Implementation of the force decomposition machine for molecular dynamics simulations.

PubMed

Borštnik, Urban; Miller, Benjamin T; Brooks, Bernard R; Janežič, Dušanka

2012-09-01

We present the design and implementation of the force decomposition machine (FDM), a cluster of personal computers (PCs) that is tailored to running molecular dynamics (MD) simulations using the distributed diagonal force decomposition (DDFD) parallelization method. The cluster interconnect architecture is optimized for the communication pattern of the DDFD method. Our implementation of the FDM relies on standard commodity components even for networking. Although the cluster is meant for DDFD MD simulations, it remains general enough for other parallel computations. An analysis of several MD simulation runs on both the FDM and a standard PC cluster demonstrates that the FDM's interconnect architecture provides a greater performance compared to a more general cluster interconnect. Copyright © 2012 Elsevier Inc. All rights reserved.

Molecular C dynamics downstream: the biochemical decomposition sequence and its impact on soil organic matter structure and function.

PubMed

Grandy, A Stuart; Neff, Jason C

2008-10-15

Advances in spectroscopic and other chemical methods have greatly enhanced our ability to characterize soil organic matter chemistry. As a result, the molecular characteristics of soil C are now known for a range of ecosystems, soil types, and management intensities. Placing this knowledge into a broader ecological and management context is difficult, however, and remains one of the fundamental challenges of soil organic matter research. Here we present a conceptual model of molecular soil C dynamics to stimulate inter-disciplinary research into the ecological implications of molecular C turnover and its management- and process-level controls. Our model describes three properties of soil C dynamics: 1) soil size fractions have unique molecular patterns that reflect varying degrees of biological and physical control over decomposition; 2) there is a common decomposition sequence independent of plant inputs or other ecosystem properties; and 3) molecular decomposition sequences, although consistent, are not uniform and can be altered by processes that accelerate or slow the microbial transformation of specific molecules. The consequences of this model include several key points. First, lignin presents a constraint to decomposition of plant litter and particulate C (>53 microm) but exerts little influence on more stable mineral-associated soil fractions <53 microm. Second, carbon stabilized onto mineral fractions has a distinct composition related more to microbially processed organic matter than to plant-related compounds. Third, disturbances, such as N fertilization and tillage, which alter decomposition rates, can have "downstream effects"; that is, a disturbance that directly alters the molecular dynamics of particulate C may have a series of indirect effects on C stabilization in silt and clay fractions.

Detecting phase-amplitude coupling with high frequency resolution using adaptive decompositions

PubMed Central

Pittman-Polletta, Benjamin; Hsieh, Wan-Hsin; Kaur, Satvinder; Lo, Men-Tzung; Hu, Kun

2014-01-01

Background Phase-amplitude coupling (PAC) – the dependence of the amplitude of one rhythm on the phase of another, lower-frequency rhythm – has recently been used to illuminate cross-frequency coordination in neurophysiological activity. An essential step in measuring PAC is decomposing data to obtain rhythmic components of interest. Current methods of PAC assessment employ narrowband Fourier-based filters, which assume that biological rhythms are stationary, harmonic oscillations. However, biological signals frequently contain irregular and nonstationary features, which may contaminate rhythms of interest and complicate comodulogram interpretation, especially when frequency resolution is limited by short data segments. New method To better account for nonstationarities while maintaining sharp frequency resolution in PAC measurement, even for short data segments, we introduce a new method of PAC assessment which utilizes adaptive and more generally broadband decomposition techniques – such as the empirical mode decomposition (EMD). To obtain high frequency resolution PAC measurements, our method distributes the PAC associated with pairs of broadband oscillations over frequency space according to the time-local frequencies of these oscillations. Comparison with existing methods We compare our novel adaptive approach to a narrowband comodulogram approach on a variety of simulated signals of short duration, studying systematically how different types of nonstationarities affect these methods, as well as on EEG data. Conclusions Our results show: (1) narrowband filtering can lead to poor PAC frequency resolution, and inaccuracy and false negatives in PAC assessment; (2) our adaptive approach attains better PAC frequency resolution and is more resistant to nonstationarities and artifacts than traditional comodulograms. PMID:24452055

Thermal decomposition of condensed-phase nitromethane from molecular dynamics from ReaxFF reactive dynamics.

PubMed

Han, Si-ping; van Duin, Adri C T; Goddard, William A; Strachan, Alejandro

2011-05-26

We studied the thermal decomposition and subsequent reaction of the energetic material nitromethane (CH(3)NO(2)) using molecular dynamics with ReaxFF, a first principles-based reactive force field. We characterize the chemistry of liquid and solid nitromethane at high temperatures (2000-3000 K) and density 1.97 g/cm(3) for times up to 200 ps. At T = 3000 K the first reaction in the decomposition of nitromethane is an intermolecular proton transfer leading to CH(3)NOOH and CH(2)NO(2). For lower temperatures (T = 2500 and 2000 K) the first reaction during decomposition is often an isomerization reaction involving the scission of the C-N bond the formation of a C-O bond to form methyl nitrate (CH(3)ONO). Also at very early times we observe intramolecular proton transfer events. The main product of these reactions is H(2)O which starts forming following those initiation steps. The appearance of H(2)O marks the beginning of the exothermic chemistry. Recent quantum-mechanics-based molecular dynamics simulations on the chemical reactions and time scales for decomposition of a crystalline sample heated to T = 3000 K for a few picoseconds are in excellent agreement with our results, providing an important, direct validation of ReaxFF.

Thermal Decomposition of Condensed-Phase Nitromethane from Molecular Dynamics from ReaxFF Reactive Dynamics

DTIC Science & Technology

2011-05-04

pubs.acs.org/JPCB Thermal Decomposition of Condensed-Phase Nitromethane from Molecular Dynamics from ReaxFF Reactive Dynamics Si-ping Han,†,‡ Adri C. T. van...ABSTRACT: We studied the thermal decomposition and subsequent reaction of the energetic material nitromethane (CH3NO2) using molec- ular dynamics...with ReaxFF, a first principles-based reactive force field. We characterize the chemistry of liquid and solid nitromethane at high temperatures (2000

Importance of Force Decomposition for Local Stress Calculations in Biomembrane Molecular Simulations.

PubMed

Vanegas, Juan M; Torres-Sánchez, Alejandro; Arroyo, Marino

2014-02-11

Local stress fields are routinely computed from molecular dynamics trajectories to understand the structure and mechanical properties of lipid bilayers. These calculations can be systematically understood with the Irving-Kirkwood-Noll theory. In identifying the stress tensor, a crucial step is the decomposition of the forces on the particles into pairwise contributions. However, such a decomposition is not unique in general, leading to an ambiguity in the definition of the stress tensor, particularly for multibody potentials. Furthermore, a theoretical treatment of constraints in local stress calculations has been lacking. Here, we present a new implementation of local stress calculations that systematically treats constraints and considers a privileged decomposition, the central force decomposition, that leads to a symmetric stress tensor by construction. We focus on biomembranes, although the methodology presented here is widely applicable. Our results show that some unphysical behavior obtained with previous implementations (e.g. nonconstant normal stress profiles along an isotropic bilayer in equilibrium) is a consequence of an improper treatment of constraints. Furthermore, other valid force decompositions produce significantly different stress profiles, particularly in the presence of dihedral potentials. Our methodology reveals the striking effect of unsaturations on the bilayer mechanics, missed by previous stress calculation implementations.

Density-dependent liquid nitromethane decomposition: molecular dynamics simulations based on ReaxFF.

PubMed

Rom, Naomi; Zybin, Sergey V; van Duin, Adri C T; Goddard, William A; Zeiri, Yehuda; Katz, Gil; Kosloff, Ronnie

2011-09-15

The decomposition mechanism of hot liquid nitromethane at various compressions was studied using reactive force field (ReaxFF) molecular dynamics simulations. A competition between two different initial thermal decomposition schemes is observed, depending on compression. At low densities, unimolecular C-N bond cleavage is the dominant route, producing CH(3) and NO(2) fragments. As density and pressure rise approaching the Chapman-Jouget detonation conditions (∼30% compression, >2500 K) the dominant mechanism switches to the formation of the CH(3)NO fragment via H-transfer and/or N-O bond rupture. The change in the decomposition mechanism of hot liquid NM leads to a different kinetic and energetic behavior, as well as products distribution. The calculated density dependence of the enthalpy change correlates with the change in initial decomposition reaction mechanism. It can be used as a convenient and useful global parameter for the detection of reaction dynamics. Atomic averaged local diffusion coefficients are shown to be sensitive to the reactions dynamics, and can be used to distinguish between time periods where chemical reactions occur and diffusion-dominated, nonreactive time periods. © 2011 American Chemical Society

Molecular characteristics of continuously released DOM during one year of root and leaf litter decomposition

NASA Astrophysics Data System (ADS)

Altmann, Jens; Jansen, Boris; Kalbitz, Karsten; Filley, Timothy

2013-04-01

Dissolved organic matter (DOM) is one of the most dynamic carbon pools linking the terrestrial with the aquatic carbon cycle. Besides the insecure contribution of terrestrial DOM to the greenhouse effect, DOM also plays an important role for the mobility and availability of heavy metals and organic pollutants in soils. These processes depend very much on the molecular characteristics of the DOM. Surprisingly the processes that determine the molecular composition of DOM are only poorly understood. DOM can originate from various sources, which influence its molecular composition. It has been recognized that DOM formation is not a static process and DOM characteristics vary not only between different carbon sources. However, molecular characteristics of DOM extracts have scarcely been studied continuously over a longer period of time. Due to constant molecular changes of the parent litter material or soil organic matter during microbial degradation, we assumed that also the molecular characteristics of litter derived DOM varies at different stages during root and needle decomposition. For this study we analyzed the chemical composition of root and leaf samples of 6 temperate tree species during one year of litter decomposition in a laboratory incubation. During this long-term experiment we measured continuously carbon and nitrogen contents of the water extracts and the remaining residues, C mineralization rates, and the chemical composition of water extracts and residues by Curie-point pyrolysis mass spectrometry with TMAH We focused on the following questions: (I) How mobile are molecules derived from plant polymers like tannin, lignin, suberin and cutin? (II) How does the composition of root and leaf derived DOM change over time in dependence on the stage of decomposition and species? Litter derived DOM was generally dominated by aromatic compounds. Substituded fatty acids as typically cutin or suberin derived were not detected in the water extracts. Fresh leaf and

Thermal Decomposition of the Solid Phase of Nitromethane: Ab Initio Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Chang, Jing; Lian, Peng; Wei, Dong-Qing; Chen, Xiang-Rong; Zhang, Qing-Ming; Gong, Zi-Zheng

2010-10-01

The Car-Parrinello molecular dynamics simulations were employed to investigate thermal decomposition of the solid nitromethane. It is found that it undergoes chemical decomposition at about 2200 K under ambient pressure. The initiation of reactions involves both proton transfer and commonly known C-N bond cleavage. About 75 species and 100 elementary reactions were observed with the final products being H2O, CO2, N2, and CNCNC. It represents the first complete simulation of solid-phase explosive reactions reported to date, which is of far-reaching implication for design and development of new energetic materials.

Evolution of complex adaptations in molecular systems

PubMed Central

Pál, Csaba; Papp, Balázs

2017-01-01

A central challenge in evolutionary biology concerns the mechanisms by which complex adaptations arise. Such adaptations depend on the fixation of multiple, highly specific mutations, where intermediate stages of evolution seemingly provide little or no benefit. It is generally assumed that the establishment of complex adaptations is very slow in nature, as evolution of such traits demands special population genetic or environmental circumstances. However, blueprints of complex adaptations in molecular systems are pervasive, indicating that they can readily evolve. We discuss the prospects and limitations of non-adaptive scenarios, which assume multiple neutral or deleterious steps in the evolution of complex adaptations. Next, we examine how complex adaptations can evolve by natural selection in changing environment. Finally, we argue that molecular ’springboards’, such as phenotypic heterogeneity and promiscuous interactions facilitate this process by providing access to new adaptive paths. PMID:28782044

Adaptive multi-step Full Waveform Inversion based on Waveform Mode Decomposition

NASA Astrophysics Data System (ADS)

Hu, Yong; Han, Liguo; Xu, Zhuo; Zhang, Fengjiao; Zeng, Jingwen

2017-04-01

Full Waveform Inversion (FWI) can be used to build high resolution velocity models, but there are still many challenges in seismic field data processing. The most difficult problem is about how to recover long-wavelength components of subsurface velocity models when seismic data is lacking of low frequency information and without long-offsets. To solve this problem, we propose to use Waveform Mode Decomposition (WMD) method to reconstruct low frequency information for FWI to obtain a smooth model, so that the initial model dependence of FWI can be reduced. In this paper, we use adjoint-state method to calculate the gradient for Waveform Mode Decomposition Full Waveform Inversion (WMDFWI). Through the illustrative numerical examples, we proved that the low frequency which is reconstructed by WMD method is very reliable. WMDFWI in combination with the adaptive multi-step inversion strategy can obtain more faithful and accurate final inversion results. Numerical examples show that even if the initial velocity model is far from the true model and lacking of low frequency information, we still can obtain good inversion results with WMD method. From numerical examples of anti-noise test, we see that the adaptive multi-step inversion strategy for WMDFWI has strong ability to resist Gaussian noise. WMD method is promising to be able to implement for the land seismic FWI, because it can reconstruct the low frequency information, lower the dominant frequency in the adjoint source, and has a strong ability to resist noise.

Molecular markers indicate different dynamics of leaves and roots during litter decomposition

NASA Astrophysics Data System (ADS)

Altmann, Jens; Jansen, Boris; Palviainen, Marjo; Kalbitz, Karsten

2010-05-01

Up to now there is only a poor understanding of the sources contributing to organic carbon in forest soils, especially the contribution of leaves and roots. Studies of the last 2 decades have shown that methods like pyrolysis and CuO oxidation are suitable tools to trace back the main contributors of organic matter in water, sediments and soils. Lignin derived monomers, extractable lipids, cutin and suberin derived compounds have been used frequently for identification of plant material. However, for the selection of suitable biomarker the decomposition patterns and stability of these compounds are of high importance but they are only poorly understood. In this study we focused on following questions: (I) Which compounds are characteristic to identify certain plant parts and plant species? (II) How stable are these compounds during the first 3 years of litter decomposition? We studied the chemical composition of samples from a 3-year litterbag decomposition experiment with roots and leaves of spruce, pine and birch which was done in Finland. Additionally to mass loss, carbon and nitrogen contents, free lipids were extracted; by alkaline hydrolysis non extractable lipids were gained. The extracts were analyzed afterwards by GC-MS, the insoluble residues were analyzed by curie-point Pyrolysis GC-MS. In addition to the identification and quantification of a variety of different compounds and compound ratios we used statistical classification methods to get deeper insights into the patterns of leaf and root-derived biomarkers during litter decomposition. The mass loss was largely different between the litter species and we always observed larger mass loss for leaf-derived litter in comparison to root derived litter. This trend was also observed by molecular analysis. The increase of the ratio of vanillic acid to vanillin was correlated to the mass loss of the samples over time. This shows that the degree of decomposition of plant material was linked with the degree of

Multi-Fault Diagnosis of Rolling Bearings via Adaptive Projection Intrinsically Transformed Multivariate Empirical Mode Decomposition and High Order Singular Value Decomposition.

PubMed

Yuan, Rui; Lv, Yong; Song, Gangbing

2018-04-16

Rolling bearings are important components in rotary machinery systems. In the field of multi-fault diagnosis of rolling bearings, the vibration signal collected from single channels tends to miss some fault characteristic information. Using multiple sensors to collect signals at different locations on the machine to obtain multivariate signal can remedy this problem. The adverse effect of a power imbalance between the various channels is inevitable, and unfavorable for multivariate signal processing. As a useful, multivariate signal processing method, Adaptive-projection has intrinsically transformed multivariate empirical mode decomposition (APIT-MEMD), and exhibits better performance than MEMD by adopting adaptive projection strategy in order to alleviate power imbalances. The filter bank properties of APIT-MEMD are also adopted to enable more accurate and stable intrinsic mode functions (IMFs), and to ease mode mixing problems in multi-fault frequency extractions. By aligning IMF sets into a third order tensor, high order singular value decomposition (HOSVD) can be employed to estimate the fault number. The fault correlation factor (FCF) analysis is used to conduct correlation analysis, in order to determine effective IMFs; the characteristic frequencies of multi-faults can then be extracted. Numerical simulations and the application of multi-fault situation can demonstrate that the proposed method is promising in multi-fault diagnoses of multivariate rolling bearing signal.

Complete ensemble local mean decomposition with adaptive noise and its application to fault diagnosis for rolling bearings

NASA Astrophysics Data System (ADS)

Wang, Lei; Liu, Zhiwen; Miao, Qiang; Zhang, Xin

2018-06-01

Mode mixing resulting from intermittent signals is an annoying problem associated with the local mean decomposition (LMD) method. Based on noise-assisted approach, ensemble local mean decomposition (ELMD) method alleviates the mode mixing issue of LMD to some degree. However, the product functions (PFs) produced by ELMD often contain considerable residual noise, and thus a relatively large number of ensemble trials are required to eliminate the residual noise. Furthermore, since different realizations of Gaussian white noise are added to the original signal, different trials may generate different number of PFs, making it difficult to take ensemble mean. In this paper, a novel method is proposed called complete ensemble local mean decomposition with adaptive noise (CELMDAN) to solve these two problems. The method adds a particular and adaptive noise at every decomposition stage for each trial. Moreover, a unique residue is obtained after separating each PF, and the obtained residue is used as input for the next stage. Two simulated signals are analyzed to illustrate the advantages of CELMDAN in comparison to ELMD and CEEMDAN. To further demonstrate the efficiency of CELMDAN, the method is applied to diagnose faults for rolling bearings in an experimental case and an engineering case. The diagnosis results indicate that CELMDAN can extract more fault characteristic information with less interference than ELMD.

Influence of density and environmental factors on decomposition kinetics of amorphous polylactide - Reactive molecular dynamics studies.

PubMed

Mlyniec, A; Ekiert, M; Morawska-Chochol, A; Uhl, T

2016-06-01

In this work, we investigate the influence of the surrounding environment and the initial density on the decomposition kinetics of polylactide (PLA). The decomposition of the amorphous PLA was investigated by means of reactive molecular dynamics simulations. A computational model simulates the decomposition of PLA polymer inside the bulk, due to the assumed lack of removal of reaction products from the polymer matrix. We tracked the temperature dependency of the water and carbon monoxide production to extract the activation energy of thermal decomposition of PLA. We found that an increased density results in decreased activation energy of decomposition by about 50%. Moreover, initiation of decomposition of the amorphous PLA is followed by a rapid decline in activation energy caused by reaction products which accelerates the hydrolysis of esters. The addition of water molecules decreases initial energy of activation as well as accelerates the decomposition process. Additionally, we have investigated the dependency of density on external loading. Comparison of pressures needed to obtain assumed densities shows that this relationship is bilinear and the slope changes around a density equal to 1.3g/cm(3). The conducted analyses provide an insight into the thermal decomposition process of the amorphous phase of PLA, which is particularly susceptible to decomposition in amorphous and semi-crystalline PLA polymers. Copyright © 2016 Elsevier Inc. All rights reserved.

Basis adaptation and domain decomposition for steady partial differential equations with random coefficients

DOE PAGES

Tipireddy, R.; Stinis, P.; Tartakovsky, A. M.

2017-09-04

In this paper, we present a novel approach for solving steady-state stochastic partial differential equations (PDEs) with high-dimensional random parameter space. The proposed approach combines spatial domain decomposition with basis adaptation for each subdomain. The basis adaptation is used to address the curse of dimensionality by constructing an accurate low-dimensional representation of the stochastic PDE solution (probability density function and/or its leading statistical moments) in each subdomain. Restricting the basis adaptation to a specific subdomain affords finding a locally accurate solution. Then, the solutions from all of the subdomains are stitched together to provide a global solution. We support ourmore » construction with numerical experiments for a steady-state diffusion equation with a random spatially dependent coefficient. Lastly, our results show that highly accurate global solutions can be obtained with significantly reduced computational costs.« less

Thermal decomposition of the solid phase of nitromethane: ab initio molecular dynamics simulations.

PubMed

Chang, Jing; Lian, Peng; Wei, Dong-Qing; Chen, Xiang-Rong; Zhang, Qing-Ming; Gong, Zi-Zheng

2010-10-29

The Car-Parrinello molecular dynamics simulations were employed to investigate thermal decomposition of the solid nitromethane. It is found that it undergoes chemical decomposition at about 2200 K under ambient pressure. The initiation of reactions involves both proton transfer and commonly known C-N bond cleavage. About 75 species and 100 elementary reactions were observed with the final products being H2O, CO2, N2, and CNCNC. It represents the first complete simulation of solid-phase explosive reactions reported to date, which is of far-reaching implication for design and development of new energetic materials.

Multi-Fault Diagnosis of Rolling Bearings via Adaptive Projection Intrinsically Transformed Multivariate Empirical Mode Decomposition and High Order Singular Value Decomposition

PubMed Central

Lv, Yong; Song, Gangbing

2018-01-01

Rolling bearings are important components in rotary machinery systems. In the field of multi-fault diagnosis of rolling bearings, the vibration signal collected from single channels tends to miss some fault characteristic information. Using multiple sensors to collect signals at different locations on the machine to obtain multivariate signal can remedy this problem. The adverse effect of a power imbalance between the various channels is inevitable, and unfavorable for multivariate signal processing. As a useful, multivariate signal processing method, Adaptive-projection has intrinsically transformed multivariate empirical mode decomposition (APIT-MEMD), and exhibits better performance than MEMD by adopting adaptive projection strategy in order to alleviate power imbalances. The filter bank properties of APIT-MEMD are also adopted to enable more accurate and stable intrinsic mode functions (IMFs), and to ease mode mixing problems in multi-fault frequency extractions. By aligning IMF sets into a third order tensor, high order singular value decomposition (HOSVD) can be employed to estimate the fault number. The fault correlation factor (FCF) analysis is used to conduct correlation analysis, in order to determine effective IMFs; the characteristic frequencies of multi-faults can then be extracted. Numerical simulations and the application of multi-fault situation can demonstrate that the proposed method is promising in multi-fault diagnoses of multivariate rolling bearing signal. PMID:29659510

Energy decomposition analysis for exciplexes using absolutely localized molecular orbitals

NASA Astrophysics Data System (ADS)

Ge, Qinghui; Mao, Yuezhi; Head-Gordon, Martin

2018-02-01

An energy decomposition analysis (EDA) scheme is developed for understanding the intermolecular interaction involving molecules in their excited states. The EDA utilizes absolutely localized molecular orbitals to define intermediate states and is compatible with excited state methods based on linear response theory such as configuration interaction singles and time-dependent density functional theory. The shift in excitation energy when an excited molecule interacts with the environment is decomposed into frozen, polarization, and charge transfer contributions, and the frozen term can be further separated into Pauli repulsion and electrostatics. These terms can be added to their counterparts obtained from the ground state EDA to form a decomposition of the total interaction energy. The EDA scheme is applied to study a variety of systems, including some model systems to demonstrate the correct behavior of all the proposed energy components as well as more realistic systems such as hydrogen-bonding complexes (e.g., formamide-water, pyridine/pyrimidine-water) and halide (F-, Cl-)-water clusters that involve charge-transfer-to-solvent excitations.

Computationally Efficient Adaptive Beamformer for Ultrasound Imaging Based on QR Decomposition.

PubMed

Park, Jongin; Wi, Seok-Min; Lee, Jin S

2016-02-01

Adaptive beamforming methods for ultrasound imaging have been studied to improve image resolution and contrast. The most common approach is the minimum variance (MV) beamformer which minimizes the power of the beamformed output while maintaining the response from the direction of interest constant. The method achieves higher resolution and better contrast than the delay-and-sum (DAS) beamformer, but it suffers from high computational cost. This cost is mainly due to the computation of the spatial covariance matrix and its inverse, which requires O(L(3)) computations, where L denotes the subarray size. In this study, we propose a computationally efficient MV beamformer based on QR decomposition. The idea behind our approach is to transform the spatial covariance matrix to be a scalar matrix σI and we subsequently obtain the apodization weights and the beamformed output without computing the matrix inverse. To do that, QR decomposition algorithm is used and also can be executed at low cost, and therefore, the computational complexity is reduced to O(L(2)). In addition, our approach is mathematically equivalent to the conventional MV beamformer, thereby showing the equivalent performances. The simulation and experimental results support the validity of our approach.

Adaptive multigrid domain decomposition solutions for viscous interacting flows

NASA Technical Reports Server (NTRS)

Rubin, Stanley G.; Srinivasan, Kumar

1992-01-01

Several viscous incompressible flows with strong pressure interaction and/or axial flow reversal are considered with an adaptive multigrid domain decomposition procedure. Specific examples include the triple deck structure surrounding the trailing edge of a flat plate, the flow recirculation in a trough geometry, and the flow in a rearward facing step channel. For the latter case, there are multiple recirculation zones, of different character, for laminar and turbulent flow conditions. A pressure-based form of flux-vector splitting is applied to the Navier-Stokes equations, which are represented by an implicit lowest-order reduced Navier-Stokes (RNS) system and a purely diffusive, higher-order, deferred-corrector. A trapezoidal or box-like form of discretization insures that all mass conservation properties are satisfied at interfacial and outflow boundaries, even for this primitive-variable, non-staggered grid computation.

Basis adaptation and domain decomposition for steady-state partial differential equations with random coefficients

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

Tipireddy, R.; Stinis, P.; Tartakovsky, A. M.

We present a novel approach for solving steady-state stochastic partial differential equations (PDEs) with high-dimensional random parameter space. The proposed approach combines spatial domain decomposition with basis adaptation for each subdomain. The basis adaptation is used to address the curse of dimensionality by constructing an accurate low-dimensional representation of the stochastic PDE solution (probability density function and/or its leading statistical moments) in each subdomain. Restricting the basis adaptation to a specific subdomain affords finding a locally accurate solution. Then, the solutions from all of the subdomains are stitched together to provide a global solution. We support our construction with numericalmore » experiments for a steady-state diffusion equation with a random spatially dependent coefficient. Our results show that highly accurate global solutions can be obtained with significantly reduced computational costs.« less

Thermal Decomposition Mechanism of CL-20 at Different Temperatures by ReaxFF Reactive Molecular Dynamics Simulations.

PubMed

Wang, Fuping; Chen, Lang; Geng, Deshen; Wu, Junying; Lu, Jianying; Wang, Chen

2018-04-26

Hexanitrohexaazaisowurtzitane (CL-20) has a high detonation velocity and pressure, but its sensitivity is also high, which somewhat limits its applications. Therefore, it is important to understand the mechanism and characteristics of thermal decomposition of CL-20. In this study, a ε-CL-20 supercell was constructed and ReaxFF-lg reactive molecular dynamics simulations were performed to investigate thermal decomposition of ε-CL-20 at various temperatures (2000, 2500, 2750, 3000, 3250, and 3500 K). The mechanism of thermal decomposition of CL-20 was analyzed from the aspects of potential energy evolution, the primary reactions, and the intermediate and final product species. The effect of temperature on thermal decomposition of CL-20 is also discussed. The initial reaction path of thermal decomposition of CL-20 is N-NO 2 cleavage to form NO 2 , followed by C-N cleavage, leading to the destruction of the cage structure. A small number of clusters appear in the early reactions and disappear at the end of the reactions. The initial reaction path of CL-20 decomposition is the same at different temperatures. However, as the temperature increases, the decomposition rate of CL-20 increases and the cage structure is destroyed earlier. The temperature greatly affects the rate constants of H 2 O and N 2 , but it has little effect on the rate constants of CO 2 and H 2 .

Regression-based adaptive sparse polynomial dimensional decomposition for sensitivity analysis

NASA Astrophysics Data System (ADS)

Tang, Kunkun; Congedo, Pietro; Abgrall, Remi

2014-11-01

Polynomial dimensional decomposition (PDD) is employed in this work for global sensitivity analysis and uncertainty quantification of stochastic systems subject to a large number of random input variables. Due to the intimate structure between PDD and Analysis-of-Variance, PDD is able to provide simpler and more direct evaluation of the Sobol' sensitivity indices, when compared to polynomial chaos (PC). Unfortunately, the number of PDD terms grows exponentially with respect to the size of the input random vector, which makes the computational cost of the standard method unaffordable for real engineering applications. In order to address this problem of curse of dimensionality, this work proposes a variance-based adaptive strategy aiming to build a cheap meta-model by sparse-PDD with PDD coefficients computed by regression. During this adaptive procedure, the model representation by PDD only contains few terms, so that the cost to resolve repeatedly the linear system of the least-square regression problem is negligible. The size of the final sparse-PDD representation is much smaller than the full PDD, since only significant terms are eventually retained. Consequently, a much less number of calls to the deterministic model is required to compute the final PDD coefficients.

A Posteriori Error Analysis and Uncertainty Quantification for Adaptive Multiscale Operator Decomposition Methods for Multiphysics Problems

DTIC Science & Technology

2014-04-01

Barrier methods for critical exponent problems in geometric analysis and mathematical physics, J. Erway and M. Holst, Submitted for publication ...TR-14-33 A Posteriori Error Analysis and Uncertainty Quantification for Adaptive Multiscale Operator Decomposition Methods for Multiphysics...Problems Approved for public release, distribution is unlimited. April 2014 HDTRA1-09-1-0036 Donald Estep and Michael

Adaptive Detection and ISI Mitigation for Mobile Molecular Communication.

PubMed

Chang, Ge; Lin, Lin; Yan, Hao

2018-03-01

Current studies on modulation and detection schemes in molecular communication mainly focus on the scenarios with static transmitters and receivers. However, mobile molecular communication is needed in many envisioned applications, such as target tracking and drug delivery. Until now, investigations about mobile molecular communication have been limited. In this paper, a static transmitter and a mobile bacterium-based receiver performing random walk are considered. In this mobile scenario, the channel impulse response changes due to the dynamic change of the distance between the transmitter and the receiver. Detection schemes based on fixed distance fail in signal detection in such a scenario. Furthermore, the intersymbol interference (ISI) effect becomes more complex due to the dynamic character of the signal which makes the estimation and mitigation of the ISI even more difficult. In this paper, an adaptive ISI mitigation method and two adaptive detection schemes are proposed for this mobile scenario. In the proposed scheme, adaptive ISI mitigation, estimation of dynamic distance, and the corresponding impulse response reconstruction are performed in each symbol interval. Based on the dynamic channel impulse response in each interval, two adaptive detection schemes, concentration-based adaptive threshold detection and peak-time-based adaptive detection, are proposed for signal detection. Simulations demonstrate that the ISI effect is significantly reduced and the adaptive detection schemes are reliable and robust for mobile molecular communication.

Solvent decompositions and physical properties of decomposition compounds in Li-ion battery electrolytes studied by DFT calculations and molecular dynamics simulations.

PubMed

Tasaki, Ken

2005-02-24

The density functional theory (DFT) calculations have been performed for the reduction decompositions of solvents widely used in Li-ion secondary battery electrolytes, ethylene carbonate (EC), propylene carbonate (PC), dimethyl carbonates (DMC), ethyl methyl carbonate (EMC), and diethyl carbonate (DEC), including a typical electrolyte additive, vinylene carbonate (VC), at the level of B3LYP/6-311+G(2d,p), both in the gas phase and solution using the polarizable conductor calculation model. In the gas phase, the first electron reduction for the cyclic carbonates and for the linear carbonates is found to be exothermic and endothermic, respectively, while the second electron reduction is endothermic for all the compounds examined. On the contrary, in solution both first and second electron reductions are exothermic for all the compounds. Among the solvents and the additive examined, the likelihood of undergoing the first electron reduction in solution was found in the order of EC > PC > VC > DMC > EMC > DEC with EC being the most likely reduced. VC, on the other hand, is most likely to undergo the second electron reduction among the compounds, in the order of VC > EC > PC. Based on the results, the experimentally demonstrated effectiveness of VC as an excellent electrolyte additive was discussed. The bulk thermodynamic properties of two dilithium alkylene glycol dicarbonates, dilithium ethylene glycol dicarbonate (Li-EDC) and dilithium 1,2-propylene glycol dicarbonate (Li-PDC), as the major component of solid-electrolyte interface (SEI) films were also examined through molecular dynamics (MD) simulations in order to understand the stability of the SEI film. It was found that film produced from a decomposition of EC, modeled by Li-EDC, has a higher density, more cohesive energy, and less solubility to the solvent than the film produced from decomposition of PC, Li-PDC. Further, MD simulations of the interface between the decomposition compound and graphite suggested

Incorporation of perceptually adaptive QIM with singular value decomposition for blind audio watermarking

NASA Astrophysics Data System (ADS)

Hu, Hwai-Tsu; Chou, Hsien-Hsin; Yu, Chu; Hsu, Ling-Yuan

2014-12-01

This paper presents a novel approach for blind audio watermarking. The proposed scheme utilizes the flexibility of discrete wavelet packet transformation (DWPT) to approximate the critical bands and adaptively determines suitable embedding strengths for carrying out quantization index modulation (QIM). The singular value decomposition (SVD) is employed to analyze the matrix formed by the DWPT coefficients and embed watermark bits by manipulating singular values subject to perceptual criteria. To achieve even better performance, two auxiliary enhancement measures are attached to the developed scheme. Performance evaluation and comparison are demonstrated with the presence of common digital signal processing attacks. Experimental results confirm that the combination of the DWPT, SVD, and adaptive QIM achieves imperceptible data hiding with satisfying robustness and payload capacity. Moreover, the inclusion of self-synchronization capability allows the developed watermarking system to withstand time-shifting and cropping attacks.

Studies on thermal decomposition behaviors of polypropylene using molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Huang, Jinbao; He, Chao; Tong, Hong; Pan, Guiying

2017-11-01

Polypropylene (PP) is one of the main components of waste plastics. In order to understand the mechanism of PP thermal decomposition, the pyrolysis behaviour of PP has been simulated from 300 to 1000 K in periodic boundary conditions by molecular dynamic method, based on AMBER force field. The simulation results show that the pyrolysis process of PP can mostly be divided into three stages: low temperature pyrolysis stage, intermediate temperature stage and high temperature pyrolysis stage. PP pyrolysis is typical of random main-chain scission, and the possible formation mechanism of major pyrolysis products was analyzed.

An ab initio molecular dynamics study of thermal decomposition of 3,6-di(azido)-1,2,4,5-tetrazine.

PubMed

Wu, Qiong; Zhu, Weihua; Xiao, Heming

2014-10-21

Ab initio molecular dynamics simulations were performed to study the thermal decomposition of isolated and crystal 3,6-di(azido)-1,2,4,5-tetrazine (DiAT). During unimolecular decomposition, the three different initiation mechanisms were observed to be N-N2 cleavage, ring opening, and isomerization, respectively. The preferential initial decomposition step is the homolysis of the N-N2 bond in the azido group. The release mechanisms of nitrogen gas are found to be very different in the early and later decomposition stages of crystal DiAT. In the early decomposition, DiAT decomposes very fast and drastically without forming any stable long-chains or heterocyclic clusters, and most of the nitrogen gases are released through rapid rupture of nitrogen-nitrogen and carbon-nitrogen bonds. But in the later decomposition stage, the release of nitrogen gas is inhibited due to low mobility, long distance from each other, and strong carbon-nitrogen bonds. To overcome the obstacles, the nitrogen gases are released through slow formation and disintegration of polycyclic networks. Our simulations suggest a new decomposition mechanism for the organic polyazido initial explosive at the atomistic level.

Molecular mechanisms of temperature adaptation

PubMed Central

Bagriantsev, Sviatoslav N; Gracheva, Elena O

2015-01-01

Thermal perception is a fundamental physiological process pertaining to the vast majority of organisms. In vertebrates, environmental temperature is detected by the primary afferents of the somatosensory neurons in the skin, which express a ‘choir’ of ion channels tuned to detect particular temperatures. Nearly two decades of research have revealed a number of receptor ion channels that mediate the perception of several temperature ranges, but most still remain molecularly orphaned. Yet even within this well-researched realm, most of our knowledge largely pertains to two closely related species of rodents, mice and rats. While these are standard biomedical research models, mice and rats provide a limited perspective to elucidate the general principles that drive somatosensory evolution. In recent years, significant advances have been made in understanding the molecular mechanism of temperature adaptation in evolutionarily distant vertebrates and in organisms with acute thermal sensitivity. These studies have revealed the remarkable versatility of the somatosensory system and highlighted adaptations at the molecular level, which often include changes in biophysical properties of ion channels from the transient receptor potential family. Exploiting non-standard animal models has the potential to provide unexpected insights into general principles of thermosensation and thermoregulation, unachievable using the rodent model alone. PMID:25433072

Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions

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

Fattebert, J.-L.; Richards, D.F.; Glosli, J.N.

2012-12-01

We present a new algorithm for automatic parallel load balancing in classical molecular dynamics. It assumes a spatial domain decomposition of particles into Voronoi cells. It is a gradient method which attempts to minimize a cost function by displacing Voronoi sites associated with each processor/sub-domain along steepest descent directions. Excellent load balance has been obtained for quasi-2D and 3D practical applications, with up to 440·10 6 particles on 65,536 MPI tasks.

Adaptive truncation of matrix decompositions and efficient estimation of NMR relaxation distributions

NASA Astrophysics Data System (ADS)

Teal, Paul D.; Eccles, Craig

2015-04-01

The two most successful methods of estimating the distribution of nuclear magnetic resonance relaxation times from two dimensional data are data compression followed by application of the Butler-Reeds-Dawson algorithm, and a primal-dual interior point method using preconditioned conjugate gradient. Both of these methods have previously been presented using a truncated singular value decomposition of matrices representing the exponential kernel. In this paper it is shown that other matrix factorizations are applicable to each of these algorithms, and that these illustrate the different fundamental principles behind the operation of the algorithms. These are the rank-revealing QR (RRQR) factorization and the LDL factorization with diagonal pivoting, also known as the Bunch-Kaufman-Parlett factorization. It is shown that both algorithms can be improved by adaptation of the truncation as the optimization process progresses, improving the accuracy as the optimal value is approached. A variation on the interior method viz, the use of barrier function instead of the primal-dual approach, is found to offer considerable improvement in terms of speed and reliability. A third type of algorithm, related to the algorithm known as Fast iterative shrinkage-thresholding algorithm, is applied to the problem. This method can be efficiently formulated without the use of a matrix decomposition.

Adaptive Filtration of Physiological Artifacts in EEG Signals in Humans Using Empirical Mode Decomposition

NASA Astrophysics Data System (ADS)

Grubov, V. V.; Runnova, A. E.; Hramov, A. E.

2018-05-01

A new method for adaptive filtration of experimental EEG signals in humans and for removal of different physiological artifacts has been proposed. The algorithm of the method includes empirical mode decomposition of EEG, determination of the number of empirical modes that are considered, analysis of the empirical modes and search for modes that contains artifacts, removal of these modes, and reconstruction of the EEG signal. The method was tested on experimental human EEG signals and demonstrated high efficiency in the removal of different types of physiological EEG artifacts.

Reactive molecular dynamics simulation of solid nitromethane impact on (010) surfaces induced and nonimpact thermal decomposition.

PubMed

Guo, Feng; Cheng, Xin-lu; Zhang, Hong

2012-04-12

Which is the first step in the decomposition process of nitromethane is a controversial issue, proton dissociation or C-N bond scission. We applied reactive force field (ReaxFF) molecular dynamics to probe the initial decomposition mechanisms of nitromethane. By comparing the impact on (010) surfaces and without impact (only heating) for nitromethane simulations, we found that proton dissociation is the first step of the pyrolysis of nitromethane, and the C-N bond decomposes in the same time scale as in impact simulations, but in the nonimpact simulation, C-N bond dissociation takes place at a later time. At the end of these simulations, a large number of clusters are formed. By analyzing the trajectories, we discussed the role of the hydrogen bond in the initial process of nitromethane decompositions, the intermediates observed in the early time of the simulations, and the formation of clusters that consisted of C-N-C-N chain/ring structures.

Ab initio molecular dynamics study on the initial chemical events in nitramines: thermal decomposition of CL-20.

PubMed

Isayev, Olexandr; Gorb, Leonid; Qasim, Mo; Leszczynski, Jerzy

2008-09-04

CL-20 (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane or HNIW) is a high-energy nitramine explosive. To improve atomistic understanding of the thermal decomposition of CL-20 gas and solid phases, we performed a series of ab initio molecular dynamics simulations. We found that during unimolecular decomposition, unlike other nitramines (e.g., RDX, HMX), CL-20 has only one distinct initial reaction channelhomolysis of the N-NO2 bond. We did not observe any HONO elimination reaction during unimolecular decomposition, whereas the ring-breaking reaction was followed by NO 2 fission. Therefore, in spite of limited sampling, that provides a mostly qualitative picture, we proposed here a scheme of unimolecular decomposition of CL-20. The averaged product population over all trajectories was estimated at four HCN, two to four NO2, two to four NO, one CO, and one OH molecule per one CL-20 molecule. Our simulations provide a detailed description of the chemical processes in the initial stages of thermal decomposition of condensed CL-20, allowing elucidation of key features of such processes as composition of primary reaction products, reaction timing, and Arrhenius behavior of the system. The primary reactions leading to NO2, NO, N 2O, and N2 occur at very early stages. We also estimated potential activation barriers for the formation of NO2, which essentially determines overall decomposition kinetics and effective rate constants for NO2 and N2. The calculated solid-phase decomposition pathways correlate with available condensed-phase experimental data.

Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

NASA Astrophysics Data System (ADS)

Guzman, Horacio V.; Junghans, Christoph; Kremer, Kurt; Stuehn, Torsten

2017-11-01

Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach, the theoretical modeling and scaling laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. These two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.

Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

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

Guzman, Horacio V.; Junghans, Christoph; Kremer, Kurt

Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach and paper, the theoretical modeling and scalingmore » laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. Finally, these two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.« less

Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

DOE PAGES

Guzman, Horacio V.; Junghans, Christoph; Kremer, Kurt; ...

2017-11-27

Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach and paper, the theoretical modeling and scalingmore » laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. Finally, these two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.« less

Advances on molecular mechanism of the adaptive evolution of Chiroptera (bats).

PubMed

Yunpeng, Liang; Li, Yu

2015-01-01

As the second biggest animal group in mammals, Chiroptera (bats) demonstrates many unique adaptive features in terms of flight, echolocation, auditory acuity, feeding habit, hibernation and immune defense, providing an excellent system for understanding the molecular basis of how organisms adapt to the living environments encountered. In this review, we summarize the researches on the molecular mechanism of the adaptive evolution of Chiroptera, especially the recent researches at the genome levels, suggesting a far more complex evolutionary pattern and functional diversity than previously thought. In the future, along with the increasing numbers of Chiroptera species genomes available, new evolutionary patterns and functional divergence will be revealed, which can promote the further understanding of this animal group and the molecular mechanism of adaptive evolution.

Molecular and cellular bases of adaptation to a changing environment in microorganisms.

PubMed

Bleuven, Clara; Landry, Christian R

2016-10-26

Environmental heterogeneity constitutes an evolutionary challenge for organisms. While evolutionary dynamics under variable conditions has been explored for decades, we still know relatively little about the cellular and molecular mechanisms involved. It is of paramount importance to examine these molecular bases because they may play an important role in shaping the course of evolution. In this review, we examine the diversity of adaptive mechanisms in the face of environmental changes. We exploit the recent literature on microbial systems because those have benefited the most from the recent emergence of genetic engineering and experimental evolution followed by genome sequencing. We identify four emerging trends: (i) an adaptive molecular change in a pathway often results in fitness trade-off in alternative environments but the effects are dependent on a mutation's genetic background; (ii) adaptive changes often modify transcriptional and signalling pathways; (iii) several adaptive changes may occur within the same molecular pathway but be associated with pleiotropy of different signs across environments; (iv) because of their large associated costs, macromolecular changes such as gene amplification and aneuploidy may be a rapid mechanism of adaptation in the short-term only. The course of adaptation in a variable environment, therefore, depends on the complexity of the environment but also on the molecular relationships among the genes involved and between the genes and the phenotypes under selection. © 2016 The Author(s).

Biomimetic molecular design tools that learn, evolve, and adapt.

PubMed

Winkler, David A

2017-01-01

A dominant hallmark of living systems is their ability to adapt to changes in the environment by learning and evolving. Nature does this so superbly that intensive research efforts are now attempting to mimic biological processes. Initially this biomimicry involved developing synthetic methods to generate complex bioactive natural products. Recent work is attempting to understand how molecular machines operate so their principles can be copied, and learning how to employ biomimetic evolution and learning methods to solve complex problems in science, medicine and engineering. Automation, robotics, artificial intelligence, and evolutionary algorithms are now converging to generate what might broadly be called in silico-based adaptive evolution of materials. These methods are being applied to organic chemistry to systematize reactions, create synthesis robots to carry out unit operations, and to devise closed loop flow self-optimizing chemical synthesis systems. Most scientific innovations and technologies pass through the well-known "S curve", with slow beginning, an almost exponential growth in capability, and a stable applications period. Adaptive, evolving, machine learning-based molecular design and optimization methods are approaching the period of very rapid growth and their impact is already being described as potentially disruptive. This paper describes new developments in biomimetic adaptive, evolving, learning computational molecular design methods and their potential impacts in chemistry, engineering, and medicine.

Molecular evolution and thermal adaptation

NASA Astrophysics Data System (ADS)

Chen, Peiqiu

2011-12-01

In this thesis, we address problems in molecular evolution, thermal adaptation, and the kinetics of adaptation of bacteria and viruses to elevated environmental temperatures. We use a nearly neutral fitness model where the replication speed of an organism is proportional to the copy number of folded proteins. Our model reproduces the distribution of stabilities of natural proteins in excellent agreement with experiment. We find that species with high mutation rates tend to have less stable proteins compared to species with low mutation rate. We found that a broad distribution of protein stabilities observed in the model and in experiment is the key determinant of thermal response for viruses and bacteria. Our results explain most of the earlier experimental observations: striking asymmetry of thermal response curves, the absence of evolutionary trade-off which was expected but not found in experiments, correlation between denaturation temperature for several protein families and the Optimal Growth Temperature (OGT) of their carrier organisms, and proximity of bacterial or viral OGTs to their evolutionary temperatures. Our theory quantitatively and with high accuracy described thermal response curves for 35 bacterial species. The model also addresses the key to adaptation is in weak-link genes (WLG), which encode least thermodynamically stable essential proteins in the proteome. We observe, as in experiment, a two-stage adaptation process. The first stage is a Luria-Delbruck type of selection, whereby rare WLG alleles, whose proteins are more stable than WLG proteins of the majority of the population (either due to standing genetic variation or due to an early acquired mutation), rapidly rise to fixation. The second stage constitutes subsequent slow accumulation of mutations in an adapted population. As adaptation progresses, selection regime changes from positive to neutral: Selection coefficient of beneficial mutations scales as a negative power of number of

Molecular determinants of enzyme cold adaptation: comparative structural and computational studies of cold- and warm-adapted enzymes.

PubMed

Papaleo, Elena; Tiberti, Matteo; Invernizzi, Gaetano; Pasi, Marco; Ranzani, Valeria

2011-11-01

The identification of molecular mechanisms underlying enzyme cold adaptation is a hot-topic both for fundamental research and industrial applications. In the present contribution, we review the last decades of structural computational investigations on cold-adapted enzymes in comparison to their warm-adapted counterparts. Comparative sequence and structural studies allow the definition of a multitude of adaptation strategies. Different enzymes carried out diverse mechanisms to adapt to low temperatures, so that a general theory for enzyme cold adaptation cannot be formulated. However, some common features can be traced in dynamic and flexibility properties of these enzymes, as well as in their intra- and inter-molecular interaction networks. Interestingly, the current data suggest that a family-centered point of view is necessary in the comparative analyses of cold- and warm-adapted enzymes. In fact, enzymes belonging to the same family or superfamily, thus sharing at least the three-dimensional fold and common features of the functional sites, have evolved similar structural and dynamic patterns to overcome the detrimental effects of low temperatures.

Biomimetic molecular design tools that learn, evolve, and adapt

PubMed Central

2017-01-01

A dominant hallmark of living systems is their ability to adapt to changes in the environment by learning and evolving. Nature does this so superbly that intensive research efforts are now attempting to mimic biological processes. Initially this biomimicry involved developing synthetic methods to generate complex bioactive natural products. Recent work is attempting to understand how molecular machines operate so their principles can be copied, and learning how to employ biomimetic evolution and learning methods to solve complex problems in science, medicine and engineering. Automation, robotics, artificial intelligence, and evolutionary algorithms are now converging to generate what might broadly be called in silico-based adaptive evolution of materials. These methods are being applied to organic chemistry to systematize reactions, create synthesis robots to carry out unit operations, and to devise closed loop flow self-optimizing chemical synthesis systems. Most scientific innovations and technologies pass through the well-known “S curve”, with slow beginning, an almost exponential growth in capability, and a stable applications period. Adaptive, evolving, machine learning-based molecular design and optimization methods are approaching the period of very rapid growth and their impact is already being described as potentially disruptive. This paper describes new developments in biomimetic adaptive, evolving, learning computational molecular design methods and their potential impacts in chemistry, engineering, and medicine. PMID:28694872

A molecular dynamics study of model SI clathrate hydrates: the effect of guest size and guest-water interaction on decomposition kinetics.

PubMed

Das, Subhadip; Baghel, Vikesh Singh; Roy, Sudip; Kumar, Rajnish

2015-04-14

One of the options suggested for methane recovery from natural gas hydrates is molecular replacement of methane by suitable guests like CO2 and N2. This approach has been found to be feasible through many experimental and molecular dynamics simulation studies. However, the long term stability of the resultant hydrate needs to be evaluated; the decomposition rate of these hydrates is expected to depend on the interaction between these guest and water molecules. In this work, molecular dynamics simulation has been performed to illustrate the effect of guest molecules with different sizes and interaction strengths with water on structure I (SI) hydrate decomposition and hence the stability. The van der Waals interaction between water of hydrate cages and guest molecules is defined by Lennard Jones potential parameters. A wide range of parameter spaces has been scanned by changing the guest molecules in the SI hydrate, which acts as a model gas for occupying the small and large cages of the SI hydrate. All atomistic simulation results show that the stability of the hydrate is sensitive to the size and interaction of the guest molecules with hydrate water. The increase in the interaction of guest molecules with water stabilizes the hydrate, which in turn shows a slower rate of hydrate decomposition. Similarly guest molecules with a reasonably small (similar to Helium) or large size increase the decomposition rate. The results were also analyzed by calculating the structural order parameter to understand the dynamics of crystal structure and correlated with the release rate of guest molecules from the solid hydrate phase. The results have been explained based on the calculation of potential energies felt by guest molecules in amorphous water, hydrate bulk and hydrate-water interface regions.

Spatial, temporal, and hybrid decompositions for large-scale vehicle routing with time windows

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

Bent, Russell W

This paper studies the use of decomposition techniques to quickly find high-quality solutions to large-scale vehicle routing problems with time windows. It considers an adaptive decomposition scheme which iteratively decouples a routing problem based on the current solution. Earlier work considered vehicle-based decompositions that partitions the vehicles across the subproblems. The subproblems can then be optimized independently and merged easily. This paper argues that vehicle-based decompositions, although very effective on various problem classes also have limitations. In particular, they do not accommodate temporal decompositions and may produce spatial decompositions that are not focused enough. This paper then proposes customer-based decompositionsmore » which generalize vehicle-based decouplings and allows for focused spatial and temporal decompositions. Experimental results on class R2 of the extended Solomon benchmarks demonstrates the benefits of the customer-based adaptive decomposition scheme and its spatial, temporal, and hybrid instantiations. In particular, they show that customer-based decompositions bring significant benefits over large neighborhood search in contrast to vehicle-based decompositions.« less

Molecular Mechanisms Underlying Cardiac Adaptation to Exercise

PubMed Central

Vega, Rick B.; Konhilas, John P.; Kelly, Daniel P.; Leinwand, Leslie A.

2017-01-01

Exercise elicits coordinated multi-organ responses including skeletal muscle, vasculature, heart and lung. In the short term, the output of the heart increases to meet the demand of strenuous exercise. Long term exercise instigates remodeling of the heart including growth and adaptive molecular and cellular re-programming. Signaling pathways such as the insulin-like growth factor 1/PI3K/Akt pathway mediate many of these responses. Exercise-induced, or physiologic, cardiac growth contrasts with growth elicited by pathological stimuli such as hypertension. Comparing the molecular and cellular underpinnings of physiologic and pathologic cardiac growth has unveiled phenotype-specific signaling pathways and transcriptional regulatory programs. Studies suggest that exercise pathways likely antagonize pathological pathways, and exercise training is often recommended for patients with chronic stable heart failure or following myocardial infarction. Herein, we summarize the current understanding of the structural and functional cardiac responses to exercise as well as signaling pathways and downstream effector molecules responsible for these adaptations. PMID:28467921

An adaptive proper orthogonal decomposition method for model order reduction of multi-disc rotor system

NASA Astrophysics Data System (ADS)

Jin, Yulin; Lu, Kuan; Hou, Lei; Chen, Yushu

2017-12-01

The proper orthogonal decomposition (POD) method is a main and efficient tool for order reduction of high-dimensional complex systems in many research fields. However, the robustness problem of this method is always unsolved, although there are some modified POD methods which were proposed to solve this problem. In this paper, a new adaptive POD method called the interpolation Grassmann manifold (IGM) method is proposed to address the weakness of local property of the interpolation tangent-space of Grassmann manifold (ITGM) method in a wider parametric region. This method is demonstrated here by a nonlinear rotor system of 33-degrees of freedom (DOFs) with a pair of liquid-film bearings and a pedestal looseness fault. The motion region of the rotor system is divided into two parts: simple motion region and complex motion region. The adaptive POD method is compared with the ITGM method for the large and small spans of parameter in the two parametric regions to present the advantage of this method and disadvantage of the ITGM method. The comparisons of the responses are applied to verify the accuracy and robustness of the adaptive POD method, as well as the computational efficiency is also analyzed. As a result, the new adaptive POD method has a strong robustness and high computational efficiency and accuracy in a wide scope of parameter.

A Novel ECG Data Compression Method Using Adaptive Fourier Decomposition With Security Guarantee in e-Health Applications.

PubMed

Ma, JiaLi; Zhang, TanTan; Dong, MingChui

2015-05-01

This paper presents a novel electrocardiogram (ECG) compression method for e-health applications by adapting an adaptive Fourier decomposition (AFD) algorithm hybridized with a symbol substitution (SS) technique. The compression consists of two stages: first stage AFD executes efficient lossy compression with high fidelity; second stage SS performs lossless compression enhancement and built-in data encryption, which is pivotal for e-health. Validated with 48 ECG records from MIT-BIH arrhythmia benchmark database, the proposed method achieves averaged compression ratio (CR) of 17.6-44.5 and percentage root mean square difference (PRD) of 0.8-2.0% with a highly linear and robust PRD-CR relationship, pushing forward the compression performance to an unexploited region. As such, this paper provides an attractive candidate of ECG compression method for pervasive e-health applications.

Materials learning from life: concepts for active, adaptive and autonomous molecular systems.

PubMed

Merindol, Rémi; Walther, Andreas

2017-09-18

Bioinspired out-of-equilibrium systems will set the scene for the next generation of molecular materials with active, adaptive, autonomous, emergent and intelligent behavior. Indeed life provides the best demonstrations of complex and functional out-of-equilibrium systems: cells keep track of time, communicate, move, adapt, evolve and replicate continuously. Stirred by the understanding of biological principles, artificial out-of-equilibrium systems are emerging in many fields of soft matter science. Here we put in perspective the molecular mechanisms driving biological functions with the ones driving synthetic molecular systems. Focusing on principles that enable new levels of functionalities (temporal control, autonomous structures, motion and work generation, information processing) rather than on specific material classes, we outline key cross-disciplinary concepts that emerge in this challenging field. Ultimately, the goal is to inspire and support new generations of autonomous and adaptive molecular devices fueled by self-regulating chemistry.

Adaptively restrained molecular dynamics in LAMMPS

NASA Astrophysics Data System (ADS)

Kant Singh, Krishna; Redon, Stephane

2017-07-01

Adaptively restrained molecular dynamics (ARMD) is a recently introduced particles simulation method that switches positional degrees of freedom on and off during simulation in order to speed up calculations. In the NVE ensemble, ARMD allows users to trade between precision and speed while, in the NVT ensemble, it makes it possible to compute statistical averages faster. Despite the conceptual simplicity of the approach, however, integrating it in existing molecular dynamics packages is non-trivial, in particular since implemented potentials should a priori be rewritten to take advantage of frozen particles and achieve a speed-up. In this paper, we present novel algorithms for integrating ARMD in LAMMPS, a popular multi-purpose molecular simulation package. In particular, we demonstrate how to enable ARMD in LAMMPS without having to re-implement all available force fields. The proposed algorithms are assessed on four different benchmarks, and show how they allow us to speed up simulations up to one order of magnitude.

Adaptive sparsest narrow-band decomposition method and its applications to rolling element bearing fault diagnosis

NASA Astrophysics Data System (ADS)

Cheng, Junsheng; Peng, Yanfeng; Yang, Yu; Wu, Zhantao

2017-02-01

Enlightened by ASTFA method, adaptive sparsest narrow-band decomposition (ASNBD) method is proposed in this paper. In ASNBD method, an optimized filter must be established at first. The parameters of the filter are determined by solving a nonlinear optimization problem. A regulated differential operator is used as the objective function so that each component is constrained to be a local narrow-band signal. Afterwards, the signal is filtered by the optimized filter to generate an intrinsic narrow-band component (INBC). ASNBD is proposed aiming at solving the problems existed in ASTFA. Gauss-Newton type method, which is applied to solve the optimization problem in ASTFA, is irreplaceable and very sensitive to initial values. However, more appropriate optimization method such as genetic algorithm (GA) can be utilized to solve the optimization problem in ASNBD. Meanwhile, compared with ASTFA, the decomposition results generated by ASNBD have better physical meaning by constraining the components to be local narrow-band signals. Comparisons are made between ASNBD, ASTFA and EMD by analyzing simulation and experimental signals. The results indicate that ASNBD method is superior to the other two methods in generating more accurate components from noise signal, restraining the boundary effect, possessing better orthogonality and diagnosing rolling element bearing fault.

Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation.

PubMed

Lopes, J S; Arenas, M; Posada, D; Beaumont, M A

2014-03-01

The estimation of parameters in molecular evolution may be biased when some processes are not considered. For example, the estimation of selection at the molecular level using codon-substitution models can have an upward bias when recombination is ignored. Here we address the joint estimation of recombination, molecular adaptation and substitution rates from coding sequences using approximate Bayesian computation (ABC). We describe the implementation of a regression-based strategy for choosing subsets of summary statistics for coding data, and show that this approach can accurately infer recombination allowing for intracodon recombination breakpoints, molecular adaptation and codon substitution rates. We demonstrate that our ABC approach can outperform other analytical methods under a variety of evolutionary scenarios. We also show that although the choice of the codon-substitution model is important, our inferences are robust to a moderate degree of model misspecification. In addition, we demonstrate that our approach can accurately choose the evolutionary model that best fits the data, providing an alternative for when the use of full-likelihood methods is impracticable. Finally, we applied our ABC method to co-estimate recombination, substitution and molecular adaptation rates from 24 published human immunodeficiency virus 1 coding data sets.

Sex speeds adaptation by altering the dynamics of molecular evolution.

PubMed

McDonald, Michael J; Rice, Daniel P; Desai, Michael M

2016-03-10

Sex and recombination are pervasive throughout nature despite their substantial costs. Understanding the evolutionary forces that maintain these phenomena is a central challenge in biology. One longstanding hypothesis argues that sex is beneficial because recombination speeds adaptation. Theory has proposed several distinct population genetic mechanisms that could underlie this advantage. For example, sex can promote the fixation of beneficial mutations either by alleviating interference competition (the Fisher-Muller effect) or by separating them from deleterious load (the ruby in the rubbish effect). Previous experiments confirm that sex can increase the rate of adaptation, but these studies did not observe the evolutionary dynamics that drive this effect at the genomic level. Here we present the first, to our knowledge, comparison between the sequence-level dynamics of adaptation in experimental sexual and asexual Saccharomyces cerevisiae populations, which allows us to identify the specific mechanisms by which sex speeds adaptation. We find that sex alters the molecular signatures of evolution by changing the spectrum of mutations that fix, and confirm theoretical predictions that it does so by alleviating clonal interference. We also show that substantially deleterious mutations hitchhike to fixation in adapting asexual populations. In contrast, recombination prevents such mutations from fixing. Our results demonstrate that sex both speeds adaptation and alters its molecular signature by allowing natural selection to more efficiently sort beneficial from deleterious mutations.

A novel fusion framework of visible light and infrared images based on singular value decomposition and adaptive DUAL-PCNN in NSST domain

NASA Astrophysics Data System (ADS)

Cheng, Boyang; Jin, Longxu; Li, Guoning

2018-06-01

Visible light and infrared images fusion has been a significant subject in imaging science. As a new contribution to this field, a novel fusion framework of visible light and infrared images based on adaptive dual-channel unit-linking pulse coupled neural networks with singular value decomposition (ADS-PCNN) in non-subsampled shearlet transform (NSST) domain is present in this paper. First, the source images are decomposed into multi-direction and multi-scale sub-images by NSST. Furthermore, an improved novel sum modified-Laplacian (INSML) of low-pass sub-image and an improved average gradient (IAVG) of high-pass sub-images are input to stimulate the ADS-PCNN, respectively. To address the large spectral difference between infrared and visible light and the occurrence of black artifacts in fused images, a local structure information operator (LSI), which comes from local area singular value decomposition in each source image, is regarded as the adaptive linking strength that enhances fusion accuracy. Compared with PCNN models in other studies, the proposed method simplifies certain peripheral parameters, and the time matrix is utilized to decide the iteration number adaptively. A series of images from diverse scenes are used for fusion experiments and the fusion results are evaluated subjectively and objectively. The results of the subjective and objective evaluation show that our algorithm exhibits superior fusion performance and is more effective than the existing typical fusion techniques.

Nutrient-enhanced decomposition of plant biomass in a freshwater wetland

USGS Publications Warehouse

Bodker, James E.; Turner, Robert Eugene; Tweel, Andrew; Schulz, Christopher; Swarzenski, Christopher M.

2015-01-01

We studied soil decomposition in a Panicum hemitomon (Schultes)-dominated freshwater marsh located in southeastern Louisiana that was unambiguously changed by secondarily-treated municipal wastewater effluent. We used four approaches to evaluate how belowground biomass decomposition rates vary under different nutrient regimes in this marsh. The results of laboratory experiments demonstrated how nutrient enrichment enhanced the loss of soil or plant organic matter by 50%, and increased gas production. An experiment demonstrated that nitrogen, not phosphorus, limited decomposition. Cellulose decomposition at the field site was higher in the flowfield of the introduced secondarily treated sewage water, and the quality of the substrate (% N or % P) was directly related to the decomposition rates. We therefore rejected the null hypothesis that nutrient enrichment had no effect on the decomposition rates of these organic soils. In response to nutrient enrichment, plants respond through biomechanical or structural adaptations that alter the labile characteristics of plant tissue. These adaptations eventually change litter type and quality (where the marsh survives) as the % N content of plant tissue rises and is followed by even higher decomposition rates of the litter produced, creating a positive feedback loop. Marsh fragmentation will increase as a result. The assumptions and conditions underlying the use of unconstrained wastewater flow within natural wetlands, rather than controlled treatment within the confines of constructed wetlands, are revealed in the loss of previously sequestered carbon, habitat, public use, and other societal benefits.

Sn - Induced decomposition of SiGeSn alloys grown on Si by molecular-beam epitaxy

NASA Astrophysics Data System (ADS)

Talochkin, A. B.; Timofeev, V. A.; Gutakovskii, A. K.; Mashanov, V. I.

2017-11-01

Structural features of Si1-x-yGexSny alloy layers grown on Si by molecular-beam epitaxy are studied. These layers with the thickness of 2.0 nm, the nominal Ge composition of x0 ≈ 0.3, and the Sn-content of y ≈ 2-6 at.% have been grown at low temperatures (100-150 °C). We have used high-resolution transmission electron microscopy to analyze atomic structure of grown layers and Raman spectroscopy to evaluate the real Ge-content x from the observed optical phonon frequencies. It is found that the x value coincides with the nominal one at low Sn-content (2-3 at.%), and when it is increased (y ≥ 5 at.%), the decomposition of alloys into two fractions occurs. One of them is enriched by Ge with x up to 0.6 and the other fraction is Si-enriched. It is shown that the observed decomposition is Sn-induced and related to increase in Ge adatoms mobility in the growth process. This mechanism is similar to that theoretically predicted by Venezuela and Tersoff (Phys. Rev. 58, 10871 (1998)) for the case of high growth temperature.

Dynamic Responses and Initial Decomposition under Shock Loading: A DFTB Calculation Combined with MSST Method for β-HMX with Molecular Vacancy.

PubMed

He, Zheng-Hua; Chen, Jun; Ji, Guang-Fu; Liu, Li-Min; Zhu, Wen-Jun; Wu, Qiang

2015-08-20

Despite extensive efforts on studying the decomposition mechanism of HMX under extreme condition, an intrinsic understanding of mechanical and chemical response processes, inducing the initial chemical reaction, is not yet achieved. In this work, the microscopic dynamic response and initial decomposition of β-HMX with (1 0 0) surface and molecular vacancy under shock condition, were explored by means of the self-consistent-charge density-functional tight-binding method (SCC-DFTB) in conjunction with multiscale shock technique (MSST). The evolutions of various bond lengths and charge transfers were analyzed to explore and understand the initial reaction mechanism of HMX. Our results discovered that the C-N bond close to major axes had less compression sensitivity and higher stretch activity. The charge was transferred mainly from the N-NO2 group along the minor axes and H atom to C atom during the early compression process. The first reaction of HMX primarily initiated with the fission of the molecular ring at the site of the C-N bond close to major axes. Further breaking of the molecular ring enhanced intermolecular interactions and promoted the cleavage of C-H and N-NO2 bonds. More significantly, the dynamic response behavior clearly depended on the angle between chemical bond and shock direction.

Adaptive-projection intrinsically transformed multivariate empirical mode decomposition in cooperative brain-computer interface applications.

PubMed

Hemakom, Apit; Goverdovsky, Valentin; Looney, David; Mandic, Danilo P

2016-04-13

An extension to multivariate empirical mode decomposition (MEMD), termed adaptive-projection intrinsically transformed MEMD (APIT-MEMD), is proposed to cater for power imbalances and inter-channel correlations in real-world multichannel data. It is shown that the APIT-MEMD exhibits similar or better performance than MEMD for a large number of projection vectors, whereas it outperforms MEMD for the critical case of a small number of projection vectors within the sifting algorithm. We also employ the noise-assisted APIT-MEMD within our proposed intrinsic multiscale analysis framework and illustrate the advantages of such an approach in notoriously noise-dominated cooperative brain-computer interface (BCI) based on the steady-state visual evoked potentials and the P300 responses. Finally, we show that for a joint cognitive BCI task, the proposed intrinsic multiscale analysis framework improves system performance in terms of the information transfer rate. © 2016 The Author(s).

Data-adaptive Harmonic Decomposition and Real-time Prediction of Arctic Sea Ice Extent

NASA Astrophysics Data System (ADS)

Kondrashov, Dmitri; Chekroun, Mickael; Ghil, Michael

2017-04-01

Decline in the Arctic sea ice extent (SIE) has profound socio-economic implications and is a focus of active scientific research. Of particular interest is prediction of SIE on subseasonal time scales, i.e. from early summer into fall, when sea ice coverage in Arctic reaches its minimum. However, subseasonal forecasting of SIE is very challenging due to the high variability of ocean and atmosphere over Arctic in summer, as well as shortness of observational data and inadequacies of the physics-based models to simulate sea-ice dynamics. The Sea Ice Outlook (SIO) by Sea Ice Prediction Network (SIPN, http://www.arcus.org/sipn) is a collaborative effort to facilitate and improve subseasonal prediction of September SIE by physics-based and data-driven statistical models. Data-adaptive Harmonic Decomposition (DAH) and Multilayer Stuart-Landau Models (MSLM) techniques [Chekroun and Kondrashov, 2017], have been successfully applied to the nonlinear stochastic modeling, as well as retrospective and real-time forecasting of Multisensor Analyzed Sea Ice Extent (MASIE) dataset in key four Arctic regions. In particular, DAH-MSLM predictions outperformed most statistical models and physics-based models in real-time 2016 SIO submissions. The key success factors are associated with DAH ability to disentangle complex regional dynamics of MASIE by data-adaptive harmonic spatio-temporal patterns that reduce the data-driven modeling effort to elemental MSLMs stacked per frequency with fixed and small number of model coefficients to estimate.

A polychromatic adaption of the Beer-Lambert model for spectral decomposition

NASA Astrophysics Data System (ADS)

Sellerer, Thorsten; Ehn, Sebastian; Mechlem, Korbinian; Pfeiffer, Franz; Herzen, Julia; Noël, Peter B.

2017-03-01

We present a semi-empirical forward-model for spectral photon-counting CT which is fully compatible with state-of-the-art maximum-likelihood estimators (MLE) for basis material line integrals. The model relies on a minimum calibration effort to make the method applicable in routine clinical set-ups with the need for periodic re-calibration. In this work we present an experimental verifcation of our proposed method. The proposed method uses an adapted Beer-Lambert model, describing the energy dependent attenuation of a polychromatic x-ray spectrum using additional exponential terms. In an experimental dual-energy photon-counting CT setup based on a CdTe detector, the model demonstrates an accurate prediction of the registered counts for an attenuated polychromatic spectrum. Thereby deviations between model and measurement data lie within the Poisson statistical limit of the performed acquisitions, providing an effectively unbiased forward-model. The experimental data also shows that the model is capable of handling possible spectral distortions introduced by the photon-counting detector and CdTe sensor. The simplicity and high accuracy of the proposed model provides a viable forward-model for MLE-based spectral decomposition methods without the need of costly and time-consuming characterization of the system response.

Climate fails to predict wood decomposition at regional scales

NASA Astrophysics Data System (ADS)

Bradford, Mark A.; Warren, Robert J., II; Baldrian, Petr; Crowther, Thomas W.; Maynard, Daniel S.; Oldfield, Emily E.; Wieder, William R.; Wood, Stephen A.; King, Joshua R.

2014-07-01

Decomposition of organic matter strongly influences ecosystem carbon storage. In Earth-system models, climate is a predominant control on the decomposition rates of organic matter. This assumption is based on the mean response of decomposition to climate, yet there is a growing appreciation in other areas of global change science that projections based on mean responses can be irrelevant and misleading. We test whether climate controls on the decomposition rate of dead wood--a carbon stock estimated to represent 73 +/- 6 Pg carbon globally--are sensitive to the spatial scale from which they are inferred. We show that the common assumption that climate is a predominant control on decomposition is supported only when local-scale variation is aggregated into mean values. Disaggregated data instead reveal that local-scale factors explain 73% of the variation in wood decomposition, and climate only 28%. Further, the temperature sensitivity of decomposition estimated from local versus mean analyses is 1.3-times greater. Fundamental issues with mean correlations were highlighted decades ago, yet mean climate-decomposition relationships are used to generate simulations that inform management and adaptation under environmental change. Our results suggest that to predict accurately how decomposition will respond to climate change, models must account for local-scale factors that control regional dynamics.

A fast new algorithm for a robot neurocontroller using inverse QR decomposition

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

Morris, A.S.; Khemaissia, S.

2000-01-01

A new adaptive neural network controller for robots is presented. The controller is based on direct adaptive techniques. Unlike many neural network controllers in the literature, inverse dynamical model evaluation is not required. A numerically robust, computationally efficient processing scheme for neutral network weight estimation is described, namely, the inverse QR decomposition (INVQR). The inverse QR decomposition and a weighted recursive least-squares (WRLS) method for neural network weight estimation is derived using Cholesky factorization of the data matrix. The algorithm that performs the efficient INVQR of the underlying space-time data matrix may be implemented in parallel on a triangular array.more » Furthermore, its systolic architecture is well suited for VLSI implementation. Another important benefit is well suited for VLSI implementation. Another important benefit of the INVQR decomposition is that it solves directly for the time-recursive least-squares filter vector, while avoiding the sequential back-substitution step required by the QR decomposition approaches.« less

Molecular Theory of Detonation Initiation: Insight from First Principles Modeling of the Decomposition Mechanisms of Organic Nitro Energetic Materials.

PubMed

Tsyshevsky, Roman V; Sharia, Onise; Kuklja, Maija M

2016-02-19

This review presents a concept, which assumes that thermal decomposition processes play a major role in defining the sensitivity of organic energetic materials to detonation initiation. As a science and engineering community we are still far away from having a comprehensive molecular detonation initiation theory in a widely agreed upon form. However, recent advances in experimental and theoretical methods allow for a constructive and rigorous approach to design and test the theory or at least some of its fundamental building blocks. In this review, we analyzed a set of select experimental and theoretical articles, which were augmented by our own first principles modeling and simulations, to reveal new trends in energetic materials and to refine known existing correlations between their structures, properties, and functions. Our consideration is intentionally limited to the processes of thermally stimulated chemical reactions at the earliest stage of decomposition of molecules and materials containing defects.

Analysis of the Sensitivity of K-Type Molecular Sieve-Deposited MWNTs for the Detection of SF₆ Decomposition Gases under Partial Discharge.

PubMed

Zhang, Xiaoxing; Li, Xin; Luo, Chenchen; Dong, Xingchen; Zhou, Lei

2015-11-11

Sulfur hexafluoride (SF6) is widely utilized in gas-insulated switchgear (GIS). However, part of SF6 decomposes into different components under partial discharge (PD) conditions. Previous research has shown that the gas responses of intrinsic and 4 Å-type molecular sieve-deposited multi-wall carbon nanotubes (MWNTs) to SOF2 and SO2F2, two important decomposition components of SF6, are not obvious. In this study, a K-type molecular sieve-deposited MWNTs sensor was developed. Its gas response characteristics and the influence of the mixture ratios of gases on the gas-sensing properties were studied. The results showed that, for sensors with gas mixture ratios of 5:1, 10:1, and 20:1, the resistance change rate increased by nearly 13.0% after SOF2 adsorption, almost 10 times that of MWNTs sensors, while the sensors' resistance change rate with a mixture ratio of 10:1 reached 17.3% after SO2F2 adsorption, nearly nine times that of intrinsic MWNT sensors. Besides, a good linear relationship was observed between concentration of decomposition components and the resistance change rate of sensors.

Adaptive Molecular Evolution for 13,000 Phage Generations

PubMed Central

Wichman, Holly A.; Millstein, Jack; Bull, J. J.

2005-01-01

Bacteriophage φX174 was evolved on a continuous supply of sensitive hosts for 180 days (∼13,000 phage generations). The average rate of nucleotide substitution was nearly 0.2% (11 substitutions)/20 days, and, surprisingly, substitutions accumulated in a clock-like manner throughout the study, except for a low rate during the first 20 days. Rates of silent and missense substitutions varied over time and among genes. Approximately 40% of the 71 missense changes and 25% of the 58 silent changes have been observed in previous adaptations; the rate of parallel substitution was highest in the early phase of the evolution, but 7% of the later changes had evolved in previous studies of much shorter duration. Several lines of evidence suggest that most of the changes were adaptive, even many of the silent substitutions. The sustained, high rate of adaptive evolution for 180 days defies a model of adaptation to a constant environment. We instead suggest that continuing molecular evolution reflects a potentially indefinite arms race, stemming from high levels of co-infection and the resulting conflict among genomes competing within the same cell. PMID:15687276

Molecular Theory of Detonation Initiation: Insight from First Principles Modeling of the Decomposition Mechanisms of Organic Nitro Energetic Materials

DOE PAGES

Tsyshevsky, Roman; Sharia, Onise; Kuklja, Maija

2016-02-19

Our review presents a concept, which assumes that thermal decomposition processes play a major role in defining the sensitivity of organic energetic materials to detonation initiation. As a science and engineering community we are still far away from having a comprehensive molecular detonation initiation theory in a widely agreed upon form. However, recent advances in experimental and theoretical methods allow for a constructive and rigorous approach to design and test the theory or at least some of its fundamental building blocks. In this review, we analyzed a set of select experimental and theoretical articles, which were augmented by our ownmore » first principles modeling and simulations, to reveal new trends in energetic materials and to refine known existing correlations between their structures, properties, and functions. Lastly, our consideration is intentionally limited to the processes of thermally stimulated chemical reactions at the earliest stage of decomposition of molecules and materials containing defects.« less

Extended dynamic mode decomposition with dictionary learning: A data-driven adaptive spectral decomposition of the Koopman operator

NASA Astrophysics Data System (ADS)

Li, Qianxiao; Dietrich, Felix; Bollt, Erik M.; Kevrekidis, Ioannis G.

2017-10-01

Numerical approximation methods for the Koopman operator have advanced considerably in the last few years. In particular, data-driven approaches such as dynamic mode decomposition (DMD)51 and its generalization, the extended-DMD (EDMD), are becoming increasingly popular in practical applications. The EDMD improves upon the classical DMD by the inclusion of a flexible choice of dictionary of observables which spans a finite dimensional subspace on which the Koopman operator can be approximated. This enhances the accuracy of the solution reconstruction and broadens the applicability of the Koopman formalism. Although the convergence of the EDMD has been established, applying the method in practice requires a careful choice of the observables to improve convergence with just a finite number of terms. This is especially difficult for high dimensional and highly nonlinear systems. In this paper, we employ ideas from machine learning to improve upon the EDMD method. We develop an iterative approximation algorithm which couples the EDMD with a trainable dictionary represented by an artificial neural network. Using the Duffing oscillator and the Kuramoto Sivashinsky partical differential equation as examples, we show that our algorithm can effectively and efficiently adapt the trainable dictionary to the problem at hand to achieve good reconstruction accuracy without the need to choose a fixed dictionary a priori. Furthermore, to obtain a given accuracy, we require fewer dictionary terms than EDMD with fixed dictionaries. This alleviates an important shortcoming of the EDMD algorithm and enhances the applicability of the Koopman framework to practical problems.

Extended dynamic mode decomposition with dictionary learning: A data-driven adaptive spectral decomposition of the Koopman operator.

PubMed

Li, Qianxiao; Dietrich, Felix; Bollt, Erik M; Kevrekidis, Ioannis G

2017-10-01

Numerical approximation methods for the Koopman operator have advanced considerably in the last few years. In particular, data-driven approaches such as dynamic mode decomposition (DMD) 51 and its generalization, the extended-DMD (EDMD), are becoming increasingly popular in practical applications. The EDMD improves upon the classical DMD by the inclusion of a flexible choice of dictionary of observables which spans a finite dimensional subspace on which the Koopman operator can be approximated. This enhances the accuracy of the solution reconstruction and broadens the applicability of the Koopman formalism. Although the convergence of the EDMD has been established, applying the method in practice requires a careful choice of the observables to improve convergence with just a finite number of terms. This is especially difficult for high dimensional and highly nonlinear systems. In this paper, we employ ideas from machine learning to improve upon the EDMD method. We develop an iterative approximation algorithm which couples the EDMD with a trainable dictionary represented by an artificial neural network. Using the Duffing oscillator and the Kuramoto Sivashinsky partical differential equation as examples, we show that our algorithm can effectively and efficiently adapt the trainable dictionary to the problem at hand to achieve good reconstruction accuracy without the need to choose a fixed dictionary a priori. Furthermore, to obtain a given accuracy, we require fewer dictionary terms than EDMD with fixed dictionaries. This alleviates an important shortcoming of the EDMD algorithm and enhances the applicability of the Koopman framework to practical problems.

Independent Molecular Basis of Convergent Highland Adaptation in Maize

PubMed Central

Takuno, Shohei; Ralph, Peter; Swarts, Kelly; Elshire, Rob J.; Glaubitz, Jeffrey C.; Buckler, Edward S.; Hufford, Matthew B.; Ross-Ibarra, Jeffrey

2015-01-01

Convergent evolution is the independent evolution of similar traits in different species or lineages of the same species; this often is a result of adaptation to similar environments, a process referred to as convergent adaptation. We investigate here the molecular basis of convergent adaptation in maize to highland climates in Mesoamerica and South America, using genome-wide SNP data. Taking advantage of archaeological data on the arrival of maize to the highlands, we infer demographic models for both populations, identifying evidence of a strong bottleneck and rapid expansion in South America. We use these models to then identify loci showing an excess of differentiation as a means of identifying putative targets of natural selection and compare our results to expectations from recently developed theory on convergent adaptation. Consistent with predictions across a wide parameter space, we see limited evidence for convergent evolution at the nucleotide level in spite of strong similarities in overall phenotypes. Instead, we show that selection appears to have predominantly acted on standing genetic variation and that introgression from wild teosinte populations appears to have played a role in highland adaptation in Mexican maize. PMID:26078279

Temperature sensitivity and enzymatic mechanisms of soil organic matter decomposition along an altitudinal gradient on Mount Kilimanjaro

NASA Astrophysics Data System (ADS)

Blagodatskaya, Evgenia; Blagodatsky, Sergey; Khomyakov, Nikita; Myachina, Olga; Kuzyakov, Yakov

2016-02-01

Short-term acceleration of soil organic matter decomposition by increasing temperature conflicts with the thermal adaptation observed in long-term studies. Here we used the altitudinal gradient on Mt. Kilimanjaro to demonstrate the mechanisms of thermal adaptation of extra- and intracellular enzymes that hydrolyze cellulose, chitin and phytate and oxidize monomers (14C-glucose) in warm- and cold-climate soils. We revealed that no response of decomposition rate to temperature occurs because of a cancelling effect consisting in an increase in half-saturation constants (Km), which counteracts the increase in maximal reaction rates (Vmax with temperature). We used the parameters of enzyme kinetics to predict thresholds of substrate concentration (Scrit) below which decomposition rates will be insensitive to global warming. Increasing values of Scrit, and hence stronger canceling effects with increasing altitude on Mt. Kilimanjaro, explained the thermal adaptation of polymer decomposition. The reduction of the temperature sensitivity of Vmax along the altitudinal gradient contributed to thermal adaptation of both polymer and monomer degradation. Extrapolating the altitudinal gradient to the large-scale latitudinal gradient, these results show that the soils of cold climates with stronger and more frequent temperature variation are less sensitive to global warming than soils adapted to high temperatures.

The control of the controller: molecular mechanisms for robust perfect adaptation and temperature compensation.

PubMed

Ni, Xiao Yu; Drengstig, Tormod; Ruoff, Peter

2009-09-02

Organisms have the property to adapt to a changing environment and keep certain components within a cell regulated at the same level (homeostasis). "Perfect adaptation" describes an organism's response to an external stepwise perturbation by regulating some of its variables/components precisely to their original preperturbation values. Numerous examples of perfect adaptation/homeostasis have been found, as for example, in bacterial chemotaxis, photoreceptor responses, MAP kinase activities, or in metal-ion homeostasis. Two concepts have evolved to explain how perfect adaptation may be understood: In one approach (robust perfect adaptation), the adaptation is a network property, which is mostly, but not entirely, independent of rate constant values; in the other approach (nonrobust perfect adaptation), a fine-tuning of rate constant values is needed. Here we identify two classes of robust molecular homeostatic mechanisms, which compensate for environmental variations in a controlled variable's inflow or outflow fluxes, and allow for the presence of robust temperature compensation. These two classes of homeostatic mechanisms arise due to the fact that concentrations must have positive values. We show that the concept of integral control (or integral feedback), which leads to robust homeostasis, is associated with a control species that has to work under zero-order flux conditions and does not necessarily require the presence of a physico-chemical feedback structure. There are interesting links between the two identified classes of homeostatic mechanisms and molecular mechanisms found in mammalian iron and calcium homeostasis, indicating that homeostatic mechanisms may underlie similar molecular control structures.

Aging-driven decomposition in zolpidem hemitartrate hemihydrate and the single-crystal structure of its decomposition products.

PubMed

Vega, Daniel R; Baggio, Ricardo; Roca, Mariana; Tombari, Dora

2011-04-01

The "aging-driven" decomposition of zolpidem hemitartrate hemihydrate (form A) has been followed by X-ray powder diffraction (XRPD), and the crystal and molecular structures of the decomposition products studied by single-crystal methods. The process is very similar to the "thermally driven" one, recently described in the literature for form E (Halasz and Dinnebier. 2010. J Pharm Sci 99(2): 871-874), resulting in a two-phase system: the neutral free base (common to both decomposition processes) and, in the present case, a novel zolpidem tartrate monohydrate, unique to the "aging-driven" decomposition. Our room-temperature single-crystal analysis gives for the free base comparable results as the high-temperature XRPD ones already reported by Halasz and Dinnebier: orthorhombic, Pcba, a = 9.6360(10) Å, b = 18.2690(5) Å, c = 18.4980(11) Å, and V = 3256.4(4) Å(3) . The unreported zolpidem tartrate monohydrate instead crystallizes in monoclinic P21 , which, for comparison purposes, we treated in the nonstandard setting P1121 with a = 20.7582(9) Å, b = 15.2331(5) Å, c = 7.2420(2) Å, γ = 90.826(2)°, and V = 2289.73(14) Å(3) . The structure presents two complete moieties in the asymmetric unit (z = 4, z' = 2). The different phases obtained in both decompositions are readily explained, considering the diverse genesis of both processes. Copyright © 2010 Wiley-Liss, Inc.

Analysis of the Sensitivity of K-Type Molecular Sieve-Deposited MWNTs for the Detection of SF6 Decomposition Gases under Partial Discharge

PubMed Central

Zhang, Xiaoxing; Li, Xin; Luo, Chenchen; Dong, Xingchen; Zhou, Lei

2015-01-01

Sulfur hexafluoride (SF6) is widely utilized in gas-insulated switchgear (GIS). However, part of SF6 decomposes into different components under partial discharge (PD) conditions. Previous research has shown that the gas responses of intrinsic and 4 Å-type molecular sieve-deposited multi-wall carbon nanotubes (MWNTs) to SOF2 and SO2F2, two important decomposition components of SF6, are not obvious. In this study, a K-type molecular sieve-deposited MWNTs sensor was developed. Its gas response characteristics and the influence of the mixture ratios of gases on the gas-sensing properties were studied. The results showed that, for sensors with gas mixture ratios of 5:1, 10:1, and 20:1, the resistance change rate increased by nearly 13.0% after SOF2 adsorption, almost 10 times that of MWNTs sensors, while the sensors’ resistance change rate with a mixture ratio of 10:1 reached 17.3% after SO2F2 adsorption, nearly nine times that of intrinsic MWNT sensors. Besides, a good linear relationship was observed between concentration of decomposition components and the resistance change rate of sensors. PMID:26569245

Thermodynamics of adaptive molecular resolution.

PubMed

Delgado-Buscalioni, R

2016-11-13

A relatively general thermodynamic formalism for adaptive molecular resolution (AMR) is presented. The description is based on the approximation of local thermodynamic equilibrium and considers the alchemic parameter λ as the conjugate variable of the potential energy difference between the atomistic and coarse-grained model Φ=U (1) -U (0) The thermodynamic formalism recovers the relations obtained from statistical mechanics of H-AdResS (Español et al, J. Chem. Phys. 142, 064115, 2015 (doi:10.1063/1.4907006)) and provides relations between the free energy compensation and thermodynamic potentials. Inspired by this thermodynamic analogy, several generalizations of AMR are proposed, such as the exploration of new Maxwell relations and how to treat λ and Φ as 'real' thermodynamic variablesThis article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'. © 2016 The Author(s).

Thermodynamics of adaptive molecular resolution

NASA Astrophysics Data System (ADS)

Delgado-Buscalioni, R.

2016-11-01

A relatively general thermodynamic formalism for adaptive molecular resolution (AMR) is presented. The description is based on the approximation of local thermodynamic equilibrium and considers the alchemic parameter λ as the conjugate variable of the potential energy difference between the atomistic and coarse-grained model Φ=U(1)-U(0). The thermodynamic formalism recovers the relations obtained from statistical mechanics of H-AdResS (Español et al., J. Chem. Phys. 142, 064115, 2015 (doi:10.1063/1.4907006)) and provides relations between the free energy compensation and thermodynamic potentials. Inspired by this thermodynamic analogy, several generalizations of AMR are proposed, such as the exploration of new Maxwell relations and how to treat λ and Φ as `real' thermodynamic variables. This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

Estimation of pulse rate from ambulatory PPG using ensemble empirical mode decomposition and adaptive thresholding.

PubMed

Pittara, Melpo; Theocharides, Theocharis; Orphanidou, Christina

2017-07-01

A new method for deriving pulse rate from PPG obtained from ambulatory patients is presented. The method employs Ensemble Empirical Mode Decomposition to identify the pulsatile component from noise-corrupted PPG, and then uses a set of physiologically-relevant rules followed by adaptive thresholding, in order to estimate the pulse rate in the presence of noise. The method was optimized and validated using 63 hours of data obtained from ambulatory hospital patients. The F1 score obtained with respect to expertly annotated data was 0.857 and the mean absolute errors of estimated pulse rates with respect to heart rates obtained from ECG collected in parallel were 1.72 bpm for "good" quality PPG and 4.49 bpm for "bad" quality PPG. Both errors are within the clinically acceptable margin-of-error for pulse rate/heart rate measurements, showing the promise of the proposed approach for inclusion in next generation wearable sensors.

1,3,5-trinitro-1,3,5-triazine decomposition and chemisorption on Al(111) surface: first-principles molecular dynamics study.

PubMed

Umezawa, Naoto; Kalia, Rajiv K; Nakano, Aiichiro; Vashista, Priya; Shimojo, Fuyuki

2007-06-21

We have investigated the decomposition and chemisorption of a 1,3,5-trinitro-1,3,5-triazine (RDX) molecule on Al(111) surface using molecular dynamics simulations, in which interatomic forces are computed quantum mechanically in the framework of the density functional theory (DFT). The real-space DFT calculations are based on higher-order finite difference and norm-conserving pseudopotential methods. Strong attractive forces between oxygen and aluminum atoms break N-O and N-N bonds in the RDX and, subsequently, the dissociated oxygen atoms and NO molecules oxidize the Al surface. In addition to these Al surface-assisted decompositions, ring cleavage of the RDX molecule is also observed. These reactions occur spontaneously without potential barriers and result in the attachment of the rest of the RDX molecule to the surface. This opens up the possibility of coating Al nanoparticles with RDX molecules to avoid the detrimental effect of oxidation in high energy density material applications.

Hugoniot curve calculation of nitromethane decomposition mixtures: A reactive force field molecular dynamics approach

NASA Astrophysics Data System (ADS)

Guo, Feng; Zhang, Hong; Hu, Hai-Quan; Cheng, Xin-Lu; Zhang, Li-Yan

2015-11-01

We investigate the Hugoniot curve, shock-particle velocity relations, and Chapman-Jouguet conditions of the hot dense system through molecular dynamics (MD) simulations. The detailed pathways from crystal nitromethane to reacted state by shock compression are simulated. The phase transition of N2 and CO mixture is found at about 10 GPa, and the main reason is that the dissociation of the C-O bond and the formation of C-C bond start at 10.0-11.0 GPa. The unreacted state simulations of nitromethane are consistent with shock Hugoniot data. The complete pathway from unreacted to reacted state is discussed. Through chemical species analysis, we find that the C-N bond breaking is the main event of the shock-induced nitromethane decomposition. Project supported by the National Natural Science Foundation of China (Grant No. 11374217) and the Shandong Provincial Natural Science Foundation, China (Grant No. ZR2014BQ008).

Molecular mechanisms of decomposition of hydrated Na+Cl- ion pairs under planar nanopore conditions

NASA Astrophysics Data System (ADS)

Shevkunov, S. V.

2017-02-01

The decomposition of Na+Cl- ion pairs under the conditions of a nanoscopic planar pore with structureless walls in a material contact with water vapor at 298 K is simulated by Monte Carlo method. The transition from the state of a contact ion pair (CIP) to the state of solvent-separated ion pair (SSIP) is shown to occur as a result of an increase in the vapor pressure over a pore after exceeding the threshold number of molecules in a hydrate shell. It is found that the planar form of a molecular cluster under the conditions of a narrow pore does not level an abrupt structural transition and the formation of hydrogen bonds in the hydrate shell starts after three molecules are added. The hydrogen bond length under pore conditions is found to be resistant to variations in the hydrate shell size and coincides with that in water under normal conditions.

Near-Ideal Xylene Selectivity in Adaptive Molecular Pillar[ n]arene Crystals.

PubMed

Jie, Kecheng; Liu, Ming; Zhou, Yujuan; Little, Marc A; Pulido, Angeles; Chong, Samantha Y; Stephenson, Andrew; Hughes, Ashlea R; Sakakibara, Fumiyasu; Ogoshi, Tomoki; Blanc, Frédéric; Day, Graeme M; Huang, Feihe; Cooper, Andrew I

2018-06-06

The energy-efficient separation of alkylaromatic compounds is a major industrial sustainability challenge. The use of selectively porous extended frameworks, such as zeolites or metal-organic frameworks, is one solution to this problem. Here, we studied a flexible molecular material, perethylated pillar[ n]arene crystals ( n = 5, 6), which can be used to separate C8 alkylaromatic compounds. Pillar[6]arene is shown to separate para-xylene from its structural isomers, meta-xylene and ortho-xylene, with 90% specificity in the solid state. Selectivity is an intrinsic property of the pillar[6]arene host, with the flexible pillar[6]arene cavities adapting during adsorption thus enabling preferential adsorption of para-xylene in the solid state. The flexibility of pillar[6]arene as a solid sorbent is rationalized using molecular conformer searches and crystal structure prediction (CSP) combined with comprehensive characterization by X-ray diffraction and 13 C solid-state NMR spectroscopy. The CSP study, which takes into account the structural variability of pillar[6]arene, breaks new ground in its own right and showcases the feasibility of applying CSP methods to understand and ultimately to predict the behavior of soft, adaptive molecular crystals.

Comparing Anisotropic Output-Based Grid Adaptation Methods by Decomposition

NASA Technical Reports Server (NTRS)

Park, Michael A.; Loseille, Adrien; Krakos, Joshua A.; Michal, Todd

2015-01-01

Anisotropic grid adaptation is examined by decomposing the steps of flow solution, ad- joint solution, error estimation, metric construction, and simplex grid adaptation. Multiple implementations of each of these steps are evaluated by comparison to each other and expected analytic results when available. For example, grids are adapted to analytic metric fields and grid measures are computed to illustrate the properties of multiple independent implementations of grid adaptation mechanics. Different implementations of each step in the adaptation process can be evaluated in a system where the other components of the adaptive cycle are fixed. Detailed examination of these properties allows comparison of different methods to identify the current state of the art and where further development should be targeted.

Roots Stimulate Expression of Decomposition Transcripts in the Soil Microbiome

NASA Astrophysics Data System (ADS)

Nuccio, E. E.; Karaoz, U.; Zhou, J.; Brodie, E.; Firestone, M.; Pett-Ridge, J.

2016-12-01

The soil surrounding plant roots, the rhizosphere, has long been recognized as a zone of great functional importance in terrestrial ecosystems. Rhizosphere microorganisms can affect the breakdown of plant tissues and root litter, and can accelerate the decomposition of detrital plant biomass, which is a process commonly described as "priming." However, the molecular mechanisms underlying rhizosphere C cycling are poorly understood, and the carbohydrate and lignolytic gene transcripts mediating the decomposition of root litter in soil are largely unidentified. We hypothesized that root exudates stimulate the expression of enzymes that are involved in decomposition of macromolecular C compounds. To assess how the abundance and diversity of decomposition enzymes differs in the rhizosphere relative to the surrounding bulk soil, we sequenced the community gene expression (metatranscriptomes) and single cell genomes of rhizosphere and bulk soil associated with wild oat (Avena fatua) over time (3, 6, 12, and 22 days). To isolate roots of a defined age in a mature plant, we used microcosms with a transparent experimental sidecar to track roots as they grew. Our results showed that a large number of C decomposition enzymes were more highly expressed in the rhizosphere compared to bulk soil, and that overall, transcripts tended to be elevated in younger roots than older roots. Genes relevant to aromatic C breakdown (nitroreductase, 4-hydroxybenzoate degradation, pectin methylesterase) and organic N cycling (ammonification) were elevated in the rhizosphere. This work identifies the potential molecular mechanisms that underpin priming in rhizosphere soil.

Molecular ecology and adaptation of visual photopigments in craniates.

PubMed

Davies, Wayne I L; Collin, Shaun P; Hunt, David M

2012-07-01

In craniates, opsin-based photopigments expressed in the eye encode molecular 'light sensors' that constitute the initial protein in photoreception and the activation of the phototransduction cascade. Since the cloning and sequencing of the first vertebrate opsin gene (bovine rod opsin) nearly 30 years ago (Ovchinnikov Yu 1982, FEBS Letters, 148, 179-191; Hargrave et al. 1983, Biophysics of Structure & Mechanism, 9, 235-244; Nathans & Hogness 1983, Cell, 34, 807-814), it is now well established that variation in the subtypes and spectral properties of the visual pigments that mediate colour and dim-light vision is a prevalent mechanism for the molecular adaptation to diverse light environments. In this review, we discuss the origins and spectral tuning of photopigments that first arose in the agnathans to sample light within the ancient aquatic landscape of the Early Cambrian, detailing the molecular changes that subsequently occurred in each of the opsin classes independently within the main branches of extant jawed gnathostomes. Specifically, we discuss the adaptive changes that have occurred in the photoreceptors of craniates as they met the ecological challenges to survive in quite differing photic niches, including brightly lit aquatic surroundings; the deep sea; the transition to and from land; diurnal, crepuscular and nocturnal environments; and light-restricted fossorial settings. The review ends with a discussion of the limitations inherent to the 'nocturnal-bottleneck' hypothesis relevant to the evolution of the mammalian visual system and a proposition that transition through a 'mesopic-bottleneck' may be a more appropriate model. © 2012 Blackwell Publishing Ltd.

A DAFT DL_POLY distributed memory adaptation of the Smoothed Particle Mesh Ewald method

NASA Astrophysics Data System (ADS)

Bush, I. J.; Todorov, I. T.; Smith, W.

2006-09-01

The Smoothed Particle Mesh Ewald method [U. Essmann, L. Perera, M.L. Berkowtz, T. Darden, H. Lee, L.G. Pedersen, J. Chem. Phys. 103 (1995) 8577] for calculating long ranged forces in molecular simulation has been adapted for the parallel molecular dynamics code DL_POLY_3 [I.T. Todorov, W. Smith, Philos. Trans. Roy. Soc. London 362 (2004) 1835], making use of a novel 3D Fast Fourier Transform (DAFT) [I.J. Bush, The Daresbury Advanced Fourier transform, Daresbury Laboratory, 1999] that perfectly matches the Domain Decomposition (DD) parallelisation strategy [W. Smith, Comput. Phys. Comm. 62 (1991) 229; M.R.S. Pinches, D. Tildesley, W. Smith, Mol. Sim. 6 (1991) 51; D. Rapaport, Comput. Phys. Comm. 62 (1991) 217] of the DL_POLY_3 code. In this article we describe software adaptations undertaken to import this functionality and provide a review of its performance.

Adaptive sampling strategies with high-throughput molecular dynamics

NASA Astrophysics Data System (ADS)

Clementi, Cecilia

Despite recent significant hardware and software developments, the complete thermodynamic and kinetic characterization of large macromolecular complexes by molecular simulations still presents significant challenges. The high dimensionality of these systems and the complexity of the associated potential energy surfaces (creating multiple metastable regions connected by high free energy barriers) does not usually allow to adequately sample the relevant regions of their configurational space by means of a single, long Molecular Dynamics (MD) trajectory. Several different approaches have been proposed to tackle this sampling problem. We focus on the development of ensemble simulation strategies, where data from a large number of weakly coupled simulations are integrated to explore the configurational landscape of a complex system more efficiently. Ensemble methods are of increasing interest as the hardware roadmap is now mostly based on increasing core counts, rather than clock speeds. The main challenge in the development of an ensemble approach for efficient sampling is in the design of strategies to adaptively distribute the trajectories over the relevant regions of the systems' configurational space, without using any a priori information on the system global properties. We will discuss the definition of smart adaptive sampling approaches that can redirect computational resources towards unexplored yet relevant regions. Our approaches are based on new developments in dimensionality reduction for high dimensional dynamical systems, and optimal redistribution of resources. NSF CHE-1152344, NSF CHE-1265929, Welch Foundation C-1570.

Surface-Accelerated Decomposition of δ-HMX.

PubMed

Sharia, Onise; Tsyshevsky, Roman; Kuklja, Maija M

2013-03-07

Despite extensive efforts to study the explosive decomposition of HMX, a cyclic nitramine widely used as a solid fuel, explosive, and propellant, an understanding of the physicochemical processes, governing the sensitivity of condensed HMX to detonation initiation is not yet achieved. Experimental and theoretical explorations of the initiation of chemistry are equally challenging because of many complex parallel processes, including the β-δ phase transition and the decomposition from both phases. Among four known polymorphs, HMX is produced in the most stable β-phase, which transforms into the most reactive δ-phase under heat or pressure. In this study, the homolytic NO2 loss and HONO elimination precursor reactions of the gas-phase, ideal crystal, and the (100) surface of δ-HMX are explored by first principles modeling. Our calculations revealed that the high sensitivity of δ-HMX is attributed to interactions of surfaces and molecular dipole moments. While both decomposition reactions coexist, the exothermic HONO-isomer formation catalyzes the N-NO2 homolysis, leading to fast violent explosions.

Decomposition of energetic molecules by interfacing with a catalytic oxide: opportunities and challenges

NASA Astrophysics Data System (ADS)

Wang, Fenggong; Tsyshevsky, Roman; Zverev, Anton; Mitrofanov, Anatoly; Kuklja, Maija

Organic-inorganic interfaces provide both intrigues and opportunities for designing systems that possess properties and functionalities inaccessible by each individual component. In particular, mixing with a photocatalyst may significantly affect the adsorption, decomposition, and photoresponse of organic molecules. Here, we choose the formulation of TiO2 and trinitrotoluene (TNT), a highly catalytic oxide and a prominent explosive, as a prototypical example to explore the interaction at the interface on the photosensitivity of energetic materials. We show that, whether or not a catalytic oxide additive can help molecular decompositions under light illumination depends largely on the band alignment between the oxide surface and the energetic molecule. Furthermore, an oxygen vacancy can lead to the electron density transfer from the surface to the energetic molecules, causing an enhancement of the bonding between molecules and surface and a reduction of the molecular decomposition activation barriers.

Molecular Bases of cyclodextrin Adapter Interactions with Engineered Protein Nanopores

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

Banerjee, A.; Mikhailova, E; Cheley, S

2010-01-01

Engineered protein pores have several potential applications in biotechnology: as sensor elements in stochastic detection and ultrarapid DNA sequencing, as nanoreactors to observe single-molecule chemistry, and in the construction of nano- and micro-devices. One important class of pores contains molecular adapters, which provide internal binding sites for small molecules. Mutants of the {alpha}-hemolysin ({alpha}HL) pore that bind the adapter {beta}-cyclodextrin ({beta}CD) {approx}10{sup 4} times more tightly than the wild type have been obtained. We now use single-channel electrical recording, protein engineering including unnatural amino acid mutagenesis, and high-resolution x-ray crystallography to provide definitive structural information on these engineered protein nanoporesmore » in unparalleled detail.« less

Anaerobic decomposition of humic substances by Clostridium from the deep subsurface

PubMed Central

Ueno, Akio; Shimizu, Satoru; Tamamura, Shuji; Okuyama, Hidetoshi; Naganuma, Takeshi; Kaneko, Katsuhiko

2016-01-01

Decomposition of humic substances (HSs) is a slow and cryptic but non-negligible component of carbon cycling in sediments. Aerobic decomposition of HSs by microorganisms in the surface environment has been well documented; however, the mechanism of anaerobic microbial decomposition of HSs is not completely understood. Moreover, no microorganisms capable of anaerobic decomposition of HSs have been isolated. Here, we report the anaerobic decomposition of humic acids (HAs) by the anaerobic bacterium Clostridium sp. HSAI-1 isolated from the deep terrestrial subsurface. The use of 14C-labelled polycatechol as an HA analogue demonstrated that the bacterium decomposed this substance up to 7.4% over 14 days. The decomposition of commercial and natural HAs by the bacterium yielded lower molecular mass fractions, as determined using high-performance size-exclusion chromatography. Fourier transform infrared spectroscopy revealed the removal of carboxyl groups and polysaccharide-related substances, as well as the generation of aliphatic components, amide and aromatic groups. Therefore, our results suggest that Clostridium sp. HSAI-1 anaerobically decomposes and transforms HSs. This study improves our understanding of the anaerobic decomposition of HSs in the hidden carbon cycling in the Earth’s subsurface. PMID:26743007

Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks.

PubMed

Shen, Lin; Yang, Weitao

2018-03-13

Direct molecular dynamics (MD) simulation with ab initio quantum mechanical and molecular mechanical (QM/MM) methods is very powerful for studying the mechanism of chemical reactions in a complex environment but also very time-consuming. The computational cost of QM/MM calculations during MD simulations can be reduced significantly using semiempirical QM/MM methods with lower accuracy. To achieve higher accuracy at the ab initio QM/MM level, a correction on the existing semiempirical QM/MM model is an attractive idea. Recently, we reported a neural network (NN) method as QM/MM-NN to predict the potential energy difference between semiempirical and ab initio QM/MM approaches. The high-level results can be obtained using neural network based on semiempirical QM/MM MD simulations, but the lack of direct MD samplings at the ab initio QM/MM level is still a deficiency that limits the applications of QM/MM-NN. In the present paper, we developed a dynamic scheme of QM/MM-NN for direct MD simulations on the NN-predicted potential energy surface to approximate ab initio QM/MM MD. Since some configurations excluded from the database for NN training were encountered during simulations, which may cause some difficulties on MD samplings, an adaptive procedure inspired by the selection scheme reported by Behler [ Behler Int. J. Quantum Chem. 2015 , 115 , 1032 ; Behler Angew. Chem., Int. Ed. 2017 , 56 , 12828 ] was employed with some adaptions to update NN and carry out MD iteratively. We further applied the adaptive QM/MM-NN MD method to the free energy calculation and transition path optimization on chemical reactions in water. The results at the ab initio QM/MM level can be well reproduced using this method after 2-4 iteration cycles. The saving in computational cost is about 2 orders of magnitude. It demonstrates that the QM/MM-NN with direct MD simulations has great potentials not only for the calculation of thermodynamic properties but also for the characterization of

Adaptively biased molecular dynamics for free energy calculations

NASA Astrophysics Data System (ADS)

Babin, Volodymyr; Roland, Christopher; Sagui, Celeste

2008-04-01

We present an adaptively biased molecular dynamics (ABMD) method for the computation of the free energy surface of a reaction coordinate using nonequilibrium dynamics. The ABMD method belongs to the general category of umbrella sampling methods with an evolving biasing potential and is inspired by the metadynamics method. The ABMD method has several useful features, including a small number of control parameters and an O(t ) numerical cost with molecular dynamics time t. The ABMD method naturally allows for extensions based on multiple walkers and replica exchange, where different replicas can have different temperatures and/or collective variables. This is beneficial not only in terms of the speed and accuracy of a calculation, but also in terms of the amount of useful information that may be obtained from a given simulation. The workings of the ABMD method are illustrated via a study of the folding of the Ace-GGPGGG-Nme peptide in a gaseous and solvated environment.

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes

PubMed Central

Castoe, Todd A.; de Koning, A. P. Jason; Hall, Kathryn T.; Card, Daren C.; Schield, Drew R.; Fujita, Matthew K.; Ruggiero, Robert P.; Degner, Jack F.; Daza, Juan M.; Gu, Wanjun; Reyes-Velasco, Jacobo; Shaney, Kyle J.; Castoe, Jill M.; Fox, Samuel E.; Poole, Alex W.; Polanco, Daniel; Dobry, Jason; Vandewege, Michael W.; Li, Qing; Schott, Ryan K.; Kapusta, Aurélie; Minx, Patrick; Feschotte, Cédric; Uetz, Peter; Ray, David A.; Hoffmann, Federico G.; Bogden, Robert; Smith, Eric N.; Chang, Belinda S. W.; Vonk, Freek J.; Casewell, Nicholas R.; Henkel, Christiaan V.; Richardson, Michael K.; Mackessy, Stephen P.; Bronikowski, Anne M.; Yandell, Mark; Warren, Wesley C.; Secor, Stephen M.; Pollock, David D.

2013-01-01

Snakes possess many extreme morphological and physiological adaptations. Identification of the molecular basis of these traits can provide novel understanding for vertebrate biology and medicine. Here, we study snake biology using the genome sequence of the Burmese python (Python molurus bivittatus), a model of extreme physiological and metabolic adaptation. We compare the python and king cobra genomes along with genomic samples from other snakes and perform transcriptome analysis to gain insights into the extreme phenotypes of the python. We discovered rapid and massive transcriptional responses in multiple organ systems that occur on feeding and coordinate major changes in organ size and function. Intriguingly, the homologs of these genes in humans are associated with metabolism, development, and pathology. We also found that many snake metabolic genes have undergone positive selection, which together with the rapid evolution of mitochondrial proteins, provides evidence for extensive adaptive redesign of snake metabolic pathways. Additional evidence for molecular adaptation and gene family expansions and contractions is associated with major physiological and phenotypic adaptations in snakes; genes involved are related to cell cycle, development, lungs, eyes, heart, intestine, and skeletal structure, including GRB2-associated binding protein 1, SSH, WNT16, and bone morphogenetic protein 7. Finally, changes in repetitive DNA content, guanine-cytosine isochore structure, and nucleotide substitution rates indicate major shifts in the structure and evolution of snake genomes compared with other amniotes. Phenotypic and physiological novelty in snakes seems to be driven by system-wide coordination of protein adaptation, gene expression, and changes in the structure of the genome. PMID:24297902

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes.

PubMed

Castoe, Todd A; de Koning, A P Jason; Hall, Kathryn T; Card, Daren C; Schield, Drew R; Fujita, Matthew K; Ruggiero, Robert P; Degner, Jack F; Daza, Juan M; Gu, Wanjun; Reyes-Velasco, Jacobo; Shaney, Kyle J; Castoe, Jill M; Fox, Samuel E; Poole, Alex W; Polanco, Daniel; Dobry, Jason; Vandewege, Michael W; Li, Qing; Schott, Ryan K; Kapusta, Aurélie; Minx, Patrick; Feschotte, Cédric; Uetz, Peter; Ray, David A; Hoffmann, Federico G; Bogden, Robert; Smith, Eric N; Chang, Belinda S W; Vonk, Freek J; Casewell, Nicholas R; Henkel, Christiaan V; Richardson, Michael K; Mackessy, Stephen P; Bronikowski, Anne M; Bronikowsi, Anne M; Yandell, Mark; Warren, Wesley C; Secor, Stephen M; Pollock, David D

2013-12-17

Snakes possess many extreme morphological and physiological adaptations. Identification of the molecular basis of these traits can provide novel understanding for vertebrate biology and medicine. Here, we study snake biology using the genome sequence of the Burmese python (Python molurus bivittatus), a model of extreme physiological and metabolic adaptation. We compare the python and king cobra genomes along with genomic samples from other snakes and perform transcriptome analysis to gain insights into the extreme phenotypes of the python. We discovered rapid and massive transcriptional responses in multiple organ systems that occur on feeding and coordinate major changes in organ size and function. Intriguingly, the homologs of these genes in humans are associated with metabolism, development, and pathology. We also found that many snake metabolic genes have undergone positive selection, which together with the rapid evolution of mitochondrial proteins, provides evidence for extensive adaptive redesign of snake metabolic pathways. Additional evidence for molecular adaptation and gene family expansions and contractions is associated with major physiological and phenotypic adaptations in snakes; genes involved are related to cell cycle, development, lungs, eyes, heart, intestine, and skeletal structure, including GRB2-associated binding protein 1, SSH, WNT16, and bone morphogenetic protein 7. Finally, changes in repetitive DNA content, guanine-cytosine isochore structure, and nucleotide substitution rates indicate major shifts in the structure and evolution of snake genomes compared with other amniotes. Phenotypic and physiological novelty in snakes seems to be driven by system-wide coordination of protein adaptation, gene expression, and changes in the structure of the genome.

Adaptive surrogate modeling by ANOVA and sparse polynomial dimensional decomposition for global sensitivity analysis in fluid simulation

NASA Astrophysics Data System (ADS)

Tang, Kunkun; Congedo, Pietro M.; Abgrall, Rémi

2016-06-01

The Polynomial Dimensional Decomposition (PDD) is employed in this work for the global sensitivity analysis and uncertainty quantification (UQ) of stochastic systems subject to a moderate to large number of input random variables. Due to the intimate connection between the PDD and the Analysis of Variance (ANOVA) approaches, PDD is able to provide a simpler and more direct evaluation of the Sobol' sensitivity indices, when compared to the Polynomial Chaos expansion (PC). Unfortunately, the number of PDD terms grows exponentially with respect to the size of the input random vector, which makes the computational cost of standard methods unaffordable for real engineering applications. In order to address the problem of the curse of dimensionality, this work proposes essentially variance-based adaptive strategies aiming to build a cheap meta-model (i.e. surrogate model) by employing the sparse PDD approach with its coefficients computed by regression. Three levels of adaptivity are carried out in this paper: 1) the truncated dimensionality for ANOVA component functions, 2) the active dimension technique especially for second- and higher-order parameter interactions, and 3) the stepwise regression approach designed to retain only the most influential polynomials in the PDD expansion. During this adaptive procedure featuring stepwise regressions, the surrogate model representation keeps containing few terms, so that the cost to resolve repeatedly the linear systems of the least-squares regression problem is negligible. The size of the finally obtained sparse PDD representation is much smaller than the one of the full expansion, since only significant terms are eventually retained. Consequently, a much smaller number of calls to the deterministic model is required to compute the final PDD coefficients.

Cellular and molecular aspects of plant adaptation to microgravity

NASA Astrophysics Data System (ADS)

Kordyum, Elizabeth; Kozeko, Liudmyla

2016-07-01

Elucidation of the range and mechanisms of the biological effects of microgravity is one of the urgent fundamental tasks of space and gravitational biology. The absence of forbidding on plant growth and development in orbital flight allows studying different aspects of plant adaptation to this factor that is directly connected with development of the technologies of bioregenerative life-support systems. Microgravity belongs to the environmental factors which cause adaptive reactions at the cellular and molecular levels in the range of physiological responses in the framework of genetically determined program of ontogenesis. It is known that cells of a multicellular organism not only take part in reactions of the organism but also carry out processes that maintain their integrity. In light of these principles, the problem of identification of biochemical, physiological and structural patterns that can have adaptive significance at the cellular and molecular levels in real and simulated microgravity is considered. It is pointed that plant cell responses in microgravity and under clinorotation vary according to growth phase, physiological state, and taxonomic position of the object. At the same time, the responses have, to some degree, a similar character reflecting the changes in the cell organelle functional load. The maintenance of the plasmalemma fluidity at the certain level, an activation of both the antioxidant system and expression of HSP genes, especially HSP70, under increasing reactive oxygen species, lipid peroxidation intensity and alteration in protein homeostasis, are a strategic paradigm of rapid (primary) cell adaptation to microgravity. In this sense, biological membranes, especially plasmalemma, and their properties and functions may be considered as the most sensitive indicators of the influence of gravity or altered gravity on a cell. The plasmalemma lipid bilayer is a border between the cell internal content and environment, so it is a mediator

Optimized molecular design of ADAPT-based HER2-imaging probes labelled with 111In and 68Ga.

PubMed

Lindbo, Sarah; Garousi, Javad; Mitran, Bogdan; Vorobyeva, Anzhelika; Oroujeni, Maryam; Orlova, Anna; Hober, Sophia; Tolmachev, Vladimir

2018-06-04

Radionuclide molecular imaging is a promising tool for visualization of cancer associated molecular abnormalities in vivo and stratification of patients for specific therapies. ADAPT is a new type of small engineered proteins based on the scaffold of an albumin binding domain of protein G. ADAPTs have been utilized to select and develop high affinity binders to different proteinaceous targets. ADAPT6 binds to human epidermal growth factor 2 (HER2) with low nanomolar affinity and can be used for its in vivo visualization. Molecular design of 111 In-labeled anti-HER2 ADAPT has been optimized in several earlier studies. In this study, we made a direct comparison of two of the most promising variants, having either a DEAVDANS or a (HE) 3 DANS sequence at the N-terminus, conjugated with a maleimido derivative of DOTA to a GSSC amino acids sequence at the C-terminus. The variants (designated DOTA-C 59 - DEAVDANS-ADAPT6-GSSC and DOTA-C 61 -(HE) 3 DANS-ADAPT6-GSSC) were stably labeled with 111 In for SPECT and 68 Ga for PET. Biodistribution of labeled ADAPT variants was evaluated in nude mice bearing human tumor xenografts with different levels of HER2 expression. Both variants enabled clear discrimination between tumors with high and low levels of HER2 expression. 111 In-labeled ADAPT6 derivatives provided higher tumor-to-organ ratios compared to 68 Ga-labeled counterparts. The best performing variant was DOTA-C 61 -(HE) 3 DANS-ADAPT6-GSSC, providing tumor-to-blood ratios of 208±36 and 109±17 at 3 h for 111 In and 68 Ga labels, respectively.

Microbial Signatures of Cadaver Gravesoil During Decomposition.

PubMed

Finley, Sheree J; Pechal, Jennifer L; Benbow, M Eric; Robertson, B K; Javan, Gulnaz T

2016-04-01

Genomic studies have estimated there are approximately 10(3)-10(6) bacterial species per gram of soil. The microbial species found in soil associated with decomposing human remains (gravesoil) have been investigated and recognized as potential molecular determinants for estimates of time since death. The nascent era of high-throughput amplicon sequencing of the conserved 16S ribosomal RNA (rRNA) gene region of gravesoil microbes is allowing research to expand beyond more subjective empirical methods used in forensic microbiology. The goal of the present study was to evaluate microbial communities and identify taxonomic signatures associated with the gravesoil human cadavers. Using 16S rRNA gene amplicon-based sequencing, soil microbial communities were surveyed from 18 cadavers placed on the surface or buried that were allowed to decompose over a range of decomposition time periods (3-303 days). Surface soil microbial communities showed a decreasing trend in taxon richness, diversity, and evenness over decomposition, while buried cadaver-soil microbial communities demonstrated increasing taxon richness, consistent diversity, and decreasing evenness. The results show that ubiquitous Proteobacteria was confirmed as the most abundant phylum in all gravesoil samples. Surface cadaver-soil communities demonstrated a decrease in Acidobacteria and an increase in Firmicutes relative abundance over decomposition, while buried soil communities were consistent in their community composition throughout decomposition. Better understanding of microbial community structure and its shifts over time may be important for advancing general knowledge of decomposition soil ecology and its potential use during forensic investigations.

Primary Molecular Disorders and Secondary Biological Adaptations in Bartter Syndrome

PubMed Central

Deschênes, Georges; Fila, Marc

2011-01-01

Bartter syndrome is a hereditary disorder that has been characterized by the association of hypokalemia, alkalosis, and the hypertrophy of the juxtaglomerular complex with secondary hyperaldosteronism and normal blood pressure. By contrast, the genetic causes of Bartter syndrome primarily affect molecular structures directly involved in the sodium reabsorption at the level of the Henle loop. The ensuing urinary sodium wasting and chronic sodium depletion are responsible for the contraction of the extracellular volume, the activation of the renin-aldosterone axis, the secretion of prostaglandins, and the biological adaptations of downstream tubular segments, meaning the distal convoluted tubule and the collecting duct. These secondary biological adaptations lead to hypokalemia and alkalosis, illustrating a close integration of the solutes regulation in the tubular structures. PMID:21941653

Daily water level forecasting using wavelet decomposition and artificial intelligence techniques

NASA Astrophysics Data System (ADS)

Seo, Youngmin; Kim, Sungwon; Kisi, Ozgur; Singh, Vijay P.

2015-01-01

Reliable water level forecasting for reservoir inflow is essential for reservoir operation. The objective of this paper is to develop and apply two hybrid models for daily water level forecasting and investigate their accuracy. These two hybrid models are wavelet-based artificial neural network (WANN) and wavelet-based adaptive neuro-fuzzy inference system (WANFIS). Wavelet decomposition is employed to decompose an input time series into approximation and detail components. The decomposed time series are used as inputs to artificial neural networks (ANN) and adaptive neuro-fuzzy inference system (ANFIS) for WANN and WANFIS models, respectively. Based on statistical performance indexes, the WANN and WANFIS models are found to produce better efficiency than the ANN and ANFIS models. WANFIS7-sym10 yields the best performance among all other models. It is found that wavelet decomposition improves the accuracy of ANN and ANFIS. This study evaluates the accuracy of the WANN and WANFIS models for different mother wavelets, including Daubechies, Symmlet and Coiflet wavelets. It is found that the model performance is dependent on input sets and mother wavelets, and the wavelet decomposition using mother wavelet, db10, can further improve the efficiency of ANN and ANFIS models. Results obtained from this study indicate that the conjunction of wavelet decomposition and artificial intelligence models can be a useful tool for accurate forecasting daily water level and can yield better efficiency than the conventional forecasting models.

Adaptive molecular evolution of the two-pore channel 1 gene TPC1 in the karst-adapted genus Primulina (Gesneriaceae)

PubMed Central

Tao, Junjie; Feng, Chao; Ai, Bin; Kang, Ming

2016-01-01

Background and Aims Limestone karst areas possess high floral diversity and endemism. The genus Primulina, which contributes to the unique calcicole flora, has high species richness and exhibit specific soil-based habitat associations that are mainly distributed on calcareous karst soils. The adaptive molecular evolutionary mechanism of the genus to karst calcium-rich environments is still not well understood. The Ca2+-permeable channel TPC1 was used in this study to test whether its gene is involved in the local adaptation of Primulina to karst high-calcium soil environments. Methods Specific amplification and sequencing primers were designed and used to amplify the full-length coding sequences of TPC1 from cDNA of 76 Primulina species. The sequence alignment without recombination and the corresponding reconstructed phylogeny tree were used in molecular evolutionary analyses at the nucleic acid level and amino acid level, respectively. Finally, the identified sites under positive selection were labelled on the predicted secondary structure of TPC1. Key Results Seventy-six full-length coding sequences of Primulina TPC1 were obtained. The length of the sequences varied between 2220 and 2286 bp and the insertion/deletion was located at the 5′ end of the sequences. No signal of substitution saturation was detected in the sequences, while significant recombination breakpoints were detected. The molecular evolutionary analyses showed that TPC1 was dominated by purifying selection and the selective pressures were not significantly different among species lineages. However, significant signals of positive selection were detected at both TPC1 codon level and amino acid level, and five sites under positive selective pressure were identified by at least three different methods. Conclusions The Ca2+-permeable channel TPC1 may be involved in the local adaptation of Primulina to karst Ca2+-rich environments. Different species lineages suffered similar selective pressure

Cerebrospinal fluid PCR analysis and biochemistry in bodies with severe decomposition.

PubMed

Palmiere, Cristian; Vanhaebost, Jessica; Ventura, Francesco; Bonsignore, Alessandro; Bonetti, Luca Reggiani

2015-02-01

The aim of this study was to assess whether Neisseria meningitidis, Listeria monocytogenes, Streptococcus pneumoniae and Haemophilus influenzae can be identified using the polymerase chain reaction technique in the cerebrospinal fluid of severely decomposed bodies with known, noninfectious causes of death or whether postmortem changes can lead to false positive results and thus erroneous diagnostic information. Biochemical investigations, postmortem bacteriology and real-time polymerase chain reaction analysis in cerebrospinal fluid were performed in a series of medico-legal autopsies that included noninfectious causes of death with decomposition, bacterial meningitis without decomposition, bacterial meningitis with decomposition, low respiratory tract infections with decomposition and abdominal infections with decomposition. In noninfectious causes of death with decomposition, postmortem investigations failed to reveal results consistent with generalized inflammation or bacterial infections at the time of death. Real-time polymerase chain reaction analysis in cerebrospinal fluid did not identify the studied bacteria in any of these cases. The results of this study highlight the usefulness of molecular approaches in bacteriology as well as the use of alternative biological samples in postmortem biochemistry in order to obtain suitable information even in corpses with severe decompositional changes. Copyright © 2014 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Molecular mechanism of metal-independent decomposition of lipid hydroperoxide 13-HPODE by halogenated quinoid carcinogens.

PubMed

Qin, Hao; Huang, Chun-Hua; Mao, Li; Xia, Hai-Ying; Kalyanaraman, Balaraman; Shao, Jie; Shan, Guo-Qiang; Zhu, Ben-Zhan

2013-10-01

Halogenated quinones are a class of carcinogenic intermediates and newly identified chlorination disinfection by-products in drinking water. 13-Hydroperoxy-9,11-octadecadienoic acid (13-HPODE) is the most extensively studied endogenous lipid hydroperoxide. Although it is well known that the decomposition of 13-HPODE can be catalyzed by transition metal ions, it is not clear whether halogenated quinones could enhance its decomposition independent of metal ions and, if so, what the unique characteristics and similarities are. Here we show that 2,5-dichloro-1,4-benzoquinone (DCBQ) could markedly enhance the decomposition of 13-HPODE and formation of reactive lipid alkyl radicals such as pentyl and 7-carboxyheptyl radicals, and the genotoxic 4-hydroxy-2-nonenal (HNE), through the complementary application of ESR spin trapping, HPLC-MS, and GC-MS methods. Interestingly, two chloroquinone-lipid alkoxyl conjugates were also detected and identified from the reaction between DCBQ and 13-HPODE. Analogous results were observed with other halogenated quinones. This represents the first report that halogenated quinoid carcinogens can enhance the decomposition of the endogenous lipid hydroperoxide 13-HPODE and formation of reactive lipid alkyl radicals and genotoxic HNE via a novel metal-independent nucleophilic substitution coupled with homolytic decomposition mechanism, which may partly explain their potential genotoxicity and carcinogenicity. Copyright © 2013 Elsevier Inc. All rights reserved.

A phylogenomic analysis of the role and timing of molecular adaptation in the aquatic transition of cetartiodactyl mammals.

PubMed

Tsagkogeorga, Georgia; McGowen, Michael R; Davies, Kalina T J; Jarman, Simon; Polanowski, Andrea; Bertelsen, Mads F; Rossiter, Stephen J

2015-09-01

Recent studies have reported multiple cases of molecular adaptation in cetaceans related to their aquatic abilities. However, none of these has included the hippopotamus, precluding an understanding of whether molecular adaptations in cetaceans occurred before or after they split from their semi-aquatic sister taxa. Here, we obtained new transcriptomes from the hippopotamus and humpback whale, and analysed these together with available data from eight other cetaceans. We identified more than 11 000 orthologous genes and compiled a genome-wide dataset of 6845 coding DNA sequences among 23 mammals, to our knowledge the largest phylogenomic dataset to date for cetaceans. We found positive selection in nine genes on the branch leading to the common ancestor of hippopotamus and whales, and 461 genes in cetaceans compared to 64 in hippopotamus. Functional annotation revealed adaptations in diverse processes, including lipid metabolism, hypoxia, muscle and brain function. By combining these findings with data on protein-protein interactions, we found evidence suggesting clustering among gene products relating to nervous and muscular systems in cetaceans. We found little support for shared ancestral adaptations in the two taxa; most molecular adaptations in extant cetaceans occurred after their split with hippopotamids.

A phylogenomic analysis of the role and timing of molecular adaptation in the aquatic transition of cetartiodactyl mammals

PubMed Central

Tsagkogeorga, Georgia; McGowen, Michael R.; Davies, Kalina T. J.; Jarman, Simon; Polanowski, Andrea; Bertelsen, Mads F.; Rossiter, Stephen J.

2015-01-01

Recent studies have reported multiple cases of molecular adaptation in cetaceans related to their aquatic abilities. However, none of these has included the hippopotamus, precluding an understanding of whether molecular adaptations in cetaceans occurred before or after they split from their semi-aquatic sister taxa. Here, we obtained new transcriptomes from the hippopotamus and humpback whale, and analysed these together with available data from eight other cetaceans. We identified more than 11 000 orthologous genes and compiled a genome-wide dataset of 6845 coding DNA sequences among 23 mammals, to our knowledge the largest phylogenomic dataset to date for cetaceans. We found positive selection in nine genes on the branch leading to the common ancestor of hippopotamus and whales, and 461 genes in cetaceans compared to 64 in hippopotamus. Functional annotation revealed adaptations in diverse processes, including lipid metabolism, hypoxia, muscle and brain function. By combining these findings with data on protein–protein interactions, we found evidence suggesting clustering among gene products relating to nervous and muscular systems in cetaceans. We found little support for shared ancestral adaptations in the two taxa; most molecular adaptations in extant cetaceans occurred after their split with hippopotamids. PMID:26473040

Ozone decomposition

PubMed Central

Batakliev, Todor; Georgiev, Vladimir; Anachkov, Metody; Rakovsky, Slavcho

2014-01-01

Catalytic ozone decomposition is of great significance because ozone is a toxic substance commonly found or generated in human environments (aircraft cabins, offices with photocopiers, laser printers, sterilizers). Considerable work has been done on ozone decomposition reported in the literature. This review provides a comprehensive summary of the literature, concentrating on analysis of the physico-chemical properties, synthesis and catalytic decomposition of ozone. This is supplemented by a review on kinetics and catalyst characterization which ties together the previously reported results. Noble metals and oxides of transition metals have been found to be the most active substances for ozone decomposition. The high price of precious metals stimulated the use of metal oxide catalysts and particularly the catalysts based on manganese oxide. It has been determined that the kinetics of ozone decomposition is of first order importance. A mechanism of the reaction of catalytic ozone decomposition is discussed, based on detailed spectroscopic investigations of the catalytic surface, showing the existence of peroxide and superoxide surface intermediates. PMID:26109880

In situ spectroscopic studies on vapor phase catalytic decomposition of dimethyl oxalate.

PubMed

Hegde, Shweta; Tharpa, Kalsang; Akuri, Satyanarayana Reddy; K, Rakesh; Kumar, Ajay; Deshpande, Raj; Nair, Sreejit A

2017-03-15

Dimethyl Oxalate (DMO) has recently gained prominence as a valuable intermediate for the production of compounds of commercial importance. The stability of DMO is poor and hence this can result in the decomposition of DMO under reaction conditions. The mechanism of DMO decomposition is however not reported and more so on catalytic surfaces. Insights into the mechanism of decomposition would help in designing catalysts for its effective molecular transformation. It is well known that DMO is sensitive to moisture, which can also be a factor contributing to its decomposition. The present work reports the results of decomposition of DMO on various catalytic materials. The materials studied consist of acidic (γ-Al 2 O 3 ), basic (MgO), weakly acidic (ZnAl 2 O 4 ) and neutral surfaces such as α-Al 2 O 3 and mesoporous precipitated SiO 2 . Infrared spectroscopy is used to identify the nature of adsorption of the molecule on the various surfaces. The spectroscopy study is done at a temperature of 200 °C, which is the onset of gas phase decomposition of DMO. The results indicate that the stability of DMO is lower than the corresponding acid, i.e. oxalic acid. It is also one of the products of decomposition. Spectroscopic data suggest that DMO decomposition is related to surface acidity and the extent of decomposition depends on the number of surface hydroxyl groups. Decomposition was also observed on α-Al 2 O 3 , which was attributed to the residual surface hydroxyl groups. DMO decomposition to oxalic acid was not observed on the basic surface (MgO).

Molecular and Metabolic Adaptations of Lactococcus lactis at Near-Zero Growth Rates

PubMed Central

Ercan, Onur; Wels, Michiel; Smid, Eddy J.

2014-01-01

This paper describes the molecular and metabolic adaptations of Lactococcus lactis during the transition from a growing to a near-zero growth state by using carbon-limited retentostat cultivation. Transcriptomic analyses revealed that metabolic patterns shifted between lactic- and mixed-acid fermentations during retentostat cultivation, which appeared to be controlled at the level of transcription of the corresponding pyruvate dissipation-encoding genes. During retentostat cultivation, cells continued to consume several amino acids but also produced specific amino acids, which may derive from the conversion of glycolytic intermediates. We identify a novel motif containing CTGTCAG in the upstream regions of several genes related to amino acid conversion, which we propose to be the target site for CodY in L. lactis KF147. Finally, under extremely low carbon availability, carbon catabolite repression was progressively relieved and alternative catabolic functions were found to be highly expressed, which was confirmed by enhanced initial acidification rates on various sugars in cells obtained from near-zero-growth cultures. The present integrated transcriptome and metabolite (amino acids and previously reported fermentation end products) study provides molecular understanding of the adaptation of L. lactis to conditions supporting low growth rates and expands our earlier analysis of the quantitative physiology of this bacterium at near-zero growth rates toward gene regulation patterns involved in zero-growth adaptation. PMID:25344239

Molecular adaptation in Rubisco: Discriminating between convergent evolution and positive selection using mechanistic and classical codon models.

PubMed

Parto, Sahar; Lartillot, Nicolas

2018-01-01

Rubisco (Ribulose-1, 5-biphosphate carboxylase/oxygenase) is the most important enzyme on earth, catalyzing the first step of photosynthetic CO2 fixation. So, without it, there would be no storing of the sun's energy in plants. Molecular adaptation of Rubisco to C4 photosynthetic pathway has attracted a lot of attention. C4 plants, which comprise less than 5% of land plants, have evolved more efficient photosynthesis compared to C3 plants. Interestingly, a large number of independent transitions from C3 to C4 phenotype have occurred. Each time, the Rubisco enzyme has been subject to similar changes in selective pressure, thus providing an excellent model for convergent evolution at the molecular level. Molecular adaptation is often identified with positive selection and is typically characterized by an elevated ratio of non-synonymous to synonymous substitution rate (dN/dS). However, convergent adaptation is expected to leave a different molecular signature, taking the form of repeated transitions toward identical or similar amino acids. Here, we used a previously introduced codon-based differential-selection model to detect and quantify consistent patterns of convergent adaptation in Rubisco in eudicots. We further contrasted our results with those obtained by classical codon models based on the estimation of dN/dS. We found that the two classes of models tend to select distinct, although overlapping, sets of positions. This discrepancy in the results illustrates the conceptual difference between these models while emphasizing the need to better discriminate between qualitatively different selective regimes, by using a broader class of codon models than those currently considered in molecular evolutionary studies.

Calibration methods influence quantitative material decomposition in photon-counting spectral CT

NASA Astrophysics Data System (ADS)

Curtis, Tyler E.; Roeder, Ryan K.

2017-03-01

Photon-counting detectors and nanoparticle contrast agents can potentially enable molecular imaging and material decomposition in computed tomography (CT). Material decomposition has been investigated using both simulated and acquired data sets. However, the effect of calibration methods on material decomposition has not been systematically investigated. Therefore, the objective of this study was to investigate the influence of the range and number of contrast agent concentrations within a modular calibration phantom on quantitative material decomposition. A commerciallyavailable photon-counting spectral micro-CT (MARS Bioimaging) was used to acquire images with five energy bins selected to normalize photon counts and leverage the contrast agent k-edge. Material basis matrix values were determined using multiple linear regression models and material decomposition was performed using a maximum a posteriori estimator. The accuracy of quantitative material decomposition was evaluated by the root mean squared error (RMSE), specificity, sensitivity, and area under the curve (AUC). An increased maximum concentration (range) in the calibration significantly improved RMSE, specificity and AUC. The effects of an increased number of concentrations in the calibration were not statistically significant for the conditions in this study. The overall results demonstrated that the accuracy of quantitative material decomposition in spectral CT is significantly influenced by calibration methods, which must therefore be carefully considered for the intended diagnostic imaging application.

Molecular Mechanisms That Underlie the Dynamic Adaptation of Innate Monocyte Memory to Varying Stimulant Strength of TLR Ligands.

PubMed

Yuan, Ruoxi; Geng, Shuo; Li, Liwu

2016-01-01

In adaptation to rising stimulant strength, innate monocytes can be dynamically programed to preferentially express either pro- or anti-inflammatory mediators. Such dynamic innate adaptation or programing may bear profound relevance in host health and disease. However, molecular mechanisms that govern innate adaptation to varying strength of stimulants are not well understood. Using lipopolysaccharide (LPS), the model stimulant of toll-like-receptor 4 (TLR4), we reported that the expressions of pro-inflammatory mediators are preferentially sustained in monocytes adapted by lower doses of LPS, and suppressed/tolerized in monocytes adapted by higher doses of LPS. Mechanistically, monocytes adapted by super-low dose LPS exhibited higher levels of transcription factor, interferon regulatory factor 5 (IRF5), and reduced levels of transcriptional modulator B lymphocyte-induced maturation protein-1 (Blimp-1). Intriguingly, the inflammatory monocyte adaptation by super-low dose LPS is dependent upon TRAM/TRIF but not MyD88. Similar to LPS, we also observed biphasic inflammatory adaptation and tolerance in monocytes challenged with varying dosages of TLR7 agonist. In sharp contrast, rising doses of TLR3 agonist preferentially caused inflammatory adaptation without inducing tolerance. At the molecular level, the differential regulation of IRF5 and Blimp-1 coincides with unique monocyte adaptation dynamics by TLR4/7 and TLR3 agonists. Our study provides novel clue toward the understanding of monocyte adaptation and memory toward distinct TLR ligands.

New molecular insights into the pools and mechanisms of Arctic soil organic matter decomposition under warming

NASA Astrophysics Data System (ADS)

Gu, B.

2017-12-01

It is estimated that Arctic permafrost soils store approximately half of the global belowground organic carbon, which is susceptible to microbial decomposition under warming climate. Studies have shown that rates of soil organic carbon (SOC) decomposition are controlled not only by temperature but also SOC substrate quality or chemical composition. However, detailed molecular-scale characterization of SOC and its susceptibility to degradation are lacking, due to extremely complex nature of SOC. Here, ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) was utilized to determine compositional changes of SOC during a microcosm warming experiment using tundra soils that were collected from the Barrow Environmental Observatory in Alaska, USA. Soil microcosm incubation was conducted with both organic and mineral active layer soils at two temperatures (-2°C and 8°C) up to 122 days, and water-extractable SOC was analyzed. Results indicate that peptides, amino sugars, and carbohydrate-like compounds are among the most labile SOC compounds to be degraded, with nitrogen-containing compounds degrading at a much faster rate than those containing no nitrogen. Refractory SOC components are dominated by the lignin- or tannin-like compounds and, to a less extent, the aliphatic compounds. Additionally, elemental ratios of O:C, H:C, and N:C were found to decrease with incubation time, and SOC in the mineral soil exhibited lower O:C and N:C ratios than those of the organic-rich soil. A biodegradation index is proposed to facilitate the incorporation of mass spectrometry data into mechanistic models of SOC degradation and thus improved prediction model of climate feedbacks in the Arctic.

New molecular insights into the pools and mechanisms of Arctic soil organic matter decomposition under warming

NASA Astrophysics Data System (ADS)

Gilbert, A.; Yamada, K.; Julien, M.; Yoshida, N.; Remaud, G.; Robins, R.

2016-12-01

It is estimated that Arctic permafrost soils store approximately half of the global belowground organic carbon, which is susceptible to microbial decomposition under warming climate. Studies have shown that rates of soil organic carbon (SOC) decomposition are controlled not only by temperature but also SOC substrate quality or chemical composition. However, detailed molecular-scale characterization of SOC and its susceptibility to degradation are lacking, due to extremely complex nature of SOC. Here, ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) was utilized to determine compositional changes of SOC during a microcosm warming experiment using tundra soils that were collected from the Barrow Environmental Observatory in Alaska, USA. Soil microcosm incubation was conducted with both organic and mineral active layer soils at two temperatures (-2°C and 8°C) up to 122 days, and water-extractable SOC was analyzed. Results indicate that peptides, amino sugars, and carbohydrate-like compounds are among the most labile SOC compounds to be degraded, with nitrogen-containing compounds degrading at a much faster rate than those containing no nitrogen. Refractory SOC components are dominated by the lignin- or tannin-like compounds and, to a less extent, the aliphatic compounds. Additionally, elemental ratios of O:C, H:C, and N:C were found to decrease with incubation time, and SOC in the mineral soil exhibited lower O:C and N:C ratios than those of the organic-rich soil. A biodegradation index is proposed to facilitate the incorporation of mass spectrometry data into mechanistic models of SOC degradation and thus improved prediction model of climate feedbacks in the Arctic.

Pi2 detection using Empirical Mode Decomposition (EMD)

NASA Astrophysics Data System (ADS)

Mieth, Johannes Z. D.; Frühauff, Dennis; Glassmeier, Karl-Heinz

2017-04-01

Empirical Mode Decomposition has been used as an alternative method to wavelet transformation to identify onset times of Pi2 pulsations in data sets of the Scandinavian Magnetometer Array (SMA). Pi2 pulsations are magnetohydrodynamic waves occurring during magnetospheric substorms. Almost always Pi2 are observed at substorm onset in mid to low latitudes on Earth's nightside. They are fed by magnetic energy release caused by dipolarization processes. Their periods lie between 40 to 150 seconds. Usually, Pi2 are detected using wavelet transformation. Here, Empirical Mode Decomposition (EMD) is presented as an alternative approach to the traditional procedure. EMD is a young signal decomposition method designed for nonlinear and non-stationary time series. It provides an adaptive, data driven, and complete decomposition of time series into slow and fast oscillations. An optimized version using Monte-Carlo-type noise assistance is used here. By displaying the results in a time-frequency space a characteristic frequency modulation is observed. This frequency modulation can be correlated with the onset of Pi2 pulsations. A basic algorithm to find the onset is presented. Finally, the results are compared to classical wavelet-based analysis. The use of different SMA stations furthermore allows the spatial analysis of Pi2 onset times. EMD mostly finds application in the fields of engineering and medicine. This work demonstrates the applicability of this method to geomagnetic time series.

Acid and alkali effects on the decomposition of HMX molecule: a computational study.

PubMed

Zhang, Chaoyang; Li, Yuzhen; Xiong, Ying; Wang, Xiaolin; Zhou, Mingfei

2011-11-03

The stored and wasted explosives are usually in an acid or alkali environment, leading to the importance of exploring the acid and alkali effects on the decomposition mechanism of explosives. The acid and alkali effects on the decomposition of HMX molecule in gaseous state and in aqueous solution at 298 K are studied using quantum chemistry and molecular force field calculations. The results show that both H(+) and OH(-) make the decomposition in gaseous state energetically favorable. However, the effect of H(+) is much different from that of OH(-) in aqueous solution: OH(-) can accelerate the decomposition but H(+) cannot. The difference is mainly caused by the large aqueous solvation energy difference between H(+) and OH(-). The results confirm that the dissociation of HMX is energetically favored only in the base solutions, in good agreement with previous HMX base hydrolysis experimental observations. The different acid and alkali effects on the HMX decomposition are dominated by the large aqueous solvation energy difference between H(+) and OH(-).

Fast polar decomposition of an arbitrary matrix

NASA Technical Reports Server (NTRS)

Higham, Nicholas J.; Schreiber, Robert S.

1988-01-01

The polar decomposition of an m x n matrix A of full rank, where m is greater than or equal to n, can be computed using a quadratically convergent algorithm. The algorithm is based on a Newton iteration involving a matrix inverse. With the use of a preliminary complete orthogonal decomposition the algorithm can be extended to arbitrary A. How to use the algorithm to compute the positive semi-definite square root of a Hermitian positive semi-definite matrix is described. A hybrid algorithm which adaptively switches from the matrix inversion based iteration to a matrix multiplication based iteration due to Kovarik, and to Bjorck and Bowie is formulated. The decision when to switch is made using a condition estimator. This matrix multiplication rich algorithm is shown to be more efficient on machines for which matrix multiplication can be executed 1.5 times faster than matrix inversion.

Thermal decomposition of solid phase nitromethane under various heating rates and target temperatures based on ab initio molecular dynamics simulations.

PubMed

Xu, Kai; Wei, Dong-Qing; Chen, Xiang-Rong; Ji, Guang-Fu

2014-10-01

The Car-Parrinello molecular dynamics simulation was applied to study the thermal decomposition of solid phase nitromethane under gradual heating and fast annealing conditions. In gradual heating simulations, we found that, rather than C-N bond cleavage, intermolecular proton transfer is more likely to be the first reaction in the decomposition process. At high temperature, the first reaction in fast annealing simulation is intermolecular proton transfer leading to CH3NOOH and CH2NO2, whereas the initial chemical event at low temperature tends to be a unimolecular C-N bond cleavage, producing CH3 and NO2 fragments. It is the first time to date that the direct rupture of a C-N bond has been reported as the first reaction in solid phase nitromethane. In addition, the fast annealing simulations on a supercell at different temperatures are conducted to validate the effect of simulation cell size on initial reaction mechanisms. The results are in qualitative agreement with the simulations on a unit cell. By analyzing the time evolution of some molecules, we also found that the time of first water molecule formation is clearly sensitive to heating rates and target temperatures when the first reaction is an intermolecular proton transfer.

Initial decomposition of the condensed-phase β-HMX under shock waves: molecular dynamics simulations.

PubMed

Ge, Ni-Na; Wei, Yong-Kai; Ji, Guang-Fu; Chen, Xiang-Rong; Zhao, Feng; Wei, Dong-Qing

2012-11-26

We have performed quantum-based multiscale simulations to study the initial chemical processes of condensed-phase octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) under shock wave loading. A self-consistent charge density-functional tight-binding (SCC-DFTB) method was employed. The results show that the initial decomposition of shocked HMX is triggered by the N-NO(2) bond breaking under the low velocity impact (8 km/s). As the shock velocity increases (11 km/s), the homolytic cleavage of the N-NO(2) bond is suppressed under high pressure, the C-H bond dissociation becomes the primary pathway for HMX decomposition in its early stages. It is accompanied by a five-membered ring formation and hydrogen transfer from the CH(2) group to the -NO(2) group. Our simulations suggest that the initial chemical processes of shocked HMX are dependent on the impact velocity, which gain new insights into the initial decomposition mechanism of HMX upon shock loading at the atomistic level, and have important implications for understanding and development of energetic materials.

Decomposition

USGS Publications Warehouse

Middleton, Beth A.

2014-01-01

A cornerstone of ecosystem ecology, decomposition was recognized as a fundamental process driving the exchange of energy in ecosystems by early ecologists such as Lindeman 1942 and Odum 1960). In the history of ecology, studies of decomposition were incorporated into the International Biological Program in the 1960s to compare the nature of organic matter breakdown in various ecosystem types. Such studies still have an important role in ecological studies of today. More recent refinements have brought debates on the relative role microbes, invertebrates and environment in the breakdown and release of carbon into the atmosphere, as well as how nutrient cycling, production and other ecosystem processes regulated by decomposition may shift with climate change. Therefore, this bibliography examines the primary literature related to organic matter breakdown, but it also explores topics in which decomposition plays a key supporting role including vegetation composition, latitudinal gradients, altered ecosystems, anthropogenic impacts, carbon storage, and climate change models. Knowledge of these topics is relevant to both the study of ecosystem ecology as well projections of future conditions for human societies.

Decomposition techniques

USGS Publications Warehouse

Chao, T.T.; Sanzolone, R.F.

1992-01-01

Sample decomposition is a fundamental and integral step in the procedure of geochemical analysis. It is often the limiting factor to sample throughput, especially with the recent application of the fast and modern multi-element measurement instrumentation. The complexity of geological materials makes it necessary to choose the sample decomposition technique that is compatible with the specific objective of the analysis. When selecting a decomposition technique, consideration should be given to the chemical and mineralogical characteristics of the sample, elements to be determined, precision and accuracy requirements, sample throughput, technical capability of personnel, and time constraints. This paper addresses these concerns and discusses the attributes and limitations of many techniques of sample decomposition along with examples of their application to geochemical analysis. The chemical properties of reagents as to their function as decomposition agents are also reviewed. The section on acid dissolution techniques addresses the various inorganic acids that are used individually or in combination in both open and closed systems. Fluxes used in sample fusion are discussed. The promising microwave-oven technology and the emerging field of automation are also examined. A section on applications highlights the use of decomposition techniques for the determination of Au, platinum group elements (PGEs), Hg, U, hydride-forming elements, rare earth elements (REEs), and multi-elements in geological materials. Partial dissolution techniques used for geochemical exploration which have been treated in detail elsewhere are not discussed here; nor are fire-assaying for noble metals and decomposition techniques for X-ray fluorescence or nuclear methods be discussed. ?? 1992.

Skeletal Muscle Remodeling in Response to Eccentric vs. Concentric Loading: Morphological, Molecular, and Metabolic Adaptations

PubMed Central

Franchi, Martino V.; Reeves, Neil D.; Narici, Marco V.

2017-01-01

Skeletal muscle contracts either by shortening or lengthening (concentrically or eccentrically, respectively); however, the two contractions substantially differ from one another in terms of mechanisms of force generation, maximum force production and energy cost. It is generally known that eccentric actions generate greater force than isometric and concentric contractions and at a lower metabolic cost. Hence, by virtue of the greater mechanical loading involved in active lengthening, eccentric resistance training (ECC RT) is assumed to produce greater hypertrophy than concentric resistance training (CON RT). Nonetheless, prevalence of either ECC RT or CON RT in inducing gains in muscle mass is still an open issue, with some studies reporting greater hypertrophy with eccentric, some with concentric and some with similar hypertrophy within both training modes. Recent observations suggest that such hypertrophic responses to lengthening vs. shortening contractions are achieved by different adaptations in muscle architecture. Whilst the changes in muscle protein synthesis in response to acute and chronic concentric and eccentric exercise bouts seem very similar, the molecular mechanisms regulating the myogenic adaptations to the two distinct loading stimuli are still incompletely understood. Thus, the present review aims to, (a) critically discuss the literature on the contribution of eccentric vs. concentric loading to muscular hypertrophy and structural remodeling, and, (b) clarify the molecular mechanisms that may regulate such adaptations. We conclude that, when matched for either maximum load or work, similar increase in muscle size is found between ECC and CON RT. However, such hypertrophic changes appear to be achieved through distinct structural adaptations, which may be regulated by different myogenic and molecular responses observed between lengthening and shortening contractions. PMID:28725197

Energy Decomposition Analysis Based on Absolutely Localized Molecular Orbitals for Large-Scale Density Functional Theory Calculations in Drug Design.

PubMed

Phipps, M J S; Fox, T; Tautermann, C S; Skylaris, C-K

2016-07-12

We report the development and implementation of an energy decomposition analysis (EDA) scheme in the ONETEP linear-scaling electronic structure package. Our approach is hybrid as it combines the localized molecular orbital EDA (Su, P.; Li, H. J. Chem. Phys., 2009, 131, 014102) and the absolutely localized molecular orbital EDA (Khaliullin, R. Z.; et al. J. Phys. Chem. A, 2007, 111, 8753-8765) to partition the intermolecular interaction energy into chemically distinct components (electrostatic, exchange, correlation, Pauli repulsion, polarization, and charge transfer). Limitations shared in EDA approaches such as the issue of basis set dependence in polarization and charge transfer are discussed, and a remedy to this problem is proposed that exploits the strictly localized property of the ONETEP orbitals. Our method is validated on a range of complexes with interactions relevant to drug design. We demonstrate the capabilities for large-scale calculations with our approach on complexes of thrombin with an inhibitor comprised of up to 4975 atoms. Given the capability of ONETEP for large-scale calculations, such as on entire proteins, we expect that our EDA scheme can be applied in a large range of biomolecular problems, especially in the context of drug design.

Vacancy-induced initial decomposition of condensed phase NTO via bimolecular hydrogen transfer mechanisms at high pressure: a DFT-D study.

PubMed

Liu, Zhichao; Wu, Qiong; Zhu, Weihua; Xiao, Heming

2015-04-28

Density functional theory with dispersion-correction (DFT-D) was employed to study the effects of vacancy and pressure on the structure and initial decomposition of crystalline 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (β-NTO), a high-energy insensitive explosive. A comparative analysis of the chemical behaviors of NTO in the ideal bulk crystal and vacancy-containing crystals under applied hydrostatic compression was considered. Our calculated formation energy, vacancy interaction energy, electron density difference, and frontier orbitals reveal that the stability of NTO can be effectively manipulated by changing the molecular environment. Bimolecular hydrogen transfer is suggested to be a potential initial chemical reaction in the vacancy-containing NTO solid at 50 GPa, which is prior to the C-NO2 bond dissociation as its initiation decomposition in the gas phase. The vacancy defects introduced into the ideal bulk NTO crystal can produce a localized site, where the initiation decomposition is preferentially accelerated and then promotes further decompositions. Our results may shed some light on the influence of the molecular environments on the initial pathways in molecular explosives.

Thermal decomposition pathways of ethane

NASA Astrophysics Data System (ADS)

Gordon, Mark S.; Truong, Thanh N.; Pople, John A.

1986-10-01

The alternate thermal decomposition pathways for ethane in its ground state have been investigated, using ab initio electronic structure calculations. Single-point energies were obtained at the full MP4/6-311 G ∗∗ level, using 6-31 G ∗ geometries for reactant, products, and transition states. The thermodynamically favored products are ethylene and molecular hydrogen, but a very large barrier (130 kcal/mol) is found for the direct 1,2-elimination of hydrogen. When calculated barriers are taken into account, the lowest-energy process is the homolytic cleavage of the C-C bond to form two methyl radicals.

Self-Attractive Hartree Decomposition: Partitioning Electron Density into Smooth Localized Fragments.

PubMed

Zhu, Tianyu; de Silva, Piotr; Van Voorhis, Troy

2018-01-09

Chemical bonding plays a central role in the description and understanding of chemistry. Many methods have been proposed to extract information about bonding from quantum chemical calculations, the majority of them resorting to molecular orbitals as basic descriptors. Here, we present a method called self-attractive Hartree (SAH) decomposition to unravel pairs of electrons directly from the electron density, which unlike molecular orbitals is a well-defined observable that can be accessed experimentally. The key idea is to partition the density into a sum of one-electron fragments that simultaneously maximize the self-repulsion and maintain regular shapes. This leads to a set of rather unusual equations in which every electron experiences self-attractive Hartree potential in addition to an external potential common for all the electrons. The resulting symmetry breaking and localization are surprisingly consistent with chemical intuition. SAH decomposition is also shown to be effective in visualization of single/multiple bonds, lone pairs, and unusual bonds due to the smooth nature of fragment densities. Furthermore, we demonstrate that it can be used to identify specific chemical bonds in molecular complexes and provides a simple and accurate electrostatic model of hydrogen bonding.

Soil Carbon Decomposition: "Quality control" or logistic challenge?

NASA Astrophysics Data System (ADS)

Kleber, M.

2011-12-01

A long tradition of soil organic matter research has generated the belief that there is "stable" soil organic carbon, thought to be recalcitrant because molecular compounds such as aromatic rings and aliphatic chains are joined to polymeric macromolecules by processes of secondary syntheses. The Carbon-Quality Temperature (CQT) theory posits that such materials should be considered "low quality" substrates, because they would require large Arrhenius activation energies for full conversion to CO2. This, in turn, has generated the notion that recalcitrant organic matter should be more temperature sensitive to elevated temperatures than less complex, more "labile" soil organic matter. Yet the molecular properties of stable carbon are elusive - so far, it has not been possible to parameterize molecular recalcitrance in a context -independent fashion. Classic humic substances and even charcoal are readily broken down when placed in an environment where microorganisms with a suitable catabolic toolbox can resort to a plentiful supply of cometabolites and oxygen. At the same time we find labile substrates such as glucose to survive for decades when enclosed within soil aggregates. What then determines the temperature sensitivity of decomposition? Should the scientific community continue to hunt for some molecular proxy for organic matter quality (such as degree of polymerization, aromaticity, aqueous solubility etc) to predict the fate of soil organic carbon in a changing world? This contribution proposes a fundamentally different approach by treating soils as reaction vessels analogous to an industrial bioreactor. Soils are considered as capable of processing dead plant material in all its molecular variations. Decomposition is seen as constrained by environmental drivers, microbial ecology and community composition, and the physical structure of the soil environment. The hypotheses is put forward that, compared to variations in the logistic status of the soil reactor

Metagenomic analysis of antibiotic resistance genes (ARGs) during refuse decomposition.

PubMed

Liu, Xi; Yang, Shu; Wang, Yangqing; Zhao, He-Ping; Song, Liyan

2018-04-12

Landfill is important reservoirs of residual antibiotics and antibiotic resistance genes (ARGs), but the mechanism of landfill application influence on antibiotic resistance remains unclear. Although refuse decomposition plays a crucial role in landfill stabilization, its impact on the antibiotic resistance has not been well characterized. To better understand the impact, we studied the dynamics of ARGs and the bacterial community composition during refuse decomposition in a bench-scale bioreactor after long term operation (265d) based on metagenomics analysis. The total abundances of ARGs increased from 431.0ppm in the initial aerobic phase (AP) to 643.9ppm in the later methanogenic phase (MP) during refuse decomposition, suggesting that application of landfill for municipal solid waste (MSW) treatment may elevate the level of ARGs. A shift from drug-specific (bacitracin, tetracycline and sulfonamide) resistance to multidrug resistance was observed during the refuse decomposition and was driven by a shift of potential bacteria hosts. The elevated abundance of Pseudomonas mainly contributed to the increasing abundance of multidrug ARGs (mexF and mexW). Accordingly, the percentage of ARGs encoding an efflux pump increased during refuse decomposition, suggesting that potential bacteria hosts developed this mechanism to adapt to the carbon and energy shortage when biodegradable substances were depleted. Overall, our findings indicate that the use of landfill for MSW treatment increased antibiotic resistance, and demonstrate the need for a comprehensive investigation of antibiotic resistance in landfill. Copyright © 2018. Published by Elsevier B.V.

Molecular adaptations of Herbaspirillum seropedicae during colonization of the maize rhizosphere.

PubMed

Balsanelli, Eduardo; Tadra-Sfeir, Michelle Z; Faoro, Helisson; Pankievicz, Vânia Cs; de Baura, Valter A; Pedrosa, Fábio O; de Souza, Emanuel M; Dixon, Ray; Monteiro, Rose A

2016-09-01

Molecular mechanisms of plant recognition and colonization by diazotrophic bacteria are barely understood. Herbaspirillum seropedicae is a Betaproteobacterium capable of colonizing epiphytically and endophytically commercial grasses, to promote plant growth. In this study, we utilized RNA-seq to compare the transcriptional profiles of planktonic and maize root-attached H. seropedicae SmR1 recovered 1 and 3 days after inoculation. The results indicated that nitrogen metabolism was strongly activated in the rhizosphere and polyhydroxybutyrate storage was mobilized in order to assist the survival of H. seropedicae during the early stages of colonization. Epiphytic cells showed altered transcription levels of several genes associated with polysaccharide biosynthesis, peptidoglycan turnover and outer membrane protein biosynthesis, suggesting reorganization of cell wall envelope components. Specific methyl-accepting chemotaxis proteins and two-component systems were differentially expressed between populations over time, suggesting deployment of an extensive bacterial sensory system for adaptation to the plant environment. An insertion mutation inactivating a methyl-accepting chemosensor induced in planktonic bacteria, decreased chemotaxis towards the plant and attachment to roots. In summary, analysis of mutant strains combined with transcript profiling revealed several molecular adaptations that enable H. seropedicae to sense the plant environment, attach to the root surface and survive during the early stages of maize colonization. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

A Systems Biology Approach to the Coordination of Defensive and Offensive Molecular Mechanisms in the Innate and Adaptive Host–Pathogen Interaction Networks

PubMed Central

Wu, Chia-Chou; Chen, Bor-Sen

2016-01-01

Infected zebrafish coordinates defensive and offensive molecular mechanisms in response to Candida albicans infections, and invasive C. albicans coordinates corresponding molecular mechanisms to interact with the host. However, knowledge of the ensuing infection-activated signaling networks in both host and pathogen and their interspecific crosstalk during the innate and adaptive phases of the infection processes remains incomplete. In the present study, dynamic network modeling, protein interaction databases, and dual transcriptome data from zebrafish and C. albicans during infection were used to infer infection-activated host–pathogen dynamic interaction networks. The consideration of host–pathogen dynamic interaction systems as innate and adaptive loops and subsequent comparisons of inferred innate and adaptive networks indicated previously unrecognized crosstalk between known pathways and suggested roles of immunological memory in the coordination of host defensive and offensive molecular mechanisms to achieve specific and powerful defense against pathogens. Moreover, pathogens enhance intraspecific crosstalk and abrogate host apoptosis to accommodate enhanced host defense mechanisms during the adaptive phase. Accordingly, links between physiological phenomena and changes in the coordination of defensive and offensive molecular mechanisms highlight the importance of host–pathogen molecular interaction networks, and consequent inferences of the host–pathogen relationship could be translated into biomedical applications. PMID:26881892

A Systems Biology Approach to the Coordination of Defensive and Offensive Molecular Mechanisms in the Innate and Adaptive Host-Pathogen Interaction Networks.

PubMed

Wu, Chia-Chou; Chen, Bor-Sen

2016-01-01

Infected zebrafish coordinates defensive and offensive molecular mechanisms in response to Candida albicans infections, and invasive C. albicans coordinates corresponding molecular mechanisms to interact with the host. However, knowledge of the ensuing infection-activated signaling networks in both host and pathogen and their interspecific crosstalk during the innate and adaptive phases of the infection processes remains incomplete. In the present study, dynamic network modeling, protein interaction databases, and dual transcriptome data from zebrafish and C. albicans during infection were used to infer infection-activated host-pathogen dynamic interaction networks. The consideration of host-pathogen dynamic interaction systems as innate and adaptive loops and subsequent comparisons of inferred innate and adaptive networks indicated previously unrecognized crosstalk between known pathways and suggested roles of immunological memory in the coordination of host defensive and offensive molecular mechanisms to achieve specific and powerful defense against pathogens. Moreover, pathogens enhance intraspecific crosstalk and abrogate host apoptosis to accommodate enhanced host defense mechanisms during the adaptive phase. Accordingly, links between physiological phenomena and changes in the coordination of defensive and offensive molecular mechanisms highlight the importance of host-pathogen molecular interaction networks, and consequent inferences of the host-pathogen relationship could be translated into biomedical applications.

[Analysis of the bacterial community developing in the course of Sphagnum moss decomposition].

PubMed

Kulichevskaia, I S; Belova, S E; Kevbrin, V V; Dedysh, S N; Zavarzin, G A

2007-01-01

Slow degradation of organic matter in acidic Sphagnum peat bogs suggests a limited activity of organotrophic microorganisms. Monitoring of the Sphagnum debris decomposition in a laboratory simulation experiment showed that this process was accompanied by a shift in the water color to brownish due to accumulation of humic substances and by the development of a specific bacterial community with a density of 2.4 x 10(7) cells ml(-1). About half of these organisms are metabolically active and detectable with rRNA-specific oligonucleotide probes. Molecular identification of the components of this microbial community showed the numerical dominance of bacteria affiliated with the phyla Alphaproteobacteria, Actinobacteria, and Phanctomycetes. The population sizes of Firmicutes and Bacteroidetes, which are believed to be the main agents of bacterially-mediated decomposition in eutrophic wetlands, were low. The numbers of planctomycetes increased at the final stage of Sphagnum decomposition. The representative isolates of Alphaproteobacteria were able to utilize galacturonic acid, the only low-molecular-weight organic compound detected in the water samples; the representatives of Planctomycetes were able to decompose some heteropolysaccharides, which points to the possible functional role of these groups of microorganisms in the community under study. Thus, the composition of the bacterial community responsible for Sphagnum decomposition in acidic and low-mineral oligotrophic conditions seems to be fundamentally different from that of the bacterial community which decomposes plant debris in eutrophic ecosystems at neutral pH.

Microbial decomposition of keratin in nature-a new hypothesis of industrial relevance.

PubMed

Lange, Lene; Huang, Yuhong; Busk, Peter Kamp

2016-03-01

Discovery of keratin-degrading enzymes from fungi and bacteria has primarily focused on finding one protease with efficient keratinase activity. Recently, an investigation was conducted of all keratinases secreted from a fungus known to grow on keratinaceous materials, such as feather, horn, and hooves. The study demonstrated that a minimum of three keratinases is needed to break down keratin, an endo-acting, an exo-acting, and an oligopeptide-acting keratinase. Further, several studies have documented that disruption of sulfur bridges of the keratin structure acts synergistically with the keratinases to loosen the molecular structure, thus giving the enzymes access to their substrate, the protein structure. With such complexity, it is relevant to compare microbial keratin decomposition with the microbial decomposition of well-studied polymers such as cellulose and chitin. Interestingly, it was recently shown that the specialized enzymes, lytic polysaccharide monoxygenases (LPMOs), shown to be important for breaking the recalcitrance of cellulose and chitin, are also found in keratin-degrading fungi. A holistic view of the complex molecular self-assembling structure of keratin and knowledge about enzymatic and boosting factors needed for keratin breakdown have been used to formulate a hypothesis for mode of action of the LPMOs in keratin decomposition and for a model for degradation of keratin in nature. Testing such hypotheses and models still needs to be done. Even now, the hypothesis can serve as an inspiration for designing industrial processes for keratin decomposition for conversion of unexploited waste streams, chicken feather, and pig bristles into bioaccessible animal feed.

Biomass pyrolysis: Thermal decomposition mechanisms of furfural and benzaldehyde

NASA Astrophysics Data System (ADS)

Vasiliou, AnGayle K.; Kim, Jong Hyun; Ormond, Thomas K.; Piech, Krzysztof M.; Urness, Kimberly N.; Scheer, Adam M.; Robichaud, David J.; Mukarakate, Calvin; Nimlos, Mark R.; Daily, John W.; Guan, Qi; Carstensen, Hans-Heinrich; Ellison, G. Barney

2013-09-01

The thermal decompositions of furfural and benzaldehyde have been studied in a heated microtubular flow reactor. The pyrolysis experiments were carried out by passing a dilute mixture of the aromatic aldehydes (roughly 0.1%-1%) entrained in a stream of buffer gas (either He or Ar) through a pulsed, heated SiC reactor that is 2-3 cm long and 1 mm in diameter. Typical pressures in the reactor are 75-150 Torr with the SiC tube wall temperature in the range of 1200-1800 K. Characteristic residence times in the reactor are 100-200 μsec after which the gas mixture emerges as a skimmed molecular beam at a pressure of approximately 10 μTorr. Products were detected using matrix infrared absorption spectroscopy, 118.2 nm (10.487 eV) photoionization mass spectroscopy and resonance enhanced multiphoton ionization. The initial steps in the thermal decomposition of furfural and benzaldehyde have been identified. Furfural undergoes unimolecular decomposition to furan + CO: C4H3O-CHO (+ M) → CO + C4H4O. Sequential decomposition of furan leads to the production of HC≡CH, CH2CO, CH3C≡CH, CO, HCCCH2, and H atoms. In contrast, benzaldehyde resists decomposition until higher temperatures when it fragments to phenyl radical plus H atoms and CO: C6H5CHO (+ M) → C6H5CO + H → C6H5 + CO + H. The H atoms trigger a chain reaction by attacking C6H5CHO: H + C6H5CHO → [C6H6CHO]* → C6H6 + CO + H. The net result is the decomposition of benzaldehyde to produce benzene and CO.

Photodegradation at day, microbial decomposition at night - decomposition in arid lands

NASA Astrophysics Data System (ADS)

Gliksman, Daniel; Gruenzweig, Jose

2014-05-01

Our current knowledge of decomposition in dry seasons and its role in carbon turnover is fragmentary. So far, decomposition during dry seasons was mostly attributed to abiotic mechanisms, mainly photochemical and thermal degradation, while the contribution of microorganisms to the decay process was excluded. We asked whether microbial decomposition occurs during the dry season and explored its interaction with photochemical degradation under Mediterranean climate. We conducted a litter bag experiment with local plant litter and manipulated litter exposure to radiation using radiation filters. We found notable rates of CO2 fluxes from litter which were related to microbial activity mainly during night-time throughout the dry season. This activity was correlated with litter moisture content and high levels of air humidity and dew. Day-time CO2 fluxes were related to solar radiation, and radiation manipulation suggested photodegradation as the underlying mechanism. In addition, a decline in microbial activity was followed by a reduction in photodegradation-related CO2 fluxes. The levels of microbial decomposition and photodegradation in the dry season were likely the factors influencing carbon mineralization during the subsequent wet season. This study showed that microbial decomposition can be a dominant contributor to CO2 emissions and mass loss in the dry season and it suggests a regulating effect of microbial activity on photodegradation. Microbial decomposition is an important contributor to the dry season decomposition and impacts the annual litter turn-over rates in dry regions. Global warming may lead to reduced moisture availability and dew deposition, which may greatly influence not only microbial decomposition of plant litter, but also photodegradation.

Toward a reaction rate model of condensed-phase RDX decomposition under high temperatures

NASA Astrophysics Data System (ADS)

Schweigert, Igor

2015-06-01

Shock ignition of energetic molecular solids is driven by microstructural heterogeneities, at which even moderate stresses can result in sufficiently high temperatures to initiate material decomposition and chemical energy release. Mesoscale modeling of these ``hot spots'' requires a reaction rate model that describes the energy release with a sub-microsecond resolution and under a wide range of temperatures. No such model is available even for well-studied energetic materials such as RDX. In this presentation, I will describe an ongoing effort to develop a reaction rate model of condensed-phase RDX decomposition under high temperatures using first-principles molecular dynamics, transition-state theory, and reaction network analysis. This work was supported by the Naval Research Laboratory, by the Office of Naval Research, and by the DoD High Performance Computing Modernization Program Software Application Institute for Multiscale Reactive Modeling of Insensitive Munitions.

Carbon cluster formation during thermal decomposition of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine and 1,3,5-triamino-2,4,6-trinitrobenzene high explosives from ReaxFF reactive molecular dynamics simulations.

PubMed

Zhang, Luzheng; Zybin, Sergey V; van Duin, Adri C T; Dasgupta, Siddharth; Goddard, William A; Kober, Edward M

2009-10-08

We report molecular dynamics (MD) simulations using the first-principles-based ReaxFF reactive force field to study the thermal decomposition of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) at various densities and temperatures. TATB is known to produce a large amount (15-30%) of high-molecular-weight carbon clusters, whereas detonation of nitramines such as HMX and RDX (1,3,5-trinitroperhydro-1,3,5-triazine) generate predominantly low-molecular-weight products. In agreement with experimental observation, these simulations predict that TATB decomposition quickly (by 30 ps) initiates the formation of large carbonaceous clusters (more than 4000 amu, or approximately 15-30% of the total system mass), and HMX decomposition leads almost exclusively to small-molecule products. We find that HMX decomposes readily on this time scale at lower temperatures, for which the decomposition rate of TATB is about an order of magnitude slower. Analyzing the ReaxFF MD results leads to the detailed atomistic structure of this carbon-rich phase of TATB and allows characterization of the kinetics and chemistry related to this phase and their dependence on system density and temperature. The carbon-rich phase formed from TATB contains mainly polyaromatic rings with large oxygen content, leading to graphitic regions. We use these results to describe the initial reaction steps of thermal decomposition of HMX and TATB in terms of the rates for forming primary and secondary products, allowing comparison to experimentally derived models. These studies show that MD using the ReaxFF reactive force field provides detailed atomistic information that explains such macroscopic observations as the dramatic difference in carbon cluster formation between TATB and HMX. This shows that ReaxFF MD captures the fundamental differences in the mechanisms of such systems and illustrates how the ReaxFF may be applied to model complex chemical phenomena

Molecular dynamics modelling of mechanical properties of polymers for adaptive aerospace structures

NASA Astrophysics Data System (ADS)

Papanikolaou, Michail; Drikakis, Dimitris; Asproulis, Nikolaos

2015-02-01

The features of adaptive structures depend on the properties of the supporting materials. For example, morphing wing structures require wing skin materials, such as rubbers that can withstand the forces imposed by the internal mechanism while maintaining the required aerodynamic properties of the aircraft. In this study, Molecular Dynamics and Minimization simulations are being used to establish well-equilibrated models of Ethylene-Propylene-Diene Monomer (EPDM) elastomer systems and investigate their mechanical properties.

Incorporation of unique molecular identifiers in TruSeq adapters improves the accuracy of quantitative sequencing.

PubMed

Hong, Jungeui; Gresham, David

2017-11-01

Quantitative analysis of next-generation sequencing (NGS) data requires discriminating duplicate reads generated by PCR from identical molecules that are of unique origin. Typically, PCR duplicates are identified as sequence reads that align to the same genomic coordinates using reference-based alignment. However, identical molecules can be independently generated during library preparation. Misidentification of these molecules as PCR duplicates can introduce unforeseen biases during analyses. Here, we developed a cost-effective sequencing adapter design by modifying Illumina TruSeq adapters to incorporate a unique molecular identifier (UMI) while maintaining the capacity to undertake multiplexed, single-index sequencing. Incorporation of UMIs into TruSeq adapters (TrUMIseq adapters) enables identification of bona fide PCR duplicates as identically mapped reads with identical UMIs. Using TrUMIseq adapters, we show that accurate removal of PCR duplicates results in improved accuracy of both allele frequency (AF) estimation in heterogeneous populations using DNA sequencing and gene expression quantification using RNA-Seq.

Factors influencing leaf litter decomposition: An intersite decomposition experiment across China

USGS Publications Warehouse

Zhou, G.; Guan, L.; Wei, X.; Tang, X.; Liu, S.; Liu, J.; Zhang, Dongxiao; Yan, J.

2008-01-01

The Long-Term Intersite Decomposition Experiment in China (hereafter referred to as LTIDE-China) was established in 2002 to study how substrate quality and macroclimate factors affect leaf litter decomposition. The LTIDE-China includes a wide variety of natural and managed ecosystems, consisting of 12 forest types (eight regional broadleaf forests, three needle-leaf plantations and one broadleaf plantation) at eight locations across China. Samples of mixed leaf litter from the south subtropical evergreen broadleaf forest in Dinghushan (referred to as the DHS sample) were translocated to all 12 forest types. The leaf litter from each of other 11 forest types was placed in its original forest to enable comparison of decomposition rates of DHS and local litters. The experiment lasted for 30 months, involving collection of litterbags from each site every 3 months. Our results show that annual decomposition rate-constants, as represented by regression fitted k-values, ranged from 0.169 to 1.454/year. Climatic factors control the decomposition rate, in which mean annual temperature and annual actual evapotranspiration are dominant and mean annual precipitation is subordinate. Initial C/N and N/P ratios were demonstrated to be important factors of regulating litter decomposition rate. Decomposition process may apparently be divided into two phases controlled by different factors. In our study, 0.75 years is believed to be the dividing line of the two phases. The fact that decomposition rates of DHS litters were slower than those of local litters may have been resulted from the acclimation of local decomposer communities to extraneous substrate. ?? 2008 Springer Science+Business Media B.V.

How does low temperature coupled with different pressures affect initiation mechanisms and subsequent decompositions in nitramine explosive HMX?

PubMed

Wu, Qiong; Xiong, Guolin; Zhu, Weihua; Xiao, Heming

2015-09-21

We have performed ab initio molecular dynamics simulations to study coupling effects of temperature (534-873 K) and pressure (1-20 GPa) on the initiation mechanisms and subsequent chemical decompositions of nitramine explosive 1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX). A new initiation decomposition mechanism of HMX was found to be the unimolecular C-H bond breaking, and this mechanism was independent of the coupling effects of different temperatures and pressures. The formed hydrogen radicals could promote subsequent decompositions of HMX. Subsequent decompositions were very sensitive to the pressure at low temperatures (534 and 608 K), while the temperature became the foremost factor that affected the decomposition at a high temperature (873 K) instead of the pressure. Our study may provide a new insight into understanding the coupling effects of the temperature and pressure on the initiation decomposition mechanisms of nitramine explosives.

Decoupling the direct and indirect effects of climate on plant litter decomposition: Accounting for stress-induced modifications in plant chemistry.

PubMed

Suseela, Vidya; Tharayil, Nishanth

2018-04-01

Decomposition of plant litter is a fundamental ecosystem process that can act as a feedback to climate change by simultaneously influencing both the productivity of ecosystems and the flux of carbon dioxide from the soil. The influence of climate on decomposition from a postsenescence perspective is relatively well known; in particular, climate is known to regulate the rate of litter decomposition via its direct influence on the reaction kinetics and microbial physiology on processes downstream of tissue senescence. Climate can alter plant metabolism during the formative stage of tissues and could shape the final chemical composition of plant litter that is available for decomposition, and thus indirectly influence decomposition; however, these indirect effects are relatively poorly understood. Climatic stress disrupts cellular homeostasis in plants and results in the reprogramming of primary and secondary metabolic pathways, which leads to changes in the quantity, composition, and organization of small molecules and recalcitrant heteropolymers, including lignins, tannins, suberins, and cuticle within the plant tissue matrix. Furthermore, by regulating metabolism during tissue senescence, climate influences the resorption of nutrients from senescing tissues. Thus, the final chemical composition of plant litter that forms the substrate of decomposition is a combined product of presenescence physiological processes through the production and resorption of metabolites. The changes in quantity, composition, and localization of the molecular construct of the litter could enhance or hinder tissue decomposition and soil nutrient cycling by altering the recalcitrance of the lignocellulose matrix, the composition of microbial communities, and the activity of microbial exo-enzymes via various complexation reactions. Also, the climate-induced changes in the molecular composition of litter could differentially influence litter decomposition and soil nutrient cycling. Compared

Decomposition Mechanism and Decomposition Promoting Factors of Waste Hard Metal for Zinc Decomposition Process (ZDP)

NASA Astrophysics Data System (ADS)

Pee, J. H.; Kim, Y. J.; Kim, J. Y.; Seong, N. E.; Cho, W. S.; Kim, K. J.

2011-10-01

Decomposition promoting factors and decomposition mechanism in the zinc decomposition process of waste hard metals which are composed mostly of tungsten carbide and cobalt were evaluated. Zinc volatility amount was suppressed and zinc steam pressure was produced in the reaction graphite crucible inside an electric furnace for ZDP. Reaction was done for 2 hrs at 650 °C, which 100 % decomposed the waste hard metals that were over 30 mm thick. As for the separation-decomposition of waste hard metals, zinc melted alloy formed a liquid composed of a mixture of γ-β1 phase from the cobalt binder layer (reaction interface). The volume of reacted zone was expanded and the waste hard metal layer was decomposed-separated horizontally from the hard metal. Zinc used in the ZDP process was almost completely removed-collected by decantation and volatilization-collection process at 1000 °C. The small amount of zinc remaining in the tungsten carbide-cobalt powder which was completely decomposed was fully removed by using phosphate solution which had a slow cobalt dissolution speed.

Metallo-organic decomposition films

NASA Technical Reports Server (NTRS)

Gallagher, B. D.

1985-01-01

A summary of metallo-organic deposition (MOD) films for solar cells was presented. The MOD materials are metal ions compounded with organic radicals. The technology is evolving quickly for solar cell metallization. Silver compounds, especially silver neodecanoate, were developed which can be applied by thick-film screening, ink-jet printing, spin-on, spray, or dip methods. Some of the advantages of MOD are: high uniform metal content, lower firing temperatures, decomposition without leaving a carbon deposit or toxic materials, and a film that is stable under ambient conditions. Molecular design criteria were explained along with compounds formulated to date, and the accompanying reactions for these compounds. Phase stability and the other experimental and analytic results of MOD films were presented.

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

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.

Trade-offs in thermal adaptation: the need for a molecular to ecological integration.

PubMed

Pörtner, Hans O; Bennett, Albert F; Bozinovic, Francisco; Clarke, Andrew; Lardies, Marco A; Lucassen, Magnus; Pelster, Bernd; Schiemer, Fritz; Stillman, Jonathon H

2006-01-01

Through functional analyses, integrative physiology is able to link molecular biology with ecology as well as evolutionary biology and is thereby expected to provide access to the evolution of molecular, cellular, and organismic functions; the genetic basis of adaptability; and the shaping of ecological patterns. This paper compiles several exemplary studies of thermal physiology and ecology, carried out at various levels of biological organization from single genes (proteins) to ecosystems. In each of those examples, trade-offs and constraints in thermal adaptation are addressed; these trade-offs and constraints may limit species' distribution and define their level of fitness. For a more comprehensive understanding, the paper sets out to elaborate the functional and conceptual connections among these independent studies and the various organizational levels addressed. This effort illustrates the need for an overarching concept of thermal adaptation that encompasses molecular, organellar, cellular, and whole-organism information as well as the mechanistic links between fitness, ecological success, and organismal physiology. For this data, the hypothesis of oxygen- and capacity-limited thermal tolerance in animals provides such a conceptual framework and allows interpreting the mechanisms of thermal limitation of animals as relevant at the ecological level. While, ideally, evolutionary studies over multiple generations, illustrated by an example study in bacteria, are necessary to test the validity of such complex concepts and underlying hypotheses, animal physiology frequently is constrained to functional studies within one generation. Comparisons of populations in a latitudinal cline, closely related species from different climates, and ontogenetic stages from riverine clines illustrate how evolutionary information can still be gained. An understanding of temperature-dependent shifts in energy turnover, associated with adjustments in aerobic scope and performance

Reliable Viscosity Calculation from Equilibrium Molecular Dynamics Simulations: A Time Decomposition Method.

PubMed

Zhang, Yong; Otani, Akihito; Maginn, Edward J

2015-08-11

Equilibrium molecular dynamics is often used in conjunction with a Green-Kubo integral of the pressure tensor autocorrelation function to compute the shear viscosity of fluids. This approach is computationally expensive and is subject to a large amount of variability because the plateau region of the Green-Kubo integral is difficult to identify unambiguously. Here, we propose a time decomposition approach for computing the shear viscosity using the Green-Kubo formalism. Instead of one long trajectory, multiple independent trajectories are run and the Green-Kubo relation is applied to each trajectory. The averaged running integral as a function of time is fit to a double-exponential function with a weighting function derived from the standard deviation of the running integrals. Such a weighting function minimizes the uncertainty of the estimated shear viscosity and provides an objective means of estimating the viscosity. While the formal Green-Kubo integral requires an integration to infinite time, we suggest an integration cutoff time tcut, which can be determined by the relative values of the running integral and the corresponding standard deviation. This approach for computing the shear viscosity can be easily automated and used in computational screening studies where human judgment and intervention in the data analysis are impractical. The method has been applied to the calculation of the shear viscosity of a relatively low-viscosity liquid, ethanol, and relatively high-viscosity ionic liquid, 1-n-butyl-3-methylimidazolium bis(trifluoromethane-sulfonyl)imide ([BMIM][Tf2N]), over a range of temperatures. These test cases show that the method is robust and yields reproducible and reliable shear viscosity values.

Free energy calculations of short peptide chains using Adaptively Biased Molecular Dynamics

NASA Astrophysics Data System (ADS)

Karpusenka, Vadzim; Babin, Volodymyr; Roland, Christopher; Sagui, Celeste

2008-10-01

We performed a computational study of monomer peptides composed of methionine, alanine, leucine, glutamate, lysine (all amino acids with a helix-forming propensities); and proline, glycine tyrosine, serine, arginine (which all have poor helix-forming propensities). The free energy landscapes as a function of the handedness and radius of gyration have been calculated using the recently introduced Adaptively Biased Molecular Dynamics (ABMD) method, combined with replica exchange, multiple walkers, and post-processing Umbrella Correction (UC). Minima that correspond to some of the left- and right-handed 310-, α- and π-helixes were identified by secondary structure assignment methods (DSSP, Stride). The resulting free energy surface (FES) and the subsequent steered molecular dynamics (SMD) simulation results are in agreement with the empirical evidence of preferred secondary structures for the peptide chains considered.

Analysis of benzoquinone decomposition in solution plasma process

NASA Astrophysics Data System (ADS)

Bratescu, M. A.; Saito, N.

2016-01-01

The decomposition of p-benzoquinone (p-BQ) in Solution Plasma Processing (SPP) was analyzed by Coherent Anti-Stokes Raman Spectroscopy (CARS) by monitoring the change of the anti-Stokes signal intensity of the vibrational transitions of the molecule, during and after SPP. Just in the beginning of the SPP treatment, the CARS signal intensities of the ring vibrational molecular transitions increased under the influence of the electric field of plasma. The results show that plasma influences the p-BQ molecules in two ways: (i) plasma produces a polarization and an orientation of the molecules in the local electric field of plasma and (ii) the gas phase plasma supplies, in the liquid phase, hydrogen and hydroxyl radicals, which reduce or oxidize the molecules, respectively, generating different carboxylic acids. The decomposition of p-BQ after SPP was confirmed by UV-visible absorption spectroscopy and liquid chromatography.

Toward a reaction rate model of condensed-phase RDX decomposition under high temperatures

NASA Astrophysics Data System (ADS)

Schweigert, Igor

2014-03-01

Shock ignition of energetic molecular solids is driven by microstructural heterogeneities, at which even moderate stresses can result in sufficiently high temperatures to initiate material decomposition and the release of the chemical energy. Mesoscale modeling of these ``hot spots'' requires a chemical reaction rate model that describes the energy release with a sub-microsecond resolution and under a wide range of temperatures. No such model is available even for well-studied energetic materials such as RDX. In this presentation, I will describe an ongoing effort to develop a reaction rate model of condensed-phase RDX decomposition under high temperatures using first-principles molecular dynamics, transition-state theory, and reaction network analysis. This work was supported by the Naval Research Laboratory, by the Office of Naval Research, and by the DOD High Performance Computing Modernization Program Software Application Institute for Multiscale Reactive Modeling of Insensitive Munitions.

Exploring Patterns of Soil Organic Matter Decomposition with Students through the Global Decomposition Project (GDP) and the Interactive Model of Leaf Decomposition (IMOLD)

NASA Astrophysics Data System (ADS)

Steiner, S. M.; Wood, J. H.

2015-12-01

As decomposition rates are affected by climate change, understanding crucial soil interactions that affect plant growth and decomposition becomes a vital part of contributing to the students' knowledge base. The Global Decomposition Project (GDP) is designed to introduce and educate students about soil organic matter and decomposition through a standardized protocol for collecting, reporting, and sharing data. The Interactive Model of Leaf Decomposition (IMOLD) utilizes animations and modeling to learn about the carbon cycle, leaf anatomy, and the role of microbes in decomposition. Paired together, IMOLD teaches the background information and allows simulation of numerous scenarios, and the GDP is a data collection protocol that allows students to gather usable measurements of decomposition in the field. Our presentation will detail how the GDP protocol works, how to obtain or make the materials needed, and how results will be shared. We will also highlight learning objectives from the three animations of IMOLD, and demonstrate how students can experiment with different climates and litter types using the interactive model to explore a variety of decomposition scenarios. The GDP demonstrates how scientific methods can be extended to educate broader audiences, and data collected by students can provide new insight into global patterns of soil decomposition. Using IMOLD, students will gain a better understanding of carbon cycling in the context of litter decomposition, as well as learn to pose questions they can answer with an authentic computer model. Using the GDP protocols and IMOLD provide a pathway for scientists and educators to interact and reach meaningful education and research goals.

Pressure-induced metallization of condensed phase β-HMX under shock loadings via molecular dynamics simulations in conjunction with multi-scale shock technique.

PubMed

Ge, Ni-Na; Wei, Yong-Kai; Zhao, Feng; Chen, Xiang-Rong; Ji, Guang-Fu

2014-07-01

The electronic structure and initial decomposition in high explosive HMX under conditions of shock loading are examined. The simulation is performed using quantum molecular dynamics in conjunction with multi-scale shock technique (MSST). A self-consistent charge density-functional tight-binding (SCC-DFTB) method is adapted. The results show that the N-N-C angle has a drastic change under shock wave compression along lattice vector b at shock velocity 11 km/s, which is the main reason that leads to an insulator-to-metal transition for the HMX system. The metallization pressure (about 130 GPa) of condensed-phase HMX is predicted firstly. We also detect the formation of several key products of condensed-phase HMX decomposition, such as NO2, NO, N2, N2O, H2O, CO, and CO2, and all of them have been observed in previous experimental studies. Moreover, the initial decomposition products include H2 due to the C-H bond breaking as a primary reaction pathway at extreme condition, which presents a new insight into the initial decomposition mechanism of HMX under shock loading at the atomistic level.

Intelligent Diagnosis Method for Rotating Machinery Using Dictionary Learning and Singular Value Decomposition.

PubMed

Han, Te; Jiang, Dongxiang; Zhang, Xiaochen; Sun, Yankui

2017-03-27

Rotating machinery is widely used in industrial applications. With the trend towards more precise and more critical operating conditions, mechanical failures may easily occur. Condition monitoring and fault diagnosis (CMFD) technology is an effective tool to enhance the reliability and security of rotating machinery. In this paper, an intelligent fault diagnosis method based on dictionary learning and singular value decomposition (SVD) is proposed. First, the dictionary learning scheme is capable of generating an adaptive dictionary whose atoms reveal the underlying structure of raw signals. Essentially, dictionary learning is employed as an adaptive feature extraction method regardless of any prior knowledge. Second, the singular value sequence of learned dictionary matrix is served to extract feature vector. Generally, since the vector is of high dimensionality, a simple and practical principal component analysis (PCA) is applied to reduce dimensionality. Finally, the K -nearest neighbor (KNN) algorithm is adopted for identification and classification of fault patterns automatically. Two experimental case studies are investigated to corroborate the effectiveness of the proposed method in intelligent diagnosis of rotating machinery faults. The comparison analysis validates that the dictionary learning-based matrix construction approach outperforms the mode decomposition-based methods in terms of capacity and adaptability for feature extraction.

Intelligent Diagnosis Method for Rotating Machinery Using Dictionary Learning and Singular Value Decomposition

PubMed Central

Han, Te; Jiang, Dongxiang; Zhang, Xiaochen; Sun, Yankui

2017-01-01

Rotating machinery is widely used in industrial applications. With the trend towards more precise and more critical operating conditions, mechanical failures may easily occur. Condition monitoring and fault diagnosis (CMFD) technology is an effective tool to enhance the reliability and security of rotating machinery. In this paper, an intelligent fault diagnosis method based on dictionary learning and singular value decomposition (SVD) is proposed. First, the dictionary learning scheme is capable of generating an adaptive dictionary whose atoms reveal the underlying structure of raw signals. Essentially, dictionary learning is employed as an adaptive feature extraction method regardless of any prior knowledge. Second, the singular value sequence of learned dictionary matrix is served to extract feature vector. Generally, since the vector is of high dimensionality, a simple and practical principal component analysis (PCA) is applied to reduce dimensionality. Finally, the K-nearest neighbor (KNN) algorithm is adopted for identification and classification of fault patterns automatically. Two experimental case studies are investigated to corroborate the effectiveness of the proposed method in intelligent diagnosis of rotating machinery faults. The comparison analysis validates that the dictionary learning-based matrix construction approach outperforms the mode decomposition-based methods in terms of capacity and adaptability for feature extraction. PMID:28346385

Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins.

PubMed

Goncearenco, Alexander; Ma, Bin-Guang; Berezovsky, Igor N

2014-03-01

DNA, RNA and proteins are major biological macromolecules that coevolve and adapt to environments as components of one highly interconnected system. We explore here sequence/structure determinants of mechanisms of adaptation of these molecules, links between them, and results of their mutual evolution. We complemented statistical analysis of genomic and proteomic sequences with folding simulations of RNA molecules, unraveling causal relations between compositional and sequence biases reflecting molecular adaptation on DNA, RNA and protein levels. We found many compositional peculiarities related to environmental adaptation and the life style. Specifically, thermal adaptation of protein-coding sequences in Archaea is characterized by a stronger codon bias than in Bacteria. Guanine and cytosine load in the third codon position is important for supporting the aerobic life style, and it is highly pronounced in Bacteria. The third codon position also provides a tradeoff between arginine and lysine, which are favorable for thermal adaptation and aerobicity, respectively. Dinucleotide composition provides stability of nucleic acids via strong base-stacking in ApG dinucleotides. In relation to coevolution of nucleic acids and proteins, thermostability-related demands on the amino acid composition affect the nucleotide content in the second codon position in Archaea.

Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins

PubMed Central

Goncearenco, Alexander; Ma, Bin-Guang; Berezovsky, Igor N.

2014-01-01

DNA, RNA and proteins are major biological macromolecules that coevolve and adapt to environments as components of one highly interconnected system. We explore here sequence/structure determinants of mechanisms of adaptation of these molecules, links between them, and results of their mutual evolution. We complemented statistical analysis of genomic and proteomic sequences with folding simulations of RNA molecules, unraveling causal relations between compositional and sequence biases reflecting molecular adaptation on DNA, RNA and protein levels. We found many compositional peculiarities related to environmental adaptation and the life style. Specifically, thermal adaptation of protein-coding sequences in Archaea is characterized by a stronger codon bias than in Bacteria. Guanine and cytosine load in the third codon position is important for supporting the aerobic life style, and it is highly pronounced in Bacteria. The third codon position also provides a tradeoff between arginine and lysine, which are favorable for thermal adaptation and aerobicity, respectively. Dinucleotide composition provides stability of nucleic acids via strong base-stacking in ApG dinucleotides. In relation to coevolution of nucleic acids and proteins, thermostability-related demands on the amino acid composition affect the nucleotide content in the second codon position in Archaea. PMID:24371267

A third-generation density-functional-theory-based method for calculating canonical molecular orbitals of large molecules.

PubMed

Hirano, Toshiyuki; Sato, Fumitoshi

2014-07-28

We used grid-free modified Cholesky decomposition (CD) to develop a density-functional-theory (DFT)-based method for calculating the canonical molecular orbitals (CMOs) of large molecules. Our method can be used to calculate standard CMOs, analytically compute exchange-correlation terms, and maximise the capacity of next-generation supercomputers. Cholesky vectors were first analytically downscaled using low-rank pivoted CD and CD with adaptive metric (CDAM). The obtained Cholesky vectors were distributed and stored on each computer node in a parallel computer, and the Coulomb, Fock exchange, and pure exchange-correlation terms were calculated by multiplying the Cholesky vectors without evaluating molecular integrals in self-consistent field iterations. Our method enables DFT and massively distributed memory parallel computers to be used in order to very efficiently calculate the CMOs of large molecules.

Physical and molecular bases of protein thermal stability and cold adaptation.

PubMed

Pucci, Fabrizio; Rooman, Marianne

2017-02-01

The molecular bases of thermal and cold stability and adaptation, which allow proteins to remain folded and functional in the temperature ranges in which their host organisms live and grow, are still only partially elucidated. Indeed, both experimental and computational studies fail to yield a fully precise and global physical picture, essentially because all effects are context-dependent and thus quite intricate to unravel. We present a snapshot of the current state of knowledge of this highly complex and challenging issue, whose resolution would enable large-scale rational protein design. Copyright © 2016 Elsevier Ltd. All rights reserved.

Modeling Oil Shale Pyrolysis: High-Temperature Unimolecular Decomposition Pathways for Thiophene.

PubMed

Vasiliou, AnGayle K; Hu, Hui; Cowell, Thomas W; Whitman, Jared C; Porterfield, Jessica; Parish, Carol A

2017-10-12

The thermal decomposition mechanism of thiophene has been investigated both experimentally and theoretically. Thermal decomposition experiments were done using a 1 mm × 3 cm pulsed silicon carbide microtubular reactor, C 4 H 4 S + Δ → Products. Unlike previous studies these experiments were able to identify the initial thiophene decomposition products. Thiophene was entrained in either Ar, Ne, or He carrier gas, passed through a heated (300-1700 K) SiC microtubular reactor (roughly ≤100 μs residence time), and exited into a vacuum chamber. The resultant molecular beam was probed by photoionization mass spectroscopy and IR spectroscopy. The pyrolysis mechanisms of thiophene were also investigated with the CBS-QB3 method using UB3LYP/6-311++G(2d,p) optimized geometries. In particular, these electronic structure methods were used to explore pathways for the formation of elemental sulfur as well as for the formation of H 2 S and 1,3-butadiyne. Thiophene was found to undergo unimolecular decomposition by five pathways: C 4 H 4 S → (1) S═C═CH 2 + HCCH, (2) CS + HCCCH 3 , (3) HCS + HCCCH 2 , (4) H 2 S + HCC-CCH, and (5) S + HCC-CH═CH 2 . The experimental and theoretical findings are in excellent agreement.

Efficient morse decompositions of vector fields.

PubMed

Chen, Guoning; Mischaikow, Konstantin; Laramee, Robert S; Zhang, Eugene

2008-01-01

Existing topology-based vector field analysis techniques rely on the ability to extract the individual trajectories such as fixed points, periodic orbits, and separatrices that are sensitive to noise and errors introduced by simulation and interpolation. This can make such vector field analysis unsuitable for rigorous interpretations. We advocate the use of Morse decompositions, which are robust with respect to perturbations, to encode the topological structures of a vector field in the form of a directed graph, called a Morse connection graph (MCG). While an MCG exists for every vector field, it need not be unique. Previous techniques for computing MCG's, while fast, are overly conservative and usually results in MCG's that are too coarse to be useful for the applications. To address this issue, we present a new technique for performing Morse decomposition based on the concept of tau-maps, which typically provides finer MCG's than existing techniques. Furthermore, the choice of tau provides a natural tradeoff between the fineness of the MCG's and the computational costs. We provide efficient implementations of Morse decomposition based on tau-maps, which include the use of forward and backward mapping techniques and an adaptive approach in constructing better approximations of the images of the triangles in the meshes used for simulation.. Furthermore, we propose the use of spatial tau-maps in addition to the original temporal tau-maps. These techniques provide additional trade-offs between the quality of the MCGs and the speed of computation. We demonstrate the utility of our technique with various examples in the plane and on surfaces including engine simulation data sets.

Adaptive Identification by Systolic Arrays.

DTIC Science & Technology

1987-12-01

BIBLIOGRIAPHY Anton , Howard, Elementary Linear Algebra , John Wiley & Sons, 19S4. Cristi, Roberto, A Parallel Structure Jor Adaptive Pole Placement...10 11. SYSTEM IDENTIFICATION M*YETHODS ....................... 12 A. LINEAR SYSTEM MODELING ......................... 12 B. SOLUTION OF SYSTEMS OF... LINEAR EQUATIONS ......... 13 C. QR DECOMPOSITION ................................ 14 D. RECURSIVE LEAST SQUARES ......................... 16 E. BLOCK

Layout decomposition of self-aligned double patterning for 2D random logic patterning

NASA Astrophysics Data System (ADS)

Ban, Yongchan; Miloslavsky, Alex; Lucas, Kevin; Choi, Soo-Han; Park, Chul-Hong; Pan, David Z.

2011-04-01

Self-aligned double pattering (SADP) has been adapted as a promising solution for sub-30nm technology nodes due to its lower overlay problem and better process tolerance. SADP is in production use for 1D dense patterns with good pitch control such as NAND Flash memory applications, but it is still challenging to apply SADP to 2D random logic patterns. The favored type of SADP for complex logic interconnects is a two mask approach using a core mask and a trim mask. In this paper, we first describe layout decomposition methods of spacer-type double patterning lithography, then report a type of SADP compliant layouts, and finally report SADP applications on Samsung 22nm SRAM layout. For SADP decomposition, we propose several SADP-aware layout coloring algorithms and a method of generating lithography-friendly core mask patterns. Experimental results on 22nm node designs show that our proposed layout decomposition for SADP effectively decomposes any given layouts.

Molecular specificity, convergence and constraint shape adaptive evolution in nutrient-poor environments.

PubMed

Hong, Jungeui; Gresham, David

2014-01-01

One of the central goals of evolutionary biology is to explain and predict the molecular basis of adaptive evolution. We studied the evolution of genetic networks in Saccharomyces cerevisiae (budding yeast) populations propagated for more than 200 generations in different nitrogen-limiting conditions. We find that rapid adaptive evolution in nitrogen-poor environments is dominated by the de novo generation and selection of copy number variants (CNVs), a large fraction of which contain genes encoding specific nitrogen transporters including PUT4, DUR3 and DAL4. The large fitness increases associated with these alleles limits the genetic heterogeneity of adapting populations even in environments with multiple nitrogen sources. Complete identification of acquired point mutations, in individual lineages and entire populations, identified heterogeneity at the level of genetic loci but common themes at the level of functional modules, including genes controlling phosphatidylinositol-3-phosphate metabolism and vacuole biogenesis. Adaptive strategies shared with other nutrient-limited environments point to selection of genetic variation in the TORC1 and Ras/PKA signaling pathways as a general mechanism underlying improved growth in nutrient-limited environments. Within a single population we observed the repeated independent selection of a multi-locus genotype, comprised of the functionally related genes GAT1, MEP2 and LST4. By studying the fitness of individual alleles, and their combination, as well as the evolutionary history of the evolving population, we find that the order in which these mutations are acquired is constrained by epistasis. The identification of repeatedly selected variation at functionally related loci that interact epistatically suggests that gene network polymorphisms (GNPs) may be a frequent outcome of adaptive evolution. Our results provide insight into the mechanistic basis by which cells adapt to nutrient-limited environments and suggest that

Molecular characterization of an adaptive response to alkylating agents in the opportunistic pathogen Aspergillus fumigatus.

PubMed

O'Hanlon, Karen A; Margison, Geoffrey P; Hatch, Amy; Fitzpatrick, David A; Owens, Rebecca A; Doyle, Sean; Jones, Gary W

2012-09-01

An adaptive response to alkylating agents based upon the conformational change of a methylphosphotriester (MPT) DNA repair protein to a transcriptional activator has been demonstrated in a number of bacterial species, but this mechanism appears largely absent from eukaryotes. Here, we demonstrate that the human pathogen Aspergillus fumigatus elicits an adaptive response to sub-lethal doses of the mono-functional alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). We have identified genes that encode MPT and O(6)-alkylguanine DNA alkyltransferase (AGT) DNA repair proteins; deletions of either of these genes abolish the adaptive response and sensitize the organism to MNNG. In vitro DNA repair assays confirm the ability of MPT and AGT to repair methylphosphotriester and O(6)-methylguanine lesions respectively. In eukaryotes, the MPT protein is confined to a select group of fungal species, some of which are major mammalian and plant pathogens. The evolutionary origin of the adaptive response is bacterial and rooted within the Firmicutes phylum. Inter-kingdom horizontal gene transfer between Firmicutes and Ascomycete ancestors introduced the adaptive response into the Fungal kingdom. Our data constitute the first detailed characterization of the molecular mechanism of the adaptive response in a lower eukaryote and has applications for development of novel fungal therapeutics targeting this DNA repair system.

Molecular characterization of an adaptive response to alkylating agents in the opportunistic pathogen Aspergillus fumigatus

PubMed Central

O’Hanlon, Karen A.; Margison, Geoffrey P.; Hatch, Amy; Fitzpatrick, David A.; Owens, Rebecca A.; Doyle, Sean; Jones, Gary W.

2012-01-01

An adaptive response to alkylating agents based upon the conformational change of a methylphosphotriester (MPT) DNA repair protein to a transcriptional activator has been demonstrated in a number of bacterial species, but this mechanism appears largely absent from eukaryotes. Here, we demonstrate that the human pathogen Aspergillus fumigatus elicits an adaptive response to sub-lethal doses of the mono-functional alkylating agent N-methyl-N′-nitro-N-nitrosoguanidine (MNNG). We have identified genes that encode MPT and O6-alkylguanine DNA alkyltransferase (AGT) DNA repair proteins; deletions of either of these genes abolish the adaptive response and sensitize the organism to MNNG. In vitro DNA repair assays confirm the ability of MPT and AGT to repair methylphosphotriester and O6-methylguanine lesions respectively. In eukaryotes, the MPT protein is confined to a select group of fungal species, some of which are major mammalian and plant pathogens. The evolutionary origin of the adaptive response is bacterial and rooted within the Firmicutes phylum. Inter-kingdom horizontal gene transfer between Firmicutes and Ascomycete ancestors introduced the adaptive response into the Fungal kingdom. Our data constitute the first detailed characterization of the molecular mechanism of the adaptive response in a lower eukaryote and has applications for development of novel fungal therapeutics targeting this DNA repair system. PMID:22669901

Adaptability in linkage of soil carbon nutrient cycles - the SEAM model

NASA Astrophysics Data System (ADS)

Wutzler, Thomas; Zaehle, Sönke; Schrumpf, Marion; Ahrens, Bernhard; Reichstein, Markus

2017-04-01

In order to understand the coupling of carbon (C) and nitrogen (N) cycles, it is necessary to understand C and N-use efficiencies of microbial soil organic matter (SOM) decomposition. While important controls of those efficiencies by microbial community adaptations have been shown at the scale of a soil pore, an abstract simplified representation of community adaptations is needed at ecosystem scale. Therefore we developed the soil enzyme allocation model (SEAM), which takes a holistic, partly optimality based approach to describe C and N dynamics at the spatial scale of an ecosystem and time-scales of years and longer. We explicitly modelled community adaptation strategies of resource allocation to extracellular enzymes and enzyme limitations on SOM decomposition. Using SEAM, we explored whether alternative strategy-hypotheses can have strong effects on SOM and inorganic N cycling. Results from prototypical simulations and a calibration to observations of an intensive pasture site showed that the so-called revenue enzyme allocation strategy was most viable. This strategy accounts for microbial adaptations to both, stoichiometry and amount of different SOM resources, and supported the largest microbial biomass under a wide range of conditions. Predictions of the SEAM model were qualitatively similar to models explicitly representing competing microbial groups. With adaptive enzyme allocation under conditions of high C/N ratio of litter inputs, N in formerly locked in slowly degrading SOM pools was made accessible, whereas with high N inputs, N was sequestered in SOM and protected from leaching. The finding that adaptation in enzyme allocation changes C and N-use efficiencies of SOM decomposition implies that concepts of C-nutrient cycle interactions should take account for the effects of such adaptations. This can be done using a holistic optimality approach.

A quantum chemical study of the decomposition of Keggin-structured heteropolyacids.

PubMed

Janik, Michael J; Bardin, Billy B; Davis, Robert J; Neurock, Matthew

2006-03-09

Heterpolyacids (HPAs) demonstrate catalytic activity for oxidative and acid-catalyzed hydrocarbon conversion processes. Deactivation and thermal instability, however, have prevented their widespread use. Herein, ab initio density functional theory is used to study the thermal decomposition of the Keggin molecular HPA structure through the desorption of constitutional water molecules. The overall reaction energy and activation barrier are computed for the overall reaction HnXM12O40-->Hn-2XM12O39+H2O. and subsequently used to predict the effect of HPA composition on thermal stability. For example, the desorption of a constitutional water molecule is found to be increasingly endothermic in the order silicomolybdic acid (H4SiMo12O40)decomposition into a bulk mixed oxide. The equilibrium concentration of defective Keggin units is determined as a function of temperature and water partial pressure. It is concluded that the loss of constitutional water molecules is a plausible deactivation mechanism of the acid catalyst. The intermediate structures along the decomposition path are proposed as possible active sites for oxidation catalysis. The results presented herein provide molecular level insight into the dynamic nature of the heteropolyacid catalyst structure.

Parallel Decomposition of the Fictitious Lagrangian Algorithm and its Accuracy for Molecular Dynamics Simulations of Semiconductors.

NASA Astrophysics Data System (ADS)

Yeh, Mei-Ling

We have performed a parallel decomposition of the fictitious Lagrangian method for molecular dynamics with tight-binding total energy expression into the hypercube computer. This is the first time in literature that the dynamical simulation of semiconducting systems containing more than 512 silicon atoms has become possible with the electrons treated as quantum particles. With the utilization of the Intel Paragon system, our timing analysis predicts that our code is expected to perform realistic simulations on very large systems consisting of thousands of atoms with time requirements of the order of tens of hours. Timing results and performance analysis of our parallel code are presented in terms of calculation time, communication time, and setup time. The accuracy of the fictitious Lagrangian method in molecular dynamics simulation is also investigated, especially the energy conservation of the total energy of ions. We find that the accuracy of the fictitious Lagrangian scheme in small silicon cluster and very large silicon system simulations is good for as long as the simulations proceed, even though we quench the electronic coordinates to the Born-Oppenheimer surface only in the beginning of the run. The kinetic energy of electrons does not increase as time goes on, and the energy conservation of the ionic subsystem remains very good. This means that, as far as the ionic subsystem is concerned, the electrons are on the average in the true quantum ground states. We also tie up some odds and ends regarding a few remaining questions about the fictitious Lagrangian method, such as the difference between the results obtained from the Gram-Schmidt and SHAKE method of orthonormalization, and differences between simulations where the electrons are quenched to the Born -Oppenheimer surface only once compared with periodic quenching.

Three-Component Decomposition of Polarimetric SAR Data Integrating Eigen-Decomposition Results

NASA Astrophysics Data System (ADS)

Lu, Da; He, Zhihua; Zhang, Huan

2018-01-01

This paper presents a novel three-component scattering power decomposition of polarimetric SAR data. There are two problems in three-component decomposition method: volume scattering component overestimation in urban areas and artificially set parameter to be a fixed value. Though volume scattering component overestimation can be partly solved by deorientation process, volume scattering still dominants some oriented urban areas. The speckle-like decomposition results introduced by artificially setting value are not conducive to further image interpretation. This paper integrates the results of eigen-decomposition to solve the aforementioned problems. Two principal eigenvectors are used to substitute the surface scattering model and the double bounce scattering model. The decomposed scattering powers are obtained using a constrained linear least-squares method. The proposed method has been verified using an ESAR PolSAR image, and the results show that the proposed method has better performance in urban area.

Single-pass incremental force updates for adaptively restrained molecular dynamics.

PubMed

Singh, Krishna Kant; Redon, Stephane

2018-03-30

Adaptively restrained molecular dynamics (ARMD) allows users to perform more integration steps in wall-clock time by switching on and off positional degrees of freedoms. This article presents new, single-pass incremental force updates algorithms to efficiently simulate a system using ARMD. We assessed different algorithms for speedup measurements and implemented them in the LAMMPS MD package. We validated the single-pass incremental force update algorithm on four different benchmarks using diverse pair potentials. The proposed algorithm allows us to perform simulation of a system faster than traditional MD in both NVE and NVT ensembles. Moreover, ARMD using the new single-pass algorithm speeds up the convergence of observables in wall-clock time. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Theoretical evidence of the observed kinetic order dependence on temperature during the N(2)O decomposition over Fe-ZSM-5.

PubMed

Guesmi, Hazar; Berthomieu, Dorothee; Bromley, Bryan; Coq, Bernard; Kiwi-Minsker, Lioubov

2010-03-28

The characterization of Fe/ZSM5 zeolite materials, the nature of Fe-sites active in N(2)O direct decomposition, as well as the rate limiting step are still a matter of debate. The mechanism of N(2)O decomposition on the binuclear oxo-hydroxo bridged extraframework iron core site [Fe(II)(mu-O)(mu-OH)Fe(II)](+) inside the ZSM-5 zeolite has been studied by combining theoretical and experimental approaches. The overall calculated path of N(2)O decomposition involves the oxidation of binuclear Fe(II) core sites by N(2)O (atomic alpha-oxygen formation) and the recombination of two surface alpha-oxygen atoms leading to the formation of molecular oxygen. Rate parameters computed using standard statistical mechanics and transition state theory reveal that elementary catalytic steps involved into N(2)O decomposition are strongly dependent on the temperature. This theoretical result was compared to the experimentally observed steady state kinetics of the N(2)O decomposition and temperature-programmed desorption (TPD) experiments. A switch of the reaction order with respect to N(2)O pressure from zero to one occurs at around 800 K suggesting a change of the rate determining step from the alpha-oxygen recombination to alpha-oxygen formation. The TPD results on the molecular oxygen desorption confirmed the mechanism proposed.

Microbial genomics, transcriptomics and proteomics: new discoveries in decomposition research using complementary methods.

PubMed

Baldrian, Petr; López-Mondéjar, Rubén

2014-02-01

Molecular methods for the analysis of biomolecules have undergone rapid technological development in the last decade. The advent of next-generation sequencing methods and improvements in instrumental resolution enabled the analysis of complex transcriptome, proteome and metabolome data, as well as a detailed annotation of microbial genomes. The mechanisms of decomposition by model fungi have been described in unprecedented detail by the combination of genome sequencing, transcriptomics and proteomics. The increasing number of available genomes for fungi and bacteria shows that the genetic potential for decomposition of organic matter is widespread among taxonomically diverse microbial taxa, while expression studies document the importance of the regulation of expression in decomposition efficiency. Importantly, high-throughput methods of nucleic acid analysis used for the analysis of metagenomes and metatranscriptomes indicate the high diversity of decomposer communities in natural habitats and their taxonomic composition. Today, the metaproteomics of natural habitats is of interest. In combination with advanced analytical techniques to explore the products of decomposition and the accumulation of information on the genomes of environmentally relevant microorganisms, advanced methods in microbial ecophysiology should increase our understanding of the complex processes of organic matter transformation.

Dominant modal decomposition method

NASA Astrophysics Data System (ADS)

Dombovari, Zoltan

2017-03-01

The paper deals with the automatic decomposition of experimental frequency response functions (FRF's) of mechanical structures. The decomposition of FRF's is based on the Green function representation of free vibratory systems. After the determination of the impulse dynamic subspace, the system matrix is formulated and the poles are calculated directly. By means of the corresponding eigenvectors, the contribution of each element of the impulse dynamic subspace is determined and the sufficient decomposition of the corresponding FRF is carried out. With the presented dominant modal decomposition (DMD) method, the mode shapes, the modal participation vectors and the modal scaling factors are identified using the decomposed FRF's. Analytical example is presented along with experimental case studies taken from machine tool industry.

Decomposition Mechanism of C5F10O: An Environmentally Friendly Insulation Medium.

PubMed

Zhang, Xiaoxing; Li, Yi; Xiao, Song; Tang, Ju; Tian, Shuangshuang; Deng, Zaitao

2017-09-05

SF 6 , the most widely used electrical-equipment-insulation gas, has serious greenhouse effects. C 5 F 10 O has attracted much attention as an alternative gas in recent two years, but the environmental impact of its decomposition products is unclear. In this work, the decomposition characteristics of C 5 F 10 O were studied based on gas chromatography-mass spectrometry and density functional theory. We found that the amount of decomposition products of C 5 F 10 O, namely, CF 4 , C 2 F 6 , C 3 F 6 , C 3 F 8 , C 4 F 10 , and C 6 F 14 , increased with increased number of discharges. Under a high-energy electric field, the C-C bond of C 5 F 10 O between carbonyl carbon and α-carbon atoms was most likely to break and generate CF 3 CO•, C 3 F 7 • or C 3 F 7 CO•, CF 3 • free radicals. CF 3 •, and C 3 F 7 • free radicals produced by the breakage more easily recombined to form small molecular products. By analyzing the ionization parameters, toxicity, and environmental effects of C 5 F 10 O and its decomposition products, we found that C 5 F 10 O gas mixtures exhibit great decomposition and environmental characteristics with low toxicity, with great potential to replace SF 6 .

Simulation of toluene decomposition in a pulse-periodic discharge operating in a mixture of molecular nitrogen and oxygen

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

Trushkin, A. N.; Kochetov, I. V.

The kinetic model of toluene decomposition in nonequilibrium low-temperature plasma generated by a pulse-periodic discharge operating in a mixture of nitrogen and oxygen is developed. The results of numerical simulation of plasma-chemical conversion of toluene are presented; the main processes responsible for C{sub 6}H{sub 5}CH{sub 3} decomposition are identified; the contribution of each process to total removal of toluene is determined; and the intermediate and final products of C{sub 6}H{sub 5}CH{sub 3} decomposition are identified. It was shown that toluene in pure nitrogen is mostly decomposed in its reactions with metastable N{sub 2}(A{sub 3}{Sigma}{sub u}{sup +}) and N{sub 2}(a Primemore » {sup 1}{Sigma}{sub u}{sup -}) molecules. In the presence of oxygen, in the N{sub 2} : O{sub 2} gas mixture, the largest contribution to C{sub 6}H{sub 5}CH{sub 3} removal is made by the hydroxyl radical OH which is generated in this mixture exclusively due to plasma-chemical reactions between toluene and oxygen decomposition products. Numerical simulation showed the existence of an optimum oxygen concentration in the mixture, at which toluene removal is maximum at a fixed energy deposition.« less

Rank-based decompositions of morphological templates.

PubMed

Sussner, P; Ritter, G X

2000-01-01

Methods for matrix decomposition have found numerous applications in image processing, in particular for the problem of template decomposition. Since existing matrix decomposition techniques are mainly concerned with the linear domain, we consider it timely to investigate matrix decomposition techniques in the nonlinear domain with applications in image processing. The mathematical basis for these investigations is the new theory of rank within minimax algebra. Thus far, only minimax decompositions of rank 1 and rank 2 matrices into outer product expansions are known to the image processing community. We derive a heuristic algorithm for the decomposition of matrices having arbitrary rank.

On the Reaction Mechanism of Acetaldehyde Decomposition on Mo(110)

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

Mei, Donghai; Karim, Ayman M.; Wang, Yong

2012-02-16

The strong Mo-O bond strength provides promising reactivity of Mo-based catalysts for the deoxygenation of biomass-derived oxygenates. Combining the novel dimer saddle point searching method with periodic spin-polarized density functional theory calculations, we investigated the reaction pathways of a acetaldehyde decomposition on the clean Mo(110) surface. Two reaction pathways were identified, a selective deoxygenation and a nonselective fragmentation pathways. We found that acetaldehyde preferentially adsorbs at the pseudo 3-fold hollow site in the η2(C,O) configuration on Mo(110). Among four possible bond (β-C-H, γ-C-H, C-O and C-C) cleavages, the initial decomposition of the adsorbed acetaldehyde produces either ethylidene via the C-Omore » bond scission or acetyl via the β-C-H bond scission while the C-C and the γ-C-H bond cleavages of acetaldehyde leading to the formation of methyl (and formyl) and formylmethyl are unlikely. Further dehydrogenations of ethylidene into either ethylidyne or vinyl are competing and very facile with low activation barriers of 0.24 and 0.31 eV, respectively. Concurrently, the formed acetyl would deoxygenate into ethylidyne via the C-O cleavage rather than breaking the C-C or the C-H bonds. The selective deoxygenation of acetaldehyde forming ethylene is inhibited by relatively weaker hydrogenation capability of the Mo(110) surface. Instead, the nonselective pathway via vinyl and vinylidene dehydrogenations to ethynyl as the final hydrocarbon fragment is kinetically favorable. On the other hand, the strong interaction between ethylene and the Mo(110) surface also leads to ethylene decomposition instead of desorption into the gas phase. This work was financially supported by the National Advanced Biofuels Consortium (NABC). Computing time was granted by a user project (emsl42292) at the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). This work was financially

Three-pattern decomposition of global atmospheric circulation: part I—decomposition model and theorems

NASA Astrophysics Data System (ADS)

Hu, Shujuan; Chou, Jifan; Cheng, Jianbo

2018-04-01

In order to study the interactions between the atmospheric circulations at the middle-high and low latitudes from the global perspective, the authors proposed the mathematical definition of three-pattern circulations, i.e., horizontal, meridional and zonal circulations with which the actual atmospheric circulation is expanded. This novel decomposition method is proved to accurately describe the actual atmospheric circulation dynamics. The authors used the NCEP/NCAR reanalysis data to calculate the climate characteristics of those three-pattern circulations, and found that the decomposition model agreed with the observed results. Further dynamical analysis indicates that the decomposition model is more accurate to capture the major features of global three dimensional atmospheric motions, compared to the traditional definitions of Rossby wave, Hadley circulation and Walker circulation. The decomposition model for the first time realized the decomposition of global atmospheric circulation using three orthogonal circulations within the horizontal, meridional and zonal planes, offering new opportunities to study the large-scale interactions between the middle-high latitudes and low latitudes circulations.

Stress-induced activation of decomposition of organic explosives: a simple way to understand.

PubMed

Zhang, Chaoyang

2013-01-01

We provide a very simply way to understand the stress-induced activation of decomposition of organic explosives by taking the simplest explosive molecule nitromethane (NM) as a prototype and constraining one or two NM molecules in a shell to represent the condensed phrase of NM against the stress caused by tension and compression, sliding and rotational shear, and imperfection. The results show that the stress loaded on NM molecule can always reduce the barriers of its decomposition. We think the origin of this stress-induced activation is due to the increased repulsive intra- and/or inter- molecular interaction potentials in explosives resulted from the stress, whose release is positive to accelerate the decomposition. Besides, by these models, we can understand that the explosives in gaseous state are easier to analyze than those in condensed state and the voids in condensed explosives make them more sensitive to external stimuli relative to the perfect crystals.

Understanding paper degradation: identification of products of cellulosic paper decomposition at the wet-dry "tideline" interface using GC-MS.

PubMed

Sladkevich, Sergey; Dupont, Anne-Laurence; Sablier, Michel; Seghouane, Dalila; Cole, Richard B

2016-11-01

Cellulose paper degradation products forming in the "tideline" area at the wet-dry interface of pure cellulose paper were analyzed using gas chromatography-electron ionization-mass spectrometry (GC-EI-MS) and high-resolution electrospray ionization-mass spectrometry (ESI-MS, LTQ Orbitrap) techniques. Different extraction protocols were employed in order to solubilize the products of oxidative cellulose decomposition, i.e., a direct solvent extraction or a more laborious chromophore release and identification (CRI) technique aiming to reveal products responsible for paper discoloration in the tideline area. Several groups of low molecular weight compounds were identified, suggesting a complex pathway of cellulose decomposition in the tidelines formed at the cellulose-water-oxygen interface. Our findings, namely the appearance of a wide range of linear saturated carboxylic acids (from formic to nonanoic), support the oxidative autocatalytic mechanism of decomposition. In addition, the identification of several furanic compounds (which can be, in part, responsible for paper discoloration) plus anhydro carbohydrate derivatives sheds more light on the pathways of cellulose decomposition. Most notably, the mechanisms of tideline formation in the presence of molecular oxygen appear surprisingly similar to pathways of pyrolytic cellulose degradation. More complex chromophore compounds were not detected in this study, thereby revealing a difference between this short-term tideline experiment and longer-term cellulose aging.

Plant adaptation to low atmospheric pressures: potential molecular responses

NASA Technical Reports Server (NTRS)

Ferl, Robert J.; Schuerger, Andrew C.; Paul, Anna-Lisa; Gurley, William B.; Corey, Kenneth; Bucklin, Ray

2002-01-01

There is an increasing realization that it may be impossible to attain Earth normal atmospheric pressures in orbital, lunar, or Martian greenhouses, simply because the construction materials do not exist to meet the extraordinary constraints imposed by balancing high engineering requirements against high lift costs. This equation essentially dictates that NASA have in place the capability to grow plants at reduced atmospheric pressure. Yet current understanding of plant growth at low pressures is limited to just a few experiments and relatively rudimentary assessments of plant vigor and growth. The tools now exist, however, to make rapid progress toward understanding the fundamental nature of plant responses and adaptations to low pressures, and to develop strategies for mitigating detrimental effects by engineering the growth conditions or by engineering the plants themselves. The genomes of rice and the model plant Arabidopsis thaliana have recently been sequenced in their entirety, and public sector and commercial DNA chips are becoming available such that thousands of genes can be assayed at once. A fundamental understanding of plant responses and adaptation to low pressures can now be approached and translated into procedures and engineering considerations to enhance plant growth at low atmospheric pressures. In anticipation of such studies, we present here the background arguments supporting these contentions, as well as informed speculation about the kinds of molecular physiological responses that might be expected of plants in low-pressure environments.

Repeated decompositions reveal the stability of infomax decomposition of fMRI data

PubMed Central

Duann, Jeng-Ren; Jung, Tzyy-Ping; Sejnowski, Terrence J.; Makeig, Scott

2010-01-01

In this study, we decomposed 12 fMRI data sets from six subjects each 101 times using the infomax algorithm. The first decomposition was taken as a reference decomposition; the others were used to form a component matrix of 100 by 100 components. Equivalence relations between components in this matrix, defined as maximum spatial correlations to the components of the reference decomposition, were found by the Hungarian sorting method and used to form 100 equivalence classes for each data set. We then tested the reproducibility of the matched components in the equivalence classes using uncertainty measures based on component distributions, time courses, and ROC curves. Infomax ICA rarely failed to derive nearly the same components in different decompositions. Very few components per data set were poorly reproduced, even using vector angle uncertainty measures stricter than correlation and detection theory measures. PMID:17281453

Molecular mechanisms underlying phosphate sensing, signaling, and adaptation in plants.

PubMed

Zhang, Zhaoliang; Liao, Hong; Lucas, William J

2014-03-01

As an essential plant macronutrient, the low availability of phosphorus (P) in most soils imposes serious limitation on crop production. Plants have evolved complex responsive and adaptive mechanisms for acquisition, remobilization and recycling of phosphate (Pi) to maintain P homeostasis. Spatio-temporal molecular, physiological, and biochemical Pi deficiency responses developed by plants are the consequence of local and systemic sensing and signaling pathways. Pi deficiency is sensed locally by the root system where hormones serve as important signaling components in terms of developmental reprogramming, leading to changes in root system architecture. Root-to-shoot and shoot-to-root signals, delivered through the xylem and phloem, respectively, involving Pi itself, hormones, miRNAs, mRNAs, and sucrose, serve to coordinate Pi deficiency responses at the whole-plant level. A combination of chromatin remodeling, transcriptional and posttranslational events contribute to globally regulating a wide range of Pi deficiency responses. In this review, recent advances are evaluated in terms of progress toward developing a comprehensive understanding of the molecular events underlying control over P homeostasis. Application of this knowledge, in terms of developing crop plants having enhanced attributes for P use efficiency, is discussed from the perspective of agricultural sustainability in the face of diminishing global P supplies. © 2014 Institute of Botany, Chinese Academy of Sciences.

Hamiltonian adaptive resolution molecular dynamics simulation of infrared dielectric functions of liquids

NASA Astrophysics Data System (ADS)

Wang, C. C.; Tan, J. Y.; Liu, L. H.

2018-05-01

Hamiltonian adaptive resolution scheme (H-AdResS), which allows to simulate materials by treating different domains of the system at different levels of resolution, is a recently proposed atomistic/coarse-grained multiscale model. In this work, a scheme to calculate the dielectric functions of liquids on account of H-AdResS is presented. In the proposed H-AdResS dielectric-function calculation scheme (DielectFunctCalS), the corrected molecular dipole moments are calculated by multiplying molecular dipole moment by the weighting fraction of the molecular mapping point. As the widths of all-atom and hybrid regions show different degrees of influence on the dielectric functions, a prefactor is multiplied to eliminate the effects of all-atom and hybrid region widths. Since one goal of using the H-AdResS method is to reduce computational costs, widths of the all-atom region and the hybrid region can be reduced considering that the coarse-grained simulation is much more timesaving compared to atomistic simulation. Liquid water and ethanol are taken as test cases to validate the DielectFunctCalS. The H-AdResS DielectFunctCalS results are in good agreement with all-atom molecular dynamics simulations. The accuracy of the H-AdResS results, together with all-atom molecular dynamics results, depends heavily on the choice of the force field and force field parameters. The H-AdResS DielectFunctCalS allows us to calculate the dielectric functions of macromolecule systems with high efficiency and makes the dielectric function calculations of large biomolecular systems possible.

Molecular Adaptation Mechanisms Employed by Ethanologenic Bacteria in Response to Lignocellulose-derived Inhibitory Compounds

PubMed Central

Ibraheem, Omodele; Ndimba, Bongani K.

2013-01-01

Current international interest in finding alternative sources of energy to the diminishing supplies of fossil fuels has encouraged research efforts in improving biofuel production technologies. In countries which lack sufficient food, the use of sustainable lignocellulosic feedstocks, for the production of bioethanol, is an attractive option. In the pre-treatment of lignocellulosic feedstocks for ethanol production, various chemicals and/or enzymatic processes are employed. These methods generally result in a range of fermentable sugars, which are subjected to microbial fermentation and distillation to produce bioethanol. However, these methods also produce compounds that are inhibitory to the microbial fermentation process. These compounds include products of sugar dehydration and lignin depolymerisation, such as organic acids, derivatised furaldehydes and phenolic acids. These compounds are known to have a severe negative impact on the ethanologenic microorganisms involved in the fermentation process by compromising the integrity of their cell membranes, inhibiting essential enzymes and negatively interact with their DNA/RNA. It is therefore important to understand the molecular mechanisms of these inhibitions, and the mechanisms by which these microorganisms show increased adaptation to such inhibitors. Presented here is a concise overview of the molecular adaptation mechanisms of ethanologenic bacteria in response to lignocellulose-derived inhibitory compounds. These include general stress response and tolerance mechanisms, which are typically those that maintain intracellular pH homeostasis and cell membrane integrity, activation/regulation of global stress responses and inhibitor substrate-specific degradation pathways. We anticipate that understanding these adaptation responses will be essential in the design of 'intelligent' metabolic engineering strategies for the generation of hyper-tolerant fermentation bacteria strains. PMID:23847442

Investigating carbon dynamics in Siberian peat bogs using molecular-level analyses

NASA Astrophysics Data System (ADS)

Kaiser, K.; Benner, R. H.

2013-12-01

Total hydrolysable carbohydrates, and lignin and cutin acid compounds were analyzed in peat cores collected 56.8 N (SIB04), 58.4 N (SIB06), 63.8 N (G137) and 66.5 N (E113) in the Western Siberian Lowland to investigate vegetation, chemical compositions and the stage of decomposition. Sphagnum mosses dominated peatland vegetation in all four cores. High-resolution molecular analyses revealed rapid vegetation changes on timescales of 50-200 years in the southern cores Sib4 and Sib6. Syringyl and vanillyl (S/V) ratios and cutin acids indicated these vegetation changes were due to varying inputs of angiosperm and gymnosperm and root material. In the G137 and E113 cores lichens briefly replaced sphagnum mosses and vascular plants. Molecular decomposition indicators used in this study tracked the decomposition of different organic constituents of peat organic matter. The carbohydrate decomposition index was sensitive to the polysaccharide component of all peat-forming plants, whereas acid/aldehyde ratios of S and V phenols (Ac/AlS,V) followed the lignin component of vascular plants. Low carbohydrate decomposition indices in peat layers corresponded well with elevated (Ad/Al)S,V ratios. This suggested both classes of biochemicals were simultaneously decomposed, and decomposition processes were associated with extensive total mass loss in these ombrotrophic systems. Selective decomposition or transformation of lignin was observed in the permafrost-influenced northern cores G137 and E113. Both cores exhibited the highest (Ad/Al)S,V ratios, almost four-fold higher than measured in peat-forming plants. The extent of decomposition in the four peat cores did not uniformly increase with age, but showed episodic extensive decomposition events. Variable decomposition events independent of climatic conditions and vegetation shifts highlight the complexity of peatland dynamics.

A comparative study of cold- and warm-adapted Endonucleases A using sequence analyses and molecular dynamics simulations.

PubMed

Michetti, Davide; Brandsdal, Bjørn Olav; Bon, Davide; Isaksen, Geir Villy; Tiberti, Matteo; Papaleo, Elena

2017-01-01

The psychrophilic and mesophilic endonucleases A (EndA) from Aliivibrio salmonicida (VsEndA) and Vibrio cholera (VcEndA) have been studied experimentally in terms of the biophysical properties related to thermal adaptation. The analyses of their static X-ray structures was no sufficient to rationalize the determinants of their adaptive traits at the molecular level. Thus, we used Molecular Dynamics (MD) simulations to compare the two proteins and unveil their structural and dynamical differences. Our simulations did not show a substantial increase in flexibility in the cold-adapted variant on the nanosecond time scale. The only exception is a more rigid C-terminal region in VcEndA, which is ascribable to a cluster of electrostatic interactions and hydrogen bonds, as also supported by MD simulations of the VsEndA mutant variant where the cluster of interactions was introduced. Moreover, we identified three additional amino acidic substitutions through multiple sequence alignment and the analyses of MD-based protein structure networks. In particular, T120V occurs in the proximity of the catalytic residue H80 and alters the interaction with the residue Y43, which belongs to the second coordination sphere of the Mg2+ ion. This makes T120V an amenable candidate for future experimental mutagenesis.

Dictionary-Based Tensor Canonical Polyadic Decomposition

NASA Astrophysics Data System (ADS)

Cohen, Jeremy Emile; Gillis, Nicolas

2018-04-01

To ensure interpretability of extracted sources in tensor decomposition, we introduce in this paper a dictionary-based tensor canonical polyadic decomposition which enforces one factor to belong exactly to a known dictionary. A new formulation of sparse coding is proposed which enables high dimensional tensors dictionary-based canonical polyadic decomposition. The benefits of using a dictionary in tensor decomposition models are explored both in terms of parameter identifiability and estimation accuracy. Performances of the proposed algorithms are evaluated on the decomposition of simulated data and the unmixing of hyperspectral images.

Molecular adaptation of a plant-bacterium outer membrane protease towards plague virulence factor Pla

PubMed Central

2011-01-01

Background Omptins are a family of outer membrane proteases that have spread by horizontal gene transfer in Gram-negative bacteria that infect vertebrates or plants. Despite structural similarity, the molecular functions of omptins differ in a manner that reflects the life style of their host bacteria. To simulate the molecular adaptation of omptins, we applied site-specific mutagenesis to make Epo of the plant pathogenic Erwinia pyrifoliae exhibit virulence-associated functions of its close homolog, the plasminogen activator Pla of Yersinia pestis. We addressed three virulence-associated functions exhibited by Pla, i.e., proteolytic activation of plasminogen, proteolytic degradation of serine protease inhibitors, and invasion into human cells. Results Pla and Epo expressed in Escherichia coli are both functional endopeptidases and cleave human serine protease inhibitors, but Epo failed to activate plasminogen and to mediate invasion into a human endothelial-like cell line. Swapping of ten amino acid residues at two surface loops of Pla and Epo introduced plasminogen activation capacity in Epo and inactivated the function in Pla. We also compared the structure of Pla and the modeled structure of Epo to analyze the structural variations that could rationalize the different proteolytic activities. Epo-expressing bacteria managed to invade human cells only after all extramembranous residues that differ between Pla and Epo and the first transmembrane β-strand had been changed. Conclusions We describe molecular adaptation of a protease from an environmental setting towards a virulence factor detrimental for humans. Our results stress the evolvability of bacterial β-barrel surface structures and the environment as a source of progenitor virulence molecules of human pathogens. PMID:21310089

Domain decomposition methods in computational fluid dynamics

NASA Technical Reports Server (NTRS)

Gropp, William D.; Keyes, David E.

1991-01-01

The divide-and-conquer paradigm of iterative domain decomposition, or substructuring, has become a practical tool in computational fluid dynamic applications because of its flexibility in accommodating adaptive refinement through locally uniform (or quasi-uniform) grids, its ability to exploit multiple discretizations of the operator equations, and the modular pathway it provides towards parallelism. These features are illustrated on the classic model problem of flow over a backstep using Newton's method as the nonlinear iteration. Multiple discretizations (second-order in the operator and first-order in the preconditioner) and locally uniform mesh refinement pay dividends separately, and they can be combined synergistically. Sample performance results are included from an Intel iPSC/860 hypercube implementation.

Molecular PET imaging for biology-guided adaptive radiotherapy of head and neck cancer.

PubMed

Hoeben, Bianca A W; Bussink, Johan; Troost, Esther G C; Oyen, Wim J G; Kaanders, Johannes H A M

2013-10-01

Integration of molecular imaging PET techniques into therapy selection strategies and radiation treatment planning for head and neck squamous cell carcinoma (HNSCC) can serve several purposes. First, pre-treatment assessments can steer decisions about radiotherapy modifications or combinations with other modalities. Second, biology-based objective functions can be introduced to the radiation treatment planning process by co-registration of molecular imaging with planning computed tomography (CT) scans. Thus, customized heterogeneous dose distributions can be generated with escalated doses to tumor areas where radiotherapy resistance mechanisms are most prevalent. Third, monitoring of temporal and spatial variations in these radiotherapy resistance mechanisms early during the course of treatment can discriminate responders from non-responders. With such information available shortly after the start of treatment, modifications can be implemented or the radiation treatment plan can be adapted tailing the biological response pattern. Currently, these strategies are in various phases of clinical testing, mostly in single-center studies. Further validation in multicenter set-up is needed. Ultimately, this should result in availability for routine clinical practice requiring stable production and accessibility of tracers, reproducibility and standardization of imaging and analysis methods, as well as general availability of knowledge and expertise. Small studies employing adaptive radiotherapy based on functional dynamics and early response mechanisms demonstrate promising results. In this context, we focus this review on the widely used PET tracer (18)F-FDG and PET tracers depicting hypoxia and proliferation; two well-known radiation resistance mechanisms.

Elucidating electrolyte decomposition under electron-rich environments at the lithium-metal anode.

PubMed

Camacho-Forero, Luis E; Balbuena, Perla B

2017-11-22

The lithium metal anode is one of the key components of the lithium-sulfur (Li-S) batteries, which are considered one of the most promising candidates for the next generation of battery systems. However, one of the main challenges that have prevented Li-metal anodes from becoming feasible to be used in commercial batteries is the continuous decomposition of the electrolyte due to its high reactivity, which leads to the formation of solid-electrolyte interphase (SEI) layers. The properties of the SEI can dramatically affect the performance of the batteries. Thus, a rigorous understanding of the electrolyte decomposition is crucial to elucidate improvements in performance of the Li-S technology. In this work, using density functional theory (DFT) and ab initio molecular dynamics simulations (AIMD), we investigate the effect of electron-rich environments on the decomposition mechanism of electrolyte species in pure 1,2-dimethoxyethane (DME) solvent and 1 M lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) and lithium bis(fluorosulfonyl)imide (LiFSI) salt solutions. It is found that systems with pure DME require an average environment of at least ∼0.9 |e| per molecule for a DME to decompose into CH 3 O - and C 2 H 4 2- via a 4-electron transfer. In the case of mixtures, the salts are very prone to react with any excess of electrons. In addition, DME dehydrogenation due to reactions with fragments coming from the salt decompositions was detected. Formation of oligomer anionic species from DME and salt fragments were also identified from the AIMD simulations. Finally, the thermodynamics and kinetics of the most relevant electrolyte decomposition reactions were characterized. DME decomposition reactions predicted from the AIMD simulations were found to be thermodynamically favorable under exposure to Li atoms and/or by reactions with salt fragments. In most cases, these reactions were shown to have low to moderate activation barriers.

Near-infrared–driven decomposition of metal precursors yields amorphous electrocatalytic films

PubMed Central

Salvatore, Danielle A.; Dettelbach, Kevan E.; Hudkins, Jesse R.; Berlinguette, Curtis P.

2015-01-01

Amorphous metal-based films lacking long-range atomic order have found utility in applications ranging from electronics applications to heterogeneous catalysis. Notwithstanding, there is a limited set of fabrication methods available for making amorphous films, particularly in the absence of a conducting substrate. We introduce herein a scalable preparative method for accessing oxidized and reduced phases of amorphous films that involves the efficient decomposition of molecular precursors, including simple metal salts, by exposure to near-infrared (NIR) radiation. The NIR-driven decomposition process provides sufficient localized heating to trigger the liberation of the ligand from solution-deposited precursors on substrates, but insufficient thermal energy to form crystalline phases. This method provides access to state-of-the-art electrocatalyst films, as demonstrated herein for the electrolysis of water, and extends the scope of usable substrates to include nonconducting and temperature-sensitive platforms. PMID:26601148

Targeting the adaptive molecular landscape of castration-resistant prostate cancer

PubMed Central

Wyatt, Alexander W; Gleave, Martin E

2015-01-01

Castration and androgen receptor (AR) pathway inhibitors induce profound and sustained responses in advanced prostate cancer. However, the inevitable recurrence is associated with reactivation of the AR and progression to a more aggressive phenotype termed castration-resistant prostate cancer (CRPC). AR reactivation can occur directly through genomic modification of the AR gene, or indirectly via co-factor and co-chaperone deregulation. This mechanistic heterogeneity is further complicated by the stress-driven induction of a myriad of overlapping cellular survival pathways. In this review, we describe the heterogeneous and evolvable molecular landscape of CRPC and explore recent successes and failures of therapeutic strategies designed to target AR reactivation and adaptive survival pathways. We also discuss exciting areas of burgeoning anti-tumour research, and their potential to improve the survival and management of patients with CRPC. PMID:25896606

Free energy landscapes of short peptide chains using adaptively biased molecular dynamics

NASA Astrophysics Data System (ADS)

Karpusenka, Vadzim; Babin, Volodymyr; Roland, Christopher; Sagui, Celeste

2009-03-01

We present the results of a computational study of the free energy landscapes of short polypeptide chains, as a function of several reaction coordinates meant to distinguish between several known types of helices. The free energy landscapes were calculated using the recently developed adaptively biased molecular dynamics method followed up with equilibrium ``umbrella correction'' runs. Specific polypeptides investigated include small chains of pure and mixed alanine, glutamate, leucine, lysine and methionine (all amino acids with strong helix-forming propensities), as well as glycine, proline(having a low helix forming propensities), tyrosine, serine and arginine. Our results are consistent with the existing experimental and other theoretical evidence.

Structural flexibility and protein adaptation to temperature: Molecular dynamics analysis of malate dehydrogenases of marine molluscs.

PubMed

Dong, Yun-Wei; Liao, Ming-Ling; Meng, Xian-Liang; Somero, George N

2018-02-06

Orthologous proteins of species adapted to different temperatures exhibit differences in stability and function that are interpreted to reflect adaptive variation in structural "flexibility." However, quantifying flexibility and comparing flexibility across proteins has remained a challenge. To address this issue, we examined temperature effects on cytosolic malate dehydrogenase (cMDH) orthologs from differently thermally adapted congeners of five genera of marine molluscs whose field body temperatures span a range of ∼60 °C. We describe consistent patterns of convergent evolution in adaptation of function [temperature effects on K M of cofactor (NADH)] and structural stability (rate of heat denaturation of activity). To determine how these differences depend on flexibilities of overall structure and of regions known to be important in binding and catalysis, we performed molecular dynamics simulation (MDS) analyses. MDS analyses revealed a significant negative correlation between adaptation temperature and heat-induced increase of backbone atom movements [root mean square deviation (rmsd) of main-chain atoms]. Root mean square fluctuations (RMSFs) of movement by individual amino acid residues varied across the sequence in a qualitatively similar pattern among orthologs. Regions of sequence involved in ligand binding and catalysis-termed mobile regions 1 and 2 (MR1 and MR2), respectively-showed the largest values for RMSF. Heat-induced changes in RMSF values across the sequence and, importantly, in MR1 and MR2 were greatest in cold-adapted species. MDS methods are shown to provide powerful tools for examining adaptation of enzymes by providing a quantitative index of protein flexibility and identifying sequence regions where adaptive change in flexibility occurs.

Critical analysis of nitramine decomposition data: Activation energies and frequency factors for HMX and RDX decomposition

NASA Technical Reports Server (NTRS)

Schroeder, M. A.

1980-01-01

A summary of a literature review on thermal decomposition of HMX and RDX is presented. The decomposition apparently fits first order kinetics. Recommended values for Arrhenius parameters for HMX and RDX decomposition in the gaseous and liquid phases and for decomposition of RDX in solution in TNT are given. The apparent importance of autocatalysis is pointed out, as are some possible complications that may be encountered in interpreting extending or extrapolating kinetic data for these compounds from measurements carried out below their melting points to the higher temperatures and pressure characteristic of combustion.

Active listening room compensation for massive multichannel sound reproduction systems using wave-domain adaptive filtering.

PubMed

Spors, Sascha; Buchner, Herbert; Rabenstein, Rudolf; Herbordt, Wolfgang

2007-07-01

The acoustic theory for multichannel sound reproduction systems usually assumes free-field conditions for the listening environment. However, their performance in real-world listening environments may be impaired by reflections at the walls. This impairment can be reduced by suitable compensation measures. For systems with many channels, active compensation is an option, since the compensating waves can be created by the reproduction loudspeakers. Due to the time-varying nature of room acoustics, the compensation signals have to be determined by an adaptive system. The problems associated with the successful operation of multichannel adaptive systems are addressed in this contribution. First, a method for decoupling the adaptation problem is introduced. It is based on a generalized singular value decomposition and is called eigenspace adaptive filtering. Unfortunately, it cannot be implemented in its pure form, since the continuous adaptation of the generalized singular value decomposition matrices to the variable room acoustics is numerically very demanding. However, a combination of this mathematical technique with the physical description of wave propagation yields a realizable multichannel adaptation method with good decoupling properties. It is called wave domain adaptive filtering and is discussed here in the context of wave field synthesis.

Residue decomposition of submodel of WEPS

USDA-ARS?s Scientific Manuscript database

The Residue Decomposition submodel of the Wind Erosion Prediction System (WEPS) simulates the decrease in crop residue biomass due to microbial activity. The decomposition process is modeled as a first-order reaction with temperature and moisture as driving variables. Decomposition is a function of ...

Hydrazine decomposition and other reactions

NASA Technical Reports Server (NTRS)

Armstrong, Warren E. (Inventor); La France, Donald S. (Inventor); Voge, Hervey H. (Inventor)

1978-01-01

This invention relates to the catalytic decomposition of hydrazine, catalysts useful for this decomposition and other reactions, and to reactions in hydrogen atmospheres generally using carbon-containing catalysts.

Decomposition of Multi-player Games

NASA Astrophysics Data System (ADS)

Zhao, Dengji; Schiffel, Stephan; Thielscher, Michael

Research in General Game Playing aims at building systems that learn to play unknown games without human intervention. We contribute to this endeavour by generalising the established technique of decomposition from AI Planning to multi-player games. To this end, we present a method for the automatic decomposition of previously unknown games into independent subgames, and we show how a general game player can exploit a successful decomposition for game tree search.

Data-adaptive harmonic spectra and multilayer Stuart-Landau models

NASA Astrophysics Data System (ADS)

Chekroun, Mickaël D.; Kondrashov, Dmitri

2017-09-01

Harmonic decompositions of multivariate time series are considered for which we adopt an integral operator approach with periodic semigroup kernels. Spectral decomposition theorems are derived that cover the important cases of two-time statistics drawn from a mixing invariant measure. The corresponding eigenvalues can be grouped per Fourier frequency and are actually given, at each frequency, as the singular values of a cross-spectral matrix depending on the data. These eigenvalues obey, furthermore, a variational principle that allows us to define naturally a multidimensional power spectrum. The eigenmodes, as far as they are concerned, exhibit a data-adaptive character manifested in their phase which allows us in turn to define a multidimensional phase spectrum. The resulting data-adaptive harmonic (DAH) modes allow for reducing the data-driven modeling effort to elemental models stacked per frequency, only coupled at different frequencies by the same noise realization. In particular, the DAH decomposition extracts time-dependent coefficients stacked by Fourier frequency which can be efficiently modeled—provided the decay of temporal correlations is sufficiently well-resolved—within a class of multilayer stochastic models (MSMs) tailored here on stochastic Stuart-Landau oscillators. Applications to the Lorenz 96 model and to a stochastic heat equation driven by a space-time white noise are considered. In both cases, the DAH decomposition allows for an extraction of spatio-temporal modes revealing key features of the dynamics in the embedded phase space. The multilayer Stuart-Landau models (MSLMs) are shown to successfully model the typical patterns of the corresponding time-evolving fields, as well as their statistics of occurrence.

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

Communication: Adaptive boundaries in multiscale simulations

NASA Astrophysics Data System (ADS)

Wagoner, Jason A.; Pande, Vijay S.

2018-04-01

Combined-resolution simulations are an effective way to study molecular properties across a range of length and time scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size and/or shape) as the simulation progresses. The number of degrees of freedom required to accurately represent even a simple molecular process can vary by several orders of magnitude throughout the course of a simulation, and adaptive boundaries react to these changes to include an appropriate but not excessive amount of detail. Here, we derive the Hamiltonian and distribution function for such a molecular simulation. We also design an algorithm that can efficiently sample the boundary as a new coordinate of the system. We apply this framework to a mixed explicit/continuum simulation of a peptide in solvent. We use this example to discuss the conditions necessary for a successful implementation of adaptive boundaries that is both efficient and accurate in reproducing molecular properties.

Elucidating electrolyte decomposition under electron-rich environments at the lithium-metal anode

DOE PAGES

Camacho-Forero, Luis E.; Balbuena, Perla B.

2017-11-07

The lithium metal anode is one of the key components of the lithium–sulfur (Li–S) batteries, which are considered one of the most promising candidates for the next generation of battery systems. However, one of the main challenges that have prevented Li-metal anodes from becoming feasible to be used in commercial batteries is the continuous decomposition of the electrolyte due to its high reactivity, which leads to the formation of solid–electrolyte interphase (SEI) layers. The properties of the SEI can dramatically affect the performance of the batteries. Thus, a rigorous understanding of the electrolyte decomposition is crucial to elucidate improvements inmore » performance of the Li–S technology. Here, in this work, using density functional theory (DFT) and ab initio molecular dynamics simulations (AIMD), we investigate the effect of electron-rich environments on the decomposition mechanism of electrolyte species in pure 1,2-dimethoxyethane (DME) solvent and 1 M lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) and lithium bis(fluorosulfonyl)imide (LiFSI) salt solutions. It is found that systems with pure DME require an average environment of at least ~0.9 |e| per molecule for a DME to decompose into CH 3O - and C 2H 4 2-via a 4-electron transfer. In the case of mixtures, the salts are very prone to react with any excess of electrons. In addition, DME dehydrogenation due to reactions with fragments coming from the salt decompositions was detected. Formation of oligomer anionic species from DME and salt fragments were also identified from the AIMD simulations. Finally, the thermodynamics and kinetics of the most relevant electrolyte decomposition reactions were characterized. DME decomposition reactions predicted from the AIMD simulations were found to be thermodynamically favorable under exposure to Li atoms and/or by reactions with salt fragments. Lastly, in most cases, these reactions were shown to have low to moderate activation barriers.« less

Elucidating electrolyte decomposition under electron-rich environments at the lithium-metal anode

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

Camacho-Forero, Luis E.; Balbuena, Perla B.

The lithium metal anode is one of the key components of the lithium–sulfur (Li–S) batteries, which are considered one of the most promising candidates for the next generation of battery systems. However, one of the main challenges that have prevented Li-metal anodes from becoming feasible to be used in commercial batteries is the continuous decomposition of the electrolyte due to its high reactivity, which leads to the formation of solid–electrolyte interphase (SEI) layers. The properties of the SEI can dramatically affect the performance of the batteries. Thus, a rigorous understanding of the electrolyte decomposition is crucial to elucidate improvements inmore » performance of the Li–S technology. Here, in this work, using density functional theory (DFT) and ab initio molecular dynamics simulations (AIMD), we investigate the effect of electron-rich environments on the decomposition mechanism of electrolyte species in pure 1,2-dimethoxyethane (DME) solvent and 1 M lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) and lithium bis(fluorosulfonyl)imide (LiFSI) salt solutions. It is found that systems with pure DME require an average environment of at least ~0.9 |e| per molecule for a DME to decompose into CH 3O - and C 2H 4 2-via a 4-electron transfer. In the case of mixtures, the salts are very prone to react with any excess of electrons. In addition, DME dehydrogenation due to reactions with fragments coming from the salt decompositions was detected. Formation of oligomer anionic species from DME and salt fragments were also identified from the AIMD simulations. Finally, the thermodynamics and kinetics of the most relevant electrolyte decomposition reactions were characterized. DME decomposition reactions predicted from the AIMD simulations were found to be thermodynamically favorable under exposure to Li atoms and/or by reactions with salt fragments. Lastly, in most cases, these reactions were shown to have low to moderate activation barriers.« less

Content-Adaptive Sketch Portrait Generation by Decompositional Representation Learning.

PubMed

Zhang, Dongyu; Lin, Liang; Chen, Tianshui; Wu, Xian; Tan, Wenwei; Izquierdo, Ebroul

2017-01-01

Sketch portrait generation benefits a wide range of applications such as digital entertainment and law enforcement. Although plenty of efforts have been dedicated to this task, several issues still remain unsolved for generating vivid and detail-preserving personal sketch portraits. For example, quite a few artifacts may exist in synthesizing hairpins and glasses, and textural details may be lost in the regions of hair or mustache. Moreover, the generalization ability of current systems is somewhat limited since they usually require elaborately collecting a dictionary of examples or carefully tuning features/components. In this paper, we present a novel representation learning framework that generates an end-to-end photo-sketch mapping through structure and texture decomposition. In the training stage, we first decompose the input face photo into different components according to their representational contents (i.e., structural and textural parts) by using a pre-trained convolutional neural network (CNN). Then, we utilize a branched fully CNN for learning structural and textural representations, respectively. In addition, we design a sorted matching mean square error metric to measure texture patterns in the loss function. In the stage of sketch rendering, our approach automatically generates structural and textural representations for the input photo and produces the final result via a probabilistic fusion scheme. Extensive experiments on several challenging benchmarks suggest that our approach outperforms example-based synthesis algorithms in terms of both perceptual and objective metrics. In addition, the proposed method also has better generalization ability across data set without additional training.

Two-dimensional NMR spectroscopy links structural moieties of soil organic matter to the temperature sensitivity of its decomposition

NASA Astrophysics Data System (ADS)

Soucemarianadin, Laure; Erhagen, Björn; Öquist, Mats; Nilsson, Mats; Schleucher, Jürgen

2015-04-01

Soil organic matter (SOM) represents a huge carbon pool, specifically in boreal ecosystems. Warming-induced release of large amounts of CO2 from the soil carbon pool might become a significant exacerbating feedback to global warming, if decomposition rates of boreal soils were more sensitive to increased temperatures. Despite a large number of studies dedicated to the topic, it has proven difficult to elucidate how the organo-chemical composition of SOM influences its decomposition, or its quality as a substrate for microbial metabolism. A great part of this challenge results from our inability to achieve a detailed characterization of the complex composition of SOM on the level of molecular structural moieties. 13C nuclear magnetic resonance (NMR) spectroscopy is a common tool to characterize SOM. However, SOM is a very complex mixture and the chemical shift regions distinguished in the 13C NMR spectra often represent many different molecular fragments. For example, in the carbohydrates region, signals of all monosaccharides present in many different polymers overlap. This overlap thwarts attempts to identify molecular moieties, resulting in insufficient information to characterize SOM composition. We applied two-dimensional (2D) NMR to characterize SOM with highly increased resolution. We directly dissolved finely ground litters and forest floors'fibric and humic horizons'of both coniferous and deciduous boreal forests in dimethyl sulfoxide and analyzed the resulting solution with a 2D 1H-13C NMR experiment. In the 2D planes of these spectra, signals of CH groups can be resolved based on their 13C and 1H chemical shifts, hence the resolving power and information content of these NMR spectra is hugely increased. The 2D spectra indeed resolved overlaps observed in 1D 13C spectra, so that hundreds of distinct CH groups could be observed and many molecular fragments could be identified. For instance, in the aromatics region, signals from individual lignin units could

TE/TM decomposition of electromagnetic sources

NASA Technical Reports Server (NTRS)

Lindell, Ismo V.

1988-01-01

Three methods are given by which bounded EM sources can be decomposed into two parts radiating transverse electric (TE) and transverse magnetic (TM) fields with respect to a given constant direction in space. The theory applies source equivalence and nonradiating source concepts, which lead to decomposition methods based on a recursive formula or two differential equations for the determination of the TE and TM components of the original source. Decompositions for a dipole in terms of point, line, and plane sources are studied in detail. The planar decomposition is seen to match to an earlier result given by Clemmow (1963). As an application of the point decomposition method, it is demonstrated that the general exact image expression for the Sommerfeld half-space problem, previously derived through heuristic reasoning, can be more straightforwardly obtained through the present decomposition method.

Adaptive frozen orbital treatment for the fragment molecular orbital method combined with density-functional tight-binding

NASA Astrophysics Data System (ADS)

Nishimoto, Yoshio; Fedorov, Dmitri G.

2018-02-01

The exactly analytic gradient is derived and implemented for the fragment molecular orbital (FMO) method combined with density-functional tight-binding (DFTB) using adaptive frozen orbitals. The response contributions which arise from freezing detached molecular orbitals on the border between fragments are computed by solving Z-vector equations. The accuracy of the energy, its gradient, and optimized structures is verified on a set of representative inorganic materials and polypeptides. FMO-DFTB is applied to optimize the structure of a silicon nano-wire, and the results are compared to those of density functional theory and experiment. FMO accelerates the DFTB calculation of a boron nitride nano-ring with 7872 atoms by a factor of 406. Molecular dynamics simulations using FMO-DFTB applied to a 10.7 μm chain of boron nitride nano-rings, consisting of about 1.2 × 106 atoms, reveal the rippling and twisting of nano-rings at room temperature.

Automated Decomposition of Model-based Learning Problems

NASA Technical Reports Server (NTRS)

Williams, Brian C.; Millar, Bill

1996-01-01

A new generation of sensor rich, massively distributed autonomous systems is being developed that has the potential for unprecedented performance, such as smart buildings, reconfigurable factories, adaptive traffic systems and remote earth ecosystem monitoring. To achieve high performance these massive systems will need to accurately model themselves and their environment from sensor information. Accomplishing this on a grand scale requires automating the art of large-scale modeling. This paper presents a formalization of [\\em decompositional model-based learning (DML)], a method developed by observing a modeler's expertise at decomposing large scale model estimation tasks. The method exploits a striking analogy between learning and consistency-based diagnosis. Moriarty, an implementation of DML, has been applied to thermal modeling of a smart building, demonstrating a significant improvement in learning rate.

Fungal community structure of fallen pine and oak wood at different stages of decomposition in the Qinling Mountains, China.

PubMed

Yuan, Jie; Zheng, Xiaofeng; Cheng, Fei; Zhu, Xian; Hou, Lin; Li, Jingxia; Zhang, Shuoxin

2017-10-24

Historically, intense forest hazards have resulted in an increase in the quantity of fallen wood in the Qinling Mountains. Fallen wood has a decisive influence on the nutrient cycling, carbon budget and ecosystem biodiversity of forests, and fungi are essential for the decomposition of fallen wood. Moreover, decaying dead wood alters fungal communities. The development of high-throughput sequencing methods has facilitated the ongoing investigation of relevant molecular forest ecosystems with a focus on fungal communities. In this study, fallen wood and its associated fungal communities were compared at different stages of decomposition to evaluate relative species abundance and species diversity. The physical and chemical factors that alter fungal communities were also compared by performing correspondence analysis according to host tree species across all stages of decomposition. Tree species were the major source of differences in fungal community diversity at all decomposition stages, and fungal communities achieved the highest levels of diversity at the intermediate and late decomposition stages. Interactions between various physical and chemical factors and fungal communities shared the same regulatory mechanisms, and there was no tree species-specific influence. Improving our knowledge of wood-inhabiting fungal communities is crucial for forest ecosystem conservation.

Transcriptome Profiling and Molecular Pathway Analysis of Genes in Association with Salinity Adaptation in Nile Tilapia Oreochromis niloticus

PubMed Central

Xu, Zhixin; Gan, Lei; Li, Tongyu; Xu, Chang; Chen, Ke; Wang, Xiaodan; Qin, Jian G.; Chen, Liqiao; Li, Erchao

2015-01-01

Nile tilapia Oreochromis niloticus is a freshwater fish but can tolerate a wide range of salinities. The mechanism of salinity adaptation at the molecular level was studied using RNA-Seq to explore the molecular pathways in fish exposed to 0, 8, or 16 (practical salinity unit, psu). Based on the change of gene expressions, the differential genes unions from freshwater to saline water were classified into three categories. In the constant change category (1), steroid biosynthesis, steroid hormone biosynthesis, fat digestion and absorption, complement and coagulation cascades were significantly affected by salinity indicating the pivotal roles of sterol-related pathways in response to salinity stress. In the change-then-stable category (2), ribosomes, oxidative phosphorylation, signaling pathways for peroxisome proliferator activated receptors, and fat digestion and absorption changed significantly with increasing salinity, showing sensitivity to salinity variation in the environment and a responding threshold to salinity change. In the stable-then-change category (3), protein export, protein processing in endoplasmic reticulum, tight junction, thyroid hormone synthesis, antigen processing and presentation, glycolysis/gluconeogenesis and glycosaminoglycan biosynthesis—keratan sulfate were the significantly changed pathways, suggesting that these pathways were less sensitive to salinity variation. This study reveals fundamental mechanism of the molecular response to salinity adaptation in O. niloticus, and provides a general guidance to understand saline acclimation in O. niloticus. PMID:26305564

Management intensity alters decomposition via biological pathways

USGS Publications Warehouse

Wickings, Kyle; Grandy, A. Stuart; Reed, Sasha; Cleveland, Cory

2011-01-01

Current conceptual models predict that changes in plant litter chemistry during decomposition are primarily regulated by both initial litter chemistry and the stage-or extent-of mass loss. Far less is known about how variations in decomposer community structure (e.g., resulting from different ecosystem management types) could influence litter chemistry during decomposition. Given the recent agricultural intensification occurring globally and the importance of litter chemistry in regulating soil organic matter storage, our objectives were to determine the potential effects of agricultural management on plant litter chemistry and decomposition rates, and to investigate possible links between ecosystem management, litter chemistry and decomposition, and decomposer community composition and activity. We measured decomposition rates, changes in litter chemistry, extracellular enzyme activity, microarthropod communities, and bacterial versus fungal relative abundance in replicated conventional-till, no-till, and old field agricultural sites for both corn and grass litter. After one growing season, litter decomposition under conventional-till was 20% greater than in old field communities. However, decomposition rates in no-till were not significantly different from those in old field or conventional-till sites. After decomposition, grass residue in both conventional- and no-till systems was enriched in total polysaccharides relative to initial litter, while grass litter decomposed in old fields was enriched in nitrogen-bearing compounds and lipids. These differences corresponded with differences in decomposer communities, which also exhibited strong responses to both litter and management type. Overall, our results indicate that agricultural intensification can increase litter decomposition rates, alter decomposer communities, and influence litter chemistry in ways that could have important and long-term effects on soil organic matter dynamics. We suggest that future

[Preface to special issue: "Molecular mechanism of the adaptation of terrestrial plants to gravity environment on Earth"].

PubMed

Kamisaka, Seiichiro

2003-08-01

Organisms borne in the primitive sea about 30 million years ago had evolved in water without a large influence of gravity on earth. About 4 million years ago, the first terrestrial organisms, plants appeared on the land from the sea. The terrestrial plants have adapted to and evolved on the land environment so that they can extend their roots downward in soil and their shoots upward against 1 g gravity. At least two functions that were acquired during the process of evolution helped the terrestrial plants to adapt to gravity environment on earth. One is gravitropism. The other is the reinforcement of the cell wall, particularly the secondary cell wall. In the present feature articles, the molecular mechanism of the adaptation of terrestrial plants to gravity environment on earth will be reviewed, paying special attention to the mechanism of the genetic control of the signaling of gravity stimulus in gravitropism, automorphogenesis, genes involved in auxin transport, gravity effect on cell wall properties and gravimorphogenesis in terrestrial plants.

Descent theory for semiorthogonal decompositions

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

Elagin, Alexei D

We put forward a method for constructing semiorthogonal decompositions of the derived category of G-equivariant sheaves on a variety X under the assumption that the derived category of sheaves on X admits a semiorthogonal decomposition with components preserved by the action of the group G on X. This method is used to obtain semiorthogonal decompositions of equivariant derived categories for projective bundles and blow-ups with a smooth centre as well as for varieties with a full exceptional collection preserved by the group action. Our main technical tool is descent theory for derived categories. Bibliography: 12 titles.

Decomposition Rate and Pattern in Hanging Pigs.

PubMed

Lynch-Aird, Jeanne; Moffatt, Colin; Simmons, Tal

2015-09-01

Accurate prediction of the postmortem interval requires an understanding of the decomposition process and the factors acting upon it. A controlled experiment, over 60 days at an outdoor site in the northwest of England, used 20 freshly killed pigs (Sus scrofa) as human analogues to study decomposition rate and pattern. Ten pigs were hung off the ground and ten placed on the surface. Observed differences in the decomposition pattern required a new decomposition scoring scale to be produced for the hanging pigs to enable comparisons with the surface pigs. The difference in the rate of decomposition between hanging and surface pigs was statistically significant (p=0.001). Hanging pigs reached advanced decomposition stages sooner, but lagged behind during the early stages. This delay is believed to result from lower variety and quantity of insects, due to restricted beetle access to the aerial carcass, and/or writhing maggots falling from the carcass. © 2015 American Academy of Forensic Sciences.

9 CFR 354.131 - Decomposition.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 9 Animals and Animal Products 2 2010-01-01 2010-01-01 false Decomposition. 354.131 Section 354.131 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE AGENCY... Carcasses and Parts § 354.131 Decomposition. Carcasses of rabbits deleteriously affected by post-mortem...

9 CFR 354.131 - Decomposition.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 9 Animals and Animal Products 2 2014-01-01 2014-01-01 false Decomposition. 354.131 Section 354.131 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE AGENCY... Carcasses and Parts § 354.131 Decomposition. Carcasses of rabbits deleteriously affected by post-mortem...

9 CFR 354.131 - Decomposition.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 9 Animals and Animal Products 2 2013-01-01 2013-01-01 false Decomposition. 354.131 Section 354.131 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE AGENCY... Carcasses and Parts § 354.131 Decomposition. Carcasses of rabbits deleteriously affected by post-mortem...

9 CFR 381.93 - Decomposition.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 9 Animals and Animal Products 2 2011-01-01 2011-01-01 false Decomposition. 381.93 Section 381.93 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE AGENCY... § 381.93 Decomposition. Carcasses of poultry deleteriously affected by post mortem changes shall be...

9 CFR 381.93 - Decomposition.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 9 Animals and Animal Products 2 2014-01-01 2014-01-01 false Decomposition. 381.93 Section 381.93 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE AGENCY... § 381.93 Decomposition. Carcasses of poultry deleteriously affected by post mortem changes shall be...

9 CFR 381.93 - Decomposition.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 9 Animals and Animal Products 2 2012-01-01 2012-01-01 false Decomposition. 381.93 Section 381.93 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE AGENCY... § 381.93 Decomposition. Carcasses of poultry deleteriously affected by post mortem changes shall be...

9 CFR 381.93 - Decomposition.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 9 Animals and Animal Products 2 2013-01-01 2013-01-01 false Decomposition. 381.93 Section 381.93 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE AGENCY... § 381.93 Decomposition. Carcasses of poultry deleteriously affected by post mortem changes shall be...

9 CFR 354.131 - Decomposition.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 9 Animals and Animal Products 2 2012-01-01 2012-01-01 false Decomposition. 354.131 Section 354.131 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE AGENCY... Carcasses and Parts § 354.131 Decomposition. Carcasses of rabbits deleteriously affected by post-mortem...

Approaches to understanding the semi-stable phase of litter decomposition

NASA Astrophysics Data System (ADS)

Preston, C. M.; Trofymow, J. A.

2012-12-01

The slowing or even apparent cessation of litter decomposition with time has been widely observed, but causes remain poorly understood. We examine the question in part through data from CIDET (the Canadian Intersite Decomposition Experiment) for 10 foliar litters at one site with MAT 6.7 degrees C. The initial rapid C loss in the first year for some litters is followed by a second phase (1-7y) with decay rates from 0.21-0.79/y, influenced by initial litter chemistry especially the ratio AUR/N (acid-unhydrolyzable residue, negative). By contrast, 10-23% of the initial litter C mass entered the semi-stable decay phase (>7 y) with modeled decay rates of 0.0021-0.0035/y. The slowing and convergence of k values was similar to trends in chemical composition. From 7-12 y, concentrations of Ca, Mg, K, P, Mn and Zn generally declined and became more similar among litters, and total N converged around 20 mg/g. Non-polar and water-soluble extractables and acid solubles continued to decrease slowly and AUR to increase. Solid-state C-13 NMR showed continuing slight declines in O- and di-O-alkyl C and increases in alkyl, methoxyl, aryl and carboxyl C. CIDET and other studies now clearly show that lignin is not selectively preserved, and that AUR is not a measure of foliar lignin as it includes components from condensed tannins and long-chain alkyl C. Interaction with soil minerals strongly enhances soil C stabilization, but what slows decomposition so much in organic horizons? The role of inherent "chemical recalcitrance" or possible formation of new covalent bonds is hotly debated in soil science, but increasingly complex or random molecular structures no doubt present greater challenges to enzymes. A relevant observation from soils and geochemistry is that decomposition results in a decline in individual compounds that can be identified from chemical analysis and a corresponding increase in the "molecularly uncharacterizable component" (MUC). Long-term declines in Ca, Mg, K

Fast algorithm of adaptive Fourier series

NASA Astrophysics Data System (ADS)

Gao, You; Ku, Min; Qian, Tao

2018-05-01

Adaptive Fourier decomposition (AFD, precisely 1-D AFD or Core-AFD) was originated for the goal of positive frequency representations of signals. It achieved the goal and at the same time offered fast decompositions of signals. There then arose several types of AFDs. AFD merged with the greedy algorithm idea, and in particular, motivated the so-called pre-orthogonal greedy algorithm (Pre-OGA) that was proven to be the most efficient greedy algorithm. The cost of the advantages of the AFD type decompositions is, however, the high computational complexity due to the involvement of maximal selections of the dictionary parameters. The present paper offers one formulation of the 1-D AFD algorithm by building the FFT algorithm into it. Accordingly, the algorithm complexity is reduced, from the original $\\mathcal{O}(M N^2)$ to $\\mathcal{O}(M N\\log_2 N)$, where $N$ denotes the number of the discretization points on the unit circle and $M$ denotes the number of points in $[0,1)$. This greatly enhances the applicability of AFD. Experiments are carried out to show the high efficiency of the proposed algorithm.

Ab initio kinetics and thermal decomposition mechanism of mononitrobiuret and 1,5-dinitrobiuret

NASA Astrophysics Data System (ADS)

Sun, Hongyan; Vaghjiani, Ghanshyam L.

2015-05-01

of (NO2 + H2O) to be the major decomposition path. Furthermore, we provide fundamental interpretations for the experimental results of Klapötke et al. [Combust. Flame 139, 358-366 (2004)] regarding the thermal stability of MNB and DNB, and their decomposition products. Notably, a fundamental understanding of fuel stability, decomposition mechanism, and key reactions leading to ignition is essential in the design and manipulation of molecular systems for the development of new energetic materials for advanced propulsion applications.

Ab Initio Kinetics and Thermal Decomposition Mechanism of Mononitrobiuret and 1,5- Dinitrobiuret

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

Sun, Hongyan; Vaghjiani, Ghanshyam G.

2015-05-26

the formation of (NO2 + H2O) to be the major decomposition path. Furthermore, we provide fundamental interpretations for the experimental results of Klapötke et al. [Combust. Flame 139, 358–366 (2004)] regarding the thermal stability of MNB and DNB, and their decomposition products. Notably, a fundamental understanding of fuel stability, decomposition mechanism, and key reactions leading to ignition is essential in the design and manipulation of molecular systems for the development of new energetic materials for advanced propulsion applications.« less

Ab initio kinetics and thermal decomposition mechanism of mononitrobiuret and 1,5-dinitrobiuret

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

Sun, Hongyan, E-mail: hongyan.sun1@gmail.com, E-mail: ghanshyam.vaghjiani@us.af.mil; Vaghjiani, Ghanshyam L., E-mail: hongyan.sun1@gmail.com, E-mail: ghanshyam.vaghjiani@us.af.mil

2015-05-28

which reveal the formation of (NO{sub 2} + H{sub 2}O) to be the major decomposition path. Furthermore, we provide fundamental interpretations for the experimental results of Klapötke et al. [Combust. Flame 139, 358–366 (2004)] regarding the thermal stability of MNB and DNB, and their decomposition products. Notably, a fundamental understanding of fuel stability, decomposition mechanism, and key reactions leading to ignition is essential in the design and manipulation of molecular systems for the development of new energetic materials for advanced propulsion applications.« less

Ab initio kinetics and thermal decomposition mechanism of mononitrobiuret and 1,5-dinitrobiuret.

PubMed

Sun, Hongyan; Vaghjiani, Ghanshyam L

2015-05-28

of (NO2 + H2O) to be the major decomposition path. Furthermore, we provide fundamental interpretations for the experimental results of Klapötke et al. [Combust. Flame 139, 358-366 (2004)] regarding the thermal stability of MNB and DNB, and their decomposition products. Notably, a fundamental understanding of fuel stability, decomposition mechanism, and key reactions leading to ignition is essential in the design and manipulation of molecular systems for the development of new energetic materials for advanced propulsion applications.

Structural optimization by multilevel decomposition

NASA Technical Reports Server (NTRS)

Sobieszczanski-Sobieski, J.; James, B.; Dovi, A.

1983-01-01

A method is described for decomposing an optimization problem into a set of subproblems and a coordination problem which preserves coupling between the subproblems. The method is introduced as a special case of multilevel, multidisciplinary system optimization and its algorithm is fully described for two level optimization for structures assembled of finite elements of arbitrary type. Numerical results are given for an example of a framework to show that the decomposition method converges and yields results comparable to those obtained without decomposition. It is pointed out that optimization by decomposition should reduce the design time by allowing groups of engineers, using different computers to work concurrently on the same large problem.

Perfluoropolyalkylether decomposition on catalytic aluminas

NASA Technical Reports Server (NTRS)

Morales, Wilfredo

1994-01-01

The decomposition of Fomblin Z25, a commercial perfluoropolyalkylether liquid lubricant, was studied using the Penn State Micro-oxidation Test, and a thermal gravimetric/differential scanning calorimetry unit. The micro-oxidation test was conducted using 440C stainless steel and pure iron metal catalyst specimens, whereas the thermal gravimetric/differential scanning calorimetry tests were conducted using catalytic alumina pellets. Analysis of the thermal data, high pressure liquid chromatography data, and x-ray photoelectron spectroscopy data support evidence that there are two different decomposition mechanisms for Fomblin Z25, and that reductive sites on the catalytic surfaces are responsible for the decomposition of Fomblin Z25.

Direct observation of nanowire growth and decomposition.

PubMed

Rackauskas, Simas; Shandakov, Sergey D; Jiang, Hua; Wagner, Jakob B; Nasibulin, Albert G

2017-09-26

Fundamental concepts of the crystal formation suggest that the growth and decomposition are determined by simultaneous embedding and removal of the atoms. Apparently, by changing the crystal formation conditions one can switch the regimes from the growth to decomposition. To the best of our knowledge, so far this has been only postulated, but never observed at the atomic level. By means of in situ environmental transmission electron microscopy we monitored and examined the atomic layer transformation at the conditions of the crystal growth and its decomposition using CuO nanowires selected as a model object. The atomic layer growth/decomposition was studied by varying an O 2 partial pressure. Three distinct regimes of the atomic layer evolution were experimentally observed: growth, transition and decomposition. The transition regime, at which atomic layer growth/decomposition switch takes place, is characterised by random nucleation of the atomic layers on the growing {111} surface. The decomposition starts on the side of the nanowire by removing the atomic layers without altering the overall crystal structure, which besides the fundamental importance offers new possibilities for the nanowire manipulation. Understanding of the crystal growth kinetics and nucleation at the atomic level is essential for the precise control of 1D crystal formation.

Uncertainty in the fate of soil organic carbon: A comparison of three conceptually different soil decomposition models

USGS Publications Warehouse

He, Yujie; Yang, Jinyan; Zhuang, Qianlai; McGuire, A. David; Zhu, Qing; Liu, Yaling; Teskey, Robert O.

2014-01-01

Conventional Q10 soil organic matter decomposition models and more complex microbial models are available for making projections of future soil carbon dynamics. However, it is unclear (1) how well the conceptually different approaches can simulate observed decomposition and (2) to what extent the trajectories of long-term simulations differ when using the different approaches. In this study, we compared three structurally different soil carbon (C) decomposition models (one Q10 and two microbial models of different complexity), each with a one- and two-horizon version. The models were calibrated and validated using 4 years of measurements of heterotrophic soil CO2 efflux from trenched plots in a Dahurian larch (Larix gmelinii Rupr.) plantation. All models reproduced the observed heterotrophic component of soil CO2 efflux, but the trajectories of soil carbon dynamics differed substantially in 100 year simulations with and without warming and increased litterfall input, with microbial models that produced better agreement with observed changes in soil organic C in long-term warming experiments. Our results also suggest that both constant and varying carbon use efficiency are plausible when modeling future decomposition dynamics and that the use of a short-term (e.g., a few years) period of measurement is insufficient to adequately constrain model parameters that represent long-term responses of microbial thermal adaption. These results highlight the need to reframe the representation of decomposition models and to constrain parameters with long-term observations and multiple data streams. We urge caution in interpreting future soil carbon responses derived from existing decomposition models because both conceptual and parameter uncertainties are substantial.

Surface-Mediated Solvent Decomposition in Li–Air Batteries: Impact of Peroxide and Superoxide Surface Terminations

DOE PAGES

Kumar, Nitin; Radin, Maxwell D.; Wood, Brandon C.; ...

2015-04-13

A viable Li/O 2 battery will require the development of stable electrolytes that do not continuously decompose during cell operation. In some recent experiments it is suggested that reactions occurring at the interface between the liquid electrolyte and the solid lithium peroxide (Li 2O 2) discharge phase are a major contributor to these instabilities. To clarify the mechanisms associated with these reactions, a variety of atomistic simulation techniques, classical Monte Carlo, van der Waals-augmented density functional theory, ab initio molecular dynamics, and various solvation models, are used to study the initial decomposition of the common electrolyte solvent, dimethoxyethane (DME), onmore » surfaces of Li 2O 2. Comparisons are made between the two predominant Li 2O 2 surface charge states by calculating decomposition pathways on peroxide-terminated (O 2 2–) and superoxide-terminated (O 2 1–) facets. For both terminations, DME decomposition proceeds exothermically via a two-step process comprised of hydrogen abstraction (H-abstraction) followed by nucleophilic attack. In the first step, abstracted H dissociates a surface O 2 dimer, and combines with a dissociated oxygen to form a hydroxide ion (OH –). In the remaining surface oxygen then attacks the DME, resulting in a DME fragment that is strongly bound to the Li 2O 2 surface. DME decomposition is predicted to be more exothermic on the peroxide facet; nevertheless, the rate of DME decomposition is faster on the superoxide termination. The impact of solvation (explicit vs implicit) and an applied electric field on the reaction energetics are investigated. Finally, our calculations suggest that surface-mediated electrolyte decomposition should out-pace liquid-phase processes such as solvent auto-oxidation by dissolved O 2.« less

Differential Decomposition Among Pig, Rabbit, and Human Remains.

PubMed

Dautartas, Angela; Kenyhercz, Michael W; Vidoli, Giovanna M; Meadows Jantz, Lee; Mundorff, Amy; Steadman, Dawnie Wolfe

2018-03-30

While nonhuman animal remains are often utilized in forensic research to develop methods to estimate the postmortem interval, systematic studies that directly validate animals as proxies for human decomposition are lacking. The current project compared decomposition rates among pigs, rabbits, and humans at the University of Tennessee's Anthropology Research Facility across three seasonal trials that spanned nearly 2 years. The Total Body Score (TBS) method was applied to quantify decomposition changes and calculate the postmortem interval (PMI) in accumulated degree days (ADD). Decomposition trajectories were analyzed by comparing the estimated and actual ADD for each seasonal trial and by fuzzy cluster analysis. The cluster analysis demonstrated that the rabbits formed one group while pigs and humans, although more similar to each other than either to rabbits, still showed important differences in decomposition patterns. The decomposition trends show that neither nonhuman model captured the pattern, rate, and variability of human decomposition. © 2018 American Academy of Forensic Sciences.

A data-driven method to enhance vibration signal decomposition for rolling bearing fault analysis

NASA Astrophysics Data System (ADS)

Grasso, M.; Chatterton, S.; Pennacchi, P.; Colosimo, B. M.

2016-12-01

Health condition analysis and diagnostics of rotating machinery requires the capability of properly characterizing the information content of sensor signals in order to detect and identify possible fault features. Time-frequency analysis plays a fundamental role, as it allows determining both the existence and the causes of a fault. The separation of components belonging to different time-frequency scales, either associated to healthy or faulty conditions, represents a challenge that motivates the development of effective methodologies for multi-scale signal decomposition. In this framework, the Empirical Mode Decomposition (EMD) is a flexible tool, thanks to its data-driven and adaptive nature. However, the EMD usually yields an over-decomposition of the original signals into a large number of intrinsic mode functions (IMFs). The selection of most relevant IMFs is a challenging task, and the reference literature lacks automated methods to achieve a synthetic decomposition into few physically meaningful modes by avoiding the generation of spurious or meaningless modes. The paper proposes a novel automated approach aimed at generating a decomposition into a minimal number of relevant modes, called Combined Mode Functions (CMFs), each consisting in a sum of adjacent IMFs that share similar properties. The final number of CMFs is selected in a fully data driven way, leading to an enhanced characterization of the signal content without any information loss. A novel criterion to assess the dissimilarity between adjacent CMFs is proposed, based on probability density functions of frequency spectra. The method is suitable to analyze vibration signals that may be periodically acquired within the operating life of rotating machineries. A rolling element bearing fault analysis based on experimental data is presented to demonstrate the performances of the method and the provided benefits.

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

Exploring Patterns of Soil Organic Matter Decomposition with Students and the Public Through the Global Decomposition Project (GDP)

NASA Astrophysics Data System (ADS)

Wood, J. H.; Natali, S.

2014-12-01

The Global Decomposition Project (GDP) is a program designed to introduce and educate students and the general public about soil organic matter and decomposition through a standardized protocol for collecting, reporting, and sharing data. This easy-to-use hands-on activity focuses on questions such as "How do environmental conditions control decomposition of organic matter in soil?" and "Why do some areas accumulate organic matter and others do not?" Soil organic matter is important to local ecosystems because it affects soil structure, regulates soil moisture and temperature, and provides energy and nutrients to soil organisms. It is also important globally because it stores a large amount of carbon, and when microbes "eat", or decompose organic matter they release greenhouse gasses such as carbon dioxide and methane into the atmosphere, which affects the earth's climate. The protocol describes a commonly used method to measure decomposition using a paper made of cellulose, a component of plant cell walls. Participants can receive pre-made cellulose decomposition bags, or make decomposition bags using instructions in the protocol and easily obtained materials (e.g., window screen and lignin-free paper). Individual results will be shared with all participants and the broader public through an online database. We will present decomposition bag results from a research site in Alaskan tundra, as well as from a middle-school-student led experiment in California. The GDP demonstrates how scientific methods can be extended to educate broader audiences, while at the same time, data collected by students and the public can provide new insight into global patterns of soil decomposition. The GDP provides a pathway for scientists and educators to interact and reach meaningful education and research goals.

Parallel Adaptive Mesh Refinement Library

NASA Technical Reports Server (NTRS)

Mac-Neice, Peter; Olson, Kevin

2005-01-01

Parallel Adaptive Mesh Refinement Library (PARAMESH) is a package of Fortran 90 subroutines designed to provide a computer programmer with an easy route to extension of (1) a previously written serial code that uses a logically Cartesian structured mesh into (2) a parallel code with adaptive mesh refinement (AMR). Alternatively, in its simplest use, and with minimal effort, PARAMESH can operate as a domain-decomposition tool for users who want to parallelize their serial codes but who do not wish to utilize adaptivity. The package builds a hierarchy of sub-grids to cover the computational domain of a given application program, with spatial resolution varying to satisfy the demands of the application. The sub-grid blocks form the nodes of a tree data structure (a quad-tree in two or an oct-tree in three dimensions). Each grid block has a logically Cartesian mesh. The package supports one-, two- and three-dimensional models.

PARAMESH: A Parallel Adaptive Mesh Refinement Community Toolkit

NASA Technical Reports Server (NTRS)

MacNeice, Peter; Olson, Kevin M.; Mobarry, Clark; deFainchtein, Rosalinda; Packer, Charles

1999-01-01

In this paper, we describe a community toolkit which is designed to provide parallel support with adaptive mesh capability for a large and important class of computational models, those using structured, logically cartesian meshes. The package of Fortran 90 subroutines, called PARAMESH, is designed to provide an application developer with an easy route to extend an existing serial code which uses a logically cartesian structured mesh into a parallel code with adaptive mesh refinement. Alternatively, in its simplest use, and with minimal effort, it can operate as a domain decomposition tool for users who want to parallelize their serial codes, but who do not wish to use adaptivity. The package can provide them with an incremental evolutionary path for their code, converting it first to uniformly refined parallel code, and then later if they so desire, adding adaptivity.

Structural characterization of alpha-terminal group of natural rubber. 2. Decomposition of branch-points by phospholipase and chemical treatments.

PubMed

Tarachiwin, Lucksanaporn; Sakdapipanich, Jitladda; Ute, Koichi; Kitayama, Tatsuki; Tanaka, Yasuyuki

2005-01-01

The treatment of deproteinized natural rubber (DPNR) latex with phospholipases A(2), B, C, and D decreased significantly the long-chain fatty acid ester contents in DPNR and also the molecular weight and Higgins' k' constant, except for phospholipase D treatment. This indicates the presence of phospholipid molecules in NR, which combine rubber molecules together. Transesterification of DPNR resulted in the decomposition of the functional group at the terminal chain-end (alpha-terminal), including phospholipids and formed linear rubber molecules. The addition of small amounts of ethanol into the DPNR solution reduced the molecular weight and shifted the molecular weight distribution (MWD) comparable to that of transesterified DPNR (TE-DPNR). The addition of diammonium hydrogen phosphate into DPNR-latex in order to remove Mg2+ ions yielded a slight decrease in molecular weight and a slight shift in MWD. The phospholipids are expected to link with mono- and diphosphate groups at the alpha-terminal by hydrogen bonding and/or ionic linkages. The decrease in the molecular weight and Huggins' k' constant of DPNR demonstrates the formation of linear molecules after decomposition of branch-points by this treatment, showing that phospholipids participate in the branching formation of NR. The branch-points formed at the alpha-terminus are postulated to originate predominantly by the association of phospholipids via micelle formation of long-chain fatty acid esters and hydrogen bonding between polar headgroups of phospholipids.

Image compression using singular value decomposition

NASA Astrophysics Data System (ADS)

Swathi, H. R.; Sohini, Shah; Surbhi; Gopichand, G.

2017-11-01

We often need to transmit and store the images in many applications. Smaller the image, less is the cost associated with transmission and storage. So we often need to apply data compression techniques to reduce the storage space consumed by the image. One approach is to apply Singular Value Decomposition (SVD) on the image matrix. In this method, digital image is given to SVD. SVD refactors the given digital image into three matrices. Singular values are used to refactor the image and at the end of this process, image is represented with smaller set of values, hence reducing the storage space required by the image. Goal here is to achieve the image compression while preserving the important features which describe the original image. SVD can be adapted to any arbitrary, square, reversible and non-reversible matrix of m × n size. Compression ratio and Mean Square Error is used as performance metrics.

Hybrid Decompositional Verification for Discovering Failures in Adaptive Flight Control Systems

NASA Technical Reports Server (NTRS)

Thompson, Sarah; Davies, Misty D.; Gundy-Burlet, Karen

2010-01-01

Adaptive flight control systems hold tremendous promise for maintaining the safety of a damaged aircraft and its passengers. However, most currently proposed adaptive control methodologies rely on online learning neural networks (OLNNs), which necessarily have the property that the controller is changing during the flight. These changes tend to be highly nonlinear, and difficult or impossible to analyze using standard techniques. In this paper, we approach the problem with a variant of compositional verification. The overall system is broken into components. Undesirable behavior is fed backwards through the system. Components which can be solved using formal methods techniques explicitly for the ranges of safe and unsafe input bounds are treated as white box components. The remaining black box components are analyzed with heuristic techniques that try to predict a range of component inputs that may lead to unsafe behavior. The composition of these component inputs throughout the system leads to overall system test vectors that may elucidate the undesirable behavior

Moisture drives surface decomposition in thawing tundra

NASA Astrophysics Data System (ADS)

Hicks Pries, Caitlin E.; Schuur, E. A. G.; Vogel, Jason G.; Natali, Susan M.

2013-07-01

Permafrost thaw can affect decomposition rates by changing environmental conditions and litter quality. As permafrost thaws, soils warm and thermokarst (ground subsidence) features form, causing some areas to become wetter while other areas become drier. We used a common substrate to measure how permafrost thaw affects decomposition rates in the surface soil in a natural permafrost thaw gradient and a warming experiment in Healy, Alaska. Permafrost thaw also changes plant community composition. We decomposed 12 plant litters in a common garden to test how changing plant litter inputs would affect decomposition. We combined species' tissue-specific decomposition rates with species and tissue-level estimates of aboveground net primary productivity to calculate community-weighted decomposition constants at both the thaw gradient and warming experiment. Moisture, specifically growing season precipitation and water table depth, was the most significant driver of decomposition. At the gradient, an increase in growing season precipitation from 200 to 300 mm increased mass loss of the common substrate by 100%. At the warming experiment, a decrease in the depth to the water table from 30 to 15 cm increased mass loss by 100%. At the gradient, community-weighted decomposition was 21% faster in extensive than in minimal thaw, but was similar when moss production was included. Overall, the effect of climate change and permafrost thaw on surface soil decomposition are driven more by precipitation and soil environment than by changes to plant communities. Increasing soil moisture is thereby another mechanism by which permafrost thaw can become a positive feedback to climate change.

Pathways of anaerobic organic matter decomposition in tundra soils from Barrow, Alaska

DOE PAGES

Herndon, Elizabeth M.; Mann, Benjamin F.; Chowdhury, Taniya Roy; ...

2015-11-23

Arctic tundra soils store a large quantity of organic carbon that is susceptible to decomposition and release to the atmosphere as methane (CH 4) and carbon dioxide (CO 2) under a warming climate. Anaerobic processes that generate CH 4 and CO 2 remain unclear because previous studies have focused on aerobic decomposition pathways. To predict releases of CO 2 and CH 4 from tundra soils, it is necessary to identify pathways of soil organic matter decomposition under the anoxic conditions that are prevalent in Arctic ecosystems. Here molecular and spectroscopic techniques were used to monitor biological degradation of water-extractable organicmore » carbon (WEOC) during anoxic incubation of tundra soils from a region of continuous permafrost in northern Alaska. Organic and mineral soils from the tundra active layer were incubated at –2, +4, or +8°C for up to 60 days to mimic the short-term thaw season. Results suggest that, under anoxic conditions, fermentation converted complex organic molecules into simple organic acids that were used in concomitant Fe-reduction and acetoclastic methanogenesis reactions. Nonaromatic compounds increased over time as WEOC increased. Organic acid metabolites initially accumulated in soils but were mostly depleted by day 60 because organic acids were consumed to produce Fe(II), CO 2, and CH 4. We conclude that fermentation of nonprotected organic matter facilitates methanogenesis and Fe reduction reactions, and that the proportion of organic acids consumed by methanogenesis increases relative to Fe reduction with increasing temperature. As a result, the decomposition pathways observed in this study are important to consider in numerical modeling of greenhouse gas production in the Arctic.« less

Nanoscale decomposition of Nb-Ru-O

NASA Astrophysics Data System (ADS)

Music, Denis; Geyer, Richard W.; Chen, Yen-Ting

2016-11-01

A correlative theoretical and experimental methodology has been employed to explore the decomposition of amorphous Nb-Ru-O at elevated temperatures. Density functional theory based molecular dynamics simulations reveal that amorphous Nb-Ru-O is structurally modified within 10 ps at 800 K giving rise to an increase in the planar metal - oxygen and metal - metal population and hence formation of large clusters, which signifies atomic segregation. The driving force for this atomic segregation process is 0.5 eV/atom. This is validated by diffraction experiments and transmission electron microscopy of sputter-synthesized Nb-Ru-O thin films. Room temperature samples are amorphous, while at 800 K nanoscale rutile RuO2 grains, self-organized in an amorphous Nb-O matrix, are observed, which is consistent with our theoretical predictions. This amorphous/crystalline interplay may be of importance for next generation of thermoelectric devices.

Direct Sum Decomposition of Groups

ERIC Educational Resources Information Center

Thaheem, A. B.

2005-01-01

Direct sum decomposition of Abelian groups appears in almost all textbooks on algebra for undergraduate students. This concept plays an important role in group theory. One simple example of this decomposition is obtained by using the kernel and range of a projection map on an Abelian group. The aim in this pedagogical note is to establish a direct…

Optimal domain decomposition strategies

NASA Technical Reports Server (NTRS)

Yoon, Yonghyun; Soni, Bharat K.

1995-01-01

The primary interest of the authors is in the area of grid generation, in particular, optimal domain decomposition about realistic configurations. A grid generation procedure with optimal blocking strategies has been developed to generate multi-block grids for a circular-to-rectangular transition duct. The focus of this study is the domain decomposition which optimizes solution algorithm/block compatibility based on geometrical complexities as well as the physical characteristics of flow field. The progress realized in this study is summarized in this paper.

A parallel domain decomposition-based implicit method for the Cahn–Hilliard–Cook phase-field equation in 3D

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

Zheng, Xiang; Yang, Chao; State Key Laboratory of Computer Science, Chinese Academy of Sciences, Beijing 100190

2015-03-15

We present a numerical algorithm for simulating the spinodal decomposition described by the three dimensional Cahn–Hilliard–Cook (CHC) equation, which is a fourth-order stochastic partial differential equation with a noise term. The equation is discretized in space and time based on a fully implicit, cell-centered finite difference scheme, with an adaptive time-stepping strategy designed to accelerate the progress to equilibrium. At each time step, a parallel Newton–Krylov–Schwarz algorithm is used to solve the nonlinear system. We discuss various numerical and computational challenges associated with the method. The numerical scheme is validated by a comparison with an explicit scheme of high accuracymore » (and unreasonably high cost). We present steady state solutions of the CHC equation in two and three dimensions. The effect of the thermal fluctuation on the spinodal decomposition process is studied. We show that the existence of the thermal fluctuation accelerates the spinodal decomposition process and that the final steady morphology is sensitive to the stochastic noise. We also show the evolution of the energies and statistical moments. In terms of the parallel performance, it is found that the implicit domain decomposition approach scales well on supercomputers with a large number of processors.« less

Alkyl ammonium cation stabilized biocidal polyiodides with adaptable high density and low pressure.

PubMed

He, Chunlin; Parrish, Damon A; Shreeve, Jean'ne M

2014-05-26

The effective application of biocidal species requires building the active moiety into a molecular back bone that can be delivered and decomposed on demand under conditions of low pressure and prolonged high-temperature detonation. The goal is to destroy storage facilities and their contents while utilizing the biocidal products arising from the released energy to destroy any remaining harmful airborne agents. Decomposition of carefully selected iodine-rich compounds can produce large amounts of the very active biocides, hydroiodic acid (HI) and iodine (I2). Polyiodide anions, namely, I3(-), I5(-), which are excellent sources of such biocides, can be stabilized through interactions with large, symmetric cations, such as alkyl ammonium salts. We have designed and synthesized suitable compounds of adaptable high density up to 3.33 g cm(-3) that are low-pressure polyiodides with various alkyl ammonium cations, deliverable iodine contents of which range between 58.0-90.9%. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Regular Decompositions for H(div) Spaces

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

Kolev, Tzanio; Vassilevski, Panayot

We study regular decompositions for H(div) spaces. In particular, we show that such regular decompositions are closely related to a previously studied “inf-sup” condition for parameter-dependent Stokes problems, for which we provide an alternative, more direct, proof.

Low-rank matrix decomposition and spatio-temporal sparse recovery for STAP radar

DOE PAGES

Sen, Satyabrata

2015-08-04

We develop space-time adaptive processing (STAP) methods by leveraging the advantages of sparse signal processing techniques in order to detect a slowly-moving target. We observe that the inherent sparse characteristics of a STAP problem can be formulated as the low-rankness of clutter covariance matrix when compared to the total adaptive degrees-of-freedom, and also as the sparse interference spectrum on the spatio-temporal domain. By exploiting these sparse properties, we propose two approaches for estimating the interference covariance matrix. In the first approach, we consider a constrained matrix rank minimization problem (RMP) to decompose the sample covariance matrix into a low-rank positivemore » semidefinite and a diagonal matrix. The solution of RMP is obtained by applying the trace minimization technique and the singular value decomposition with matrix shrinkage operator. Our second approach deals with the atomic norm minimization problem to recover the clutter response-vector that has a sparse support on the spatio-temporal plane. We use convex relaxation based standard sparse-recovery techniques to find the solutions. With extensive numerical examples, we demonstrate the performances of proposed STAP approaches with respect to both the ideal and practical scenarios, involving Doppler-ambiguous clutter ridges, spatial and temporal decorrelation effects. As a result, the low-rank matrix decomposition based solution requires secondary measurements as many as twice the clutter rank to attain a near-ideal STAP performance; whereas the spatio-temporal sparsity based approach needs a considerably small number of secondary data.« less

CT Image Sequence Restoration Based on Sparse and Low-Rank Decomposition

PubMed Central

Gou, Shuiping; Wang, Yueyue; Wang, Zhilong; Peng, Yong; Zhang, Xiaopeng; Jiao, Licheng; Wu, Jianshe

2013-01-01

Blurry organ boundaries and soft tissue structures present a major challenge in biomedical image restoration. In this paper, we propose a low-rank decomposition-based method for computed tomography (CT) image sequence restoration, where the CT image sequence is decomposed into a sparse component and a low-rank component. A new point spread function of Weiner filter is employed to efficiently remove blur in the sparse component; a wiener filtering with the Gaussian PSF is used to recover the average image of the low-rank component. And then we get the recovered CT image sequence by combining the recovery low-rank image with all recovery sparse image sequence. Our method achieves restoration results with higher contrast, sharper organ boundaries and richer soft tissue structure information, compared with existing CT image restoration methods. The robustness of our method was assessed with numerical experiments using three different low-rank models: Robust Principle Component Analysis (RPCA), Linearized Alternating Direction Method with Adaptive Penalty (LADMAP) and Go Decomposition (GoDec). Experimental results demonstrated that the RPCA model was the most suitable for the small noise CT images whereas the GoDec model was the best for the large noisy CT images. PMID:24023764

Hyperspectral chemical plume detection algorithms based on multidimensional iterative filtering decomposition.

PubMed

Cicone, A; Liu, J; Zhou, H

2016-04-13

Chemicals released in the air can be extremely dangerous for human beings and the environment. Hyperspectral images can be used to identify chemical plumes, however the task can be extremely challenging. Assuming we know a priori that some chemical plume, with a known frequency spectrum, has been photographed using a hyperspectral sensor, we can use standard techniques such as the so-called matched filter or adaptive cosine estimator, plus a properly chosen threshold value, to identify the position of the chemical plume. However, due to noise and inadequate sensing, the accurate identification of chemical pixels is not easy even in this apparently simple situation. In this paper, we present a post-processing tool that, in a completely adaptive and data-driven fashion, allows us to improve the performance of any classification methods in identifying the boundaries of a plume. This is done using the multidimensional iterative filtering (MIF) algorithm (Cicone et al. 2014 (http://arxiv.org/abs/1411.6051); Cicone & Zhou 2015 (http://arxiv.org/abs/1507.07173)), which is a non-stationary signal decomposition method like the pioneering empirical mode decomposition method (Huang et al. 1998 Proc. R. Soc. Lond. A 454, 903. (doi:10.1098/rspa.1998.0193)). Moreover, based on the MIF technique, we propose also a pre-processing method that allows us to decorrelate and mean-centre a hyperspectral dataset. The cosine similarity measure, which often fails in practice, appears to become a successful and outperforming classifier when equipped with such a pre-processing method. We show some examples of the proposed methods when applied to real-life problems. © 2016 The Author(s).

Uncoupling of Bacterial and Terrigenous Dissolved Organic Matter Dynamics in Decomposition Experiments

PubMed Central

Herlemann, Daniel P. R.; Manecki, Marcus; Meeske, Christian; Pollehne, Falk; Labrenz, Matthias; Schulz-Bull, Detlef; Dittmar, Thorsten; Jürgens, Klaus

2014-01-01

The biodegradability of terrigenous dissolved organic matter (tDOM) exported to the sea has a major impact on the global carbon cycle, but our understanding of tDOM bioavailability is fragmentary. In this study, the effects of preparative tDOM isolation on microbial decomposition were investigated in incubation experiments consisting of mesocosms containing mesohaline water from the Baltic Sea. Dissolved organic carbon (DOC) consumption, molecular DOM composition, bacterial activities, and shifts in bacterial community structure were compared between mesocosms supplemented with riverine tDOM, either as filtered, particle-free river water or as a concentrate obtained by lyophilization/tangential ultrafiltration, and those containing only Baltic Sea water or river water. As shown using ultra-high-resolution mass spectrometry (15 Tesla Fourier-transform ion cyclotron resonance mass spectrometry, FT-ICR-MS) covering approximately 4600 different DOM compounds, the three DOM preparation protocols resulted in distinct patterns of molecular DOM composition. However, despite DOC losses of 4–16% and considerable bacterial production, there was no significant change in DOM composition during the 28-day experiment. Moreover, tDOM addition affected neither DOC degradation nor bacterial dynamics significantly, regardless of the tDOM preparation. This result suggested that the introduced tDOM was largely not bioavailable, at least on the temporal scale of our experiment, and that the observed bacterial activity and DOC decomposition mainly reflected the degradation of unknown, labile, colloidal and low-molecular weight DOM, both of which escape the analytical window of FT-ICR-MS. In contrast to the different tDOM preparations, the initial bacterial inoculum and batch culture conditions determined bacterial community succession and superseded the effects of tDOM addition. The uncoupling of tDOM and bacterial dynamics suggests that mesohaline bacterial communities cannot

Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

NASA Astrophysics Data System (ADS)

Zhang, Gaigong; Lin, Lin; Hu, Wei; Yang, Chao; Pask, John E.

2017-04-01

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn-Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann-Feynman forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Since the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann-Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H2 and liquid Al-Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.

Cluster decomposition of full configuration interaction wave functions: A tool for chemical interpretation of systems with strong correlation

NASA Astrophysics Data System (ADS)

Lehtola, Susi; Tubman, Norm M.; Whaley, K. Birgitta; Head-Gordon, Martin

2017-10-01

Approximate full configuration interaction (FCI) calculations have recently become tractable for systems of unforeseen size, thanks to stochastic and adaptive approximations to the exponentially scaling FCI problem. The result of an FCI calculation is a weighted set of electronic configurations, which can also be expressed in terms of excitations from a reference configuration. The excitation amplitudes contain information on the complexity of the electronic wave function, but this information is contaminated by contributions from disconnected excitations, i.e., those excitations that are just products of independent lower-level excitations. The unwanted contributions can be removed via a cluster decomposition procedure, making it possible to examine the importance of connected excitations in complicated multireference molecules which are outside the reach of conventional algorithms. We present an implementation of the cluster decomposition analysis and apply it to both true FCI wave functions, as well as wave functions generated from the adaptive sampling CI algorithm. The cluster decomposition is useful for interpreting calculations in chemical studies, as a diagnostic for the convergence of various excitation manifolds, as well as as a guidepost for polynomially scaling electronic structure models. Applications are presented for (i) the double dissociation of water, (ii) the carbon dimer, (iii) the π space of polyacenes, and (iv) the chromium dimer. While the cluster amplitudes exhibit rapid decay with an increasing rank for the first three systems, even connected octuple excitations still appear important in Cr2, suggesting that spin-restricted single-reference coupled-cluster approaches may not be tractable for some problems in transition metal chemistry.

An analysis of scatter decomposition

NASA Technical Reports Server (NTRS)

Nicol, David M.; Saltz, Joel H.

1990-01-01

A formal analysis of a powerful mapping technique known as scatter decomposition is presented. Scatter decomposition divides an irregular computational domain into a large number of equal sized pieces, and distributes them modularly among processors. A probabilistic model of workload in one dimension is used to formally explain why, and when scatter decomposition works. The first result is that if correlation in workload is a convex function of distance, then scattering a more finely decomposed domain yields a lower average processor workload variance. The second result shows that if the workload process is stationary Gaussian and the correlation function decreases linearly in distance until becoming zero and then remains zero, scattering a more finely decomposed domain yields a lower expected maximum processor workload. Finally it is shown that if the correlation function decreases linearly across the entire domain, then among all mappings that assign an equal number of domain pieces to each processor, scatter decomposition minimizes the average processor workload variance. The dependence of these results on the assumption of decreasing correlation is illustrated with situations where a coarser granularity actually achieves better load balance.

Eliminating the zero spectrum in Fourier transform profilometry using empirical mode decomposition.

PubMed

Li, Sikun; Su, Xianyu; Chen, Wenjing; Xiang, Liqun

2009-05-01

Empirical mode decomposition is introduced into Fourier transform profilometry to extract the zero spectrum included in the deformed fringe pattern without the need for capturing two fringe patterns with pi phase difference. The fringe pattern is subsequently demodulated using a standard Fourier transform profilometry algorithm. With this method, the deformed fringe pattern is adaptively decomposed into a finite number of intrinsic mode functions that vary from high frequency to low frequency by means of an algorithm referred to as a sifting process. Then the zero spectrum is separated from the high-frequency components effectively. Experiments validate the feasibility of this method.

Error reduction in EMG signal decomposition

PubMed Central

Kline, Joshua C.

2014-01-01

Decomposition of the electromyographic (EMG) signal into constituent action potentials and the identification of individual firing instances of each motor unit in the presence of ambient noise are inherently probabilistic processes, whether performed manually or with automated algorithms. Consequently, they are subject to errors. We set out to classify and reduce these errors by analyzing 1,061 motor-unit action-potential trains (MUAPTs), obtained by decomposing surface EMG (sEMG) signals recorded during human voluntary contractions. Decomposition errors were classified into two general categories: location errors representing variability in the temporal localization of each motor-unit firing instance and identification errors consisting of falsely detected or missed firing instances. To mitigate these errors, we developed an error-reduction algorithm that combines multiple decomposition estimates to determine a more probable estimate of motor-unit firing instances with fewer errors. The performance of the algorithm is governed by a trade-off between the yield of MUAPTs obtained above a given accuracy level and the time required to perform the decomposition. When applied to a set of sEMG signals synthesized from real MUAPTs, the identification error was reduced by an average of 1.78%, improving the accuracy to 97.0%, and the location error was reduced by an average of 1.66 ms. The error-reduction algorithm in this study is not limited to any specific decomposition strategy. Rather, we propose it be used for other decomposition methods, especially when analyzing precise motor-unit firing instances, as occurs when measuring synchronization. PMID:25210159

Reduced rank regression via adaptive nuclear norm penalization

PubMed Central

Chen, Kun; Dong, Hongbo; Chan, Kung-Sik

2014-01-01

Summary We propose an adaptive nuclear norm penalization approach for low-rank matrix approximation, and use it to develop a new reduced rank estimation method for high-dimensional multivariate regression. The adaptive nuclear norm is defined as the weighted sum of the singular values of the matrix, and it is generally non-convex under the natural restriction that the weight decreases with the singular value. However, we show that the proposed non-convex penalized regression method has a global optimal solution obtained from an adaptively soft-thresholded singular value decomposition. The method is computationally efficient, and the resulting solution path is continuous. The rank consistency of and prediction/estimation performance bounds for the estimator are established for a high-dimensional asymptotic regime. Simulation studies and an application in genetics demonstrate its efficacy. PMID:25045172

Nitromethane decomposition under high static pressure.

PubMed

Citroni, Margherita; Bini, Roberto; Pagliai, Marco; Cardini, Gianni; Schettino, Vincenzo

2010-07-29

The room-temperature pressure-induced reaction of nitromethane has been studied by means of infrared spectroscopy in conjunction with ab initio molecular dynamics simulations. The evolution of the IR spectrum during the reaction has been monitored at 32.2 and 35.5 GPa performing the measurements in a diamond anvil cell. The simulations allowed the characterization of the onset of the high-pressure reaction, showing that its mechanism has a complex bimolecular character and involves the formation of the aci-ion of nitromethane. The growth of a three-dimensional disordered polymer has been evidenced both in the experiments and in the simulations. On decompression of the sample, after the reaction, a continuous evolution of the product is observed with a decomposition into smaller molecules. This behavior has been confirmed by the simulations and represents an important novelty in the scene of the known high-pressure reactions of molecular systems. The major reaction product on decompression is N-methylformamide, the smallest molecule containing the peptide bond. The high-pressure reaction of crystalline nitromethane under irradiation at 458 nm was also experimentally studied. The reaction threshold pressure is significantly lowered by the electronic excitation through two-photon absorption, and methanol, not detected in the purely pressure-induced reaction, is formed. The presence of ammonium carbonate is also observed.

Reactive Goal Decomposition Hierarchies for On-Board Autonomy

NASA Astrophysics Data System (ADS)

Hartmann, L.

2002-01-01

As our experience grows, space missions and systems are expected to address ever more complex and demanding requirements with fewer resources (e.g., mass, power, budget). One approach to accommodating these higher expectations is to increase the level of autonomy to improve the capabilities and robustness of on- board systems and to simplify operations. The goal decomposition hierarchies described here provide a simple but powerful form of goal-directed behavior that is relatively easy to implement for space systems. A goal corresponds to a state or condition that an operator of the space system would like to bring about. In the system described here goals are decomposed into simpler subgoals until the subgoals are simple enough to execute directly. For each goal there is an activation condition and a set of decompositions. The decompositions correspond to different ways of achieving the higher level goal. Each decomposition contains a gating condition and a set of subgoals to be "executed" sequentially or in parallel. The gating conditions are evaluated in order and for the first one that is true, the corresponding decomposition is executed in order to achieve the higher level goal. The activation condition specifies global conditions (i.e., for all decompositions of the goal) that need to hold in order for the goal to be achieved. In real-time, parameters and state information are passed between goals and subgoals in the decomposition; a termination indication (success, failure, degree) is passed up when a decomposition finishes executing. The lowest level decompositions include servo control loops and finite state machines for generating control signals and sequencing i/o. Semaphores and shared memory are used to synchronize and coordinate decompositions that execute in parallel. The goal decomposition hierarchy is reactive in that the generated behavior is sensitive to the real-time state of the system and the environment. That is, the system is able to react

Litter quality versus soil microbial community controls over decomposition: a quantitative analysis

USGS Publications Warehouse

Cleveland, Cory C.; Reed, Sasha C.; Keller, Adrienne B.; Nemergut, Diana R.; O'Neill, Sean P.; Ostertag, Rebecca; Vitousek, Peter M.

2014-01-01

The possible effects of soil microbial community structure on organic matter decomposition rates have been widely acknowledged, but are poorly understood. Understanding these relationships is complicated by the fact that microbial community structure and function are likely to both affect and be affected by organic matter quality and chemistry, thus it is difficult to draw mechanistic conclusions from field studies. We conducted a reciprocal soil inoculum × litter transplant laboratory incubation experiment using samples collected from a set of sites that have similar climate and plant species composition but vary significantly in bacterial community structure and litter quality. The results showed that litter quality explained the majority of variation in decomposition rates under controlled laboratory conditions: over the course of the 162-day incubation, litter quality explained nearly two-thirds (64 %) of variation in decomposition rates, and a smaller proportion (25 %) was explained by variation in the inoculum type. In addition, the relative importance of inoculum type on soil respiration increased over the course of the experiment, and was significantly higher in microcosms with lower litter quality relative to those with higher quality litter. We also used molecular phylogenetics to examine the relationships between bacterial community composition and soil respiration in samples through time. Pyrosequencing revealed that bacterial community composition explained 32 % of the variation in respiration rates. However, equal portions (i.e., 16 %) of the variation in bacterial community composition were explained by inoculum type and litter quality, reflecting the importance of both the meta-community and the environment in bacterial assembly. Taken together, these results indicate that the effects of changing microbial community composition on decomposition are likely to be smaller than the potential effects of climate change and/or litter quality changes in

Basis material decomposition in spectral CT using a semi-empirical, polychromatic adaption of the Beer-Lambert model.

PubMed

Ehn, S; Sellerer, T; Mechlem, K; Fehringer, A; Epple, M; Herzen, J; Pfeiffer, F; Noël, P B

2017-01-07

Following the development of energy-sensitive photon-counting detectors using high-Z sensor materials, application of spectral x-ray imaging methods to clinical practice comes into reach. However, these detectors require extensive calibration efforts in order to perform spectral imaging tasks like basis material decomposition. In this paper, we report a novel approach to basis material decomposition that utilizes a semi-empirical estimator for the number of photons registered in distinct energy bins in the presence of beam-hardening effects which can be termed as a polychromatic Beer-Lambert model. A maximum-likelihood estimator is applied to the model in order to obtain estimates of the underlying sample composition. Using a Monte-Carlo simulation of a typical clinical CT acquisition, the performance of the proposed estimator was evaluated. The estimator is shown to be unbiased and efficient according to the Cramér-Rao lower bound. In particular, the estimator is capable of operating with a minimum number of calibration measurements. Good results were obtained after calibration using less than 10 samples of known composition in a two-material attenuation basis. This opens up the possibility for fast re-calibration in the clinical routine which is considered an advantage of the proposed method over other implementations reported in the literature.

Basis material decomposition in spectral CT using a semi-empirical, polychromatic adaption of the Beer-Lambert model

NASA Astrophysics Data System (ADS)

Ehn, S.; Sellerer, T.; Mechlem, K.; Fehringer, A.; Epple, M.; Herzen, J.; Pfeiffer, F.; Noël, P. B.

2017-01-01

Following the development of energy-sensitive photon-counting detectors using high-Z sensor materials, application of spectral x-ray imaging methods to clinical practice comes into reach. However, these detectors require extensive calibration efforts in order to perform spectral imaging tasks like basis material decomposition. In this paper, we report a novel approach to basis material decomposition that utilizes a semi-empirical estimator for the number of photons registered in distinct energy bins in the presence of beam-hardening effects which can be termed as a polychromatic Beer-Lambert model. A maximum-likelihood estimator is applied to the model in order to obtain estimates of the underlying sample composition. Using a Monte-Carlo simulation of a typical clinical CT acquisition, the performance of the proposed estimator was evaluated. The estimator is shown to be unbiased and efficient according to the Cramér-Rao lower bound. In particular, the estimator is capable of operating with a minimum number of calibration measurements. Good results were obtained after calibration using less than 10 samples of known composition in a two-material attenuation basis. This opens up the possibility for fast re-calibration in the clinical routine which is considered an advantage of the proposed method over other implementations reported in the literature.

Fast and robust reconstruction for fluorescence molecular tomography via a sparsity adaptive subspace pursuit method.

PubMed

Ye, Jinzuo; Chi, Chongwei; Xue, Zhenwen; Wu, Ping; An, Yu; Xu, Han; Zhang, Shuang; Tian, Jie

2014-02-01

Fluorescence molecular tomography (FMT), as a promising imaging modality, can three-dimensionally locate the specific tumor position in small animals. However, it remains challenging for effective and robust reconstruction of fluorescent probe distribution in animals. In this paper, we present a novel method based on sparsity adaptive subspace pursuit (SASP) for FMT reconstruction. Some innovative strategies including subspace projection, the bottom-up sparsity adaptive approach, and backtracking technique are associated with the SASP method, which guarantees the accuracy, efficiency, and robustness for FMT reconstruction. Three numerical experiments based on a mouse-mimicking heterogeneous phantom have been performed to validate the feasibility of the SASP method. The results show that the proposed SASP method can achieve satisfactory source localization with a bias less than 1mm; the efficiency of the method is much faster than mainstream reconstruction methods; and this approach is robust even under quite ill-posed condition. Furthermore, we have applied this method to an in vivo mouse model, and the results demonstrate the feasibility of the practical FMT application with the SASP method.

Chinese Orthographic Decomposition and Logographic Structure

ERIC Educational Resources Information Center

Cheng, Chao-Ming; Lin, Shan-Yuan

2013-01-01

"Chinese orthographic decomposition" refers to a sense of uncertainty about the writing of a well-learned Chinese character following a prolonged inspection of the character. This study investigated the decomposition phenomenon in a test situation in which Chinese characters were repeatedly presented in a word context and assessed…

Nitrosonium-Catalyzed Decomposition of S-Nitrosothiols in Solution

PubMed Central

Zhao, Yi-Lei; McCarren, Patrick R.; Houk, K. N.; Choi, Bo Yoon; Toone, Eric J.

2008-01-01

The decomposition of S-nitrosothiols (RSNO) in solution under oxidative conditions is significantly faster than can be accounted for by homolysis of the S-N bond. Here we propose a cationic chain mechanism in which nitrosylation of nitrosothiol produces a nitrosylated cation that, in turn, reacts with a second nitrosothiol to produce disulfide and the NO dimer. Nitrosylated dimer acts as a source of nitrosonium for nitrosothiol nitrosylation, completing the catalytic cycle. The mechanism accounts for several unexplained facets of nitrosothiol chemistry in solution, including the observation that the decomposition of an RSNO is accelerated by O2, mixtures of O2 and NO, and other oxidants, that decomposition is inhibited by thiols and other antioxidants, that decomposition is dependent on sulfur substitution, and that decomposition often shows non-integral kinetic orders. PMID:16076198

Nanofiller Presence Enhances Polycyclic Aromatic Hydrocarbon (PAH) Profile on Nanoparticles Released during Thermal Decomposition of Nano-enabled Thermoplastics: Potential Environmental Health Implications.

PubMed

Singh, Dilpreet; Schifman, Laura Arabella; Watson-Wright, Christa; Sotiriou, Georgios A; Oyanedel-Craver, Vinka; Wohlleben, Wendel; Demokritou, Philip

2017-05-02

Nano-enabled products are ultimately destined to reach end-of-life with an important fraction undergoing thermal degradation through waste incineration or accidental fires. Although previous studies have investigated the physicochemical properties of released lifecycle particulate matter (called LCPM) from thermal decomposition of nano-enabled thermoplastics, critical questions about the effect of nanofiller on the chemical composition of LCPM still persist. Here, we investigate the potential nanofiller effects on the profiles of 16 Environmental Protection Agency (EPA)-priority polycyclic aromatic hydrocarbons (PAHs) adsorbed on LCPM from thermal decomposition of nano-enabled thermoplastics. We found that nanofiller presence in thermoplastics significantly enhances not only the total PAH concentration in LCPM but most importantly also the high molecular weight (HMW, 4-6 ring) PAHs that are considerably more toxic than the low molecular weight (LMW, 2-3 ring) PAHs. This nano-specific effect was also confirmed during in vitro cellular toxicological evaluation of LCPM for the case of polyurethane thermoplastic enabled with carbon nanotubes (PU-CNT). LCPM from PU-CNT shows significantly higher cytotoxicity compared to PU which could be attributed to its higher HMW PAH concentration. These findings are crucial and make the case that nanofiller presence in thermoplastics can significantly affect the physicochemical and toxicological properties of LCPM released during thermal decomposition.

Chemistry of decomposition of freshwater wetland sedimentary organic material during ramped pyrolysis

NASA Astrophysics Data System (ADS)

Williams, E. K.; Rosenheim, B. E.

2011-12-01

Ramped pyrolysis methodology, such as that used in the programmed-temperature pyrolysis/combustion system (PTP/CS), improves radiocarbon analysis of geologic materials devoid of authigenic carbonate compounds and with low concentrations of extractable authochthonous organic molecules. The approach has improved sediment chronology in organic-rich sediments proximal to Antarctic ice shelves (Rosenheim et al., 2008) and constrained the carbon sequestration potential of suspended sediments in the lower Mississippi River (Roe et al., in review). Although ramped pyrolysis allows for separation of sedimentary organic material based upon relative reactivity, chemical information (i.e. chemical composition of pyrolysis products) is lost during the in-line combustion of pyrolysis products. A first order approximation of ramped pyrolysis/combustion system CO2 evolution, employing a simple Gaussian decomposition routine, has been useful (Rosenheim et al., 2008), but improvements may be possible. First, without prior compound-specific extractions, the molecular composition of sedimentary organic matter is unknown and/or unidentifiable. Second, even if determined as constituents of sedimentary organic material, many organic compounds have unknown or variable decomposition temperatures. Third, mixtures of organic compounds may result in significant chemistry within the pyrolysis reactor, prior to introduction of oxygen along the flow path. Gaussian decomposition of the reaction rate may be too simple to fully explain the combination of these factors. To relate both the radiocarbon age over different temperature intervals and the pyrolysis reaction thermograph (temperature (°C) vs. CO2 evolved (μmol)) obtained from PTP/CS to chemical composition of sedimentary organic material, we present a modeling framework developed based upon the ramped pyrolysis decomposition of simple mixtures of organic compounds (i.e. cellulose, lignin, plant fatty acids, etc.) often found in sedimentary

Geochemical drivers of organic matter decomposition in Arctic tundra soils

DOE PAGES

Herndon, Elizabeth M.; Yang, Ziming; Graham, David E.; ...

2015-12-07

Climate change is warming tundra ecosystems in the Arctic, resulting in the decomposition of previously-frozen soil organic matter (SOM) and release of carbon (C) to the atmosphere; however, the processes that control SOM decomposition and C emissions remain highly uncertain. In this study, we evaluate geochemical factors that influence anaerobic production of carbon dioxide (CO 2) and methane (CH 4) in the active layers of four ice-wedge polygons. Surface and soil pore waters were collected during the annual thaw season over a two-year period in an area containing waterlogged, low-centered polygons and well-drained, high-centered polygons. We report spatial and seasonalmore » patterns of dissolved gases in relation to the geochemical properties of Fe and organic C as determined using spectroscopic and chromatographic techniques. Iron was present as Fe(II) in soil solution near the permafrost boundary but enriched as Fe(III) in the middle of the active layer, similar to dissolved aromatic-C and organic acids. Dissolved CH 4 increased relative to dissolved CO 2 with depth and varied with soil moisture in the middle of the active layer in patterns that were positively correlated with the proportion of dissolved Fe(III) in transitional and low-centered polygon soils but negatively correlated in the drier flat- and high-centered polygons. These results suggest that microbial-mediated Fe oxidation and reduction influence respiration/fermentation of SOM and production of substrates (e.g., low-molecular-weight organic acids) for methanogenesis. As a result, we infer that geochemical differences induced by water saturation dictate microbial products of SOM decomposition, and Fe geochemistry is an important factor regulating methanogenesis in anoxic tundra soils.« less

Atomic and molecular adsorption on Au(111)

DOE PAGES

Santiago-Rodriguez, Yohaselly; Herron, Jeffrey A.; Curet-Arana, Maria C.; ...

2014-05-02

Periodic self-consistent density functional theory (DFT-GGA) calculations were used to study the adsorption of several atomic species, molecular species and molecular fragments on the Au(111) surface with a coverage of 1/4 monolayer (ML). Binding geometries, binding energies, and diffusion barriers were calculated for 27 species. Furthermore, we calculated the surface deformation energy associated with the binding events. The binding strength for all the analyzed species can be ordered as follows: NH 3 < NO < CO < CH 3 < HCO < NH 2 < COOH < OH < HCOO < CNH 2 < H < N < NH molecular species and fragments. The intramolecular and adsorbate-surface vibrational frequencies were calculated for all the adsorbates on their most energetically stable adsorption site. Most of the theoretical binding energies and frequencies agreed with experimental values reported in the literature. In general, the values obtained with the PW91 functional are more accurate than RPBE in reproducing these experimental binding energies. The energies of the adsorbed species were used to calculate the thermochemical potential energy surfaces for decomposition of CO, NO, N 2, NH 3 and CH 4, oxidation of CO, and hydrogenation of CO, CO 2 and NO, giving insight into the thermochemistry of these reactions on gold nanoparticles. As a result, these potential energy surfaces demonstrated that: the decomposition of species is not energetically favorable on Au(111); the desorption of NH 3, NO and CO are more favorable than their decomposition; the oxidation of CO and hydrogenation of CO and NO on Au(111) to form HCO and HNO, respectively, are also thermodynamically favorable.« less

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

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

Zhang, Gaigong; Lin, Lin, E-mail: linlin@math.berkeley.edu; Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Since the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H{sub 2} and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

DOE PAGES

Zhang, Gaigong; Lin, Lin; Hu, Wei; ...

2017-01-27

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Sin ce the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H 2 and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

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

Zhang, Gaigong; Lin, Lin; Hu, Wei

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Sin ce the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H 2 and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

Adaptation and diversity along an altitudinal gradient in Ethiopian barley (Hordeum vulgare L.) landraces revealed by molecular analysis

PubMed Central

2010-01-01

Background Among the cereal crops, barley is the species with the greatest adaptability to a wide range of environments. To determine the level and structure of genetic diversity in barley (Hordeum vulgare L.) landraces from the central highlands of Ethiopia, we have examined the molecular variation at seven nuclear microsatellite loci. Results A total of 106 landrace populations were sampled in the two growing seasons (Meher and Belg; the long and short rainy seasons, respectively), across three districts (Ankober, Mojanawadera and Tarmaber), and within each district along an altitudinal gradient (from 1,798 to 3,324 m a.s.l). Overall, although significant, the divergence (e.g. FST) is very low between seasons and geographical districts, while it is high between different classes of altitude. Selection for adaptation to different altitudes appears to be the main factor that has determined the observed clinal variation, along with population-size effects. Conclusions Our data show that barley landraces from Ethiopia are constituted by highly variable local populations (farmer's fields) that have large within-population diversity. These landraces are also shown to be locally adapted, with the major driving force that has shaped their population structure being consistent with selection for adaptation along an altitudinal gradient. Overall, our study highlights the potential of such landraces as a source of useful alleles. Furthermore, these landraces also represent an ideal system to study the processes of adaptation and for the identification of genes and genomic regions that have adaptive roles in crop species. PMID:20565982

On the hadron mass decomposition

NASA Astrophysics Data System (ADS)

Lorcé, Cédric

2018-02-01

We argue that the standard decompositions of the hadron mass overlook pressure effects, and hence should be interpreted with great care. Based on the semiclassical picture, we propose a new decomposition that properly accounts for these pressure effects. Because of Lorentz covariance, we stress that the hadron mass decomposition automatically comes along with a stability constraint, which we discuss for the first time. We show also that if a hadron is seen as made of quarks and gluons, one cannot decompose its mass into more than two contributions without running into trouble with the consistency of the physical interpretation. In particular, the so-called quark mass and trace anomaly contributions appear to be purely conventional. Based on the current phenomenological values, we find that in average quarks exert a repulsive force inside nucleons, balanced exactly by the gluon attractive force.

Thermal decomposition of ammonium hexachloroosmate.

PubMed

Asanova, T I; Kantor, I; Asanov, I P; Korenev, S V; Yusenko, K V

2016-12-07

Structural changes of (NH 4 ) 2 [OsCl 6 ] occurring during thermal decomposition in a reduction atmosphere have been studied in situ using combined energy-dispersive X-ray absorption spectroscopy (ED-XAFS) and powder X-ray diffraction (PXRD). According to PXRD, (NH 4 ) 2 [OsCl 6 ] transforms directly to metallic Os without the formation of any crystalline intermediates but through a plateau where no reactions occur. XANES and EXAFS data by means of Multivariate Curve Resolution (MCR) analysis show that thermal decomposition occurs with the formation of an amorphous intermediate {OsCl 4 } x with a possible polymeric structure. Being revealed for the first time the intermediate was subjected to determine the local atomic structure around osmium. The thermal decomposition of hexachloroosmate is much more complex and occurs within a minimum two-step process, which has never been observed before.

Conductimetric determination of decomposition of silicate melts

NASA Technical Reports Server (NTRS)

Kroeger, C.; Lieck, K.

1986-01-01

A description of a procedure is given to detect decomposition of silicate systems in the liquid state by conductivity measurements. Onset of decomposition can be determined from the temperature curves of resistances measured on two pairs of electrodes, one above the other. Degree of decomposition can be estimated from temperature and concentration dependency of conductivity of phase boundaries. This procedure was tested with systems PbO-B2O3 and PbO-B2O3-SiO2.

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

Early stage litter decomposition across biomes

Treesearch

Ika Djukic; Sebastian Kepfer-Rojas; Inger Kappel Schmidt; Klaus Steenberg Larsen; Claus Beier; Björn Berg; Kris Verheyen; Adriano Caliman; Alain Paquette; Alba Gutiérrez-Girón; Alberto Humber; Alejandro Valdecantos; Alessandro Petraglia; Heather Alexander; Algirdas Augustaitis; Amélie Saillard; Ana Carolina Ruiz Fernández; Ana I. Sousa; Ana I. Lillebø; Anderson da Rocha Gripp; André-Jean Francez; Andrea Fischer; Andreas Bohner; Andrey Malyshev; Andrijana Andrić; Andy Smith; Angela Stanisci; Anikó Seres; Anja Schmidt; Anna Avila; Anne Probst; Annie Ouin; Anzar A. Khuroo; Arne Verstraeten; Arely N. Palabral-Aguilera; Artur Stefanski; Aurora Gaxiola; Bart Muys; Bernard Bosman; Bernd Ahrends; Bill Parker; Birgit Sattler; Bo Yang; Bohdan Juráni; Brigitta Erschbamer; Carmen Eugenia Rodriguez Ortiz; Casper T. Christiansen; E. Carol Adair; Céline Meredieu; Cendrine Mony; Charles A. Nock; Chi-Ling Chen; Chiao-Ping Wang; Christel Baum; Christian Rixen; Christine Delire; Christophe Piscart; Christopher Andrews; Corinna Rebmann; Cristina Branquinho; Dana Polyanskaya; David Fuentes Delgado; Dirk Wundram; Diyaa Radeideh; Eduardo Ordóñez-Regil; Edward Crawford; Elena Preda; Elena Tropina; Elli Groner; Eric Lucot; Erzsébet Hornung; Esperança Gacia; Esther Lévesque; Evanilde Benedito; Evgeny A. Davydov; Evy Ampoorter; Fabio Padilha Bolzan; Felipe Varela; Ferdinand Kristöfel; Fernando T. Maestre; Florence Maunoury-Danger; Florian Hofhansl; Florian Kitz; Flurin Sutter; Francisco Cuesta; Francisco de Almeida Lobo; Franco Leandro de Souza; Frank Berninger; Franz Zehetner; Georg Wohlfahrt; George Vourlitis; Geovana Carreño-Rocabado; Gina Arena; Gisele Daiane Pinha; Grizelle González; Guylaine Canut; Hanna Lee; Hans Verbeeck; Harald Auge; Harald Pauli; Hassan Bismarck Nacro; Héctor A. Bahamonde; Heike Feldhaar; Heinke Jäger; Helena C. Serrano; Hélène Verheyden; Helge Bruelheide; Henning Meesenburg; Hermann Jungkunst; Hervé Jactel; Hideaki Shibata; Hiroko Kurokawa; Hugo López Rosas; Hugo L. Rojas Villalobos; Ian Yesilonis; Inara Melece; Inge Van Halder; Inmaculada García Quirós; Isaac Makelele; Issaka Senou; István Fekete; Ivan Mihal; Ivika Ostonen; Jana Borovská; Javier Roales; Jawad Shoqeir; Jean-Christophe Lata; Jean-Paul Theurillat; Jean-Luc Probst; Jess Zimmerman; Jeyanny Vijayanathan; Jianwu Tang; Jill Thompson; Jiří Doležal; Joan-Albert Sanchez-Cabeza; Joël Merlet; Joh Henschel; Johan Neirynck; Johannes Knops; John Loehr; Jonathan von Oppen; Jónína Sigríður Þorláksdóttir; Jörg Löffler; José-Gilberto Cardoso-Mohedano; José-Luis Benito-Alonso; Jose Marcelo Torezan; Joseph C. Morina; Juan J. Jiménez; Juan Dario Quinde; Juha Alatalo; Julia Seeber; Jutta Stadler; Kaie Kriiska; Kalifa Coulibaly; Karibu Fukuzawa; Katalin Szlavecz; Katarína Gerhátová; Kate Lajtha; Kathrin Käppeler; Katie A. Jennings; Katja Tielbörger; Kazuhiko Hoshizaki; Ken Green; Lambiénou Yé; Laryssa Helena Ribeiro Pazianoto; Laura Dienstbach; Laura Williams; Laura Yahdjian; Laurel M. Brigham; Liesbeth van den Brink; Lindsey Rustad; al. et

2018-01-01

Through litter decomposition enormous amounts of carbon is emitted to the atmosphere. Numerous large-scale decomposition experiments have been conducted focusing on this fundamental soil process in order to understand the controls on the terrestrial carbon transfer to the atmosphere. However, previous studies were mostly based on site-specific litter and methodologies...

Plant Identity Influences Decomposition through More Than One Mechanism

PubMed Central

McLaren, Jennie R.; Turkington, Roy

2011-01-01

Plant litter decomposition is a critical ecosystem process representing a major pathway for carbon flux, but little is known about how it is affected by changes in plant composition and diversity. Single plant functional groups (graminoids, legumes, non-leguminous forbs) were removed from a grassland in northern Canada to examine the impacts of functional group identity on decomposition. Removals were conducted within two different environmental contexts (fertilization and fungicide application) to examine the context-dependency of these identity effects. We examined two different mechanisms by which the loss of plant functional groups may impact decomposition: effects of the living plant community on the decomposition microenvironment, and changes in the species composition of the decomposing litter, as well as the interaction between these mechanisms. We show that the identity of the plant functional group removed affects decomposition through both mechanisms. Removal of both graminoids and forbs slowed decomposition through changes in the decomposition microenvironment. We found non-additive effects of litter mixing, with both the direction and identity of the functional group responsible depending on year; in 2004 graminoids positively influenced decomposition whereas in 2006 forbs negatively influenced decomposition rate. Although these two mechanisms act independently, their effects may be additive if both mechanisms are considered simultaneously. It is essential to understand the variety of mechanisms through which even a single ecosystem property is affected if we are to predict the future consequences of biodiversity loss. PMID:21858210

Offset-sparsity decomposition for enhancement of color microscopic image of stained specimen in histopathology: further results

NASA Astrophysics Data System (ADS)

Kopriva, Ivica; Popović Hadžija, Marijana; Hadžija, Mirko; Aralica, Gorana

2016-03-01

Recently, novel data-driven offset-sparsity decomposition (OSD) method was proposed by us to increase colorimetric difference between tissue-structures present in the color microscopic image of stained specimen in histopathology. The OSD method performs additive decomposition of vectorized spectral images into image-adapted offset term and sparse term. Thereby, the sparse term represents an enhanced image. The method was tested on images of the histological slides of human liver stained with hematoxylin and eosin, anti-CD34 monoclonal antibody and Sudan III. Herein, we present further results related to increase of colorimetric difference between tissue structures present in the images of human liver specimens with pancreatic carcinoma metastasis stained with Gomori, CK7, CDX2 and LCA, and with colon carcinoma metastasis stained with Gomori, CK20 and PAN CK. Obtained relative increase of colorimetric difference is in the range [19.36%, 103.94%].

Traits drive global wood decomposition rates more than climate.

PubMed

Hu, Zhenhong; Michaletz, Sean T; Johnson, Daniel J; McDowell, Nate G; Huang, Zhiqun; Zhou, Xuhui; Xu, Chonggang

2018-06-14

Wood decomposition is a major component of the global carbon cycle. Decomposition rates vary across climate gradients, which is thought to reflect the effects of temperature and moisture on the metabolic kinetics of decomposers. However, decomposition rates also vary with wood traits, which may reflect the influence of stoichiometry on decomposer metabolism as well as geometry relating the surface areas that decomposers colonize with the volumes they consume. In this paper, we combined metabolic and geometric scaling theories to formalize hypotheses regarding the drivers of wood decomposition rates, and assessed these hypotheses using a global compilation of data on climate, wood traits, and wood decomposition rates. Our results are consistent with predictions from both metabolic and geometric scaling theories. Approximately half of the global variation in decomposition rates was explained by wood traits (nitrogen content and diameter), while only a fifth was explained by climate variables (air temperature, precipitation, and relative humidity). These results indicate that global variation in wood decomposition rates is best explained by stoichiometric and geometric wood traits. Our findings suggest that inclusion of wood traits in global carbon cycle models can improve predictions of carbon fluxes from wood decomposition. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics

NASA Astrophysics Data System (ADS)

Xie, Dexuan

2014-10-01

The Poisson-Boltzmann equation (PBE) is one widely-used implicit solvent continuum model in the calculation of electrostatic potential energy for biomolecules in ionic solvent, but its numerical solution remains a challenge due to its strong singularity and nonlinearity caused by its singular distribution source terms and exponential nonlinear terms. To effectively deal with such a challenge, in this paper, new solution decomposition and minimization schemes are proposed, together with a new PBE analysis on solution existence and uniqueness. Moreover, a PBE finite element program package is developed in Python based on the FEniCS program library and GAMer, a molecular surface and volumetric mesh generation program package. Numerical tests on proteins and a nonlinear Born ball model with an analytical solution validate the new solution decomposition and minimization schemes, and demonstrate the effectiveness and efficiency of the new PBE finite element program package.

Ab initio kinetics of gas phase decomposition reactions.

PubMed

Sharia, Onise; Kuklja, Maija M

2010-12-09

The thermal and kinetic aspects of gas phase decomposition reactions can be extremely complex due to a large number of parameters, a variety of possible intermediates, and an overlap in thermal decomposition traces. The experimental determination of the activation energies is particularly difficult when several possible reaction pathways coexist in the thermal decomposition. Ab initio calculations intended to provide an interpretation of the experiment are often of little help if they produce only the activation barriers and ignore the kinetics of the decomposition process. To overcome this ambiguity, a theoretical study of a complete picture of gas phase thermo-decomposition, including reaction energies, activation barriers, and reaction rates, is illustrated with the example of the β-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) molecule by means of quantum-chemical calculations. We study three types of major decomposition reactions characteristic of nitramines: the HONO elimination, the NONO rearrangement, and the N-NO(2) homolysis. The reaction rates were determined using the conventional transition state theory for the HONO and NONO decompositions and the variational transition state theory for the N-NO(2) homolysis. Our calculations show that the HMX decomposition process is more complex than it was previously believed to be and is defined by a combination of reactions at any given temperature. At all temperatures, the direct N-NO(2) homolysis prevails with the activation barrier at 38.1 kcal/mol. The nitro-nitrite isomerization and the HONO elimination, with the activation barriers at 46.3 and 39.4 kcal/mol, respectively, are slow reactions at all temperatures. The obtained conclusions provide a consistent interpretation for the reported experimental data.

Optimization by nonhierarchical asynchronous decomposition

NASA Technical Reports Server (NTRS)

Shankar, Jayashree; Ribbens, Calvin J.; Haftka, Raphael T.; Watson, Layne T.

1992-01-01

Large scale optimization problems are tractable only if they are somehow decomposed. Hierarchical decompositions are inappropriate for some types of problems and do not parallelize well. Sobieszczanski-Sobieski has proposed a nonhierarchical decomposition strategy for nonlinear constrained optimization that is naturally parallel. Despite some successes on engineering problems, the algorithm as originally proposed fails on simple two dimensional quadratic programs. The algorithm is carefully analyzed for quadratic programs, and a number of modifications are suggested to improve its robustness.

Adaptively biased molecular dynamics: An umbrella sampling method with a time-dependent potential

NASA Astrophysics Data System (ADS)

Babin, Volodymyr; Karpusenka, Vadzim; Moradi, Mahmoud; Roland, Christopher; Sagui, Celeste

We discuss an adaptively biased molecular dynamics (ABMD) method for the computation of a free energy surface for a set of reaction coordinates. The ABMD method belongs to the general category of umbrella sampling methods with an evolving biasing potential. It is characterized by a small number of control parameters and an O(t) numerical cost with simulation time t. The method naturally allows for extensions based on multiple walkers and replica exchange mechanism. The workings of the method are illustrated with a number of examples, including sugar puckering, and free energy landscapes for polymethionine and polyproline peptides, and for a short β-turn peptide. ABMD has been implemented into the latest version (Case et al., AMBER 10; University of California: San Francisco, 2008) of the AMBER software package and is freely available to the simulation community.

Randomized Dynamic Mode Decomposition

NASA Astrophysics Data System (ADS)

Erichson, N. Benjamin; Brunton, Steven L.; Kutz, J. Nathan

2017-11-01

The dynamic mode decomposition (DMD) is an equation-free, data-driven matrix decomposition that is capable of providing accurate reconstructions of spatio-temporal coherent structures arising in dynamical systems. We present randomized algorithms to compute the near-optimal low-rank dynamic mode decomposition for massive datasets. Randomized algorithms are simple, accurate and able to ease the computational challenges arising with `big data'. Moreover, randomized algorithms are amenable to modern parallel and distributed computing. The idea is to derive a smaller matrix from the high-dimensional input data matrix using randomness as a computational strategy. Then, the dynamic modes and eigenvalues are accurately learned from this smaller representation of the data, whereby the approximation quality can be controlled via oversampling and power iterations. Here, we present randomized DMD algorithms that are categorized by how many passes the algorithm takes through the data. Specifically, the single-pass randomized DMD does not require data to be stored for subsequent passes. Thus, it is possible to approximately decompose massive fluid flows (stored out of core memory, or not stored at all) using single-pass algorithms, which is infeasible with traditional DMD algorithms.

Multi-scale pixel-based image fusion using multivariate empirical mode decomposition.

PubMed

Rehman, Naveed ur; Ehsan, Shoaib; Abdullah, Syed Muhammad Umer; Akhtar, Muhammad Jehanzaib; Mandic, Danilo P; McDonald-Maier, Klaus D

2015-05-08

A novel scheme to perform the fusion of multiple images using the multivariate empirical mode decomposition (MEMD) algorithm is proposed. Standard multi-scale fusion techniques make a priori assumptions regarding input data, whereas standard univariate empirical mode decomposition (EMD)-based fusion techniques suffer from inherent mode mixing and mode misalignment issues, characterized respectively by either a single intrinsic mode function (IMF) containing multiple scales or the same indexed IMFs corresponding to multiple input images carrying different frequency information. We show that MEMD overcomes these problems by being fully data adaptive and by aligning common frequency scales from multiple channels, thus enabling their comparison at a pixel level and subsequent fusion at multiple data scales. We then demonstrate the potential of the proposed scheme on a large dataset of real-world multi-exposure and multi-focus images and compare the results against those obtained from standard fusion algorithms, including the principal component analysis (PCA), discrete wavelet transform (DWT) and non-subsampled contourlet transform (NCT). A variety of image fusion quality measures are employed for the objective evaluation of the proposed method. We also report the results of a hypothesis testing approach on our large image dataset to identify statistically-significant performance differences.

Multi-Scale Pixel-Based Image Fusion Using Multivariate Empirical Mode Decomposition

PubMed Central

Rehman, Naveed ur; Ehsan, Shoaib; Abdullah, Syed Muhammad Umer; Akhtar, Muhammad Jehanzaib; Mandic, Danilo P.; McDonald-Maier, Klaus D.

2015-01-01

A novel scheme to perform the fusion of multiple images using the multivariate empirical mode decomposition (MEMD) algorithm is proposed. Standard multi-scale fusion techniques make a priori assumptions regarding input data, whereas standard univariate empirical mode decomposition (EMD)-based fusion techniques suffer from inherent mode mixing and mode misalignment issues, characterized respectively by either a single intrinsic mode function (IMF) containing multiple scales or the same indexed IMFs corresponding to multiple input images carrying different frequency information. We show that MEMD overcomes these problems by being fully data adaptive and by aligning common frequency scales from multiple channels, thus enabling their comparison at a pixel level and subsequent fusion at multiple data scales. We then demonstrate the potential of the proposed scheme on a large dataset of real-world multi-exposure and multi-focus images and compare the results against those obtained from standard fusion algorithms, including the principal component analysis (PCA), discrete wavelet transform (DWT) and non-subsampled contourlet transform (NCT). A variety of image fusion quality measures are employed for the objective evaluation of the proposed method. We also report the results of a hypothesis testing approach on our large image dataset to identify statistically-significant performance differences. PMID:26007714

Cadaver decomposition in terrestrial ecosystems

NASA Astrophysics Data System (ADS)

Carter, David O.; Yellowlees, David; Tibbett, Mark

2007-01-01

A dead mammal (i.e. cadaver) is a high quality resource (narrow carbon:nitrogen ratio, high water content) that releases an intense, localised pulse of carbon and nutrients into the soil upon decomposition. Despite the fact that as much as 5,000 kg of cadaver can be introduced to a square kilometre of terrestrial ecosystem each year, cadaver decomposition remains a neglected microsere. Here we review the processes associated with the introduction of cadaver-derived carbon and nutrients into soil from forensic and ecological settings to show that cadaver decomposition can have a greater, albeit localised, effect on belowground ecology than plant and faecal resources. Cadaveric materials are rapidly introduced to belowground floral and faunal communities, which results in the formation of a highly concentrated island of fertility, or cadaver decomposition island (CDI). CDIs are associated with increased soil microbial biomass, microbial activity (C mineralisation) and nematode abundance. Each CDI is an ephemeral natural disturbance that, in addition to releasing energy and nutrients to the wider ecosystem, acts as a hub by receiving these materials in the form of dead insects, exuvia and puparia, faecal matter (from scavengers, grazers and predators) and feathers (from avian scavengers and predators). As such, CDIs contribute to landscape heterogeneity. Furthermore, CDIs are a specialised habitat for a number of flies, beetles and pioneer vegetation, which enhances biodiversity in terrestrial ecosystems.

Mapping of the extinction in giant molecular clouds using optical star counts

NASA Astrophysics Data System (ADS)

Cambrésy, L.

1999-05-01

This paper presents large scale extinction maps of most nearby Giant Molecular Clouds of the Galaxy (Lupus, rho Ophiuchus, Scorpius, Coalsack, Taurus, Chamaeleon, Musca, Corona Australis, Serpens, IC 5146, Vela, Orion, Monoceros R1 and R2, Rosette, Carina) derived from a star count method using an adaptive grid and a wavelet decomposition applied to the optical data provided by the USNO-Precision Measuring Machine. The distribution of the extinction in the clouds leads to estimate their total individual masses M and their maximum of extinction. I show that the relation between the mass contained within an iso-extinction contour and the extinction is similar from cloud to cloud and allows the extrapolation of the maximum of extinction in the range 5.7 to 25.5 magnitudes. I found that about half of the mass is contained in regions where the visual extinction is smaller than 1 magnitude. The star count method used on large scale ( ~ 250 square degrees) is a powerful and relatively straightforward method to estimate the mass of molecular complexes. A systematic study of the all sky would lead to discover new clouds as I did in the Lupus complex for which I found a sixth cloud of about 10(4) M_⊙.

A test of the hierarchical model of litter decomposition.

PubMed

Bradford, Mark A; Veen, G F Ciska; Bonis, Anne; Bradford, Ella M; Classen, Aimee T; Cornelissen, J Hans C; Crowther, Thomas W; De Long, Jonathan R; Freschet, Gregoire T; Kardol, Paul; Manrubia-Freixa, Marta; Maynard, Daniel S; Newman, Gregory S; Logtestijn, Richard S P; Viketoft, Maria; Wardle, David A; Wieder, William R; Wood, Stephen A; van der Putten, Wim H

2017-12-01

Our basic understanding of plant litter decomposition informs the assumptions underlying widely applied soil biogeochemical models, including those embedded in Earth system models. Confidence in projected carbon cycle-climate feedbacks therefore depends on accurate knowledge about the controls regulating the rate at which plant biomass is decomposed into products such as CO 2 . Here we test underlying assumptions of the dominant conceptual model of litter decomposition. The model posits that a primary control on the rate of decomposition at regional to global scales is climate (temperature and moisture), with the controlling effects of decomposers negligible at such broad spatial scales. Using a regional-scale litter decomposition experiment at six sites spanning from northern Sweden to southern France-and capturing both within and among site variation in putative controls-we find that contrary to predictions from the hierarchical model, decomposer (microbial) biomass strongly regulates decomposition at regional scales. Furthermore, the size of the microbial biomass dictates the absolute change in decomposition rates with changing climate variables. Our findings suggest the need for revision of the hierarchical model, with decomposers acting as both local- and broad-scale controls on litter decomposition rates, necessitating their explicit consideration in global biogeochemical models.

Through-wall image enhancement using fuzzy and QR decomposition.

PubMed

Riaz, Muhammad Mohsin; Ghafoor, Abdul

2014-01-01

QR decomposition and fuzzy logic based scheme is proposed for through-wall image enhancement. QR decomposition is less complex compared to singular value decomposition. Fuzzy inference engine assigns weights to different overlapping subspaces. Quantitative measures and visual inspection are used to analyze existing and proposed techniques.

Reactivity continuum modeling of leaf, root, and wood decomposition across biomes

NASA Astrophysics Data System (ADS)

Koehler, Birgit; Tranvik, Lars J.

2015-07-01

Large carbon dioxide amounts are released to the atmosphere during organic matter decomposition. Yet the large-scale and long-term regulation of this critical process in global carbon cycling by litter chemistry and climate remains poorly understood. We used reactivity continuum (RC) modeling to analyze the decadal data set of the "Long-term Intersite Decomposition Experiment," in which fine litter and wood decomposition was studied in eight biome types (224 time series). In 32 and 46% of all sites the litter content of the acid-unhydrolyzable residue (AUR, formerly referred to as lignin) and the AUR/nitrogen ratio, respectively, retarded initial decomposition rates. This initial rate-retarding effect generally disappeared within the first year of decomposition, and rate-stimulating effects of nutrients and a rate-retarding effect of the carbon/nitrogen ratio became more prevalent. For needles and leaves/grasses, the influence of climate on decomposition decreased over time. For fine roots, the climatic influence was initially smaller but increased toward later-stage decomposition. The climate decomposition index was the strongest climatic predictor of decomposition. The similar variability in initial decomposition rates across litter categories as across biome types suggested that future changes in decomposition may be dominated by warming-induced changes in plant community composition. In general, the RC model parameters successfully predicted independent decomposition data for the different litter-biome combinations (196 time series). We argue that parameterization of large-scale decomposition models with RC model parameters, as opposed to the currently common discrete multiexponential models, could significantly improve their mechanistic foundation and predictive accuracy across climate zones and litter categories.

VDR gene methylation as a molecular adaption to light exposure: Historic, recent and genetic influences.

PubMed

Beckett, Emma L; Jones, Patrice; Veysey, Martin; Duesing, Konsta; Martin, Charlotte; Furst, John; Yates, Zoe; Jablonski, Nina G; Chaplin, George; Lucock, Mark

2017-09-10

The vitamin D receptor (VDR) is a member of the nuclear receptor family of transcription factors. We examined whether degree of VDR gene methylation acts as a molecular adaptation to light exposure. We explored this in the context of photoperiod at conception, recent UV irradiance at 305 nm, and gene-latitude effects. Eighty subjects were examined for VDR gene-CpG island methylation density. VDR gene variants were also examined by PCR-RFLP. Photoperiod at conception was significantly positively related to VDR methylation density, explaining 17% of the variance in methylation (r 2  = 0.17; P = .001). Within this model, photoperiod at conception and plasma 25(OH)D independently predicted methylation density at the VDR-CpG island. Recent UV exposure at 305 nm led to a fivefold increase in mean methylation density (P = .02). Again, UV exposure and plasma 25(OH)D independently predicted methylation density at the VDR-CpG island. In the presence of the BsmI mutant allele, methylation density was increased (P = .01), and in the presence of the TaqI or FokI mutant allele, methylation density was decreased (P = .007 and .04 respectively). Multivariate modelling suggests plasma 25(OH)D, photoperiod at conception, recent solar irradiance, and VDR genotype combine as independent predictors of methylation at the VDR-CpG island, explaining 34% of the variance in methylation (R 2  = 0.34, P < .0001). Duration of early-life light exposure and strength of recent irradiance, along with latitudinal genetic factors, influence degree of VDR gene methylation consistent with this epigenetic phenomenon being a molecular adaptation to variation in ambient light exposure. Findings contribute to our understanding of human biology. © 2017 Wiley Periodicals, Inc.

Organic Carbon Sorption and Decomposition in Selected Global Soils

DOE Data Explorer

Jagadamma, S.; Mayes, M. A.; Steinweg, J. M.; Wang, G.; Post, W. M.

2014-01-01

This data set reports the results of lab-scale experiments conducted to investigate the dynamics of organic carbon (C) decomposition from several soils from temperate, tropical, arctic, and sub-arctic environments. Results were used to test the newly developed soil microbe decomposition C model--Microbial-ENzyme-medicated Decomposition (MEND).

Isothermal Decomposition of Hydrogen Peroxide Dihydrate

NASA Technical Reports Server (NTRS)

Loeffler, M. J.; Baragiola, R. A.

2011-01-01

We present a new method of growing pure solid hydrogen peroxide in an ultra high vacuum environment and apply it to determine thermal stability of the dihydrate compound that forms when water and hydrogen peroxide are mixed at low temperatures. Using infrared spectroscopy and thermogravimetric analysis, we quantified the isothermal decomposition of the metastable dihydrate at 151.6 K. This decomposition occurs by fractional distillation through the preferential sublimation of water, which leads to the formation of pure hydrogen peroxide. The results imply that in an astronomical environment where condensed mixtures of H2O2 and H2O are shielded from radiolytic decomposition and warmed to temperatures where sublimation is significant, highly concentrated or even pure hydrogen peroxide may form.

Domain Decomposition By the Advancing-Partition Method

NASA Technical Reports Server (NTRS)

Pirzadeh, Shahyar Z.

2008-01-01

A new method of domain decomposition has been developed for generating unstructured grids in subdomains either sequentially or using multiple computers in parallel. Domain decomposition is a crucial and challenging step for parallel grid generation. Prior methods are generally based on auxiliary, complex, and computationally intensive operations for defining partition interfaces and usually produce grids of lower quality than those generated in single domains. The new technique, referred to as "Advancing Partition," is based on the Advancing-Front method, which partitions a domain as part of the volume mesh generation in a consistent and "natural" way. The benefits of this approach are: 1) the process of domain decomposition is highly automated, 2) partitioning of domain does not compromise the quality of the generated grids, and 3) the computational overhead for domain decomposition is minimal. The new method has been implemented in NASA's unstructured grid generation code VGRID.

Decomposition of sulfamethoxazole and trimethoprim by continuous UVA/LED/TiO2 photocatalysis: Decomposition pathways, residual antibacterial activity and toxicity.

PubMed

Cai, Qinqing; Hu, Jiangyong

2017-02-05

In this study, continuous LED/UVA/TiO 2 photocatalytic decomposition of sulfamethoxazole (SMX) and trimethoprim (TMP) was investigated. More than 90% of SMX and TMP were removed within 20min by the continuous photoreactor (with the initial concentration of 400ppb for each). The removal rates of SMX and TMP decreased with higher initial antibiotics loadings. SMX was much easier decomposed in acidic condition, while pH affected little on TMP's decomposition. 0.003% was found to be the optimum H 2 O 2 dosage to enhance SMX photocatalytic decomposition. Decomposition pathways of SMX and TMP were proposed based on the intermediates identified by using LC-MS-MS and GC-MS. Aniline was identified as a new intermediate generated during SMX photocatalytic decomposition. Antibacterial activity study with a reference Escherichia coli strain was also conducted during the photocatalytic process. Results indicated that with every portion of TMP removed, the residual antibacterial activity decreased by one portion. However, the synergistic effect between SMX and TMP tended to slow down the antibacterial activity removal of SMX and TMP mixture. Chronic toxicity studies conducted with Vibrio fischeri exhibited 13-20% bioluminescence inhibition during the decomposition of 1ppm SMX and 1ppm TMP, no acute toxicity to V. fischeri was observed during the photocatalytic process. Copyright © 2016 Elsevier B.V. All rights reserved.

Mechanisms of charcoal degradation during its initial stages of decomposition

NASA Astrophysics Data System (ADS)

Singh, Nimisha; Abiven, Samuel; Schmidt, Michael W. I.

2010-05-01

Future climatic changes might result in an increased potential for wildfires, whereby incorporation of charred biomass into soil would increase. The incomplete combustion of biomass results in the production of a chemically heterogeneous class of highly condensed compounds known as pyrogenic C (PyC), which is generally considered resistant to microbial degradation. Recently, studies based on short-term laboratory incubations with soil have indicated that PyC can also eventually degrade (Baldock and Smernik, 2002; Hamer et al., 2004) and it is now widely accepted that a significant quantity of these resistant fraction of soil must have undergone degradation in terrestrial environments. Charcoal has been shown to decompose faster in the initial stages (first 2-3 months) and stabilize later (Kuzyakov et al., 2009). However, studies describing charcoal transformation processes remain scarce. The different potential degradation mechanisms have not yet been studied in combination, and therefore the relative importance for PyC degradation has not been evaluated. We are conducting an incubation experiment to study the biological, chemical and physical degradation/stabilization processes of PyC in soil under controlled conditions. We use Pinus ponderosa 13C/15N labeled (13C: 800 per mil, 15N: 4.2 atom %) wood and charcoal (pyrolysed at 450 °C under N2 atmosphere). We incubate soil from Lägeren forest (Wettingen, Switzerland) with three kind of organic inputs, labeled wood, char and no littler control. The decomposition rates would be estimated based on 13C of CO2 entrapped in NaOH. Time course destructive sampling would be done during the study. Lyophilized soil subsamples will be used for analysis of the amount of 13C incorporation in the microbial biomass using fumigation extraction method and phospholipids fatty acid analysis (PLFA). The remaining PyC in the soil would be characterized for the changes in its chemistry at the molecular level using Benzenepolycarboxlic

Biogeochemistry of Decomposition and Detrital Processing

NASA Astrophysics Data System (ADS)

Sanderman, J.; Amundson, R.

2003-12-01

Decomposition is a key ecological process that roughly balances net primary production in terrestrial ecosystems and is an essential process in resupplying nutrients to the plant community. Decomposition consists of three concurrent processes: communition or fragmentation, leaching of water-soluble compounds, and microbial catabolism. Decomposition can also be viewed as a sequential process, what Eijsackers and Zehnder (1990) compare to a Russian matriochka doll. Soil macrofauna fragment and partially solubilize plant residues, facilitating establishment of a community of decomposer microorganisms. This decomposer community will gradually shift as the most easily degraded plant compounds are utilized and the more recalcitrant materials begin to accumulate. Given enough time and the proper environmental conditions, most naturally occurring compounds can completely be mineralized to inorganic forms. Simultaneously with mineralization, the process of humification acts to transform a fraction of the plant residues into stable soil organic matter (SOM) or humus. For reference, Schlesinger (1990) estimated that only ˜0.7% of detritus eventually becomes stabilized into humus.Decomposition plays a key role in the cycling of most plant macro- and micronutrients and in the formation of humus. Figure 1 places the roles of detrital processing and mineralization within the context of the biogeochemical cycling of essential plant nutrients. Chapin (1991) found that while the atmosphere supplied 4% and mineral weathering supplied no nitrogen and <1% of phosphorus, internal nutrient recycling is the source for >95% of all the nitrogen and phosphorus uptake by tundra species in Barrow, Alaska. In a cool temperate forest, nutrient recycling accounted for 93%, 89%, 88%, and 65% of total sources for nitrogen, phosphorus, potassium, and calcium, respectively ( Chapin, 1991). (13K)Figure 1. A decomposition-centric biogeochemical model of nutrient cycling. Although there is significant

An adaptive interpolation scheme for molecular potential energy surfaces

NASA Astrophysics Data System (ADS)

Kowalewski, Markus; Larsson, Elisabeth; Heryudono, Alfa

2016-08-01

The calculation of potential energy surfaces for quantum dynamics can be a time consuming task—especially when a high level of theory for the electronic structure calculation is required. We propose an adaptive interpolation algorithm based on polyharmonic splines combined with a partition of unity approach. The adaptive node refinement allows to greatly reduce the number of sample points by employing a local error estimate. The algorithm and its scaling behavior are evaluated for a model function in 2, 3, and 4 dimensions. The developed algorithm allows for a more rapid and reliable interpolation of a potential energy surface within a given accuracy compared to the non-adaptive version.

Decomposition rates and termite assemblage composition in semiarid Africa

USGS Publications Warehouse

Schuurman, G.

2005-01-01

Outside of the humid tropics, abiotic factors are generally considered the dominant regulators of decomposition, and biotic influences are frequently not considered in predicting decomposition rates. In this study, I examined the effect of termite assemblage composition and abundance on decomposition of wood litter of an indigenous species (Croton megalobotrys) in five terrestrial habitats of the highly seasonal semiarid Okavango Delta region of northern Botswana, to determine whether natural variation in decomposer community composition and abundance influences decomposition rates. 1 conducted the study in two areas, Xudum and Santawani, with the Xudum study preceding the Santawani study. I assessed termite assemblage composition and abundance using a grid of survey baits (rolls of toilet paper) placed on the soil surface and checked 2-4 times/month. I placed a billet (a section of wood litter) next to each survey bait and measured decomposition in a plot by averaging the mass loss of its billets. Decomposition rates varied up to sixfold among plots within the same habitat and locality, despite the fact that these plots experienced the same climate. In addition, billets decomposed significantly faster during the cooler and drier Santawani study, contradicting climate-based predictions. Because termite incidence was generally higher in Santawani plots, termite abundance initially seemed a likely determinant of decomposition in this system. However, no significant effect of termite incidence on billet mass loss rates was observed among the Xudum plots, where decomposition rates remained low even though termite incidence varied considerably. Considering the incidences of fungus-growing termites and non-fungus-growing termites separately resolves this apparent contradiction: in both Santawani and Xudum, only fungus-growing termites play a significant role in decomposition. This result is mirrored in an analysis of the full data set of combined Xudum and Santawani data

ADVANCED OXIDATION: OXALATE DECOMPOSITION TESTING WITH OZONE

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

Ketusky, E.; Subramanian, K.

At the Savannah River Site (SRS), oxalic acid is currently considered the preferred agent for chemically cleaning the large underground Liquid Radioactive Waste Tanks. It is applied only in the final stages of emptying a tank when generally less than 5,000 kg of waste solids remain, and slurrying based removal methods are no-longer effective. The use of oxalic acid is preferred because of its combined dissolution and chelating properties, as well as the fact that corrosion to the carbon steel tank walls can be controlled. Although oxalic acid is the preferred agent, there are significant potential downstream impacts. Impacts include:more » (1) Degraded evaporator operation; (2) Resultant oxalate precipitates taking away critically needed operating volume; and (3) Eventual creation of significant volumes of additional feed to salt processing. As an alternative to dealing with the downstream impacts, oxalate decomposition using variations of ozone based Advanced Oxidation Process (AOP) were investigated. In general AOPs use ozone or peroxide and a catalyst to create hydroxyl radicals. Hydroxyl radicals have among the highest oxidation potentials, and are commonly used to decompose organics. Although oxalate is considered among the most difficult organic to decompose, the ability of hydroxyl radicals to decompose oxalate is considered to be well demonstrated. In addition, as AOPs are considered to be 'green' their use enables any net chemical additions to the waste to be minimized. In order to test the ability to decompose the oxalate and determine the decomposition rates, a test rig was designed, where 10 vol% ozone would be educted into a spent oxalic acid decomposition loop, with the loop maintained at 70 C and recirculated at 40L/min. Each of the spent oxalic acid streams would be created from three oxalic acid strikes of an F-area simulant (i.e., Purex = high Fe/Al concentration) and H-area simulant (i.e., H area modified Purex = high Al/Fe concentration) after

Origins of adaptive immunity.

PubMed

Liongue, Clifford; John, Liza B; Ward, Alister

2011-01-01

Adaptive immunity, involving distinctive antibody- and cell-mediated responses to specific antigens based on "memory" of previous exposure, is a hallmark of higher vertebrates. It has been argued that adaptive immunity arose rapidly, as articulated in the "big bang theory" surrounding its origins, which stresses the importance of coincident whole-genome duplications. Through a close examination of the key molecules and molecular processes underpinning adaptive immunity, this review suggests a less-extreme model, in which adaptive immunity emerged as part of longer evolutionary journey. Clearly, whole-genome duplications provided additional raw genetic materials that were vital to the emergence of adaptive immunity, but a variety of other genetic events were also required to generate some of the key molecules, whereas others were preexisting and simply co-opted into adaptive immunity.

Investigation of shock-induced chemical decomposition of sensitized nitromethane through time-resolved Raman spectroscopy

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

Pangilinan, G.I.; Constantinou, C.P.; Gruzdkov, Y.A.

1996-07-01

Molecular processes associated with shock induced chemical decomposition of a mixture of nitromethane with ethylenediamine (0.1 wt%) are examined using time-resolved, Raman scattering. When shocked by stepwise loading to 14.2 GPa pressure, changes in the nitromethane vibrational modes and the spectral background characterize the onset of reaction. The CN stretch mode softens and disappears even as the NO{sub 2} and CH{sub 3} stretch modes, though modified, retain their identities. The shape and intensity of the spectral background also shows changes characteristic of reaction. Changes in the background, which are observed even at lower peak pressures of 11.4 GPa, are assignedmore » to luminescence from reaction intermediates. The implications of these results to various molecular models of sensitization are discussed.« less

Decomposition of silicon carbide at high pressures and temperatures

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

Daviau, Kierstin; Lee, Kanani K. M.

We measure the onset of decomposition of silicon carbide, SiC, to silicon and carbon (e.g., diamond) at high pressures and high temperatures in a laser-heated diamond-anvil cell. We identify decomposition through x-ray diffraction and multiwavelength imaging radiometry coupled with electron microscopy analyses on quenched samples. We find that B3 SiC (also known as 3C or zinc blende SiC) decomposes at high pressures and high temperatures, following a phase boundary with a negative slope. The high-pressure decomposition temperatures measured are considerably lower than those at ambient, with our measurements indicating that SiC begins to decompose at ~ 2000 K at 60more » GPa as compared to ~ 2800 K at ambient pressure. Once B3 SiC transitions to the high-pressure B1 (rocksalt) structure, we no longer observe decomposition, despite heating to temperatures in excess of ~ 3200 K. The temperature of decomposition and the nature of the decomposition phase boundary appear to be strongly influenced by the pressure-induced phase transitions to higher-density structures in SiC, silicon, and carbon. The decomposition of SiC at high pressure and temperature has implications for the stability of naturally forming moissanite on Earth and in carbon-rich exoplanets.« less

Evaluating litter decomposition and soil organic matter dynamics in earth system models: contrasting analysis of long-term litter decomposition and steady-state soil carbon

NASA Astrophysics Data System (ADS)

Bonan, G. B.; Wieder, W. R.

2012-12-01

Decomposition is a large term in the global carbon budget, but models of the earth system that simulate carbon cycle-climate feedbacks are largely untested with respect to litter decomposition. Here, we demonstrate a protocol to document model performance with respect to both long-term (10 year) litter decomposition and steady-state soil carbon stocks. First, we test the soil organic matter parameterization of the Community Land Model version 4 (CLM4), the terrestrial component of the Community Earth System Model, with data from the Long-term Intersite Decomposition Experiment Team (LIDET). The LIDET dataset is a 10-year study of litter decomposition at multiple sites across North America and Central America. We show results for 10-year litter decomposition simulations compared with LIDET for 9 litter types and 20 sites in tundra, grassland, and boreal, conifer, deciduous, and tropical forest biomes. We show additional simulations with DAYCENT, a version of the CENTURY model, to ask how well an established ecosystem model matches the observations. The results reveal large discrepancy between the laboratory microcosm studies used to parameterize the CLM4 litter decomposition and the LIDET field study. Simulated carbon loss is more rapid than the observations across all sites, despite using the LIDET-provided climatic decomposition index to constrain temperature and moisture effects on decomposition. Nitrogen immobilization is similarly biased high. Closer agreement with the observations requires much lower decomposition rates, obtained with the assumption that nitrogen severely limits decomposition. DAYCENT better replicates the observations, for both carbon mass remaining and nitrogen, without requirement for nitrogen limitation of decomposition. Second, we compare global observationally-based datasets of soil carbon with simulated steady-state soil carbon stocks for both models. The models simulations were forced with observationally-based estimates of annual

Domain decomposition for aerodynamic and aeroacoustic analyses, and optimization

NASA Technical Reports Server (NTRS)

Baysal, Oktay

1995-01-01

The overarching theme was the domain decomposition, which intended to improve the numerical solution technique for the partial differential equations at hand; in the present study, those that governed either the fluid flow, or the aeroacoustic wave propagation, or the sensitivity analysis for a gradient-based optimization. The role of the domain decomposition extended beyond the original impetus of discretizing geometrical complex regions or writing modular software for distributed-hardware computers. It induced function-space decompositions and operator decompositions that offered the valuable property of near independence of operator evaluation tasks. The objectives have gravitated about the extensions and implementations of either the previously developed or concurrently being developed methodologies: (1) aerodynamic sensitivity analysis with domain decomposition (SADD); (2) computational aeroacoustics of cavities; and (3) dynamic, multibody computational fluid dynamics using unstructured meshes.

English and Turkish Pupils' Understanding of Decomposition

ERIC Educational Resources Information Center

Cetin, Gulcan

2007-01-01

This study aimed to describe seventh grade English and Turkish students' levels of understanding of decomposition. Data were analyzed descriptively from the students' written responses to four diagnostic questions about decomposition. Results revealed that the English students had considerably higher sound understanding and lower no understanding…

Scare Tactics: Evaluating Problem Decompositions Using Failure Scenarios

NASA Technical Reports Server (NTRS)

Helm, B. Robert; Fickas, Stephen

1992-01-01

Our interest is in the design of multi-agent problem-solving systems, which we refer to as composite systems. We have proposed an approach to composite system design by decomposition of problem statements. An automated assistant called Critter provides a library of reusable design transformations which allow a human analyst to search the space of decompositions for a problem. In this paper we describe a method for evaluating and critiquing problem decompositions generated by this search process. The method uses knowledge stored in the form of failure decompositions attached to design transformations. We suggest the benefits of our critiquing method by showing how it could re-derive steps of a published development example. We then identify several open issues for the method.

Decomposition of forest products buried in landfills

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

Wang, Xiaoming, E-mail: xwang25@ncsu.edu; Padgett, Jennifer M.; Powell, John S.

Highlights: • This study tracked chemical changes of wood and paper in landfills. • A decomposition index was developed to quantify carbohydrate biodegradation. • Newsprint biodegradation as measured here is greater than previous reports. • The field results correlate well with previous laboratory measurements. - Abstract: The objective of this study was to investigate the decomposition of selected wood and paper products in landfills. The decomposition of these products under anaerobic landfill conditions results in the generation of biogenic carbon dioxide and methane, while the un-decomposed portion represents a biogenic carbon sink. Information on the decomposition of these municipal wastemore » components is used to estimate national methane emissions inventories, for attribution of carbon storage credits, and to assess the life-cycle greenhouse gas impacts of wood and paper products. Hardwood (HW), softwood (SW), plywood (PW), oriented strand board (OSB), particleboard (PB), medium-density fiberboard (MDF), newsprint (NP), corrugated container (CC) and copy paper (CP) were buried in landfills operated with leachate recirculation, and were excavated after approximately 1.5 and 2.5 yr. Samples were analyzed for cellulose (C), hemicellulose (H), lignin (L), volatile solids (VS), and organic carbon (OC). A holocellulose decomposition index (HOD) and carbon storage factor (CSF) were calculated to evaluate the extent of solids decomposition and carbon storage. Samples of OSB made from HW exhibited cellulose plus hemicellulose (C + H) loss of up to 38%, while loss for the other wood types was 0–10% in most samples. The C + H loss was up to 81%, 95% and 96% for NP, CP and CC, respectively. The CSFs for wood and paper samples ranged from 0.34 to 0.47 and 0.02 to 0.27 g OC g{sup −1} dry material, respectively. These results, in general, correlated well with an earlier laboratory-scale study, though NP and CC decomposition measured in this study were

WAKES: Wavelet Adaptive Kinetic Evolution Solvers

NASA Astrophysics Data System (ADS)

Mardirian, Marine; Afeyan, Bedros; Larson, David

2016-10-01

We are developing a general capability to adaptively solve phase space evolution equations mixing particle and continuum techniques in an adaptive manner. The multi-scale approach is achieved using wavelet decompositions which allow phase space density estimation to occur with scale dependent increased accuracy and variable time stepping. Possible improvements on the SFK method of Larson are discussed, including the use of multiresolution analysis based Richardson-Lucy Iteration, adaptive step size control in explicit vs implicit approaches. Examples will be shown with KEEN waves and KEEPN (Kinetic Electrostatic Electron Positron Nonlinear) waves, which are the pair plasma generalization of the former, and have a much richer span of dynamical behavior. WAKES techniques are well suited for the study of driven and released nonlinear, non-stationary, self-organized structures in phase space which have no fluid, limit nor a linear limit, and yet remain undamped and coherent well past the drive period. The work reported here is based on the Vlasov-Poisson model of plasma dynamics. Work supported by a Grant from the AFOSR.

Parallel processing for pitch splitting decomposition

NASA Astrophysics Data System (ADS)

Barnes, Levi; Li, Yong; Wadkins, David; Biederman, Steve; Miloslavsky, Alex; Cork, Chris

2009-10-01

Decomposition of an input pattern in preparation for a double patterning process is an inherently global problem in which the influence of a local decomposition decision can be felt across an entire pattern. In spite of this, a large portion of the work can be massively distributed. Here, we discuss the advantages of geometric distribution for polygon operations with limited range of influence. Further, we have found that even the naturally global "coloring" step can, in large part, be handled in a geometrically local manner. In some practical cases, up to 70% of the work can be distributed geometrically. We also describe the methods for partitioning the problem into local pieces and present scaling data up to 100 CPUs. These techniques reduce DPT decomposition runtime by orders of magnitude.

An adaptive interpolation scheme for molecular potential energy surfaces

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

Kowalewski, Markus, E-mail: mkowalew@uci.edu; Larsson, Elisabeth; Heryudono, Alfa

The calculation of potential energy surfaces for quantum dynamics can be a time consuming task—especially when a high level of theory for the electronic structure calculation is required. We propose an adaptive interpolation algorithm based on polyharmonic splines combined with a partition of unity approach. The adaptive node refinement allows to greatly reduce the number of sample points by employing a local error estimate. The algorithm and its scaling behavior are evaluated for a model function in 2, 3, and 4 dimensions. The developed algorithm allows for a more rapid and reliable interpolation of a potential energy surface within amore » given accuracy compared to the non-adaptive version.« less

Nucleon Momentum and Spin Decompositions

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

Cho, Y. M.

We construct a gauge invariant canonical momentum operator which satisfies the canonical commutation relation to resolve the old controversy on the canonical versus kinematic momentum of a charged particle in gauge theories. With this we show how to obtain the gauge independent momentum and spin decompositions of composite particles to those of the constituents in QED and QCD, which has been thought to be impossible. Moerover, we show that there are two logically acceptable nucleom momentum and spin decompositions, depending on which gluons we identify as the constituent of nucleons.

Sucrose in Aqueous Solution Revisited: 2. Adaptively Biased Molecular Dynamics Simulations and Computational Analysis of NMR Relaxation

PubMed Central

Xia, Junchao; Case, David A.

2012-01-01

We report 100 ns molecular dynamics simulations, at various temperatures, of sucrose in water (with concentrations of sucrose ranging from 0.02 to 4 M), and in a 7:3 water-DMSO mixture. Convergence of the resulting conformational ensembles was checked using adaptive-biased simulations along the glycosidic φ and ψ torsion angles. NMR relaxation parameters, including longitudinal (R1) and transverse (R2) relaxation rates, nuclear Overhauser enhancements (NOE), and generalized order parameter (S2) were computed from the resulting time-correlation functions. The amplitude and time scales of molecular motions change with temperature and concentration in ways that track closely with experimental results, and are consistent with a model in which sucrose conformational fluctuations are limited (with 80–90% of the conformations having φ – ψ values within 20° of an average conformation), but with some important differences in conformation between pure water and DMSO-water mixtures. PMID:22058066

Climate fails to predict wood decomposition at regional scales

Treesearch

Mark A. Bradford; Robert J. Warren; Petr Baldrian; Thomas W. Crowther; Daniel S. Maynard; Emily E. Oldfield; William R. Wieder; Stephen A. Wood; Joshua R. King

2014-01-01

Decomposition of organic matter strongly influences ecosystem carbon storage1. In Earth-system models, climate is a predominant control on the decomposition rates of organic matter2, 3, 4, 5. This assumption is based on the mean response of decomposition to climate, yet there is a growing appreciation in other areas of global change science that projections based on...

Bi-dimensional empirical mode decomposition based fringe-like pattern suppression in polarization interference imaging spectrometer

NASA Astrophysics Data System (ADS)

Ren, Wenyi; Cao, Qizhi; Wu, Dan; Jiang, Jiangang; Yang, Guoan; Xie, Yingge; Wang, Guodong; Zhang, Sheqi

2018-01-01

Many observers using interference imaging spectrometer were plagued by the fringe-like pattern(FP) that occurs for optical wavelengths in red and near-infrared region. It brings us more difficulties in the data processing such as the spectrum calibration, information retrieval, and so on. An adaptive method based on the bi-dimensional empirical mode decomposition was developed to suppress the nonlinear FP in polarization interference imaging spectrometer. The FP and corrected interferogram were separated effectively. Meanwhile, the stripes introduced by CCD mosaic was suppressed. The nonlinear interferogram background removal and the spectrum distortion correction were implemented as well. It provides us an alternative method to adaptively suppress the nonlinear FP without prior experimental data and knowledge. This approach potentially is a powerful tool in the fields of Fourier transform spectroscopy, holographic imaging, optical measurement based on moire fringe, etc.

Decomposition of forest products buried in landfills.

PubMed

Wang, Xiaoming; Padgett, Jennifer M; Powell, John S; Barlaz, Morton A

2013-11-01

The objective of this study was to investigate the decomposition of selected wood and paper products in landfills. The decomposition of these products under anaerobic landfill conditions results in the generation of biogenic carbon dioxide and methane, while the un-decomposed portion represents a biogenic carbon sink. Information on the decomposition of these municipal waste components is used to estimate national methane emissions inventories, for attribution of carbon storage credits, and to assess the life-cycle greenhouse gas impacts of wood and paper products. Hardwood (HW), softwood (SW), plywood (PW), oriented strand board (OSB), particleboard (PB), medium-density fiberboard (MDF), newsprint (NP), corrugated container (CC) and copy paper (CP) were buried in landfills operated with leachate recirculation, and were excavated after approximately 1.5 and 2.5yr. Samples were analyzed for cellulose (C), hemicellulose (H), lignin (L), volatile solids (VS), and organic carbon (OC). A holocellulose decomposition index (HOD) and carbon storage factor (CSF) were calculated to evaluate the extent of solids decomposition and carbon storage. Samples of OSB made from HW exhibited cellulose plus hemicellulose (C+H) loss of up to 38%, while loss for the other wood types was 0-10% in most samples. The C+H loss was up to 81%, 95% and 96% for NP, CP and CC, respectively. The CSFs for wood and paper samples ranged from 0.34 to 0.47 and 0.02 to 0.27gOCg(-1) dry material, respectively. These results, in general, correlated well with an earlier laboratory-scale study, though NP and CC decomposition measured in this study were higher than previously reported. Copyright © 2013 Elsevier Ltd. All rights reserved.

Are litter decomposition and fire linked through plant species traits?

PubMed

Cornelissen, Johannes H C; Grootemaat, Saskia; Verheijen, Lieneke M; Cornwell, William K; van Bodegom, Peter M; van der Wal, René; Aerts, Rien

2017-11-01

Contents 653 I. 654 II. 657 III. 659 IV. 661 V. 662 VI. 663 VII. 665 665 References 665 SUMMARY: Biological decomposition and wildfire are connected carbon release pathways for dead plant material: slower litter decomposition leads to fuel accumulation. Are decomposition and surface fires also connected through plant community composition, via the species' traits? Our central concept involves two axes of trait variation related to decomposition and fire. The 'plant economics spectrum' (PES) links biochemistry traits to the litter decomposability of different fine organs. The 'size and shape spectrum' (SSS) includes litter particle size and shape and their consequent effect on fuel bed structure, ventilation and flammability. Our literature synthesis revealed that PES-driven decomposability is largely decoupled from predominantly SSS-driven surface litter flammability across species; this finding needs empirical testing in various environmental settings. Under certain conditions, carbon release will be dominated by decomposition, while under other conditions litter fuel will accumulate and fire may dominate carbon release. Ecosystem-level feedbacks between decomposition and fire, for example via litter amounts, litter decomposition stage, community-level biotic interactions and altered environment, will influence the trait-driven effects on decomposition and fire. Yet, our conceptual framework, explicitly comparing the effects of two plant trait spectra on litter decomposition vs fire, provides a promising new research direction for better understanding and predicting Earth surface carbon dynamics. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Density functional theory and RRKM calculations of decompositions of the metastable E-2,4-pentadienal molecular ions.

PubMed

Solano Espinoza, Eduardo A; Vallejo Narváez, Wilmer E

2010-07-01

The potential energy profiles for the fragmentations that lead to [C(5)H(5)O](+) and [C(4)H(6)](+*) ions from the molecular ions [C(5)H(6)O](+*) of E-2,4-pentadienal were obtained from calculations at the UB3LYP/6-311G + + (3df,3pd)//UB3LYP/6-31G(d,p) level of theory. Kinetic barriers and harmonic frequencies obtained by the density functional method were then employed in Rice-Ramsperger-Kassel-Marcus calculations of individual rate coefficients for a large number of reaction steps. The pre-equilibrium and rate-controlling step approximations were applied to different regions of the complex potential energy surface, allowing the overall rate of decomposition to be calculated and discriminated between three rival pathways: C-H bond cleavage, decarbonylation and cyclization. These processes should have to compete for an equilibrated mixture of four conformers of the E-2,4-pentadienal ions. The direct dissociation, however, can only become important in the high-energy regime. In contrast, loss of CO and cyclization are observable processes in the metastable kinetic window. The former involves a slow 1,2-hydrogen shift from the carbonyl group that is immediately followed by the formation of an ion-neutral complex which, in turn, decomposes rapidly to the s-trans-1,3-butadiene ion [C(4)H(6)](+*). The predominating metastable channel is the second one, that is, a multi-step ring closure which starts with a rate-limiting cis-trans isomerization. This process yields a mixture of interconverting pyran ions that dissociates to the pyrylium ions [C(5)H(5)O](+). These results can be used to rationalize the CID mass spectrum of E-2,4-pentadienal in a low-energy regime. 2010 John Wiley & Sons, Ltd.

A density functional theory study of the decomposition mechanism of nitroglycerin.

PubMed

Pei, Liguan; Dong, Kehai; Tang, Yanhui; Zhang, Bo; Yu, Chang; Li, Wenzuo

2017-08-21

The detailed decomposition mechanism of nitroglycerin (NG) in the gas phase was studied by examining reaction pathways using density functional theory (DFT) and canonical variational transition state theory combined with a small-curvature tunneling correction (CVT/SCT). The mechanism of NG autocatalytic decomposition was investigated at the B3LYP/6-31G(d,p) level of theory. Five possible decomposition pathways involving NG were identified and the rate constants for the pathways at temperatures ranging from 200 to 1000 K were calculated using CVT/SCT. There was found to be a lower energy barrier to the β-H abstraction reaction than to the α-H abstraction reaction during the initial step in the autocatalytic decomposition of NG. The decomposition pathways for CHOCOCHONO 2 (a product obtained following the abstraction of three H atoms from NG by NO 2 ) include O-NO 2 cleavage or isomer production, meaning that the autocatalytic decomposition of NG has two reaction pathways, both of which are exothermic. The rate constants for these two reaction pathways are greater than the rate constants for the three pathways corresponding to unimolecular NG decomposition. The overall process of NG decomposition can be divided into two stages based on the NO 2 concentration, which affects the decomposition products and reactions. In the first stage, the reaction pathway corresponding to O-NO 2 cleavage is the main pathway, but the rates of the two autocatalytic decomposition pathways increase with increasing NO 2 concentration. However, when a threshold NO 2 concentration is reached, the NG decomposition process enters its second stage, with the two pathways for NG autocatalytic decomposition becoming the main and secondary reaction pathways.

A New Adaptive Framework for Collaborative Filtering Prediction.

PubMed

Almosallam, Ibrahim A; Shang, Yi

2008-06-01

Collaborative filtering is one of the most successful techniques for recommendation systems and has been used in many commercial services provided by major companies including Amazon, TiVo and Netflix. In this paper we focus on memory-based collaborative filtering (CF). Existing CF techniques work well on dense data but poorly on sparse data. To address this weakness, we propose to use z-scores instead of explicit ratings and introduce a mechanism that adaptively combines global statistics with item-based values based on data density level. We present a new adaptive framework that encapsulates various CF algorithms and the relationships among them. An adaptive CF predictor is developed that can self adapt from user-based to item-based to hybrid methods based on the amount of available ratings. Our experimental results show that the new predictor consistently obtained more accurate predictions than existing CF methods, with the most significant improvement on sparse data sets. When applied to the Netflix Challenge data set, our method performed better than existing CF and singular value decomposition (SVD) methods and achieved 4.67% improvement over Netflix's system.

Domain decomposition: A bridge between nature and parallel computers

NASA Technical Reports Server (NTRS)

Keyes, David E.

1992-01-01

Domain decomposition is an intuitive organizing principle for a partial differential equation (PDE) computation, both physically and architecturally. However, its significance extends beyond the readily apparent issues of geometry and discretization, on one hand, and of modular software and distributed hardware, on the other. Engineering and computer science aspects are bridged by an old but recently enriched mathematical theory that offers the subject not only unity, but also tools for analysis and generalization. Domain decomposition induces function-space and operator decompositions with valuable properties. Function-space bases and operator splittings that are not derived from domain decompositions generally lack one or more of these properties. The evolution of domain decomposition methods for elliptically dominated problems has linked two major algorithmic developments of the last 15 years: multilevel and Krylov methods. Domain decomposition methods may be considered descendants of both classes with an inheritance from each: they are nearly optimal and at the same time efficiently parallelizable. Many computationally driven application areas are ripe for these developments. A progression is made from a mathematically informal motivation for domain decomposition methods to a specific focus on fluid dynamics applications. To be introductory rather than comprehensive, simple examples are provided while convergence proofs and algorithmic details are left to the original references; however, an attempt is made to convey their most salient features, especially where this leads to algorithmic insight.

Kinetics of the cellular decomposition of supersaturated solid solutions

NASA Astrophysics Data System (ADS)

Ivanov, M. A.; Naumuk, A. Yu.

2014-09-01

A consistent description of the kinetics of the cellular decomposition of supersaturated solid solutions with the development of a spatially periodic structure of lamellar (platelike) type, which consists of alternating phases of precipitates on the basis of the impurity component and depleted initial solid solution, is given. One of the equations, which determines the relationship between the parameters that describe the process of decomposition, has been obtained from a comparison of two approaches in order to determine the rate of change in the free energy of the system. The other kinetic parameters can be described with the use of a variational method, namely, by the maximum velocity of motion of the decomposition boundary at a given temperature. It is shown that the mutual directions of growth of the lamellae of different phases are determined by the minimum value of the interphase surface energy. To determine the parameters of the decomposition, a simple thermodynamic model of states with a parabolic dependence of the free energy on the concentrations has been used. As a result, expressions that describe the decomposition rate, interlamellar distance, and the concentration of impurities in the phase that remain after the decomposition have been derived. This concentration proves to be equal to the half-sum of the initial concentration and the equilibrium concentration corresponding to the decomposition temperature.

Efficient Delaunay Tessellation through K-D Tree Decomposition

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

Morozov, Dmitriy; Peterka, Tom

Delaunay tessellations are fundamental data structures in computational geometry. They are important in data analysis, where they can represent the geometry of a point set or approximate its density. The algorithms for computing these tessellations at scale perform poorly when the input data is unbalanced. We investigate the use of k-d trees to evenly distribute points among processes and compare two strategies for picking split points between domain regions. Because resulting point distributions no longer satisfy the assumptions of existing parallel Delaunay algorithms, we develop a new parallel algorithm that adapts to its input and prove its correctness. We evaluatemore » the new algorithm using two late-stage cosmology datasets. The new running times are up to 50 times faster using k-d tree compared with regular grid decomposition. Moreover, in the unbalanced data sets, decomposing the domain into a k-d tree is up to five times faster than decomposing it into a regular grid.« less

Using Microwave Sample Decomposition in Undergraduate Analytical Chemistry

NASA Astrophysics Data System (ADS)

Griff Freeman, R.; McCurdy, David L.

1998-08-01

A shortcoming of many undergraduate classes in analytical chemistry is that students receive little exposure to sample preparation in chemical analysis. This paper reports the progress made in introducing microwave sample decomposition into several quantitative analysis experiments at Truman State University. Two experiments being performed in our current laboratory rotation include closed vessel microwave decomposition applied to the classical gravimetric determination of nickel and the determination of sodium in snack foods by flame atomic emission spectrometry. A third lab, using open-vessel microwave decomposition for the Kjeldahl nitrogen determination is now ready for student trial. Microwave decomposition reduces the time needed to complete these experiments and significantly increases the student awareness of the importance of sample preparation in quantitative chemical analyses, providing greater breadth and realism in the experiments.

Steganography based on pixel intensity value decomposition

NASA Astrophysics Data System (ADS)

Abdulla, Alan Anwar; Sellahewa, Harin; Jassim, Sabah A.

2014-05-01

This paper focuses on steganography based on pixel intensity value decomposition. A number of existing schemes such as binary, Fibonacci, Prime, Natural, Lucas, and Catalan-Fibonacci (CF) are evaluated in terms of payload capacity and stego quality. A new technique based on a specific representation is proposed to decompose pixel intensity values into 16 (virtual) bit-planes suitable for embedding purposes. The proposed decomposition has a desirable property whereby the sum of all bit-planes does not exceed the maximum pixel intensity value, i.e. 255. Experimental results demonstrate that the proposed technique offers an effective compromise between payload capacity and stego quality of existing embedding techniques based on pixel intensity value decomposition. Its capacity is equal to that of binary and Lucas, while it offers a higher capacity than Fibonacci, Prime, Natural, and CF when the secret bits are embedded in 1st Least Significant Bit (LSB). When the secret bits are embedded in higher bit-planes, i.e., 2nd LSB to 8th Most Significant Bit (MSB), the proposed scheme has more capacity than Natural numbers based embedding. However, from the 6th bit-plane onwards, the proposed scheme offers better stego quality. In general, the proposed decomposition scheme has less effect in terms of quality on pixel value when compared to most existing pixel intensity value decomposition techniques when embedding messages in higher bit-planes.

Wood decomposition as influenced by invertebrates.

PubMed

Ulyshen, Michael D

2016-02-01

The diversity and habitat requirements of invertebrates associated with dead wood have been the subjects of hundreds of studies in recent years but we still know very little about the ecological or economic importance of these organisms. The purpose of this review is to examine whether, how and to what extent invertebrates affect wood decomposition in terrestrial ecosystems. Three broad conclusions can be reached from the available literature. First, wood decomposition is largely driven by microbial activity but invertebrates also play a significant role in both temperate and tropical environments. Primary mechanisms include enzymatic digestion (involving both endogenous enzymes and those produced by endo- and ectosymbionts), substrate alteration (tunnelling and fragmentation), biotic interactions and nitrogen fertilization (i.e. promoting nitrogen fixation by endosymbiotic and free-living bacteria). Second, the effects of individual invertebrate taxa or functional groups can be accelerative or inhibitory but the cumulative effect of the entire community is generally to accelerate wood decomposition, at least during the early stages of the process (most studies are limited to the first 2-3 years). Although methodological differences and design limitations preclude meta-analysis, studies aimed at quantifying the contributions of invertebrates to wood decomposition commonly attribute 10-20% of wood loss to these organisms. Finally, some taxa appear to be particularly influential with respect to promoting wood decomposition. These include large wood-boring beetles (Coleoptera) and termites (Termitoidae), especially fungus-farming macrotermitines. The presence or absence of these species may be more consequential than species richness and the influence of invertebrates is likely to vary biogeographically. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

Phlogopite Decomposition, Water, and Venus

NASA Technical Reports Server (NTRS)

Johnson, N. M.; Fegley, B., Jr.

2005-01-01

Venus is a hot and dry planet with a surface temperature of 660 to 740 K and 30 parts per million by volume (ppmv) water vapor in its lower atmosphere. In contrast Earth has an average surface temperature of 288 K and 1-4% water vapor in its troposphere. The hot and dry conditions on Venus led many to speculate that hydrous minerals on the surface of Venus would not be there today even though they might have formed in a potentially wetter past. Thermodynamic calculations predict that many hydrous minerals are unstable under current Venusian conditions. Thermodynamics predicts whether a particular mineral is stable or not, but we need experimental data on the decomposition rate of hydrous minerals to determine if they survive on Venus today. Previously, we determined the decomposition rate of the amphibole tremolite, and found that it could exist for billions of years at current surface conditions. Here, we present our initial results on the decomposition of phlogopite mica, another common hydrous mineral on Earth.

CRISPR-Cas adaptation: insights into the mechanism of action.

PubMed

Amitai, Gil; Sorek, Rotem

2016-02-01

Since the first demonstration that CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against phages and plasmids, numerous studies have yielded key insights into the molecular mechanisms governing how these systems attack and degrade foreign DNA. However, the molecular mechanisms underlying the adaptation stage, in which new immunological memory is formed, have until recently represented a major unresolved question. In this Progress article, we discuss recent discoveries that have shown both how foreign DNA is identified by the CRISPR-Cas adaptation machinery and the molecular basis for its integration into the chromosome to form an immunological memory. Furthermore, we describe the roles of each of the specific CRISPR-Cas components that are involved in memory formation, and consider current models for their evolutionary origin.

Structural adaptation of cold-active RTX lipase from Pseudomonas sp. strain AMS8 revealed via homology and molecular dynamics simulation approaches.

PubMed

Mohamad Ali, Mohd Shukuri; Mohd Fuzi, Siti Farhanie; Ganasen, Menega; Abdul Rahman, Raja Noor Zaliha Raja; Basri, Mahiran; Salleh, Abu Bakar

2013-01-01

The psychrophilic enzyme is an interesting subject to study due to its special ability to adapt to extreme temperatures, unlike typical enzymes. Utilizing computer-aided software, the predicted structure and function of the enzyme lipase AMS8 (LipAMS8) (isolated from the psychrophilic Pseudomonas sp., obtained from the Antarctic soil) are studied. The enzyme shows significant sequence similarities with lipases from Pseudomonas sp. MIS38 and Serratia marcescens. These similarities aid in the prediction of the 3D molecular structure of the enzyme. In this study, 12 ns MD simulation is performed at different temperatures for structural flexibility and stability analysis. The results show that the enzyme is most stable at 0°C and 5°C. In terms of stability and flexibility, the catalytic domain (N-terminus) maintained its stability more than the noncatalytic domain (C-terminus), but the non-catalytic domain showed higher flexibility than the catalytic domain. The analysis of the structure and function of LipAMS8 provides new insights into the structural adaptation of this protein at low temperatures. The information obtained could be a useful tool for low temperature industrial applications and molecular engineering purposes, in the near future.

Spatiotemporal Domain Decomposition for Massive Parallel Computation of Space-Time Kernel Density

NASA Astrophysics Data System (ADS)

Hohl, A.; Delmelle, E. M.; Tang, W.

2015-07-01

Accelerated processing capabilities are deemed critical when conducting analysis on spatiotemporal datasets of increasing size, diversity and availability. High-performance parallel computing offers the capacity to solve computationally demanding problems in a limited timeframe, but likewise poses the challenge of preventing processing inefficiency due to workload imbalance between computing resources. Therefore, when designing new algorithms capable of implementing parallel strategies, careful spatiotemporal domain decomposition is necessary to account for heterogeneity in the data. In this study, we perform octtree-based adaptive decomposition of the spatiotemporal domain for parallel computation of space-time kernel density. In order to avoid edge effects near subdomain boundaries, we establish spatiotemporal buffers to include adjacent data-points that are within the spatial and temporal kernel bandwidths. Then, we quantify computational intensity of each subdomain to balance workloads among processors. We illustrate the benefits of our methodology using a space-time epidemiological dataset of Dengue fever, an infectious vector-borne disease that poses a severe threat to communities in tropical climates. Our parallel implementation of kernel density reaches substantial speedup compared to sequential processing, and achieves high levels of workload balance among processors due to great accuracy in quantifying computational intensity. Our approach is portable of other space-time analytical tests.

The Fourier decomposition method for nonlinear and non-stationary time series analysis.

PubMed

Singh, Pushpendra; Joshi, Shiv Dutt; Patney, Rakesh Kumar; Saha, Kaushik

2017-03-01

for many decades, there has been a general perception in the literature that Fourier methods are not suitable for the analysis of nonlinear and non-stationary data. In this paper, we propose a novel and adaptive Fourier decomposition method (FDM), based on the Fourier theory, and demonstrate its efficacy for the analysis of nonlinear and non-stationary time series. The proposed FDM decomposes any data into a small number of 'Fourier intrinsic band functions' (FIBFs). The FDM presents a generalized Fourier expansion with variable amplitudes and variable frequencies of a time series by the Fourier method itself. We propose an idea of zero-phase filter bank-based multivariate FDM (MFDM), for the analysis of multivariate nonlinear and non-stationary time series, using the FDM. We also present an algorithm to obtain cut-off frequencies for MFDM. The proposed MFDM generates a finite number of band-limited multivariate FIBFs (MFIBFs). The MFDM preserves some intrinsic physical properties of the multivariate data, such as scale alignment, trend and instantaneous frequency. The proposed methods provide a time-frequency-energy (TFE) distribution that reveals the intrinsic structure of a data. Numerical computations and simulations have been carried out and comparison is made with the empirical mode decomposition algorithms.

The Fourier decomposition method for nonlinear and non-stationary time series analysis

PubMed Central

Joshi, Shiv Dutt; Patney, Rakesh Kumar; Saha, Kaushik

2017-01-01

for many decades, there has been a general perception in the literature that Fourier methods are not suitable for the analysis of nonlinear and non-stationary data. In this paper, we propose a novel and adaptive Fourier decomposition method (FDM), based on the Fourier theory, and demonstrate its efficacy for the analysis of nonlinear and non-stationary time series. The proposed FDM decomposes any data into a small number of ‘Fourier intrinsic band functions’ (FIBFs). The FDM presents a generalized Fourier expansion with variable amplitudes and variable frequencies of a time series by the Fourier method itself. We propose an idea of zero-phase filter bank-based multivariate FDM (MFDM), for the analysis of multivariate nonlinear and non-stationary time series, using the FDM. We also present an algorithm to obtain cut-off frequencies for MFDM. The proposed MFDM generates a finite number of band-limited multivariate FIBFs (MFIBFs). The MFDM preserves some intrinsic physical properties of the multivariate data, such as scale alignment, trend and instantaneous frequency. The proposed methods provide a time–frequency–energy (TFE) distribution that reveals the intrinsic structure of a data. Numerical computations and simulations have been carried out and comparison is made with the empirical mode decomposition algorithms. PMID:28413352

Density functional theory studies of HCOOH decomposition on Pd(111)

DOE PAGES

Scaranto, Jessica; Mavrikakis, Manos

2015-12-02

Here, the investigation of formic acid (HCOOH) decomposition on transition metal surfaces is important to derive useful insights for vapor phase catalysis involving HCOOH and for the development of direct HCOOH fuel cells (DFAFC). Here we present the results obtained from periodic, self-consistent, density functional theory (DFT-GGA) calculations for the elementary steps involved in the gas-phase decomposition of HCOOH on Pd(111). Accordingly, we analyzed the minimum energy paths for HCOOH dehydrogenation to CO 2 + H 2 and dehydration to CO + H 2O through the carboxyl (COOH) and formate (HCOO) intermediates. Our results suggest that HCOO formation is easiermore » than COOH formation, but HCOO decomposition is more difficult than COOH decomposition, in particular in presence of co-adsorbed O and OH species. Therefore, both paths may contribute to HCOOH decomposition. CO formation goes mainly through COOH decomposition.« less

Density functional theory studies of HCOOH decomposition on Pd(111)

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

Scaranto, Jessica; Mavrikakis, Manos

Here, the investigation of formic acid (HCOOH) decomposition on transition metal surfaces is important to derive useful insights for vapor phase catalysis involving HCOOH and for the development of direct HCOOH fuel cells (DFAFC). Here we present the results obtained from periodic, self-consistent, density functional theory (DFT-GGA) calculations for the elementary steps involved in the gas-phase decomposition of HCOOH on Pd(111). Accordingly, we analyzed the minimum energy paths for HCOOH dehydrogenation to CO 2 + H 2 and dehydration to CO + H 2O through the carboxyl (COOH) and formate (HCOO) intermediates. Our results suggest that HCOO formation is easiermore » than COOH formation, but HCOO decomposition is more difficult than COOH decomposition, in particular in presence of co-adsorbed O and OH species. Therefore, both paths may contribute to HCOOH decomposition. CO formation goes mainly through COOH decomposition.« less

Evolution-Based Functional Decomposition of Proteins

PubMed Central

Rivoire, Olivier; Reynolds, Kimberly A.; Ranganathan, Rama

2016-01-01

The essential biological properties of proteins—folding, biochemical activities, and the capacity to adapt—arise from the global pattern of interactions between amino acid residues. The statistical coupling analysis (SCA) is an approach to defining this pattern that involves the study of amino acid coevolution in an ensemble of sequences comprising a protein family. This approach indicates a functional architecture within proteins in which the basic units are coupled networks of amino acids termed sectors. This evolution-based decomposition has potential for new understandings of the structural basis for protein function. To facilitate its usage, we present here the principles and practice of the SCA and introduce new methods for sector analysis in a python-based software package (pySCA). We show that the pattern of amino acid interactions within sectors is linked to the divergence of functional lineages in a multiple sequence alignment—a model for how sector properties might be differentially tuned in members of a protein family. This work provides new tools for studying proteins and for generally testing the concept of sectors as the principal units of function and adaptive variation. PMID:27254668

Critical Analysis of Nitramine Decomposition Data: Activation Energies and Frequency Factors for HMX and RDX Decomposition

DTIC Science & Technology

1985-09-01

larger than the net energies of reaction for the same transitions ) represent energy needed for "freeing-up" of HMX or RDX molecules 70E. R. Lee, R. H...FACTORS FOR HMX AND RDX DECOMPOSITION Michael A. Schroeder DT!C .AECTE September 1985 SEP 3 0 8 * APPROVED FOR PUBUC RELEASE; DISTIR!UTION UNLIMITED. US...Final Activation Energies and Frequency Factors for HMX and RDX Decomposition b PERFORMING ORG. REPORT N, %1ER 7. AUTHOR(@) 6 CONTRACT OR GRANT NuMP

Comparison of decomposition rates between autopsied and non-autopsied human remains.

PubMed

Bates, Lennon N; Wescott, Daniel J

2016-04-01

Penetrating trauma has been cited as a significant factor in the rate of decomposition. Therefore, penetrating trauma may have an effect on estimations of time-since-death in medicolegal investigations and on research examining decomposition rates and processes when autopsied human bodies are used. The goal of this study was to determine if there are differences in the rate of decomposition between autopsied and non-autopsied human remains in the same environment. The purpose is to shed light on how large incisions, such as those from a thorocoabdominal autopsy, effect time-since-death estimations and research on the rate of decomposition that use both autopsied and non-autopsied human remains. In this study, 59 non-autopsied and 24 autopsied bodies were studied. The number of accumulated degree days required to reach each decomposition stage was then compared between autopsied and non-autopsied remains. Additionally, both types of bodies were examined for seasonal differences in decomposition rates. As temperature affects the rate of decomposition, this study also compared the internal body temperatures of autopsied and non-autopsied remains to see if differences between the two may be leading to differential decomposition. For this portion of this study, eight non-autopsied and five autopsied bodies were investigated. Internal temperature was collected once a day for two weeks. The results showed that differences in the decomposition rate between autopsied and non-autopsied remains was not statistically significant, though the average ADD needed to reach each stage of decomposition was slightly lower for autopsied bodies than non-autopsied bodies. There was also no significant difference between autopsied and non-autopsied bodies in the rate of decomposition by season or in internal temperature. Therefore, this study suggests that it is unnecessary to separate autopsied and non-autopsied remains when studying gross stages of human decomposition in Central Texas

SU-F-J-138: An Extension of PCA-Based Respiratory Deformation Modeling Via Multi-Linear Decomposition

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

Iliopoulos, AS; Sun, X; Pitsianis, N

Purpose: To address and lift the limited degree of freedom (DoF) of globally bilinear motion components such as those based on principal components analysis (PCA), for encoding and modeling volumetric deformation motion. Methods: We provide a systematic approach to obtaining a multi-linear decomposition (MLD) and associated motion model from deformation vector field (DVF) data. We had previously introduced MLD for capturing multi-way relationships between DVF variables, without being restricted by the bilinear component format of PCA-based models. PCA-based modeling is commonly used for encoding patient-specific deformation as per planning 4D-CT images, and aiding on-board motion estimation during radiotherapy. However, themore » bilinear space-time decomposition inherently limits the DoF of such models by the small number of respiratory phases. While this limit is not reached in model studies using analytical or digital phantoms with low-rank motion, it compromises modeling power in the presence of relative motion, asymmetries and hysteresis, etc, which are often observed in patient data. Specifically, a low-DoF model will spuriously couple incoherent motion components, compromising its adaptability to on-board deformation changes. By the multi-linear format of extracted motion components, MLD-based models can encode higher-DoF deformation structure. Results: We conduct mathematical and experimental comparisons between PCA- and MLD-based models. A set of temporally-sampled analytical trajectories provides a synthetic, high-rank DVF; trajectories correspond to respiratory and cardiac motion factors, including different relative frequencies and spatial variations. Additionally, a digital XCAT phantom is used to simulate a lung lesion deforming incoherently with respect to the body, which adheres to a simple respiratory trend. In both cases, coupling of incoherent motion components due to a low model DoF is clearly demonstrated. Conclusion: Multi

Generalized decompositions of dynamic systems and vector Lyapunov functions

NASA Astrophysics Data System (ADS)

Ikeda, M.; Siljak, D. D.

1981-10-01

The notion of decomposition is generalized to provide more freedom in constructing vector Lyapunov functions for stability analysis of nonlinear dynamic systems. A generalized decomposition is defined as a disjoint decomposition of a system which is obtained by expanding the state-space of a given system. An inclusion principle is formulated for the solutions of the expansion to include the solutions of the original system, so that stability of the expansion implies stability of the original system. Stability of the expansion can then be established by standard disjoint decompositions and vector Lyapunov functions. The applicability of the new approach is demonstrated using the Lotka-Volterra equations.

Climate history shapes contemporary leaf litter decomposition

Treesearch

Michael S. Strickland; Ashley D. Keiser; Mark A. Bradford

2015-01-01

Litter decomposition is mediated by multiple variables, of which climate is expected to be a dominant factor at global scales. However, like other organisms, traits of decomposers and their communities are shaped not just by the contemporary climate but also their climate history. Whether or not this affects decomposition rates is underexplored. Here we source...

Moisture controls decomposition rate in thawing tundra

Treesearch

C.E. Hicks-Pries; E.A.G. Schuur; S.M. Natali; J.G. Vogel

2013-01-01

Permafrost thaw can affect decomposition rates by changing environmental conditions and litter quality. As permafrost thaws, soils warm and thermokarst (ground subsidence) features form, causing some areas to become wetter while other areas become drier. We used a common substrate to measure how permafrost thaw affects decomposition rates in the surface soil in a...

Electrochemical and Infrared Absorption Spectroscopy Detection of SF₆ Decomposition Products.

PubMed

Dong, Ming; Zhang, Chongxing; Ren, Ming; Albarracín, Ricardo; Ye, Rixin

2017-11-15

Sulfur hexafluoride (SF₆) gas-insulated electrical equipment is widely used in high-voltage (HV) and extra-high-voltage (EHV) power systems. Partial discharge (PD) and local heating can occur in the electrical equipment because of insulation faults, which results in SF₆ decomposition and ultimately generates several types of decomposition products. These SF₆ decomposition products can be qualitatively and quantitatively detected with relevant detection methods, and such detection contributes to diagnosing the internal faults and evaluating the security risks of the equipment. At present, multiple detection methods exist for analyzing the SF₆ decomposition products, and electrochemical sensing (ES) and infrared (IR) spectroscopy are well suited for application in online detection. In this study, the combination of ES with IR spectroscopy is used to detect SF₆ gas decomposition. First, the characteristics of these two detection methods are studied, and the data analysis matrix is established. Then, a qualitative and quantitative analysis ES-IR model is established by adopting a two-step approach. A SF₆ decomposition detector is designed and manufactured by combining an electrochemical sensor and IR spectroscopy technology. The detector is used to detect SF₆ gas decomposition and is verified to reliably and accurately detect the gas components and concentrations.

Theoretical study of the decomposition mechanism of environmentally friendly insulating medium C3F7CN in the presence of H2O in a discharge

NASA Astrophysics Data System (ADS)

Zhang, Xiaoxing; Li, Yi; Xiao, Song; Tian, Shuangshuang; Deng, Zaitao; Tang, Ju

2017-08-01

C3F7CN has been the focus of the alternative gas research field over the past two years because of its excellent insulation properties and environmental characteristics. Experimental studies on its insulation performance have made many achievements. However, few studies on the formation mechanism of the decomposition components exist. A discussion of the decomposition characteristics of insulating media will provide guidance for scientific experimental research and the work that must be completed before further engineering application. In this study, the decomposition mechanism of C3F7CN in the presence of trace H2O under discharge was calculated based on the density functional theory and transition state theory. The reaction heat, Gibbs free energy, and activation energy of different decomposition pathways were investigated. The ionization parameters and toxicity of C3F7CN and various decomposition products were analyzed from the molecular structure perspective. The formation mechanism of the C3F7CN discharge decomposition components and the influence of trace water were evaluated. This paper confirms that C3F7CN has excellent decomposition characteristics, which provide theoretical support for later experiments and related engineering applications. However, the existence of trace water has a negative impact on C3F7CN’s insulation performance. Thus, strict trace water content standards should be developed to ensure dielectric insulation and the safety of maintenance personnel.

HCOOH decomposition on Pt(111): A DFT study

DOE PAGES

Scaranto, Jessica; Mavrikakis, Manos

2015-10-13

Formic acid (HCOOH) decomposition on transition metal surfaces is important for hydrogen production and for its electro-oxidation in direct HCOOH fuel cells. HCOOH can decompose through dehydrogenation leading to formation of CO 2 and H 2 or dehydration leading to CO and H 2O; because CO can poison metal surfaces, dehydrogenation is typically the desirable decomposition path. Here we report a mechanistic analysis of HCOOH decomposition on Pt(111), obtained from a plane wave density functional theory (DFT-PW91) study. We analyzed the dehydrogenation mechanism by considering the two possible pathways involving the formate (HCOO) or the carboxyl (COOH) intermediate. We alsomore » considered several possible dehydration paths leading to CO formation. We studied HCOO and COOH decomposition both on the clean surface and in the presence of other relevant co-adsorbates. The results suggest that COOH formation is energetically more difficult than HCOO formation. In contrast, COOH dehydrogenation is easier than HCOO decomposition. Here, we found that CO 2 is the main product through both pathways and that CO is produced mainly through the dehydroxylation of the COOH intermediate.« less

HCOOH decomposition on Pt(111): A DFT study

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

Scaranto, Jessica; Mavrikakis, Manos

Formic acid (HCOOH) decomposition on transition metal surfaces is important for hydrogen production and for its electro-oxidation in direct HCOOH fuel cells. HCOOH can decompose through dehydrogenation leading to formation of CO 2 and H 2 or dehydration leading to CO and H 2O; because CO can poison metal surfaces, dehydrogenation is typically the desirable decomposition path. Here we report a mechanistic analysis of HCOOH decomposition on Pt(111), obtained from a plane wave density functional theory (DFT-PW91) study. We analyzed the dehydrogenation mechanism by considering the two possible pathways involving the formate (HCOO) or the carboxyl (COOH) intermediate. We alsomore » considered several possible dehydration paths leading to CO formation. We studied HCOO and COOH decomposition both on the clean surface and in the presence of other relevant co-adsorbates. The results suggest that COOH formation is energetically more difficult than HCOO formation. In contrast, COOH dehydrogenation is easier than HCOO decomposition. Here, we found that CO 2 is the main product through both pathways and that CO is produced mainly through the dehydroxylation of the COOH intermediate.« less

Microbial ecological succession during municipal solid waste decomposition.

PubMed

Staley, Bryan F; de Los Reyes, Francis L; Wang, Ling; Barlaz, Morton A

2018-04-28

The decomposition of landfilled refuse proceeds through distinct phases, each defined by varying environmental factors such as volatile fatty acid concentration, pH, and substrate quality. The succession of microbial communities in response to these changing conditions was monitored in a laboratory-scale simulated landfill to minimize measurement difficulties experienced at field scale. 16S rRNA gene sequences retrieved at separate stages of decomposition showed significant succession in both Bacteria and methanogenic Archaea. A majority of Bacteria sequences in landfilled refuse belong to members of the phylum Firmicutes, while Proteobacteria levels fluctuated and Bacteroidetes levels increased as decomposition proceeded. Roughly 44% of archaeal sequences retrieved under conditions of low pH and high acetate were strictly hydrogenotrophic (Methanomicrobiales, Methanobacteriales). Methanosarcina was present at all stages of decomposition. Correspondence analysis showed bacterial population shifts were attributed to carboxylic acid concentration and solids hydrolysis, while archaeal populations were affected to a higher degree by pH. T-RFLP analysis showed specific taxonomic groups responded differently and exhibited unique responses during decomposition, suggesting that species composition and abundance within Bacteria and Archaea are highly dynamic. This study shows landfill microbial demographics are highly variable across both spatial and temporal transects.

A variance-decomposition approach to investigating multiscale habitat associations

USGS Publications Warehouse

Lawler, J.J.; Edwards, T.C.

2006-01-01

The recognition of the importance of spatial scale in ecology has led many researchers to take multiscale approaches to studying habitat associations. However, few of the studies that investigate habitat associations at multiple spatial scales have considered the potential effects of cross-scale correlations in measured habitat variables. When cross-scale correlations in such studies are strong, conclusions drawn about the relative strength of habitat associations at different spatial scales may be inaccurate. Here we adapt and demonstrate an analytical technique based on variance decomposition for quantifying the influence of cross-scale correlations on multiscale habitat associations. We used the technique to quantify the variation in nest-site locations of Red-naped Sapsuckers (Sphyrapicus nuchalis) and Northern Flickers (Colaptes auratus) associated with habitat descriptors at three spatial scales. We demonstrate how the method can be used to identify components of variation that are associated only with factors at a single spatial scale as well as shared components of variation that represent cross-scale correlations. Despite the fact that no explanatory variables in our models were highly correlated (r < 0.60), we found that shared components of variation reflecting cross-scale correlations accounted for roughly half of the deviance explained by the models. These results highlight the importance of both conducting habitat analyses at multiple spatial scales and of quantifying the effects of cross-scale correlations in such analyses. Given the limits of conventional analytical techniques, we recommend alternative methods, such as the variance-decomposition technique demonstrated here, for analyzing habitat associations at multiple spatial scales. ?? The Cooper Ornithological Society 2006.

Model-based multiple patterning layout decomposition

NASA Astrophysics Data System (ADS)

Guo, Daifeng; Tian, Haitong; Du, Yuelin; Wong, Martin D. F.

2015-10-01

As one of the most promising next generation lithography technologies, multiple patterning lithography (MPL) plays an important role in the attempts to keep in pace with 10 nm technology node and beyond. With feature size keeps shrinking, it has become impossible to print dense layouts within one single exposure. As a result, MPL such as double patterning lithography (DPL) and triple patterning lithography (TPL) has been widely adopted. There is a large volume of literature on DPL/TPL layout decomposition, and the current approach is to formulate the problem as a classical graph-coloring problem: Layout features (polygons) are represented by vertices in a graph G and there is an edge between two vertices if and only if the distance between the two corresponding features are less than a minimum distance threshold value dmin. The problem is to color the vertices of G using k colors (k = 2 for DPL, k = 3 for TPL) such that no two vertices connected by an edge are given the same color. This is a rule-based approach, which impose a geometric distance as a minimum constraint to simply decompose polygons within the distance into different masks. It is not desired in practice because this criteria cannot completely capture the behavior of the optics. For example, it lacks of sufficient information such as the optical source characteristics and the effects between the polygons outside the minimum distance. To remedy the deficiency, a model-based layout decomposition approach to make the decomposition criteria base on simulation results was first introduced at SPIE 2013.1 However, the algorithm1 is based on simplified assumption on the optical simulation model and therefore its usage on real layouts is limited. Recently AMSL2 also proposed a model-based approach to layout decomposition by iteratively simulating the layout, which requires excessive computational resource and may lead to sub-optimal solutions. The approach2 also potentially generates too many stiches. In this

The trait contribution to wood decomposition rates of 15 Neotropical tree species.

PubMed

van Geffen, Koert G; Poorter, Lourens; Sass-Klaassen, Ute; van Logtestijn, Richard S P; Cornelissen, Johannes H C

2010-12-01

The decomposition of dead wood is a critical uncertainty in models of the global carbon cycle. Despite this, relatively few studies have focused on dead wood decomposition, with a strong bias to higher latitudes. Especially the effect of interspecific variation in species traits on differences in wood decomposition rates remains unknown. In order to fill these gaps, we applied a novel method to study long-term wood decomposition of 15 tree species in a Bolivian semi-evergreen tropical moist forest. We hypothesized that interspecific differences in species traits are important drivers of variation in wood decomposition rates. Wood decomposition rates (fractional mass loss) varied between 0.01 and 0.31 yr(-1). We measured 10 different chemical, anatomical, and morphological traits for all species. The species' average traits were useful predictors of wood decomposition rates, particularly the average diameter (dbh) of the tree species (R2 = 0.41). Lignin concentration further increased the proportion of explained inter-specific variation in wood decomposition (both negative relations, cumulative R2 = 0.55), although it did not significantly explain variation in wood decomposition rates if considered alone. When dbh values of the actual dead trees sampled for decomposition rate determination were used as a predictor variable, the final model (including dead tree dbh and lignin concentration) explained even more variation in wood decomposition rates (R2 = 0.71), underlining the importance of dbh in wood decomposition. Other traits, including wood density, wood anatomical traits, macronutrient concentrations, and the amount of phenolic extractives could not significantly explain the variation in wood decomposition rates. The surprising results of this multi-species study, in which for the first time a large set of traits is explicitly linked to wood decomposition rates, merits further testing in other forest ecosystems.

Vanishing-Overhead Linear-Scaling Random Phase Approximation by Cholesky Decomposition and an Attenuated Coulomb-Metric.

PubMed

Luenser, Arne; Schurkus, Henry F; Ochsenfeld, Christian

2017-04-11

A reformulation of the random phase approximation within the resolution-of-the-identity (RI) scheme is presented, that is competitive to canonical molecular orbital RI-RPA already for small- to medium-sized molecules. For electronically sparse systems drastic speedups due to the reduced scaling behavior compared to the molecular orbital formulation are demonstrated. Our reformulation is based on two ideas, which are independently useful: First, a Cholesky decomposition of density matrices that reduces the scaling with basis set size for a fixed-size molecule by one order, leading to massive performance improvements. Second, replacement of the overlap RI metric used in the original AO-RPA by an attenuated Coulomb metric. Accuracy is significantly improved compared to the overlap metric, while locality and sparsity of the integrals are retained, as is the effective linear scaling behavior.

About decomposition approach for solving the classification problem

NASA Astrophysics Data System (ADS)

Andrianova, A. A.

2016-11-01

This article describes the features of the application of an algorithm with using of decomposition methods for solving the binary classification problem of constructing a linear classifier based on Support Vector Machine method. Application of decomposition reduces the volume of calculations, in particular, due to the emerging possibilities to build parallel versions of the algorithm, which is a very important advantage for the solution of problems with big data. The analysis of the results of computational experiments conducted using the decomposition approach. The experiment use known data set for binary classification problem.

Molecular evolution of the hyaluronan synthase 2 gene in mammals: implications for adaptations to the subterranean niche and cancer resistance

PubMed Central

Faulkes, Christopher G.; Davies, Kalina T. J.; Rossiter, Stephen J.; Bennett, Nigel C.

2015-01-01

The naked mole-rat (NMR) Heterocephalus glaber is a unique and fascinating mammal exhibiting many unusual adaptations to a subterranean lifestyle. The recent discovery of their resistance to cancer and exceptional longevity has opened up new and important avenues of research. Part of this resistance to cancer has been attributed to the fact that NMRs produce a modified form of hyaluronan—a key constituent of the extracellular matrix—that is thought to confer increased elasticity of the skin as an adaptation for living in narrow tunnels. This so-called high molecular mass hyaluronan (HMM-HA) stems from two apparently unique substitutions in the hyaluronan synthase 2 enzyme (HAS2). To test whether other subterranean mammals with similar selection pressures also show molecular adaptation in their HAS2 gene, we sequenced the HAS2 gene for 11 subterranean mammals and closely related species, and combined these with data from 57 other mammals. Comparative screening revealed that one of the two putatively important HAS2 substitutions in the NMR predicted to have a significant effect on hyaluronan synthase function was uniquely shared by all African mole-rats. Interestingly, we also identified multiple other amino acid substitutions in key domains of the HAS2 molecule, although the biological consequences of these for hyaluronan synthesis remain to be determined. Despite these results, we found evidence of strong purifying selection acting on the HAS2 gene across all mammals, and the NMR remains unique in its particular HAS2 sequence. Our results indicate that more work is needed to determine whether the apparent cancer resistance seen in NMR is shared by other members of the African mole-rat clade. PMID:25948568

Molecular carbon isotopic evidence for the origin of geothermal hydrocarbons

NASA Technical Reports Server (NTRS)

Des Marais, D. J.; Donchin, J. H.; Nehring, N. L.; Truesdell, A. H.

1981-01-01

Isotopic measurements of individual geothermal hydrocarbons that are, as a group, of higher molecular weight than methane are reported. It is believed in light of this data that the principal source of hydrocarbons in four geothermal areas in western North America is the thermal decomposition of sedimentary or groundwater organic matter.

Metascalable molecular dynamics simulation of nano-mechano-chemistry

NASA Astrophysics Data System (ADS)

Shimojo, F.; Kalia, R. K.; Nakano, A.; Nomura, K.; Vashishta, P.

2008-07-01

We have developed a metascalable (or 'design once, scale on new architectures') parallel application-development framework for first-principles based simulations of nano-mechano-chemical processes on emerging petaflops architectures based on spatiotemporal data locality principles. The framework consists of (1) an embedded divide-and-conquer (EDC) algorithmic framework based on spatial locality to design linear-scaling algorithms, (2) a space-time-ensemble parallel (STEP) approach based on temporal locality to predict long-time dynamics, and (3) a tunable hierarchical cellular decomposition (HCD) parallelization framework to map these scalable algorithms onto hardware. The EDC-STEP-HCD framework exposes and expresses maximal concurrency and data locality, thereby achieving parallel efficiency as high as 0.99 for 1.59-billion-atom reactive force field molecular dynamics (MD) and 17.7-million-atom (1.56 trillion electronic degrees of freedom) quantum mechanical (QM) MD in the framework of the density functional theory (DFT) on adaptive multigrids, in addition to 201-billion-atom nonreactive MD, on 196 608 IBM BlueGene/L processors. We have also used the framework for automated execution of adaptive hybrid DFT/MD simulation on a grid of six supercomputers in the US and Japan, in which the number of processors changed dynamically on demand and tasks were migrated according to unexpected faults. The paper presents the application of the framework to the study of nanoenergetic materials: (1) combustion of an Al/Fe2O3 thermite and (2) shock initiation and reactive nanojets at a void in an energetic crystal.

Towards a representation of priming on soil carbon decomposition in the global land biosphere model ORCHIDEE (version 1.9.5.2)

NASA Astrophysics Data System (ADS)

Guenet, Bertrand; Esteban Moyano, Fernando; Peylin, Philippe; Ciais, Philippe; Janssens, Ivan A.

2016-03-01

Priming of soil carbon decomposition encompasses different processes through which the decomposition of native (already present) soil organic matter is amplified through the addition of new organic matter, with new inputs typically being more labile than the native soil organic matter. Evidence for priming comes from laboratory and field experiments, but to date there is no estimate of its impact at global scale and under the current anthropogenic perturbation of the carbon cycle. Current soil carbon decomposition models do not include priming mechanisms, thereby introducing uncertainty when extrapolating short-term local observations to ecosystem and regional to global scale. In this study we present a simple conceptual model of decomposition priming, called PRIM, able to reproduce laboratory (incubation) and field (litter manipulation) priming experiments. Parameters for this model were first optimized against data from 20 soil incubation experiments using a Bayesian framework. The optimized parameter values were evaluated against another set of soil incubation data independent from the ones used for calibration and the PRIM model reproduced the soil incubations data better than the original, CENTURY-type soil decomposition model, whose decomposition equations are based only on first-order kinetics. We then compared the PRIM model and the standard first-order decay model incorporated into the global land biosphere model ORCHIDEE (Organising Carbon and Hydrology In Dynamic Ecosystems). A test of both models was performed at ecosystem scale using litter manipulation experiments from five sites. Although both versions were equally able to reproduce observed decay rates of litter, only ORCHIDEE-PRIM could simulate the observed priming (R2 = 0.54) in cases where litter was added or removed. This result suggests that a conceptually simple and numerically tractable representation of priming adapted to global models is able to capture the sign and magnitude of the

Towards a representation of priming on soil carbon decomposition in the global land biosphere model ORCHIDEE (version 1.9.5.2)

NASA Astrophysics Data System (ADS)

Guenet, B.; Moyano, F. E.; Peylin, P.; Ciais, P.; Janssens, I. A.

2015-10-01

Priming of soil carbon decomposition encompasses different processes through which the decomposition of native (already present) soil organic matter is amplified through the addition of new organic matter, with new inputs typically being more labile than the native soil organic matter. Evidence for priming comes from laboratory and field experiments, but to date there is no estimate of its impact at global scale and under the current anthropogenic perturbation of the carbon cycle. Current soil carbon decomposition models do not include priming mechanisms, thereby introducing uncertainty when extrapolating short-term local observations to ecosystem and regional to global scale. In this study we present a simple conceptual model of decomposition priming, called PRIM, able to reproduce laboratory (incubation) and field (litter manipulation) priming experiments. Parameters for this model were first optimized against data from 20 soil incubation experiments using a Bayesian framework. The optimized parameter values were evaluated against another set of soil incubation data independent from the ones used for calibration and the PRIM model reproduced the soil incubations data better than the original, CENTURY-type soil decomposition model, whose decomposition equations are based only on first order kinetics. We then compared the PRIM model and the standard first order decay model incorporated into the global land biosphere model ORCHIDEE. A test of both models was performed at ecosystem scale using litter manipulation experiments from 5 sites. Although both versions were equally able to reproduce observed decay rates of litter, only ORCHIDEE-PRIM could simulate the observed priming (R2 = 0.54) in cases where litter was added or removed. This result suggests that a conceptually simple and numerically tractable representation of priming adapted to global models is able to capture the sign and magnitude of the priming of litter and soil organic matter.

Assessing the effect of different treatments on decomposition rate of dairy manure.

PubMed

Khalil, Tariq M; Higgins, Stewart S; Ndegwa, Pius M; Frear, Craig S; Stöckle, Claudio O

2016-11-01

Confined animal feeding operations (CAFOs) contribute to greenhouse gas emission, but the magnitude of these emissions as a function of operation size, infrastructure, and manure management are difficult to assess. Modeling is a viable option to estimate gaseous emission and nutrient flows from CAFOs. These models use a decomposition rate constant for carbon mineralization. However, this constant is usually determined assuming a homogenous mix of manure, ignoring the effects of emerging manure treatments. The aim of this study was to measure and compare the decomposition rate constants of dairy manure in single and three-pool decomposition models, and to develop an empirical model based on chemical composition of manure for prediction of a decomposition rate constant. Decomposition rate constants of manure before and after an anaerobic digester (AD), following coarse fiber separation, and fine solids removal were determined under anaerobic conditions for single and three-pool decomposition models. The decomposition rates of treated manure effluents differed significantly from untreated manure for both single and three-pool decomposition models. In the single-pool decomposition model, AD effluent containing only suspended solids had a relatively high decomposition rate of 0.060 d(-1), while liquid with coarse fiber and fine solids removed had the lowest rate of 0.013 d(-1). In the three-pool decomposition model, fast and slow decomposition rate constants (0.25 d(-1) and 0.016 d(-1) respectively) of untreated AD influent were also significantly different from treated manure fractions. A regression model to predict the decomposition rate of treated dairy manure fitted well (R(2) = 0.83) to observed data. Copyright © 2016 Elsevier Ltd. All rights reserved.

Atomic decomposition of the protein solvation free energy and its application to amyloid-beta protein in water

NASA Astrophysics Data System (ADS)

Chong, Song-Ho; Ham, Sihyun

2011-07-01

We report the development of an atomic decomposition method of the protein solvation free energy in water, which ascribes global change in the solvation free energy to local changes in protein conformation as well as in hydration structure. So far, empirical decomposition analyses based on simple continuum solvation models have prevailed in the study of protein-protein interactions, protein-ligand interactions, as well as in developing scoring functions for computer-aided drug design. However, the use of continuum solvation model suffers serious drawbacks since it yields the protein free energy landscape which is quite different from that of the explicit solvent model and since it does not properly account for the non-polar hydrophobic effects which play a crucial role in biological processes in water. Herein, we develop an exact and general decomposition method of the solvation free energy that overcomes these hindrances. We then apply this method to elucidate the molecular origin for the solvation free energy change upon the conformational transitions of 42-residue amyloid-beta protein (Aβ42) in water, whose aggregation has been implicated as a primary cause of Alzheimer's disease. We address why Aβ42 protein exhibits a great propensity to aggregate when transferred from organic phase to aqueous phase.

Lossless and Sufficient - Invariant Decomposition of Deterministic Target

NASA Astrophysics Data System (ADS)

Paladini, Riccardo; Ferro Famil, Laurent; Pottier, Eric; Martorella, Marco; Berizzi, Fabrizio

2011-03-01

The symmetric radar scattering matrix of a reciprocal target is projected on the circular polarization basis and is decomposed into four orientation invariant parameters, relative phase and relative orientation. The physical interpretation of this results is found in the wave-particle nature of radar scattering due to the circular polarization nature of elemental packets of energy. The proposed decomposition, is based on left orthogonal to left Special Unitary basis, providing the target description in term of a unitary vector. A comparison between the proposed CTD and Cameron, Kennaugh and Krogager decompositions is also pointed out. A validation by the use of both anechoic chamber data and airborne EMISAR data of DTU is used to show the effectiveness of this decomposition for the analysis of coherent targets. In the second paper we will show the application of the rotation group U(3) for the decomposition of distributed targets into nine meaningful parameters.

Distributed Damage Estimation for Prognostics based on Structural Model Decomposition

NASA Technical Reports Server (NTRS)

Daigle, Matthew; Bregon, Anibal; Roychoudhury, Indranil

2011-01-01

Model-based prognostics approaches capture system knowledge in the form of physics-based models of components, and how they fail. These methods consist of a damage estimation phase, in which the health state of a component is estimated, and a prediction phase, in which the health state is projected forward in time to determine end of life. However, the damage estimation problem is often multi-dimensional and computationally intensive. We propose a model decomposition approach adapted from the diagnosis community, called possible conflicts, in order to both improve the computational efficiency of damage estimation, and formulate a damage estimation approach that is inherently distributed. Local state estimates are combined into a global state estimate from which prediction is performed. Using a centrifugal pump as a case study, we perform a number of simulation-based experiments to demonstrate the approach.

Root traits predict decomposition across a landscape-scale grazing experiment

PubMed Central

Smith, Stuart W; Woodin, Sarah J; Pakeman, Robin J; Johnson, David; van der Wal, René

2014-01-01

Root litter is the dominant soil carbon and nutrient input in many ecosystems, yet few studies have considered how root decomposition is regulated at the landscape scale and how this is mediated by land-use management practices. Large herbivores can potentially influence below-ground decomposition through changes in soil microclimate (temperature and moisture) and changes in plant species composition (root traits). To investigate such herbivore-induced changes, we quantified annual root decomposition of upland grassland species in situ across a landscape-scale livestock grazing experiment, in a common-garden experiment and in laboratory microcosms evaluating the influence of key root traits on decomposition. Livestock grazing increased soil temperatures, but this did not affect root decomposition. Grazing had no effect on soil moisture, but wetter soils retarded root decomposition. Species-specific decomposition rates were similar across all grazing treatments, and species differences were maintained in the common-garden experiment, suggesting an overriding importance of litter type. Supporting this, in microcosms, roots with lower specific root area (m2 g−1) or those with higher phosphorus concentrations decomposed faster. Our results suggest that large herbivores alter below-ground carbon and nitrogen dynamics more through their effects on plant species composition and associated root traits than through effects on the soil microclimate. PMID:24841886

Extension of the AMBER molecular dynamics software to Intel's Many Integrated Core (MIC) architecture

NASA Astrophysics Data System (ADS)

Needham, Perri J.; Bhuiyan, Ashraf; Walker, Ross C.

2016-04-01

We present an implementation of explicit solvent particle mesh Ewald (PME) classical molecular dynamics (MD) within the PMEMD molecular dynamics engine, that forms part of the AMBER v14 MD software package, that makes use of Intel Xeon Phi coprocessors by offloading portions of the PME direct summation and neighbor list build to the coprocessor. We refer to this implementation as pmemd MIC offload and in this paper present the technical details of the algorithm, including basic models for MPI and OpenMP configuration, and analyze the resultant performance. The algorithm provides the best performance improvement for large systems (>400,000 atoms), achieving a ∼35% performance improvement for satellite tobacco mosaic virus (1,067,095 atoms) when 2 Intel E5-2697 v2 processors (2 ×12 cores, 30M cache, 2.7 GHz) are coupled to an Intel Xeon Phi coprocessor (Model 7120P-1.238/1.333 GHz, 61 cores). The implementation utilizes a two-fold decomposition strategy: spatial decomposition using an MPI library and thread-based decomposition using OpenMP. We also present compiler optimization settings that improve the performance on Intel Xeon processors, while retaining simulation accuracy.

Heterometallic molecular precursors for a lithium-iron oxide material: synthesis, solid state structure, solution and gas-phase behaviour, and thermal decomposition.

PubMed

Han, Haixiang; Wei, Zheng; Barry, Matthew C; Filatov, Alexander S; Dikarev, Evgeny V

2017-05-02

Three heterometallic single-source precursors with a Li : Fe = 1 : 1 ratio for a LiFeO 2 oxide material are reported. Heterometallic compounds LiFeL 3 (L = tbaoac (1), ptac (2), and acac(3)) have been obtained on a large scale, in nearly quantitative yields by one-step reactions that employ readily available reagents. The heterometallic precursor LiFe(acac) 3 (3) with small, symmetric substituents on the ligand (acac = pentane-2,4-dionate), maintains a 1D polymeric structure in the solid state that limits its volatility and prevents solubility in non-coordinating solvents. The application of the unsymmetrical ligands, tbaoac (tert-butyl acetoacetate) and ptac (1,1,1-trifluoro-5,5-dimethyl-2,4-hexanedionate), that exhibit different bridging properties at the two ends of the ligand, allowed us to change the connectivity pattern within the heterometallic assembly. The latter was demonstrated by structural characterization of heterometallic complexes LiFe(tbaoac) 3 (1) and LiFe(ptac) 3 (2) that consist of discrete heterocyclic tetranuclear molecules Li 2 Fe 2 L 6 . The compounds are highly volatile and exhibit a congruent sublimation character. DART mass spectrometric investigation revealed the presence of heterometallic molecules in the gas phase. The positive mode spectra are dominated by the presence of [M - L] + peaks (M = Li 2 Fe 2 L 6 ). In accord with their discrete molecular structure, complexes 1 and 2 are highly soluble in nearly all common solvents. In order to test the retention of the heterometallic structure in solution, the diamagnetic analog of 1, LiMg(tbaoac) 3 (4), has been isolated. Its tetranuclear molecular structure was found to be isomorphous to that of the iron counterpart. 1 H and 7 Li NMR spectroscopy unambiguously confirmed the presence of heterometallic molecules in solutions of non-coordinating solvents. The heterometallic precursor 1 was shown to exhibit clean thermal decomposition in air that results in phase-pure �

Iterative image-domain decomposition for dual-energy CT

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

Niu, Tianye; Dong, Xue; Petrongolo, Michael

2014-04-15

Purpose: Dual energy CT (DECT) imaging plays an important role in advanced imaging applications due to its capability of material decomposition. Direct decomposition via matrix inversion suffers from significant degradation of image signal-to-noise ratios, which reduces clinical values of DECT. Existing denoising algorithms achieve suboptimal performance since they suppress image noise either before or after the decomposition and do not fully explore the noise statistical properties of the decomposition process. In this work, the authors propose an iterative image-domain decomposition method for noise suppression in DECT, using the full variance-covariance matrix of the decomposed images. Methods: The proposed algorithm ismore » formulated in the form of least-square estimation with smoothness regularization. Based on the design principles of a best linear unbiased estimator, the authors include the inverse of the estimated variance-covariance matrix of the decomposed images as the penalty weight in the least-square term. The regularization term enforces the image smoothness by calculating the square sum of neighboring pixel value differences. To retain the boundary sharpness of the decomposed images, the authors detect the edges in the CT images before decomposition. These edge pixels have small weights in the calculation of the regularization term. Distinct from the existing denoising algorithms applied on the images before or after decomposition, the method has an iterative process for noise suppression, with decomposition performed in each iteration. The authors implement the proposed algorithm using a standard conjugate gradient algorithm. The method performance is evaluated using an evaluation phantom (Catphan©600) and an anthropomorphic head phantom. The results are compared with those generated using direct matrix inversion with no noise suppression, a denoising method applied on the decomposed images, and an existing algorithm with similar formulation

High temperature decomposition of hydrogen peroxide

NASA Technical Reports Server (NTRS)

Parrish, Clyde F. (Inventor)

2004-01-01

Nitric oxide (NO) is oxidized into nitrogen dioxide (NO.sub.2) by the high temperature decomposition of a hydrogen peroxide solution to produce the oxidative free radicals, hydroxyl and hydroperoxyl. The hydrogen peroxide solution is impinged upon a heated surface in a stream of nitric oxide where it decomposes to produce the oxidative free radicals. Because the decomposition of the hydrogen peroxide solution occurs within the stream of the nitric oxide, rapid gas-phase oxidation of nitric oxide into nitrogen dioxide occurs.

High temperature decomposition of hydrogen peroxide

NASA Technical Reports Server (NTRS)

Parrish, Clyde F. (Inventor)

2011-01-01

Nitric oxide (NO) is oxidized into nitrogen dioxide (NO.sub.2) by the high temperature decomposition of a hydrogen peroxide solution to produce the oxidative free radicals, hydroxyl and hydroperoxyl. The hydrogen peroxide solution is impinged upon a heated surface in a stream of nitric oxide where it decomposes to produce the oxidative free radicals. Because the decomposition of the hydrogen peroxide solution occurs within the stream of the nitric oxide, rapid gas-phase oxidation of nitric oxide into nitrogen dioxide occurs.

High temperature decomposition of hydrogen peroxide

NASA Technical Reports Server (NTRS)

Parrish, Clyde F. (Inventor)

2005-01-01

Nitric oxide (NO) is oxidized into nitrogen dioxide (NO2) by the high temperature decomposition of a hydrogen peroxide solution to produce the oxidative free radicals, hydroxyl and hydroperoxyl. The hydrogen peroxide solution is impinged upon a heated surface in a stream of nitric oxide where it decomposes to produce the oxidative free radicals. Because the decomposition of the hydrogen peroxide solution occurs within the stream of the nitric oxide, rapid gas-phase oxidation of nitric oxide into nitrogen dioxide occurs.

High Temperature Decomposition of Hydrogen Peroxide

NASA Technical Reports Server (NTRS)

Parrish, Clyde F. (Inventor)

2004-01-01

Nitric oxide (NO) is oxidized into nitrogen dioxide (NO2) by the high temperature decomposition of a hydrogen peroxide solution to produce the oxidative free radicals, hydroxyl and hydropemxyl. The hydrogen peroxide solution is impinged upon a heated surface in a stream of nitric oxide where it decomposes to produce the oxidative free radicals. Because the decomposition of the hydrogen peroxide solution occurs within the stream of the nitric oxide, rapid gas-phase oxidation of nitric oxide into nitrogen dioxide occurs.

Study on US/O3 mechanism in p-chlorophenol decomposition

PubMed Central

Xu, Xian-wen; Xu, Xin-hua; Shi, Hui-xiang; Wang, Da-hui

2005-01-01

Study on the effects of sonolysis, ozonolysis and US/O3 system on the decomposition of p-chlorophenol in aqueous solutions indicated that in the cases of US/O3 system, individual ozonolysis and sonolysis, the decomposition rate of p-chlorophenol reached 78.78%, 56.20%, 2.79% after a 16-min reaction while its CODcr (chemical oxygen demand) removal rate was 97.02%, 62.17%, 3.67% after a 120-min reaction. The decomposition reaction of p-chlorophenol follows pseudo-first-order kinetics. The enhancement factors of p-chlorophenol and its CODcr under US/O3 system reached 63% and 237% respectively. The main intermediates during the decomposition include catechol, hydroquinone, p-benzoquinone, phenol, fumaric acid, maleic acid, oxalic acid and formic acid. The decomposition mechanism of p-chlorophenol was also discussed. PMID:15909343

Culture- and molecular-based detection of swine-adapted Salmonella shed by avian scavengers.

PubMed

Blanco, Guillermo; Díaz de Tuesta, Juan A

2018-09-01

Salmonella can play an important role as a disease agent in wildlife, which can then act as carriers and reservoirs of sanitary importance at the livestock-human interface. Transmission from livestock to avian scavengers can occur when these species consume contaminated carcasses and meat remains in supplementary feeding stations and rubbish dumps. We compared the performance of PCR-based detection with conventional culture-based methods to detect Salmonella in the faeces of red kites (Milvus milvus) and griffon vultures (Gyps fulvus) in central Spain. The occurrence of culturable Salmonella was intermediate in red kites (1.9%, n=52) and high in griffon vultures (26.3%, n=99). These proportions were clearly higher with PCR-based detection (13.5% and 40.4%, respectively). Confirmation cultures failed to grow Salmonella in all faecal samples positive by the molecular assay but negative by the initial conventional culture in both scavenger species, indicating the occurrence of false (non-culturable) positives by PCR-based detection. This suggests that the molecular assay is highly sensitive to detecting viable Salmonella in cultures, but also partial genomes and dead or unviable bacteria from past infections or contamination. Thus, the actual occurrence of Salmonella in a particular sampling time period can be underestimated when using only culture detection. The serovars found in the scavenger faeces were among the most frequently isolated in pigs from Spain and other EU countries, especially those generally recognized as swine-adapted monophasic variants of S. Typhimurium. Because the studied species obtain much of their food from pig carcasses, this livestock may be the primary source of Salmonella via direct ingestion of infected carcasses and indirectly via contamination due to the unsanitary conditions found in supplementary feeding stations established for scavenger conservation. Combining culture- and molecular-based detection is encouraged to understand the

Bimolecular Coupling as a Vector for Decomposition of Fast-Initiating Olefin Metathesis Catalysts.

PubMed

Bailey, Gwendolyn A; Foscato, Marco; Higman, Carolyn S; Day, Craig S; Jensen, Vidar R; Fogg, Deryn E

2018-06-06

The correlation between rapid initiation and rapid decomposition in olefin metathesis is probed for a series of fast-initiating, phosphine-free Ru catalysts: the Hoveyda catalyst HII, RuCl 2 (L)(═CHC 6 H 4 - o-O i Pr); the Grela catalyst nG (a derivative of HII with a nitro group para to O i Pr); the Piers catalyst PII, [RuCl 2 (L)(═CHPCy 3 )]OTf; the third-generation Grubbs catalyst GIII, RuCl 2 (L)(py) 2 (═CHPh); and dianiline catalyst DA, RuCl 2 (L)( o-dianiline)(═CHPh), in all of which L = H 2 IMes = N,N'-bis(mesityl)imidazolin-2-ylidene. Prior studies of ethylene metathesis have established that various Ru metathesis catalysts can decompose by β-elimination of propene from the metallacyclobutane intermediate RuCl 2 (H 2 IMes)(κ 2 -C 3 H 6 ), Ru-2. The present work demonstrates that in metathesis of terminal olefins, β-elimination yields only ca. 25-40% propenes for HII, nG, PII, or DA, and none for GIII. The discrepancy is attributed to competing decomposition via bimolecular coupling of methylidene intermediate RuCl 2 (H 2 IMes)(═CH 2 ), Ru-1. Direct evidence for methylidene coupling is presented, via the controlled decomposition of transiently stabilized adducts of Ru-1, RuCl 2 (H 2 IMes)L n (═CH 2 ) (L n = py n' ; n' = 1, 2, or o-dianiline). These adducts were synthesized by treating in situ-generated metallacyclobutane Ru-2 with pyridine or o-dianiline, and were isolated by precipitating at low temperature (-116 or -78 °C, respectively). On warming, both undergo methylidene coupling, liberating ethylene and forming RuCl 2 (H 2 IMes)L n . A mechanism is proposed based on kinetic studies and molecular-level computational analysis. Bimolecular coupling emerges as an important contributor to the instability of Ru-1, and a potentially major pathway for decomposition of fast-initiating, phosphine-free metathesis catalysts.

Dynamics in the Decompositions Approach to Quantum Mechanics

NASA Astrophysics Data System (ADS)

Harding, John

2017-12-01

In Harding (Trans. Amer. Math. Soc. 348(5), 1839-1862 1996) it was shown that the direct product decompositions of any non-empty set, group, vector space, and topological space X form an orthomodular poset Fact X. This is the basis for a line of study in foundational quantum mechanics replacing Hilbert spaces with other types of structures. Here we develop dynamics and an abstract version of a time independent Schrödinger's equation in the setting of decompositions by considering representations of the group of real numbers in the automorphism group of the orthomodular poset Fact X of decompositions.

Land-use legacies regulate decomposition dynamics following bioenergy crop conversion

DOE PAGES

Kallenbach, Cynthia M.; Stuart Grandy, A.

2014-07-14

Land-use conversion into bioenergy crop production can alter litter decomposition processes tightly coupled to soil carbon and nutrient dynamics. Yet, litter decomposition has been poorly described in bioenergy production systems, especially following land-use conversion. Predicting decomposition dynamics in postconversion bioenergy production systems is challenging because of the combined influence of land-use legacies with current management and litter quality. To evaluate how land-use legacies interact with current bioenergy crop management to influence litter decomposition in different litter types, we conducted a landscape-scale litterbag decomposition experiment. We proposed land-use legacies regulate decomposition, but their effects are weakened under higher quality litter andmore » when current land use intensifies ecosystem disturbance relative to prior land use. We compared sites left in historical land uses of either agriculture (AG) or Conservation Reserve Program grassland (CRP) to those that were converted to corn or switchgrass bioenergy crop production. Enzyme activities, mass loss, microbial biomass, and changes in litter chemistry were monitored in corn stover and switchgrass litter over 485 days, accompanied by similar soil measurements. Across all measured variables, legacy had the strongest effect (P < 0.05) relative to litter type and current management, where CRP sites maintained higher soil and litter enzyme activities and microbial biomass relative to AG sites. Decomposition responses to conversion depended on legacy but also current management and litter type. Within the CRP sites, conversion into corn increased litter enzymes, microbial biomass, and litter protein and lipid abundances, especially on decomposing corn litter, relative to nonconverted CRP. However, conversion into switchgrass from CRP, a moderate disturbance, often had no effect on switchgrass litter decomposition parameters. Thus, legacies shape the direction and

Climbing plants: attachment adaptations and bioinspired innovations.

PubMed

Burris, Jason N; Lenaghan, Scott C; Stewart, C Neal

2018-04-01

Climbing plants have unique adaptations to enable them to compete for sunlight, for which they invest minimal resources for vertical growth. Indeed, their stems bear relatively little weight, as they traverse their host substrates skyward. Climbers possess high tensile strength and flexibility, which allows them to utilize natural and manmade structures for support and growth. The climbing strategies of plants have intrigued scientists for centuries, yet our understanding about biochemical adaptations and their molecular undergirding is still in the early stages of research. Nonetheless, recent discoveries are promising, not only from a basic knowledge perspective, but also for bioinspired product development. Several adaptations, including nanoparticle and adhesive production will be reviewed, as well as practical translation of these adaptations to commercial applications. We will review the botanical literature on the modes of adaptation to climb, as well as specialized organs-and cellular innovations. Finally, recent molecular and biochemical data will be reviewed to assess the future needs and new directions for potential practical products that may be bioinspired by climbing plants.

The Effect of Body Mass on Outdoor Adult Human Decomposition.

PubMed

Roberts, Lindsey G; Spencer, Jessica R; Dabbs, Gretchen R

2017-09-01

Forensic taphonomy explores factors impacting human decomposition. This study investigated the effect of body mass on the rate and pattern of adult human decomposition. Nine males and three females aged 49-95 years ranging in mass from 73 to 159 kg who were donated to the Complex for Forensic Anthropology Research between December 2012 and September 2015 were included in this study. Kelvin accumulated degree days (KADD) were used to assess the thermal energy required for subjects to reach several total body score (TBS) thresholds: early decomposition (TBS ≥6.0), TBS ≥12.5, advanced decomposition (TBS ≥19.0), TBS ≥23.0, and skeletonization (TBS ≥27.0). Results indicate no significant correlation between body mass and KADD at any TBS threshold. Body mass accounted for up to 24.0% of variation in decomposition rate depending on stage, and minor differences in decomposition pattern were observed. Body mass likely has a minimal impact on postmortem interval estimation. © 2017 American Academy of Forensic Sciences.

Randomized interpolative decomposition of separated representations

NASA Astrophysics Data System (ADS)

Biagioni, David J.; Beylkin, Daniel; Beylkin, Gregory

2015-01-01

We introduce an algorithm to compute tensor interpolative decomposition (dubbed CTD-ID) for the reduction of the separation rank of Canonical Tensor Decompositions (CTDs). Tensor ID selects, for a user-defined accuracy ɛ, a near optimal subset of terms of a CTD to represent the remaining terms via a linear combination of the selected terms. CTD-ID can be used as an alternative to or in combination with the Alternating Least Squares (ALS) algorithm. We present examples of its use within a convergent iteration to compute inverse operators in high dimensions. We also briefly discuss the spectral norm as a computational alternative to the Frobenius norm in estimating approximation errors of tensor ID. We reduce the problem of finding tensor IDs to that of constructing interpolative decompositions of certain matrices. These matrices are generated via randomized projection of the terms of the given tensor. We provide cost estimates and several examples of the new approach to the reduction of separation rank.

Primary decomposition of zero-dimensional ideals over finite fields

NASA Astrophysics Data System (ADS)

Gao, Shuhong; Wan, Daqing; Wang, Mingsheng

2009-03-01

A new algorithm is presented for computing primary decomposition of zero-dimensional ideals over finite fields. Like Berlekamp's algorithm for univariate polynomials, the new method is based on the invariant subspace of the Frobenius map acting on the quotient algebra. The dimension of the invariant subspace equals the number of primary components, and a basis of the invariant subspace yields a complete decomposition. Unlike previous approaches for decomposing multivariate polynomial systems, the new method does not need primality testing nor any generic projection, instead it reduces the general decomposition problem directly to root finding of univariate polynomials over the ground field. Also, it is shown how Groebner basis structure can be used to get partial primary decomposition without any root finding.

Molecular adaptation to an extreme environment: origin of the thermal stability of the pompeii worm collagen.

PubMed

Sicot, F X; Mesnage, M; Masselot, M; Exposito, J Y; Garrone, R; Deutsch, J; Gaill, F

2000-09-29

The annelid Alvinella pompejana is probably the most heat-tolerant metazoan organism known. Previous results have shown that the level of thermal stability of its interstitial collagen is significantly greater than that of coastal annelids and of vent organisms, such as the vestimentiferan Riftia pachyptila, living in colder parts of the deep-sea hydrothermal environment. In order to investigate the molecular basis of this thermal behavior, we cloned and sequenced a large cDNA molecule coding the fibrillar collagen of Alvinella, including one half of the helical domain and the entire C-propeptide domain. For comparison, we also cloned the 3' part of the homologous cDNA from Riftia. Comparison of the corresponding helical domains of these two species, together with that of the previously sequenced domain of the coastal lugworm Arenicola marina, showed that the increase in proline content and in the number of stabilizing triplets correlate with the outstanding thermostability of the interstitial collagen of A. pompejana. Phylogenetic analysis showed that triple helical and the C-propeptide parts of the same collagen molecule evolve at different rates, in favor of an adaptive mechanism at the molecular level. Copyright 2000 Academic Press.

From classical to quantum and back: Hamiltonian adaptive resolution path integral, ring polymer, and centroid molecular dynamics

NASA Astrophysics Data System (ADS)

Kreis, Karsten; Kremer, Kurt; Potestio, Raffaello; Tuckerman, Mark E.

2017-12-01

Path integral-based methodologies play a crucial role for the investigation of nuclear quantum effects by means of computer simulations. However, these techniques are significantly more demanding than corresponding classical simulations. To reduce this numerical effort, we recently proposed a method, based on a rigorous Hamiltonian formulation, which restricts the quantum modeling to a small but relevant spatial region within a larger reservoir where particles are treated classically. In this work, we extend this idea and show how it can be implemented along with state-of-the-art path integral simulation techniques, including path-integral molecular dynamics, which allows for the calculation of quantum statistical properties, and ring-polymer and centroid molecular dynamics, which allow the calculation of approximate quantum dynamical properties. To this end, we derive a new integration algorithm that also makes use of multiple time-stepping. The scheme is validated via adaptive classical-path-integral simulations of liquid water. Potential applications of the proposed multiresolution method are diverse and include efficient quantum simulations of interfaces as well as complex biomolecular systems such as membranes and proteins.

DHA-fluorescent probe is sensitive to membrane order and reveals molecular adaptation of DHA in ordered lipid microdomains☆

PubMed Central

Teague, Heather; Ross, Ron; Harris, Mitchel; Mitchell, Drake C.; Shaikh, Saame Raza

2012-01-01

Docosahexaenoic acid (DHA) disrupts the size and order of plasma membrane lipid microdomains in vitro and in vivo. However, it is unknown how the highly disordered structure of DHA mechanistically adapts to increase the order of tightly packed lipid microdomains. Therefore, we studied a novel DHA-Bodipy fluorescent probe to address this issue. We first determined if the DHA-Bodipy probe localized to the plasma membrane of primary B and immortal EL4 cells. Image analysis revealed that DHA-Bodipy localized into the plasma membrane of primary B cells more efficiently than EL4 cells. We then determined if the probe detected changes in plasma membrane order. Quantitative analysis of time-lapse movies established that DHA-Bodipy was sensitive to membrane molecular order. This allowed us to investigate how DHA-Bodipy physically adapted to ordered lipid microdomains. To accomplish this, we employed steady-state and time-resolved fluorescence anisotropy measurements in lipid vesicles of varying composition. Similar to cell culture studies, the probe was highly sensitive to membrane order in lipid vesicles. Moreover, these experiments revealed, relative to controls, that upon incorporation into highly ordered microdomains, DHA-Bodipy underwent an increase in its fluorescence lifetime and molecular order. In addition, the probe displayed a significant reduction in its rotational diffusion compared to controls. Altogether, DHA-Bodipy was highly sensitive to membrane order and revealed for the first time that DHA, despite its flexibility, could become ordered with less rotational motion inside ordered lipid microdomains. Mechanistically, this explains how DHA acyl chains can increase order upon formation of lipid microdomains in vivo. PMID:22841541

Associational Patterns of Scavenger Beetles to Decomposition Stages.

PubMed

Zanetti, Noelia I; Visciarelli, Elena C; Centeno, Nestor D

2015-07-01

Beetles associated with carrion play an important role in recycling organic matter in an ecosystem. Four experiments on decomposition, one per season, were conducted in a semirural area in Bahía Blanca, Argentina. Melyridae are reported for the first time of forensic interest. Apart from adults and larvae of Scarabaeidae, thirteen species and two genera of other coleopteran families are new forensic records in Argentina. Diversity, abundance, and species composition of beetles showed differences between stages and seasons. Our results differed from other studies conducted in temperate regions. Four guilds and succession patterns were established in relation to decomposition stages and seasons. Dermestidae (necrophages) predominated in winter during the decomposition process; Staphylinidae (necrophiles) in Fresh and Bloat stages during spring, summer, and autumn; and Histeridae (necrophiles) and Cleridae (omnivores) in the following stages during those seasons. Finally, coleopteran activity, diversity and abundance, and decomposition rate change with biogeoclimatic characteristics, which is of significance in forensics. © 2015 American Academy of Forensic Sciences.

Molecular basis of a novel adaptation to hypoxic-hypercapnia in a strictly fossorial mole.

PubMed

Campbell, Kevin L; Storz, Jay F; Signore, Anthony V; Moriyama, Hideaki; Catania, Kenneth C; Payson, Alexander P; Bonaventura, Joseph; Stetefeld, Jörg; Weber, Roy E

2010-07-16

Elevated blood O(2) affinity enhances survival at low O(2) pressures, and is perhaps the best known and most broadly accepted evolutionary adjustment of terrestrial vertebrates to environmental hypoxia. This phenotype arises by increasing the intrinsic O(2) affinity of the hemoglobin (Hb) molecule, by decreasing the intracellular concentration of allosteric effectors (e.g., 2,3-diphosphoglycerate; DPG), or by suppressing the sensitivity of Hb to these physiological cofactors. Here we report that strictly fossorial eastern moles (Scalopus aquaticus) have evolved a low O(2) affinity, DPG-insensitive Hb - contrary to expectations for a mammalian species that is adapted to the chronic hypoxia and hypercapnia of subterranean burrow systems. Molecular modelling indicates that this functional shift is principally attributable to a single charge altering amino acid substitution in the beta-type delta-globin chain (delta136Gly-->Glu) of this species that perturbs electrostatic interactions between the dimer subunits via formation of an intra-chain salt-bridge with delta82Lys. However, this replacement also abolishes key binding sites for the red blood cell effectors Cl-, lactate and DPG (the latter of which is virtually absent from the red cells of this species) at delta82Lys, thereby markedly reducing competition for carbamate formation (CO(2) binding) at the delta-chain N-termini. We propose this Hb phenotype illustrates a novel mechanism for adaptively elevating the CO(2) carrying capacity of eastern mole blood during burst tunnelling activities associated with subterranean habitation.

Adaptation in Living Systems

NASA Astrophysics Data System (ADS)

Tu, Yuhai; Rappel, Wouter-Jan

2018-03-01

Adaptation refers to the biological phenomenon where living systems change their internal states in response to changes in their environments in order to maintain certain key functions critical for their survival and fitness. Adaptation is one of the most ubiquitous and arguably one of the most fundamental properties of living systems. It occurs throughout all biological scales, from adaptation of populations of species over evolutionary time to adaptation of a single cell to different environmental stresses during its life span. In this article, we review some of the recent progress made in understanding molecular mechanisms of cellular-level adaptation. We take the minimalist (or the physicist) approach and study the simplest systems that exhibit generic adaptive behaviors, namely chemotaxis in bacterium cells (Escherichia coli) and eukaryotic cells (Dictyostelium). We focus on understanding the basic biochemical interaction networks that are responsible for adaptation dynamics. By combining theoretical modeling with quantitative experimentation, we demonstrate universal features in adaptation as well as important differences in different cellular systems. Future work in extending the modeling framework to study adaptation in more complex systems such as sensory neurons is also discussed.

TENSOR DECOMPOSITIONS AND SPARSE LOG-LINEAR MODELS

PubMed Central

Johndrow, James E.; Bhattacharya, Anirban; Dunson, David B.

2017-01-01

Contingency table analysis routinely relies on log-linear models, with latent structure analysis providing a common alternative. Latent structure models lead to a reduced rank tensor factorization of the probability mass function for multivariate categorical data, while log-linear models achieve dimensionality reduction through sparsity. Little is known about the relationship between these notions of dimensionality reduction in the two paradigms. We derive several results relating the support of a log-linear model to nonnegative ranks of the associated probability tensor. Motivated by these findings, we propose a new collapsed Tucker class of tensor decompositions, which bridge existing PARAFAC and Tucker decompositions, providing a more flexible framework for parsimoniously characterizing multivariate categorical data. Taking a Bayesian approach to inference, we illustrate empirical advantages of the new decompositions. PMID:29332971

New evidence favoring multilevel decomposition and optimization

NASA Technical Reports Server (NTRS)

Padula, Sharon L.; Polignone, Debra A.

1990-01-01

The issue of the utility of multilevel decomposition and optimization remains controversial. To date, only the structural optimization community has actively developed and promoted multilevel optimization techniques. However, even this community acknowledges that multilevel optimization is ideally suited for a rather limited set of problems. It is warned that decomposition typically requires eliminating local variables by using global variables and that this in turn causes ill-conditioning of the multilevel optimization by adding equality constraints. The purpose is to suggest a new multilevel optimization technique. This technique uses behavior variables, in addition to design variables and constraints, to decompose the problem. The new technique removes the need for equality constraints, simplifies the decomposition of the design problem, simplifies the programming task, and improves the convergence speed of multilevel optimization compared to conventional optimization.

Seasonal necrophagous insect community assembly during vertebrate carrion decomposition.

PubMed

Benbow, M E; Lewis, A J; Tomberlin, J K; Pechal, J L

2013-03-01

Necrophagous invertebrates have been documented to be a predominant driver of vertebrate carrion decomposition; however, very little is understood about the assembly of these communities both within and among seasons. The objective of this study was to evaluate the seasonal differences in insect taxa composition, richness, and diversity on carrion over decomposition with the intention that such data will be useful for refining error estimates in forensic entomology. Sus scrofa (L.) carcasses (n = 3-6, depending on season) were placed in a forested habitat near Xenia, OH, during spring, summer, autumn, and winter. Taxon richness varied substantially among seasons but was generally lower (1-2 taxa) during early decomposition and increased (3-8 taxa) through intermediate stages of decomposition. Autumn and winter showed the highest richness during late decomposition. Overall, taxon richness was higher during active decay for all seasons. While invertebrate community composition was generally consistent among seasons, the relative abundance of five taxa significantly differed across seasons, demonstrating different source communities for colonization depending on the time of year. There were significantly distinct necrophagous insect communities for each stage of decomposition, and between summer and autumn and summer and winter, but the communities were similar between autumn and winter. Calliphoridae represented significant indicator taxa for summer and autumn but replaced by Coleoptera during winter. Here we demonstrated substantial variability in necrophagous communities and assembly on carrion over decomposition and among seasons. Recognizing this variation has important consequences for forensic entomology and future efforts to provide error rates for estimates of the postmortem interval using arthropod succession data as evidence during criminal investigations.

Microbial Community Functional Change during Vertebrate Carrion Decomposition

PubMed Central

Pechal, Jennifer L.; Crippen, Tawni L.; Tarone, Aaron M.; Lewis, Andrew J.; Tomberlin, Jeffery K.; Benbow, M. Eric

2013-01-01

Microorganisms play a critical role in the decomposition of organic matter, which contributes to energy and nutrient transformation in every ecosystem. Yet, little is known about the functional activity of epinecrotic microbial communities associated with carrion. The objective of this study was to provide a description of the carrion associated microbial community functional activity using differential carbon source use throughout decomposition over seasons, between years and when microbial communities were isolated from eukaryotic colonizers (e.g., necrophagous insects). Additionally, microbial communities were identified at the phyletic level using high throughput sequencing during a single study. We hypothesized that carrion microbial community functional profiles would change over the duration of decomposition, and that this change would depend on season, year and presence of necrophagous insect colonization. Biolog EcoPlates™ were used to measure the variation in epinecrotic microbial community function by the differential use of 29 carbon sources throughout vertebrate carrion decomposition. Pyrosequencing was used to describe the bacterial community composition in one experiment to identify key phyla associated with community functional changes. Overall, microbial functional activity increased throughout decomposition in spring, summer and winter while it decreased in autumn. Additionally, microbial functional activity was higher in 2011 when necrophagous arthropod colonizer effects were tested. There were inconsistent trends in the microbial function of communities isolated from remains colonized by necrophagous insects between 2010 and 2011, suggesting a greater need for a mechanistic understanding of the process. These data indicate that functional analyses can be implemented in carrion studies and will be important in understanding the influence of microbial communities on an essential ecosystem process, carrion decomposition. PMID:24265741

Tree species diversity affects decomposition through modified micro-environmental conditions across European forests.

PubMed

Joly, François-Xavier; Milcu, Alexandru; Scherer-Lorenzen, Michael; Jean, Loreline-Katia; Bussotti, Filippo; Dawud, Seid Muhie; Müller, Sandra; Pollastrini, Martina; Raulund-Rasmussen, Karsten; Vesterdal, Lars; Hättenschwiler, Stephan

2017-05-01

Different tree species influence litter decomposition directly through species-specific litter traits, and indirectly through distinct modifications of the local decomposition environment. Whether these indirect effects on decomposition are influenced by tree species diversity is presently not clear. We addressed this question by studying the decomposition of two common substrates, cellulose paper and wood sticks, in a total of 209 forest stands of varying tree species diversity across six major forest types at the scale of Europe. Tree species richness showed a weak but positive correlation with the decomposition of cellulose but not with that of wood. Surprisingly, macroclimate had only a minor effect on cellulose decomposition and no effect on wood decomposition despite the wide range in climatic conditions among sites from Mediterranean to boreal forests. Instead, forest canopy density and stand-specific litter traits affected the decomposition of both substrates, with a particularly clear negative effect of the proportion of evergreen tree litter. Our study suggests that species richness and composition of tree canopies modify decomposition indirectly through changes in microenvironmental conditions. These canopy-induced differences in the local decomposition environment control decomposition to a greater extent than continental-scale differences in macroclimatic conditions. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Family Wide Molecular Adaptations to Underground Life in African Mole-Rats Revealed by Phylogenomic Analysis.

PubMed

Davies, Kalina T J; Bennett, Nigel C; Tsagkogeorga, Georgia; Rossiter, Stephen J; Faulkes, Christopher G

2015-12-01

During their evolutionary radiation, mammals have colonized diverse habitats. Arguably the subterranean niche is the most inhospitable of these, characterized by reduced oxygen, elevated carbon dioxide, absence of light, scarcity of food, and a substrate that is energetically costly to burrow through. Of all lineages to have transitioned to a subterranean niche, African mole-rats are one of the most successful. Much of their ecological success can be attributed to a diet of plant storage organs, which has allowed them to colonize climatically varied habitats across sub-Saharan Africa, and has probably contributed to the evolution of their diverse social systems. Yet despite their many remarkable phenotypic specializations, little is known about molecular adaptations underlying these traits. To address this, we sequenced the transcriptomes of seven mole-rat taxa, including three solitary species, and combined new sequences with existing genomic data sets. Alignments of more than 13,000 protein-coding genes encompassed, for the first time, all six genera and the full spectrum of ecological and social variation in the clade. We detected positive selection within the mole-rat clade and along ancestral branches in approximately 700 genes including loci associated with tumorigenesis, aging, morphological development, and sociality. By combining these results with gene ontology annotation and protein-protein networks, we identified several clusters of functionally related genes. This family wide analysis of molecular evolution in mole-rats has identified a suite of positively selected genes, deepening our understanding of the extreme phenotypic traits exhibited by this group. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

A New Adaptive Framework for Collaborative Filtering Prediction

PubMed Central

Almosallam, Ibrahim A.; Shang, Yi

2010-01-01

Collaborative filtering is one of the most successful techniques for recommendation systems and has been used in many commercial services provided by major companies including Amazon, TiVo and Netflix. In this paper we focus on memory-based collaborative filtering (CF). Existing CF techniques work well on dense data but poorly on sparse data. To address this weakness, we propose to use z-scores instead of explicit ratings and introduce a mechanism that adaptively combines global statistics with item-based values based on data density level. We present a new adaptive framework that encapsulates various CF algorithms and the relationships among them. An adaptive CF predictor is developed that can self adapt from user-based to item-based to hybrid methods based on the amount of available ratings. Our experimental results show that the new predictor consistently obtained more accurate predictions than existing CF methods, with the most significant improvement on sparse data sets. When applied to the Netflix Challenge data set, our method performed better than existing CF and singular value decomposition (SVD) methods and achieved 4.67% improvement over Netflix’s system. PMID:21572924

Characteristic of root decomposition in a tropical rainforest in Sarawak, Malaysi

NASA Astrophysics Data System (ADS)

Ohashi, Mizue; Makita, Naoki; Katayam, Ayumi; Kume, Tomonori; Matsumoto, Kazuho; Khoon Kho, L.

2016-04-01

Woody roots play a significant role in forest carbon cycling, as up to 60 percent of tree photosynthetic production can be allocated to belowground. Root decay is one of the main processes of soil C dynamics and potentially relates to soil C sequestration. However, much less attention has been paid for root litter decomposition compared to the studies of leaf litter because roots are hidden from view. Previous studies have revealed that physico-chemical quality of roots, climate, and soil organisms affect root decomposition significantly. However, patterns and mechanisms of root decomposition are still poorly understood because of the high variability of root properties, field environment and potential decomposers. For example, root size would be a factor controlling decomposition rates, but general understanding of the difference between coarse and fine root decompositions is still lacking. Also, it is known that root decomposition is performed by soil animals, fungi and bacteria, but their relative importance is poorly understood. In this study, therefore, we aimed to characterize the root decomposition in a tropical rainforest in Sarawak, Malaysia, and clarify the impact of soil living organisms and root sizes on root litter decomposition. We buried soil cores with fine and coarse root litter bags in soil in Lambir Hills National Park. Three different types of soil cores that are covered by 1.5 cm plastic mesh, root-impermeable sheet (50um) and fungi-impermeable sheet (1um) were prepared. The soil cores were buried in February 2013 and collected 4 times, 134 days, 226 days, 786 days and 1151 days after the installation. We found that nearly 80 percent of the coarse root litter was decomposed after two years, whereas only 60 percent of the fine root litter was decomposed. Our results also showed significantly different ratio of decomposition between different cores, suggesting the different contribution of soil living organisms to decomposition process.

Thermal Decomposition Synthesis of Iron Oxide Nanoparticles with Diminished Magnetic Dead Layer by Controlled Addition of Oxygen.

PubMed

Unni, Mythreyi; Uhl, Amanda M; Savliwala, Shehaab; Savitzky, Benjamin H; Dhavalikar, Rohan; Garraud, Nicolas; Arnold, David P; Kourkoutis, Lena F; Andrew, Jennifer S; Rinaldi, Carlos

2017-02-28

Decades of research focused on size and shape control of iron oxide nanoparticles have led to methods of synthesis that afford excellent control over physical size and shape but comparatively poor control over magnetic properties. Popular synthesis methods based on thermal decomposition of organometallic precursors in the absence of oxygen have yielded particles with mixed iron oxide phases, crystal defects, and poorer than expected magnetic properties, including the existence of a thick "magnetically dead layer" experimentally evidenced by a magnetic diameter significantly smaller than the physical diameter. Here, we show how single-crystalline iron oxide nanoparticles with few defects and similar physical and magetic diameter distributions can be obtained by introducing molecular oxygen as one of the reactive species in the thermal decomposition synthesis. This is achieved without the need for any postsynthesis oxidation or thermal annealing. These results address a significant challenge in the synthesis of nanoparticles with predictable magnetic properties and could lead to advances in applications of magnetic nanoparticles.

Thermal decomposition of gaseous ammonium nitrate at low pressure: kinetic modeling of product formation and heterogeneous decomposition of nitric acid.

PubMed

Park, J; Lin, M C

2009-12-03

The thermal decomposition of ammonium nitrate, NH(4)NO(3) (AN), in the gas phase has been studied at 423-56 K by pyrolysis/mass spectrometry under low-pressure conditions using a Saalfeld reactor coated with boric acid. The sublimation of NH(4)NO(3) at 423 K was proposed to produce equal amounts of NH(3) and HNO(3), followed by the decomposition reaction of HNO(3), HNO(3) + M --> OH + NO(2) + M (where M = third-body and reactor surface). The absolute yields of N(2), N(2)O, H(2)O, and NH(3), which can be unambiguously measured and quantitatively calibrated under a constant pressure at 5-6.2 torr He are kinetically modeled using the detailed [H,N,O]-mechanism established earlier for the simulation of NH(3)-NO(2) (Park, J.; Lin, M. C. Technologies and Combustion for a Clean Environment. Proc. 4th Int. Conf. 1997, 34-1, 1-5) and ADN decomposition reactions (Park, J.; Chakraborty, D.; Lin, M. C. Proc. Combust. Inst. 1998, 27, 2351-2357). Since the homogeneous decomposition reaction of HNO(3) itself was found to be too slow to account for the consumption of reactants and the formation of products, we also introduced the heterogeneous decomposition of HNO(3) in our kinetic modeling. The heterogeneous decomposition rate of HNO(3), HNO(3) + (B(2)O(3)/SiO(2)) --> OH + NO(2) + (B(2)O(3)/SiO(2)), was determined by varying its rate to match the modeled result to the measured concentrations of NH(3) and H(2)O; the rate could be represented by k(2b) = 7.91 x 10(7) exp(-12 600/T) s(-1), which appears to be consistent with those reported by Johnston and co-workers (Johnston, H. S.; Foering, L.; Tao, Y.-S.; Messerly, G. H. J. Am. Chem. Soc. 1951, 73, 2319-2321) for HNO(3) decomposition on glass reactors at higher temperatures. Notably, the concentration profiles of all species measured could be satisfactorily predicted by the existing [H,N,O]-mechanism with the heterogeneous initiation process.

Thermal Decomposition of Gaseous Ammonium Nitrate at Low Pressure: Kinetic Modeling of Product Formation and Heterogeneous Decomposition of Nitric Acid

NASA Astrophysics Data System (ADS)

Park, J.; Lin, M. C.

2009-10-01

The thermal decomposition of ammonium nitrate, NH4NO3 (AN), in the gas phase has been studied at 423-56 K by pyrolysis/mass spectrometry under low-pressure conditions using a Saalfeld reactor coated with boric acid. The sublimation of NH4NO3 at 423 K was proposed to produce equal amounts of NH3 and HNO3, followed by the decomposition reaction of HNO3, HNO3 + M → OH + NO2 + M (where M = third-body and reactor surface). The absolute yields of N2, N2O, H2O, and NH3, which can be unambiguously measured and quantitatively calibrated under a constant pressure at 5-6.2 torr He are kinetically modeled using the detailed [H,N,O]-mechanism established earlier for the simulation of NH3-NO2 (Park, J.; Lin, M. C. Technologies and Combustion for a Clean Environment. Proc. 4th Int. Conf. 1997, 34-1, 1-5) and ADN decomposition reactions (Park, J.; Chakraborty, D.; Lin, M. C. Proc. Combust. Inst. 1998, 27, 2351-2357). Since the homogeneous decomposition reaction of HNO3 itself was found to be too slow to account for the consumption of reactants and the formation of products, we also introduced the heterogeneous decomposition of HNO3 in our kinetic modeling. The heterogeneous decomposition rate of HNO3, HNO3 + (B2O3/SiO2) → OH + NO2 + (B2O3/SiO2), was determined by varying its rate to match the modeled result to the measured concentrations of NH3 and H2O; the rate could be represented by k2b = 7.91 × 107 exp(-12 600/T) s-1, which appears to be consistent with those reported by Johnston and co-workers (Johnston, H. S.; Foering, L.; Tao, Y.-S.; Messerly, G. H. J. Am. Chem. Soc. 1951, 73, 2319-2321) for HNO3 decomposition on glass reactors at higher temperatures. Notably, the concentration profiles of all species measured could be satisfactorily predicted by the existing [H,N,O]-mechanism with the heterogeneous initiation process.

Thermal decomposition of high-nitrogen energetic compounds: TAGzT and GUzT

NASA Astrophysics Data System (ADS)

Hayden, Heather F.

The U.S. Navy is exploring high-nitrogen compounds as burning-rate additives to meet the growing demands of future high-performance gun systems. Two high-nitrogen compounds investigated as potential burning-rate additives are bis(triaminoguanidinium) 5,5-azobitetrazolate (TAGzT) and bis(guanidinium) 5,5'-azobitetrazolate (GUzT). Small-scale tests showed that formulations containing TAGzT exhibit significant increases in the burning rates of RDX-based gun propellants. However, when GUzT, a similarly structured molecule was incorporated into the formulation, there was essentially no effect on the burning rate of the propellant. Through the use of simultaneous thermogravimetric modulated beam mass spectrometry (STMBMS) and Fourier-Transform ion cyclotron resonance (FTICR) mass spectrometry methods, an investigation of the underlying chemical and physical processes that control the thermal decomposition behavior of TAGzT and GUzT alone and in the presence of RDX, was conducted. The objective was to determine why GUzT is not as good a burning-rate enhancer in RDX-based gun propellants as compared to TAGzT. The results show that TAGzT is an effective burning-rate modifier in the presence of RDX because the decomposition of TAGzT alters the initial stages of the decomposition of RDX. Hydrazine, formed in the decomposition of TAGzT, reacts faster with RDX than RDX can decompose itself. The reactions occur at temperatures below the melting point of RDX and thus the TAGzT decomposition products react with RDX in the gas phase. Although there is no hydrazine formed in the decomposition of GUzT, amines formed in the decomposition of GUzT react with aldehydes, formed in the decomposition of RDX, resulting in an increased reaction rate of RDX in the presence of GUzT. However, GUzT is not an effective burning-rate modifier because its decomposition does not alter the initial gas-phase decomposition of RDX. The decomposition of GUzT occurs at temperatures above the melting point

Decomposition of aquatic plants in lakes

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

Godshalk, G.L.

1977-01-01

This study was carried out to systematically determine the effects of temperature and oxygen concentration, two environmental parameters crucial to lake metabolism in general, on decomposition of five species of aquatic vascular plants of three growth forms in a Michigan lake. Samples of dried plant material were decomposed in flasks in the laboratory under three different oxygen regimes, aerobic-to-anaerobic, strict anaerobic, and aerated, each at 10/sup 0/C and 25/sup 0/C. In addition, in situ decomposition of the same species was monitored using the litter bag technique under four conditions.

Singlet molecular oxygen generated by biological hydroperoxides.

PubMed

Miyamoto, Sayuri; Martinez, Glaucia R; Medeiros, Marisa H G; Di Mascio, Paolo

2014-10-05

The chemistry behind the phenomenon of ultra-weak photon emission has been subject of considerable interest for decades. Great progress has been made on the understanding of the chemical generation of electronically excited states that are involved in these processes. Proposed mechanisms implicated the production of excited carbonyl species and singlet molecular oxygen in the mechanism of generation of chemiluminescence in biological system. In particular, attention has been focused on the potential generation of singlet molecular oxygen in the recombination reaction of peroxyl radicals by the Russell mechanism. In the last ten years, our group has demonstrated the generation of singlet molecular oxygen from reactions involving the decomposition of biologically relevant hydroperoxides, especially from lipid hydroperoxides in the presence of metal ions, peroxynitrite, HOCl and cytochrome c. In this review we will discuss details on the chemical aspects related to the mechanism of singlet molecular oxygen generation from different biological hydroperoxides. Copyright © 2014 Elsevier B.V. All rights reserved.

Applications of molecular modeling in coal research

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

Carlson, G.A.; Faulon, J.L.

Over the past several years, molecular modeling has been applied to study various characteristics of coal molecular structures. Powerful workstations coupled with molecular force-field-based software packages have been used to study coal and coal-related molecules. Early work involved determination of the minimum-energy three-dimensional conformations of various published coal structures (Given, Wiser, Solomon and Shinn), and the dominant role of van der Waals and hydrogen bonding forces in defining the energy-minimized structures. These studies have been extended to explore various physical properties of coal structures, including density, microporosity, surface area, and fractal dimension. Other studies have related structural characteristics to cross-linkmore » density and have explored small molecule interactions with coal. Finally, recent studies using a structural elucidation (molecular builder) technique have constructed statistically diverse coal structures based on quantitative and qualitative data on coal and its decomposition products. This technique is also being applied to study coalification processes based on postulated coalification chemistry.« less

Review on Thermal Decomposition of Ammonium Nitrate

NASA Astrophysics Data System (ADS)

Chaturvedi, Shalini; Dave, Pragnesh N.

2013-01-01

In this review data from the literature on thermal decomposition of ammonium nitrate (AN) and the effect of additives to their thermal decomposition are summarized. The effect of additives like oxides, cations, inorganic acids, organic compounds, phase-stablized CuO, etc., is discussed. The effect of an additive mainly occurs at the exothermic peak of pure AN in a temperature range of 200°C to 140°C.

Thermal Decomposition Mechanism of Butyraldehyde

NASA Astrophysics Data System (ADS)

Hatten, Courtney D.; Warner, Brian; Wright, Emily; Kaskey, Kevin; McCunn, Laura R.

2013-06-01

The thermal decomposition of butyraldehyde, CH_3CH_2CH_2C(O)H, has been studied in a resistively heated SiC tubular reactor. Products of pyrolysis were identified via matrix-isolation FTIR spectroscopy and photoionization mass spectrometry in separate experiments. Carbon monoxide, ethene, acetylene, water and ethylketene were among the products detected. To unravel the mechanism of decomposition, pyrolysis of a partially deuterated sample of butyraldehyde was studied. Also, the concentration of butyraldehyde in the carrier gas was varied in experiments to determine the presence of bimolecular reactions. The results of these experiments can be compared to the dissociation pathways observed in similar aldehydes and are relevant to the processing of biomass, foods, and tobacco.

Low-rank canonical-tensor decomposition of potential energy surfaces: application to grid-based diagrammatic vibrational Green's function theory

NASA Astrophysics Data System (ADS)

Rai, Prashant; Sargsyan, Khachik; Najm, Habib; Hermes, Matthew R.; Hirata, So

2017-09-01

A new method is proposed for a fast evaluation of high-dimensional integrals of potential energy surfaces (PES) that arise in many areas of quantum dynamics. It decomposes a PES into a canonical low-rank tensor format, reducing its integral into a relatively short sum of products of low-dimensional integrals. The decomposition is achieved by the alternating least squares (ALS) algorithm, requiring only a small number of single-point energy evaluations. Therefore, it eradicates a force-constant evaluation as the hotspot of many quantum dynamics simulations and also possibly lifts the curse of dimensionality. This general method is applied to the anharmonic vibrational zero-point and transition energy calculations of molecules using the second-order diagrammatic vibrational many-body Green's function (XVH2) theory with a harmonic-approximation reference. In this application, high dimensional PES and Green's functions are both subjected to a low-rank decomposition. Evaluating the molecular integrals over a low-rank PES and Green's functions as sums of low-dimensional integrals using the Gauss-Hermite quadrature, this canonical-tensor-decomposition-based XVH2 (CT-XVH2) achieves an accuracy of 0.1 cm-1 or higher and nearly an order of magnitude speedup as compared with the original algorithm using force constants for water and formaldehyde.

Crop residue decomposition in Minnesota biochar-amended plots

NASA Astrophysics Data System (ADS)

Weyers, S. L.; Spokas, K. A.

2014-06-01

Impacts of biochar application at laboratory scales are routinely studied, but impacts of biochar application on decomposition of crop residues at field scales have not been widely addressed. The priming or hindrance of crop residue decomposition could have a cascading impact on soil processes, particularly those influencing nutrient availability. Our objectives were to evaluate biochar effects on field decomposition of crop residue, using plots that were amended with biochars made from different plant-based feedstocks and pyrolysis platforms in the fall of 2008. Litterbags containing wheat straw material were buried in July of 2011 below the soil surface in a continuous-corn cropped field in plots that had received one of seven different biochar amendments or a uncharred wood-pellet amendment 2.5 yr prior to start of this study. Litterbags were collected over the course of 14 weeks. Microbial biomass was assessed in treatment plots the previous fall. Though first-order decomposition rate constants were positively correlated to microbial biomass, neither parameter was statistically affected by biochar or wood-pellet treatments. The findings indicated only a residual of potentially positive and negative initial impacts of biochars on residue decomposition, which fit in line with established feedstock and pyrolysis influences. Overall, these findings indicate that no significant alteration in the microbial dynamics of the soil decomposer communities occurred as a consequence of the application of plant-based biochars evaluated here.

Crop residue decomposition in Minnesota biochar amended plots

NASA Astrophysics Data System (ADS)

Weyers, S. L.; Spokas, K. A.

2014-02-01

Impacts of biochar application at laboratory scales are routinely studied, but impacts of biochar application on decomposition of crop residues at field scales have not been widely addressed. The priming or hindrance of crop residue decomposition could have a cascading impact on soil processes, particularly those influencing nutrient availability. Our objectives were to evaluate biochar effects on field decomposition of crop residue, using plots that were amended with biochars made from different feedstocks and pyrolysis platforms prior to the start of this study. Litterbags containing wheat straw material were buried below the soil surface in a continuous-corn cropped field in plots that had received one of seven different biochar amendments or a non-charred wood pellet amendment 2.5 yr prior to start of this study. Litterbags were collected over the course of 14 weeks. Microbial biomass was assessed in treatment plots the previous fall. Though first-order decomposition rate constants were positively correlated to microbial biomass, neither parameter was statistically affected by biochar or wood-pellet treatments. The findings indicated only a residual of potentially positive and negative initial impacts of biochars on residue decomposition, which fit in line with established feedstock and pyrolysis influences. Though no significant impacts were observed with field-weathered biochars, effective soil management may yet have to account for repeat applications of biochar.

Robust and automated three-dimensional segmentation of densely packed cell nuclei in different biological specimens with Lines-of-Sight decomposition.

PubMed

Mathew, B; Schmitz, A; Muñoz-Descalzo, S; Ansari, N; Pampaloni, F; Stelzer, E H K; Fischer, S C

2015-06-08

Due to the large amount of data produced by advanced microscopy, automated image analysis is crucial in modern biology. Most applications require reliable cell nuclei segmentation. However, in many biological specimens cell nuclei are densely packed and appear to touch one another in the images. Therefore, a major difficulty of three-dimensional cell nuclei segmentation is the decomposition of cell nuclei that apparently touch each other. Current methods are highly adapted to a certain biological specimen or a specific microscope. They do not ensure similarly accurate segmentation performance, i.e. their robustness for different datasets is not guaranteed. Hence, these methods require elaborate adjustments to each dataset. We present an advanced three-dimensional cell nuclei segmentation algorithm that is accurate and robust. Our approach combines local adaptive pre-processing with decomposition based on Lines-of-Sight (LoS) to separate apparently touching cell nuclei into approximately convex parts. We demonstrate the superior performance of our algorithm using data from different specimens recorded with different microscopes. The three-dimensional images were recorded with confocal and light sheet-based fluorescence microscopes. The specimens are an early mouse embryo and two different cellular spheroids. We compared the segmentation accuracy of our algorithm with ground truth data for the test images and results from state-of-the-art methods. The analysis shows that our method is accurate throughout all test datasets (mean F-measure: 91%) whereas the other methods each failed for at least one dataset (F-measure≤69%). Furthermore, nuclei volume measurements are improved for LoS decomposition. The state-of-the-art methods required laborious adjustments of parameter values to achieve these results. Our LoS algorithm did not require parameter value adjustments. The accurate performance was achieved with one fixed set of parameter values. We developed a novel and

Cyclic Mario worlds — color-decomposition for one-loop QCD

NASA Astrophysics Data System (ADS)

Kälin, Gregor

2018-04-01

We present a new color decomposition for QCD amplitudes at one-loop level as a generalization of the Del Duca-Dixon-Maltoni and Johansson-Ochirov decomposition at tree level. Starting from a minimal basis of planar primitive amplitudes we write down a color decomposition that is free of linear dependencies among appearing primitive amplitudes or color factors. The conjectured decomposition applies to any number of quark flavors and is independent of the choice of gauge group and matter representation. The results also hold for higher-dimensional or supersymmetric extensions of QCD. We provide expressions for any number of external quark-antiquark pairs and gluons. [Figure not available: see fulltext.

Interface conditions for domain decomposition with radical grid refinement

NASA Technical Reports Server (NTRS)

Scroggs, Jeffrey S.

1991-01-01

Interface conditions for coupling the domains in a physically motivated domain decomposition method are discussed. The domain decomposition is based on an asymptotic-induced method for the numerical solution of hyperbolic conservation laws with small viscosity. The method consists of multiple stages. The first stage is to obtain a first approximation using a first-order method, such as the Godunov scheme. Subsequent stages of the method involve solving internal-layer problem via a domain decomposition. The method is derived and justified via singular perturbation techniques.

Testing the Use of Pigs as Human Proxies in Decomposition Studies.

PubMed

Connor, Melissa; Baigent, Christiane; Hansen, Eriek S

2017-12-28

Pigs are a common human analogue in taphonomic study, yet data comparing the trajectory of decomposition between the two groups are lacking. This study compared decomposition rate and gross tissue change in 17 pigs and 22 human remains placed in the Forensic Investigation Research Station in western Colorado between 2012 and 2015. Accumulated degree days (ADD) were used to assess the number of thermal units required to reach a given total body score (TBS) (1) which was used as the measure of decomposition. A comparison of slopes in linear mixed effects model indicated that decomposition rates significantly differed between human donors and pig remains χ 2 (1) = 5.662, p = 0.017. Neither the pig nor the human trajectory compared well to the TBS model. Thus, (i) pigs are not an adequate proxy for human decomposition studies, and (ii) in the semiarid environment of western Colorado, there is a need to develop a regional decomposition model. © 2017 American Academy of Forensic Sciences.

Differential decomposition of bacterial and viral fecal indicators in common human pollution types.

PubMed

Wanjugi, Pauline; Sivaganesan, Mano; Korajkic, Asja; Kelty, Catherine A; McMinn, Brian; Ulrich, Robert; Harwood, Valerie J; Shanks, Orin C

2016-11-15

Understanding the decomposition of microorganisms associated with different human fecal pollution types is necessary for proper implementation of many water quality management practices, as well as predicting associated public health risks. Here, the decomposition of select cultivated and molecular indicators of fecal pollution originating from fresh human feces, septage, and primary effluent sewage in a subtropical marine environment was assessed over a six day period with an emphasis on the influence of ambient sunlight and indigenous microbiota. Ambient water mixed with each fecal pollution type was placed in dialysis bags and incubated in situ in a submersible aquatic mesocosm. Genetic and cultivated fecal indicators including fecal indicator bacteria (enterococci, E. coli, and Bacteroidales), coliphage (somatic and F+), Bacteroides fragilis phage (GB-124), and human-associated genetic indicators (HF183/BacR287 and HumM2) were measured in each sample. Simple linear regression assessing treatment trends in each pollution type over time showed significant decay (p ≤ 0.05) in most treatments for feces and sewage (27/28 and 32/40, respectively), compared to septage (6/26). A two-way analysis of variance of log 10 reduction values for sewage and feces experiments indicated that treatments differentially impact survival of cultivated bacteria, cultivated phage, and genetic indicators. Findings suggest that sunlight is critical for phage decay, and indigenous microbiota play a lesser role. For bacterial cultivated and genetic indicators, the influence of indigenous microbiota varied by pollution type. This study offers new insights on the decomposition of common human fecal pollution types in a subtropical marine environment with important implications for water quality management applications. Published by Elsevier Ltd.

9 CFR 354.131 - Decomposition.

Code of Federal Regulations, 2011 CFR

2011-01-01

... CERTIFICATION VOLUNTARY INSPECTION OF RABBITS AND EDIBLE PRODUCTS THEREOF Disposition of Diseased Rabbit Carcasses and Parts § 354.131 Decomposition. Carcasses of rabbits deleteriously affected by post-mortem...

On the elastic–plastic decomposition of crystal deformation at the atomic scale

DOE PAGES

Stukowski, Alexander; Arsenlis, A.

2012-03-02

Given two snapshots of an atomistic system, taken at different stages of the deformation process, one can compute the incremental deformation gradient field, F, as defined by continuum mechanics theory, from the displacements of atoms. However, such a kinematic analysis of the total deformation does not reveal the respective contributions of elastic and plastic deformation. We develop a practical technique to perform the multiplicative decomposition of the deformation field, F = F eF p, into elastic and plastic parts for the case of crystalline materials. The described computational analysis method can be used to quantify plastic deformation in a materialmore » due to crystal slip-based mechanisms in molecular dynamics and molecular statics simulations. The knowledge of the plastic deformation field, F p, and its variation with time can provide insight into the number, motion and localization of relevant crystal defects such as dislocations. As a result, the computed elastic field, F e, provides information about inhomogeneous lattice strains and lattice rotations induced by the presence of defects.« less

Adaptation in CRISPR-Cas Systems.

PubMed

Sternberg, Samuel H; Richter, Hagen; Charpentier, Emmanuelle; Qimron, Udi

2016-03-17

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins constitute an adaptive immune system in prokaryotes. The system preserves memories of prior infections by integrating short segments of foreign DNA, termed spacers, into the CRISPR array in a process termed adaptation. During the past 3 years, significant progress has been made on the genetic requirements and molecular mechanisms of adaptation. Here we review these recent advances, with a focus on the experimental approaches that have been developed, the insights they generated, and a proposed mechanism for self- versus non-self-discrimination during the process of spacer selection. We further describe the regulation of adaptation and the protein players involved in this fascinating process that allows bacteria and archaea to harbor adaptive immunity. Copyright © 2016 Elsevier Inc. All rights reserved.

Long-time atomistic dynamics through a new self-adaptive accelerated molecular dynamics method

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

Gao, N.; Yang, L.; Gao, F.

2017-02-27

A self-adaptive accelerated molecular dynamics method is developed to model infrequent atomic- scale events, especially those events that occur on a rugged free-energy surface. Key in the new development is the use of the total displacement of the system at a given temperature to construct a boost-potential, which is slowly increased to accelerate the dynamics. The temperature is slowly increased to accelerate the dynamics. By allowing the system to evolve from one steady-state con guration to another by overcoming the transition state, this self-evolving approach makes it possible to explore the coupled motion of species that migrate on vastly differentmore » time scales. The migrations of single vacancy (V) and small He-V clusters, and the growth of nano-sized He-V clusters in Fe for times in the order of seconds are studied by this new method. An interstitial- assisted mechanism is rst explored for the migration of a helium-rich He-V cluster, while a new two-component Ostwald ripening mechanism is suggested for He-V cluster growth.« less

An optimization approach for fitting canonical tensor decompositions.

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

Dunlavy, Daniel M.; Acar, Evrim; Kolda, Tamara Gibson

Tensor decompositions are higher-order analogues of matrix decompositions and have proven to be powerful tools for data analysis. In particular, we are interested in the canonical tensor decomposition, otherwise known as the CANDECOMP/PARAFAC decomposition (CPD), which expresses a tensor as the sum of component rank-one tensors and is used in a multitude of applications such as chemometrics, signal processing, neuroscience, and web analysis. The task of computing the CPD, however, can be difficult. The typical approach is based on alternating least squares (ALS) optimization, which can be remarkably fast but is not very accurate. Previously, nonlinear least squares (NLS) methodsmore » have also been recommended; existing NLS methods are accurate but slow. In this paper, we propose the use of gradient-based optimization methods. We discuss the mathematical calculation of the derivatives and further show that they can be computed efficiently, at the same cost as one iteration of ALS. Computational experiments demonstrate that the gradient-based optimization methods are much more accurate than ALS and orders of magnitude faster than NLS.« less

X-Ray Thomson Scattering Without the Chihara Decomposition

NASA Astrophysics Data System (ADS)

Magyar, Rudolph; Baczewski, Andrew; Shulenburger, Luke; Hansen, Stephanie B.; Desjarlais, Michael P.; Sandia National Laboratories Collaboration

X-Ray Thomson Scattering is an important experimental technique used in dynamic compression experiments to measure the properties of warm dense matter. The fundamental property probed in these experiments is the electronic dynamic structure factor that is typically modeled using an empirical three-term decomposition (Chihara, J. Phys. F, 1987). One of the crucial assumptions of this decomposition is that the system's electrons can be either classified as bound to ions or free. This decomposition may not be accurate for materials in the warm dense regime. We present unambiguous first principles calculations of the dynamic structure factor independent of the Chihara decomposition that can be used to benchmark these assumptions. Results are generated using a finite-temperature real-time time-dependent density functional theory applied for the first time in these conditions. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Security Administration under contract DE-AC04-94AL85000.

Decomposition of energetic chemicals contaminated with iron or stainless steel.

PubMed

Chervin, Sima; Bodman, Glenn T; Barnhart, Richard W

2006-03-17

Contamination of chemicals or reaction mixtures with iron or stainless steel is likely to take place during chemical processing. If energetic and thermally unstable chemicals are involved in a manufacturing process, contamination with iron or stainless steel can impact the decomposition characteristics of these chemicals and, subsequently, the safety of the processes, and should be investigated. The goal of this project was to undertake a systematic approach to study the impact of iron or stainless steel contamination on the decomposition characteristics of different chemical classes. Differential scanning calorimetry (DSC) was used to study the decomposition reaction by testing each chemical pure, and in mixtures with iron and stainless steel. The following classes of energetic chemicals were investigated: nitrobenzenes, tetrazoles, hydrazines, hydroxylamines and oximes, sulfonic acid derivatives and monomers. The following non-energetic groups were investigated for contributing effects: halogens, hydroxyls, amines, amides, nitriles, sulfonic acid esters, carbonyl halides and salts of hydrochloric acid. Based on the results obtained, conclusions were drawn regarding the sensitivity of the decomposition reaction to contamination with iron and stainless steel for the chemical classes listed above. It was demonstrated that the most sensitive classes are hydrazines and hydroxylamines/oximes. Contamination of these chemicals with iron or stainless steel not only destabilizes them, leading to decomposition at significantly lower temperatures, but also sometimes causes increased severity of the decomposition. The sensitivity of nitrobenzenes to contamination with iron or stainless steel depended upon the presence of other contributing groups: the presence of such groups as acid chlorides or chlorine/fluorine significantly increased the effect of contamination on decomposition characteristics of nitrobenzenes. The decomposition of sulfonic acid derivatives and tetrazoles

Soil fauna and plant litter decomposition in tropical and subalpine forests

Treesearch

G. Gonzalez; T.R. Seastedt

2001-01-01

The decomposition of plant residues is influenced by their chemical composition, the physical-chemical environment, and the decomposer organisms. Most studies interested in latitudinal gradients of decomposition have focused on substrate quality and climate effects on decomposition, and have excluded explicit recognition of the soil organisms involved in the process....

On distributed wavefront reconstruction for large-scale adaptive optics systems.

PubMed

de Visser, Cornelis C; Brunner, Elisabeth; Verhaegen, Michel

2016-05-01

The distributed-spline-based aberration reconstruction (D-SABRE) method is proposed for distributed wavefront reconstruction with applications to large-scale adaptive optics systems. D-SABRE decomposes the wavefront sensor domain into any number of partitions and solves a local wavefront reconstruction problem on each partition using multivariate splines. D-SABRE accuracy is within 1% of a global approach with a speedup that scales quadratically with the number of partitions. The D-SABRE is compared to the distributed cumulative reconstruction (CuRe-D) method in open-loop and closed-loop simulations using the YAO adaptive optics simulation tool. D-SABRE accuracy exceeds CuRe-D for low levels of decomposition, and D-SABRE proved to be more robust to variations in the loop gain.

Fourier transform wavefront control with adaptive prediction of the atmosphere.

PubMed

Poyneer, Lisa A; Macintosh, Bruce A; Véran, Jean-Pierre

2007-09-01

Predictive Fourier control is a temporal power spectral density-based adaptive method for adaptive optics that predicts the atmosphere under the assumption of frozen flow. The predictive controller is based on Kalman filtering and a Fourier decomposition of atmospheric turbulence using the Fourier transform reconstructor. It provides a stable way to compensate for arbitrary numbers of atmospheric layers. For each Fourier mode, efficient and accurate algorithms estimate the necessary atmospheric parameters from closed-loop telemetry and determine the predictive filter, adjusting as conditions change. This prediction improves atmospheric rejection, leading to significant improvements in system performance. For a 48x48 actuator system operating at 2 kHz, five-layer prediction for all modes is achievable in under 2x10(9) floating-point operations/s.

Electrochemical and Infrared Absorption Spectroscopy Detection of SF6 Decomposition Products

PubMed Central

Dong, Ming; Ren, Ming; Ye, Rixin

2017-01-01

Sulfur hexafluoride (SF6) gas-insulated electrical equipment is widely used in high-voltage (HV) and extra-high-voltage (EHV) power systems. Partial discharge (PD) and local heating can occur in the electrical equipment because of insulation faults, which results in SF6 decomposition and ultimately generates several types of decomposition products. These SF6 decomposition products can be qualitatively and quantitatively detected with relevant detection methods, and such detection contributes to diagnosing the internal faults and evaluating the security risks of the equipment. At present, multiple detection methods exist for analyzing the SF6 decomposition products, and electrochemical sensing (ES) and infrared (IR) spectroscopy are well suited for application in online detection. In this study, the combination of ES with IR spectroscopy is used to detect SF6 gas decomposition. First, the characteristics of these two detection methods are studied, and the data analysis matrix is established. Then, a qualitative and quantitative analysis ES-IR model is established by adopting a two-step approach. A SF6 decomposition detector is designed and manufactured by combining an electrochemical sensor and IR spectroscopy technology. The detector is used to detect SF6 gas decomposition and is verified to reliably and accurately detect the gas components and concentrations. PMID:29140268

Termites promote resistance of decomposition to spatiotemporal variability in rainfall.

PubMed

Veldhuis, Michiel P; Laso, Francisco J; Olff, Han; Berg, Matty P

2017-02-01

The ecological impact of rapid environmental change will depend on the resistance of key ecosystems processes, which may be promoted by species that exert strong control over local environmental conditions. Recent theoretical work suggests that macrodetritivores increase the resistance of African savanna ecosystems to changing climatic conditions, but experimental evidence is lacking. We examined the effect of large fungus-growing termites and other non-fungus-growing macrodetritivores on decomposition rates empirically with strong spatiotemporal variability in rainfall and temperature. Non-fungus-growing larger macrodetritivores (earthworms, woodlice, millipedes) promoted decomposition rates relative to microbes and small soil fauna (+34%) but both groups reduced their activities with decreasing rainfall. However, fungus-growing termites increased decomposition rates strongest (+123%) under the most water-limited conditions, making overall decomposition rates mostly independent from rainfall. We conclude that fungus-growing termites are of special importance in decoupling decomposition rates from spatiotemporal variability in rainfall due to the buffered environment they create within their extended phenotype (mounds), that allows decomposition to continue when abiotic conditions outside are less favorable. This points at a wider class of possibly important ecological processes, where soil-plant-animal interactions decouple ecosystem processes from large-scale climatic gradients. This may strongly alter predictions from current climate change models. © 2016 by the Ecological Society of America.

Full Quantum Dynamics Simulation of a Realistic Molecular System Using the Adaptive Time-Dependent Density Matrix Renormalization Group Method.

PubMed

Yao, Yao; Sun, Ke-Wei; Luo, Zhen; Ma, Haibo

2018-01-18

The accurate theoretical interpretation of ultrafast time-resolved spectroscopy experiments relies on full quantum dynamics simulations for the investigated system, which is nevertheless computationally prohibitive for realistic molecular systems with a large number of electronic and/or vibrational degrees of freedom. In this work, we propose a unitary transformation approach for realistic vibronic Hamiltonians, which can be coped with using the adaptive time-dependent density matrix renormalization group (t-DMRG) method to efficiently evolve the nonadiabatic dynamics of a large molecular system. We demonstrate the accuracy and efficiency of this approach with an example of simulating the exciton dissociation process within an oligothiophene/fullerene heterojunction, indicating that t-DMRG can be a promising method for full quantum dynamics simulation in large chemical systems. Moreover, it is also shown that the proper vibronic features in the ultrafast electronic process can be obtained by simulating the two-dimensional (2D) electronic spectrum by virtue of the high computational efficiency of the t-DMRG method.

Hydrogen iodide decomposition

DOEpatents

O'Keefe, Dennis R.; Norman, John H.

1983-01-01

Liquid hydrogen iodide is decomposed to form hydrogen and iodine in the presence of water using a soluble catalyst. Decomposition is carried out at a temperature between about 350.degree. K. and about 525.degree. K. and at a corresponding pressure between about 25 and about 300 atmospheres in the presence of an aqueous solution which acts as a carrier for the homogeneous catalyst. Various halides of the platinum group metals, particularly Pd, Rh and Pt, are used, particularly the chlorides and iodides which exhibit good solubility. After separation of the H.sub.2, the stream from the decomposer is countercurrently extracted with nearly dry HI to remove I.sub.2. The wet phase contains most of the catalyst and is recycled directly to the decomposition step. The catalyst in the remaining almost dry HI-I.sub.2 phase is then extracted into a wet phase which is also recycled. The catalyst-free HI-I.sub.2 phase is finally distilled to separate the HI and I.sub.2. The HI is recycled to the reactor; the I.sub.2 is returned to a reactor operating in accordance with the Bunsen equation to create more HI.

An adaptive molecular timer in p53-meidated cell fate decision

NASA Astrophysics Data System (ADS)

Zhang, Xiao-Peng; Wang, Ping; Liu, Feng; Wang, Wei

The tumor suppressor p53 decides cellular outcomes in the DNA damage response. It is intriguing to explore the link between p53 dynamics and cell fates. We developed a theoretical model of p53 signaling network to clarify the mechanism of cell fate decision mediated by its dynamics. We found that the interplay between p53-Mdm2 negative feedback loop and p53-PTEN-Mdm2 positive feedback loop shapes p53 dynamics. Depending on the intensity of DNA damage, p53 shows three modes of dynamics: persistent pulses, two-phase dynamics with pulses followed by sustained high levels and straightforward high levels. Especially, p53 shows two-phase dynamics upon moderated damage and the required number of p53 pulses before apoptosis induction decreases with increasing DNA damage. Our results suggested there exists an adaptive molecular timer that determines whether and when the apoptosis switch should be triggered. We clarified the mechanism behind the switching of p53 dynamical modes by bifurcation analysis. Moreover, we reproduced the experimental results that drug additions alter p53 pulses to sustained p53 activation and leads to senescence. Our work may advance the understanding the significance of p53 dynamics in tumor suppression. This work was supported by National Natural Science Foundation of China (Nos. 11175084, 11204126 and 31361163003).

Investigation of Molecular Structure and Thermal Properties of Thermo-Oxidative Aged SBS in Blends and Their Relations

PubMed Central

Xu, Xiong; Yu, Jianying; Xue, Lihui; Zhang, Canlin; Zha, Yagang; Gu, Yi

2017-01-01

Tri-block copolymer styrene–butadiene (SBS) is extensively applied in bituminous highway construction due to its high elasticity and excellent weather resistance. With the extension of time, tri-block structural SBS automatically degrades into bi-block structural SB- with some terminal oxygen-containing groups under the comprehensive effects of light, heat, oxygen, etc. In this paper, the effects of aging temperature, aging time and oxygen concentration on the molecular structure of thermo-oxidative aged SBS were mainly investigated using Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS), and the correlation between oxygen-containing groups and thermal properties (TG–DTG) was further discussed. The FTIR and XPS results show that rapid decomposition of SBS will occur with increments of aging temperature, aging time and oxygen concentration, and a large number of oxygen-containing groups such as –OH, C=O, –COOH, etc. will be formed during thermo-oxidative aging. In short-term aging, changes in aging temperature and oxygen concentration have a significant impact on the structural damage of SBS. However, in long-term aging, it has no further effect on the molecular structure of SBS or on increasing oxygen concentration. The TG and DTG results indicate that the concentration of substances with low molecular weight gradually increases with the improvement of the degree of aging of the SBS, while the initial decomposition rate increases at the beginning of thermal weightlessness and the decomposition rate slows down in comparison with neat SBS. From the relation between the XPS and TG results, it can be seen that the initial thermal stability of SBS rapidly reduces as the relative concentration of the oxygen-containing groups accumulates around 3%, while the maximum decomposition temperature slowly decreases when the relative concentration of the oxygen-containing groups is more than 3%, due to the difficult damage to strong

Investigation of Molecular Structure and Thermal Properties of Thermo-Oxidative Aged SBS in Blends and Their Relations.

PubMed

Xu, Xiong; Yu, Jianying; Xue, Lihui; Zhang, Canlin; Zha, Yagang; Gu, Yi

2017-07-07

Tri-block copolymer styrene-butadiene (SBS) is extensively applied in bituminous highway construction due to its high elasticity and excellent weather resistance. With the extension of time, tri-block structural SBS automatically degrades into bi-block structural SB- with some terminal oxygen-containing groups under the comprehensive effects of light, heat, oxygen, etc. In this paper, the effects of aging temperature, aging time and oxygen concentration on the molecular structure of thermo-oxidative aged SBS were mainly investigated using Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS), and the correlation between oxygen-containing groups and thermal properties (TG-DTG) was further discussed. The FTIR and XPS results show that rapid decomposition of SBS will occur with increments of aging temperature, aging time and oxygen concentration, and a large number of oxygen-containing groups such as -OH, C=O, -COOH, etc. will be formed during thermo-oxidative aging. In short-term aging, changes in aging temperature and oxygen concentration have a significant impact on the structural damage of SBS. However, in long-term aging, it has no further effect on the molecular structure of SBS or on increasing oxygen concentration. The TG and DTG results indicate that the concentration of substances with low molecular weight gradually increases with the improvement of the degree of aging of the SBS, while the initial decomposition rate increases at the beginning of thermal weightlessness and the decomposition rate slows down in comparison with neat SBS. From the relation between the XPS and TG results, it can be seen that the initial thermal stability of SBS rapidly reduces as the relative concentration of the oxygen-containing groups accumulates around 3%, while the maximum decomposition temperature slowly decreases when the relative concentration of the oxygen-containing groups is more than 3%, due to the difficult damage to strong bonds

Unraveling the physical meaning of the Jaffe-Manohar decomposition of the nucleon spin

NASA Astrophysics Data System (ADS)

Wakamatsu, M.

2016-09-01

A general consensus now is that there are two physically inequivalent complete decompositions of the nucleon spin, i.e. the decomposition of the canonical type and that of mechanical type. The well-known Jaffe-Manohar decomposition is of the former type. Unfortunately, there is a wide-spread misbelief that this decomposition matches the partonic picture, which states that motion of quarks in the nucleon is approximately free. In the present monograph, we reveal that this understanding is not necessarily correct and that the Jaffe-Manohar decomposition is not such a decomposition, which natively reflects the intrinsic (or static) orbital angular momentum structure of the nucleon.

Molecular basis of a novel adaptation to hypoxic-hypercapnia in a strictly fossorial mole

PubMed Central

2010-01-01

Background Elevated blood O2 affinity enhances survival at low O2 pressures, and is perhaps the best known and most broadly accepted evolutionary adjustment of terrestrial vertebrates to environmental hypoxia. This phenotype arises by increasing the intrinsic O2 affinity of the hemoglobin (Hb) molecule, by decreasing the intracellular concentration of allosteric effectors (e.g., 2,3-diphosphoglycerate; DPG), or by suppressing the sensitivity of Hb to these physiological cofactors. Results Here we report that strictly fossorial eastern moles (Scalopus aquaticus) have evolved a low O2 affinity, DPG-insensitive Hb - contrary to expectations for a mammalian species that is adapted to the chronic hypoxia and hypercapnia of subterranean burrow systems. Molecular modelling indicates that this functional shift is principally attributable to a single charge altering amino acid substitution in the β-type δ-globin chain (δ136Gly→Glu) of this species that perturbs electrostatic interactions between the dimer subunits via formation of an intra-chain salt-bridge with δ82Lys. However, this replacement also abolishes key binding sites for the red blood cell effectors Cl-, lactate and DPG (the latter of which is virtually absent from the red cells of this species) at δ82Lys, thereby markedly reducing competition for carbamate formation (CO2 binding) at the δ-chain N-termini. Conclusions We propose this Hb phenotype illustrates a novel mechanism for adaptively elevating the CO2 carrying capacity of eastern mole blood during burst tunnelling activities associated with subterranean habitation. PMID:20637064

Thermal decomposition hazard evaluation of hydroxylamine nitrate.

PubMed

Wei, Chunyang; Rogers, William J; Mannan, M Sam

2006-03-17

Hydroxylamine nitrate (HAN) is an important member of the hydroxylamine family and it is a liquid propellant when combined with alkylammonium nitrate fuel in an aqueous solution. Low concentrations of HAN are used primarily in the nuclear industry as a reductant in nuclear material processing and for decontamination of equipment. Also, HAN has been involved in several incidents because of its instability and autocatalytic decomposition behavior. This paper presents calorimetric measurement for the thermal decomposition of 24 mass% HAN/water. Gas phase enthalpy of formation of HAN is calculated using both semi-empirical methods with MOPAC and high-level quantum chemical methods of Gaussian 03. CHETAH is used to estimate the energy release potential of HAN. A Reactive System Screening Tool (RSST) and an Automatic Pressure Tracking Adiabatic Calorimeter (APTAC) are used to characterize thermal decomposition of HAN and to provide guidance about safe conditions for handling and storing of HAN.

Sparse Solution of Fiber Orientation Distribution Function by Diffusion Decomposition

PubMed Central

Yeh, Fang-Cheng; Tseng, Wen-Yih Isaac

2013-01-01

Fiber orientation is the key information in diffusion tractography. Several deconvolution methods have been proposed to obtain fiber orientations by estimating a fiber orientation distribution function (ODF). However, the L 2 regularization used in deconvolution often leads to false fibers that compromise the specificity of the results. To address this problem, we propose a method called diffusion decomposition, which obtains a sparse solution of fiber ODF by decomposing the diffusion ODF obtained from q-ball imaging (QBI), diffusion spectrum imaging (DSI), or generalized q-sampling imaging (GQI). A simulation study, a phantom study, and an in-vivo study were conducted to examine the performance of diffusion decomposition. The simulation study showed that diffusion decomposition was more accurate than both constrained spherical deconvolution and ball-and-sticks model. The phantom study showed that the angular error of diffusion decomposition was significantly lower than those of constrained spherical deconvolution at 30° crossing and ball-and-sticks model at 60° crossing. The in-vivo study showed that diffusion decomposition can be applied to QBI, DSI, or GQI, and the resolved fiber orientations were consistent regardless of the diffusion sampling schemes and diffusion reconstruction methods. The performance of diffusion decomposition was further demonstrated by resolving crossing fibers on a 30-direction QBI dataset and a 40-direction DSI dataset. In conclusion, diffusion decomposition can improve angular resolution and resolve crossing fibers in datasets with low SNR and substantially reduced number of diffusion encoding directions. These advantages may be valuable for human connectome studies and clinical research. PMID:24146772

Theoretical studies of the decomposition mechanisms of 1,2,4-butanetriol trinitrate.

PubMed

Pei, Liguan; Dong, Kehai; Tang, Yanhui; Zhang, Bo; Yu, Chang; Li, Wenzuo

2017-12-06

Density functional theory (DFT) and canonical variational transition-state theory combined with a small-curvature tunneling correction (CVT/SCT) were used to explore the decomposition mechanisms of 1,2,4-butanetriol trinitrate (BTTN) in detail. The results showed that the γ-H abstraction reaction is the initial pathway for autocatalytic BTTN decomposition. The three possible hydrogen atom abstraction reactions are all exothermic. The rate constants for autocatalytic BTTN decomposition are 3 to 10 40 times greater than the rate constants for the two unimolecular decomposition reactions (O-NO 2 cleavage and HONO elimination). The process of BTTN decomposition can be divided into two stages according to whether the NO 2 concentration is above a threshold value. HONO elimination is the main reaction channel during the first stage because autocatalytic decomposition requires NO 2 and the concentration of NO 2 is initially low. As the reaction proceeds, the concentration of NO 2 gradually increases; when it exceeds the threshold value, the second stage begins, with autocatalytic decomposition becoming the main reaction channel.