fed soil litter treated with lead or zinc at concentrations that ranged from 100 to 12,800 ppm. The survival of the adults, the maximum number of young alive, and the average number of young alive, were recorded over 64 weeks. Lead at 12,800 ppm and zinc at 1,600 ppm or more had statistically significant (p < 0.05) negative effects on the populations. These results agree with field observations suggesting that lead and zinc have reduced populations of decomposers in contaminated forest soil litter, and concentrations are similar to those reported to be associated with reductions in natural populations of decomposers. Poisoning of decomposers may disrupt nutrient cycling, reduce the numbers of invertebrates available to other wildlife for food, and contribute to the contamination of food chains.

Cat got your tongue? Using the tip-of-the-tongue state to investigate fixed expressions.

PubMed

Nordmann, Emily; Cleland, Alexandra A; Bull, Rebecca

2013-01-01

Despite the fact that they play a prominent role in everyday speech, the representation and processing of fixed expressions during language production is poorly understood. Here, we report a study investigating the processes underlying fixed expression production. "Tip-of-the-tongue" (TOT) states were elicited for well-known idioms (e.g., hit the nail on the head) and participants were asked to report any information they could regarding the content of the phrase. Participants were able to correctly report individual words for idioms that they could not produce. In addition, participants produced both figurative (e.g., pretty for easy on the eye) and literal errors (e.g., hammer for hit the nail on the head) when in a TOT state, suggesting that both figurative and literal meanings are active during production. There was no effect of semantic decomposability on overall TOT incidence; however, participants recalled a greater proportion of words for decomposable rather than non-decomposable idioms. This finding suggests there may be differences in how decomposable and non-decomposable idioms are retrieved during production. Copyright © 2013 Cognitive Science Society, Inc.

A hierarchical approach to cooperativity in macromolecular and self-assembling binding systems.

PubMed

Garcés, Josep Lluís; Acerenza, Luis; Mizraji, Eduardo; Mas, Francesc

2008-04-01

The study of complex macromolecular binding systems reveals that a high number of states and processes are involved in their mechanism of action, as has become more apparent with the sophistication of the experimental techniques used. The resulting information is often difficult to interpret because of the complexity of the scheme (large size and profuse interactions, including cooperative and self-assembling interactions) and the lack of transparency that this complexity introduces into the interpretation of the indexes traditionally used to describe the binding properties. In particular, cooperative behaviour can be attributed to very different causes, such as direct chemical modification of the binding sites, conformational changes in the whole structure of the macromolecule, aggregation processes between different subunits, etc. In this paper, we propose a novel approach for the analysis of the binding properties of complex macromolecular and self-assembling systems. To quantify the binding behaviour, we use the global association quotient defined as K(c) = [occupied sites]/([free sites] L), L being the free ligand concentration. K(c) can be easily related to other measures of cooperativity (such as the Hill number or the Scatchard plot) and to the free energies involved in the binding processes at each ligand concentration. In a previous work, it was shown that K(c) could be decomposed as an average of equilibrium constants in two ways: intrinsic constants for Adair binding systems and elementary constants for the general case. In this study, we show that these two decompositions are particular cases of a more general expression, where the average is over partial association quotients, associated with subsystems from which the system is composed. We also show that if the system is split into different subsystems according to a binding hierarchy that starts from the lower, microscopic level and ends at the higher, aggregation level, the global association quotient can be decomposed following the hierarchical levels of macromolecular organisation. In this process, the partial association quotients of one level are expressed, in a recursive way, as a function of the partial quotients of the level that is immediately below, until the microscopic level is reached. As a result, the binding properties of very complex macromolecular systems can be analysed in detail, making the mechanistic explanation of their behaviour transparent. In addition, our approach provides a model-independent interpretation of the intrinsic equilibrium constants in terms of the elementary ones.

Dye-sensitized TiO2-catalyzed photodegradation of sulfamethoxazole under blue or yellow light.

PubMed

Lu, Norman; Yeh, Yun-Peng; Wang, Guan-Bo; Feng, Tsung-Yao; Shih, Yang-Hsin; Chen, Dong

2017-01-01

Visible light-induced photocatalysis is potentially advantageous and could be an efficient approach to degrade contaminants because it can be used to selectively target specific wavelength for decomposition of organic contaminants in water and wastewater. This study demonstrates the photodegradation of sulfamethoxazole (SMX) using [Pt(3,3'-dicarboxy-2,2'-bpy)(1,2-benzenedithiolate)] (Complex 1)-sensitized and [Pt(4,4'-dicarboxy-2,2'-bpy)(1,2-benzenedithiolate)] (Complex 2)-sensitized titanium dioxide (TiO 2 ) under blue or yellow light (420 or 580 nm, respectively) irradiation in water. The Complex 1-sensitized TiO 2 photocatalytic oxidation of SMX reached almost 100 % removal under 420 nm irradiation for 3 h in water. In addition, the formation of hydroxyl radicals can be facilitated by bubbling O 2 during the photodegradation in which an effective decomposition of SMX was observed. Based on HPLC and UV-Vis studies of the decomposed products, it was found that SMX underwent cleavage of aromatic rings during the photodegradation process.

A novel encryption scheme for high-contrast image data in the Fresnelet domain

PubMed Central

Bibi, Nargis; Farwa, Shabieh; Jahngir, Adnan; Usman, Muhammad

2018-01-01

In this paper, a unique and more distinctive encryption algorithm is proposed. This is based on the complexity of highly nonlinear S box in Flesnelet domain. The nonlinear pattern is transformed further to enhance the confusion in the dummy data using Fresnelet technique. The security level of the encrypted image boosts using the algebra of Galois field in Fresnelet domain. At first level, the Fresnelet transform is used to propagate the given information with desired wavelength at specified distance. It decomposes given secret data into four complex subbands. These complex sub-bands are separated into two components of real subband data and imaginary subband data. At second level, the net subband data, produced at the first level, is deteriorated to non-linear diffused pattern using the unique S-box defined on the Galois field F28. In the diffusion process, the permuted image is substituted via dynamic algebraic S-box substitution. We prove through various analysis techniques that the proposed scheme enhances the cipher security level, extensively. PMID:29608609

Anatomical Network Analysis Shows Decoupling of Modular Lability and Complexity in the Evolution of the Primate Skull

PubMed Central

Esteve-Altava, Borja; Boughner, Julia C.; Diogo, Rui; Villmoare, Brian A.; Rasskin-Gutman, Diego

2015-01-01

Modularity and complexity go hand in hand in the evolution of the skull of primates. Because analyses of these two parameters often use different approaches, we do not know yet how modularity evolves within, or as a consequence of, an also-evolving complex organization. Here we use a novel network theory-based approach (Anatomical Network Analysis) to assess how the organization of skull bones constrains the co-evolution of modularity and complexity among primates. We used the pattern of bone contacts modeled as networks to identify connectivity modules and quantify morphological complexity. We analyzed whether modularity and complexity evolved coordinately in the skull of primates. Specifically, we tested Herbert Simon’s general theory of near-decomposability, which states that modularity promotes the evolution of complexity. We found that the skulls of extant primates divide into one conserved cranial module and up to three labile facial modules, whose composition varies among primates. Despite changes in modularity, statistical analyses reject a positive feedback between modularity and complexity. Our results suggest a decoupling of complexity and modularity that translates to varying levels of constraint on the morphological evolvability of the primate skull. This study has methodological and conceptual implications for grasping the constraints that underlie the developmental and functional integration of the skull of humans and other primates. PMID:25992690

Resolving Properties of Polymers and Nanoparticle Assembly through Coarse-Grained Computational Studies.

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

Grest, Gary S.

2017-09-01

Coupled length and time scales determine the dynamic behavior of polymers and polymer nanocomposites and underlie their unique properties. To resolve the properties over large time and length scales it is imperative to develop coarse grained models which retain the atomistic specificity. Here we probe the degree of coarse graining required to simultaneously retain significant atomistic details a nd access large length and time scales. The degree of coarse graining in turn sets the minimum length scale instrumental in defining polymer properties and dynamics. Using polyethylene as a model system, we probe how the coarse - graining scale affects themore » measured dynamics with different number methylene group s per coarse - grained beads. Using these models we simulate polyethylene melts for times over 500 ms to study the viscoelastic properties of well - entangled polymer melts and large nanoparticle assembly as the nanoparticles are driven close enough to form nanostructures.« less

Parallel Anisotropic Tetrahedral Adaptation

NASA Technical Reports Server (NTRS)

Park, Michael A.; Darmofal, David L.

2008-01-01

An adaptive method that robustly produces high aspect ratio tetrahedra to a general 3D metric specification without introducing hybrid semi-structured regions is presented. The elemental operators and higher-level logic is described with their respective domain-decomposed parallelizations. An anisotropic tetrahedral grid adaptation scheme is demonstrated for 1000-1 stretching for a simple cube geometry. This form of adaptation is applicable to more complex domain boundaries via a cut-cell approach as demonstrated by a parallel 3D supersonic simulation of a complex fighter aircraft. To avoid the assumptions and approximations required to form a metric to specify adaptation, an approach is introduced that directly evaluates interpolation error. The grid is adapted to reduce and equidistribute this interpolation error calculation without the use of an intervening anisotropic metric. Direct interpolation error adaptation is illustrated for 1D and 3D domains.

Intermolecular symmetry-adapted perturbation theory study of large organic complexes.

PubMed

Heßelmann, Andreas; Korona, Tatiana

2014-09-07

Binding energies for the complexes of the S12L database by Grimme [Chem. Eur. J. 18, 9955 (2012)] were calculated using intermolecular symmetry-adapted perturbation theory combined with a density-functional theory description of the interacting molecules. The individual interaction energy decompositions revealed no particular change in the stabilisation pattern as compared to smaller dimer systems at equilibrium structures. This demonstrates that, to some extent, the qualitative description of the interaction of small dimer systems may be extrapolated to larger systems, a method that is widely used in force-fields in which the total interaction energy is decomposed into atom-atom contributions. A comparison of the binding energies with accurate experimental reference values from Grimme, the latter including thermodynamic corrections from semiempirical calculations, has shown a fairly good agreement to within the error range of the reference binding energies.

Prospects and challenges for fungal metatranscriptomes of complex communities

DOE PAGES

Kuske, Cheryl Rae; Hesse, Cedar Nelson; Challacombe, Jean Faust; ...

2015-01-22

We report that the ability to extract and purify messenger RNA directly from plants, decomposing organic matter and soil, followed by high-throughput sequencing of the pool of expressed genes, has spawned the emerging research area of metatranscriptomics. Each metatranscriptome provides a snapshot of the composition and relative abundance of actively transcribed genes, and thus provides an assessment of the interactions between soil microorganisms and plants, and collective microbial metabolic processes in many environments. We highlight current approaches for analysis of fungal transcriptome and metatranscriptome datasets across a gradient of community complexity, and note benefits and pitfalls associated with those approaches.more » Finally, we discuss knowledge gaps that limit our current ability to interpret metatranscriptome datasets and suggest future research directions that will require concerted efforts within the scientific community.« less

Wave theory of turbulence in compressible media (acoustic theory of turbulence)

NASA Technical Reports Server (NTRS)

Kentzer, C. P.

1975-01-01

The generation and the transmission of sound in turbulent flows are treated as one of the several aspects of wave propagation in turbulence. Fluid fluctuations are decomposed into orthogonal Fourier components, with five interacting modes of wave propagation: two vorticity modes, one entropy mode, and two acoustic modes. Wave interactions, governed by the inhomogeneous and nonlinear terms of the perturbed Navier-Stokes equations, are modeled by random functions which give the rates of change of wave amplitudes equal to the averaged interaction terms. The statistical framework adopted is a quantum-like formulation in terms of complex distribution functions. The spatial probability distributions are given by the squares of the absolute values of the complex characteristic functions. This formulation results in nonlinear diffusion-type transport equations for the probability densities of the five modes of wave propagation.

A web interface for easy flexible protein-protein docking with ATTRACT.

PubMed

de Vries, Sjoerd J; Schindler, Christina E M; Chauvot de Beauchêne, Isaure; Zacharias, Martin

2015-02-03

Protein-protein docking programs can give valuable insights into the structure of protein complexes in the absence of an experimental complex structure. Web interfaces can facilitate the use of docking programs by structural biologists. Here, we present an easy web interface for protein-protein docking with the ATTRACT program. While aimed at nonexpert users, the web interface still covers a considerable range of docking applications. The web interface supports systematic rigid-body protein docking with the ATTRACT coarse-grained force field, as well as various kinds of protein flexibility. The execution of a docking protocol takes up to a few hours on a standard desktop computer. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Redox and fungicidal properties of phthalocyanine metal complexes as related to active oxygen.

PubMed

Vol'pin, M E; Novodarova, G N; Krainova NYu; Lapikova, V P; Aver'yanov, A A

2000-10-01

Some chemical and fungicidal effects of 20 phthalocyanines of Co, Fe, Cu, and Al were studied. Under dark conditions, these complexes reduced nitroblue tetrazolium in the presence of KCN, accelerated the autoxidation of ascorbate or hydroquinone and decomposed hydrogen peroxide. In the later reaction, hydroxyl radical was generated as evidenced with the deoxyribose assay. The inhibition by superoxide dismutase and catalase of catalyzed autoxidation of ascorbate suggests the participation of superoxide anion-radical and hydrogen peroxide in the reaction. Most complexes were toxic to the fungus Magnaporthe grisea which causes blast disease of rice. The toxicity was enhanced by light being diminished by antioxidant reagents sequestering active oxygen species. Some complexes (including nontoxic ones), after 1-day contact with a leaf surface of the disease-susceptible rice cultivar, induced the fungitoxicity of leaf diffusate. This toxicity was also light-activated and sensitive to antioxidant reagents. Several complexes, when added to inocula, decreased 2-3 times the frequency of the compatible symptoms of the blast. It is suggested that in planta, the dark redox activity of phthalocyanines along with their photosensitization promote the generation of active oxygen, which damages the parasite and, therefore, favors disease resistance.