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Sample records for adaptive molecular decomposition

  1. Non-equilibrium molecular dynamics simulation of nanojet injection with adaptive-spatial decomposition parallel algorithm.

    PubMed

    Shin, Hyun-Ho; Yoon, Woong-Sup

    2008-07-01

    An Adaptive-Spatial Decomposition parallel algorithm was developed to increase computation efficiency for molecular dynamics simulations of nano-fluids. Injection of a liquid argon jet with a scale of 17.6 molecular diameters was investigated. A solid annular platinum injector was also solved simultaneously with the liquid injectant by adopting a solid modeling technique which incorporates phantom atoms. The viscous heat was naturally discharged through the solids so the liquid boiling problem was avoided with no separate use of temperature controlling methods. Parametric investigations of injection speed, wall temperature, and injector length were made. A sudden pressure drop at the orifice exit causes flash boiling of the liquid departing the nozzle exit with strong evaporation on the surface of the liquids, while rendering a slender jet. The elevation of the injection speed and the wall temperature causes an activation of the surface evaporation concurrent with reduction in the jet breakup length and the drop size. PMID:19051924

  2. Nonlinear mode decomposition: A noise-robust, adaptive decomposition method

    NASA Astrophysics Data System (ADS)

    Iatsenko, Dmytro; McClintock, Peter V. E.; Stefanovska, Aneta

    2015-09-01

    The signals emanating from complex systems are usually composed of a mixture of different oscillations which, for a reliable analysis, should be separated from each other and from the inevitable background of noise. Here we introduce an adaptive decomposition tool—nonlinear mode decomposition (NMD)—which decomposes a given signal into a set of physically meaningful oscillations for any wave form, simultaneously removing the noise. NMD is based on the powerful combination of time-frequency analysis techniques—which, together with the adaptive choice of their parameters, make it extremely noise robust—and surrogate data tests used to identify interdependent oscillations and to distinguish deterministic from random activity. We illustrate the application of NMD to both simulated and real signals and demonstrate its qualitative and quantitative superiority over other approaches, such as (ensemble) empirical mode decomposition, Karhunen-Loève expansion, and independent component analysis. We point out that NMD is likely to be applicable and useful in many different areas of research, such as geophysics, finance, and the life sciences. The necessary matlab codes for running NMD are freely available for download.

  3. Nonlinear mode decomposition: a noise-robust, adaptive decomposition method.

    PubMed

    Iatsenko, Dmytro; McClintock, Peter V E; Stefanovska, Aneta

    2015-09-01

    The signals emanating from complex systems are usually composed of a mixture of different oscillations which, for a reliable analysis, should be separated from each other and from the inevitable background of noise. Here we introduce an adaptive decomposition tool-nonlinear mode decomposition (NMD)-which decomposes a given signal into a set of physically meaningful oscillations for any wave form, simultaneously removing the noise. NMD is based on the powerful combination of time-frequency analysis techniques-which, together with the adaptive choice of their parameters, make it extremely noise robust-and surrogate data tests used to identify interdependent oscillations and to distinguish deterministic from random activity. We illustrate the application of NMD to both simulated and real signals and demonstrate its qualitative and quantitative superiority over other approaches, such as (ensemble) empirical mode decomposition, Karhunen-Loève expansion, and independent component analysis. We point out that NMD is likely to be applicable and useful in many different areas of research, such as geophysics, finance, and the life sciences. The necessary matlab codes for running NMD are freely available for download. PMID:26465549

  4. Autocatalytic Decomposition Mechanisms in Energetic Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Kuklja, Maija; Rashkeev, Sergey

    2009-06-01

    Atomic scale mechanisms of the initiation of chemical processes in energetic molecular crystals, which lead to the decomposition and ultimately to an explosive chain reaction, are still far from being understood. In this work, we investigate the onset of the initiation processes in two high explosive crystals - diamino-dinitroethylene (DADNE) and triamino- trinitrobenzene (TATB). We found that an autocatalytic decomposition mechanism is likely to take place in DADNE crystal that consists of corrugated, dashboard-shaped molecular layers. The presence of a dissociated NO2 group in the interstitial space between two layers induces a significant shear-strain between these layers, which, in turn, facilitates the further dissociation of NO2 groups from surrounding molecules through lowering the C-NO2 decomposition barrier. Unlike this, in TATB (that consists of flat, graphite-like molecular layers), an interstitial NO2 group positioned between two layers tends to produce a tensile stress (rather than a shear-strain), which leads to local molecular disorder in these layers without any significant modification of the C-NO2 decomposition barrier. The observed differences between the two materials are discussed in terms of their structural, electronic, and chemical properties.

  5. Decomposition of Amino Diazeniumdiolates (NONOates): Molecular Mechanisms

    SciTech Connect

    Shaikh, Nizamuddin; Valiev, Marat; Lymar, Sergei V.

    2014-08-23

    Although diazeniumdiolates (X[N(O)NO]-) are extensively used in biochemical, physiological, and pharmacological studies due to their ability to slowly release NO and/or its congeneric nitroxyl, the mechanisms of these processes remain obscure. In this work, we used a combination of spectroscopic, kinetic, and computational techniques to arrive at a qualitatively consistent molecular mechanism for decomposition of amino diazeniumdiolates (amino NONOates: R2N[N(O)NO]-, where R = -N(C2H5)2 (1), -N(C3H4NH2)2 (2), or -N(C2H4NH2)2 (3)). Decomposition of these NONOates is triggered by protonation of their [NN(O)NO]- group with apparent pKa and decomposition rate constants of 4.6 and 1 s-1 for 1-H, 3.5 and 83 x 10-3 s-1 for 2-H, and 3.8 and 3.3 x 10-3 s-1 for 3-H. Although protonation occurs mainly on the O atoms of the functional group, only the minor R2N(H)N(O)NO tautomer (population ~0.01%, for 1) undergoes the N-N heterolytic bond cleavage (k ~102 s-1 for 1) leading to amine and NO. Decompositions of protonated amino NONOates are strongly temperature-dependent; activation enthalpies are 20.4 and 19.4 kcal/mol for 1 and 2, respectively, which includes contributions from both the tautomerization and bond cleavage. The bond cleavage rates exhibit exceptional sensitivity to the nature of R substituents which strongly modulate activation entropy. At pH < 2, decompositions of all these NONOates are subject to additional acid catalysis that occurs through di-protonation of the [NN(O)NO]- group.

  6. Decomposition of amino diazeniumdiolates (NONOates): Molecular mechanisms

    DOE PAGESBeta

    Shaikh, Nizamuddin; Valiev, Marat; Lymar, Sergei V.

    2014-08-23

    Although diazeniumdiolates (X[N(O)NO]-) are extensively used in biochemical, physiological, and pharmacological studies due to their ability to release NO and/or its congeneric nitroxyl, the mechanisms of these processes remain obscure. In this work, we used a combination of spectroscopic, kinetic, and computational techniques to arrive at a quantitatively consistent molecular mechanism for decomposition of amino diazeniumdiolates (amino NONOates: R2N[N(O)NO]-, where R = —N(C2H5)2(1), —N(C3H4NH2)2(2), or —N(C2H4NH2)2(3)). Decomposition of these NONOates is triggered by protonation of their [NN(O)NO]- group with the apparent pKa and decomposition rate constants of 4.6 and 1 s-1 for 1; 3.5 and 0.083 s-1 for 2; andmore » 3.8 and 0.0033 s-1 for 3. Although protonation occurs mainly on the O atoms of the functional group, only the minor R2N(H)N(O)NO tautomer (population ~ 10-7, for 1) undergoes the N—N heterolytic bond cleavage (kd ~ 107 s-1 for 1) leading to amine and NO. Decompositions of protonated amino NONOates are strongly temperature-dependent; activation enthalpies are 20.4 and 19.4 kcal/mol for 1 and 2, respectively, which includes contributions from both the tautomerization and bond cleavage. Thus, the bond cleavage rates exhibit exceptional sensitivity to the nature of R substituents which strongly modulate activation entropy. At pH < 2, decompositions of all three NONOates that have been investigated are subject to additional acid catalysis that occurs through di-protonation of the [NN(O)NO]- group.« less

  7. TRIANGLE-SHAPED DC CORONA DISCHARGE DEVICE FOR MOLECULAR DECOMPOSITION

    EPA Science Inventory

    The paper discusses the evaluation of electrostatic DC corona discharge devices for the application of molecular decomposition. A point-to-plane geometry corona device with a rectangular cross section demonstrated low decomposition efficiencies in earlier experimental work. The n...

  8. Adaptive polyphase subband decomposition structures for image compression.

    PubMed

    Gerek, O N; Cetin, A E

    2000-01-01

    Subband decomposition techniques have been extensively used for data coding and analysis. In most filter banks, the goal is to obtain subsampled signals corresponding to different spectral regions of the original data. However, this approach leads to various artifacts in images having spatially varying characteristics, such as images containing text, subtitles, or sharp edges. In this paper, adaptive filter banks with perfect reconstruction property are presented for such images. The filters of the decomposition structure which can be either linear or nonlinear vary according to the nature of the signal. This leads to improved image compression ratios. Simulation examples are presented. PMID:18262904

  9. Image super-resolution based on image adaptive decomposition

    NASA Astrophysics Data System (ADS)

    Xie, Qiwei; Wang, Haiyan; Shen, Lijun; Chen, Xi; Han, Hua

    2011-11-01

    In this paper we propose an image super-resolution algorithm based on Gaussian Mixture Model (GMM) and a new adaptive image decomposition algorithm. The new image decomposition algorithm uses local extreme of image to extract the cartoon and oscillating part of image. In this paper, we first decompose an image into oscillating and piecewise smooth (cartoon) parts, then enlarge the cartoon part with interpolation. Because GMM accurately characterizes the oscillating part, we specify it as the prior distribution and then formulate the image super-resolution problem as a constrained optimization problem to acquire the enlarged texture part and finally we obtain a fine result.

  10. Limited-memory adaptive snapshot selection for proper orthogonal decomposition

    SciTech Connect

    Oxberry, Geoffrey M.; Kostova-Vassilevska, Tanya; Arrighi, Bill; Chand, Kyle

    2015-04-02

    Reduced order models are useful for accelerating simulations in many-query contexts, such as optimization, uncertainty quantification, and sensitivity analysis. However, offline training of reduced order models can have prohibitively expensive memory and floating-point operation costs in high-performance computing applications, where memory per core is limited. To overcome this limitation for proper orthogonal decomposition, we propose a novel adaptive selection method for snapshots in time that limits offline training costs by selecting snapshots according an error control mechanism similar to that found in adaptive time-stepping ordinary differential equation solvers. The error estimator used in this work is related to theory bounding the approximation error in time of proper orthogonal decomposition-based reduced order models, and memory usage is minimized by computing the singular value decomposition using a single-pass incremental algorithm. Results for a viscous Burgers’ test problem demonstrate convergence in the limit as the algorithm error tolerances go to zero; in this limit, the full order model is recovered to within discretization error. The resulting method can be used on supercomputers to generate proper orthogonal decomposition-based reduced order models, or as a subroutine within hyperreduction algorithms that require taking snapshots in time, or within greedy algorithms for sampling parameter space.

  11. Adaptive domain decomposition methods for advection-diffusion problems

    SciTech Connect

    Carlenzoli, C.; Quarteroni, A.

    1995-12-31

    Domain decomposition methods can perform poorly on advection-diffusion equations if diffusion is dominated by advection. Indeed, the hyperpolic part of the equations could affect the behavior of iterative schemes among subdomains slowing down dramatically their rate of convergence. Taking into account the direction of the characteristic lines we introduce suitable adaptive algorithms which are stable with respect to the magnitude of the convective field in the equations and very effective on bear boundary value problems.

  12. The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations.

    PubMed

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

    2011-11-15

    Parallelization is an effective way to reduce the computational time needed for molecular dynamics simulations. We describe a new parallelization method, the distributed-diagonal force decomposition method, with which we extend and improve the existing force decomposition methods. Our new method requires less data communication during molecular dynamics simulations than replicated data and current force decomposition methods, increasing the parallel efficiency. It also dynamically load-balances the processors' computational load throughout the simulation. The method is readily implemented in existing molecular dynamics codes and it has been incorporated into the CHARMM program, allowing its immediate use in conjunction with the many molecular dynamics simulation techniques that are already present in the program. We also present the design of the Force Decomposition Machine, a cluster of personal computers and networks that is tailored to running molecular dynamics simulations using the distributed diagonal force decomposition method. The design is expandable and provides various degrees of fault resilience. This approach is easily adaptable to computers with Graphics Processing Units because it is independent of the processor type being used. PMID:21793007

  13. Sparse time-frequency decomposition based on dictionary adaptation.

    PubMed

    Hou, Thomas Y; Shi, Zuoqiang

    2016-04-13

    In this paper, we propose a time-frequency analysis method to obtain instantaneous frequencies and the corresponding decomposition by solving an optimization problem. In this optimization problem, the basis that is used to decompose the signal is not known a priori. Instead, it is adapted to the signal and is determined as part of the optimization problem. In this sense, this optimization problem can be seen as a dictionary adaptation problem, in which the dictionary is adaptive to one signal rather than a training set in dictionary learning. This dictionary adaptation problem is solved by using the augmented Lagrangian multiplier (ALM) method iteratively. We further accelerate the ALM method in each iteration by using the fast wavelet transform. We apply our method to decompose several signals, including signals with poor scale separation, signals with outliers and polluted by noise and a real signal. The results show that this method can give accurate recovery of both the instantaneous frequencies and the intrinsic mode functions. PMID:26953172

  14. Nonequilibrium adiabatic molecular dynamics simulations of methane clathrate hydrate decomposition

    NASA Astrophysics Data System (ADS)

    Alavi, Saman; Ripmeester, J. A.

    2010-04-01

    Nonequilibrium, constant energy, constant volume (NVE) molecular dynamics simulations are used to study the decomposition of methane clathrate hydrate in contact with water. Under adiabatic conditions, the rate of methane clathrate decomposition is affected by heat and mass transfer arising from the breakup of the clathrate hydrate framework and release of the methane gas at the solid-liquid interface and diffusion of methane through water. We observe that temperature gradients are established between the clathrate and solution phases as a result of the endothermic clathrate decomposition process and this factor must be considered when modeling the decomposition process. Additionally we observe that clathrate decomposition does not occur gradually with breakup of individual cages, but rather in a concerted fashion with rows of structure I cages parallel to the interface decomposing simultaneously. Due to the concerted breakup of layers of the hydrate, large amounts of methane gas are released near the surface which can form bubbles that will greatly affect the rate of mass transfer near the surface of the clathrate phase. The effects of these phenomena on the rate of methane hydrate decomposition are determined and implications on hydrate dissociation in natural methane hydrate reservoirs are discussed.

  15. 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.

  16. Dynamic-domain-decomposition parallel molecular dynamics

    NASA Astrophysics Data System (ADS)

    Srinivasan, S. G.; Ashok, I.; Jônsson, Hannes; Kalonji, Gretchen; Zahorjan, John

    1997-05-01

    Parallel molecular dynamics with short-range forces can suffer from load-imbalance problems and attendant performance degradation due to density variations in the simulated system. In this paper, we describe an approach to dynamical load balancing, enabled by the Ādhāra runtime system. The domain assigned to each processor is automatically and dynamically resized so as to evenly distribute the molecular dynamics computations across all the processors. The algorithm was tested on an Intel Paragon parallel computer for two and three-dimensional Lennard-Jones systems containing 99 458 and 256000 atoms, respectively, and using up to 256 processors. In these benchmarks, the overhead for carrying out the load-balancing operations was found to be small and the total computation time was reduced by as much as 50%.

  17. Adaptive evolution of molecular phenotypes

    NASA Astrophysics Data System (ADS)

    Held, Torsten; Nourmohammad, Armita; Lässig, Michael

    2014-09-01

    Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a quantitative trait under time-dependent selection, which arises from environmental changes or through fitness interactions with other co-evolving phenotypes. We analyze a model of trait evolution under mutations and genetic drift in a single-peak fitness seascape. The fitness peak performs a constrained random walk in the trait amplitude, which determines the time-dependent trait optimum in a given population. We derive analytical expressions for the distribution of the time-dependent trait divergence between populations and of the trait diversity within populations. Based on this solution, we develop a method to infer adaptive evolution of quantitative traits. Specifically, we show that the ratio of the average trait divergence and the diversity is a universal function of evolutionary time, which predicts the stabilizing strength and the driving rate of the fitness seascape. From an information-theoretic point of view, this function measures the macro-evolutionary entropy in a population ensemble, which determines the predictability of the evolutionary process. Our solution also quantifies two key characteristics of adapting populations: the cumulative fitness flux, which measures the total amount of adaptation, and the adaptive load, which is the fitness cost due to a population's lag behind the fitness peak.

  18. 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

  19. 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

  20. Molecular mechanisms of temperature adaptation.

    PubMed

    Bagriantsev, Sviatoslav N; Gracheva, Elena O

    2015-08-15

    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

  1. Efficient and accurate sound propagation using adaptive rectangular decomposition.

    PubMed

    Raghuvanshi, Nikunj; Narain, Rahul; Lin, Ming C

    2009-01-01

    Accurate sound rendering can add significant realism to complement visual display in interactive applications, as well as facilitate acoustic predictions for many engineering applications, like accurate acoustic analysis for architectural design. Numerical simulation can provide this realism most naturally by modeling the underlying physics of wave propagation. However, wave simulation has traditionally posed a tough computational challenge. In this paper, we present a technique which relies on an adaptive rectangular decomposition of 3D scenes to enable efficient and accurate simulation of sound propagation in complex virtual environments. It exploits the known analytical solution of the Wave Equation in rectangular domains, and utilizes an efficient implementation of the Discrete Cosine Transform on Graphics Processors (GPU) to achieve at least a 100-fold performance gain compared to a standard Finite-Difference Time-Domain (FDTD) implementation with comparable accuracy, while also being 10-fold more memory efficient. Consequently, we are able to perform accurate numerical acoustic simulation on large, complex scenes in the kilohertz range. To the best of our knowledge, it was not previously possible to perform such simulations on a desktop computer. Our work thus enables acoustic analysis on large scenes and auditory display for complex virtual environments on commodity hardware. PMID:19590105

  2. 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. PMID:23085166

  3. Efficient implementation of the adaptive scale pixel decomposition algorithm

    NASA Astrophysics Data System (ADS)

    Zhang, L.; Bhatnagar, S.; Rau, U.; Zhang, M.

    2016-08-01

    Context. Most popular algorithms in use to remove the effects of a telescope's point spread function (PSF) in radio astronomy are variants of the CLEAN algorithm. Most of these algorithms model the sky brightness using the delta-function basis, which results in undesired artefacts when used to image extended emission. The adaptive scale pixel decomposition (Asp-Clean) algorithm models the sky brightness on a scale-sensitive basis and thus gives a significantly better imaging performance when imaging fields that contain both resolved and unresolved emission. Aims: However, the runtime cost of Asp-Clean is higher than that of scale-insensitive algorithms. In this paper, we identify the most expensive step in the original Asp-Clean algorithm and present an efficient implementation of it, which significantly reduces the computational cost while keeping the imaging performance comparable to the original algorithm. The PSF sidelobe levels of modern wide-band telescopes are significantly reduced, allowing us to make approximations to reduce the computational cost, which in turn allows for the deconvolution of larger images on reasonable timescales. Methods: As in the original algorithm, scales in the image are estimated through function fitting. Here we introduce an analytical method to model extended emission, and a modified method for estimating the initial values used for the fitting procedure, which ultimately leads to a lower computational cost. Results: The new implementation was tested with simulated EVLA data and the imaging performance compared well with the original Asp-Clean algorithm. Tests show that the current algorithm can recover features at different scales with lower computational cost.

  4. 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.

  5. Adaptive soft molecular self-assemblies.

    PubMed

    Wang, Andong; Shi, Wenyue; Huang, Jianbin; Yan, Yun

    2016-01-14

    Adaptive molecular self-assemblies provide possibility of constructing smart and functional materials in a non-covalent bottom-up manner. Exploiting the intrinsic properties of responsiveness of non-covalent interactions, a great number of fancy self-assemblies have been achieved. In this review, we try to highlight the recent advances in this field. The following contents are focused: (1) environmental adaptiveness, including smart self-assemblies adaptive to pH, temperature, pressure, and moisture; (2) special chemical adaptiveness, including nanostructures adaptive to important chemicals, such as enzymes, CO2, metal ions, redox agents, explosives, biomolecules; (3) field adaptiveness, including self-assembled materials that are capable of adapting to external fields such as magnetic field, electric field, light irradiation, and shear forces. PMID:26509717

  6. Adaptive dynamic load-balancing with irregular domain decomposition for particle simulations

    NASA Astrophysics Data System (ADS)

    Begau, Christoph; Sutmann, Godehard

    2015-05-01

    We present a flexible and fully adaptive dynamic load-balancing scheme, which is designed for particle simulations of three-dimensional systems with short ranged interactions. The method is based on domain decomposition with non-orthogonal non-convex domains, which are constructed based on a local repartitioning of computational work between neighbouring processors. Domains are dynamically adjusted in a flexible way under the condition that the original topology is not changed, i.e. neighbour relations between domains are retained, which guarantees a fixed communication pattern for each domain during a simulation. Extensions of this scheme are discussed and illustrated with examples, which generalise the communication patterns and do not fully restrict data exchange to direct neighbours. The proposed method relies on a linked cell algorithm, which makes it compatible with existing implementations in particle codes and does not modify the underlying algorithm for calculating the forces between particles. The method has been implemented into the molecular dynamics community code IMD and performance has been measured for various molecular dynamics simulations of systems representing realistic problems from materials science. It is found that the method proves to balance the work between processors in simulations with strongly inhomogeneous and dynamically changing particle distributions, which results in a significant increase of the efficiency of the parallel code compared both to unbalanced simulations and conventional load-balancing strategies.

  7. Adaptive control of molecular alignment

    SciTech Connect

    Horn, C.; Wollenhaupt, M.; Krug, M.; Baumert, T.; Nalda, R. de; Banares, L.

    2006-03-15

    We demonstrate control on nonadiabatic molecular alignment by using a spectrally phase-shaped laser pulse. An evolutionary algorithm in a closed feedback loop has been used in order to find pulse shapes that maximize a given effect. In particular, this scheme has been applied to the optimization of total alignment, and to the control of the temporal structure of the alignment transient within a revival. Asymmetric temporal pulse shapes have been found to be very effective for the latter and have been studied separately in a single-parameter control scheme. Our experimental results are supported by numerical simulations.

  8. Denoising preterm EEG by signal decomposition and adaptive filtering: a comparative study.

    PubMed

    Navarro, X; Porée, F; Beuchée, A; Carrault, G

    2015-03-01

    Electroencephalography (EEG) from preterm infant monitoring systems is usually contaminated by several sources of noise that have to be removed in order to correctly interpret signals and perform automated analysis reliably. Band-pass and adaptive filters (AF) continue to be systematically applied, but their efficacy may be decreased facing preterm EEG patterns such as the tracé alternant and slow delta-waves. In this paper, we propose the combination of EEG decomposition with AF to improve the overall denoising process. Using artificially contaminated signals from real EEGs, we compared the quality of filtered signals applying different decomposition techniques: the discrete wavelet transform, the empirical mode decomposition (EMD) and a recent improved version, the complete ensemble EMD with adaptive noise. Simulations demonstrate that introducing EMD-based techniques prior to AF can reduce up to 30% the root mean squared errors in denoised EEGs. PMID:25659233

  9. 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.

  10. Adaptive kinetic Monte Carlo simulation of methanol decomposition on Cu(100)

    SciTech Connect

    Xu, Lijun; Mei, Donghai; Henkelman, Graeme A.

    2009-12-31

    The adaptive kinetic Monte Carlo method was used to calculate the dynamics of methanol decomposition on Cu(100) at room temperature over a time scale of minutes. Mechanisms of reaction were found using min-mode following saddle point searches based upon forces and energies from density functional theory. Rates of reaction were calculated with harmonic transition state theory. The dynamics followed a pathway from CH3-OH, CH3-O, CH2-O, CH-O and finally C-O. Our calculations confirm that methanol decomposition starts with breaking the O-H bond followed by breaking C-H bonds in the dehydrogenated intermediates until CO is produced. The bridge site on the Cu(100) surface is the active site for scissoring chemical bonds. Reaction intermediates are mobile on the surface which allows them to find this active reaction site. This study illustrates how the adaptive kinetic Monte Carlo method can model the dynamics of surface chemistry from first principles.

  11. Molecular adaptations in Antarctic fish and bacteria

    NASA Astrophysics Data System (ADS)

    Russo, Roberta; Riccio, Alessia; di Prisco, Guido; Verde, Cinzia; Giordano, Daniela

    2010-08-01

    Marine organisms, living in the cold waters of the Southern Ocean, are exposed to high oxygen concentrations. Cold-adapted organisms have developed networks of defence mechanisms to protect themselves against oxidative stress. The dominant suborder Notothenioidei of the Southern Ocean is one of the most interesting models, within vertebrates, to study the evolutionary biological responses to extreme environment. Within bacteria, the psychrophilic Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 gives the opportunity to explore the cellular strategies adopted in vivo by cold-adapted microorganisms to cope with cold and high oxygen concentration. Understanding the molecular mechanisms underlying how a range of Antarctic organisms have responded to climate change in the past will enable predictions as to how they and other species will adapt to global climate change, in terms of physiological function, distribution patterns and ecosystem balance.

  12. ADAPTIVE MULTILEVEL SPLITTING IN MOLECULAR DYNAMICS SIMULATIONS*

    PubMed Central

    Aristoff, David; Lelièvre, Tony; Mayne, Christopher G.; Teo, Ivan

    2014-01-01

    Adaptive Multilevel Splitting (AMS) is a replica-based rare event sampling method that has been used successfully in high-dimensional stochastic simulations to identify trajectories across a high potential barrier separating one metastable state from another, and to estimate the probability of observing such a trajectory. An attractive feature of AMS is that, in the limit of a large number of replicas, it remains valid regardless of the choice of reaction coordinate used to characterize the trajectories. Previous studies have shown AMS to be accurate in Monte Carlo simulations. In this study, we extend the application of AMS to molecular dynamics simulations and demonstrate its effectiveness using a simple test system. Our conclusion paves the way for useful applications, such as molecular dynamics calculations of the characteristic time of drug dissociation from a protein target. PMID:26005670

  13. Adaptive mode control of a few-mode fiber by real-time mode decomposition.

    PubMed

    Huang, Liangjin; Leng, Jinyong; Zhou, Pu; Guo, Shaofeng; Lü, Haibin; Cheng, Xiang'ai

    2015-10-19

    A novel approach to adaptively control the beam profile in a few-mode fiber is experimentally demonstrated. We stress the fiber through an electric-controlled polarization controller, whose driven voltage depends on the current and target modal content difference obtained with the real-time mode decomposition. We have achieved selective excitations of LP01 and LP11 modes, as well as significant improvement of the beam quality factor, which may play crucial roles for high-power fiber lasers, fiber based telecommunication systems and other fundamental researches and applications. PMID:26480466

  14. 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.

  15. Dip-separated structural filtering using seislet transform and adaptive empirical mode decomposition based dip filter

    NASA Astrophysics Data System (ADS)

    Chen, Yangkang

    2016-07-01

    The seislet transform has been demonstrated to have a better compression performance for seismic data compared with other well-known sparsity promoting transforms, thus it can be used to remove random noise by simply applying a thresholding operator in the seislet domain. Since the seislet transform compresses the seismic data along the local structures, the seislet thresholding can be viewed as a simple structural filtering approach. Because of the dependence on a precise local slope estimation, the seislet transform usually suffers from low compression ratio and high reconstruction error for seismic profiles that have dip conflicts. In order to remove the limitation of seislet thresholding in dealing with conflicting-dip data, I propose a dip-separated filtering strategy. In this method, I first use an adaptive empirical mode decomposition based dip filter to separate the seismic data into several dip bands (5 or 6). Next, I apply seislet thresholding to each separated dip component to remove random noise. Then I combine all the denoised components to form the final denoised data. Compared with other dip filters, the empirical mode decomposition based dip filter is data-adaptive. One only needs to specify the number of dip components to be separated. Both complicated synthetic and field data examples show superior performance of my proposed approach than the traditional alternatives. The dip-separated structural filtering is not limited to seislet thresholding, and can also be extended to all those methods that require slope information.

  16. Dip-separated structural filtering using seislet transform and adaptive empirical mode decomposition based dip filter

    NASA Astrophysics Data System (ADS)

    Chen, Yangkang

    2016-04-01

    The seislet transform has been demonstrated to have a better compression performance for seismic data compared with other well-known sparsity promoting transforms, thus it can be used to remove random noise by simply applying a thresholding operator in the seislet domain. Since the seislet transform compresses the seismic data along the local structures, the seislet thresholding can be viewed as a simple structural filtering approach. Because of the dependence on a precise local slope estimation, the seislet transform usually suffers from low compression ratio and high reconstruction error for seismic profiles that have dip conflicts. In order to remove the limitation of seislet thresholding in dealing with conflicting-dip data, I propose a dip-separated filtering strategy. In this method, I first use an adaptive empirical mode decomposition based dip filter to separate the seismic data into several dip bands (5 or 6). Next, I apply seislet thresholding to each separated dip component to remove random noise. Then I combine all the denoised components to form the final denoised data. Compared with other dip filters, the empirical mode decomposition based dip filter is data-adaptive. One only need to specify the number of dip components to be separated. Both complicated synthetic and field data examples show superior performance of my proposed approach than the traditional alternatives. The dip-separated structural filtering is not limited to seislet thresholding, and can also be extended to all those methods that require slope information.

  17. 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

  18. Face illumination manipulation using a single reference image by adaptive layer decomposition.

    PubMed

    Chen, Xiaowu; Wu, Hongyu; Jin, Xin; Zhao, Qinping

    2013-11-01

    This paper proposes a novel image-based framework to manipulate the illumination of human face through adaptive layer decomposition. According to our framework, only a single reference image, without any knowledge of the 3D geometry or material information of the input face, is needed. To transfer the illumination effects of a reference face image to a normal lighting face, we first decompose the lightness layers of the reference and the input images into large-scale and detail layers through weighted least squares (WLS) filter with adaptive smoothing parameters according to the gradient values of the face images. The large-scale layer of the reference image is filtered with the guidance of the input image by guided filter with adaptive smoothing parameters according to the face structures. The relit result is obtained by replacing the largescale layer of the input image with that of the reference image. To normalize the illumination effects of a non-normal lighting face (i.e., face delighting), we introduce similar reflectance prior to the layer decomposition stage by WLS filter, which make the normalized result less affected by the high contrast light and shadow effects of the input face. Through these two procedures, we can change the illumination effects of a non-normal lighting face by first normalizing the illumination and then transferring the illumination of another reference face to it. We acquire convincing relit results of both face relighting and delighting on numerous input and reference face images with various illumination effects and genders. Comparisons with previous papers show that our framework is less affected by geometry differences and can preserve better the identification structure and skin color of the input face. PMID:23807447

  19. 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.

  20. Ab inito molecular-dynamics study of EC decomposition process on Li2O2 surfaces

    NASA Astrophysics Data System (ADS)

    Ando, Yasunobu; Ikeshoji, Tamio; Otani, Minoru

    2015-03-01

    We have simulated electrochemical reactions of the EC molecule decomposition on Li2O2 substrate by ab initio molecular dynamics combined with the effective screening medium method. EC molecules adsorb onto the peroxide spontaneously. We find through the analysis of density of states that the adsorption state is stabilized by hybridization of the sp2 orbital and the surface states of the Li2O2. After adsorption, EC ring opens, which leads to the decomposition of the peroxide and the formation of a carboxy group. This kind of alkyl carbonates formed on the Li2O2 substrate was found in experiments actually Nanosystem Research Institute, AIST; ESICB, Kyoto University

  1. 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.

  2. 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. PMID:26580046

  3. ERP and Adaptive Autoregressive identification with spectral power decomposition to study rapid auditory processing in infants.

    PubMed

    Piazza, C; Cantiani, C; Tacchino, G; Molteni, M; Reni, G; Bianchi, A M

    2014-01-01

    The ability to process rapidly-occurring auditory stimuli plays an important role in the mechanisms of language acquisition. For this reason, the research community has begun to investigate infant auditory processing, particularly using the Event Related Potentials (ERP) technique. In this paper we approach this issue by means of time domain and time-frequency domain analysis. For the latter, we propose the use of Adaptive Autoregressive (AAR) identification with spectral power decomposition. Results show EEG delta-theta oscillation enhancement related to the processing of acoustic frequency and duration changes, suggesting that, as expected, power modulation encodes rapid auditory processing (RAP) in infants and that the time-frequency analysis method proposed is able to identify this modulation. PMID:25571014

  4. 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. PMID:26953174

  5. Independent molecular basis of convergent highland adaptation in maize

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  6. Anaerobic Decomposition of Switchgrass by Tropical Soil-Derived Feedstock-Adapted Consortia

    PubMed Central

    DeAngelis, Kristen M.; Fortney, Julian L.; Borglin, Sharon; Silver, Whendee L.; Simmons, Blake A.; Hazen, Terry C.

    2012-01-01

    ABSTRACT Tropical forest soils decompose litter rapidly with frequent episodes of anoxic conditions, making it likely that bacteria using alternate terminal electron acceptors (TEAs) play a large role in decomposition. This makes these soils useful templates for improving biofuel production. To investigate how TEAs affect decomposition, we cultivated feedstock-adapted consortia (FACs) derived from two tropical forest soils collected from the ends of a rainfall gradient: organic matter-rich tropical cloud forest (CF) soils, which experience sustained low redox, and iron-rich tropical rain forest (RF) soils, which experience rapidly fluctuating redox. Communities were anaerobically passed through three transfers of 10 weeks each with switchgrass as a sole carbon (C) source; FACs were then amended with nitrate, sulfate, or iron oxide. C mineralization and cellulase activities were higher in CF-FACs than in RF-FACs. Pyrosequencing of the small-subunit rRNA revealed members of the Firmicutes, Bacteroidetes, and Alphaproteobacteria as dominant. RF- and CF-FAC communities were not different in microbial diversity or biomass. The RF-FACs, derived from fluctuating redox soils, were the most responsive to the addition of TEAs, while the CF-FACs were overall more efficient and productive, both on a per-gram switchgrass and a per-cell biomass basis. These results suggest that decomposing microbial communities in fluctuating redox environments are adapted to the presence of a diversity of TEAs and ready to take advantage of them. More importantly, these data highlight the role of local environmental conditions in shaping microbial community function that may be separate from phylogenetic structure. PMID:22354956

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

    SciTech Connect

    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 440·106 particles on 65,536 MPI tasks.

  8. Adaptive instant record signals applied to detection with time reversal operator decomposition.

    PubMed

    Folegot, Thomas; de Rosny, Julien; Prada, Claire; Fink, Mathias

    2005-06-01

    Time reversal arrays are becoming common tools whether for detection or tomography. These applications require the measurement of the response from the array to one or several receivers. The most natural way to record the impulse responses for several sources is to generate pulses successively from each emitting point and record simultaneously the signals from the receivers. However, this method is very time consuming or inefficient in terms of signal-to-noise ratio. To overcome this limitation quasi-orthogonal pseudonoise signals like Kasami sequences can be used. For guided wave propagation, a very high degree of orthogonality between the signal is necessary to allow an accurate measure of the whole multipath structure of the transfer function. Hence, in this work, we propose a new family of pseudo-orthogonal signals that is adapted to the environment and more specifically, to highly dispersive media. These adaptive instant records signals are used experimentally to detect targets using the time reversal operator decomposition method. The accuracy of the 15 x 15 transfer functions acquired simultaneously, and therefore the detection capability, are demonstrated in an experimental ultrasonic waveguide as a small-scale model of shallow water propagation including bottom absorption and reverberation. PMID:16018479

  9. 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.

  10. Linking temperature sensitivity of soil organic matter decomposition to its molecular structure, accessibility, and microbial physiology.

    PubMed

    Wagai, Rota; Kishimoto-Mo, Ayaka W; Yonemura, Seiichiro; Shirato, Yasuhito; Hiradate, Syuntaro; Yagasaki, Yasumi

    2013-04-01

    Temperature sensitivity of soil organic matter (SOM) decomposition may have a significant impact on global warming. Enzyme-kinetic hypothesis suggests that decomposition of low-quality substrate (recalcitrant molecular structure) requires higher activation energy and thus has greater temperature sensitivity than that of high-quality, labile substrate. Supporting evidence, however, relies largely on indirect indices of substrate quality. Furthermore, the enzyme-substrate reactions that drive decomposition may be regulated by microbial physiology and/or constrained by protective effects of soil mineral matrix. We thus tested the kinetic hypothesis by directly assessing the carbon molecular structure of low-density fraction (LF) which represents readily accessible, mineral-free SOM pool. Using five mineral soil samples of contrasting SOM concentrations, we conducted 30-days incubations (15, 25, and 35 °C) to measure microbial respiration and quantified easily soluble C as well as microbial biomass C pools before and after the incubations. Carbon structure of LFs (<1.6 and 1.6-1.8 g cm(-3) ) and bulk soil was measured by solid-state (13) C-NMR. Decomposition Q10 was significantly correlated with the abundance of aromatic plus alkyl-C relative to O-alkyl-C groups in LFs but not in bulk soil fraction or with the indirect C quality indices based on microbial respiration or biomass. The warming did not significantly change the concentration of biomass C or the three types of soluble C despite two- to three-fold increase in respiration. Thus, enhanced microbial maintenance respiration (reduced C-use efficiency) especially in the soils rich in recalcitrant LF might lead to the apparent equilibrium between SOM solubilization and microbial C uptake. Our results showed physical fractionation coupled with direct assessment of molecular structure as an effective approach and supported the enzyme-kinetic interpretation of widely observed C quality-temperature relationship for

  11. 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

  12. 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

  13. Metabolic flux estimation--a self-adaptive evolutionary algorithm with singular value decomposition.

    PubMed

    Yang, Jing; Wongsa, Sarawan; Kadirkamanathan, Visakan; Billings, Stephen A; Wright, Phillip C

    2007-01-01

    Metabolic flux analysis is important for metabolic system regulation and intracellular pathway identification. A popular approach for intracellular flux estimation involves using 13C tracer experiments to label states that can be measured by nuclear magnetic resonance spectrometry or gas chromatography mass spectrometry. However, the bilinear balance equations derived from 13C tracer experiments and the noisy measurements require a nonlinear optimization approach to obtain the optimal solution. In this paper, the flux quantification problem is formulated as an error-minimization problem with equality and inequality constraints through the 13C balance and stoichiometric equations. The stoichiometric constraints are transformed to a null space by singular value decomposition. Self-adaptive evolutionary algorithms are then introduced for flux quantification. The performance of the evolutionary algorithm is compared with ordinary least squares estimation by the simulation of the central pentose phosphate pathway. The proposed algorithm is also applied to the central metabolism of Corynebacterium glutamicum under lysine-producing conditions. A comparison between the results from the proposed algorithm and data from the literature is given. The complexity of a metabolic system with bidirectional reactions is also investigated by analyzing the fluctuations in the flux estimates when available measurements are varied. PMID:17277420

  14. Despeckling algorithm on ultrasonic image using adaptive block-based singular value decomposition

    NASA Astrophysics Data System (ADS)

    Sae-Bae, Napa; Udomhunsakul, Somkait

    2008-03-01

    Speckle noise reduction is an important technique to enhance the quality of ultrasonic image. In this paper, a despeckling algorithm based on an adaptive block-based singular value decomposition filtering (BSVD) applied on ultrasonic images is presented. Instead of applying BSVD directly to ultrasonic image, we propose to apply BSVD on the noisy edge image version obtained from the difference between the logarithmic transformations of the original image and blur image version of its. The recovered image is performed by combining the speckle noise-free edge image with blur image version of its. Finally, exponential transformation is applied in order to get the reconstructed image. To evaluate our algorithm compared with well-know algorithms such as Lee filter, Kuan filter, Homomorphic Wiener filter, median filter and wavelet soft thresholding, four image quality measurements, which are Mean Square Error (MSE), Signal to MSE (S/MSE), Edge preservation (β), and Correlation measurement (ρ), are used. From the results, it clearly shows that the proposed algorithm outperforms other methods in terms of quantitative and subjective assessments.

  15. Adaptive optical biocompact disk for molecular recognition

    NASA Astrophysics Data System (ADS)

    Peng, Leilei; Varma, Manoj M.; Regnier, Fred E.; Nolte, David D.

    2005-05-01

    We report the use of adaptive interferometry to detect a monolayer of protein immobilized in a periodic pattern on a spinning glass disk. A photorefractive quantum-well device acting as an adaptive beam mixer in a two-wave mixing geometry stabilizes the interferometric quadrature in the far field. Phase modulation generated by the spinning biolayer pattern in the probe beam is detected as a homodyne signal free of amplitude modulation. Binding between antibodies and immobilized antigens in a two-analyte immunoassay was tested with high specificity and without observable cross reactivity.

  16. Empirical mode decomposition, an adaptive approach for interpreting shaft vibratory signals of large rotating machinery

    NASA Astrophysics Data System (ADS)

    Yang, Wenxian; Tavner, P. J.

    2009-04-01

    The Fourier transform (FT) has been the most popular method for analyzing large rotating machine shaft vibration problems, but it assumes that these vibration signals are linear and stationary. However, in reality this is not always true. Nonlinear and non-stationary shaft vibration signals are often encountered during the start-up and shut-down processes of the machines. Additionally, mechanical faults, for example rotor-to-stator rubbing, fluid excitation, part-loosening, and shaft cracking, are nonlinear. Owing to these reasons, an accurate analysis of shaft vibration cannot always be achieved by using the FT. An alternative tool, the wavelet transform (WT), is now being used to improve the situation. But the efficiency is a problem especially when applying the WT to the accurate analysis of a large-scale, lengthy data. In view of the powerful capability of empirical mode decomposition (EMD) to process nonlinear/non-stationary signals, its algorithm efficiency and its satisfactory performance in minimizing energy leakage, the EMD is used in this paper to analyze the problem, the signals investigated are adaptively decomposed into a finite number of intrinsic mode functions (IMFs). The principal IMFs, identified using an energy-distribution threshold, dominate the signals' oscillation. So, 'purified' shaft vibration signals can be reconstructed from these principal IMFs. To remove interference present in principal IMFs, an adaptive band-pass filter is designed, whose central frequency is automatically set to the frequency dominating the IMF being investigated. To facilitate the observation of transient shaft vibration, a transient shaft orbit (TSO) is constructed by introducing timescale into the orbit drawing process. Nine mathematical criteria are also proposed to evaluate the shaft vibrations exhibited in the IMFs and TSOs. The novelty of this approach is that the EMD provides an adaptive, effective, and efficient way to obtain 'purified' shaft vibration

  17. Energy dissipation in an adaptive molecular circuit

    NASA Astrophysics Data System (ADS)

    Wang, Shou-Wen; Lan, Yueheng; Tang, Lei-Han

    2015-07-01

    The ability to monitor nutrient and other environmental conditions with high sensitivity is crucial for cell growth and survival. Sensory adaptation allows a cell to recover its sensitivity after a transient response to a shift in the strength of extracellular stimulus. The working principles of adaptation have been established previously based on rate equations which do not consider fluctuations in a thermal environment. Recently, Lan et al (2012 Nat. Phys. 8 422-8) performed a detailed analysis of a stochastic model for the Escherichia coli sensory network. They showed that accurate adaptation is possible only when the system operates in a nonequilibrium steady-state (NESS). They further proposed an energy-speed-accuracy (ESA) trade-off relation. We present here analytic results on the NESS of the model through a mapping to a one-dimensional birth-death process. An exact expression for the entropy production rate is also derived. Based on these results, we are able to discuss the ESA relation in a more general setting. Our study suggests that the adaptation error can be reduced exponentially as the methylation range increases. Finally, we show that a nonequilibrium phase transition exists in the infinite methylation range limit, despite the fact that the model contains only two discrete variables.

  18. Kinetic model for thermal decomposition of energetic materials from ReaxFF molecular dynamics

    NASA Astrophysics Data System (ADS)

    Sergeev, Oleg; Yanilkin, Alexey

    2015-06-01

    In the present work we perform molecular dynamics simulations of the thermal decomposition of isolated molecules and single crystals of PETN, RDX and HMX. For isolated molecules we use multi-replica approach with different preconditioned atomic velocities to obtain statistics of the decomposition. In this model we only consider the initial stage of the reactions, that shows first order kinetics. In the model of single crystal, we directly observe reaction pathways that result in product formation, as well as the dependences of concentrations of main chemical species on time after heating. Initial temperatures are in the range of 1000 to 2800 K. On the basis of the obtained dependences of concentrations we propose a kinetic model that describes thermal decomposition process. Reaction rate constants are well described by the Arrhenius law. Activation energies for the initial stage appear to be lowered by 30-60 kJ/mole in condensed phase compared to the isolated molecule. We compare these results between different ReaxFF parametrizations and DFT calculations. Please refer the correspondence to this author.

  19. Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Jung, Jaewoon; Kobayashi, Chigusa; Imamura, Toshiyuki; Sugita, Yuji

    2016-03-01

    Three-dimensional Fast Fourier Transform (3D FFT) plays an important role in a wide variety of computer simulations and data analyses, including molecular dynamics (MD) simulations. In this study, we develop hybrid (MPI+OpenMP) parallelization schemes of 3D FFT based on two new volumetric decompositions, mainly for the particle mesh Ewald (PME) calculation in MD simulations. In one scheme, (1d_Alltoall), five all-to-all communications in one dimension are carried out, and in the other, (2d_Alltoall), one two-dimensional all-to-all communication is combined with two all-to-all communications in one dimension. 2d_Alltoall is similar to the conventional volumetric decomposition scheme. We performed benchmark tests of 3D FFT for the systems with different grid sizes using a large number of processors on the K computer in RIKEN AICS. The two schemes show comparable performances, and are better than existing 3D FFTs. The performances of 1d_Alltoall and 2d_Alltoall depend on the supercomputer network system and number of processors in each dimension. There is enough leeway for users to optimize performance for their conditions. In the PME method, short-range real-space interactions as well as long-range reciprocal-space interactions are calculated. Our volumetric decomposition schemes are particularly useful when used in conjunction with the recently developed midpoint cell method for short-range interactions, due to the same decompositions of real and reciprocal spaces. The 1d_Alltoall scheme of 3D FFT takes 4.7 ms to simulate one MD cycle for a virus system containing more than 1 million atoms using 32,768 cores on the K computer.

  20. Molecular aspects of adaptation to extreme cold environments

    NASA Technical Reports Server (NTRS)

    Finegold, Leonard

    1986-01-01

    Some of the various strategies adopted by living organisms for survival at low temperatures are discussed from the molecular and membrane points of view. Two examples of connections between biological cold adaptation and the molecular level are considered: (1) antifreeze proteins in fish from cold sea water and (2) the fluidity characteristics of cell membranes in a wide variety of organisms. Emphasis is placed on the occurrence of s-phases.

  1. Molecular Adaptation during Adaptive Radiation in the Hawaiian Endemic Genus Schiedea

    PubMed Central

    Kapralov, Maxim V.; Filatov, Dmitry A.

    2006-01-01

    Background “Explosive” adaptive radiations on islands remain one of the most puzzling evolutionary phenomena. The rate of phenotypic and ecological adaptations is extremely fast during such events, suggesting that many genes may be under fairly strong selection. However, no evidence for adaptation at the level of protein coding genes was found, so it has been suggested that selection may work mainly on regulatory elements. Here we report the first evidence that positive selection does operate at the level of protein coding genes during rapid adaptive radiations. We studied molecular adaptation in Hawaiian endemic plant genus Schiedea (Caryophyllaceae), which includes closely related species with a striking range of morphological and ecological forms, varying from rainforest vines to woody shrubs growing in desert-like conditions on cliffs. Given the remarkable difference in photosynthetic performance between Schiedea species from different habitats, we focused on the “photosynthetic” Rubisco enzyme, the efficiency of which is known to be a limiting step in plant photosynthesis. Results We demonstrate that the chloroplast rbcL gene, encoding the large subunit of Rubisco enzyme, evolved under strong positive selection in Schiedea. Adaptive amino acid changes occurred in functionally important regions of Rubisco that interact with Rubisco activase, a chaperone which promotes and maintains the catalytic activity of Rubisco. Interestingly, positive selection acting on the rbcL might have caused favorable cytotypes to spread across several Schiedea species. Significance We report the first evidence for adaptive changes at the DNA and protein sequence level that may have been associated with the evolution of photosynthetic performance and colonization of new habitats during a recent adaptive radiation in an island plant genus. This illustrates how small changes at the molecular level may change ecological species performance and helps us to understand the

  2. 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).

  3. Decomposition of unitary matrices for finding quantum circuits: application to molecular Hamiltonians.

    PubMed

    Daskin, Anmer; Kais, Sabre

    2011-04-14

    Constructing appropriate unitary matrix operators for new quantum algorithms and finding the minimum cost gate sequences for the implementation of these unitary operators is of fundamental importance in the field of quantum information and quantum computation. Evolution of quantum circuits faces two major challenges: complex and huge search space and the high costs of simulating quantum circuits on classical computers. Here, we use the group leaders optimization algorithm to decompose a given unitary matrix into a proper-minimum cost quantum gate sequence. We test the method on the known decompositions of Toffoli gate, the amplification step of the Grover search algorithm, the quantum Fourier transform, and the sender part of the quantum teleportation. Using this procedure, we present the circuit designs for the simulation of the unitary propagators of the Hamiltonians for the hydrogen and the water molecules. The approach is general and can be applied to generate the sequence of quantum gates for larger molecular systems. PMID:21495747

  4. 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. PMID:26909573

  5. 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. PMID:25222961

  6. Parallel feedback active noise control of MRI acoustic noise with signal decomposition using hybrid RLS-NLMS adaptive algorithms.

    PubMed

    Ganguly, Anshuman; Krishna Vemuri, Sri Hari; Panahi, Issa

    2014-01-01

    This paper presents a cost-effective adaptive feedback Active Noise Control (FANC) method for controlling functional Magnetic Resonance Imaging (fMRI) acoustic noise by decomposing it into dominant periodic components and residual random components. Periodicity of fMRI acoustic noise is exploited by using linear prediction (LP) filtering to achieve signal decomposition. A hybrid combination of adaptive filters-Recursive Least Squares (RLS) and Normalized Least Mean Squares (NLMS) are then used to effectively control each component separately. Performance of the proposed FANC system is analyzed and Noise attenuation levels (NAL) up to 32.27 dB obtained by simulation are presented which confirm the effectiveness of the proposed FANC method. PMID:25570676

  7. Coherent Control of Molecular Torsion and the Active-space Decomposition Method

    NASA Astrophysics Data System (ADS)

    Parker, Shane Matthew

    This dissertation discusses schemes and applications for the strong-field control of molecular torsions as well as introduces the active-space decomposition method. In the first part, a route to realize general control over the torsional motions of a class of biaryl compounds is proposed. Torsion in biaryl compounds--molecules with two aromatic moieties connected by a bond about which the barrier to rotation is small--mediates the electronic coupling between the two rings in the molecule. Thus, by controlling the torsion angle, one also controls the electron transfer and transport rates, the absorption and emission spectra, and the molecule's chirality. In our scheme, a non-resonant half-cycle pulse interacts with the permanent dipole of only one moiety of the pre-oriented biaryl compound. In the non-adiabatic regime, coherent motion is initiated by the half-cycle pulse. In the adiabatic regime, the torsion angle is tuned by the pulse. By properly choosing the parameters and polarization of the half-cycle pulse, we show that free internal rotation can be started or that the molecular chirality can be inverted. Then, with the aid of optimal control theory, we design "deracemizing" control pulses, i.e., control pulses that convert a racemic mixture into an enantiopure mixture. Finally, we explore the potential for this type of control in a single-molecule pulling experiment. In the second part, we describe the active space decomposition method for computing excited states of molecular dimers. In this method, the dimer's wavefunction is expressed as a linear combination of direct products of orthogonal localized monomer states. The adiabatic dimer states are found by diagonalizing the Hamiltonian in this direct product space. Matrix elements between direct product states are computed directly, without ever explicitly forming the dimer wavefunction, thus enabling calculations of dimers with active space sizes that would be otherwise impossible. The decomposed

  8. An adaptively fast ensemble empirical mode decomposition method and its applications to rolling element bearing fault diagnosis

    NASA Astrophysics Data System (ADS)

    Xue, Xiaoming; Zhou, Jianzhong; Xu, Yanhe; Zhu, Wenlong; Li, Chaoshun

    2015-10-01

    Ensemble empirical mode decomposition (EEMD) represents a significant improvement over the original empirical mode decomposition (EMD) method for eliminating the mode mixing problem. However, the added white noises generate some tough problems including the high computational cost, the determination of the two critical parameters (the amplitude of the added white noise and the number of ensemble trials), and the contamination of the residue noise in the signal reconstruction. To solve these problems, an adaptively fast EEMD (AFEEMD) method combined with complementary EEMD (CEEMD) is proposed in this paper. In the proposed method, the two critical parameters are respectively fixed as 0.01 times standard deviation of the original signal and two ensemble trials. Instead, the upper frequency limit of the added white noise is the key parameter which needs to be prescribed beforehand. Unlike the original EEMD method, only two high-frequency white noises are added to the signal to be investigated with anti-phase in AFEEMD. Furthermore, an index termed relative root-mean-square error is employed for the adaptive selection of the proper upper frequency limit of the added white noises. Simulation test and vibration signals based fault diagnosis of rolling element bearing under different fault types are utilized to demonstrate the feasibility and effectiveness of the proposed method. The analysis results indicate that the AFEEMD method represents a sound improvement over the original EEMD method, and has strong practicability.

  9. Adaptive modelling of structured molecular representations for toxicity prediction

    NASA Astrophysics Data System (ADS)

    Bertinetto, Carlo; Duce, Celia; Micheli, Alessio; Solaro, Roberto; Tiné, Maria Rosaria

    2012-12-01

    We investigated the possibility of modelling structure-toxicity relationships by direct treatment of the molecular structure (without using descriptors) through an adaptive model able to retain the appropriate structural information. With respect to traditional descriptor-based approaches, this provides a more general and flexible way to tackle prediction problems that is particularly suitable when little or no background knowledge is available. Our method employs a tree-structured molecular representation, which is processed by a recursive neural network (RNN). To explore the realization of RNN modelling in toxicological problems, we employed a data set containing growth impairment concentrations (IGC50) for Tetrahymena pyriformis.

  10. 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

  11. 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

  12. Adaptive multilayer method of fundamental solutions using a weighted greedy QR decomposition for the Laplace equation

    NASA Astrophysics Data System (ADS)

    Shigeta, Takemi; Young, D. L.; Liu, Chein-Shan

    2012-08-01

    The mixed boundary value problem of the Laplace equation is considered. The method of fundamental solutions (MFS) approximates the exact solution to the Laplace equation by a linear combination of independent fundamental solutions with different source points. The accuracy of the numerical solution depends on the distribution of source points. In this paper, a weighted greedy QR decomposition (GQRD) is proposed to choose significant source points by introducing a weighting parameter. An index called an average degree of approximation is defined to show the efficiency of the proposed method. From numerical experiments, it is concluded that the numerical solution tends to be more accurate when the average degree of approximation is larger, and that the proposed method can yield more accurate solutions with a less number of source points than the conventional GQRD.

  13. 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. PMID:26574439

  14. 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

  15. Noise reduction in Doppler ultrasound signals using an adaptive decomposition algorithm.

    PubMed

    Zhang, Yufeng; Wang, Le; Gao, Yali; Chen, Jianhua; Shi, Xinling

    2007-07-01

    A novel de-noising method for improving the signal-to-noise ratio (SNR) of Doppler ultrasound blood flow signals, called the matching pursuit method, has been proposed. Using this method, the Doppler ultrasound signal was first decomposed into a linear expansion of waveforms, called time-frequency atoms, which were selected from a redundant dictionary named Gabor functions. Subsequently, a decay parameter-based algorithm was employed to determine the decomposition times. Finally, the de-noised Doppler signal was reconstructed using the selected components. The SNR improvements, the amount of the lost component in the original signal and the maximum frequency estimation precision with simulated Doppler blood flow signals, have been used to evaluate a performance comparison, based on the wavelet, the wavelet packets and the matching pursuit de-noising algorithms. From the simulation and clinical experiment results, it was concluded that the performance of the matching pursuit approach was better than those of the DWT and the WPs methods for the Doppler ultrasound signal de-noising. PMID:16996774

  16. A Posteriori Analysis of Adaptive Multiscale Operator Decomposition Methods for Multiphysics Problems

    SciTech Connect

    Donald Estep; Michael Holst; Simon Tavener

    2010-02-08

    This project was concerned with the accurate computational error estimation for numerical solutions of multiphysics, multiscale systems that couple different physical processes acting across a large range of scales relevant to the interests of the DOE. Multiscale, multiphysics models are characterized by intimate interactions between different physics across a wide range of scales. This poses significant computational challenges addressed by the proposal, including: (1) Accurate and efficient computation; (2) Complex stability; and (3) Linking different physics. The research in this project focused on Multiscale Operator Decomposition methods for solving multiphysics problems. The general approach is to decompose a multiphysics problem into components involving simpler physics over a relatively limited range of scales, and then to seek the solution of the entire system through some sort of iterative procedure involving solutions of the individual components. MOD is a very widely used technique for solving multiphysics, multiscale problems; it is heavily used throughout the DOE computational landscape. This project made a major advance in the analysis of the solution of multiscale, multiphysics problems.

  17. Molecular adaptation of telomere associated genes in mammals

    PubMed Central

    2013-01-01

    Background Placental mammals display a huge range of life history traits, including size, longevity, metabolic rate and germ line generation time. Although a number of general trends have been proposed between these traits, there are exceptions that warrant further investigation. Species such as naked mole rat, human and certain bat species all exhibit extreme longevity with respect to body size. It has long been established that telomeres and telomere maintenance have a clear role in ageing but it has not yet been established whether there is evidence for adaptation in telomere maintenance proteins that could account for increased longevity in these species. Results Here we carry out a molecular investigation of selective pressure variation, specifically focusing on telomere associated genes across placental mammals. In general we observe a large number of instances of positive selection acting on telomere genes. Although these signatures of selection overall are not significantly correlated with either longevity or body size we do identify positive selection in the microbat species Myotis lucifugus in functionally important regions of the telomere maintenance genes DKC1 and TERT, and in naked mole rat in the DNA repair gene BRCA1. Conclusion These results demonstrate the multifarious selective pressures acting across the mammal phylogeny driving lineage-specific adaptations of telomere associated genes. Our results show that regardless of the longevity of a species, these proteins have evolved under positive selection thereby removing increased longevity as the single selective force driving this rapid rate of evolution. However, evidence of molecular adaptations specific to naked mole rat and Myotis lucifugus highlight functionally significant regions in genes that may alter the way in which telomeres are regulated and maintained in these longer-lived species. PMID:24237966

  18. 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.

  19. 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

    2016-01-01

    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. PMID:26907231

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

    DOE PAGESBeta

    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

  1. Symmetry-adapted perturbation theory interaction energy decomposition for some noble gas complexes

    NASA Astrophysics Data System (ADS)

    Cukras, Janusz; Sadlej, Joanna

    2008-06-01

    This Letter contains a study of the interaction energy in HArF⋯N 2 and HArF⋯P 2 complexes. Symmetry-adapted perturbation theory (SAPT) has been applied to analyze the electrostatic, induction, dispersion and exchange contributions to the total interaction energy. The interaction energy has also been obtained by supermolecular method at the MP2, MP4, CCSD, CCSD(T) levels. The interaction energy for the studied complexes results from a partial cancelation of large attractive electrostatic, induction, dispersion terms by a strong repulsive exchange contribution. The induction and dispersion effects proved to be crucial in establishing the preference for the colinear HArF⋯N 2 and HArF⋯P 2 structures and shift direction of νHAr stretching vibrations.

  2. Using adaptive proper orthogonal decomposition to solve the reaction-diffusion equation

    SciTech Connect

    Singer, M A; Green, W H

    2007-12-03

    We introduce an adaptive POD method to reduce the computational cost of reacting flow simulations. The scheme is coupled with an operator-splitting algorithm to solve the reaction-diffusion equation. For the reaction sub-steps, locally valid basis vectors, obtained via POD and the method of snapshots, are used to project the minor species mass fractions onto a reduced dimensional space thereby decreasing the number of equations that govern combustion chemistry. The method is applied to a one-dimensional laminar premixed CH{sub 4}-air flame using GRImech 3.0; with errors less than 0:25%, a speed-up factor of 3:5 is observed. The speed-up results from fewer source term evaluations required to compute the Jacobian matrices.

  3. Influence of molecular structure on anisotropic photoinduced decomposition of polyimide molecules

    NASA Astrophysics Data System (ADS)

    Usami, Kiyoaki; Sakamoto, Kenji; Ushioda, Sukekatsu

    2001-05-01

    We have investigated the anisotropic decomposition of polyimide molecules induced by irradiation of linearly polarized ultraviolet light (LPUVL). Three polyimides were examined: poly [4,4'-oxydiphenylene-pyromellitimide], poly [4,4'-oxydiphenylene-1,2,3,4-butanetetracarboximide] and poly [4,4'-oxydiphenylene-1,2,3,4-cyclobutanetetracarboximide] (CBDA-ODA). Anisotropic decomposition was monitored by measuring the polarized infrared absorption spectra of ˜10 nm thick films as a function of LPUVL exposure. Among the three polyimides, CBDA-ODA showed the largest anisotropy of decomposition in the initial stage of LPUVL exposure. This result suggests that CBDA-ODA is a suitable polyimide material for photoinduced liquid crystal alignment based on photodecomposition reactions. The details of the LPUVL exposure dependence of the film anisotropy are discussed.

  4. NON-CONFORMING FINITE ELEMENTS; MESH GENERATION, ADAPTIVITY AND RELATED ALGEBRAIC MULTIGRID AND DOMAIN DECOMPOSITION METHODS IN MASSIVELY PARALLEL COMPUTING ENVIRONMENT

    SciTech Connect

    Lazarov, R; Pasciak, J; Jones, J

    2002-02-01

    Construction, analysis and numerical testing of efficient solution techniques for solving elliptic PDEs that allow for parallel implementation have been the focus of the research. A number of discretization and solution methods for solving second order elliptic problems that include mortar and penalty approximations and domain decomposition methods for finite elements and finite volumes have been investigated and analyzed. Techniques for parallel domain decomposition algorithms in the framework of PETC and HYPRE have been studied and tested. Hierarchical parallel grid refinement and adaptive solution methods have been implemented and tested on various model problems. A parallel code implementing the mortar method with algebraically constructed multiplier spaces was developed.

  5. 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.

  6. Gearbox fault diagnosis using adaptive zero phase time-varying filter based on multi-scale chirplet sparse signal decomposition

    NASA Astrophysics Data System (ADS)

    Wu, Chunyan; Liu, Jian; Peng, Fuqiang; Yu, Dejie; Li, Rong

    2013-07-01

    When used for separating multi-component non-stationary signals, the adaptive time-varying filter(ATF) based on multi-scale chirplet sparse signal decomposition(MCSSD) generates phase shift and signal distortion. To overcome this drawback, the zero phase filter is introduced to the mentioned filter, and a fault diagnosis method for speed-changing gearbox is proposed. Firstly, the gear meshing frequency of each gearbox is estimated by chirplet path pursuit. Then, according to the estimated gear meshing frequencies, an adaptive zero phase time-varying filter(AZPTF) is designed to filter the original signal. Finally, the basis for fault diagnosis is acquired by the envelope order analysis to the filtered signal. The signal consisting of two time-varying amplitude modulation and frequency modulation(AM-FM) signals is respectively analyzed by ATF and AZPTF based on MCSSD. The simulation results show the variances between the original signals and the filtered signals yielded by AZPTF based on MCSSD are 13.67 and 41.14, which are far less than variances (323.45 and 482.86) between the original signals and the filtered signals obtained by ATF based on MCSSD. The experiment results on the vibration signals of gearboxes indicate that the vibration signals of the two speed-changing gearboxes installed on one foundation bed can be separated by AZPTF effectively. Based on the demodulation information of the vibration signal of each gearbox, the fault diagnosis can be implemented. Both simulation and experiment examples prove that the proposed filter can extract a mono-component time-varying AM-FM signal from the multi-component time-varying AM-FM signal without distortion.

  7. 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. PMID:24417933

  8. Adaptive neuro-fuzzy inference system for acoustic analysis of 4-channel phonocardiograms using empirical mode decomposition.

    PubMed

    Becerra, Miguel A; Orrego, Diana A; Delgado-Trejos, Edilson

    2013-01-01

    The heart's mechanical activity can be appraised by auscultation recordings, taken from the 4-Standard Auscultation Areas (4-SAA), one for each cardiac valve, as there are invisible murmurs when a single area is examined. This paper presents an effective approach for cardiac murmur detection based on adaptive neuro-fuzzy inference systems (ANFIS) over acoustic representations derived from Empirical Mode Decomposition (EMD) and Hilbert-Huang Transform (HHT) of 4-channel phonocardiograms (4-PCG). The 4-PCG database belongs to the National University of Colombia. Mel-Frequency Cepstral Coefficients (MFCC) and statistical moments of HHT were estimated on the combination of different intrinsic mode functions (IMFs). A fuzzy-rough feature selection (FRFS) was applied in order to reduce complexity. An ANFIS network was implemented on the feature space, randomly initialized, adjusted using heuristic rules and trained using a hybrid learning algorithm made up by least squares and gradient descent. Global classification for 4-SAA was around 98.9% with satisfactory sensitivity and specificity, using a 50-fold cross-validation procedure (70/30 split). The representation capability of the EMD technique applied to 4-PCG and the neuro-fuzzy inference of acoustic features offered a high performance to detect cardiac murmurs. PMID:24109851

  9. Competing channels in the thermal decomposition of azidoacetone studied by pyrolysis in combination with molecular beam mass spectrometric techniques.

    PubMed

    O'Keeffe, Patrick; Scotti, Giorgio; Stranges, Domenico; Rodrigues, Paula; Barros, M Teresa; Costa, Maria L

    2008-04-10

    The thermal decomposition of azidoacetone (CH3COCH2N3) was studied using a combined experimental and computational approach. Flash pyrolysis at a range of temperatures (296-1250 K) was used to induce thermal decomposition, and the resulting products were expanded into a molecular beam and subsequently analyzed using electron bombardment ionization coupled to a quadrupole mass spectrometer. The advantages of this technique are that the parent molecules spend a very short time in the pyrolysis zone (20-30 mus) and that the subsequent expansion permits the stabilization of thermal products that are not observable using conventional pyrolysis methods. A detailed analysis of the mass spectra as a function of pyrolysis temperature revealed the participation of five thermal decomposition channels. Ab initio calculations on the stable structures and transition states of the azidoacetone system in combination with an analysis of the dissociative ionization pattern of each channel allowed the identity and mechanism of each channel to be elucidated. At low temperatures (296-800 K) the azide decomposes principally by the loss of N2 to yield the imine (CH3COCHNH), which can further decompose to CH3CO and CHNH. At low and intermediate temperatures a process involving the loss of N2 to yield CH3CHO and HCN is also open. Finally, at high temperatures (800-1250 K) a channel in which the azide decomposes to a stable cyclic amine (CO(CH2)2NH) (after loss of N2) is active. The last channel involves subsequent thermal decomposition of this cyclic amine to ketene (H2CCO) and methanimine (H2CNH). PMID:18341306

  10. Molecular basis of chill resistance adaptations in poikilothermic animals.

    PubMed

    Hayward, Scott A L; Manso, Bruno; Cossins, Andrew R

    2014-01-01

    Chill and freeze represent very different components of low temperature stress. Whilst the principal mechanisms of tissue damage and of acquired protection from freeze-induced effects are reasonably well established, those for chill damage and protection are not. Non-freeze cold exposure (i.e. chill) can lead to serious disruption to normal life processes, including disruption to energy metabolism, loss of membrane perm-selectivity and collapse of ion gradients, as well as loss of neuromuscular coordination. If the primary lesions are not relieved then the progressive functional debilitation can lead to death. Thus, identifying the underpinning molecular lesions can point to the means of building resistance to subsequent chill exposures. Researchers have focused on four specific lesions: (i) failure of neuromuscular coordination, (ii) perturbation of bio-membrane structure and adaptations due to altered lipid composition, (iii) protein unfolding, which might be mitigated by the induced expression of compatible osmolytes acting as 'chemical chaperones', (iv) or the induced expression of protein chaperones along with the suppression of general protein synthesis. Progress in all these potential mechanisms has been ongoing but not substantial, due in part to an over-reliance on straightforward correlative approaches. Also, few studies have intervened by adoption of single gene ablation, which provides much more direct and compelling evidence for the role of specific genes, and thus processes, in adaptive phenotypes. Another difficulty is the existence of multiple mechanisms, which often act together, thus resulting in compensatory responses to gene manipulations, which may potentially mask disruptive effects on the chill tolerance phenotype. Consequently, there is little direct evidence of the underpinning regulatory mechanisms leading to induced resistance to chill injury. Here, we review recent advances mainly in lower vertebrates and in arthropods, but increasingly

  11. Molecular mechanisms involved in plant adaptation to low K(+) availability.

    PubMed

    Chérel, Isabelle; Lefoulon, Cécile; Boeglin, Martin; Sentenac, Hervé

    2014-03-01

    Potassium is a major inorganic constituent of the living cell and the most abundant cation in the cytosol. It plays a role in various functions at the cell level, such as electrical neutralization of anionic charges, protein synthesis, long- and short-term control of membrane polarization, and regulation of the osmotic potential. Through the latter function, K(+) is involved at the whole-plant level in osmotically driven functions such as cell movements, regulation of stomatal aperture, or phloem transport. Thus, plant growth and development require that large amounts of K(+) are taken up from the soil and translocated to the various organs. In most ecosystems, however, soil K(+) availability is low and fluctuating, so plants have developed strategies to take up K(+) more efficiently and preserve vital functions and growth when K(+) availability is becoming limited. These strategies include increased capacity for high-affinity K(+) uptake from the soil, K(+) redistribution between the cytosolic and vacuolar pools, ensuring cytosolic homeostasis, and modification of root system development and architecture. Our knowledge about the mechanisms and signalling cascades involved in these different adaptive responses has been rapidly growing during the last decade, revealing a highly complex network of interacting processes. This review is focused on the different physiological responses induced by K(+) deprivation, their underlying molecular events, and the present knowledge and hypotheses regarding the mechanisms responsible for K(+) sensing and signalling. PMID:24293613

  12. Molecular mechanisms of Tetranychus urticae chemical adaptation in hop fields.

    PubMed

    Piraneo, Tara G; Bull, Jon; Morales, Mariany A; Lavine, Laura C; Walsh, Douglas B; Zhu, Fang

    2015-01-01

    The two-spotted spider mite, Tetranychus urticae Koch is a major pest that feeds on >1,100 plant species. Many perennial crops including hop (Humulus lupulus) are routinely plagued by T. urticae infestations. Hop is a specialty crop in Pacific Northwest states, where 99% of all U.S. hops are produced. To suppress T. urticae, growers often apply various acaricides. Unfortunately T. urticae has been documented to quickly develop resistance to these acaricides which directly cause control failures. Here, we investigated resistance ratios and distribution of multiple resistance-associated mutations in field collected T. urticae samples compared with a susceptible population. Our research revealed that a mutation in the cytochrome b gene (G126S) in 35% tested T. urticae populations and a mutation in the voltage-gated sodium channel gene (F1538I) in 66.7% populations may contribute resistance to bifenazate and bifenthrin, respectively. No mutations were detected in Glutamate-gated chloride channel subunits tested, suggesting target site insensitivity may not be important in our hop T. urticae resistance to abamectin. However, P450-mediated detoxification was observed and is a putative mechanism for abamectin resistance. Molecular mechanisms of T. urticae chemical adaptation in hopyards is imperative new information that will help growers develop effective and sustainable management strategies. PMID:26621458

  13. Molecular mechanisms of Tetranychus urticae chemical adaptation in hop fields

    PubMed Central

    Piraneo, Tara G.; Bull, Jon; Morales, Mariany A.; Lavine, Laura C.; Walsh, Douglas B.; Zhu, Fang

    2015-01-01

    The two-spotted spider mite, Tetranychus urticae Koch is a major pest that feeds on >1,100 plant species. Many perennial crops including hop (Humulus lupulus) are routinely plagued by T. urticae infestations. Hop is a specialty crop in Pacific Northwest states, where 99% of all U.S. hops are produced. To suppress T. urticae, growers often apply various acaricides. Unfortunately T. urticae has been documented to quickly develop resistance to these acaricides which directly cause control failures. Here, we investigated resistance ratios and distribution of multiple resistance-associated mutations in field collected T. urticae samples compared with a susceptible population. Our research revealed that a mutation in the cytochrome b gene (G126S) in 35% tested T. urticae populations and a mutation in the voltage-gated sodium channel gene (F1538I) in 66.7% populations may contribute resistance to bifenazate and bifenthrin, respectively. No mutations were detected in Glutamate-gated chloride channel subunits tested, suggesting target site insensitivity may not be important in our hop T. urticae resistance to abamectin. However, P450-mediated detoxification was observed and is a putative mechanism for abamectin resistance. Molecular mechanisms of T. urticae chemical adaptation in hopyards is imperative new information that will help growers develop effective and sustainable management strategies. PMID:26621458

  14. Temperature Adaptations in the Terminal Processes of Anaerobic Decomposition of Yellowstone National Park and Icelandic Hot Spring Microbial Mats

    PubMed Central

    Sandbeck, Kenneth A.; Ward, David M.

    1982-01-01

    The optimum temperatures for methanogenesis in microbial mats of four neutral to alkaline, low-sulfate hot springs in Yellowstone National Park were between 50 and 60°C, which was 13 to 23°C lower than the upper temperature for mat development. Significant methanogenesis at 65°C was only observed in one of the springs. Methane production in samples collected at a 51 or 62°C site in Octopus Spring was increased by incubation at higher temperatures and was maximal at 70°C. Strains of Methanobacterium thermoautotrophicum were isolated from 50, 55, 60, and 65°C sites in Octopus Spring at the temperatures of the collection sites. The optimum temperature for growth and methanogenesis of each isolate was 65°C. Similar results were found for the potential rate of sulfate reduction in an Icelandic hot spring microbial mat in which sulfate reduction dominated methane production as a terminal process in anaerobic decomposition. The potential rate of sulfate reduction along the thermal gradient of the mat was greatest at 50°C, but incubation at 60°C of the samples obtained at 50°C increased the rate. Adaptation to different mat temperatures, common among various microorganisms and processes in the mats, did not appear to occur in the processes and microorganisms which terminate the anaerobic food chain. Other factors must explain why the maximal rates of these processes are restricted to moderate temperatures of the mat ecosystem. PMID:16346109

  15. Spherical-Harmonic Decomposition for Molecular Recognition in Electron-Density Maps

    PubMed Central

    DiMaio, Frank P.; Soni, Ameet B.; Phillips, George N.; Shavlik, Jude W.

    2008-01-01

    An important problem in high-throughput protein crystallography is constructing a protein model from an electron-density map. DiMaio et al. (2006) describe an automated approach to this otherwise time-consuming process. One important step involves searching the density map for many small protein fragments, or templates. The previous approach uses Fourier convolution to quickly compare some rotation of the template to the entire density map. We propose to instead use the spherical-harmonic decomposition of the template and of some region in the density map. In this new framework, we are able to eliminate areas of the map from the search process if they are unlikely to match to any templates. We design several “first-pass filters” for this elimination task, including one filter which uses a set of rotation-invariant descriptors (derived from the spherical-harmonic decomposition) of a sphere of density to train an accurate classifier. We show our new template-matching method improves accuracy and reduces running time, compared to our previous approach. Protein models constructed using this matching also show significant accuracy improvement. We extend our method to produce a structural-homology detection algorithm that, due to its use of electron-density maps, is more sensitive than sequence-only methods. PMID:19517990

  16. Solid Molecular Phosphine Catalysts for Formic Acid Decomposition in the Biorefinery.

    PubMed

    Hausoul, Peter J C; Broicher, Cornelia; Vegliante, Roberta; Göb, Christian; Palkovits, Regina

    2016-04-25

    The co-production of formic acid during the conversion of cellulose to levulinic acid offers the possibility for on-site hydrogen production and reductive transformations. Phosphorus-based porous polymers loaded with Ru complexes exhibit high activity and selectivity in the base-free decomposition of formic acid to CO2 and H2 . A polymeric analogue of 1,2-bis(diphenylphosphino)ethane (DPPE) gave the best results in terms of performance and stability. Recycling tests revealed low levels of leaching and only a gradual decrease in the activity over seven runs. An applicability study revealed that these catalysts even facilitate selective removal of formic acid from crude product mixtures arising from the synthesis of levulinic acid. PMID:27043017

  17. 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. PMID:21827423

  18. Shock-induced decomposition of high energy materials: A ReaxFF molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Tiwari, Subodh; Mishra, Ankit; Nomura, Ken-Ichi; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya

    Atomistic simulations of shock-induced detonation provide critical information about high-energy (HE) materials such as sensitivity, crystallographic anisotropy, detonation velocity, and reaction pathways. However, first principles methods are unable to handle systems large enough to describe shock appropriately. We report reactive-force-field ReaxFF simulations of shock-induced decomposition of 1, 3, 5-triamino-2, 3, 6-trinitrobenzene (TATB) and 1,1-diamino 2-2-dinitroethane (FOX-7) crystal. A flyer acts as mechanical stimuli to introduce a shock, which in turn initiated chemical reactions. Our simulation showed a shock speed of 9.8 km/s and 8.23 km/s for TATB and FOX-7, respectively. Reactivity analysis proves that FOX-7 is more reactive than TATB. Chemical reaction pathways analysis revealed similar pathways for the formation of N2 and H2O in both TATB and FOX-7. However, abundance of NH3 formation is specific to FOX-7. Large clusters formed during the reactions also shows different compositions between TATB and FOX-7. Carbon soot formation is much more pronounced in TATB. Overall, this study provides a detailed comparison between shock induced reaction pathway between FOX-7 and TATB. This work was supported by the Office of Naval Research Grant No. N000014-12-1-0555.

  19. An adaptive interpolation scheme for molecular potential energy surfaces.

    PubMed

    Kowalewski, Markus; Larsson, Elisabeth; Heryudono, Alfa

    2016-08-28

    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. PMID:27586901

  20. Crossed Molecular Beam Studies and Dynamics of Decomposition of Chemically Activated Radicals

    DOE R&D Accomplishments Database

    Lee, Y. T.

    1973-09-01

    The power of the crossed molecular beams method in the investigation of the dynamics of chemical reactions lies mainly in the direct observation of the consequences of single collisions of well controlled reactant molecules. The primary experimental observations which provide information on reaction dynamics are the measurements of angular and velocity distributions of reaction products.

  1. 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. PMID:27248370

  2. Probing non-covalent interactions with a second generation energy decomposition analysis using absolutely localized molecular orbitals.

    PubMed

    Horn, Paul R; Mao, Yuezhi; Head-Gordon, Martin

    2016-08-17

    An energy decomposition analysis (EDA) separates a calculated interaction energy into as many interpretable contributions as possible; for instance, permanent and induced electrostatics, Pauli repulsions, dispersion and charge transfer. The challenge is to construct satisfactory definitions of all terms in the chemically relevant regime where fragment densities overlap, rendering unique definitions impossible. Towards this goal, we present an improved EDA for Kohn-Sham density functional theory (DFT) with properties that have previously not been simultaneously attained. Building on the absolutely localized molecular orbital (ALMO)-EDA, this second generation ALMO-EDA is variational and employs valid antisymmetric electronic wavefunctions to produce all five contributions listed above. These contributions moreover all have non-trivial complete basis set limits. We apply the EDA to the water dimer, the T-shaped and parallel-displaced benzene dimer, the p-biphthalate dimer "anti-electrostatic" hydrogen bonding complex, the biologically relevant binding of adenine and thymine in stacked and hydrogen-bonded configurations, the triply hydrogen-bonded guanine-cytosine complex, the interaction of Cl(-) with s-triazine and with the 1,3-dimethyl imidazolium cation, which is relevant to the study of ionic liquids, and the water-formaldehyde-vinyl alcohol ter-molecular radical cationic complex formed in the dissociative photoionization of glycerol. PMID:27492057

  3. Spatial decomposition of molecular ions within 3D atom probe reconstructions.

    PubMed

    Breen, Andrew; Moody, Michael P; Gault, Baptiste; Ceguerra, Anna V; Xie, Kelvin Y; Du, Sichao; Ringer, Simon P

    2013-09-01

    Two methods for separating the constituent atoms of molecular ions within atom probe tomography reconstructions are presented. The Gaussian Separation Method efficiently deconvolutes molecular ions containing two constituent atoms and is tested on simulated data before being applied to an experimental HSLA steel dataset containing NbN. The Delaunay Separation Method extends separation to larger complex ions and is also tested on simulated data before being applied to an experimental GaAs dataset containing many large (>3 atoms) complex ions. First nearest neighbour (1NN) distributions and images of the reconstruction before and after the separations are used to show the effect of the algorithms and their validity and practicality are also discussed. PMID:23522847

  4. A Linked-Cell Domain Decomposition Method for Molecular Dynamics Simulation on a Scalable Multiprocessor

    DOE PAGESBeta

    Yang, L. H.; Brooks III, E. D.; Belak, J.

    1992-01-01

    A molecular dynamics algorithm for performing large-scale simulations using the Parallel C Preprocessor (PCP) programming paradigm on the BBN TC2000, a massively parallel computer, is discussed. The algorithm uses a linked-cell data structure to obtain the near neighbors of each atom as time evoles. Each processor is assigned to a geometric domain containing many subcells and the storage for that domain is private to the processor. Within this scheme, the interdomain (i.e., interprocessor) communication is minimized.

  5. Multi-Orbital Molecular Compound (TTM-TTP)I3: Effective Model and Fragment Decomposition

    NASA Astrophysics Data System (ADS)

    Tsuchiizu, Masahisa; Omori, Yukiko; Suzumura, Yoshikazu; Bonnet, Marie-Laure; Robert, Vincent; Ishibashi, Shoji; Seo, Hitoshi

    2011-01-01

    The electronic structure of the molecular compound (TTM-TTP)I3, which exhibits a peculiar intra-molecular charge ordering, has been studied using multi-configuration ab initio calculations. First we derive an effective Hubbard-type model based on the molecular orbitals (MOs) of TTM-TTP; we set up a two-orbital Hamiltonian for the two MOs near the Fermi energy and determine its full parameters: the transfer integrals, the Coulomb and exchange interactions. The tight-binding band structure obtained from these transfer integrals is consistent with the result of the direct band calculation based on density functional theory. Then, by decomposing the frontier MOs into two parts, i.e., fragments, we find that the stacked TTM-TTP molecules can be described by a two-leg ladder model, while the inter-fragment Coulomb energies are scaled to the inverse of their distances. This result indicates that the fragment picture that we proposed earlier [M.-L. Bonnet et al.: J. Chem. Phys. 132 (2010) 214705] successfully describes the low-energy properties of this compound.

  6. Molecular-level tradeoffs and metabolic adaptation to simultaneous stressors

    PubMed Central

    Carlson, Ross P.; Taffs, Reed L.

    2010-01-01

    Summary Life is a dynamic process driven by the complex interplay between physical constraints and selection pressures, ranging from nutrient limitation to inhibitory substances to predators. These stressors are not mutually exclusive; microbes have faced concurrent challenges for eons. Genome-enabled systems biology approaches are adapting economic and ecological concepts like tradeoff curves and strategic resource allocation theory to analyze metabolic adaptations to simultaneous stressors. These methodologies can accurately describe and predict metabolic adaptations to concurrent stresses by considering the tradeoff between investment of limiting resources into enzymatic machinery and the resulting cellular function. The approaches represent promising links between computational biology and well established economic and ecological methodologies for analyzing the interplay between physical constraints and microbial fitness. PMID:20637598

  7. Car-Parrinello molecular dynamics study of the thermal decomposition of sodium fulminate.

    PubMed

    Damianos, Konstantina; Frank, Irmgard

    2010-07-19

    Depending on the metal cation, metal fulminates exhibit a characteristic sensitivity with respect to heat and mechanical stress. In the present paper we study the high-temperature reactions of bulk sodium fulminate using Car-Parrinello molecular dynamics simulations. We find that the initiating reaction is the formation of the fulminate dimer, while in earlier studies an electron transfer was assumed to be the first reaction step. The initial carbon--carbon bond formation is followed by fast consecutive reactions leading to polymerisation. The resulting species remain charged on the timescale of the simulations. PMID:20521277

  8. Free energy calculations from adaptive molecular dynamics simulations with adiabatic reweighting

    NASA Astrophysics Data System (ADS)

    Cao, Lingling; Stoltz, Gabriel; Lelièvre, Tony; Marinica, Mihai-Cosmin; Athènes, Manuel

    2014-03-01

    We propose an adiabatic reweighting algorithm for computing the free energy along an external parameter from adaptive molecular dynamics simulations. The adaptive bias is estimated using Bayes identity and information from all the sampled configurations. We apply the algorithm to a structural transition in a cluster and to the migration of a crystalline defect along a reaction coordinate. Compared to standard adaptive molecular dynamics, we observe an acceleration of convergence. With the aid of the algorithm, it is also possible to iteratively construct the free energy along the reaction coordinate without having to differentiate the gradient of the reaction coordinate or any biasing potential.

  9. Ethanol decomposition on transition metal nanoparticles during carbon nanotube growth: ab initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Shibuta, Yasushi; Shimamura, Kohei; Oguri, Tomoya; Arifin, Rizal; Shimojo, Fuyuki; Yamaguchi, Shu

    2015-03-01

    The growth mechanism of carbon nanotubes (CNT) has been widely discussed both from experimental and computational studies. Regarding the computational studies, most of the studies focuses on the aggregation of isolate carbon atoms on the catalytic metal nanoparticle, whereas the initial dissociation of carbon source molecules should affect the yield and quality of the products. On the other hand, we have studied the dissociation process of carbon source molecules on the metal surface by the ab initio molecular dynamics simulation. In the study, we investigate the ethanol dissociation on Pt and Ni clusters by ab initio MD simulations to discuss the initial stage of CNT growth by alcohol CVD technique. Part of this research is supported by the Grant-in-Aid for Young Scientists (a) (No. 24686026) from MEXT, Japan.

  10. Thermal decomposition of a honeycomb-network sheet: A molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Paturej, J.; Popova, H.; Milchev, A.; Vilgis, T. A.

    2012-08-01

    The thermal degradation of a graphene-like two-dimensional honeycomb membrane with bonds undergoing temperature-induced scission is studied by means of Molecular Dynamics simulation using Langevin thermostat. We demonstrate that at lower temperature the probability distribution of breaking bonds is highly peaked at the rim of the membrane sheet whereas at higher temperature bonds break at random everywhere in the hexagonal flake. The mean breakage time τ is found to decrease with the total number of network nodes N by a power law τ ∝ N-0.5 and reveals an Arrhenian dependence on temperature T. Scission times are themselves exponentially distributed. The fragmentation kinetics of the average number of clusters can be described by first-order chemical reactions between network nodes ni of different coordination. The distribution of fragments sizes evolves with time elapsed from initially a δ-function through a bimodal one into a single-peaked again at late times. Our simulation results are complemented by a set of 1st-order kinetic differential equations for ni which can be solved exactly and compared to data derived from the computer experiment, providing deeper insight into the thermolysis mechanism.

  11. Spinodal decomposition of polymer solutions: molecular dynamics simulations of the two-dimensional case

    NASA Astrophysics Data System (ADS)

    Reith, Daniel; Bucior, Katarzyna; Yelash, Leonid; Virnau, Peter; Binder, Kurt

    2012-03-01

    As a generic model system for phase separation in polymer solutions, a coarse-grained model for hexadecane/carbon dioxide mixtures has been studied in two-dimensional geometry. Both the phase diagram in equilibrium (obtained from a finite size scaling analysis of Monte Carlo data) and the kinetics of state changes caused by pressure jumps (studied by large scale molecular dynamics simulations) are presented. The results are compared to previous work where the same model was studied in three-dimensional geometry and under confinement in slit geometry. For deep quenches the characteristic length scale ℓ(t) of the formed domains grows with time t according to a power law close to \\ell (t)\\propto \\sqrt{t}. Since in this problem both the polymer density ρp and the solvent density ρs matter, the time evolution of the density distribution PL(ρp,ρs,t) in L × L subboxes of the system is also analyzed. It is found that in the first stage of phase separation the system separates locally into low density carbon dioxide regions that contain no polymers and regions of high density polymer melt that are supersaturated with this solvent. The further coarsening proceeds via the growth of domains of rather irregular shapes. A brief comparison of our findings with results of other models is given.

  12. An energy decomposition analysis for second-order Møller–Plesset perturbation theory based on absolutely localized molecular orbitals

    SciTech Connect

    Thirman, Jonathan Head-Gordon, Martin

    2015-08-28

    An energy decomposition analysis (EDA) of intermolecular interactions is proposed for second-order Møller–Plesset perturbation theory (MP2) based on absolutely localized molecular orbitals (ALMOs), as an extension to a previous ALMO-based EDA for self-consistent field methods. It decomposes the canonical MP2 binding energy by dividing the double excitations that contribute to the MP2 wave function into classes based on how the excitations involve different molecules. The MP2 contribution to the binding energy is decomposed into four components: frozen interaction, polarization, charge transfer, and dispersion. Charge transfer is defined by excitations that change the number of electrons on a molecule, dispersion by intermolecular excitations that do not transfer charge, and polarization and frozen interactions by intra-molecular excitations. The final two are separated by evaluations of the frozen, isolated wave functions in the presence of the other molecules, with adjustments for orbital response. Unlike previous EDAs for electron correlation methods, this one includes components for the electrostatics, which is vital as adjustment to the electrostatic behavior of the system is in some cases the dominant effect of the treatment of electron correlation. The proposed EDA is then applied to a variety of different systems to demonstrate that all proposed components behave correctly. This includes systems with one molecule and an external electric perturbation to test the separation between polarization and frozen interactions and various bimolecular systems in the equilibrium range and beyond to test the rest of the EDA. We find that it performs well on these tests. We then apply the EDA to a halogen bonded system to investigate the nature of the halogen bond.

  13. [Molecular mechanisms of tissue hypoxia and organism adaptation].

    PubMed

    Luk'ianova, L D

    2003-01-01

    The mechanism for participation of aerobic energy metabolism in formation of urgent and long-term adaptation to hypoxia is under consideration. It is stated that changes in kinetic properties of mitochondrial enzyme complexes (MEC), primarily enzymes of the respiratory chain substrate region (MEC I), in response to oxygen shortage underlie diverse stages of bioenergetic (tissue) hypoxia. It was shown that economization of energy metabolism in adaptation to hypoxia occurs due to formation of a new mitochondrial population. The mitochondria possess lesser size and decreased content of cytochromes; however, they are characterized by higher activities of enzymes and lower affinity of the enzymes to their substrates as well as high efficiency of oxidative phosphorylation. Furthermore the amount of mitochondria increases in the cell. It was demonstrated that oxygen shortage can both directly affect the bioenergetic apparatus of cell and indirectly influence it via stress activation of the neuro-humoral system. The latter triggers a non-specific cascade of functional and metabolic responses and eventually disturbs oxygen delivery to cells, which also promotes bioenergetic hypoxia. Genotypically determined differences in kinetic properties of MEC are established, which play a leading role in formation of the functional and metabolic "portrait" of resistant and non-resistant to hypoxia animals and also in development of urgent and long-term mechanisms of adaptation to hypoxia. It was shown that these mechanisms can be used not only for development of the tactics and strategy for pharmacological correction of hypoxic states, but also for optimization of non-drug methods for enhancing the non-specific resistance of the organism. PMID:12918247

  14. Molecular and ecological signs of mitochondrial adaptation: consequences for introgression?

    PubMed Central

    Boratyński, Z; Melo-Ferreira, J; Alves, P C; Berto, S; Koskela, E; Pentikäinen, O T; Tarroso, P; Ylilauri, M; Mappes, T

    2014-01-01

    The evolution of the mitochondrial genome and its potential adaptive impact still generates vital debates. Even if mitochondria have a crucial functional role, as they are the main cellular energy suppliers, mitochondrial DNA (mtDNA) introgression is common in nature, introducing variation in populations upon which selection may act. Here we evaluated whether the evolution of mtDNA in a rodent species affected by mtDNA introgression is explained by neutral expectations alone. Variation in one mitochondrial and six nuclear markers in Myodes glareolus voles was examined, including populations that show mtDNA introgression from its close relative, Myodes rutilus. In addition, we modelled protein structures of the mtDNA marker (cytochrome b) and estimated the environmental envelopes of mitotypes. We found that massive mtDNA introgression occurred without any trace of introgression in the analysed nuclear genes. The results show that the native glareolus mtDNA evolved under past positive selection, suggesting that mtDNA in this system has selective relevance. The environmental models indicate that the rutilus mitotype inhabits colder and drier habitats than the glareolus one that can result from local adaptation or from the geographic context of introgression. Finally, homology models of the cytochrome b protein revealed a substitution in rutilus mtDNA in the vicinity of the catalytic fraction, suggesting that differences between mitotypes may result in functional changes. These results suggest that the evolution of mtDNA in Myodes may have functional, ecological and adaptive significance. This work opens perspective onto future experimental tests of the role of natural selection in mtDNA introgression in this system. PMID:24690754

  15. Molecular and ecological signs of mitochondrial adaptation: consequences for introgression?

    PubMed

    Boratyński, Z; Melo-Ferreira, J; Alves, P C; Berto, S; Koskela, E; Pentikäinen, O T; Tarroso, P; Ylilauri, M; Mappes, T

    2014-10-01

    The evolution of the mitochondrial genome and its potential adaptive impact still generates vital debates. Even if mitochondria have a crucial functional role, as they are the main cellular energy suppliers, mitochondrial DNA (mtDNA) introgression is common in nature, introducing variation in populations upon which selection may act. Here we evaluated whether the evolution of mtDNA in a rodent species affected by mtDNA introgression is explained by neutral expectations alone. Variation in one mitochondrial and six nuclear markers in Myodes glareolus voles was examined, including populations that show mtDNA introgression from its close relative, Myodes rutilus. In addition, we modelled protein structures of the mtDNA marker (cytochrome b) and estimated the environmental envelopes of mitotypes. We found that massive mtDNA introgression occurred without any trace of introgression in the analysed nuclear genes. The results show that the native glareolus mtDNA evolved under past positive selection, suggesting that mtDNA in this system has selective relevance. The environmental models indicate that the rutilus mitotype inhabits colder and drier habitats than the glareolus one that can result from local adaptation or from the geographic context of introgression. Finally, homology models of the cytochrome b protein revealed a substitution in rutilus mtDNA in the vicinity of the catalytic fraction, suggesting that differences between mitotypes may result in functional changes. These results suggest that the evolution of mtDNA in Myodes may have functional, ecological and adaptive significance. This work opens perspective onto future experimental tests of the role of natural selection in mtDNA introgression in this system. PMID:24690754

  16. Molecular networks of human muscle adaptation to exercise and age.

    PubMed

    Phillips, Bethan E; Williams, John P; Gustafsson, Thomas; Bouchard, Claude; Rankinen, Tuomo; Knudsen, Steen; Smith, Kenneth; Timmons, James A; Atherton, Philip J

    2013-03-01

    Physical activity and molecular ageing presumably interact to precipitate musculoskeletal decline in humans with age. Herein, we have delineated molecular networks for these two major components of sarcopenic risk using multiple independent clinical cohorts. We generated genome-wide transcript profiles from individuals (n = 44) who then undertook 20 weeks of supervised resistance-exercise training (RET). Expectedly, our subjects exhibited a marked range of hypertrophic responses (3% to +28%), and when applying Ingenuity Pathway Analysis (IPA) up-stream analysis to ~580 genes that co-varied with gain in lean mass, we identified rapamycin (mTOR) signaling associating with growth (P = 1.4 × 10(-30)). Paradoxically, those displaying most hypertrophy exhibited an inhibited mTOR activation signature, including the striking down-regulation of 70 rRNAs. Differential analysis found networks mimicking developmental processes (activated all-trans-retinoic acid (ATRA, Z-score = 4.5; P = 6 × 10(-13)) and inhibited aryl-hydrocarbon receptor signaling (AhR, Z-score = -2.3; P = 3 × 10(-7))) with RET. Intriguingly, as ATRA and AhR gene-sets were also a feature of endurance exercise training (EET), they appear to represent "generic" physical activity responsive gene-networks. For age, we found that differential gene-expression methods do not produce consistent molecular differences between young versus old individuals. Instead, utilizing two independent cohorts (n = 45 and n = 52), with a continuum of subject ages (18-78 y), the first reproducible set of age-related transcripts in human muscle was identified. This analysis identified ~500 genes highly enriched in post-transcriptional processes (P = 1 × 10(-6)) and with negligible links to the aforementioned generic exercise regulated gene-sets and some overlap with ribosomal genes. The RNA signatures from multiple compounds all targeting serotonin, DNA topoisomerase antagonism, and RXR activation were significantly related to

  17. Molecular Networks of Human Muscle Adaptation to Exercise and Age

    PubMed Central

    Phillips, Bethan E.; Williams, John P.; Gustafsson, Thomas; Bouchard, Claude; Rankinen, Tuomo; Knudsen, Steen; Smith, Kenneth

    2013-01-01

    Physical activity and molecular ageing presumably interact to precipitate musculoskeletal decline in humans with age. Herein, we have delineated molecular networks for these two major components of sarcopenic risk using multiple independent clinical cohorts. We generated genome-wide transcript profiles from individuals (n = 44) who then undertook 20 weeks of supervised resistance-exercise training (RET). Expectedly, our subjects exhibited a marked range of hypertrophic responses (3% to +28%), and when applying Ingenuity Pathway Analysis (IPA) up-stream analysis to ∼580 genes that co-varied with gain in lean mass, we identified rapamycin (mTOR) signaling associating with growth (P = 1.4×10−30). Paradoxically, those displaying most hypertrophy exhibited an inhibited mTOR activation signature, including the striking down-regulation of 70 rRNAs. Differential analysis found networks mimicking developmental processes (activated all-trans-retinoic acid (ATRA, Z-score = 4.5; P = 6×10−13) and inhibited aryl-hydrocarbon receptor signaling (AhR, Z-score = −2.3; P = 3×10−7)) with RET. Intriguingly, as ATRA and AhR gene-sets were also a feature of endurance exercise training (EET), they appear to represent “generic” physical activity responsive gene-networks. For age, we found that differential gene-expression methods do not produce consistent molecular differences between young versus old individuals. Instead, utilizing two independent cohorts (n = 45 and n = 52), with a continuum of subject ages (18–78 y), the first reproducible set of age-related transcripts in human muscle was identified. This analysis identified ∼500 genes highly enriched in post-transcriptional processes (P = 1×10−6) and with negligible links to the aforementioned generic exercise regulated gene-sets and some overlap with ribosomal genes. The RNA signatures from multiple compounds all targeting serotonin, DNA topoisomerase antagonism, and RXR

  18. A Fast Variational Method for the Construction of Resolution Adaptive C-Smooth Molecular Surfaces.

    PubMed

    Bajaj, Chandrajit L; Xu, Guoliang; Zhang, Qin

    2009-05-01

    We present a variational approach to smooth molecular (proteins, nucleic acids) surface constructions, starting from atomic coordinates, as available from the protein and nucleic-acid data banks. Molecular dynamics (MD) simulations traditionally used in understanding protein and nucleic-acid folding processes, are based on molecular force fields, and require smooth models of these molecular surfaces. To accelerate MD simulations, a popular methodology is to employ coarse grained molecular models, which represent clusters of atoms with similar physical properties by psuedo- atoms, resulting in coarser resolution molecular surfaces. We consider generation of these mixed-resolution or adaptive molecular surfaces. Our approach starts from deriving a general form second order geometric partial differential equation in the level-set formulation, by minimizing a first order energy functional which additionally includes a regularization term to minimize the occurrence of chemically infeasible molecular surface pockets or tunnel-like artifacts. To achieve even higher computational efficiency, a fast cubic B-spline C(2) interpolation algorithm is also utilized. A narrow band, tri-cubic B-spline level-set method is then used to provide C(2) smooth and resolution adaptive molecular surfaces. PMID:19802355

  19. Natural gas leak location with K-L divergence-based adaptive selection of Ensemble Local Mean Decomposition components and high-order ambiguity function

    NASA Astrophysics Data System (ADS)

    Sun, Jiedi; Xiao, Qiyang; Wen, Jiangtao; Zhang, Ying

    2015-07-01

    In this study, a time-delay estimation method based on Ensemble Local Mean Decomposition (ELMD) method and high-order ambiguity function (HAF) is proposed for locating natural gas pipeline leaks. The leakage signals were decomposed using ELMD, and numerous production functions (PFs) were obtained. An adaptive selection method based on Kullback-Leibler (K-L) divergence was proposed to process these PF components and choose the characteristic PFs that contain most of the leakage information. The HAF was employed to analyze the instantaneous parameters of the characteristic PFs and calculate the difference in arrival time of characteristic frequencies. From the time difference and the signal propagation speed, the natural gas pipeline leakage location can be determined. The experiment results show that the proposed method can locate leaks with higher accuracy than cross-correlation method.

  20. Demodulation for hydraulic pump fault signals based on local mean decomposition and improved adaptive multiscale morphology analysis

    NASA Astrophysics Data System (ADS)

    Jiang, Wanlu; Zheng, Zhi; Zhu, Yong; Li, Yang

    2015-06-01

    Scales of IAMMA are adaptively determined by morphological features of signal, thus fault features of a hydraulic pump fault signal presented in multi-scales can be adaptively demodulated. In some coefficient range, IAMMA outperforms AMMA in demodulation ability based on the same SE, and it is less susceptible to noises than AMMA. The best performance of IAMMA with triangle SE is stronger than that of IAMMA with plat and semi-circle SE when they demodulate the same fault signal of hydraulic pump. Compared with traditional demodulation methods of HT and TKEO, IAMMA is adaptive and has stronger demodulation ability. An evaluation method based on kurtosis, power and standard deviation is proposed, by which some PFs which are rich in fault features can be selected as data source.

  1. Towards the adaptive optimization of field-free molecular alignment

    NASA Astrophysics Data System (ADS)

    Rouzée, Arnaud; Hertz, Edouard; Lavorel, Bruno; Faucher, Olivier

    2008-04-01

    We theoretically report the optimization of field-free molecular alignment by spectral phase shaping of femtosecond laser pulses. Optimal pulse shapes are designed iteratively by an evolutionary algorithm in conjunction with a non-perturbative regime calculation. The investigation is conducted in O2 and N2 under realistic conditions of intensity, temperature and pulse shaping. We demonstrate that specific tailored pulses can provide significant maximization of field-free alignment compared to the Fourier transform limited pulses of the same energy. The underlying control mechanism is discussed. The effect of pulse energy and temperature is analysed leading to the identification of a general criteria for a successful optimization. Finally, the optimal spectral phase learned from the algorithm is rather smooth and can be described by a representation in terms of a sigmoidal function. We show that the use of a low-dimensional parametrization of the phase yields an efficient optimization of the alignment within a highly reduced convergence time.

  2. The Coevolution of Phycobilisomes: Molecular Structure Adapting to Functional Evolution

    PubMed Central

    Shi, Fei; Qin, Song; Wang, Yin-Chu

    2011-01-01

    Phycobilisome is the major light-harvesting complex in cyanobacteria and red alga. It consists of phycobiliproteins and their associated linker peptides which play key role in absorption and unidirectional transfer of light energy and the stability of the whole complex system, respectively. Former researches on the evolution among PBPs and linker peptides had mainly focused on the phylogenetic analysis and selective evolution. Coevolution is the change that the conformation of one residue is interrupted by mutation and a compensatory change selected for in its interacting partner. Here, coevolutionary analysis of allophycocyanin, phycocyanin, and phycoerythrin and covariation analysis of linker peptides were performed. Coevolution analyses reveal that these sites are significantly correlated, showing strong evidence of the functional and structural importance of interactions among these residues. According to interprotein coevolution analysis, less interaction was found between PBPs and linker peptides. Our results also revealed the correlations between the coevolution and adaptive selection in PBS were not directly related, but probably demonstrated by the sites coupled under physical-chemical interactions. PMID:21904470

  3. Molecular mechanisms of genetic adaptation to xenobiotic compounds.

    PubMed Central

    van der Meer, J R; de Vos, W M; Harayama, S; Zehnder, A J

    1992-01-01

    Microorganisms in the environment can often adapt to use xenobiotic chemicals as novel growth and energy substrates. Specialized enzyme systems and metabolic pathways for the degradation of man-made compounds such as chlorobiphenyls and chlorobenzenes have been found in microorganisms isolated from geographically separated areas of the world. The genetic characterization of an increasing number of aerobic pathways for degradation of (substituted) aromatic compounds in different bacteria has made it possible to compare the similarities in genetic organization and in sequence which exist between genes and proteins of these specialized catabolic routes and more common pathways. These data suggest that discrete modules containing clusters of genes have been combined in different ways in the various catabolic pathways. Sequence information further suggests divergence of catabolic genes coding for specialized enzymes in the degradation of xenobiotic chemicals. An important question will be to find whether these specialized enzymes evolved from more common isozymes only after the introduction of xenobiotic chemicals into the environment. Evidence is presented that a range of genetic mechanisms, such as gene transfer, mutational drift, and genetic recombination and transposition, can accelerate the evolution of catabolic pathways in bacteria. However, there is virtually no information concerning the rates at which these mechanisms are operating in bacteria living in nature and the response of such rates to the presence of potential (xenobiotic) substrates. Quantitative data on the genetic processes in the natural environment and on the effect of environmental parameters on the rate of evolution are needed. PMID:1480115

  4. 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. PMID:25767053

  5. Flexibility and enzymatic cold-adaptation: a comparative molecular dynamics investigation of the elastase family.

    PubMed

    Papaleo, Elena; Riccardi, Laura; Villa, Chiara; Fantucci, Piercarlo; De Gioia, Luca

    2006-08-01

    Molecular dynamics simulations of representative mesophilic and psycrophilic elastases have been carried out at different temperatures to explore the molecular basis of cold adaptation inside a specific enzymatic family. The molecular dynamics trajectories have been compared and analyzed in terms of secondary structure, molecular flexibility, intramolecular and protein-solvent interactions, unravelling molecular features relevant to rationalize the efficient catalytic activity of psychrophilic elastases at low temperature. The comparative molecular dynamics investigation reveals that modulation of the number of protein-solvent interactions is not the evolutionary strategy followed by the psycrophilic elastase to enhance catalytic activity at low temperature. In addition, flexibility and solvent accessibility of the residues forming the catalytic triad and the specificity pocket are comparable in the cold- and warm-adapted enzymes. Instead, loop regions with different amino acid composition in the two enzymes, and clustered around the active site or the specificity pocket, are characterized by enhanced flexibility in the cold-adapted enzyme. Remarkably, the psycrophilic elastase is characterized by reduced flexibility, when compared to the mesophilic counterpart, in some scattered regions distant from the functional sites, in agreement with hypothesis suggesting that local rigidity in regions far from functional sites can be beneficial for the catalytic activity of psychrophilic enzymes. PMID:16920043

  6. Water adaptation strategy in anuran amphibians: molecular diversity of aquaporin.

    PubMed

    Ogushi, Yuji; Akabane, Gen; Hasegawa, Takahiro; Mochida, Hiroshi; Matsuda, Manabu; Suzuki, Masakazu; Tanaka, Shigeyasu

    2010-01-01

    Most adult anuran amphibians except for the aquatic species absorb water across the ventral pelvic skin and reabsorb it from urine in the urinary bladder. Many terrestrial and arboreal species use a region in the posterior or pelvic region of the ventral skin that is specialized for rapid rehydration from shallow water sources or moist substrates. Periods of terrestrial activity can be prolonged by reabsorption of dilute urine from the urinary bladder. Aquaporin (AQP), a water channel protein, plays a fundamental role in these water absorption/reabsorption processes, which are regulated by antidiuretic hormone. Characterization of AQPs from various anurans revealed that the unique water homeostasis is basically mediated by two types of anuran-specific AQPs, i.e. ventral pelvic skin and urinary bladder type, respectively. The bladder-type AQP is further expressed in the pelvic skin of terrestrial and arboreal species, together with the pelvic skin-type AQP. In contrast, the pelvic skin-type AQP (AQP-x3) of the aquatic Xenopus has lost the ability of efficient protein production. The extra C-terminal tail in AQP-x3 consisting of 33 nucleotides within the coding region appears to participate in the posttranscriptional regulation of AQP-x3 gene expression by attenuating protein expression. The positive transcriptional regulation of bladder-type AQP in the pelvic skin and negative posttranscriptional regulation of pelvic skin-type AQP provide flexibility in the water regulation mechanisms, which might have contributed to the evolutionary adaptation of anurans to a wide variety of water environments. PMID:19854867

  7. Molecular mechanisms underlying the exceptional adaptations of batoid fins

    PubMed Central

    Nakamura, Tetsuya; Klomp, Jeff; Pieretti, Joyce; Schneider, Igor; Gehrke, Andrew R.; Shubin, Neil H.

    2015-01-01

    Extreme novelties in the shape and size of paired fins are exemplified by extinct and extant cartilaginous and bony fishes. Pectoral fins of skates and rays, such as the little skate (Batoid, Leucoraja erinacea), show a strikingly unique morphology where the pectoral fin extends anteriorly to ultimately fuse with the head. This results in a morphology that essentially surrounds the body and is associated with the evolution of novel swimming mechanisms in the group. In an approach that extends from RNA sequencing to in situ hybridization to functional assays, we show that anterior and posterior portions of the pectoral fin have different genetic underpinnings: canonical genes of appendage development control posterior fin development via an apical ectodermal ridge (AER), whereas an alternative Homeobox (Hox)–Fibroblast growth factor (Fgf)–Wingless type MMTV integration site family (Wnt) genetic module in the anterior region creates an AER-like structure that drives anterior fin expansion. Finally, we show that GLI family zinc finger 3 (Gli3), which is an anterior repressor of tetrapod digits, is expressed in the posterior half of the pectoral fin of skate, shark, and zebrafish but in the anterior side of the pelvic fin. Taken together, these data point to both highly derived and deeply ancestral patterns of gene expression in skate pectoral fins, shedding light on the molecular mechanisms behind the evolution of novel fin morphologies. PMID:26644578

  8. Molecular mechanisms underlying the exceptional adaptations of batoid fins.

    PubMed

    Nakamura, Tetsuya; Klomp, Jeff; Pieretti, Joyce; Schneider, Igor; Gehrke, Andrew R; Shubin, Neil H

    2015-12-29

    Extreme novelties in the shape and size of paired fins are exemplified by extinct and extant cartilaginous and bony fishes. Pectoral fins of skates and rays, such as the little skate (Batoid, Leucoraja erinacea), show a strikingly unique morphology where the pectoral fin extends anteriorly to ultimately fuse with the head. This results in a morphology that essentially surrounds the body and is associated with the evolution of novel swimming mechanisms in the group. In an approach that extends from RNA sequencing to in situ hybridization to functional assays, we show that anterior and posterior portions of the pectoral fin have different genetic underpinnings: canonical genes of appendage development control posterior fin development via an apical ectodermal ridge (AER), whereas an alternative Homeobox (Hox)-Fibroblast growth factor (Fgf)-Wingless type MMTV integration site family (Wnt) genetic module in the anterior region creates an AER-like structure that drives anterior fin expansion. Finally, we show that GLI family zinc finger 3 (Gli3), which is an anterior repressor of tetrapod digits, is expressed in the posterior half of the pectoral fin of skate, shark, and zebrafish but in the anterior side of the pelvic fin. Taken together, these data point to both highly derived and deeply ancestral patterns of gene expression in skate pectoral fins, shedding light on the molecular mechanisms behind the evolution of novel fin morphologies. PMID:26644578

  9. Molecular evolution and adaptation of the mitochondrial cytochrome b gene in the subgenus Martes.

    PubMed

    Li, B; Malyarchuk, B; He, X B; Derenko, M

    2013-01-01

    Martes species represent a typical example of rapid evolutionary radiation and a recent speciation event. To identify regions of the genome that experienced adaptive evolution, which might provide clues to their functional importance and may be informative about the features that make each species unique, we sought evidence of molecular adaptation in the mitochondrial DNA (mtDNA) cytochrome b gene in the subgenus Martes. Complete sequences of the cytochrome b gene were obtained from 87 samples, including 49 sables, 28 pine martens, and 10 stone martens, and were combined with mtDNA sequences of other true martens, such as M. melampus and M. americana. Analysis of the cytochrome b gene variation in true martens has shown that the evolution of this gene is under negative selection. In contrast, positive selection on the cytochrome b protein has been detected by means of the software TreeSAAP using a phylogenetic reconstruction of Martes taxa. Signatures of adaptive variation in cytochrome b were restricted to the transmembrane domains, which likely function as proton pumps. We compared results of different methods for testing selection and molecular adaptation, and we supposed that the radical changes of the cytochrome b amino acid residues in the subgenus Martes may be the result of molecular adaptation to specific environmental conditions coupled with species dispersals. PMID:24085456

  10. A density-based adaptive quantum mechanical/molecular mechanical method.

    PubMed

    Waller, Mark P; Kumbhar, Sadhana; Yang, Jack

    2014-10-20

    We present a density-based adaptive quantum mechanical/molecular mechanical (DBA-QM/MM) method, whereby molecules can switch layers from the QM to the MM region and vice versa. The adaptive partitioning of the molecular system ensures that the layer assignment can change during the optimization procedure, that is, on the fly. The switch from a QM molecule to a MM molecule is determined if there is an absence of noncovalent interactions to any atom of the QM core region. The presence/absence of noncovalent interactions is determined by analysis of the reduced density gradient. Therefore, the location of the QM/MM boundary is based on physical arguments, and this neatly removes some empiricism inherent in previous adaptive QM/MM partitioning schemes. The DBA-QM/MM method is validated by using a water-in-water setup and an explicitly solvated L-alanyl-L-alanine dipeptide. PMID:24954803

  11. Real-Time Molecular Monitoring of Chemical Environment in ObligateAnaerobes during Oxygen Adaptive Response

    SciTech Connect

    Holman, Hoi-Ying N.; Wozei, Eleanor; Lin, Zhang; Comolli, Luis R.; Ball, David. A.; Borglin, Sharon; Fields, Matthew W.; Hazen, Terry C.; Downing, Kenneth H.

    2009-02-25

    Determining the transient chemical properties of the intracellular environment canelucidate the paths through which a biological system adapts to changes in its environment, for example, the mechanisms which enable some obligate anaerobic bacteria to survive a sudden exposure to oxygen. Here we used high-resolution Fourier Transform Infrared (FTIR) spectromicroscopy to continuously follow cellular chemistry within living obligate anaerobes by monitoring hydrogen bonding in their cellular water. We observed a sequence of wellorchestrated molecular events that correspond to changes in cellular processes in those cells that survive, but only accumulation of radicals in those that do not. We thereby can interpret the adaptive response in terms of transient intracellular chemistry and link it to oxygen stress and survival. This ability to monitor chemical changes at the molecular level can yield important insights into a wide range of adaptive responses.

  12. Chemical reaction dynamics of PeCB and TCDD decomposition: A tight-binding quantum chemical molecular dynamics study with first-principles parameterization

    NASA Astrophysics Data System (ADS)

    Suzuki, Ai; Selvam, Parasuraman; Kusagaya, Tomonori; Takami, Seiichi; Kubo, Momoji; Imamura, Akira; Miyamoto, Akira

    The decomposition reaction dynamics of 2,3,4,4',5-penta-chlorinated biphenyl (2,3,4,4',5-PeCB), 3,3',4,4',5-penta-chlorinated biphenyl (3,3',4,4',5-PeCB), and 2,3,7,8-tetra-chlorinated dibenzo-p-dioxin (2,3,7,8-TCDD) was clarified for the first time at atomic and electronic levels, using our novel tight-binding quantum chemical molecular dynamics method with first-principles parameterization. The calculation speed of our new method is over 5000 times faster than that of the conventional first-principles molecular dynamics method. We confirmed that the structure, energy, and electronic states of the above molecules calculated by our new method are quantitatively consistent with those by first-principles calculations. After the confirmation of our methodology, we investigated the decomposition reaction dynamics of the above molecules and the calculated dynamic behaviors indicate that the oxidation of the 2,3,4,4',5-PeCB, 3,3',4,4',5-PeCB, and 2,3,7,8-TCDD proceeds through an epoxide intermediate, which is in good agreement with the previous experimental reports and consistent with our static density functional theory calculations. These results proved that our new tight-binding quantum chemical molecular dynamics method with first-principles parameterization is an effective tool to clarify the chemical reaction dynamics at reaction temperatures.

  13. 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

  14. 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

  15. Determining the Energetics of Small β-Sheet Peptides using Adaptive Steered Molecular Dynamics.

    PubMed

    Bureau, Hailey R; Hershkovits, Eli; Quirk, Stephen; Hernandez, Rigoberto

    2016-04-12

    Mechanically driven unfolding is a useful computational tool for extracting the energetics and stretching pathway of peptides. In this work, two representative β-hairpin peptides, chignolin (PDB: 1UAO ) and trpzip1 (PDB: 1LE0 ), were investigated using an adaptive variant of the original steered molecular dynamics method called adaptive steered molecular dynamics (ASMD). The ASMD method makes it possible to perform energetic calculations on increasingly complex biological systems. Although the two peptides are similar in length and have similar secondary structures, their unfolding energetics are quite different. The hydrogen bonding profile and specific residue pair interaction energies provide insight into the differing stabilities of these peptides and reveal which of the pairs provides the most significant stabilization. PMID:26930270

  16. Symmetry-adapted non-equilibrium molecular dynamics of chiral carbon nanotubes under tensile loading

    NASA Astrophysics Data System (ADS)

    Aghaei, Amin; Dayal, Kaushik

    2011-06-01

    We report on non-equilibrium molecular dynamics calculations of chiral single-wall carbon nanotubes using the framework of Objective Structures. This enables us to adapt molecular dynamics to the symmetry of chiral nanotubes and efficiently simulate these systems with small unit cells. We outline the method and the adaptation of a conventional thermostat and barostat to this setting. We then apply the method in order to examine the behavior of nanotubes with various chiralities subject to a constant extensional strain rate. We examine the effects of temperature, strain rate, and pre-compression/pre-tension. We find a range of failure mechanisms, including the formation of Stone-Wales defects, the opening of voids, and the motion of atoms out of the cross-section.

  17. 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.

  18. Molecular and cellular neurocardiology: development, and cellular and molecular adaptations to heart disease.

    PubMed

    Habecker, Beth A; Anderson, Mark E; Birren, Susan J; Fukuda, Keiichi; Herring, Neil; Hoover, Donald B; Kanazawa, Hideaki; Paterson, David J; Ripplinger, Crystal M

    2016-07-15

    The nervous system and cardiovascular system develop in concert and are functionally interconnected in both health and disease. This white paper focuses on the cellular and molecular mechanisms that underlie neural-cardiac interactions during development, during normal physiological function in the mature system, and during pathological remodelling in cardiovascular disease. The content on each subject was contributed by experts, and we hope that this will provide a useful resource for newcomers to neurocardiology as well as aficionados. PMID:27060296

  19. Calculating IP Tuning Knobs for the PEP II High Energy Ring using Singular Value Decomposition, Response Matrices and an Adapted Moore Penrose Method

    SciTech Connect

    Wittmer, W.; /SLAC

    2007-11-07

    The PEP II lattices are unique in their detector solenoid field compensation scheme by utilizing a set of skew quadrupoles in the IR region and the adjacent arcs left and right of the IP. Additionally, the design orbit through this region is nonzero. This combined with the strong local coupling wave makes it very difficult to calculate IP tuning knobs which are orthogonal and closed. The usual approach results either in non-closure, not being orthogonal or the change in magnet strength being too big. To find a solution, the set of tuning quads had to be extended which resulted having more degrees of freedom than constraints. To find the optimal set of quadrupoles which creates a linear, orthogonal and closed knob and simultaneously minimizing the changes in magnet strength, the method using Singular Value Decomposition, Response Matrices and an Adapted Moore Penrose method had to be extended. The results of these simulations are discussed below and the results of first implementation in the machine are shown.

  20. Adaptive autoregressive identification with spectral power decomposition for studying movement-related activity in scalp EEG signals and basal ganglia local field potentials

    NASA Astrophysics Data System (ADS)

    Foffani, Guglielmo; Bianchi, Anna M.; Priori, Alberto; Baselli, Giuseppe

    2004-09-01

    We propose a method that combines adaptive autoregressive (AAR) identification and spectral power decomposition for the study of movement-related spectral changes in scalp EEG signals and basal ganglia local field potentials (LFPs). This approach introduces the concept of movement-related poles, allowing one to study not only the classical event-related desynchronizations (ERD) and synchronizations (ERS), which correspond to modulations of power, but also event-related modulations of frequency. We applied the method to analyze movement-related EEG signals and LFPs contemporarily recorded from the sensorimotor cortex, the globus pallidus internus (GPi) and the subthalamic nucleus (STN) in a patient with Parkinson's disease who underwent stereotactic neurosurgery for the implant of deep brain stimulation (DBS) electrodes. In the AAR identification we compared the whale and the exponential forgetting factors, showing that the whale forgetting provides a better disturbance rejection and it is therefore more suitable to investigate movement-related brain activity. Movement-related power modulations were consistent with previous studies. In addition, movement-related frequency modulations were observed from both scalp EEG signals and basal ganglia LFPs. The method therefore represents an effective approach to the study of movement-related brain activity.

  1. 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. PMID:24297902

  2. 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

  3. 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

  4. 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

    2015-01-01

    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

  5. Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns

    PubMed Central

    2011-01-01

    forward the conclusion that this evolutionary scenario has been possible through a complex interplay between adaptive mutations, often structurally destabilizing, and compensatory mutations. Our results unearth patterns of evolution that have likely optimized the Rubisco activity and uncover mutational dynamics useful in the molecular engineering of enzymatic activities. Reviewers This article was reviewed by Prof. Christian Blouin (nominated by Dr W Ford Doolittle), Dr Endre Barta (nominated by Dr Sandor Pongor), and Dr Nicolas Galtier. PMID:21639885

  6. A parallel adaptive finite element simplified spherical harmonics approximation solver for frequency domain fluorescence molecular imaging.

    PubMed

    Lu, Yujie; Zhu, Banghe; Shen, Haiou; Rasmussen, John C; Wang, Ge; Sevick-Muraca, Eva M

    2010-08-21

    Fluorescence molecular imaging/tomography may play an important future role in preclinical research and clinical diagnostics. Time- and frequency-domain fluorescence imaging can acquire more measurement information than the continuous wave (CW) counterpart, improving the image quality of fluorescence molecular tomography. Although diffusion approximation (DA) theory has been extensively applied in optical molecular imaging, high-order photon migration models need to be further investigated to match quantitation provided by nuclear imaging. In this paper, a frequency-domain parallel adaptive finite element solver is developed with simplified spherical harmonics (SP(N)) approximations. To fully evaluate the performance of the SP(N) approximations, a fast time-resolved tetrahedron-based Monte Carlo fluorescence simulator suitable for complex heterogeneous geometries is developed using a convolution strategy to realize the simulation of the fluorescence excitation and emission. The validation results show that high-order SP(N) can effectively correct the modeling errors of the diffusion equation, especially when the tissues have high absorption characteristics or when high modulation frequency measurements are used. Furthermore, the parallel adaptive mesh evolution strategy improves the modeling precision and the simulation speed significantly on a realistic digital mouse phantom. This solver is a promising platform for fluorescence molecular tomography using high-order approximations to the radiative transfer equation. PMID:20671350

  7. Molecular Specificity, Convergence and Constraint Shape Adaptive Evolution in Nutrient-Poor Environments

    PubMed Central

    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

  8. Ab initio molecular dynamics simulation of ethanol decomposition on platinum cluster at initial stage of carbon nanotube growth

    NASA Astrophysics Data System (ADS)

    Shibuta, Yasushi; Shimamura, Kohei; Arifin, Rizal; Shimojo, Fuyuki

    2015-09-01

    Ethanol decomposition on a platinum cluster is investigated by ab initio MD simulation. As the dehydrogenation proceeds, the Mulliken charge of the methylene carbon becomes a positive value, whereas that of the methyl carbon keeps a negative value. Especially, the Mulliken charge of the methylene carbon in CHxCO (x = 0, 1, 2 and 3) fragment molecules takes a large positive value. These fragment molecules correspond to those with Csbnd C bond that dissociated in the MD simulation. It suggests the large deviation in the Mulliken charge between methylene and methyl carbons is the key factor inducing the Csbnd C bond dissociation.

  9. A LOW-COST PROCESS FOR THE SYNTHESIS OF NANOSIZE YTTRIA-STABILIZED ZIRCONIA (YSZ) BY MOLECULAR DECOMPOSITION

    SciTech Connect

    Anil V. Virkar

    2004-05-06

    This report summarizes the results of work done during the performance period on this project, between October 1, 2002 and December 31, 2003, with a three month no-cost extension. The principal objective of this work was to develop a low-cost process for the synthesis of sinterable, fine powder of YSZ. The process is based on molecular decomposition (MD) wherein very fine particles of YSZ are formed by: (1) Mixing raw materials in a powder form, (2) Synthesizing compound containing YSZ and a fugitive constituent by a conventional process, and (3) Selectively leaching (decomposing) the fugitive constituent, thus leaving behind insoluble YSZ of a very fine particle size. While there are many possible compounds, which can be used as precursors, the one selected for the present work was Y-doped Na{sub 2}ZrO{sub 3}, where the fugitive constituent is Na{sub 2}O. It can be readily demonstrated that the potential cost of the MD process for the synthesis of very fine (or nanosize) YSZ is considerably lower than the commonly used processes, namely chemical co-precipitation and combustion synthesis. Based on the materials cost alone, for a 100 kg batch, the cost of YSZ made by chemical co-precipitation is >$50/kg, while that of the MD process should be <$10/kg. Significant progress was made during the performance period on this project. The highlights of the progress are given here in a bullet form. (1) From the two selected precursors listed in Phase I proposal, namely Y-doped BaZrO{sub 3} and Y-doped Na{sub 2}ZrO{sub 3}, selection of Y-doped Na{sub 2}ZrO{sub 3} was made for the synthesis of nanosize (or fine) YSZ. This was based on the potential cost of the precursor, the need to use only water for leaching, and the short time required for the process. (2) For the synthesis of calcia-stabilized zirconia (CSZ), which has the potential for use in place of YSZ in the anode of SOFC, Ca-doped Na{sub 2}ZrO{sub 3} was demonstrated as a suitable precursor. (3) Synthesis of Y

  10. 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

  11. The Molecular Basis of High-Altitude Adaptation in Deer Mice

    PubMed Central

    Storz, Jay F; Sabatino, Stephen J; Hoffmann, Federico G; Gering, Eben J; Moriyama, Hideaki; Ferrand, Nuno; Monteiro, Bruno; Nachman, Michael W

    2007-01-01

    Elucidating genetic mechanisms of adaptation is a goal of central importance in evolutionary biology, yet few empirical studies have succeeded in documenting causal links between molecular variation and organismal fitness in natural populations. Here we report a population genetic analysis of a two-locus α-globin polymorphism that underlies physiological adaptation to high-altitude hypoxia in natural populations of deer mice, Peromyscus maniculatus. This system provides a rare opportunity to examine the molecular underpinnings of fitness-related variation in protein function that can be related to a well-defined selection pressure. We surveyed DNA sequence variation in the duplicated α-globin genes of P. maniculatus from high- and low-altitude localities (i) to identify the specific mutations that may be responsible for the divergent fine-tuning of hemoglobin function and (ii) to test whether the genes exhibit the expected signature of diversifying selection between populations that inhabit different elevational zones. Results demonstrate that functionally distinct protein alleles are maintained as a long-term balanced polymorphism and that adaptive modifications of hemoglobin function are produced by the independent or joint effects of five amino acid mutations that modulate oxygen-binding affinity. PMID:17397259

  12. Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution.

    PubMed

    Galtier, Nicolas; Duret, Laurent

    2007-06-01

    The analysis of evolutionary rates is a popular approach to characterizing the effect of natural selection at the molecular level. Sequences contributing to species adaptation are expected to evolve faster than nonfunctional sequences because favourable mutations have a higher fixation probability than neutral ones. Such an accelerated rate of evolution might be due to factors other than natural selection, in particular GC-biased gene conversion. This is true of neutral sequences, but also of constrained sequences, which can be illustrated using the mouse Fxy gene. Several criteria can discriminate between the natural selection and biased gene conversion models. These criteria suggest that the recently reported human accelerated regions are most likely the result of biased gene conversion. We argue that these regions, far from contributing to human adaptation, might represent the Achilles' heel of our genome. PMID:17418442

  13. Elucidating the molecular architecture of adaptation via evolve and resequence experiments

    PubMed Central

    Long, Anthony; Liti, Gianni; Luptak, Andrej; Tenaillon, Olivier

    2016-01-01

    Evolve and resequence (E&R) experiments use experimental evolution to adapt populations to a novel environment, followed by next-generation sequencing. They enable molecular evolution to be monitored in real time at a genome-wide scale. We review the field of E&R experiments across diverse systems, ranging from simple non-living RNA to bacteria, yeast and complex multicellular Drosophila melanogaster. We explore how different evolutionary outcomes in these systems are largely consistent with common population genetics principles. Differences in outcomes across systems are largely explained by different: starting population sizes, levels of pre-existing genetic variation, recombination rates, and adaptive landscapes. We highlight emerging themes and inconsistencies that future experiments must address. PMID:26347030

  14. Molecular characterization of insulin from squamate reptiles reveals sequence diversity and possible adaptive evolution.

    PubMed

    Yamagishi, Genki; Yoshida, Ayaka; Kobayashi, Aya; Park, Min Kyun

    2016-01-01

    The Squamata are the most adaptive and prosperous group among ectothermic amniotes, reptiles, due to their species-richness and geographically wide habitat. Although the molecular mechanisms underlying their prosperity remain largely unknown, unique features have been reported from hormones that regulate energy metabolism. Insulin, a central anabolic hormone, is one such hormone, as its roles and effectiveness in regulation of blood glucose levels remain to be examined in squamates. In the present study, cDNAs coding for insulin were isolated from multiple species that represent various groups of squamates. The deduced amino acid sequences showed a high degree of divergence, with four lineages showing obviously higher number of amino acid substitutions than most of vertebrates, from teleosts to mammals. Among 18 sites presented to comprise the two receptor binding surfaces (one with 12 sites and the other with 6 sites), substitutions were observed in 13 sites. Among them was the substitution of HisB10, which results in the loss of the ability to hexamerize. Furthermore, three of these substitutions were reported to increase mitogenicity in human analogues. These substitutions were also reported from insulin of hystricomorph rodents and agnathan fishes, whose mitogenic potency have been shown to be increased. The estimated value of the non-synonymous-to-synonymous substitution ratio (ω) for the Squamata clade was larger than those of the other reptiles and aves. Even higher values were estimated for several lineages among squamates. These results, together with the regulatory mechanisms of digestion and nutrient assimilation in squamates, suggested a possible adaptive process through the molecular evolution of squamate INS. Further studies on the roles of insulin, in relation to the physiological and ecological traits of squamate species, will provide an insight into the molecular mechanisms that have led to the adaptivity and prosperity of squamates. PMID:26344944

  15. Adaptation.

    PubMed

    Broom, Donald M

    2006-01-01

    The term adaptation is used in biology in three different ways. It may refer to changes which occur at the cell and organ level, or at the individual level, or at the level of gene action and evolutionary processes. Adaptation by cells, especially nerve cells helps in: communication within the body, the distinguishing of stimuli, the avoidance of overload and the conservation of energy. The time course and complexity of these mechanisms varies. Adaptive characters of organisms, including adaptive behaviours, increase fitness so this adaptation is evolutionary. The major part of this paper concerns adaptation by individuals and its relationships to welfare. In complex animals, feed forward control is widely used. Individuals predict problems and adapt by acting before the environmental effect is substantial. Much of adaptation involves brain control and animals have a set of needs, located in the brain and acting largely via motivational mechanisms, to regulate life. Needs may be for resources but are also for actions and stimuli which are part of the mechanism which has evolved to obtain the resources. Hence pigs do not just need food but need to be able to carry out actions like rooting in earth or manipulating materials which are part of foraging behaviour. The welfare of an individual is its state as regards its attempts to cope with its environment. This state includes various adaptive mechanisms including feelings and those which cope with disease. The part of welfare which is concerned with coping with pathology is health. Disease, which implies some significant effect of pathology, always results in poor welfare. Welfare varies over a range from very good, when adaptation is effective and there are feelings of pleasure or contentment, to very poor. A key point concerning the concept of individual adaptation in relation to welfare is that welfare may be good or poor while adaptation is occurring. Some adaptation is very easy and energetically cheap and

  16. The molecular symmetry adapted non - adiabatic coupling terms and diabatic Hamiltonian matrix

    NASA Astrophysics Data System (ADS)

    Mukherjee, Saikat; Bandyopadhyay, Sudip; Paul, Amit Kumar; Adhikari, Satrajit

    2013-04-01

    We calculate the adiabatic Potential Energy Surfaces (PESs) and the Non - Adiabatic Coupling Terms (NACTs) for the excited electronic states (22 E' and 12 A'1) of Na3 cluster at the MRCI level by using ab initio quantum chemistry package (MOLPRO), where the NACTs are adapted with Molecular Symmetry (MS) by employing appropriate Irreducible Representations (IREPs). Such terms are incorporated into the Adiabatic to Diabatic Transformation (ADT) equations to obtain the ADT angles to construct the continuous, single - valued, symmetric and smooth 3 × 3 diabatic Hamiltonian matrix.

  17. 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.

  18. Grand-Canonical Adaptive Resolution Centroid Molecular Dynamics: Implementation and application

    NASA Astrophysics Data System (ADS)

    Agarwal, Animesh; Delle Site, Luigi

    2016-09-01

    We have implemented the Centroid Molecular Dynamics scheme (CMD) into the Grand Canonical-like version of the Adaptive Resolution Simulation Molecular Dynamics (GC-AdResS) method. We have tested the implementation on two different systems, liquid parahydrogen at extreme thermodynamic conditions and liquid water at ambient conditions; the reproduction of structural as well as dynamical results of reference systems are highly satisfactory. The capability of performing GC-AdResS CMD simulations allows for the treatment of a system characterized by some quantum features and open boundaries. This latter characteristic not only is of computational convenience, allowing for equivalent results of much larger and computationally more expensive systems, but also suggests a tool of analysis so far not explored, that is the unambiguous identification of the essential degrees of freedom required for a given property.

  19. Effects of molecular complexity and reservoir conditions on the discharge coefficient of adapted planar nozzles

    NASA Astrophysics Data System (ADS)

    Guardone, Alberto

    2015-09-01

    The transonic flow at throat section of a convergent-divergent nozzle is studied in adapted conditions to assess the influence of the fluid molecular complexity and total thermodynamic state on the discharge coefficient. The standard Sauer method is applied to solve the transonic perturbation potential equation in the vicinity of the nozzle throat. An analytic expression is derived that allows one to compute the discharge coefficient in terms of the nozzle curvature at the throat section and of the value of the fundamental derivative of gasdynamics at sonic conditions, which depends on the fluid molecular complexity and on the thermodynamic state in the reservoir. A linear dependence of the discharge coefficient on the sonic value of the fundamental derivative of gasdynamics is exposed.

  20. An energy decomposition analysis for intermolecular interactions from an absolutely localized molecular orbital reference at the coupled-cluster singles and doubles level

    SciTech Connect

    Azar, R. Julian; Head-Gordon, Martin

    2012-01-14

    We propose a wave function-based method for the decomposition of intermolecular interaction energies into chemically-intuitive components, isolating both mean-field- and explicit correlation-level contributions. We begin by solving the locally-projected self-consistent field for molecular interactions equations for a molecular complex, obtaining an intramolecularly polarized reference of self-consistently optimized, absolutely-localized molecular orbitals (ALMOs), determined with the constraint that each fragment MO be composed only of atomic basis functions belonging to its own fragment. As explicit inter-electronic correlation is integral to an accurate description of weak forces underlying intermolecular interaction potentials, namely, coordinated fluctuations in weakly interacting electronic densities, we add dynamical correlation to the ALMO polarized reference at the coupled-cluster singles and doubles level, accounting for explicit dispersion and charge-transfer effects, which map naturally onto the cluster operator. We demonstrate the stability of energy components with basis set extension, follow the hydrogen bond-breaking coordinate in the C{sub s}-symmetry water dimer, decompose the interaction energies of dispersion-bound rare gas dimers and other van der Waals complexes, and examine charge transfer-dominated donor-acceptor interactions in borane adducts. We compare our results with high-level calculations and experiment when possible.

  1. 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

  2. Ozone decomposition.

    PubMed

    Batakliev, Todor; Georgiev, Vladimir; Anachkov, Metody; Rakovsky, Slavcho; Zaikov, Gennadi E

    2014-06-01

    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

  3. Rich diversity and potency of skin antioxidant peptides revealed a novel molecular basis for high-altitude adaptation of amphibians

    PubMed Central

    Yang, Xinwang; Wang, Ying; Zhang, Yue; Lee, Wen-Hui; Zhang, Yun

    2016-01-01

    Elucidating the mechanisms of high-altitude adaptation is an important research area in modern biology. To date, however, knowledge has been limited to the genetic mechanisms of adaptation to the lower oxygen and temperature levels prevalent at high altitudes, with adaptation to UV radiation largely neglected. Furthermore, few proteomic or peptidomic analyses of these factors have been performed. In this study, the molecular adaptation of high-altitude Odorrana andersonii and cavernicolous O. wuchuanensis to elevated UV radiation was investigated. Compared with O. wuchuanensis, O. andersonii exhibited greater diversity and free radical scavenging potentiality of skin antioxidant peptides to cope with UV radiation. This implied that O. andersonii evolved a much more complicated and powerful skin antioxidant peptide system to survive high-altitude UV levels. Our results provided valuable peptidomic clues for understanding the novel molecular basis for adaptation to high elevation habitats. PMID:26813022

  4. 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. PMID:25923055

  5. Molecular Aspects of Plant Adaptation to Life in the Chernobyl Zone1[w

    PubMed Central

    Kovalchuk, Igor; Abramov, Vladimir; Pogribny, Igor; Kovalchuk, Olga

    2004-01-01

    With each passing year since the Chernobyl accident of 1986, more questions arise about the potential for organisms to adapt to radiation exposure. Often this is thought to be attributed to somatic and germline mutation rates in various organisms. We analyzed the adaptability of native Arabidopsis plants collected from areas with different levels of contamination around the Chernobyl nuclear power plant from 1986 to 1992. Notably, progeny of Chernobyl plants resisted higher concentrations of the mutagens Rose Bengal and methyl methane sulfonate. We analyzed the possible molecular mechanisms of their resistance to mutagens and found a more than 10-fold lower frequency of extrachromosomal homologous recombination, significant differences in the expression of radical scavenging (CAT1 and FSD3) and DNA-repair (RAD1 and RAD51-like) genes upon exposure to mutagens (Rose Bengal and x-rays), and a higher level of global genome methylation. This data suggests that adaptation to ionizing radiation is a complex process involving epigenetic regulation of gene expression and genome stabilization that improves plants' resistance to environmental mutagens. PMID:15133154

  6. Uncovering the differential molecular basis of adaptive diversity in three Echinochloa leaf transcriptomes.

    PubMed

    Nah, Gyoungju; Im, Ji-Hoon; Kim, Jin-Won; Park, Hae-Rim; Yook, Min-Jung; Yang, Tae-Jin; Fischer, Albert J; Kim, Do-Soon

    2015-01-01

    Echinochloa is a major weed that grows almost everywhere in farmed land. This high prevalence results from its high adaptability to various water conditions, including upland and paddy fields, and its ability to grow in a wide range of climates, ranging from tropical to temperate regions. Three Echinochloa crus-galli accessions (EC-SNU1, EC-SNU2, and EC-SNU3) collected in Korea have shown diversity in their responses to flooding, with EC-SNU1 exhibiting the greatest growth among three accessions. In the search for molecular components underlying adaptive diversity among the three Echinochloa crus-galli accessions, we performed de novo assembly of leaf transcriptomes and investigated the pattern of differentially expressed genes (DEGs). Although the overall composition of the three leaf transcriptomes was well-conserved, the gene expression patterns of particular gene ontology (GO) categories were notably different among the three accessions. Under non-submergence growing conditions, five protein categories (serine/threonine kinase, leucine-rich repeat kinase, signaling-related, glycoprotein, and glycosidase) were significantly (FDR, q < 0.05) enriched in up-regulated DEGs from EC-SNU1. These up-regulated DEGs include major components of signal transduction pathways, such as receptor-like kinase (RLK) and calcium-dependent protein kinase (CDPK) genes, as well as previously known abiotic stress-responsive genes. Our results therefore suggest that diversified gene expression regulation of upstream signaling components conferred the molecular basis of adaptive diversity in Echinochloa crus-galli. PMID:26266806

  7. Uncovering the Differential Molecular Basis of Adaptive Diversity in Three Echinochloa Leaf Transcriptomes

    PubMed Central

    Nah, Gyoungju; Im, Ji-Hoon; Kim, Jin-Won; Park, Hae-Rim; Yook, Min-Jung; Yang, Tae-Jin; Fischer, Albert J.; Kim, Do-Soon

    2015-01-01

    Echinochloa is a major weed that grows almost everywhere in farmed land. This high prevalence results from its high adaptability to various water conditions, including upland and paddy fields, and its ability to grow in a wide range of climates, ranging from tropical to temperate regions. Three Echinochloa crus-galli accessions (EC-SNU1, EC-SNU2, and EC-SNU3) collected in Korea have shown diversity in their responses to flooding, with EC-SNU1 exhibiting the greatest growth among three accessions. In the search for molecular components underlying adaptive diversity among the three Echinochloa crus-galli accessions, we performed de novo assembly of leaf transcriptomes and investigated the pattern of differentially expressed genes (DEGs). Although the overall composition of the three leaf transcriptomes was well-conserved, the gene expression patterns of particular gene ontology (GO) categories were notably different among the three accessions. Under non-submergence growing conditions, five protein categories (serine/threonine kinase, leucine-rich repeat kinase, signaling-related, glycoprotein, and glycosidase) were significantly (FDR, q < 0.05) enriched in up-regulated DEGs from EC-SNU1. These up-regulated DEGs include major components of signal transduction pathways, such as receptor-like kinase (RLK) and calcium-dependent protein kinase (CDPK) genes, as well as previously known abiotic stress-responsive genes. Our results therefore suggest that diversified gene expression regulation of upstream signaling components conferred the molecular basis of adaptive diversity in Echinochloa crus-galli. PMID:26266806

  8. 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

  9. Molecular adaptation mechanisms employed by ethanologenic bacteria in response to lignocellulose-derived inhibitory compounds.

    PubMed

    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

  10. 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.

  11. Adaptive GPU-accelerated force calculation for interactive rigid molecular docking using haptics.

    PubMed

    Iakovou, Georgios; Hayward, Steven; Laycock, Stephen D

    2015-09-01

    Molecular docking systems model and simulate in silico the interactions of intermolecular binding. Haptics-assisted docking enables the user to interact with the simulation via their sense of touch but a stringent time constraint on the computation of forces is imposed due to the sensitivity of the human haptic system. To simulate high fidelity smooth and stable feedback the haptic feedback loop should run at rates of 500Hz to 1kHz. We present an adaptive force calculation approach that can be executed in parallel on a wide range of Graphics Processing Units (GPUs) for interactive haptics-assisted docking with wider applicability to molecular simulations. Prior to the interactive session either a regular grid or an octree is selected according to the available GPU memory to determine the set of interatomic interactions within a cutoff distance. The total force is then calculated from this set. The approach can achieve force updates in less than 2ms for molecular structures comprising hundreds of thousands of atoms each, with performance improvements of up to 90 times the speed of current CPU-based force calculation approaches used in interactive docking. Furthermore, it overcomes several computational limitations of previous approaches such as pre-computed force grids, and could potentially be used to model receptor flexibility at haptic refresh rates. PMID:26186491

  12. Adapt

    NASA Astrophysics Data System (ADS)

    Bargatze, L. F.

    2015-12-01

    Active Data Archive Product Tracking (ADAPT) is a collection of software routines that permits one to generate XML metadata files to describe and register data products in support of the NASA Heliophysics Virtual Observatory VxO effort. ADAPT is also a philosophy. The ADAPT concept is to use any and all available metadata associated with scientific data to produce XML metadata descriptions in a consistent, uniform, and organized fashion to provide blanket access to the full complement of data stored on a targeted data server. In this poster, we present an application of ADAPT to describe all of the data products that are stored by using the Common Data File (CDF) format served out by the CDAWEB and SPDF data servers hosted at the NASA Goddard Space Flight Center. These data servers are the primary repositories for NASA Heliophysics data. For this purpose, the ADAPT routines have been used to generate data resource descriptions by using an XML schema named Space Physics Archive, Search, and Extract (SPASE). SPASE is the designated standard for documenting Heliophysics data products, as adopted by the Heliophysics Data and Model Consortium. The set of SPASE XML resource descriptions produced by ADAPT includes high-level descriptions of numerical data products, display data products, or catalogs and also includes low-level "Granule" descriptions. A SPASE Granule is effectively a universal access metadata resource; a Granule associates an individual data file (e.g. a CDF file) with a "parent" high-level data resource description, assigns a resource identifier to the file, and lists the corresponding assess URL(s). The CDAWEB and SPDF file systems were queried to provide the input required by the ADAPT software to create an initial set of SPASE metadata resource descriptions. Then, the CDAWEB and SPDF data repositories were queried subsequently on a nightly basis and the CDF file lists were checked for any changes such as the occurrence of new, modified, or deleted

  13. Ab initio molecular orbital investigation of the unimolecular decomposition of CH[sub 3]SiH[sub 2][sup +

    SciTech Connect

    Gordon, M.S.; Pederson, L.A. Ames Research Lab., IA ); Bakhtiar, R.; Jacobson, D.B. )

    1995-01-05

    The potential energy surface for the decomposition of CH[sub 3]SiH[sub 2][sup +] was studied by ab initio electronic structure theory. At the MP2/6-31G(d,p) level of theory, CH[sub 3]SiH[sub 2][sup +] is the only minimum energy structure on the SiCH[sub 3][sup +] potential energy surface. Lower levels of theory reported that [sup +]CH[sub 2]SiH[sub 3] was also a local minimum, about 40 kcal/mol higher in energy with only a small (ca. 1-2 kcal/mol) barrier for conversion back to CH[sub 3]SiH[sub 2][sup +]. However, at higher levels of theory, the C[sub s] structure of [sup +]CH[sub 2]SiH[sub 3] has an imaginary frequency, indicating that it is a saddle point rather than a local minimum on the potential energy surface. The 0 K reaction enthalpies for 1,1-dehydrogenation from silicon, 1,2-dehydrogenation, 1,1-dehydrogenation from carbon, and demethanation were calculated to be 30.2, 69.1, 107.3, and 45.3 kcal/mol, respectively. Activation energies (0 K) were calculated at the MP4/6-311++G(2df,2pd) level of theory with the classical barriers subsequently adjusted for zero-point vibrational energies. The 0 K activation energies for 1,1-dehydrogenation from silicon, 1,2-dehydrogenation, and demethanation are predicted to be 66.6, 72.7, and 73.0 kcal/mol, respectively. 52 refs., 5 figs., 2 tabs.

  14. Molecular mechanisms of Saccharomyces cerevisiae stress adaptation and programmed cell death in response to acetic acid

    PubMed Central

    Giannattasio, Sergio; Guaragnella, Nicoletta; Ždralević, Maša; Marra, Ersilia

    2013-01-01

    Beyond its classical biotechnological applications such as food and beverage production or as a cell factory, the yeast Saccharomyces cerevisiae is a valuable model organism to study fundamental mechanisms of cell response to stressful environmental changes. Acetic acid is a physiological product of yeast fermentation and it is a well-known food preservative due to its antimicrobial action. Acetic acid has recently been shown to cause yeast cell death and aging. Here we shall focus on the molecular mechanisms of S. cerevisiae stress adaptation and programmed cell death in response to acetic acid. We shall elaborate on the intracellular signaling pathways involved in the cross-talk of pro-survival and pro-death pathways underlying the importance of understanding fundamental aspects of yeast cell homeostasis to improve the performance of a given yeast strain in biotechnological applications. PMID:23430312

  15. Molecular mechanisms of Saccharomyces cerevisiae stress adaptation and programmed cell death in response to acetic acid.

    PubMed

    Giannattasio, Sergio; Guaragnella, Nicoletta; Zdralević, Maša; Marra, Ersilia

    2013-01-01

    Beyond its classical biotechnological applications such as food and beverage production or as a cell factory, the yeast Saccharomyces cerevisiae is a valuable model organism to study fundamental mechanisms of cell response to stressful environmental changes. Acetic acid is a physiological product of yeast fermentation and it is a well-known food preservative due to its antimicrobial action. Acetic acid has recently been shown to cause yeast cell death and aging. Here we shall focus on the molecular mechanisms of S. cerevisiae stress adaptation and programmed cell death in response to acetic acid. We shall elaborate on the intracellular signaling pathways involved in the cross-talk of pro-survival and pro-death pathways underlying the importance of understanding fundamental aspects of yeast cell homeostasis to improve the performance of a given yeast strain in biotechnological applications. PMID:23430312

  16. 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

  17. Molecular views of damaged DNA: Adaptation of the Program DUPLEX to parallel architectures

    SciTech Connect

    Hingerty, B.E.; Crawford, O.H.; Broyde, S.; Wagner, R.A.

    1994-09-01

    The nucleic acids molecular mechanics program DUPLEX has been designed with useful features for surveying the potential energy surface of polynucleotides, especially ones that are modified by polycyclic aromatic carcinogens. The program features helpful strategies for addressing the multiple minimum problem: (1) the reduced variable domain of torsion angle space; (2) search strategies that emphasize large scale searches for smaller subunits, followed by building to larger units by a variety of strategies; (3) the use of penalty functions to aid the minimizer in locating selected structural types in first stage minimizations; penalty functions are released in terminal minimizations to yield final unrestrained minimum energy conformations. Predictive capability is illustrated by DNA modified by activated benzo[a]pyrenes. The first stage of adaptation to parallel computers is described.

  18. Molecular Assortment of Lens Species with Different Adaptations to Drought Conditions Using SSR Markers.

    PubMed

    Singh, Dharmendra; Singh, Chandan Kumar; Tomar, Ram Sewak Singh; Taunk, Jyoti; Singh, Ranjeet; Maurya, Sadhana; Chaturvedi, Ashish Kumar; Pal, Madan; Singh, Rajendra; Dubey, Sarawan Kumar

    2016-01-01

    The success of drought tolerance breeding programs can be enhanced through molecular assortment of germplasm. This study was designed to characterize molecular diversity within and between Lens species with different adaptations to drought stress conditions using SSR markers. Drought stress was applied at seedling stage to study the effects on morpho-physiological traits under controlled condition, where tolerant cultivars and wilds showed 12.8-27.6% and 9.5-23.2% reduction in seed yield per plant respectively. When juxtaposed to field conditions, the tolerant cultivars (PDL-1 and PDL-2) and wild (ILWL-314 and ILWL-436) accessions showed 10.5-26.5% and 7.5%-15.6% reduction in seed yield per plant, respectively under rain-fed conditions. The reductions in seed yield in the two tolerant cultivars and wilds under severe drought condition were 48-49% and 30.5-45.3% respectively. A set of 258 alleles were identified among 278 genotypes using 35 SSR markers. Genetic diversity and polymorphism information contents varied between 0.321-0.854 and 0.299-0.836, with mean value of 0.682 and 0.643, respectively. All the genotypes were clustered into 11 groups based on SSR markers. Tolerant genotypes were grouped in cluster 6 while sensitive ones were mainly grouped into cluster 7. Wild accessions were separated from cultivars on the basis of both population structure and cluster analysis. Cluster analysis has further grouped the wild accessions on the basis of species and sub-species into 5 clusters. Physiological and morphological characters under drought stress were significantly (P = 0.05) different among microsatellite clusters. These findings suggest that drought adaptation is variable among wild and cultivated genotypes. Also, genotypes from contrasting clusters can be selected for hybridization which could help in evolution of better segregants for improving drought tolerance in lentil. PMID:26808306

  19. Molecular Assortment of Lens Species with Different Adaptations to Drought Conditions Using SSR Markers

    PubMed Central

    Singh, Dharmendra; Singh, Chandan Kumar; Tomar, Ram Sewak Singh; Taunk, Jyoti; Singh, Ranjeet; Maurya, Sadhana; Chaturvedi, Ashish Kumar; Pal, Madan; Singh, Rajendra; Dubey, Sarawan Kumar

    2016-01-01

    The success of drought tolerance breeding programs can be enhanced through molecular assortment of germplasm. This study was designed to characterize molecular diversity within and between Lens species with different adaptations to drought stress conditions using SSR markers. Drought stress was applied at seedling stage to study the effects on morpho-physiological traits under controlled condition, where tolerant cultivars and wilds showed 12.8–27.6% and 9.5–23.2% reduction in seed yield per plant respectively. When juxtaposed to field conditions, the tolerant cultivars (PDL-1 and PDL-2) and wild (ILWL-314 and ILWL-436) accessions showed 10.5–26.5% and 7.5%–15.6% reduction in seed yield per plant, respectively under rain-fed conditions. The reductions in seed yield in the two tolerant cultivars and wilds under severe drought condition were 48–49% and 30.5–45.3% respectively. A set of 258 alleles were identified among 278 genotypes using 35 SSR markers. Genetic diversity and polymorphism information contents varied between 0.321–0.854 and 0.299–0.836, with mean value of 0.682 and 0.643, respectively. All the genotypes were clustered into 11 groups based on SSR markers. Tolerant genotypes were grouped in cluster 6 while sensitive ones were mainly grouped into cluster 7. Wild accessions were separated from cultivars on the basis of both population structure and cluster analysis. Cluster analysis has further grouped the wild accessions on the basis of species and sub-species into 5 clusters. Physiological and morphological characters under drought stress were significantly (P = 0.05) different among microsatellite clusters. These findings suggest that drought adaptation is variable among wild and cultivated genotypes. Also, genotypes from contrasting clusters can be selected for hybridization which could help in evolution of better segregants for improving drought tolerance in lentil. PMID:26808306

  20. Woodland Decomposition.

    ERIC Educational Resources Information Center

    Napier, J.

    1988-01-01

    Outlines the role of the main organisms involved in woodland decomposition and discusses some of the variables affecting the rate of nutrient cycling. Suggests practical work that may be of value to high school students either as standard practice or long-term projects. (CW)

  1. Unfolding Thermodynamics of Cysteine-Rich Proteins and Molecular Thermal-Adaptation of Marine Ciliates

    PubMed Central

    Cazzolli, Giorgia; Škrbić, Tatjana; Guella, Graziano; Faccioli, Pietro

    2013-01-01

    Euplotes nobilii and Euplotes raikovi are phylogenetically closely allied species of marine ciliates, living in polar and temperate waters, respectively. Their evolutional relation and the sharply different temperatures of their natural environments make them ideal organisms to investigate thermal-adaptation. We perform a comparative study of the thermal unfolding of disulfide-rich protein pheromones produced by these ciliates. Recent circular dichroism (CD) measurements have shown that the two psychrophilic (E. nobilii) and mesophilic (E. raikovi) protein families are characterized by very different melting temperatures, despite their close structural homology. The enhanced thermal stability of the E. raikovi pheromones is realized notwithstanding the fact that these proteins form, as a rule, a smaller number of disulfide bonds. We perform Monte Carlo (MC) simulations in a structure-based coarse-grained (CG) model to show that the higher stability of the E. raikovi pheromones is due to the lower locality of the disulfide bonds, which yields a lower entropy increase in the unfolding process. Our study suggests that the higher stability of the mesophilic E. raikovi phermones is not mainly due to the presence of a strongly hydrophobic core, as it was proposed in the literature. In addition, we argue that the molecular adaptation of these ciliates may have occurred from cold to warm, and not from warm to cold. To provide a testable prediction, we identify a point-mutation of an E. nobilii pheromone that should lead to an unfolding temperature typical of that of E. raikovi pheromones. PMID:24970199

  2. Searching for the dust/molecular torus in a typical AGN using adaptive optics

    NASA Astrophysics Data System (ADS)

    Marco, O.; Alloin, D.

    Adaptive optics systems are now routinely operated on several 4 meter class telescopes, allowing to achieve angular resolutions down to 70 msec in the near-infrared. Although these systems have excellent performances, their use for exploring the physics and structure of AGN is still limited for the following reasons: the limiting magnitude of the wavefront sensor is too high, the sensitivity of infrared detectors does not give access to medium/high spectral solution spectroscopy and the angular resolution achieved does not always fit the apparent size of the physical components responsible for emission features close to the central engine. The new generation of 8-10m class telescopes bring improvements in this matter. However, some interesting results have been obtained so far with Adonis, the ESO La Silla adaptive optics system on the 3.60 meter telescope, in the investigation of AGN structure. In particular, a prominent structure has been detected in the central arcsec core of NGC 1068, which might feature the dusty/molecular torus expected on theoretical grounds.

  3. Searching for the Dust/Molecular Torus in a Typical AGN using Adaptive Optics

    NASA Astrophysics Data System (ADS)

    Marco, O.; Alloin, D.

    Adaptive Optics systems are now routinely operated on several 4 meter class telescopes, allowing to achieve angular resolutions down to 70 msec in the near-infrared. Although these systems have excellent performances, their use for exploring the physics and structure of AGN is still limited for the following reasons: the limiting magnitude of the wavefront sensor is too high, the sensitivity of infrared detectors does not give access to medium/high spectral resolution spectroscopy and the angular resolution achieved does not always fit the apparent size of the physical components responsible for emission features close to the central engine. The new generation of 8-10 m class telescopes bring improvements in this matter. However, some interesting results have been obtained so far with Adonis, the ESO La Silla adaptive optics system on the 3.60 meter telescope, in the investigation of AGN structure. In particular, a prominent structure has been detected in the central arcs! ec core of NGC1068, which might feature the dusty/molecular torus expected on theoretical grounds.

  4. Molecular individuality and adaptation of the tick Rhipicephalus appendiculatus in changed feeding environments.

    PubMed

    Wang, H; Kaufman, W R; Cui, W W; Nuttall, P A

    2001-12-01

    The tick Rhipicephalus appendiculatus Neumann (Acari: Ixodidae) naturally infests many host species. However, the mechanisms that enable it to feed on such a wide range of hosts are unclear. One possibility is that a tick population maintains molecular (genotypic and/or phenotypic) diversity among individuals such that individuals vary in their competency in taking bloodmeals under different feeding conditions. As a first step in testing this hypothesis, we showed that the polymorphism of salivary gland proteins, previously demonstrated in unfed ticks, was maintained during feeding on guinea-pigs. We then compared feeding performance under standard laboratory rearing conditions: one instar (adults or nymphs) feeding on guinea-pigs, with three changed conditions: (1) two instars (adults and nymphs) feeding together on guinea-pigs; (2) one instar (adults or nymphs) feeding on hamsters; and (3) two instars (adults and nymphs) feeding together on hamsters. The mean engorged weight of adult females was significantly reduced under all changed conditions, indicating that most of the adult individuals were significantly challenged by the changed conditions. However, some individuals achieved successful engorgement, indicating competence to the changed condition, and demonstrating variation in adaptive ability among individuals. Engorged females produced egg masses positively correlated to the engorged weights. More interestingly, the correlation coefficient (R) increased when feeding condition was changed. This may lead to more efficient selection for population adaptation under the changed conditions. As the feeding success of ixodid ticks depends on the efficiency of the cocktail of immunomodulatory saliva, the relevance of the polymorphism of salivary gland proteins and host adaptation is discussed. PMID:11776459

  5. 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. PMID:10993725

  6. Dolphin genome provides evidence for adaptive evolution of nervous system genes and a molecular rate slowdown

    PubMed Central

    McGowen, Michael R.; Grossman, Lawrence I.; Wildman, Derek E.

    2012-01-01

    Cetaceans (dolphins and whales) have undergone a radical transformation from the original mammalian bodyplan. In addition, some cetaceans have evolved large brains and complex cognitive capacities. We compared approximately 10 000 protein-coding genes culled from the bottlenose dolphin genome with nine other genomes to reveal molecular correlates of the remarkable phenotypic features of these aquatic mammals. Evolutionary analyses demonstrated that the overall synonymous substitution rate in dolphins has slowed compared with other studied mammals, and is within the range of primates and elephants. We also discovered 228 genes potentially under positive selection (dN/dS > 1) in the dolphin lineage. Twenty-seven of these genes are associated with the nervous system, including those related to human intellectual disabilities, synaptic plasticity and sleep. In addition, genes expressed in the mitochondrion have a significantly higher mean dN/dS ratio in the dolphin lineage than others examined, indicating evolution in energy metabolism. We encountered selection in other genes potentially related to cetacean adaptations such as glucose and lipid metabolism, dermal and lung development, and the cardiovascular system. This study underlines the parallel molecular trajectory of cetaceans with other mammalian groups possessing large brains. PMID:22740643

  7. Adaptive steered molecular dynamics: Validation of the selection criterion and benchmarking energetics in vacuum

    NASA Astrophysics Data System (ADS)

    Ozer, Gungor; Quirk, Stephen; Hernandez, Rigoberto

    2012-06-01

    The potential of mean force (PMF) for stretching decaalanine in vacuum was determined earlier by Park and Schulten [J. Chem. Phys. 120, 5946 (2004)] in a landmark article demonstrating the efficacy of combining steered molecular dynamics and Jarzynski's nonequilibrium relation. In this study, the recently developed adaptive steered molecular dynamics (ASMD) algorithm [G. Ozer, E. Valeev, S. Quirk, and R. Hernandez, J. Chem. Theory Comput. 6, 3026 (2010)] is used to reproduce the PMF of the unraveling of decaalanine in vacuum by averaging over fewer nonequilibrium trajectories. The efficiency and accuracy of the method are demonstrated through the agreement with the earlier work by Park and Schulten, a series of convergence checks compared to alternate SMD pulling strategies, and an analytical proof. The nonequilibrium trajectories obtained through ASMD have also been used to analyze the intrapeptide hydrogen bonds along the stretching coordinate. As the decaalanine helix is stretched, the initially stabilized i → i + 4 contacts (α-helix) is replaced by i → i + 3 contacts (310-helix). No significant formation of i → i + 5 hydrogen bonds (π-helix) is observed.

  8. Evolution of the fruit endocarp: molecular mechanisms underlying adaptations in seed protection and dispersal strategies

    PubMed Central

    Dardick, Chris; Callahan, Ann M.

    2014-01-01

    Plant evolution is largely driven by adaptations in seed protection and dispersal strategies that allow diversification into new niches. This is evident by the tremendous variation in flowering and fruiting structures present both across and within different plant lineages. Within a single plant family a staggering variety of fruit types can be found such as fleshy fruits including berries, pomes, and drupes and dry fruit structures like achenes, capsules, and follicles. What are the evolutionary mechanisms that enable such dramatic shifts to occur in a relatively short period of time? This remains a fundamental question of plant biology today. On the surface it seems that these extreme differences in form and function must be the consequence of very different developmental programs that require unique sets of genes. Yet as we begin to decipher the molecular and genetic basis underlying fruit form it is becoming apparent that simple genetic changes in key developmental regulatory genes can have profound anatomical effects. In this review, we discuss recent advances in understanding the molecular mechanisms of fruit endocarp tissue differentiation that have contributed to species diversification within three plant lineages. PMID:25009543

  9. 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

  10. 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. PMID:26473040

  11. Effects of temperature on anaerobic decomposition of high-molecular weight organic matter under sulfate-reducing conditions

    NASA Astrophysics Data System (ADS)

    Matsui, Takato; Kojima, Hisaya; Fukui, Manabu

    2013-03-01

    Most sedimentary mineralization occurs along coasts under anaerobic conditions. In the absence of oxygen, high-molecular weight organic matter in marine sediments is gradually decomposed by hydrolysis, fermentation and sulfate reduction. Because of the different responses of the respective steps to temperature, degradation may be specifically slowed or stopped in certain step. To evaluate the effect of temperature on cellobiose degradation, culture experiments were performed at six different temperatures (3 °C, 8 °C, 13 °C, 18 °C, 23 °C, and 28 °C) under sulfate-reducing conditions. This study measured the concentrations of sulfide, dissolved organic carbon (DOC), and organic acids during that degradation. Degradation patterns were divided into three temperature groups: 3 °C, 8/13 °C, and 18/23/28 °C. The decrease in DOC proceeded in two steps, except at 3 °C. The length of the stagnant phase separating these two steps differed greatly between temperatures of 8/13 °C and 18/23/28 °C. In the first step, organic carbon was consumed by hydrolysis, fermentation and sulfate reduction. In the second step, acetate accumulated during the first step was oxidized by sulfate reduction. Bacterial communities in the cultures were analyzed by denaturing gradient gel electrophoresis (DGGE); the major differences among the three temperature groups were attributed to shifts in acetate-using sulfate reducers of the genus Desulfobacter. This suggests that temperature characteristics of dominant acetate oxidizers are important factors in determining the response of carbon flow in coastal marine sediments in relation to the changes in temperature.

  12. Tracking adaptive evolution in the structure, function and molecular phylogeny of haemoglobin in non-Antarctic notothenioid fish species

    NASA Astrophysics Data System (ADS)

    Verde, Cinzia; Parisi, Elio; di Prisco, Guido

    2006-04-01

    With the notable exception of Antarctic icefishes, haemoglobin (Hb) is present in all vertebrates. In polar fish, Hb evolution has included adaptations with implications at the biochemical, physiological and molecular levels. Cold adaptation has been shown to be also linked to small changes in primary structure and post-translational modifications in proteins, including hydrophobic remodelling and increased flexibility. A wealth of knowledge is available on the oxygen-transport system of fish inhabiting Antarctic waters, but very little is known on the structure and function of Hb of non-Antarctic notothenioid fishes. The comparison of the biochemical and physiological adaptations between cold-adapted and non-cold-adapted species is a powerful tool to understand whether (and to what extent) extreme environments require specific adaptations or simply select for phenotypically different life styles. This study focuses on structure, function and molecular phylogeny of Hb in Antarctic and non-Antarctic notothenioid fishes. The rationale is to use the primary structure of Hb as tool of choice to gain insight into the pathways of the evolution history of α and β globins of notothenioids and also as a basis for reconstructing the phylogenetic relationships among Antarctic and non-Antarctic species.

  13. Improved Discovery of Molecular Interactions in Genome-Scale Data with Adaptive Model-Based Normalization

    PubMed Central

    Brown, Patrick O.

    2013-01-01

    Background High throughput molecular-interaction studies using immunoprecipitations (IP) or affinity purifications are powerful and widely used in biology research. One of many important applications of this method is to identify the set of RNAs that interact with a particular RNA-binding protein (RBP). Here, the unique statistical challenge presented is to delineate a specific set of RNAs that are enriched in one sample relative to another, typically a specific IP compared to a non-specific control to model background. The choice of normalization procedure critically impacts the number of RNAs that will be identified as interacting with an RBP at a given significance threshold – yet existing normalization methods make assumptions that are often fundamentally inaccurate when applied to IP enrichment data. Methods In this paper, we present a new normalization methodology that is specifically designed for identifying enriched RNA or DNA sequences in an IP. The normalization (called adaptive or AD normalization) uses a basic model of the IP experiment and is not a variant of mean, quantile, or other methodology previously proposed. The approach is evaluated statistically and tested with simulated and empirical data. Results and Conclusions The adaptive (AD) normalization method results in a greatly increased range in the number of enriched RNAs identified, fewer false positives, and overall better concordance with independent biological evidence, for the RBPs we analyzed, compared to median normalization. The approach is also applicable to the study of pairwise RNA, DNA and protein interactions such as the analysis of transcription factors via chromatin immunoprecipitation (ChIP) or any other experiments where samples from two conditions, one of which contains an enriched subset of the other, are studied. PMID:23349766

  14. Molecular Mechanisms Mediating the Adaptive Regulation of Intestinal Riboflavin Uptake Process

    PubMed Central

    Subramanian, Veedamali S.; Ghosal, Abhisek; Kapadia, Rubina; Nabokina, Svetlana M.; Said, Hamid M.

    2015-01-01

    The intestinal absorption process of vitamin B2 (riboflavin, RF) is carrier-mediated, and all three known human RF transporters, i.e., hRFVT-1, -2, and -3 (products of the SLC52A1, 2 & 3 genes, respectively) are expressed in the gut. We have previously shown that the intestinal RF uptake process is adaptively regulated by substrate level, but little is known about the molecular mechanism(s) involved. Using human intestinal epithelial NCM460 cells maintained under RF deficient and over-supplemented (OS) conditions, we now show that the induction in RF uptake in RF deficiency is associated with an increase in expression of the hRFVT-2 & -3 (but not hRFVT-1) at the protein and mRNA levels. Focusing on hRFVT-3, the predominant transporter in the intestine, we also observed an increase in the level of expression of its hnRNA and activity of its promoter in the RF deficiency state. An increase in the level of expression of the nuclear factor Sp1 (which is important for activity of the SLC52A3 promoter) was observed in RF deficiency, while mutating the Sp1/GC site in the SLC52A3 promoter drastically decreased the level of induction in SLC52A3 promoter activity in RF deficiency. We also observed specific epigenetic changes in the SLC52A3 promoter in RF deficiency. Finally, an increase in hRFVT-3 protein expression at the cell surface was observed in RF deficiency. Results of these investigations show, for the first time, that transcriptional and post-transcriptional mechanisms are involved in the adaptive regulation of intestinal RF uptake by the prevailing substrate level. PMID:26121134

  15. 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

  16. Family Wide Molecular Adaptations to Underground Life in African Mole-Rats Revealed by Phylogenomic Analysis

    PubMed Central

    Davies, Kalina T.J.; Bennett, Nigel C.; Tsagkogeorga, Georgia; Rossiter, Stephen J.; Faulkes, Christopher G.

    2015-01-01

    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. PMID:26318402

  17. Adaptation of the Black Yeast Wangiella dermatitidis to Ionizing Radiation: Molecular and Cellular Mechanisms

    PubMed Central

    Robertson, Kelly L.; Mostaghim, Anahita; Cuomo, Christina A.; Soto, Carissa M.; Lebedev, Nikolai; Bailey, Robert F.; Wang, Zheng

    2012-01-01

    Observations of enhanced growth of melanized fungi under low-dose ionizing radiation in the laboratory and in the damaged Chernobyl nuclear reactor suggest they have adapted the ability to survive or even benefit from exposure to ionizing radiation. However, the cellular and molecular mechanism of fungal responses to such radiation remains poorly understood. Using the black yeast Wangiella dermatitidis as a model, we confirmed that ionizing radiation enhanced cell growth by increasing cell division and cell size. Using RNA-seq technology, we compared the transcriptomic profiles of the wild type and the melanin-deficient wdpks1 mutant under irradiation and non-irradiation conditions. It was found that more than 3000 genes were differentially expressed when these two strains were constantly exposed to a low dose of ionizing radiation and that half were regulated at least two fold in either direction. Functional analysis indicated that many genes for amino acid and carbohydrate metabolism and cell cycle progression were down-regulated and that a number of antioxidant genes and genes affecting membrane fluidity were up-regulated in both irradiated strains. However, the expression of ribosomal biogenesis genes was significantly up-regulated in the irradiated wild-type strain but not in the irradiated wdpks1 mutant, implying that melanin might help to contribute radiation energy for protein translation. Furthermore, we demonstrated that long-term exposure to low doses of radiation significantly increased survivability of both the wild-type and the wdpks1 mutant, which was correlated with reduced levels of reactive oxygen species (ROS), increased production of carotenoid and induced expression of genes encoding translesion DNA synthesis. Our results represent the first functional genomic study of how melanized fungal cells respond to low dose ionizing radiation and provide clues for the identification of biological processes, molecular pathways and individual genes

  18. Adaptation of the black yeast Wangiella dermatitidis to ionizing radiation: molecular and cellular mechanisms.

    PubMed

    Robertson, Kelly L; Mostaghim, Anahita; Cuomo, Christina A; Soto, Carissa M; Lebedev, Nikolai; Bailey, Robert F; Wang, Zheng

    2012-01-01

    Observations of enhanced growth of melanized fungi under low-dose ionizing radiation in the laboratory and in the damaged Chernobyl nuclear reactor suggest they have adapted the ability to survive or even benefit from exposure to ionizing radiation. However, the cellular and molecular mechanism of fungal responses to such radiation remains poorly understood. Using the black yeast Wangiella dermatitidis as a model, we confirmed that ionizing radiation enhanced cell growth by increasing cell division and cell size. Using RNA-seq technology, we compared the transcriptomic profiles of the wild type and the melanin-deficient wdpks1 mutant under irradiation and non-irradiation conditions. It was found that more than 3000 genes were differentially expressed when these two strains were constantly exposed to a low dose of ionizing radiation and that half were regulated at least two fold in either direction. Functional analysis indicated that many genes for amino acid and carbohydrate metabolism and cell cycle progression were down-regulated and that a number of antioxidant genes and genes affecting membrane fluidity were up-regulated in both irradiated strains. However, the expression of ribosomal biogenesis genes was significantly up-regulated in the irradiated wild-type strain but not in the irradiated wdpks1 mutant, implying that melanin might help to contribute radiation energy for protein translation. Furthermore, we demonstrated that long-term exposure to low doses of radiation significantly increased survivability of both the wild-type and the wdpks1 mutant, which was correlated with reduced levels of reactive oxygen species (ROS), increased production of carotenoid and induced expression of genes encoding translesion DNA synthesis. Our results represent the first functional genomic study of how melanized fungal cells respond to low dose ionizing radiation and provide clues for the identification of biological processes, molecular pathways and individual genes

  19. Comprehensive molecular characterization of Methylobacterium extorquens AM1 adapted for 1-butanol tolerance

    DOE PAGESBeta

    Hu, Bo; Yang, Yi -Ming; Beck, David A. C.; Wang, Qian -Wen; Chen, Wen -Jing; Yang, Jing; Lidstrom, Mary E.; Yang, Song

    2016-04-11

    In this study, the toxicity of alcohols is one of the major roadblocks of biological fermentation for biofuels production. Methylobacterium extorquens AM1, a facultative methylotrophic α-proteobacterium, has been engineered to generate 1-butanol from cheap carbon feedstocks through a synthetic metabolic pathway. However, M. extorquens AM1 is vulnerable to solvent stress, which impedes further development for 1-butanol production. Only a few studies have reported the general stress response of M. extorquens AM1 to solvent stress. Therefore, it is highly desirable to obtain a strain with ameliorated 1-butanol tolerance and elucidate the molecular mechanism of 1-butnaol tolerance in M. extorquens AM1 formore » future strain improvement. In this work, adaptive laboratory evolution was used as a tool to isolate mutants with 1-butanol tolerance up to 0.5 %. The evolved strains, BHBT3 and BHBT5, demonstrated increased growth rates and higher survival rates with the existence of 1-butanol. Whole genome sequencing revealed a SNP mutation at kefB in BHBT5, which was confirmed to be responsible for increasing 1-butanol tolerance through an allelic exchange experiment. Global metabolomic analysis further discovered that the pools of multiple key metabolites, including fatty acids, amino acids, and disaccharides, were increased in BHBT5 in response to 1-butanol stress. Additionally, the carotenoid synthesis pathway was significantly down-regulated in BHBT5. In conclusion, we successfully screened mutants resistant to 1-butanol and provided insights into the molecular mechanism of 1-butanol tolerance in M. extorquens AM1. This research will be useful for uncovering the mechanism of cellular response of M. extorquens AM1 to solvent stress, and will provide the genetic blueprint for the rational design of a strain of M. extorquens AM1 with increased 1-butanol tolerance in the future.« less

  20. 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. PMID:26318402

  1. Adaptive Multilevel Splitting Method for Molecular Dynamics Calculation of Benzamidine-Trypsin Dissociation Time.

    PubMed

    Teo, Ivan; Mayne, Christopher G; Schulten, Klaus; Lelièvre, Tony

    2016-06-14

    Adaptive multilevel splitting (AMS) is a rare event sampling method that requires minimal parameter tuning and allows unbiased sampling of transition pathways of a given rare event. Previous simulation studies have verified the efficiency and accuracy of AMS in the calculation of transition times for simple systems in both Monte Carlo and molecular dynamics (MD) simulations. Now, AMS is applied for the first time to an MD simulation of protein-ligand dissociation, representing a leap in complexity from the previous test cases. Of interest is the dissociation rate, which is typically too low to be accessible to conventional MD. The present study joins other recent efforts to develop advanced sampling techniques in MD to calculate dissociation rates, which are gaining importance in the pharmaceutical field as indicators of drug efficacy. The system investigated here, benzamidine bound to trypsin, is an example common to many of these efforts. The AMS estimate of the dissociation rate was found to be (2.6 ± 2.4) × 10(2) s(-1), which compares well with the experimental value. PMID:27159059

  2. Targeted metagenomics unveils the molecular basis for adaptive evolution of enzymes to their environment

    PubMed Central

    Suenaga, Hikaru

    2015-01-01

    Microorganisms have a wonderful ability to adapt rapidly to new or altered environmental conditions. Enzymes are the basis of metabolism in all living organisms and, therefore, enzyme adaptation plays a crucial role in the adaptation of microorganisms. Comparisons of homology and parallel beneficial mutations in an enzyme family provide valuable hints of how an enzyme adapted to an ecological system; consequently, a series of enzyme collections is required to investigate enzyme evolution. Targeted metagenomics is a promising tool for the construction of enzyme pools and for studying the adaptive evolution of enzymes. This perspective article presents a summary of targeted metagenomic approaches useful for this purpose. PMID:26441940

  3. Targeted metagenomics unveils the molecular basis for adaptive evolution of enzymes to their environment.

    PubMed

    Suenaga, Hikaru

    2015-01-01

    Microorganisms have a wonderful ability to adapt rapidly to new or altered environmental conditions. Enzymes are the basis of metabolism in all living organisms and, therefore, enzyme adaptation plays a crucial role in the adaptation of microorganisms. Comparisons of homology and parallel beneficial mutations in an enzyme family provide valuable hints of how an enzyme adapted to an ecological system; consequently, a series of enzyme collections is required to investigate enzyme evolution. Targeted metagenomics is a promising tool for the construction of enzyme pools and for studying the adaptive evolution of enzymes. This perspective article presents a summary of targeted metagenomic approaches useful for this purpose. PMID:26441940

  4. Decomposition of indwelling EMG signals

    PubMed Central

    Nawab, S. Hamid; Wotiz, Robert P.; De Luca, Carlo J.

    2008-01-01

    Decomposition of indwelling electromyographic (EMG) signals is challenging in view of the complex and often unpredictable behaviors and interactions of the action potential trains of different motor units that constitute the indwelling EMG signal. These phenomena create a myriad of problem situations that a decomposition technique needs to address to attain completeness and accuracy levels required for various scientific and clinical applications. Starting with the maximum a posteriori probability classifier adapted from the original precision decomposition system (PD I) of LeFever and De Luca (25, 26), an artificial intelligence approach has been used to develop a multiclassifier system (PD II) for addressing some of the experimentally identified problem situations. On a database of indwelling EMG signals reflecting such conditions, the fully automatic PD II system is found to achieve a decomposition accuracy of 86.0% despite the fact that its results include low-amplitude action potential trains that are not decomposable at all via systems such as PD I. Accuracy was established by comparing the decompositions of indwelling EMG signals obtained from two sensors. At the end of the automatic PD II decomposition procedure, the accuracy may be enhanced to nearly 100% via an interactive editor, a particularly significant fact for the previously indecomposable trains. PMID:18483170

  5. Differential Molecular Responses of Rapeseed Cotyledons to Light and Dark Reveal Metabolic Adaptations toward Autotrophy Establishment

    PubMed Central

    He, Dongli; Damaris, Rebecca N.; Fu, Jinlei; Tu, Jinxing; Fu, Tingdong; Xi, Chen; Yi, Bin; Yang, Pingfang

    2016-01-01

    Photosynthesis competent autotrophy is established during the postgerminative stage of plant growth. Among the multiple factors, light plays a decisive role in the switch from heterotrophic to autotrophic growth. Under dark conditions, the rapeseed hypocotyl extends quickly with an apical hook, and the cotyledon is yellow and folded, and maintains high levels of the isocitrate lyase (ICL). By contrast, in the light, the hypocotyl extends slowly, the cotyledon unfolds and turns green, the ICL content changes in parallel with cotyledon greening. To reveal metabolic adaptations during the establishment of postgerminative autotrophy in rapeseed, we conducted comparative proteomic and metabolomic analyses of the cotyledons of seedlings grown under light versus dark conditions. Under both conditions, the increase in proteases, fatty acid β-oxidation and glyoxylate-cycle related proteins was accompanied by rapid degradation of the stored proteins and lipids with an accumulation of the amino acids. While light condition partially retarded these conversions. Light significantly induced the expression of chlorophyll-binding and photorespiration related proteins, resulting in an increase in reducing-sugars. However, the levels of some chlorophyllide conversion, Calvin-cycle and photorespiration related proteins also accumulated in dark grown cotyledons, implying that the transition from heterotrophy to autotrophy is programmed in the seed rather than induced by light. Various anti-stress systems, e.g., redox related proteins, salicylic acid, proline and chaperones, were employed to decrease oxidative stress, which was mainly derived from lipid oxidation or photorespiration, under both conditions. This study provides a comprehensive understanding of the differential molecular responses of rapeseed cotyledons to light and dark conditions, which will facilitate further study on the complex mechanism underlying the transition from heterotrophy to autotrophy. PMID:27471506

  6. Molecular adaptation and resilience of the insect’s nuclear receptor USP

    PubMed Central

    2012-01-01

    propose a model in which the molecular adaptation of this protein is seen as a process of resilience for the maintenance of the ecdysone receptor functionality. PMID:23039844

  7. Differential Molecular Responses of Rapeseed Cotyledons to Light and Dark Reveal Metabolic Adaptations toward Autotrophy Establishment.

    PubMed

    He, Dongli; Damaris, Rebecca N; Fu, Jinlei; Tu, Jinxing; Fu, Tingdong; Xi, Chen; Yi, Bin; Yang, Pingfang

    2016-01-01

    Photosynthesis competent autotrophy is established during the postgerminative stage of plant growth. Among the multiple factors, light plays a decisive role in the switch from heterotrophic to autotrophic growth. Under dark conditions, the rapeseed hypocotyl extends quickly with an apical hook, and the cotyledon is yellow and folded, and maintains high levels of the isocitrate lyase (ICL). By contrast, in the light, the hypocotyl extends slowly, the cotyledon unfolds and turns green, the ICL content changes in parallel with cotyledon greening. To reveal metabolic adaptations during the establishment of postgerminative autotrophy in rapeseed, we conducted comparative proteomic and metabolomic analyses of the cotyledons of seedlings grown under light versus dark conditions. Under both conditions, the increase in proteases, fatty acid β-oxidation and glyoxylate-cycle related proteins was accompanied by rapid degradation of the stored proteins and lipids with an accumulation of the amino acids. While light condition partially retarded these conversions. Light significantly induced the expression of chlorophyll-binding and photorespiration related proteins, resulting in an increase in reducing-sugars. However, the levels of some chlorophyllide conversion, Calvin-cycle and photorespiration related proteins also accumulated in dark grown cotyledons, implying that the transition from heterotrophy to autotrophy is programmed in the seed rather than induced by light. Various anti-stress systems, e.g., redox related proteins, salicylic acid, proline and chaperones, were employed to decrease oxidative stress, which was mainly derived from lipid oxidation or photorespiration, under both conditions. This study provides a comprehensive understanding of the differential molecular responses of rapeseed cotyledons to light and dark conditions, which will facilitate further study on the complex mechanism underlying the transition from heterotrophy to autotrophy. PMID:27471506

  8. Exploring the Molecular and Metabolic Factors Contributing to the Adaptation of Maize Seedlings to Nitrate Limitation

    PubMed Central

    El-kereamy, Ashraf; Guevara, David; Bi, Yong-Mei; Chen, Xi; Rothstein, Steven J.

    2011-01-01

    Crop production on soils containing sub-optimal levels of nitrogen (N) severely compromises yield potential. The development of plant varieties displaying high N use efficiency (NUE) will optimize N fertilizer use and reduce the environmental damage caused by excess N application. Maize is one of the most important crops cultivated worldwide. Identification of the genotypes with an enhanced NUE in the field is both time and resource consuming and sometime is difficult due to the regulation in the biotechnology programs. Identification of traits associated with adaptation to N limitation at an early vegetative stage which could reflect NUE at maturity is in need. We developed a hydroponic growth system and used it to test two genotypes that were different in their NUE at maturity under N limitation. One genotype SRG-200 showed a higher NUE than the other genotype SRG-100 and we used its hybrid SRG-150 as a reference for NUE. A number of phenotypic, molecular, and metabolic factors were tested using these three genetic lines at an early vegetative stage to determine which of these could be more indicative of predicting improved NUE at an early seedling stage. These include a transcriptional analysis which showed that the higher NUE in SRG-200 genotype is associated with higher transcript levels for the genes involved in nitrate transport, N assimilation, and GS and that the SRG-200 genotype maintained higher sugar content in leaves. Those identified in this study could be useful indicators for selecting promising maize lines at early stages to help develop elite varieties showing an enhanced NUE. PMID:22666225

  9. Variation and decomposition of the partial molar volume of small gas molecules in different organic solvents derived from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Klähn, Marco; Martin, Alistair; Cheong, Daniel W.; Garland, Marc V.

    2013-12-01

    The partial molar volumes, bar V_i, of the gas solutes H2, CO, and CO2, solvated in acetone, methanol, heptane, and diethylether are determined computationally in the limit of infinite dilution and standard conditions. Solutions are described with molecular dynamics simulations in combination with the OPLS-aa force field for solvents and customized force field for solutes. bar V_i is determined with the direct method, while the composition of bar V_i is studied with Kirkwood-Buff integrals (KBIs). Subsequently, the amount of unoccupied space and size of pre-formed cavities in pure solvents is determined. Additionally, the shape of individual solvent cages is analyzed. Calculated bar V_i deviate only 3.4 cm3 mol-1 (7.1%) from experimental literature values. Experimental bar V_i variations across solutions are reproduced qualitatively and also quantitatively in most cases. The KBI analysis identifies differences in solute induced solvent reorganization in the immediate vicinity of H2 (<0.7 nm) and solvent reorganization up to the third solvation shell of CO and CO2 (<1.6 nm) as the origin of bar V_i variations. In all solutions, larger bar V_i are found in solvents that exhibit weak internal interactions, low cohesive energy density and large compressibility. Weak internal interactions facilitate solvent displacement by thermal solute movement, which enhances the size of solvent cages and thus bar V_i. Additionally, attractive electrostatic interactions of CO2 and the solvents, which do not depend on internal solvent interactions only, partially reversed the bar V_i trends observed in H2 and CO solutions where electrostatic interactions with the solvents are absent. More empty space and larger pre-formed cavities are found in solvents with weak internal interactions, however, no evidence is found that solutes in any considered solvent are accommodated in pre-formed cavities. Individual solvent cages are found to be elongated in the negative direction of solute

  10. RNA Sequencing of Populus x canadensis Roots Identifies Key Molecular Mechanisms Underlying Physiological Adaption to Excess Zinc

    PubMed Central

    Ariani, Andrea; Di Baccio, Daniela; Romeo, Stefania; Lombardi, Lara; Andreucci, Andrea; Lux, Alexander; Horner, David Stephen; Sebastiani, Luca

    2015-01-01

    Populus x canadensis clone I-214 exhibits a general indicator phenotype in response to excess Zn, and a higher metal uptake in roots than in shoots with a reduced translocation to aerial parts under hydroponic conditions. This physiological adaptation seems mainly regulated by roots, although the molecular mechanisms that underlie these processes are still poorly understood. Here, differential expression analysis using RNA-sequencing technology was used to identify the molecular mechanisms involved in the response to excess Zn in root. In order to maximize specificity of detection of differentially expressed (DE) genes, we consider the intersection of genes identified by three distinct statistical approaches (61 up- and 19 down-regulated) and validate them by RT-qPCR, yielding an agreement of 93% between the two experimental techniques. Gene Ontology (GO) terms related to oxidation-reduction processes, transport and cellular iron ion homeostasis were enriched among DE genes, highlighting the importance of metal homeostasis in adaptation to excess Zn by P. x canadensis clone I-214. We identified the up-regulation of two Populus metal transporters (ZIP2 and NRAMP1) probably involved in metal uptake, and the down-regulation of a NAS4 gene involved in metal translocation. We identified also four Fe-homeostasis transcription factors (two bHLH38 genes, FIT and BTS) that were differentially expressed, probably for reducing Zn-induced Fe-deficiency. In particular, we suggest that the down-regulation of FIT transcription factor could be a mechanism to cope with Zn-induced Fe-deficiency in Populus. These results provide insight into the molecular mechanisms involved in adaption to excess Zn in Populus spp., but could also constitute a starting point for the identification and characterization of molecular markers or biotechnological targets for possible improvement of phytoremediation performances of poplar trees. PMID:25671786

  11. 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

  12. Cyto•IQ: an adaptive cytometer for extracting the noisy dynamics of molecular interactions in live cells

    NASA Astrophysics Data System (ADS)

    Ball, David A.; Moody, Stephen E.; Peccoud, Jean

    2010-02-01

    We have developed a fundamentally new type of cytometer to track the statistics of dynamic molecular interactions in hundreds of individual live cells within a single experiment. This entirely new high-throughput experimental system, which we have named Cyto•IQ, reports statistical, rather than image-based data for a large cellular population. Like a flow cytometer, Cyto•IQ rapidly measures several fluorescent probes in a large population of cells to yield a reduced statistical model that is matched to the experimental goals set by the user. However, Cyto•IQ moves beyond flow cytometry by tracking multiple probes in individual cells over time. Using adaptive learning algorithms, we process data in real time to maximize the convergence of the statistical model parameter estimators. Software controlling Cyto•IQ integrates existing open source applications to interface hardware components, process images, and adapt the data acquisition strategy based on previously acquired data. These innovations allow the study of larger populations of cells, and molecular interactions with more complex dynamics, than is possible with traditional microscope-based approaches. Cyto•IQ supports research to characterize the noisy dynamics of molecular interactions controlling biological processes.

  13. Evidence of Molecular Adaptation to Extreme Environments and Applicability to Space Environments

    NASA Astrophysics Data System (ADS)

    Filipovic, M. D.; Ognjanovic, S.; Ognjanovic, M.

    2008-06-01

    This is initial investigation of gene signatures responsible for adapting microscopic life to the extreme Earth environments. We present preliminary results on identification of the clusters of orthologous groups (COGs) common to several hyperthermophiles and exclusion of those common to a mesophile (non-hyperthermophile): Escherichia coli (E. coli K12), will yield a group of proteins possibly involved in adaptation to life under extreme temperatures. Comparative genome analyses represent a powerful tool in discovery of novel genes responsible for adaptation to specific extreme environments. Methanogens stand out as the only group of organisms that have species capable of growth at 0° C (Metarhizium frigidum (M.~frigidum) and Methanococcoides burtonii (M.~burtonii)) and 110° C (Methanopyrus kandleri (M.~kandleri)). Although not all the components of heat adaptation can be attributed to novel genes, the chaperones known as heat shock proteins stabilize the enzymes under elevated temperature. However, highly conserved chaperons found in bacteria and eukaryots are not present in hyperthermophilic Archea, rather, they have a unique chaperone TF55. Our aim was to use software which we specifically developed for extremophile genome comparative analyses in order to search for additional novel genes involved in hyperthermophile adaptation. The following hyperthermophile genomes incorporated in this software were used for these studies: Methanocaldococcus jannaschii (M.~jannaschii), M.~kandleri, Archaeoglobus fulgidus (A.~fulgidus) and three species of Pyrococcus. Common genes were annotated and grouped according to their roles in cellular processes where such information was available and proteins not previously implicated in the heat-adaptation of hyperthermophiles were identified. Additional experimental data are needed in order to learn more about these proteins. To address non-gene based components of thermal adaptation, all sequenced extremophiles were analysed for

  14. Glycogen synthase kinase 3 is part of the molecular machinery regulating the adaptive response to LPS stimulation in microglial cells.

    PubMed

    Ajmone-Cat, Maria Antonietta; D'Urso, Maria Cristina; di Blasio, Giorgia; Brignone, Maria Stefania; De Simone, Roberta; Minghetti, Luisa

    2016-07-01

    Repeated stimulation of TLR4 signaling by lipopolysaccharide (LPS) in microglia induces a state of tolerance/sensitization consisting in the reprogramming of the expression of pro-inflammatory genes in favor of anti-inflammatory ones. The molecular mechanisms underlying this adaptive response are far to be elucidated. Glycogen synthase kinase 3 (GSK3) has emerged as crucial regulator of TLR signaling, mediating the balance between pro- and anti-inflammatory functions in both periphery and central nervous system. The present study extends this notion identifying GSK3 as part of the molecular machinery regulating the LPS-adaptive response in microglial cells, by using primary microglial cultures and organotypic hippocampal slices (OHSCs). We found that lithium chloride (LiCl), a widely used GSK3 inhibitor and the mainstay treatment for bipolar disorder, reinforced the LPS adaptive response by enhancing both downregulation of pro-inflammatory genes (inducible nitric oxide synthase, interleukin 1β, interleukin 6, tumor necrosis factor α), and upregulation of genes typically associated to anti-inflammatory functions (interleukin 10 and MRC1). The effects of GSK3 inhibition were mimicked by Wnt3a, added exogenously, and reversed by Inhibitor of Wnt-Response-1-endo, a pharmacological disruptor of the canonical Wnt/β-catenin pathway, and GW9662, a selective peroxisome proliferator activated receptor γ antagonist, suggesting that these two pathways are involved in the regulation of LPS-tolerance/sensitization by GSK. Finally, LiCl treatment of OHSCs enhanced the protective functional consequences of the microglial adaptive response to LPS on oligodendrocyte maturation, as indicated by MBP mRNA upregulation. These results further indicate GSK3 as key component in the orchestration of neuroinflammation and target for neuroprotective strategies. PMID:26593276

  15. Canonical Huynen decomposition of radar targets

    NASA Astrophysics Data System (ADS)

    Li, Dong; Zhang, Yunhua

    2015-10-01

    Huynen decomposition prefers the world of basic symmetry and regularity (SR) in which we live. However, this preference restricts its applicability to ideal SR scatterer only. As for the complex non-symmetric (NS) and irregular (IR) scatterers such as forest and building, Huynen decomposition fails to analyze their scattering. The canonical Huynen dichotomy is devised to extend Huynen decomposition to the preferences for IR and NS. From the physical realizability conditions of polarimetric scattering description, two other dichotomies of polarimetric radar target are developed, which prefer scattering IR, and NS, respectively, and provide two competent supplements to Huynen decomposition. The canonical Huynen dichotomy is the combination of the two dichotomies and Huynen decomposition. In virtue of an Adaptive selection, the canonical Huynen dichotomy is used in target extraction, and the experiments on AIRSAR San Francisco data demonstrate its high efficiency and excellent discrimination of radar targets.

  16. The excited states of K3 cluster: The molecular symmetry adapted non-adiabatic coupling terms and diabatic Hamiltonian matrix

    NASA Astrophysics Data System (ADS)

    Mukherjee, Saikat; Adhikari, Satrajit

    2014-08-01

    We calculate the adiabatic potential energy surfaces (PESs) and the non-adiabatic coupling terms (NACTs) for the excited electronic states of K3 cluster by MRCI approach using MOLPRO. The NACTs are adapted with molecular symmetry to assign appropriate IREPs so that the elements of the Hamiltonian matrix are totally symmetric. We incorporate those NACTs into three-state adiabatic-to-diabatic transformation (ADT) equations to obtain ADT angles for constructing continuous, single-valued, smooth and symmetric diabatic Hamiltonian matrix, where its elements are fitted with analytic functions. Finally, we demonstrate that the dressed diabatic and adiabatic-via-dressed diabatic PECs show prominent topological effect over dressed adiabatic curves.

  17. Network-based integration of molecular and physiological data elucidates regulatory mechanisms underlying adaptation to high-fat diet.

    PubMed

    Derous, Davina; Kelder, Thomas; van Schothorst, Evert M; van Erk, Marjan; Voigt, Anja; Klaus, Susanne; Keijer, Jaap; Radonjic, Marijana

    2015-07-01

    Health is influenced by interplay of molecular, physiological and environmental factors. To effectively maintain health and prevent disease, health-relevant relations need to be understood at multiple levels of biological complexity. Network-based methods provide a powerful platform for integration and mining of data and knowledge characterizing different aspects of health. Previously, we have reported physiological and gene expression changes associated with adaptation of murine epididymal white adipose tissue (eWAT) to 5 days and 12 weeks of high-fat diet (HFD) and low-fat diet feeding (Voigt et al. in Mol Nutr Food Res 57:1423-1434, 2013. doi: 10.1002/mnfr.201200671 ). In the current study, we apply network analysis on this dataset to comprehensively characterize mechanisms driving the short- and long-term adaptation of eWAT to HFD across multiple levels of complexity. We built a three-layered interaction network comprising enriched biological processes, their transcriptional regulators and associated changes in physiological parameters. The multi-layered network model reveals that early eWAT adaptation to HFD feeding involves major changes at a molecular level, including activation of TGF-β signalling pathway, immune and stress response and downregulation of mitochondrial functioning. Upon prolonged HFD intake, initial transcriptional response tails off, mitochondrial functioning is even further diminished, and in turn the relation between eWAT gene expression and physiological changes becomes more prominent. In particular, eWAT weight and total energy intake negatively correlate with cellular respiration process, revealing mitochondrial dysfunction as a hallmark of late eWAT adaptation to HFD. Apart from global understanding of the time-resolved adaptation to HFD, the multi-layered network model allows several novel mechanistic hypotheses to emerge: (1) early activation of TGF-β signalling as a trigger for structural and morphological changes in

  18. Evolution of the fruit endocarp: molecular mechanisms underlying adaptations in seed protection and dispersal strategies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant evolution is largely driven by adaptations in seed protection and dispersal strategies that allow diversification into new niches. This is evident by the tremendous variation in flowering and fruiting structures present both across and within different plant lineages. Within a single plant f...

  19. Adaptive neuro-fuzzy inference system multi-objective optimization using the genetic algorithm/singular value decomposition method for modelling the discharge coefficient in rectangular sharp-crested side weirs

    NASA Astrophysics Data System (ADS)

    Khoshbin, Fatemeh; Bonakdari, Hossein; Hamed Ashraf Talesh, Seyed; Ebtehaj, Isa; Zaji, Amir Hossein; Azimi, Hamed

    2016-06-01

    In the present article, the adaptive neuro-fuzzy inference system (ANFIS) is employed to model the discharge coefficient in rectangular sharp-crested side weirs. The genetic algorithm (GA) is used for the optimum selection of membership functions, while the singular value decomposition (SVD) method helps in computing the linear parameters of the ANFIS results section (GA/SVD-ANFIS). The effect of each dimensionless parameter on discharge coefficient prediction is examined in five different models to conduct sensitivity analysis by applying the above-mentioned dimensionless parameters. Two different sets of experimental data are utilized to examine the models and obtain the best model. The study results indicate that the model designed through GA/SVD-ANFIS predicts the discharge coefficient with a good level of accuracy (mean absolute percentage error = 3.362 and root mean square error = 0.027). Moreover, comparing this method with existing equations and the multi-layer perceptron-artificial neural network (MLP-ANN) indicates that the GA/SVD-ANFIS method has superior performance in simulating the discharge coefficient of side weirs.

  20. Genome Sequencing of the Perciform Fish Larimichthys crocea Provides Insights into Molecular and Genetic Mechanisms of Stress Adaptation

    PubMed Central

    Shi, Qiong; Zhu, Lv-Yun; Li, Ting; Ding, Yang; Nie, Li; Li, Qiuhua; Dong, Wei-ren; Jiang, Liang; Sun, Bing; Zhang, XinHui; Li, Mingyu; Zhang, Hai-Qi; Xie, ShangBo; Zhu, YaBing; Jiang, XuanTing; Wang, Xianhui; Mu, Pengfei; Chen, Wei; Yue, Zhen; Wang, Zhuo; Wang, Jun; Shao, Jian-Zhong; Chen, Xinhua

    2015-01-01

    The large yellow croaker Larimichthys crocea (L. crocea) is one of the most economically important marine fish in China and East Asian countries. It also exhibits peculiar behavioral and physiological characteristics, especially sensitive to various environmental stresses, such as hypoxia and air exposure. These traits may render L. crocea a good model for investigating the response mechanisms to environmental stress. To understand the molecular and genetic mechanisms underlying the adaptation and response of L. crocea to environmental stress, we sequenced and assembled the genome of L. crocea using a bacterial artificial chromosome and whole-genome shotgun hierarchical strategy. The final genome assembly was 679 Mb, with a contig N50 of 63.11 kb and a scaffold N50 of 1.03 Mb, containing 25,401 protein-coding genes. Gene families underlying adaptive behaviours, such as vision-related crystallins, olfactory receptors, and auditory sense-related genes, were significantly expanded in the genome of L. crocea relative to those of other vertebrates. Transcriptome analyses of the hypoxia-exposed L. crocea brain revealed new aspects of neuro-endocrine-immune/metabolism regulatory networks that may help the fish to avoid cerebral inflammatory injury and maintain energy balance under hypoxia. Proteomics data demonstrate that skin mucus of the air-exposed L. crocea had a complex composition, with an unexpectedly high number of proteins (3,209), suggesting its multiple protective mechanisms involved in antioxidant functions, oxygen transport, immune defence, and osmotic and ionic regulation. Our results reveal the molecular and genetic basis of fish adaptation and response to hypoxia and air exposure. The data generated by this study will provide valuable resources for the genetic improvement of stress resistance and yield potential in L. crocea. PMID:25835551

  1. Molecular evolution of the hyaluronan synthase 2 gene in mammals: implications for adaptations to the subterranean niche and cancer resistance.

    PubMed

    Faulkes, Christopher G; Davies, Kalina T J; Rossiter, Stephen J; Bennett, Nigel C

    2015-05-01

    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

  2. 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

  3. Thermal decomposition products of butyraldehyde

    NASA Astrophysics Data System (ADS)

    Hatten, Courtney D.; Kaskey, Kevin R.; Warner, Brian J.; Wright, Emily M.; McCunn, Laura R.

    2013-12-01

    The thermal decomposition of gas-phase butyraldehyde, CH3CH2CH2CHO, was studied in the 1300-1600 K range with a hyperthermal nozzle. Products were identified via matrix-isolation Fourier transform infrared spectroscopy and photoionization mass spectrometry in separate experiments. There are at least six major initial reactions contributing to the decomposition of butyraldehyde: a radical decomposition channel leading to propyl radical + CO + H; molecular elimination to form H2 + ethylketene; a keto-enol tautomerism followed by elimination of H2O producing 1-butyne; an intramolecular hydrogen shift and elimination producing vinyl alcohol and ethylene, a β-C-C bond scission yielding ethyl and vinoxy radicals; and a γ-C-C bond scission yielding methyl and CH2CH2CHO radicals. The first three reactions are analogous to those observed in the thermal decomposition of acetaldehyde, but the latter three reactions are made possible by the longer alkyl chain structure of butyraldehyde. The products identified following thermal decomposition of butyraldehyde are CO, HCO, CH3CH2CH2, CH3CH2CH=C=O, H2O, CH3CH2C≡CH, CH2CH2, CH2=CHOH, CH2CHO, CH3, HC≡CH, CH2CCH, CH3C≡CH, CH3CH=CH2, H2C=C=O, CH3CH2CH3, CH2=CHCHO, C4H2, C4H4, and C4H8. The first ten products listed are direct products of the six reactions listed above. The remaining products can be attributed to further decomposition reactions or bimolecular reactions in the nozzle.

  4. ADAPT, a Novel Scaffold Protein-Based Probe for Radionuclide Imaging of Molecular Targets That Are Expressed in Disseminated Cancers.

    PubMed

    Garousi, Javad; Lindbo, Sarah; Nilvebrant, Johan; Åstrand, Mikael; Buijs, Jos; Sandström, Mattias; Honarvar, Hadis; Orlova, Anna; Tolmachev, Vladimir; Hober, Sophia

    2015-10-15

    Small engineered scaffold proteins have attracted attention as probes for radionuclide-based molecular imaging. One class of these imaging probes, termed ABD-Derived Affinity Proteins (ADAPT), has been created using the albumin-binding domain (ABD) of streptococcal protein G as a stable protein scaffold. In this study, we report the development of a clinical lead probe termed ADAPT6 that binds HER2, an oncoprotein overexpressed in many breast cancers that serves as a theranostic biomarker for several approved targeting therapies. Surface-exposed amino acids of ABD were randomized to create a combinatorial library enabling selection of high-affinity binders to various proteins. Furthermore, ABD was engineered to enable rapid purification, to eradicate its binding to albumin, and to enable rapid blood clearance. Incorporation of a unique cysteine allowed site-specific conjugation to a maleimido derivative of a DOTA chelator, enabling radionuclide labeling, ¹¹¹In for SPECT imaging and ⁶⁸Ga for PET imaging. Pharmacologic studies in mice demonstrated that the fully engineered molecule (111)In/⁶⁸Ga-DOTA-(HE)3-ADAPT6 was specifically bound and taken up by HER2-expressing tumors, with a high tumor-to-normal tissue ratio in xenograft models of human cancer. Unbound tracer underwent rapid renal clearance followed by high renal reabsorption. HER2-expressing xenografts were visualized by gamma-camera or PET at 1 hour after infusion. PET experiments demonstrated feasibility for discrimination of xenografts with high or low HER2 expression. Our results offer a preclinical proof of concept for the use of ADAPT probes for noninvasive in vivo imaging. PMID:26297736

  5. Convergence Analysis of a Domain Decomposition Paradigm

    SciTech Connect

    Bank, R E; Vassilevski, P S

    2006-06-12

    We describe a domain decomposition algorithm for use in several variants of the parallel adaptive meshing paradigm of Bank and Holst. This algorithm has low communication, makes extensive use of existing sequential solvers, and exploits in several important ways data generated as part of the adaptive meshing paradigm. We show that for an idealized version of the algorithm, the rate of convergence is independent of both the global problem size N and the number of subdomains p used in the domain decomposition partition. Numerical examples illustrate the effectiveness of the procedure.

  6. Path integral molecular dynamics within the grand canonical-like adaptive resolution technique: Simulation of liquid water

    NASA Astrophysics Data System (ADS)

    Agarwal, Animesh; Delle Site, Luigi

    2015-09-01

    Quantum effects due to the spatial delocalization of light atoms are treated in molecular simulation via the path integral technique. Among several methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to investigate properties induced by spatial delocalization of atoms; however, computationally this technique is very demanding. The above mentioned limitation implies the restriction of PIMD applications to relatively small systems and short time scales. One of the possible solutions to overcome size and time limitation is to introduce PIMD algorithms into the Adaptive Resolution Simulation Scheme (AdResS). AdResS requires a relatively small region treated at path integral level and embeds it into a large molecular reservoir consisting of generic spherical coarse grained molecules. It was previously shown that the realization of the idea above, at a simple level, produced reasonable results for toy systems or simple/test systems like liquid parahydrogen. Encouraged by previous results, in this paper, we show the simulation of liquid water at room conditions where AdResS, in its latest and more accurate Grand-Canonical-like version (GC-AdResS), is merged with two of the most relevant PIMD techniques available in the literature. The comparison of our results with those reported in the literature and/or with those obtained from full PIMD simulations shows a highly satisfactory agreement.

  7. Path integral molecular dynamics within the grand canonical-like adaptive resolution technique: Simulation of liquid water

    SciTech Connect

    Agarwal, Animesh Delle Site, Luigi

    2015-09-07

    Quantum effects due to the spatial delocalization of light atoms are treated in molecular simulation via the path integral technique. Among several methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to investigate properties induced by spatial delocalization of atoms; however, computationally this technique is very demanding. The above mentioned limitation implies the restriction of PIMD applications to relatively small systems and short time scales. One of the possible solutions to overcome size and time limitation is to introduce PIMD algorithms into the Adaptive Resolution Simulation Scheme (AdResS). AdResS requires a relatively small region treated at path integral level and embeds it into a large molecular reservoir consisting of generic spherical coarse grained molecules. It was previously shown that the realization of the idea above, at a simple level, produced reasonable results for toy systems or simple/test systems like liquid parahydrogen. Encouraged by previous results, in this paper, we show the simulation of liquid water at room conditions where AdResS, in its latest and more accurate Grand-Canonical-like version (GC-AdResS), is merged with two of the most relevant PIMD techniques available in the literature. The comparison of our results with those reported in the literature and/or with those obtained from full PIMD simulations shows a highly satisfactory agreement.

  8. Genome-wide analysis of adaptive molecular evolution in the carnivorous plant Utricularia gibba.

    PubMed

    Carretero-Paulet, Lorenzo; Chang, Tien-Hao; Librado, Pablo; Ibarra-Laclette, Enrique; Herrera-Estrella, Luis; Rozas, Julio; Albert, Victor A

    2015-02-01

    The genome of the bladderwort Utricularia gibba provides an unparalleled opportunity to uncover the adaptive landscape of an aquatic carnivorous plant with unique phenotypic features such as absence of roots, development of water-filled suction bladders, and a highly ramified branching pattern. Despite its tiny size, the U. gibba genome accommodates approximately as many genes as other plant genomes. To examine the relationship between the compactness of its genome and gene turnover, we compared the U. gibba genome with that of four other eudicot species, defining a total of 17,324 gene families (orthogroups). These families were further classified as either 1) lineage-specific expanded/contracted or 2) stable in size. The U. gibba-expanded families are generically related to three main phenotypic features: 1) trap physiology, 2) key plant morphogenetic/developmental pathways, and 3) response to environmental stimuli, including adaptations to life in aquatic environments. Further scans for signatures of protein functional specialization permitted identification of seven candidate genes with amino acid changes putatively fixed by positive Darwinian selection in the U. gibba lineage. The Arabidopsis orthologs of these genes (AXR, UMAMIT41, IGS, TAR2, SOL1, DEG9, and DEG10) are involved in diverse plant biological functions potentially relevant for U. gibba phenotypic diversification, including 1) auxin metabolism and signal transduction, 2) flowering induction and floral meristem transition, 3) root development, and 4) peptidases. Taken together, our results suggest numerous candidate genes and gene families as interesting targets for further experimental confirmation of their functional and adaptive roles in the U. gibba's unique lifestyle and highly specialized body plan. PMID:25577200

  9. Genome-Wide Analysis of Adaptive Molecular Evolution in the Carnivorous Plant Utricularia gibba

    PubMed Central

    Librado, Pablo; Ibarra-Laclette, Enrique; Herrera-Estrella, Luis; Rozas, Julio; Albert, Victor A.

    2015-01-01

    The genome of the bladderwort Utricularia gibba provides an unparalleled opportunity to uncover the adaptive landscape of an aquatic carnivorous plant with unique phenotypic features such as absence of roots, development of water-filled suction bladders, and a highly ramified branching pattern. Despite its tiny size, the U. gibba genome accommodates approximately as many genes as other plant genomes. To examine the relationship between the compactness of its genome and gene turnover, we compared the U. gibba genome with that of four other eudicot species, defining a total of 17,324 gene families (orthogroups). These families were further classified as either 1) lineage-specific expanded/contracted or 2) stable in size. The U. gibba-expanded families are generically related to three main phenotypic features: 1) trap physiology, 2) key plant morphogenetic/developmental pathways, and 3) response to environmental stimuli, including adaptations to life in aquatic environments. Further scans for signatures of protein functional specialization permitted identification of seven candidate genes with amino acid changes putatively fixed by positive Darwinian selection in the U. gibba lineage. The Arabidopsis orthologs of these genes (AXR, UMAMIT41, IGS, TAR2, SOL1, DEG9, and DEG10) are involved in diverse plant biological functions potentially relevant for U. gibba phenotypic diversification, including 1) auxin metabolism and signal transduction, 2) flowering induction and floral meristem transition, 3) root development, and 4) peptidases. Taken together, our results suggest numerous candidate genes and gene families as interesting targets for further experimental confirmation of their functional and adaptive roles in the U. gibba’s unique lifestyle and highly specialized body plan. PMID:25577200

  10. Simulation of macromolecular liquids with the adaptive resolution molecular dynamics technique

    NASA Astrophysics Data System (ADS)

    Peters, J. H.; Klein, R.; Delle Site, L.

    2016-08-01

    We extend the application of the adaptive resolution technique (AdResS) to liquid systems composed of alkane chains of different lengths. The aim of the study is to develop and test the modifications of AdResS required in order to handle the change of representation of large molecules. The robustness of the approach is shown by calculating several relevant structural properties and comparing them with the results of full atomistic simulations. The extended scheme represents a robust prototype for the simulation of macromolecular systems of interest in several fields, from material science to biophysics.

  11. Multi-objective molecular de novo design by adaptive fragment prioritization.

    PubMed

    Reutlinger, Michael; Rodrigues, Tiago; Schneider, Petra; Schneider, Gisbert

    2014-04-14

    We present the development and application of a computational molecular de novo design method for obtaining bioactive compounds with desired on- and off-target binding. The approach translates the nature-inspired concept of ant colony optimization to combinatorial building block selection. By relying on publicly available structure-activity data, we developed a predictive quantitative polypharmacology model for 640 human drug targets. By taking reductive amination as an example of a privileged reaction, we obtained novel subtype-selective and multitarget-modulating dopamine D4 antagonists, as well as ligands selective for the sigma-1 receptor with accurately predicted affinities. The nanomolar potencies of the hits obtained, their high ligand efficiencies, and an overall success rate of 90 % demonstrate that this ligand-based computer-aided molecular design method may guide target-focused combinatorial chemistry. PMID:24623390

  12. Assessing the Effect of Litter Species on the Dynamic of Bacterial and Fungal Communities during Leaf Decomposition in Microcosm by Molecular Techniques

    PubMed Central

    Xu, Wenjing; Shi, Lingling; Chan, Onchim; Li, Jiao; Casper, Peter; Zou, Xiaoming

    2013-01-01

    Although bacteria and fungi are well-known to be decomposers of leaf litter, few studies have examined their compositions and diversities during the decomposition process in tropical stream water. Xishuangbanna is a tropical region preserving one of the highest floristic diversity areas in China. In this study, leaf litter of four dominant plant species in Xishuangbanna was incubated in stream water for 42 days during which samples were taken regularly. Following DNA extraction, PCR-DGGE (denaturing gradient gel electrophoresis) and clone-sequencing analyses were performed using bacterial and fungal specific primers. Leaf species have slightly influences on bacterial community rather than fungal community. The richness and diversity of bacteria was higher than that of fungi, which increased towards the end of the 42-day-incubation. The bacterial community was initially more specific upon the type of leaves and gradually became similar at the later stage of decomposition with alpha-proteobacteria as major component. Sequences affiliated to methanotrophs were obtained that indicates potentially occurrence of methane oxidation and methanogenesis. For the fungal community, sequences affiliated to Aspergillus were predominant at the beginning and then shifted to Pleosporales. Our results suggest that the microorganisms colonizing leaf biofilm in tropical stream water were mostly generalists that could exploit the resources of leaves of various species equally well. PMID:24367682

  13. Transcriptome Analysis in Tardigrade Species Reveals Specific Molecular Pathways for Stress Adaptations

    PubMed Central

    Förster, Frank; Beisser, Daniela; Grohme, Markus A.; Liang, Chunguang; Mali, Brahim; Siegl, Alexander Matthias; Engelmann, Julia C.; Shkumatov, Alexander V.; Schokraie, Elham; Müller, Tobias; Schnölzer, Martina; Schill, Ralph O.; Frohme, Marcus; Dandekar, Thomas

    2012-01-01

    Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum. These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant. PMID:22563243

  14. Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life

    PubMed Central

    Faddeeva, A.; Studer, R. A.; Kraaijeveld, K.; Sie, D.; Ylstra, B.; Mariën, J.; op den Camp, H. J. M.; Datema, E.; den Dunnen, J. T.; van Straalen, N. M.; Roelofs, D.

    2015-01-01

    Background Collembola (springtails) represent a soil-living lineage of hexapods in between insects and crustaceans. Consequently, their genomes may hold key information on the early processes leading to evolution of Hexapoda from a crustacean ancestor. Method We assembled and annotated transcriptomes of the Collembola Folsomia candida and Orchesella cincta, and performed comparative analysis with protein-coding gene sequences of three crustaceans and three insects to identify adaptive signatures associated with the evolution of hexapods within the pancrustacean clade. Results Assembly of the springtail transcriptomes resulted in 37,730 transcripts with predicted open reading frames for F. candida and 32,154 for O. cincta, of which 34.2% were functionally annotated for F. candida and 38.4% for O. cincta. Subsequently, we predicted orthologous clusters among eight species and applied the branch-site test to detect episodic positive selection in the Hexapoda and Collembola lineages. A subset of 250 genes showed significant positive selection along the Hexapoda branch and 57 in the Collembola lineage. Gene Ontology categories enriched in these genes include metabolism, stress response (i.e. DNA repair, immune response), ion transport, ATP metabolism, regulation and development-related processes (i.e. eye development, neurological development). Conclusions We suggest that the identified gene families represent processes that have played a key role in the divergence of hexapods within the pancrustacean clade that eventually evolved into the most species-rich group of all animals, the hexapods. Furthermore, some adaptive signatures in collembolans may provide valuable clues to understand evolution of hexapods on land. PMID:26075903

  15. Quantitative Proteomic Analysis Reveals Molecular Adaptations in the Hippocampal Synaptic Active Zone of Chronic Mild Stress-Unsusceptible Rats

    PubMed Central

    Zhou, Jian; Liu, Zhao; Yu, Jia; Han, Xin; Fan, Songhua; Shao, Weihua; Chen, Jianjun; Qiao, Rui

    2016-01-01

    Background: While stressful events are recognized as an important cause of major depressive disorder, some individuals exposed to life stressors maintain normal psychological functioning. The molecular mechanism(s) underlying this phenomenon remain unclear. Abnormal transmission and plasticity of hippocampal synapses have been implied to play a key role in the pathoetiology of major depressive disorder. Methods: A chronic mild stress protocol was applied to separate susceptible and unsusceptible rat subpopulations. Proteomic analysis using an isobaric tag for relative and absolute quantitation coupled with tandem mass spectrometry was performed to identify differential proteins in enriched hippocampal synaptic junction preparations. Results: A total of 4318 proteins were quantified, and 89 membrane proteins were present in differential amounts. Of these, SynaptomeDB identified 81 (91%) having a synapse-specific localization. The unbiased profiles identified several candidate proteins within the synaptic junction that may be associated with stress vulnerability or insusceptibility. Subsequent functional categorization revealed that protein systems particularly involved in membrane trafficking at the synaptic active zone exhibited a positive strain as potential molecular adaptations in the unsusceptible rats. Moreover, through STRING and immunoblotting analysis, membrane-associated GTP-bound Rab3a and Munc18-1 appear to coregulate syntaxin-1/SNAP25/VAMP2 assembly at the hippocampal presynaptic active zone of unsusceptible rats, facilitating SNARE-mediated membrane fusion and neurotransmitter release, and may be part of a stress-protection mechanism in actively maintaining an emotional homeostasis. Conclusions: The present results support the concept that there is a range of potential protein adaptations in the hippocampal synaptic active zone of unsusceptible rats, revealing new investigative targets that may contribute to a better understanding of stress

  16. Adaptation to the sky: Defining the feather with integument fossils from Mesozoic China and experimental evidence from molecular laboratories

    PubMed Central

    Chuong, Cheng-Ming; Wu, Ping; Zhang, Fu-Cheng; Xu, Xing; Yu, Minke; Widelitz, Randall B.; Jiang, Ting-Xin; Hou, Lianhai

    2015-01-01

    In this special issue of Evo-Devo of the amniote integument, Alibardi has discussed the adaptation of the integument to the land. Here we will discuss the adaptation to the sky. We first review a series of fossil discoveries representing intermediate forms of feathers or feather-like appendages from dinosaurs and Mesozoic birds from the Jehol Biota of China. We then discuss results from the molecular and developmental biological experiments using chicken integument as the model. Feather forms can be modulated using retrovirus mediated gene mis-expression that mimics those found in nature today and in the evolutionary past. The molecular conversions among different types of integument appendages (feather, scale, tooth) are discussed. From these evidences, we recognize that not all organisms with feathers are birds, and that not all skin appendages with hierarchical branches are feathers. We develop a set of criteria for true avian feathers: 1) possessing actively proliferating cells in the proximal follicle for a proximo – distal growth mode; 2) forming hierarchical branches of rachis, barbs and barbules, with barbs shaped by differential cell death into either bilaterally or radially symmetric structures; 3) having a follicle structure, with a mesenchyme core during development; 4) maturing into a structure consisting of epithelia without a mesenchyme core with two sides of the vane facing the previous basal and supra-basal layer, respectively; and 5) having stem cells and dermal papilla in the follicle and hence the ability to molt and regenerate. A model of feather evolution from feather bud → barbs → barbules → rachis is presented, which is opposite to the old view of scale plate → rachis → barbs → barbules. PMID:12949768

  17. Nested Taylor decomposition in multivariate function decomposition

    NASA Astrophysics Data System (ADS)

    Baykara, N. A.; Gürvit, Ercan

    2014-12-01

    Fluctuationlessness approximation applied to the remainder term of a Taylor decomposition expressed in integral form is already used in many articles. Some forms of multi-point Taylor expansion also are considered in some articles. This work is somehow a combination these where the Taylor decomposition of a function is taken where the remainder is expressed in integral form. Then the integrand is decomposed to Taylor again, not necessarily around the same point as the first decomposition and a second remainder is obtained. After taking into consideration the necessary change of variables and converting the integration limits to the universal [0;1] interval a multiple integration system formed by a multivariate function is formed. Then it is intended to apply the Fluctuationlessness approximation to each of these integrals one by one and get better results as compared with the single node Taylor decomposition on which the Fluctuationlessness is applied.

  18. Molecular Phylogeny Supports Repeated Adaptation to Burrowing within Small-Eared Shrews Genus of Cryptotis (Eulipotyphla, Soricidae)

    PubMed Central

    He, Kai; Woodman, Neal; Boaglio, Sean; Roberts, Mariel; Supekar, Sunjana; Maldonado, Jesús E.

    2015-01-01

    Small-eared shrews of the New World genus Cryptotis (Eulipotyphla, Soricidae) comprise at least 42 species that traditionally have been partitioned among four or more species groups based on morphological characters. The Cryptotis mexicana species group is of particular interest, because its member species inhibit a subtly graded series of forelimb adaptations that appear to correspond to locomotory behaviors that range from more ambulatory to more fossorial. Unfortunately, the evolutionary relationships both among species in the C. mexicana group and among the species groups remain unclear. To better understand the phylogeny of this group of shrews, we sequenced two mitochondrial and two nuclear genes. To help interpret the pattern and direction of morphological changes, we also generated a matrix of morphological characters focused on the evolutionarily plastic humerus. We found significant discordant between the resulting molecular and morphological trees, suggesting considerable convergence in the evolution of the humerus. Our results indicate that adaptations for increased burrowing ability evolved repeatedly within the genus Cryptotis. PMID:26489020

  19. Molecular Phylogeny Supports Repeated Adaptation to Burrowing within Small-Eared Shrews Genus of Cryptotis (Eulipotyphla, Soricidae).

    PubMed

    He, Kai; Woodman, Neal; Boaglio, Sean; Roberts, Mariel; Supekar, Sunjana; Maldonado, Jesús E

    2015-01-01

    Small-eared shrews of the New World genus Cryptotis (Eulipotyphla, Soricidae) comprise at least 42 species that traditionally have been partitioned among four or more species groups based on morphological characters. The Cryptotis mexicana species group is of particular interest, because its member species inhibit a subtly graded series of forelimb adaptations that appear to correspond to locomotory behaviors that range from more ambulatory to more fossorial. Unfortunately, the evolutionary relationships both among species in the C. mexicana group and among the species groups remain unclear. To better understand the phylogeny of this group of shrews, we sequenced two mitochondrial and two nuclear genes. To help interpret the pattern and direction of morphological changes, we also generated a matrix of morphological characters focused on the evolutionarily plastic humerus. We found significant discordant between the resulting molecular and morphological trees, suggesting considerable convergence in the evolution of the humerus. Our results indicate that adaptations for increased burrowing ability evolved repeatedly within the genus Cryptotis. PMID:26489020

  20. Selective transport systems mediate sequestration of plant glucosides in leaf beetles: A molecular basis for adaptation and evolution

    PubMed Central

    Kuhn, Jürgen; Pettersson, Eva M.; Feld, Birte K.; Burse, Antje; Termonia, Arnaud; Pasteels, Jacques M.; Boland, Wilhelm

    2004-01-01

    Chrysomeline larvae respond to disturbance and attack by everting dorsal glandular reservoirs, which release defensive secretions. The ancestral defense is based on the de novo synthesis of monoterpene iridoids. The catabolization of the host-plant O-glucoside salicin into salicylaldehyde is a character state that evolved later in two distinct lineages, which specialized on Salicaceae. By using two species producing monoterpenes (Hydrothassa marginella and Phratora laticollis) and two sequestering species (Chrysomela populi and Phratora vitellinae), we studied the molecular basis of sequestration by feeding the larvae structurally different thioglucosides resembling natural O-glucosides. Their accumulation in the defensive systems demonstrated that the larvae possess transport systems, which are evolutionarily adapted to the glycosides of their host plants. Minor structural modifications in the aglycon result in drastically reduced transport rates of the test compounds. Moreover, the ancestral iridoid-producing leaf beetles already possess a fully functional import system for an early precursor of the iridoid defenses. Our data confirm an evolutionary scenario in which, after a host-plant change, the transport system of the leaf beetles may play a pivotal role in the adaptation on new hosts by selecting plant-derived glucosides that can be channeled to the defensive system. PMID:15365181

  1. 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. PMID:26881892

  2. 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

  3. Explosive type of moderate-resistance training induces functional, cardiovascular, and molecular adaptations in the elderly.

    PubMed

    Beltran Valls, Maria Reyes; Dimauro, Ivan; Brunelli, Andrea; Tranchita, Eliana; Ciminelli, Emanuela; Caserotti, Paolo; Duranti, Guglielmo; Sabatini, Stefania; Parisi, Paolo; Parisi, Attilio; Caporossi, Daniela

    2014-04-01

    Current recommendations aimed at reducing neuromuscular and functional loss in aged muscle have identified muscle power as a key target for intervention trials, although little is known about the biological and cardiovascular systemic response in the elderly. This study investigated the effects of 12 weeks of low-frequency, moderate-intensity, explosive-type resistance training (EMRT) on muscle strength and power in old community-dwelling people (70-75 years), monitoring functional performance linked to daily living activities (ADL) and cardiovascular response, as well as biomarkers of muscle damage, cardiovascular risk, and cellular stress response. The present study provides the first evidence that EMRT was highly effective in achieving a significant enhancement in muscular strength and power as well as in functional performance without causing any detrimental modification in cardiovascular, inflammatory, and damage parameters. Moreover, trained elderly subjects showed an adaptive response at both systemic and cellular levels by modulation of antioxidant and stress-induced markers such as myeloperoxidase (MPO), heat shock protein 70 (Hsp70) and 27 (Hsp27), and thioredoxin reductase 1 (TrxR1). PMID:24136652

  4. Life-history evolution at the molecular level: adaptive amino acid composition of avian vitellogenins

    PubMed Central

    Hughes, Austin L.

    2015-01-01

    Avian genomes typically encode three distinct vitellogenin (VTG) egg yolk proteins (VTG1, VTG2 and VTG3), which arose by gene duplication prior to the most recent common ancestor of birds. Analysis of VTG sequences from 34 avian species in a phylogenetic framework supported the hypothesis that VTG amino acid composition has co-evolved with embryo incubation time. Embryo incubation time was positively correlated with the proportions of dietary essential amino acids (EAAs) in VTG1 and VTG2, and with the proportion of sulfur-containing amino acids in VTG3. These patterns were seen even when only semi-altricial and/or altricial species were considered, suggesting that the duration of embryo incubation is a major selective factor on the amino acid composition of VTGs, rather than developmental mode alone. The results are consistent with the hypothesis that the level of EAAs provided to the egg represents an adaptation to the loss of amino acids through breakdown over the course of incubation and imply that life-history phenotypes and VTG amino acid composition have co-evolved throughout the evolutionary history of birds. PMID:26224713

  5. Parallel molecular routes to cold adaptation in eight genera of New Zealand stick insects

    PubMed Central

    Dennis, Alice B.; Dunning, Luke T.; Sinclair, Brent J.; Buckley, Thomas R.

    2015-01-01

    The acquisition of physiological strategies to tolerate novel thermal conditions allows organisms to exploit new environments. As a result, thermal tolerance is a key determinant of the global distribution of biodiversity, yet the constraints on its evolution are not well understood. Here we investigate parallel evolution of cold tolerance in New Zealand stick insects, an endemic radiation containing three montane-occurring species. Using a phylogeny constructed from 274 orthologous genes, we show that stick insects have independently colonized montane environments at least twice. We compare supercooling point and survival of internal ice formation among ten species from eight genera, and identify both freeze tolerance and freeze avoidance in separate montane lineages. Freeze tolerance is also verified in both lowland and montane populations of a single, geographically widespread, species. Transcriptome sequencing following cold shock identifies a set of structural cuticular genes that are both differentially regulated and under positive sequence selection in each species. However, while cuticular proteins in general are associated with cold shock across the phylogeny, the specific genes at play differ among species. Thus, while processes related to cuticular structure are consistently associated with adaptation for cold, this may not be the consequence of shared ancestral genetic constraints. PMID:26355841

  6. Molecular Genetic Analysis of Orf Virus: A Poxvirus That Has Adapted to Skin

    PubMed Central

    Fleming, Stephen B.; Wise, Lyn M.; Mercer, Andrew A.

    2015-01-01

    Orf virus is the type species of the Parapoxvirus genus of the family Poxviridae. It induces acute pustular skin lesions in sheep and goats and is transmissible to humans. The genome is G+C rich, 138 kbp and encodes 132 genes. It shares many essential genes with vaccinia virus that are required for survival but encodes a number of unique factors that allow it to replicate in the highly specific immune environment of skin. Phylogenetic analysis suggests that both viral interleukin-10 and vascular endothelial growth factor genes have been “captured” from their host during the evolution of the parapoxviruses. Genes such as a chemokine binding protein and a protein that binds granulocyte-macrophage colony-stimulating factor and interleukin-2 appear to have evolved from a common poxvirus ancestral gene while three parapoxvirus nuclear factor (NF)-κB signalling pathway inhibitors have no homology to other known NF-κB inhibitors. A homologue of an anaphase-promoting complex subunit that is believed to manipulate the cell cycle and enhance viral DNA synthesis appears to be a specific adaptation for viral-replication in keratinocytes. The review focuses on the unique genes of orf virus, discusses their evolutionary origins and their role in allowing viral-replication in the skin epidermis. PMID:25807056

  7. Molecular basis of adaptation to high soil boron in wheat landraces and elite cultivars.

    PubMed

    Pallotta, Margaret; Schnurbusch, Thorsten; Hayes, Julie; Hay, Alison; Baumann, Ute; Paull, Jeff; Langridge, Peter; Sutton, Tim

    2014-10-01

    Environmental constraints severely restrict crop yields in most production environments, and expanding the use of variation will underpin future progress in breeding. In semi-arid environments boron toxicity constrains productivity, and genetic improvement is the only effective strategy for addressing the problem. Wheat breeders have sought and used available genetic diversity from landraces to maintain yield in these environments; however, the identity of the genes at the major tolerance loci was unknown. Here we describe the identification of near-identical, root-specific boron transporter genes underlying the two major-effect quantitative trait loci for boron tolerance in wheat, Bo1 and Bo4 (ref. 2). We show that tolerance to a high concentration of boron is associated with multiple genomic changes including tetraploid introgression, dispersed gene duplication, and variation in gene structure and transcript level. An allelic series was identified from a panel of bread and durum wheat cultivars and landraces originating from diverse agronomic zones. Our results demonstrate that, during selection, breeders have matched functionally different boron tolerance alleles to specific environments. The characterization of boron tolerance in wheat illustrates the power of the new wheat genomic resources to define key adaptive processes that have underpinned crop improvement. PMID:25043042

  8. Adaptation of Stenotrophomonas maltophilia in cystic fibrosis: molecular diversity, mutation frequency and antibiotic resistance.

    PubMed

    Vidigal, P G; Dittmer, S; Steinmann, E; Buer, J; Rath, P-M; Steinmann, J

    2014-07-01

    Due to the continuous exposure to a challenging environment and repeated antibiotic treatment courses, bacterial populations in cystic fibrosis (CF) patients experience selective pressure causing the emergence of mutator phenotypes. In this study we investigated the genotypic diversity, mutation frequency and antibiotic resistance of S. maltophilia isolates chronically colonizing CF patients. S. maltophilia was isolated from a total of 90 sputum samples, collected sequentially from 19 CF patients admitted between January 2008 and March 2012 at the University Hospital Essen, Germany. DNA fingerprinting by repetitive-sequence-based PCR revealed that 68.4% (n=13) of CF patients harbored different S. maltophilia genotypes during the 4-year study course. Out of 90 S. maltophilia isolates obtained from chronically colonized CF patients, 17.8% (n=16) were hypomutators, 27.7% (n=25), normomutators, 23.3% (n=21), weak hypermutators and 31.2% (n=28) strong hypermutators. We also found that mutation rates of the most clonally related genotypes varied over time with the tendency to become less mutable. Mutator isolates were found to have no significant increase in resistance against eight different antibiotics versus nonmutators. Sequencing of the mismatch repair genes mutL, mutS and uvrD revealed alterations that resulted in amino acid changes in their corresponding proteins. Here, we could demonstrate that several different S. maltophilia genotypes are present in CF patients and as a sign of adaption their mutation status switches over time to a less mutator phenotype without increasing resistance. These results suggest that S. maltophilia attempts to sustain its biological fitness as mechanism for long-term persistence in the CF lung. PMID:24836944

  9. Adaptation of bird hemoglobins to high altitudes: demonstration of molecular mechanism by protein engineering.

    PubMed

    Jessen, T H; Weber, R E; Fermi, G; Tame, J; Braunitzer, G

    1991-08-01

    Of two closely related species of geese, one, the greylag goose, lives in the Indian plains all year round, while the other, the bar-headed goose, lives at the Tibetan lakes and migrates across the Himalayas to winter in India. Another species, the Andean goose, lives in the High Andes all year round. Possession of a Hb with high oxygen affinity helps to adapt bar-headed and Andean geese to high altitudes. The Hb amino acid sequences of the bar-headed and the greylag geese differ by four substitutions, of which only one is unique among bird sequences: Pro-119 alpha (H2)----Ala. Perutz proposed that the two-carbon gap left by this substitution at the alpha 1 beta 1 contact raises the oxygen affinity, because it relaxes the tension in the deoxy or T structure [Perutz, M. F. (1983) Mol. Biol. Evol. 1, 1-28]. It was later found that the Hb of the Andean goose has a gap in the same position, due to the complementary substitution Leu-55 beta (D6)----Ser. We have tested Perutz's hypothesis by introducing each of these substitutions into human globin synthesized in Escherichia coli. The reconstituted Hbs combine cooperatively with oxygen. Their oxygen affinities exceed that of normal human Hb by an even larger factor than that found between the high-flying geese and the greylag goose. The mutant Hb Met-55 beta (D6)----Ser was crystallized. Its structure is the same as that of HbA, except in the immediate environment of the gap left by the substitution of the serine for the methionine side chain, which evidently causes the increased oxygen affinity of this Hb. PMID:1862080

  10. HIF-1-driven skeletal muscle adaptations to chronic hypoxia: molecular insights into muscle physiology.

    PubMed

    Favier, F B; Britto, F A; Freyssenet, D G; Bigard, X A; Benoit, H

    2015-12-01

    Skeletal muscle is a metabolically active tissue and the major body protein reservoir. Drop in ambient oxygen pressure likely results in a decrease in muscle cells oxygenation, reactive oxygen species (ROS) overproduction and stabilization of the oxygen-sensitive hypoxia-inducible factor (HIF)-1α. However, skeletal muscle seems to be quite resistant to hypoxia compared to other organs, probably because it is accustomed to hypoxic episodes during physical exercise. Few studies have observed HIF-1α accumulation in skeletal muscle during ambient hypoxia probably because of its transient stabilization. Nevertheless, skeletal muscle presents adaptations to hypoxia that fit with HIF-1 activation, although the exact contribution of HIF-2, I kappa B kinase and activating transcription factors, all potentially activated by hypoxia, needs to be determined. Metabolic alterations result in the inhibition of fatty acid oxidation, while activation of anaerobic glycolysis is less evident. Hypoxia causes mitochondrial remodeling and enhanced mitophagy that ultimately lead to a decrease in ROS production, and this acclimatization in turn contributes to HIF-1α destabilization. Likewise, hypoxia has structural consequences with muscle fiber atrophy due to mTOR-dependent inhibition of protein synthesis and transient activation of proteolysis. The decrease in muscle fiber area improves oxygen diffusion into muscle cells, while inhibition of protein synthesis, an ATP-consuming process, and reduction in muscle mass decreases energy demand. Amino acids released from muscle cells may also have protective and metabolic effects. Collectively, these results demonstrate that skeletal muscle copes with the energetic challenge imposed by O2 rarefaction via metabolic optimization. PMID:26298291

  11. Molecular dynamics studies on the adaptability of an ionic liquid in the extraction of solid nanoparticles.

    PubMed

    Frost, Denzil S; Machas, Michael; Dai, Lenore L

    2012-10-01

    Recently, a number of publications have suggested that ionic liquids (ILs) can absorb solid particles. This development may have implications in fields like oil sand processing, oil spill beach cleanup, and water treatment. In this Article, we provide a computational investigation of this phenomenon via molecular dynamics simulations. Two particle surface chemistries were investigated: (1) hydrocarbon-saturated and (2) silanol-saturated, representing hydrophobic and hydrophilic particles, respectively. Employing 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF(6)]) as a model IL, these nanoparticles were allowed to equilibrate at the IL/water and IL/hexane interfaces to observe the interfacial self-assembled structures. At the IL/water interface, the hydrocarbon-based nanoparticles were nearly completely absorbed by the IL, while the silica nanoparticles maintained equal volume in both phases. At the IL/hexane interface, the hydrocarbon nanoparticles maintained minimal interactions with the IL, whereas the silica nanoparticles were nearly completely absorbed by it. Studies of these two types of nanoparticles immersed in the bulk IL indicate that the surface chemistry has a great effect on the corresponding IL liquid structure. These effects include layering of the ions, hydrogen bonding, and irreversible absorption of some ions to the silica nanoparticle surface. We quantify these effects with respect to each nanoparticle. The results suggest that ILs likely exhibit this absorption capability because they can form solvation layers with reduced dynamics around the nanoparticles. PMID:22950605

  12. Cellular, physiological, and molecular adaptive responses of Erwinia amylovora to starvation.

    PubMed

    Santander, Ricardo D; Oliver, James D; Biosca, Elena G

    2014-05-01

    Erwinia amylovora causes fire blight, a destructive disease of rosaceous plants distributed worldwide. This bacterium is a nonobligate pathogen able to survive outside the host under starvation conditions, allowing its spread by various means such as rainwater. We studied E. amylovora responses to starvation using water microcosms to mimic natural oligotrophy. Initially, survivability under optimal (28 °C) and suboptimal (20 °C) growth temperatures was compared. Starvation induced a loss of culturability much more pronounced at 28 °C than at 20 °C. Natural water microcosms at 20 °C were then used to characterize cellular, physiological, and molecular starvation responses of E. amylovora. Challenged cells developed starvation-survival and viable but nonculturable responses, reduced their size, acquired rounded shapes and developed surface vesicles. Starved cells lost motility in a few days, but a fraction retained flagella. The expression of genes related to starvation, oxidative stress, motility, pathogenicity, and virulence was detected during the entire experimental period with different regulation patterns observed during the first 24 h. Further, starved cells remained as virulent as nonstressed cells. Overall, these results provide new knowledge on the biology of E. amylovora under conditions prevailing in nature, which could contribute to a better understanding of the life cycle of this pathogen. PMID:24476337

  13. Adapting SAFT-γ perturbation theory to site-based molecular dynamics simulation. I. Homogeneous fluids

    SciTech Connect

    Ghobadi, Ahmadreza F.; Elliott, J. Richard

    2013-12-21

    In this work, we aim to develop a version of the Statistical Associating Fluid Theory (SAFT)-γ equation of state (EOS) that is compatible with united-atom force fields, rather than experimental data. We rely on the accuracy of the force fields to provide the relation to experimental data. Although, our objective is a transferable theory of interfacial properties for soft and fused heteronuclear chains, we first clarify the details of the SAFT-γ approach in terms of site-based simulations for homogeneous fluids. We show that a direct comparison of Helmholtz free energy to molecular simulation, in the framework of a third order Weeks-Chandler-Andersen perturbation theory, leads to an EOS that takes force field parameters as input and reproduces simulation results for Vapor-Liquid Equilibria (VLE) calculations. For example, saturated liquid density and vapor pressure of n-alkanes ranging from methane to dodecane deviate from those of the Transferable Potential for Phase Equilibria (TraPPE) force field by about 0.8% and 4%, respectively. Similar agreement between simulation and theory is obtained for critical properties and second virial coefficient. The EOS also reproduces simulation data of mixtures with about 5% deviation in bubble point pressure. Extension to inhomogeneous systems and united-atom site types beyond those used in description of n-alkanes will be addressed in succeeding papers.

  14. Molecular Characterization of HIV-1 Subtype C gp-120 Regions Potentially Involved in Virus Adaptive Mechanisms

    PubMed Central

    Cenci, Alessandra; D'Avenio, Giuseppe; Tavoschi, Lara; Chiappi, Michele; Becattini, Simone; Narino, Maria del Pilar; Picconi, Orietta; Bernasconi, Daniela; Fanales-Belasio, Emanuele; Vardas, Eftyhia; Sukati, Hosea; Presti, Alessandra Lo; Ciccozzi, Massimo; Monini, Paolo; Ensoli, Barbara; Grigioni, Mauro; Buttò, Stefano

    2014-01-01

    The role of variable regions of HIV-1 gp120 in immune escape of HIV has been investigated. However, there is scant information on how conserved gp120 regions contribute to virus escaping. Here we have studied how molecular sequence characteristics of conserved C3, C4 and V3 regions of clade C HIV-1 gp120 that are involved in HIV entry and are target of the immune response, are modulated during the disease course. We found an increase of “shifting” putative N-glycosylation sites (PNGSs) in the α2 helix (in C3) and in C4 and an increase of sites under positive selection pressure in the α2 helix during the chronic stage of disease. These sites are close to CD4 and to co-receptor binding sites. We also found a negative correlation between electric charges of C3 and V4 during the late stage of disease counteracted by a positive correlation of electric charges of α2 helix and V5 during the same stage. These data allow us to hypothesize possible mechanisms of virus escape involving constant and variable regions of gp120. In particular, new mutations, including new PNGSs occurring near the CD4 and CCR5 binding sites could potentially affect receptor binding affinity and shield the virus from the immune response. PMID:24788065

  15. Molecular systematics and adaptive radiation of Hawaii's endemic Damselfly genus Megalagrion (Odonata: Coenagrionidae).

    PubMed

    Jordan, Steve; Simon, Chris; Polhemus, Dan

    2003-02-01

    Damselflies of the endemic Hawaiian genus Megalagrion have radiated into a wide variety of habitats and are an excellent model group for the study of adaptive radiation. Past phylogenetic analysis based on morphological characters has been problematic. Here, we examine relationships among 56 individuals from 20 of the 23 described species using maximum likelihood (ML) and Bayesian phylogenetic analysis of mitochondrial (1287 bp) and nuclear (1039 bp) DNA sequence data. Models of evolution were chosen using the Akaike information criterion. Problems with distant outgroups were accommodated by constraining the best ML ingroup topology but allowing the outgroups to attach to any ingroup branch in a bootstrap analysis. No strong contradictions were obtained between either data partition and the combined data set. Areas of disagreement are mainly confined to clades that are strongly supported by the mitochondrial DNA and weakly supported by the elongation factor 1alpha data because of lack of changes. However, the combined analysis resulted in a unique tree. Correlation between Bayesian posterior probabilities and bootstrap percentages decreased in concert with decreasing information in the data partitions. In cases where nodes were supported by single characters bootstrap proportions were dramatically reduced compared with posterior probabilities. Two speciation patterns were evident from the phylogenetic analysis. First, most speciation is interisland and occurred as members of established ecological guilds colonized new volcanoes after they emerged from the sea. Second, there are several instances of rapid radiation into a variety of specialized habitats, in one case entirely within the island of Kauai. Application of a local clock procedure to the mitochondrial DNA topology suggests that two of these radiations correspond to the development of habitat on the islands of Kauai and Oahu. About 4.0 million years ago, species simultaneously moved into fast streams and

  16. Adhesion beyond the interface: Molecular adaptations of the mussel byssus to the intertidal zone

    NASA Astrophysics Data System (ADS)

    MIller, Dusty Rose

    -derived mechanisms for adhesion protection, we also tested for direct chemical mechanisms by tracking redox in the mussel adhesive plaques and found a persistent reservoir of antioxidant activity that can protect Dopa from oxidation. Overall, the mussel byssus represents an excellent model system for understanding adaptive mechanisms of both underwater adhesives and tough materials and I propose in this dissertation that these supporting mechanisms are intimately linked and ultimately responsible for the durable and dynamic underwater adhesion of mussels in the intertidal zone.

  17. Molecular Dynamics of Mesophilic-Like Mutants of a Cold-Adapted Enzyme: Insights into Distal Effects Induced by the Mutations

    PubMed Central

    Papaleo, Elena; Pasi, Marco; Tiberti, Matteo; De Gioia, Luca

    2011-01-01

    Networks and clusters of intramolecular interactions, as well as their “communication” across the three-dimensional architecture have a prominent role in determining protein stability and function. Special attention has been dedicated to their role in thermal adaptation. In the present contribution, seven previously experimentally characterized mutants of a cold-adapted α-amylase, featuring mesophilic-like behavior, have been investigated by multiple molecular dynamics simulations, essential dynamics and analyses of correlated motions and electrostatic interactions. Our data elucidate the molecular mechanisms underlying the ability of single and multiple mutations to globally modulate dynamic properties of the cold-adapted α-amylase, including both local and complex unpredictable distal effects. Our investigation also shows, in agreement with the experimental data, that the conversion of the cold-adapted enzyme in a warm-adapted variant cannot be completely achieved by the introduction of few mutations, also providing the rationale behind these effects. Moreover, pivotal residues, which are likely to mediate the effects induced by the mutations, have been identified from our analyses, as well as a group of suitable candidates for protein engineering. In fact, a subset of residues here identified (as an isoleucine, or networks of mesophilic-like salt bridges in the proximity of the catalytic site) should be considered, in experimental studies, to get a more efficient modification of the features of the cold-adapted enzyme. PMID:21915299

  18. Molecular evolution of the odorant and gustatory receptor genes in lepidopteran insects: implications for their adaptation and speciation.

    PubMed

    Engsontia, Patamarerk; Sangket, Unitsa; Chotigeat, Wilaiwan; Satasook, Chutamas

    2014-08-01

    Lepidoptera (comprised of butterflies and moths) is one of the largest groups of insects, including more than 160,000 described species. Chemoreception plays important roles in the adaptation of these species to a wide range of niches, e.g., plant hosts, egg-laying sites, and mates. This study investigated the molecular evolution of the lepidopteran odorant (Or) and gustatory receptor (Gr) genes using recently identified genes from Bombyx mori, Danaus plexippus, Heliconius melpomene, Plutella xylostella, Heliothis virescens, Manduca sexta, Cydia pomonella, and Spodoptera littoralis. A limited number of cases of large lineage-specific gene expansion are observed (except in the P. xylostella lineage), possibly due to selection against tandem gene duplication. There has been strong purifying selection during the evolution of both lepidopteran odorant and gustatory genes, as shown by the low ω values estimated through CodeML analysis, ranging from 0.0093 to 0.3926. However, purifying selection has been relaxed on some amino acid sites in these receptors, leading to sequence divergence, which is a precursor of positive selection on these sequences. Signatures of positive selection were detected only in a few loci from the lineage-specific analysis. Estimation of gene gains and losses suggests that the common ancestor of the Lepidoptera had fewer Or genes compared to extant species and an even more reduced number of Gr genes, particularly within the bitter receptor clade. Multiple gene gains and a few gene losses occurred during the evolution of Lepidoptera. Gene family expansion may be associated with the adaptation of lepidopteran species to plant hosts, especially after angiosperm radiation. Phylogenetic analysis of the moth sex pheromone receptor genes suggested that chromosomal translocations have occurred several times. New sex pheromone receptors have arisen through tandem gene duplication. Positive selection was detected at some amino acid sites predicted to be

  19. ALV-J GP37 Molecular Analysis Reveals Novel Virus-Adapted Sites and Three Tyrosine-Based Env Species

    PubMed Central

    Shang, Jianjun; Tian, Xiaoyan; Yang, Jialiang; Chen, Hongjun; Shao, Hongxia; Qin, Aijian

    2015-01-01

    Compared to other avian leukosis viruses (ALV), ALV-J primarily induces myeloid leukemia and hemangioma and causes significant economic loss for the poultry industry. The ALV-J Env protein is hypothesized to be related to its unique pathogenesis. However, the molecular determinants of Env for ALV-J pathogenesis are unclear. In this study, we compared and analyzed GP37 of ALV-J Env and the EAV-HP sequence, which has high homology to that of ALV-J Env. Phylogenetic analysis revealed five groups of ALV-J GP37 and two novel ALV-J Envs with endemic GP85 and EAV-HP-like GP37. Furthermore, at least 15 virus-adapted mutations were detected in GP37 compared to the EAV-HP sequence. Further analysis demonstrated that three tyrosine-based motifs (YxxM, ITIM (immune tyrosine-based inhibitory motif) and ITAM-like (immune tyrosine-based active motif like)) associated with immune disease and oncogenesis were found in the cytoplasmic tail of GP37. Based on the potential function and distribution of these motifs in GP37, ALV-J Env was grouped into three species, inhibitory Env, bifunctional Env and active Env. Accordingly, 36.91%, 61.74% and 1.34% of ALV-J Env sequences from GenBank are classified as inhibitory, bifunctional and active Env, respectively. Additionally, the Env of the ALV-J prototype strain, HPRS-103, and 17 of 18 EAV-HP sequences belong to the inhibitory Env. And models for signal transduction of the three ALV-J Env species were predicted. Our findings and models provide novel insights for identifying the roles and molecular mechanism of ALV-J Env in the unique pathogenesis of ALV-J. PMID:25849207

  20. Inferring the Frequency Spectrum of Derived Variants to Quantify Adaptive Molecular Evolution in Protein-Coding Genes of Drosophila melanogaster.

    PubMed

    Keightley, Peter D; Campos, José L; Booker, Tom R; Charlesworth, Brian

    2016-06-01

    Many approaches for inferring adaptive molecular evolution analyze the unfolded site frequency spectrum (SFS), a vector of counts of sites with different numbers of copies of derived alleles in a sample of alleles from a population. Accurate inference of the high-copy-number elements of the SFS is difficult, however, because of misassignment of alleles as derived vs. ancestral. This is a known problem with parsimony using outgroup species. Here we show that the problem is particularly serious if there is variation in the substitution rate among sites brought about by variation in selective constraint levels. We present a new method for inferring the SFS using one or two outgroups that attempts to overcome the problem of misassignment. We show that two outgroups are required for accurate estimation of the SFS if there is substantial variation in selective constraints, which is expected to be the case for nonsynonymous sites in protein-coding genes. We apply the method to estimate unfolded SFSs for synonymous and nonsynonymous sites in a population of Drosophila melanogaster from phase 2 of the Drosophila Population Genomics Project. We use the unfolded spectra to estimate the frequency and strength of advantageous and deleterious mutations and estimate that ∼50% of amino acid substitutions are positively selected but that <0.5% of new amino acid mutations are beneficial, with a scaled selection strength of Nes ≈ 12. PMID:27098912

  1. On the salty side of life: molecular, physiological and anatomical adaptation and acclimation of trees to extreme habitats.

    PubMed

    Polle, Andrea; Chen, Shaoliang

    2015-09-01

    Saline and sodic soils that cannot be used for agriculture occur worldwide. Cultivating stress-tolerant trees to obtain biomass from salinized areas has been suggested. Various tree species of economic importance for fruit, fibre and timber production exhibit high salinity tolerance. Little is known about the mechanisms enabling tree crops to cope with high salinity for extended periods. Here, the molecular, physiological and anatomical adjustments underlying salt tolerance in glycophytic and halophytic model tree species, such as Populus euphratica in terrestrial habitats, and mangrove species along coastlines are reviewed. Key mechanisms that have been identified as mediating salt tolerance are discussed at scales from the genetic to the morphological level, including leaf succulence and structural adjustments of wood anatomy. The genetic and transcriptomic bases for physiological salt acclimation are salt sensing and signalling networks that activate target genes; the target genes keep reactive oxygen species under control, maintain the ion balance and restore water status. Evolutionary adaptation includes gene duplication in these pathways. Strategies for and limitations to tree improvement, particularly transgenic approaches for increasing salt tolerance by transforming trees with single and multiple candidate genes, are discussed. PMID:25159181

  2. Photosynthesis, environmental change, and plant adaptation: Research topics in plant molecular ecology. Summary report of a workshop

    SciTech Connect

    1995-07-01

    As we approach the 21st Century, it is becoming increasingly clear that human activities, primarily related to energy extraction and use, will lead to marked environmental changes at the local, regional, and global levels. The realized and the potential photosynthetic performance of plants is determined by a combination of intrinsic genetic information and extrinsic environmental factors, especially climate. It is essential that the effects of environmental changes on the photosynthetic competence of individual species, communities, and ecosystems be accurately assessed. From October 24 to 26, 1993, a group of scientists specializing in various aspects of plant science met to discuss how our predictive capabilities could be improved by developing a more rational, mechanistic approach to relating photosynthetic processes to environmental factors. A consensus emerged that achieving this goal requires multidisciplinary research efforts that combine tools and techniques of genetics, molecular biology, biophysics, biochemistry, and physiology to understand the principles, mechanisms, and limitations of evolutional adaptation and physiological acclimation of photosynthetic processes. Many of these basic tools and techniques, often developed in other fields of science, already are available but have not been applied in a coherent, coordinated fashion to ecological research. The efforts of this research program are related to the broader efforts to develop more realistic prognostic models to forecast climate change that include photosynthetic responses and feedbacks at the regional and ecosystem levels.

  3. The Molecular Mechanism Underlying Continuous Exercise Training-Induced Adaptive Changes of Lipolysis in White Adipose Cells.

    PubMed

    Ogasawara, Junetsu; Izawa, Tetsuya; Sakurai, Tomonobu; Sakurai, Takuya; Shirato, Ken; Ishibashi, Yoshinaga; Ishida, Hitoshi; Ohno, Hideki; Kizaki, Takako

    2015-01-01

    Physical exercise accelerates the mobilization of free fatty acids from white adipocytes to provide fuel for energy. This happens in several tissues and helps to regulate a whole-body state of metabolism. Under these conditions, the hydrolysis of triacylglycerol (TG) that is found in white adipocytes is known to be augmented via the activation of these lipolytic events, which is referred to as the "lipolytic cascade." Indeed, evidence has shown that the lipolytic responses in white adipocytes are upregulated by continuous exercise training (ET) through the adaptive changes in molecules that constitute the lipolytic cascade. During the past few decades, many lipolysis-related molecules have been identified. Of note, the discovery of a new lipase, known as adipose triglyceride lipase, has redefined the existing concepts of the hormone-sensitive lipase-dependent hydrolysis of TG in white adipocytes. This review outlines the alterations in the lipolytic molecules of white adipocytes that result from ET, which includes the molecular regulation of TG lipases through the lipolytic cascade. PMID:26075089

  4. Effect of heterologous expression of molecular chaperone DnaK from Tetragenococcus halophilus on salinity adaptation of Escherichia coli.

    PubMed

    Sugimoto, Shinya; Nakayama, Jiro; Fukuda, Daisuke; Sonezaki, Shino; Watanabe, Maki; Tosukhowong, Amonlaya; Sonomoto, Kenji

    2003-01-01

    Molecular chaperone DnaK of halophilic Tetragenococcus halophilus JCM5888 was characterized under salinity conditions both in vitro and in vivo. The dnaK gene was cloned into an expression vector and transformed into Escherichia coli. The DnaK protein obtained from the recombinant E. coli showed a significantly higher refolding activity of denatured lactate dehydrogenase than that from non-halophilic Lactococcus lactis under NaCl concentrations higher than 1 M. E. coli without the overexpression of DnaK exhibited a growth profile with a prolonged lag phase and suppressed maximum cell density in Luria-Bertani medium containing 5% (0.86 M) NaCl. On the contrary, the overexpression of T. halophilus DnaK greatly shortened this prolonged lag phase with no effect on maximum growth, while that of L. lactis DnaK decreased maximum growth. The amount of protein aggregates was increased by salt stress in the E. coli cells, while this aggregation was greatly suppressed by the overexpression of T, halophilus DnaK. These results suggest that heterologous overexpression of T. halophilus DnaK, via its chaperone activity, promotes salinity adaptation of E. coli. PMID:16233497

  5. Prolyl Isomerization as a Molecular Memory in the Allosteric Regulation of the Signal Adapter Protein c-CrkII

    PubMed Central

    Schmidpeter, Philipp A. M.; Schmid, Franz X.

    2015-01-01

    c-CrkII is a central signal adapter protein. A domain opening/closing reaction between its N- and C-terminal Src homology 3 domains (SH3N and SH3C, respectively) controls signal propagation from upstream tyrosine kinases to downstream targets. In chicken but not in human c-CrkII, opening/closing is coupled with cis/trans isomerization at Pro-238 in SH3C. Here, we used advanced double-mixing experiments and kinetic simulations to uncover dynamic domain interactions in c-CrkII and to elucidate how they are linked with cis/trans isomerization and how this regulates substrate binding to SH3N. Pro-238 trans → cis isomerization is not a simple on/off switch but converts chicken c-CrkII from a high affinity to a low affinity form. We present a double-box model that describes c-CrkII as an allosteric system consisting of an open, high affinity R state and a closed, low affinity T state. Coupling of the T-R transition with an intrinsically slow prolyl isomerization provides c-CrkII with a kinetic memory and possibly functions as a molecular attenuator during signal transduction. PMID:25488658

  6. Prolyl isomerization as a molecular memory in the allosteric regulation of the signal adapter protein c-CrkII.

    PubMed

    Schmidpeter, Philipp A M; Schmid, Franz X

    2015-01-30

    c-CrkII is a central signal adapter protein. A domain opening/closing reaction between its N- and C-terminal Src homology 3 domains (SH3N and SH3C, respectively) controls signal propagation from upstream tyrosine kinases to downstream targets. In chicken but not in human c-CrkII, opening/closing is coupled with cis/trans isomerization at Pro-238 in SH3C. Here, we used advanced double-mixing experiments and kinetic simulations to uncover dynamic domain interactions in c-CrkII and to elucidate how they are linked with cis/trans isomerization and how this regulates substrate binding to SH3N. Pro-238 trans → cis isomerization is not a simple on/off switch but converts chicken c-CrkII from a high affinity to a low affinity form. We present a double-box model that describes c-CrkII as an allosteric system consisting of an open, high affinity R state and a closed, low affinity T state. Coupling of the T-R transition with an intrinsically slow prolyl isomerization provides c-CrkII with a kinetic memory and possibly functions as a molecular attenuator during signal transduction. PMID:25488658

  7. Mineral respiration under extreme acidic conditions: from a supramolecular organization to a molecular adaptation in Acidithiobacillus ferrooxidans.

    PubMed

    Roger, Magali; Castelle, Cindy; Guiral, Marianne; Infossi, Pascale; Lojou, Elisabeth; Giudici-Orticoni, Marie-Thérèse; Ilbert, Marianne

    2012-12-01

    Acidithiobacillus ferrooxidans is an acidophilic chemolithoautotrophic Gram-negative bacterium that can derive energy from the oxidation of ferrous iron at pH 2 using oxygen as electron acceptor. The study of this bacterium has economic and fundamental biological interest because of its use in the industrial extraction of copper and uranium from ores. For this reason, its respiratory chain has been analysed in detail in recent years. Studies have shown the presence of a functional supercomplex that spans the outer and the inner membranes and allows a direct electron transfer from the extracellular Fe2+ ions to the inner membrane cytochrome c oxidase. Iron induces the expression of two operons encoding proteins implicated in this complex as well as in the regeneration of the reducing power. Most of these are metalloproteins that have been characterized biochemically, structurally and biophysically. For some of them, the molecular basis of their adaptation to the periplasmic acidic environment has been described. Modifications in the metal surroundings have been highlighted for cytochrome c and rusticyanin, whereas, for the cytochrome c oxidase, an additional partner that maintains its stability and activity has been demonstrated recently. PMID:23176476

  8. The Molecular Mechanism Underlying Continuous Exercise Training-Induced Adaptive Changes of Lipolysis in White Adipose Cells

    PubMed Central

    Ogasawara, Junetsu; Sakurai, Tomonobu; Sakurai, Takuya; Ishibashi, Yoshinaga; Ishida, Hitoshi; Ohno, Hideki

    2015-01-01

    Physical exercise accelerates the mobilization of free fatty acids from white adipocytes to provide fuel for energy. This happens in several tissues and helps to regulate a whole-body state of metabolism. Under these conditions, the hydrolysis of triacylglycerol (TG) that is found in white adipocytes is known to be augmented via the activation of these lipolytic events, which is referred to as the “lipolytic cascade.” Indeed, evidence has shown that the lipolytic responses in white adipocytes are upregulated by continuous exercise training (ET) through the adaptive changes in molecules that constitute the lipolytic cascade. During the past few decades, many lipolysis-related molecules have been identified. Of note, the discovery of a new lipase, known as adipose triglyceride lipase, has redefined the existing concepts of the hormone-sensitive lipase-dependent hydrolysis of TG in white adipocytes. This review outlines the alterations in the lipolytic molecules of white adipocytes that result from ET, which includes the molecular regulation of TG lipases through the lipolytic cascade. PMID:26075089

  9. An atomic charge-charge flux-dipole flux atom-in-molecule decomposition for molecular dipole-moment derivatives and infrared fundamental intensities.

    PubMed

    Haiduke, Roberto L A; Bruns, Roy E

    2005-03-24

    The molecular dipole moment and its derivatives are determined from atomic charges, atomic dipoles, and their fluxes obtained from AIM formalism and calculated at the MP2(FC)/6-311++G(3d,3p) level for 16 molecules: 6 diatomic hydrides, CO, HCN, OCS, CO2, CS2, C2H2, C2N2, H2O, H2CO, and CH4. Root-mean-square (rms) errors of 0.052 D and 0.019 e are found for the dipole moments and their derivatives calculated using AIM parameters when compared with those obtained directly from the MP2(FC)/6-311++G(3d,3p) calculations and 0.097 D and 0.049 e when compared to the experimental values. The major deviations occur for the NaH, HF, and H2O molecules. Parallel polar tensor elements for the diatomic and linear polyatomic molecules, except H2, HF, LiH, and NaH, have values resulting from cancellations of substantial contributions from atomic charge fluxes and atomic dipole fluxes. These fluxes have a large negative correlation coefficient, -0.97. IR fundamental intensity sums for CO, HCN, OCS, CO2, CS2, C2H2, C2N2, H2CO, and CH4 calculated using AIM charges, charge fluxes, and atomic dipole fluxes have rms errors of 14.9 km mol(-1) when compared with sums calculated directly from the molecular wave function and 36.2 km mol(-1) relative to experimental values. The classical model proposed here to calculate dipole-moment derivatives is compared with the charge-charge flux-overlap model long used by spectroscopists for interpreting IR vibrational intensities. The utility of the AIM atomic charges and dipoles was illustrated by calculating the forces exerted on molecules by a charged particle. AIM quantities were able to reproduce forces due to a +0.1 e particle over a 3-8-A separation range for the CO and HF molecules in collinear and perpendicular arrangements. These results show that IR intensities do contain information relevant to the study of intermolecular interactions. PMID:16833574

  10. Comparative analysis of nucleotide translocation through protein nanopores using steered molecular dynamics and an adaptive biasing force

    PubMed Central

    Martin, Hugh S C; Jha, Shantenu; Coveney, Peter V

    2014-01-01

    The translocation of nucleotide molecules across biological and synthetic nanopores has attracted attention as a next generation technique for sequencing DNA. Computer simulations have the ability to provide atomistic-level insight into important states and processes, delivering a means to develop a fundamental understanding of the translocation event, for example, by extracting the free energy of the process. Even with current supercomputing facilities, the simulation of many-atom systems in fine detail is limited to shorter timescales than the real events they attempt to recreate. This imposes the need for enhanced simulation techniques that expand the scope of investigation in a given timeframe. There are numerous free energy calculation and translocation methodologies available, and it is by no means clear which method is best applied to a particular problem. This article explores the use of two popular free energy calculation methodologies in a nucleotide-nanopore translocation system, using the α-hemolysin nanopore. The first uses constant velocity-steered molecular dynamics (cv-SMD) in conjunction with Jarzynski's equality. The second applies an adaptive biasing force (ABF), which has not previously been applied to the nucleotide-nanpore system. The purpose of this study is to provide a comprehensive comparison of these methodologies, allowing for a detailed comparative assessment of the scientific merits, the computational cost, and the statistical quality of the data obtained from each technique. We find that the ABF method produces results that are closer to experimental measurements than those from cv-SMD, whereas the net errors are smaller for the same computational cost. © 2014 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:24403093

  11. Prolonged Residence Time of a Noncovalent Molecular Adapter, β-Cyclodextrin, within the Lumen of Mutant α-Hemolysin Pores

    PubMed Central

    Gu, Li-Qun; Cheley, Stephen; Bayley, Hagan

    2001-01-01

    Noncovalent molecular adapters, such as cyclodextrins, act as binding sites for channel blockers when lodged in the lumen of the α-hemolysin (αHL) pore, thereby offering a basis for the detection of a variety of organic molecules with αHL as a sensor element. β-Cyclodextrin (βCD) resides in the wild-type αHL pore for several hundred microseconds. The residence time can be extended to several milliseconds by the manipulation of pH and transmembrane potential. Here, we describe mutant homoheptameric αHL pores that are capable of accommodating βCD for tens of seconds. The mutants were obtained by site-directed mutagenesis at position 113, which is a residue that lies near a constriction in the lumen of the transmembrane β barrel, and fall into two classes. Members of the tight-binding class, M113D, M113N, M113V, M113H, M113F and M113Y, bind βCD ∼104-fold more avidly than the remaining αHL pores, including WT-αHL. The lower Kd values of these mutants are dominated by reduced values of koff. The major effect of the mutations is most likely a remodeling of the binding site for βCD in the vicinity of position 113. In addition, there is a smaller voltage-sensitive component of the binding, which is also affected by the residue at 113 and may result from transport of the neutral βCD molecule by electroosmotic flow. The mutant pores for which the dwell time of βCD is prolonged can serve as improved components for stochastic sensors. PMID:11696607

  12. Orthogonal tensor decompositions

    SciTech Connect

    Tamara G. Kolda

    2000-03-01

    The authors explore the orthogonal decomposition of tensors (also known as multi-dimensional arrays or n-way arrays) using two different definitions of orthogonality. They present numerous examples to illustrate the difficulties in understanding such decompositions. They conclude with a counterexample to a tensor extension of the Eckart-Young SVD approximation theorem by Leibovici and Sabatier [Linear Algebra Appl. 269(1998):307--329].

  13. Physicochemical Evolution and Molecular Adaptation of the Cetacean Osmoregulation-related Gene UT-A2 and Implications for Functional Studies

    PubMed Central

    Wang, Jingzhen; Yu, Xueying; Hu, Bo; Zheng, Jinsong; Xiao, Wuhan; Hao, Yujiang; Liu, Wenhua; Wang, Ding

    2015-01-01

    Cetaceans have an enigmatic evolutionary history of re-invading aquatic habitats. One of their essential adaptabilities that has enabled this process is their homeostatic strategy adjustment. Here, we investigated the physicochemical evolution and molecular adaptation of the cetacean urea transporter UT-A2, which plays an important role in urine concentration and water homeostasis. First, we cloned UT-A2 from the freshwater Yangtze finless porpoise, after which bioinformatics analyses were conducted based on available datasets (including freshwater baiji and marine toothed and baleen whales) using MEGA, PAML, DataMonkey, TreeSAAP and Consurf. Our findings suggest that the UT-A2 protein shows folding similar to that of dvUT and UT-B, whereas some variations occurred in the functional So and Si regions of the selectivity filter. Additionally, several regions of the cetacean UT-A2 protein have experienced molecular adaptations. We suggest that positive-destabilizing selection could contribute to adaptations by influencing its biochemical and conformational character. The conservation of amino acid residues within the selectivity filter of the urea conduction pore is likely to be necessary for urea conduction, whereas the non-conserved amino acid replacements around the entrance and exit of the conduction pore could potentially affect the activity, which could be interesting target sites for future mutagenesis studies. PMID:25762239

  14. 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.

  15. Molecular and immunogenic characterization of BHK-21 cell line adapted CVS-11 strain of rabies virus and future prospect in vaccination strategy.

    PubMed

    Patel, Arunkumar C; Upmanyu, Vikramaditya; Ramasamy, Santhamani; Gupta, Praveen Kumar; Singh, Rajendra; Singh, Rabindra Prasad

    2015-12-01

    Development of a cost effective quality vaccine is a key issue in rabies control programme in developing countries. With this perspective, in the present study, challenge virus standard (CVS)-11 strain of rabies virus was adapted to grow in BHK-21 cells, characterized, compared with other viruses including global vaccine strains and field isolates from Indian subcontinent and China at molecular level. This cell adapted virus was evaluated for the production of cost effective veterinary vaccine. The maximum virus titre achieved was 10(7) fluorescent focus unit (FFU)/mL at 10th passage level. There was no nucleotide difference in the nucleoprotein (N) and glycoprotein (G) genes after adaptation in cell line. Phylogenetic analysis showed that adapted virus was grouped with global vaccine strains, closest being with other CVS strains but distinct from the Indian field isolates. Global vaccine strains including cell adapted CVS-11 virus have 83-87 % identity at nucleotide level of G gene with Indian field viruses. Growth kinetics of cell culture adapted virus showed that the optimum virus titer (around 10(7) FFU/mL) could be obtained at around 48 h post infection by co-cultivation method using 0.1 multiplicity of infection inoculums at 37 °C. These findings can be used for up scaling of vaccine production. The protective efficacy of test vaccine produced using 10(6.95) FFU/mL cell culture harvest showed 1.17 IU/mL relative potency by NIH test. Further, adapted virus was found to be suitable for use in rapid fluorescent focus inhibition test. PMID:26645040

  16. 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. PMID:26748499

  17. Autocatalytic Decomposition at Shear-Strain Interfaces

    NASA Astrophysics Data System (ADS)

    Kuklja, M. M.; Rashkeev, Sergey N.

    2009-12-01

    Atomic scale mechanisms of the initiation of chemical processes in energetic molecular crystals leading to the decomposition and ultimately to an explosive chain reaction, are far from being completely understood. We investigated the onset of the initiation processes in two energetic crystals—diamino-dinitroethylene (DADNE, C2H4N4O4) and triamino-trinitrobenzene (TATB, C6H6N6O6). We suggest that an autocatalytic decomposition mechanism is likely to take place in DADNE crystal that is built out of corrugated, dashboard-shaped molecular layers, and the level of the induced shear-strain perturbation between the layers strongly depends upon the presence of interstitial NO2 groups. Unlike this, in TATB, which consists of flat, graphite-like molecular layers, an interstitial NO2 group positioned between two layers produces a local molecular orientation disorder and barely affects the C-NO2 decomposition barrier. Split off NO2 groups in the interstitial exhibit a series of exothermic reactions. In DADNE, these reactions start at a lower concentration of interstitial nitro-groups which may be correlated to the higher sensitivity of this material to the initiation as compared to TATB.

  18. Molecular characterization of mammalian-adapted Korean-type avian H9N2 virus and evaluation of its virulence in mice.

    PubMed

    Park, Kuk Jin; Song, Min-Suk; Kim, Eun-Ha; Kwon, Hyeok-Il; Baek, Yun Hee; Choi, Eun-Hye; Park, Su-Jin; Kim, Se Mi; Kim, Young-Il; Choi, Won-Suk; Yoo, Dae-Won; Kim, Chul-Joong; Choi, Young Ki

    2015-08-01

    Avian influenza A virus (AIV) is commonly isolated from domestic poultry and wild migratory birds, and the H9N2 subtype is the most prevalent and the major cause of severe disease in poultry in Korea. In addition to the veterinary concerns regarding the H9N2 subtype, it is also considered to be the next potential human pandemic strain due to its rapid evolution and interspecies transmission. In this study, we utilize serial lung-to-lung passage of a low pathogenic avian influenza virus (LPAI) H9N2 (A/Ck/Korea/163/04, WT163) (Y439-lineage) in mice to increase pathogenicity and investigate the potential virulence marker. Mouse-adapted H9N2 virus obtained high virulence (100% mortality) in mice after 98 serial passages. Sequence results show that the mouse adaptation (ma163) possesses several mutations within seven gene segments (PB2, PA, HA, NP, NA, M, and NS) relative to the wild-type strain. The HA gene showed the most mutations (at least 11) with one resulting in the loss of an N-glycosylation site (at amino acid 166). Moreover, reverse genetic studies established that an E627K substitution in PB2 and the loss of the N-glycosylation site in the HA protein (aa166) are critical virulence markers in the mouse-adapted H9N2 virus. Thus, these results add to the increasing body of mutational analysis data defining the function of the viral polymerase and HA genes and their roles in mammalian host adaptation. To our knowledge, this is first report of the generation of a mammalian-adapted Korea H9N2 virus (Y493-lineages). Therefore, this study offers valuable insights into the molecular evolution of the LPAI Korean H9N2 in a new host and adds to the current knowledge of the molecular markers associated with increased virulence. PMID:26224460

  19. Cold Adaptation of Zinc Metalloproteases in the Thermolysin Family from Deep Sea and Arctic Sea Ice Bacteria Revealed by Catalytic and Structural Properties and Molecular Dynamics

    PubMed Central

    Xie, Bin-Bin; Bian, Fei; Chen, Xiu-Lan; He, Hai-Lun; Guo, Jun; Gao, Xiang; Zeng, Yin-Xin; Chen, Bo; Zhou, Bai-Cheng; Zhang, Yu-Zhong

    2009-01-01

    Increased conformational flexibility is the prevailing explanation for the high catalytic efficiency of cold-adapted enzymes at low temperatures. However, less is known about the structural determinants of flexibility. We reported two novel cold-adapted zinc metalloproteases in the thermolysin family, vibriolysin MCP-02 from a deep sea bacterium and vibriolysin E495 from an Arctic sea ice bacterium, and compared them with their mesophilic homolog, pseudolysin from a terrestrial bacterium. Their catalytic efficiencies, kcat/Km (10–40 °C), followed the order pseudolysin < MCP-02 < E495 with a ratio of ∼1:2:4. MCP-02 and E495 have the same optimal temperature (Topt, 57 °C, 5 °C lower than pseudolysin) and apparent melting temperature (Tm = 64 °C, ∼10 °C lower than pseudolysin). Structural analysis showed that the slightly lower stabilities resulted from a decrease in the number of salt bridges. Fluorescence quenching experiments and molecular dynamics simulations showed that the flexibilities of the proteins were pseudolysin < MCP-02 < E495, suggesting that optimization of flexibility is a strategy for cold adaptation. Molecular dynamics results showed that the ordinal increase in flexibility from pseudolysin to MCP-02 and E495, especially the increase from MCP-02 to E495, mainly resulted from the decrease of hydrogen-bond stability in the dynamic structure, which was due to the increase in asparagine, serine, and threonine residues. Finally, a model for the cold adaptation of MCP-02 and E495 was proposed. This is the first report of the optimization of hydrogen-bonding dynamics as a strategy for cold adaptation and provides new insights into the structural basis underlying conformational flexibility. PMID:19181663

  20. Combining molecular evolution and environmental genomics to unravel adaptive processes of MHC class IIB diversity in European minnows (Phoxinus phoxinus)

    PubMed Central

    Collin, Helene; Burri, Reto; Comtesse, Fabien; Fumagalli, Luca

    2013-01-01

    Abstract Host–pathogen interactions are a major evolutionary force promoting local adaptation. Genes of the major histocompatibility complex (MHC) represent unique candidates to investigate evolutionary processes driving local adaptation to parasite communities. The present study aimed at identifying the relative roles of neutral and adaptive processes driving the evolution of MHC class IIB (MHCIIB) genes in natural populations of European minnows (Phoxinus phoxinus). To this end, we isolated and genotyped exon 2 of two MHCIIB gene duplicates (DAB1 and DAB3) and 1′665 amplified fragment length polymorphism (AFLP) markers in nine populations, and characterized local bacterial communities by 16S rDNA barcoding using 454 amplicon sequencing. Both MHCIIB loci exhibited signs of historical balancing selection. Whereas genetic differentiation exceeded that of neutral markers at both loci, the populations' genetic diversities were positively correlated with local pathogen diversities only at DAB3. Overall, our results suggest pathogen-mediated local adaptation in European minnows at both MHCIIB loci. While at DAB1 selection appears to favor different alleles among populations, this is only partially the case in DAB3, which appears to be locally adapted to pathogen communities in terms of genetic diversity. These results provide new insights into the importance of host–pathogen interactions in driving local adaptation in the European minnow, and highlight that the importance of adaptive processes driving MHCIIB gene evolution may differ among duplicates within species, presumably as a consequence of alternative selective regimes or different genomic context. Using next-generation sequencing, the present manuscript identifies the relative roles of neutral and adaptive processes driving the evolution of MHC class IIB (MHCIIB) genes in natural populations of a cyprinid fish: the European minnow (Phoxinus phoxinus). We highlight that the relative importance of neutral

  1. Decomposing Nekrasov decomposition

    NASA Astrophysics Data System (ADS)

    Morozov, A.; Zenkevich, Y.

    2016-02-01

    AGT relations imply that the four-point conformal block admits a decomposition into a sum over pairs of Young diagrams of essentially rational Nekrasov functions — this is immediately seen when conformal block is represented in the form of a matrix model. However, the q-deformation of the same block has a deeper decomposition — into a sum over a quadruple of Young diagrams of a product of four topological vertices. We analyze the interplay between these two decompositions, their properties and their generalization to multi-point conformal blocks. In the latter case we explain how Dotsenko-Fateev all-with-all (star) pair "interaction" is reduced to the quiver model nearest-neighbor (chain) one. We give new identities for q-Selberg averages of pairs of generalized Macdonald polynomials. We also translate the slicing invariance of refined topological strings into the language of conformal blocks and interpret it as abelianization of generalized Macdonald polynomials.

  2. NTO decomposition studies

    SciTech Connect

    Oxley, J.C.; Smith, J.L.; Yeager, K.E.; Rogers, E.; Dong, X.X.

    1996-07-01

    To examine the thermal decomposition of 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO) in detail, isotopic labeling studies were undertaken. NTO samples labeled with {sup 15}N in three different locations [N(1) and N(2), N(4), and N(6)] were prepared. Upon thermolysis, the majority of the NTO condensed-phase product was a brown, insoluble residue, but small quantities of 2,4-dihydro-3H-1,2,4-triazol-3-one (TO) and triazole were detected. Gases comprised the remainder of the NTO decomposition products. The analysis of these gases is reported along with mechanistic implications of these observations.

  3. 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.

  4. Characterizing early molecular biomarkers of zinc-induced adaptive and adverseoxidative stress responses in human bronchial epithelial cells

    EPA Science Inventory

    Determining mechanism-based biomarkers that distinguish adaptive and adverse cellular processes is critical to understanding the health effects of environmental exposures. Here, we examined cellular responses of the tracheobronchial airway to zinc (Zn) exposure. A pharmacokinetic...

  5. Optimal Decomposition of Service Level Objectives into Policy Assertions.

    PubMed

    Rastegari, Yousef; Shams, Fereidoon

    2015-01-01

    WS-agreement specifies quality objectives that each partner is obligated to provide. To meet quality objectives, the corresponding partner should apply appropriate policy assertions to its web services and adjust their parameters accordingly. Transformation of WS-CDL to WSBPEL is addressed in some related works, but neither of them considers quality aspects of transformation nor run-time adaptation. Here, in conformance with web services standards, we propose an optimal decomposition method to make a set of WS-policy assertions. Assertions can be applied to WSBPEL elements and affect their run-time behaviors. The decomposition method achieves the best outcome for a performance indicator. It also guarantees the lowest adaptation overhead by reducing the number of service reselections. We considered securities settlement case study to prototype and evaluate the decomposition method. The results show an acceptable threshold between customer satisfaction-the targeted performance indicator in our case study-and adaptation overhead. PMID:26962544

  6. Optimal Decomposition of Service Level Objectives into Policy Assertions

    PubMed Central

    Rastegari, Yousef; Shams, Fereidoon

    2015-01-01

    WS-agreement specifies quality objectives that each partner is obligated to provide. To meet quality objectives, the corresponding partner should apply appropriate policy assertions to its web services and adjust their parameters accordingly. Transformation of WS-CDL to WSBPEL is addressed in some related works, but neither of them considers quality aspects of transformation nor run-time adaptation. Here, in conformance with web services standards, we propose an optimal decomposition method to make a set of WS-policy assertions. Assertions can be applied to WSBPEL elements and affect their run-time behaviors. The decomposition method achieves the best outcome for a performance indicator. It also guarantees the lowest adaptation overhead by reducing the number of service reselections. We considered securities settlement case study to prototype and evaluate the decomposition method. The results show an acceptable threshold between customer satisfaction—the targeted performance indicator in our case study—and adaptation overhead. PMID:26962544

  7. 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.

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

    SciTech Connect

    Bent, Russell W

    2010-01-01

    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 decompositions 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.

  9. Multicriteria approximation through decomposition

    SciTech Connect

    Burch, C. |; Krumke, S.; Marathe, M.; Phillips, C.; Sundberg, E. |

    1997-12-01

    The authors propose a general technique called solution decomposition to devise approximation algorithms with provable performance guarantees. The technique is applicable to a large class of combinatorial optimization problems that can be formulated as integer linear programs. Two key ingredients of the technique involve finding a decomposition of a fractional solution into a convex combination of feasible integral solutions and devising generic approximation algorithms based on calls to such decompositions as oracles. The technique is closely related to randomized rounding. The method yields as corollaries unified solutions to a number of well studied problems and it provides the first approximation algorithms with provable guarantees for a number of new problems. The particular results obtained in this paper include the following: (1) The authors demonstrate how the technique can be used to provide more understanding of previous results and new algorithms for classical problems such as Multicriteria Spanning Trees, and Suitcase Packing. (2) They show how the ideas can be extended to apply to multicriteria optimization problems, in which they wish to minimize a certain objective function subject to one or more budget constraints. As corollaries they obtain first non-trivial multicriteria approximation algorithms for problems including the k-Hurdle and the Network Inhibition problems.

  10. Multicriteria approximation through decomposition

    SciTech Connect

    Burch, C.; Krumke, S.; Marathe, M.; Phillips, C.; Sundberg, E.

    1998-06-01

    The authors propose a general technique called solution decomposition to devise approximation algorithms with provable performance guarantees. The technique is applicable to a large class of combinatorial optimization problems that can be formulated as integer linear programs. Two key ingredients of their technique involve finding a decomposition of a fractional solution into a convex combination of feasible integral solutions and devising generic approximation algorithms based on calls to such decompositions as oracles. The technique is closely related to randomized rounding. Their method yields as corollaries unified solutions to a number of well studied problems and it provides the first approximation algorithms with provable guarantees for a number of new problems. The particular results obtained in this paper include the following: (1) the authors demonstrate how the technique can be used to provide more understanding of previous results and new algorithms for classical problems such as Multicriteria Spanning Trees, and Suitcase Packing; (2) they also show how the ideas can be extended to apply to multicriteria optimization problems, in which they wish to minimize a certain objective function subject to one or more budget constraints. As corollaries they obtain first non-trivial multicriteria approximation algorithms for problems including the k-Hurdle and the Network Inhibition problems.

  11. Cardiac hypertrophy and failure--a disease of adaptation. Modifications in membrane proteins provide a molecular basis for arrhythmogenicity.

    PubMed

    Moalic, J M; Charlemagne, D; Mansier, P; Chevalier, B; Swynghedauw, B

    1993-05-01

    Cardiac hypertrophy is the physiological adaptation of the heart to chronic mechanical overload. Cardiac failure indicates the limits of the process. Cardiac hypertrophy is only one example of biological adaptation and results from the induction of several changes in gene expression, mostly of the fetal type, including those coding for the myosin heavy chain or the alpha-subunit of the Na+,K(+)-ATPase. From a thermodynamic point of view, the decrease in Vmax allows the heart to produce a normal tension at a lower cost. This process results from changes both in the sarcomere and in the expression of certain membrane proteins. The decrease in calcium transient is determined by several changes in membrane proteins that result in a rather fragile equilibrium in terms of calcium homeostasis. Any abnormal input in calcium will have exaggerated detrimental consequences on a hypertrophied myocyte and may cause automaticity and arrhythmias or an exaggerated response to anoxia in terms of compliance. PMID:8485830

  12. Rolling bearing feature frequency extraction using extreme average envelope decomposition

    NASA Astrophysics Data System (ADS)

    Shi, Kunju; Liu, Shulin; Jiang, Chao; Zhang, Hongli

    2015-12-01

    The vibration signal contains a wealth of sensitive information which reflects the running status of the equipment. It is one of the most important steps for precise diagnosis to decompose the signal and extracts the effective information properly. The traditional classical adaptive signal decomposition method, such as EMD, exists the problems of mode mixing, low decomposition accuracy etc. Aiming at those problems, EAED(extreme average envelope decomposition) method is presented based on EMD. EAED method has three advantages. Firstly, it is completed through midpoint envelopment method rather than using maximum and minimum envelopment respectively as used in EMD. Therefore, the average variability of the signal can be described accurately. Secondly, in order to reduce the envelope errors during the signal decomposition, replacing two envelopes with one envelope strategy is presented. Thirdly, the similar triangle principle is utilized to calculate the time of extreme average points accurately. Thus, the influence of sampling frequency on the calculation results can be significantly reduced. Experimental results show that EAED could separate out single frequency components from a complex signal gradually. EAED could not only isolate three kinds of typical bearing fault characteristic of vibration frequency components but also has fewer decomposition layers. EAED replaces quadratic enveloping to an envelope which ensuring to isolate the fault characteristic frequency under the condition of less decomposition layers. Therefore, the precision of signal decomposition is improved.

  13. Genomic analysis identified a potential novel molecular mechanism for high-altitude adaptation in sheep at the Himalayas.

    PubMed

    Gorkhali, Neena Amatya; Dong, Kunzhe; Yang, Min; Song, Shen; Kader, Adiljian; Shrestha, Bhola Shankar; He, Xiaohong; Zhao, Qianjun; Pu, Yabin; Li, Xiangchen; Kijas, James; Guan, Weijun; Han, Jianlin; Jiang, Lin; Ma, Yuehui

    2016-01-01

    Sheep has successfully adapted to the extreme high-altitude Himalayan region. To identify genes underlying such adaptation, we genotyped genome-wide single nucleotide polymorphisms (SNPs) of four major sheep breeds living at different altitudes in Nepal and downloaded SNP array data from additional Asian and Middle East breeds. Using a di value-based genomic comparison between four high-altitude and eight lowland Asian breeds, we discovered the most differentiated variants at the locus of FGF-7 (Keratinocyte growth factor-7), which was previously reported as a good protective candidate for pulmonary injuries. We further found a SNP upstream of FGF-7 that appears to contribute to the divergence signature. First, the SNP occurred at an extremely conserved site. Second, the SNP showed an increasing allele frequency with the elevated altitude in Nepalese sheep. Third, the electrophoretic mobility shift assays (EMSA) analysis using human lung cancer cells revealed the allele-specific DNA-protein interactions. We thus hypothesized that FGF-7 gene potentially enhances lung function by regulating its expression level in high-altitude sheep through altering its binding of specific transcription factors. Especially, FGF-7 gene was not implicated in previous studies of other high-altitude species, suggesting a potential novel adaptive mechanism to high altitude in sheep at the Himalayas. PMID:27444145

  14. Genomic analysis identified a potential novel molecular mechanism for high-altitude adaptation in sheep at the Himalayas

    PubMed Central

    Gorkhali, Neena Amatya; Dong, Kunzhe; Yang, Min; Song, Shen; Kader, Adiljian; Shrestha, Bhola Shankar; He, Xiaohong; Zhao, Qianjun; Pu, Yabin; Li, Xiangchen; Kijas, James; Guan, Weijun; Han, Jianlin; Jiang, Lin; Ma, Yuehui

    2016-01-01

    Sheep has successfully adapted to the extreme high-altitude Himalayan region. To identify genes underlying such adaptation, we genotyped genome-wide single nucleotide polymorphisms (SNPs) of four major sheep breeds living at different altitudes in Nepal and downloaded SNP array data from additional Asian and Middle East breeds. Using a di value-based genomic comparison between four high-altitude and eight lowland Asian breeds, we discovered the most differentiated variants at the locus of FGF-7 (Keratinocyte growth factor-7), which was previously reported as a good protective candidate for pulmonary injuries. We further found a SNP upstream of FGF-7 that appears to contribute to the divergence signature. First, the SNP occurred at an extremely conserved site. Second, the SNP showed an increasing allele frequency with the elevated altitude in Nepalese sheep. Third, the electrophoretic mobility shift assays (EMSA) analysis using human lung cancer cells revealed the allele-specific DNA-protein interactions. We thus hypothesized that FGF-7 gene potentially enhances lung function by regulating its expression level in high-altitude sheep through altering its binding of specific transcription factors. Especially, FGF-7 gene was not implicated in previous studies of other high-altitude species, suggesting a potential novel adaptive mechanism to high altitude in sheep at the Himalayas. PMID:27444145

  15. Adapting SAFT-γ perturbation theory to site-based molecular dynamics simulation. III. Molecules with partial charges at bulk phases, confined geometries and interfaces

    SciTech Connect

    Ghobadi, Ahmadreza F.; Elliott, J. Richard

    2014-09-07

    In Paper I [A. F. Ghobadi and J. R. Elliott, J. Chem. Phys. 139(23), 234104 (2013)], we showed that how a third-order Weeks–Chandler–Anderson (WCA) Thermodynamic Perturbation Theory and molecular simulation can be integrated to characterize the repulsive and dispersive contributions to the Helmholtz free energy for realistic molecular conformations. To this end, we focused on n-alkanes to develop a theory for fused and soft chains. In Paper II [A. F. Ghobadi and J. R. Elliott, J. Chem. Phys. 141(2), 024708 (2014)], we adapted the classical Density Functional Theory and studied the microstructure of the realistic molecular fluids in confined geometries and vapor-liquid interfaces. We demonstrated that a detailed consistency between molecular simulation and theory can be achieved for both bulk and inhomogeneous phases. In this paper, we extend the methodology to molecules with partial charges such as carbon dioxide, water, 1-alkanols, nitriles, and ethers. We show that the electrostatic interactions can be captured via an effective association potential in the framework of Statistical Associating Fluid Theory (SAFT). Implementation of the resulting association contribution in assessing the properties of these molecules at confined geometries and interfaces presents satisfactory agreement with molecular simulation and experimental data. For example, the predicted surface tension deviates less than 4% comparing to full potential simulations. Also, the theory, referred to as SAFT-γ WCA, is able to reproduce the specific orientation of hydrophilic head and hydrophobic tail of 1-alkanols at the vapor-liquid interface of water.

  16. Adapting SAFT-γ perturbation theory to site-based molecular dynamics simulation. III. Molecules with partial charges at bulk phases, confined geometries and interfaces

    NASA Astrophysics Data System (ADS)

    Ghobadi, Ahmadreza F.; Elliott, J. Richard

    2014-09-01

    In Paper I [A. F. Ghobadi and J. R. Elliott, J. Chem. Phys. 139(23), 234104 (2013)], we showed that how a third-order Weeks-Chandler-Anderson (WCA) Thermodynamic Perturbation Theory and molecular simulation can be integrated to characterize the repulsive and dispersive contributions to the Helmholtz free energy for realistic molecular conformations. To this end, we focused on n-alkanes to develop a theory for fused and soft chains. In Paper II [A. F. Ghobadi and J. R. Elliott, J. Chem. Phys. 141(2), 024708 (2014)], we adapted the classical Density Functional Theory and studied the microstructure of the realistic molecular fluids in confined geometries and vapor-liquid interfaces. We demonstrated that a detailed consistency between molecular simulation and theory can be achieved for both bulk and inhomogeneous phases. In this paper, we extend the methodology to molecules with partial charges such as carbon dioxide, water, 1-alkanols, nitriles, and ethers. We show that the electrostatic interactions can be captured via an effective association potential in the framework of Statistical Associating Fluid Theory (SAFT). Implementation of the resulting association contribution in assessing the properties of these molecules at confined geometries and interfaces presents satisfactory agreement with molecular simulation and experimental data. For example, the predicted surface tension deviates less than 4% comparing to full potential simulations. Also, the theory, referred to as SAFT-γ WCA, is able to reproduce the specific orientation of hydrophilic head and hydrophobic tail of 1-alkanols at the vapor-liquid interface of water.

  17. Fulvenallene decomposition kinetics.

    PubMed

    Polino, Daniela; Cavallotti, Carlo

    2011-09-22

    While the decomposition kinetics of the benzyl radical has been studied in depth both from the experimental and the theoretical standpoint, much less is known about the reactivity of what is likely to be its main decomposition product, fulvenallene. In this work the high temperature reactivity of fulvenallene was investigated on a Potential Energy Surface (PES) consisting of 10 wells interconnected through 11 transition states using a 1 D Master Equation (ME). Rate constants were calculated using RRKM theory and the ME was integrated using a stochastic kinetic Monte Carlo code. It was found that two main decomposition channels are possible, the first is active on the singlet PES and leads to the formation of the fulvenallenyl radical and atomic hydrogen. The second requires intersystem crossing to the triplet PES and leads to acetylene and cyclopentadienylidene. ME simulations were performed calculating the microcanonical intersystem crossing frequency using Landau-Zener theory convoluting the crossing probability with RRKM rates evaluated at the conical intersection. It was found that the reaction channel leading to the cyclopentadienylidene diradical is only slightly faster than that leading to the fulvenallenyl radical, so that it can be concluded that both reactions are likely to be active in the investigated temperature (1500-2000 K) and pressure (0.05-50 bar) ranges. However, the simulations show that intersystem crossing is rate limiting for the first reaction channel, as the removal of this barrier leads to an increase of the rate constant by a factor of 2-3. Channel specific rate constants are reported as a function of temperature and pressure. PMID:21819060

  18. Hydrogen peroxide catalytic decomposition

    NASA Technical Reports Server (NTRS)

    Parrish, Clyde F. (Inventor)

    2010-01-01

    Nitric oxide in a gaseous stream is converted to nitrogen dioxide using oxidizing species generated through the use of concentrated hydrogen peroxide fed as a monopropellant into a catalyzed thruster assembly. The hydrogen peroxide is preferably stored at stable concentration levels, i.e., approximately 50%-70% by volume, and may be increased in concentration in a continuous process preceding decomposition in the thruster assembly. The exhaust of the thruster assembly, rich in hydroxyl and/or hydroperoxy radicals, may be fed into a stream containing oxidizable components, such as nitric oxide, to facilitate their oxidation.

  19. Mode decomposition evolution equations

    PubMed Central

    Wang, Yang; Wei, Guo-Wei; Yang, Siyang

    2011-01-01

    Partial differential equation (PDE) based methods have become some of the most powerful tools for exploring the fundamental problems in signal processing, image processing, computer vision, machine vision and artificial intelligence in the past two decades. The advantages of PDE based approaches are that they can be made fully automatic, robust for the analysis of images, videos and high dimensional data. A fundamental question is whether one can use PDEs to perform all the basic tasks in the image processing. If one can devise PDEs to perform full-scale mode decomposition for signals and images, the modes thus generated would be very useful for secondary processing to meet the needs in various types of signal and image processing. Despite of great progress in PDE based image analysis in the past two decades, the basic roles of PDEs in image/signal analysis are only limited to PDE based low-pass filters, and their applications to noise removal, edge detection, segmentation, etc. At present, it is not clear how to construct PDE based methods for full-scale mode decomposition. The above-mentioned limitation of most current PDE based image/signal processing methods is addressed in the proposed work, in which we introduce a family of mode decomposition evolution equations (MoDEEs) for a vast variety of applications. The MoDEEs are constructed as an extension of a PDE based high-pass filter (Europhys. Lett., 59(6): 814, 2002) by using arbitrarily high order PDE based low-pass filters introduced by Wei (IEEE Signal Process. Lett., 6(7): 165, 1999). The use of arbitrarily high order PDEs is essential to the frequency localization in the mode decomposition. Similar to the wavelet transform, the present MoDEEs have a controllable time-frequency localization and allow a perfect reconstruction of the original function. Therefore, the MoDEE operation is also called a PDE transform. However, modes generated from the present approach are in the spatial or time domain and can be

  20. Reviewing molecular adaptations of Lyme borreliosis spirochetes in the context of reproductive fitness in natural transmission cycles

    PubMed Central

    Tsao, Jean I.

    2009-01-01

    Lyme borreliosis (LB) is caused by a group of pathogenic spirochetes – most often Borrelia burgdorferi, B. afzelii, and B. garinii – that are vectored by hard ticks in the Ixodes ricinus-persulcatus complex, which feed on a variety of mammals, birds, and lizards. Although LB is one of the best-studied vector-borne zoonoses, the annual incidence in North America and Europe leads other vector-borne diseases and continues to increase. What factors make the LB system so successful, and how can researchers hope to reduce disease risk – either through vaccinating humans or reducing the risk of contacting infected ticks in nature? Discoveries of molecular interactions involved in the transmission of LB spirochetes have accelerated recently, revealing complex interactions among the spirochete-tick-vertebrate triad. These interactions involve multiple, and often redundant, pathways that reflect the evolution of general and specific mechanisms by which the spirochetes survive and reproduce. Previous reviews have focused on the molecular interactions or population biology of the system. Here molecular interactions among the LB spirochete, its vector, and vertebrate hosts are reviewed in the context of natural maintenance cycles, which represent the ecological and evolutionary contexts that shape these interactions. This holistic system approach may help researchers develop additional testable hypotheses about transmission processes, interpret laboratory results, and guide development of future LB control measures and management. PMID:19368764

  1. Reviewing molecular adaptations of Lyme borreliosis spirochetes in the context of reproductive fitness in natural transmission cycles.

    PubMed

    Tsao, Jean I

    2009-01-01

    Lyme borreliosis (LB) is caused by a group of pathogenic spirochetes - most often Borrelia burgdorferi, B. afzelii, and B. garinii - that are vectored by hard ticks in the Ixodes ricinus-persulcatus complex, which feed on a variety of mammals, birds, and lizards. Although LB is one of the best-studied vector-borne zoonoses, the annual incidence in North America and Europe leads other vector-borne diseases and continues to increase. What factors make the LB system so successful, and how can researchers hope to reduce disease risk - either through vaccinating humans or reducing the risk of contacting infected ticks in nature? Discoveries of molecular interactions involved in the transmission of LB spirochetes have accelerated recently, revealing complex interactions among the spirochete-tick-vertebrate triad. These interactions involve multiple, and often redundant, pathways that reflect the evolution of general and specific mechanisms by which the spirochetes survive and reproduce. Previous reviews have focused on the molecular interactions or population biology of the system. Here molecular interactions among the LB spirochete, its vector, and vertebrate hosts are reviewed in the context of natural maintenance cycles, which represent the ecological and evolutionary contexts that shape these interactions. This holistic system approach may help researchers develop additional testable hypotheses about transmission processes, interpret laboratory results, and guide development of future LB control measures and management. PMID:19368764

  2. Molecular characterization of E2 glycoprotein of classical swine fever virus: adaptation and propagation in porcine kidney cells.

    PubMed

    Kumar, Rakesh; Barman, Nagendra N; Khatoon, Elina; Rajbongshi, Gitika; Deka, Nipu; Morla, Sudhir; Kumar, Sachin

    2015-05-01

    Classical swine fever virus (CSFV) is the causative agent of a highly contagious disease, hog cholera in pigs. The disease is endemic in many parts of the world, and vaccination is the only way to protect the animals from CSFV infection. The lapinized vaccine strains are occasionally not protective because of animal to animal passage, inadequate vaccination strategy, suboptimal vaccine dose, and emergence of new variants. The surface glycoprotein E2 of CSFV is a major antigenic determinant and can modulate the disease outcome in pigs. In the present study, we characterized the CSFV in porcine kidney cells. The CSFV vaccine strains showed enhanced replication following 15 passages in porcine kidney cells. Nucleotide sequence analysis of the E2 protein gene of the cell culture-adapted vaccine strain of CSFV showed a mutation in putative amino acid sequences that are identical to its virulent counterpart. The study suggests the possibility of exaltation in vaccine strains following its adaptation in host cells and paves the way for a further exploration of the biology of its outbreak. PMID:25552311

  3. Functional and molecular adaptation of Cl/HCO3- exchanger to chronic alkaline media in renal cells.

    PubMed

    Rivarola, Valeria; Ford, Paula; Chara, Osvaldo; Parisi, Mario; Capurro, Claudia

    2005-01-01

    The Cl(-)/HCO3- exchanger (AE) is one of the mechanisms that cells have developed to adjust pH Despite its importance, the role of AE isoforms in controlling steady-state pH during alkalosis has not been widely investigated. In the present study, we have evaluated whether conditions simulating acute and chronic metabolic alkalosis affected the transport activity and protein levels of Cl-/HCO3- exchangers in a rat cortical collecting duct cell line (RCCD1). pH(i) was monitored using the fluorescent dye BCECF in monolayers grown on permeable supports. Anion exchanger function was assessed by the response of pH(i) to acute chloride removal. RT-PCR and immunoblot assays were also performed. Our results showed that RCCD1 cells express two members of the anion exchanger gene family: AE2 and AE4. Functional studies demonstrated that while in acute alkalosis pH(i) became alkaline and was not regulated, after 48 h adaptation; steady-state pH(i) reached a value similar to the physiological one. Chronic treated cells also resulted in a 3-fold rise in Cl(-)/HCO3- exchange activity together with a 2.2-fold increase in AE2, but not AE4, protein abundance. We conclude that RCCD1 cells can adapt to chronic extracellular alkalosis reestablishing its steady-state pH(i) and that AE2 would play a key role in cell homeostasis. PMID:16301827

  4. Molecular interaction between natural IgG and ficolin - mechanistic insights on adaptive-innate immune crosstalk

    NASA Astrophysics Data System (ADS)

    Panda, Saswati; Zhang, Jing; Yang, Lifeng; Anand, Ganesh S.; Ding, Jeak L.

    2014-01-01

    Recently, we found that natural IgG (nIgG; a non-specific immunoglobulin of adaptive immunity) is not quiescent, but plays a crucial role in immediate immune defense by collaborating with ficolin (an innate immune protein). However, how the nIgG and ficolin interplay and what factors control the complex formation during infection is unknown. Here, we found that mild acidosis and hypocalcaemia induced by infection- inflammation condition increased the nIgG:ficolin complex formation. Hydrogen-deuterium exchange mass spectrometry delineated the binding interfaces to the CH2-CH3 region of nIgG Fc and P-subdomain of ficolin FBG domain. Infection condition exposes novel binding sites. Site-directed mutagenesis and surface plasmon resonance analyses of peptides, derived from nIgG and ficolin, defined the interacting residues between the proteins. These results provide mechanistic insights on the interaction between two molecules representing the adaptive and innate immune pathways, prompting potential development of immunomodulatory/prophylactic peptides tunable to prevailing infection conditions.

  5. The origin of litter chemical complexity during decomposition.

    PubMed

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

    2012-10-01

    The chemical complexity of decomposing plant litter is a central feature shaping the terrestrial carbon (C) cycle, but explanations of the origin of this complexity remain contentious. Here, we ask: How does litter chemistry change during decomposition, and what roles do decomposers play in these changes? During a long-term (730 days) litter decomposition experiment, we tracked concurrent changes in decomposer community structure and function and litter chemistry using high-resolution molecular techniques. Contrary to the current paradigm, we found that the chemistry of different litter types diverged, rather than converged, during decomposition due to the activities of decomposers. Furthermore, the same litter type exposed to different decomposer communities exhibited striking differences in chemistry, even after > 90% mass loss. Our results show that during decomposition, decomposer community characteristics regulate changes in litter chemistry, which could influence the functionality of litter-derived soil organic matter (SOM) and the turnover and stabilisation of soil C. PMID:22897741

  6. 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.

  7. Coxeter decompositions of hyperbolic simplexes

    SciTech Connect

    Felikson, A A

    2002-12-31

    A Coxeter decomposition of a polyhedron in a hyperbolic space H{sup n} is a decomposition of it into finitely many Coxeter polyhedra such that any two tiles having a common facet are symmetric with respect to it. The classification of Coxeter decompositions is closely related to the problem of the classification of finite-index subgroups generated by reflections in discrete hyperbolic groups generated by reflections. All Coxeter decompositions of simplexes in the hyperbolic spaces H{sup n} with n>3 are described in this paper.

  8. Intermolecular forces and molecular dynamics simulation of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) using symmetry adapted perturbation theory.

    PubMed

    Taylor, DeCarlos E

    2013-04-25

    The dimer potential energy surface (PES) of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) has been explored using symmetry adapted perturbation theory based on a Kohn-Sham density functional theory description of the monomers [SAPT(DFT)]. An intermolecular potential energy function was parametrized using a grid of 880 ab initio SAPT(DFT) dimer interaction energies, and the function was used to identify stationary points on the SAPT(DFT) dimer PES. It is shown that there exists a variety of minima with a range of bonding configurations and ab initio analyses of the interaction energy components, along with radial cross sections of the PES near each minimum, are presented. Results of isothermal-isostress molecular dynamics simulations are reported, and the simulated structure, thermal expansion, sublimation enthalpy, and bulk modulus of the TATB crystal, based on the SAPT(DFT) interaction potential, are in good agreement with experiment. PMID:23565605

  9. Comparative Transcriptomic Exploration Reveals Unique Molecular Adaptations of Neuropathogenic Trichobilharzia to Invade and Parasitize Its Avian Definitive Host.

    PubMed

    Leontovyč, Roman; Young, Neil D; Korhonen, Pasi K; Hall, Ross S; Tan, Patrick; Mikeš, Libor; Kašný, Martin; Horák, Petr; Gasser, Robin B

    2016-02-01

    To date, most molecular investigations of schistosomatids have focused principally on blood flukes (schistosomes) of humans. Despite the clinical importance of cercarial dermatitis in humans caused by Trichobilharzia regenti and the serious neuropathologic disease that this parasite causes in its permissive avian hosts and accidental mammalian hosts, almost nothing is known about the molecular aspects of how this fluke invades its hosts, migrates in host tissues and how it interacts with its hosts' immune system. Here, we explored selected aspects using a transcriptomic-bioinformatic approach. To do this, we sequenced, assembled and annotated the transcriptome representing two consecutive life stages (cercariae and schistosomula) of T. regenti involved in the first phases of infection of the avian host. We identified key biological and metabolic pathways specific to each of these two developmental stages and also undertook comparative analyses using data available for taxonomically related blood flukes of the genus Schistosoma. Detailed comparative analyses revealed the unique involvement of carbohydrate metabolism, translation and amino acid metabolism, and calcium in T. regenti cercariae during their invasion and in growth and development, as well as the roles of cell adhesion molecules, microaerobic metabolism (citrate cycle and oxidative phosphorylation), peptidases (cathepsins) and other histolytic and lysozomal proteins in schistosomula during their particular migration in neural tissues of the avian host. In conclusion, the present transcriptomic exploration provides new and significant insights into the molecular biology of T. regenti, which should underpin future genomic and proteomic investigations of T. regenti and, importantly, provides a useful starting point for a range of comparative studies of schistosomatids and other trematodes. PMID:26863542

  10. Comparative Transcriptomic Exploration Reveals Unique Molecular Adaptations of Neuropathogenic Trichobilharzia to Invade and Parasitize Its Avian Definitive Host

    PubMed Central

    Leontovyč, Roman; Young, Neil D.; Korhonen, Pasi K.; Hall, Ross S.; Tan, Patrick; Mikeš, Libor; Kašný, Martin; Horák, Petr; Gasser, Robin B.

    2016-01-01

    To date, most molecular investigations of schistosomatids have focused principally on blood flukes (schistosomes) of humans. Despite the clinical importance of cercarial dermatitis in humans caused by Trichobilharzia regenti and the serious neuropathologic disease that this parasite causes in its permissive avian hosts and accidental mammalian hosts, almost nothing is known about the molecular aspects of how this fluke invades its hosts, migrates in host tissues and how it interacts with its hosts’ immune system. Here, we explored selected aspects using a transcriptomic-bioinformatic approach. To do this, we sequenced, assembled and annotated the transcriptome representing two consecutive life stages (cercariae and schistosomula) of T. regenti involved in the first phases of infection of the avian host. We identified key biological and metabolic pathways specific to each of these two developmental stages and also undertook comparative analyses using data available for taxonomically related blood flukes of the genus Schistosoma. Detailed comparative analyses revealed the unique involvement of carbohydrate metabolism, translation and amino acid metabolism, and calcium in T. regenti cercariae during their invasion and in growth and development, as well as the roles of cell adhesion molecules, microaerobic metabolism (citrate cycle and oxidative phosphorylation), peptidases (cathepsins) and other histolytic and lysozomal proteins in schistosomula during their particular migration in neural tissues of the avian host. In conclusion, the present transcriptomic exploration provides new and significant insights into the molecular biology of T. regenti, which should underpin future genomic and proteomic investigations of T. regenti and, importantly, provides a useful starting point for a range of comparative studies of schistosomatids and other trematodes. PMID:26863542

  11. Micro- and Macro-Geographic Scale Effect on the Molecular Imprint of Selection and Adaptation in Norway Spruce

    PubMed Central

    Scalfi, Marta; Mosca, Elena; Di Pierro, Erica Adele; Troggio, Michela; Vendramin, Giovanni Giuseppe; Sperisen, Christoph; La Porta, Nicola; Neale, David B.

    2014-01-01

    Forest tree species of temperate and boreal regions have undergone a long history of demographic changes and evolutionary adaptations. The main objective of this study was to detect signals of selection in Norway spruce (Picea abies [L.] Karst), at different sampling-scales and to investigate, accounting for population structure, the effect of environment on species genetic diversity. A total of 384 single nucleotide polymorphisms (SNPs) representing 290 genes were genotyped at two geographic scales: across 12 populations distributed along two altitudinal-transects in the Alps (micro-geographic scale), and across 27 populations belonging to the range of Norway spruce in central and south-east Europe (macro-geographic scale). At the macrogeographic scale, principal component analysis combined with Bayesian clustering revealed three major clusters, corresponding to the main areas of southern spruce occurrence, i.e. the Alps, Carpathians, and Hercynia. The populations along the altitudinal transects were not differentiated. To assess the role of selection in structuring genetic variation, we applied a Bayesian and coalescent-based FST-outlier method and tested for correlations between allele frequencies and climatic variables using regression analyses. At the macro-geographic scale, the FST-outlier methods detected together 11 FST-outliers. Six outliers were detected when the same analyses were carried out taking into account the genetic structure. Regression analyses with population structure correction resulted in the identification of two (micro-geographic scale) and 38 SNPs (macro-geographic scale) significantly correlated with temperature and/or precipitation. Six of these loci overlapped with FST-outliers, among them two loci encoding an enzyme involved in riboflavin biosynthesis and a sucrose synthase. The results of this study indicate a strong relationship between genetic and environmental variation at both geographic scales. It also suggests that an

  12. Developing ab initio quality force fields from condensed phase quantum-mechanics/molecular-mechanics calculations through the adaptive force matching method

    NASA Astrophysics Data System (ADS)

    Akin-Ojo, Omololu; Song, Yang; Wang, Feng

    2008-08-01

    A new method called adaptive force matching (AFM) has been developed that is capable of producing high quality force fields for condensed phase simulations. This procedure involves the parametrization of force fields to reproduce ab initio forces obtained from condensed phase quantum-mechanics/molecular-mechanics (QM/MM) calculations. During the procedure, the MM part of the QM/MM is iteratively improved so as to approach ab initio quality. In this work, the AFM method has been tested to parametrize force fields for liquid water so that the resulting force fields reproduce forces calculated using the ab initio MP2 and the Kohn-Sham density functional theory with the Becke-Lee-Yang-Parr (BLYP) and Becke three-parameter LYP (B3LYP) exchange correlation functionals. The AFM force fields generated in this work are very simple to evaluate and are supported by most molecular dynamics (MD) codes. At the same time, the quality of the forces predicted by the AFM force fields rivals that of very expensive ab initio calculations and are found to successfully reproduce many experimental properties. The site-site radial distribution functions (RDFs) obtained from MD simulations using the force field generated from the BLYP functional through AFM compare favorably with the previously published RDFs from Car-Parrinello MD simulations with the same functional. Technical aspects of AFM such as the optimal QM cluster size, optimal basis set, and optimal QM method to be used with the AFM procedure are discussed in this paper.

  13. Erbium hydride decomposition kinetics.

    SciTech Connect

    Ferrizz, Robert Matthew

    2006-11-01

    Thermal desorption spectroscopy (TDS) is used to study the decomposition kinetics of erbium hydride thin films. The TDS results presented in this report are analyzed quantitatively using Redhead's method to yield kinetic parameters (E{sub A} {approx} 54.2 kcal/mol), which are then utilized to predict hydrogen outgassing in vacuum for a variety of thermal treatments. Interestingly, it was found that the activation energy for desorption can vary by more than 7 kcal/mol (0.30 eV) for seemingly similar samples. In addition, small amounts of less-stable hydrogen were observed for all erbium dihydride films. A detailed explanation of several approaches for analyzing thermal desorption spectra to obtain kinetic information is included as an appendix.

  14. Art of spin decomposition

    SciTech Connect

    Chen Xiangsong; Sun Weimin; Wang Fan; Goldman, T.

    2011-04-01

    We analyze the problem of spin decomposition for an interacting system from a natural perspective of constructing angular-momentum eigenstates. We split, from the total angular-momentum operator, a proper part which can be separately conserved for a stationary state. This part commutes with the total Hamiltonian and thus specifies the quantum angular momentum. We first show how this can be done in a gauge-dependent way, by seeking a specific gauge in which part of the total angular-momentum operator vanishes identically. We then construct a gauge-invariant operator with the desired property. Our analysis clarifies what is the most pertinent choice among the various proposals for decomposing the nucleon spin. A similar analysis is performed for extracting a proper part from the total Hamiltonian to construct energy eigenstates.

  15. Decomposition of Furan on Pd(111)

    SciTech Connect

    Xu, Ye

    2012-01-01

    Periodic density functional theory calculations (GGA-PBE) have been performed to investigate the mechanism for the decomposition of furan up to CO formation on the Pd(111) surface. At 1/9 ML coverage, furan adsorbs with its molecular plane parallel to the surface in several states with nearly identical adsorption energies of -1.0 eV. The decomposition of furan begins with the opening of the ring at the C-O position with an activation barrier of E{sub a} = 0.82 eV, which yields a C{sub 4}H{sub 4}O aldehyde species that rapidly loses the {alpha} H to form C{sub 4}H{sub 3}O (E{sub a} = 0.40 eV). C{sub 4}H{sub 3}O further dehydrogenates at the {delta} position to form C{sub 4}H{sub 2}O (E{sub a} = 0.83 eV), before the {alpha}-{beta} C-C bond dissociates (E{sub a} = 1.08 eV) to form CO. Each step is the lowest-barrier dissociation step in the respective species. A simple kinetic analysis suggests that furan decomposition begins at 240-270 K and is mostly complete by 320 K, in close agreement with previous experiments. It is suggested that the C{sub 4}H{sub 2}O intermediate delays the decarbonylation step up to 350 K.

  16. Molecular chaperone accumulation as a function of stress evidences adaptation to high hydrostatic pressure in the piezophilic archaeon Thermococcus barophilus

    PubMed Central

    Cario, Anaïs; Jebbar, Mohamed; Thiel, Axel; Kervarec, Nelly; Oger, Phil M.

    2016-01-01

    The accumulation of mannosyl-glycerate (MG), the salinity stress response osmolyte of Thermococcales, was investigated as a function of hydrostatic pressure in Thermococcus barophilus strain MP, a hyperthermophilic, piezophilic archaeon isolated from the Snake Pit site (MAR), which grows optimally at 40 MPa. Strain MP accumulated MG primarily in response to salinity stress, but in contrast to other Thermococcales, MG was also accumulated in response to thermal stress. MG accumulation peaked for combined stresses. The accumulation of MG was drastically increased under sub-optimal hydrostatic pressure conditions, demonstrating that low pressure is perceived as a stress in this piezophile, and that the proteome of T. barophilus is low-pressure sensitive. MG accumulation was strongly reduced under supra-optimal pressure conditions clearly demonstrating the structural adaptation of this proteome to high hydrostatic pressure. The lack of MG synthesis only slightly altered the growth characteristics of two different MG synthesis deletion mutants. No shift to other osmolytes was observed. Altogether our observations suggest that the salinity stress response in T. barophilus is not essential and may be under negative selective pressure, similarly to what has been observed for its thermal stress response. PMID:27378270

  17. Molecular chaperone accumulation as a function of stress evidences adaptation to high hydrostatic pressure in the piezophilic archaeon Thermococcus barophilus.

    PubMed

    Cario, Anaïs; Jebbar, Mohamed; Thiel, Axel; Kervarec, Nelly; Oger, Phil M

    2016-01-01

    The accumulation of mannosyl-glycerate (MG), the salinity stress response osmolyte of Thermococcales, was investigated as a function of hydrostatic pressure in Thermococcus barophilus strain MP, a hyperthermophilic, piezophilic archaeon isolated from the Snake Pit site (MAR), which grows optimally at 40 MPa. Strain MP accumulated MG primarily in response to salinity stress, but in contrast to other Thermococcales, MG was also accumulated in response to thermal stress. MG accumulation peaked for combined stresses. The accumulation of MG was drastically increased under sub-optimal hydrostatic pressure conditions, demonstrating that low pressure is perceived as a stress in this piezophile, and that the proteome of T. barophilus is low-pressure sensitive. MG accumulation was strongly reduced under supra-optimal pressure conditions clearly demonstrating the structural adaptation of this proteome to high hydrostatic pressure. The lack of MG synthesis only slightly altered the growth characteristics of two different MG synthesis deletion mutants. No shift to other osmolytes was observed. Altogether our observations suggest that the salinity stress response in T. barophilus is not essential and may be under negative selective pressure, similarly to what has been observed for its thermal stress response. PMID:27378270

  18. 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…

  19. Linear array for covariance differencing via hyperbolic singular value decomposition

    NASA Astrophysics Data System (ADS)

    Bojanczyk, A. W.; Steinhardt, A. O.

    1989-11-01

    We consider a problem pertaining to bearing estimation in unknown noise using the covariance differencing approach, and propose a linear array of processors which exhibits a linear speed-up with respect to a uniprocessor system. Our solution hinges on a new canonic matrix factorization which we term the hyperbolic singular value decomposition. The parallel algorithm for hyperbolic SVD based bearing estimation is an adaptation of a well known biorthogonalization technique developed by Hestenes. Parallel implementations of the algorithm are based on earlier works on one-sided Jacobi methods. It turns out that strategies for parallelization of Jacobi methods are equally well applicable for computing the hyperbolic singular value decomposition.

  20. Adapting SAFT-γ perturbation theory to site-based molecular dynamics simulation. I. Homogeneous fluids

    NASA Astrophysics Data System (ADS)

    Ghobadi, Ahmadreza F.; Elliott, J. Richard

    2013-12-01

    In this work, we aim to develop a version of the Statistical Associating Fluid Theory (SAFT)-γ equation of state (EOS) that is compatible with united-atom force fields, rather than experimental data. We rely on the accuracy of the force fields to provide the relation to experimental data. Although, our objective is a transferable theory of interfacial properties for soft and fused heteronuclear chains, we first clarify the details of the SAFT-γ approach in terms of site-based simulations for homogeneous fluids. We show that a direct comparison of Helmholtz free energy to molecular simulation, in the framework of a third order Weeks-Chandler-Andersen perturbation theory, leads to an EOS that takes force field parameters as input and reproduces simulation results for Vapor-Liquid Equilibria (VLE) calculations. For example, saturated liquid density and vapor pressure of n-alkanes ranging from methane to dodecane deviate from those of the Transferable Potential for Phase Equilibria (TraPPE) force field by about 0.8% and 4%, respectively. Similar agreement between simulation and theory is obtained for critical properties and second virial coefficient. The EOS also reproduces simulation data of mixtures with about 5% deviation in bubble point pressure. Extension to inhomogeneous systems and united-atom site types beyond those used in description of n-alkanes will be addressed in succeeding papers.

  1. Computational Design of a pH Stable Enzyme: Understanding Molecular Mechanism of Penicillin Acylase's Adaptation to Alkaline Conditions

    PubMed Central

    Suplatov, Dmitry; Panin, Nikolay; Kirilin, Evgeny; Shcherbakova, Tatyana; Kudryavtsev, Pavel; Švedas, Vytas

    2014-01-01

    Protein stability provides advantageous development of novel properties and can be crucial in affording tolerance to mutations that introduce functionally preferential phenotypes. Consequently, understanding the determining factors for protein stability is important for the study of structure-function relationship and design of novel protein functions. Thermal stability has been extensively studied in connection with practical application of biocatalysts. However, little work has been done to explore the mechanism of pH-dependent inactivation. In this study, bioinformatic analysis of the Ntn-hydrolase superfamily was performed to identify functionally important subfamily-specific positions in protein structures. Furthermore, the involvement of these positions in pH-induced inactivation was studied. The conformational mobility of penicillin acylase in Escherichia coli was analyzed through molecular modeling in neutral and alkaline conditions. Two functionally important subfamily-specific residues, Gluβ482 and Aspβ484, were found. Ionization of these residues at alkaline pH promoted the collapse of a buried network of stabilizing interactions that consequently disrupted the functional protein conformation. The subfamily-specific position Aspβ484 was selected as a hotspot for mutation to engineer enzyme variant tolerant to alkaline medium. The corresponding Dβ484N mutant was produced and showed 9-fold increase in stability at alkaline conditions. Bioinformatic analysis of subfamily-specific positions can be further explored to study mechanisms of protein inactivation and to design more stable variants for the engineering of homologous Ntn-hydrolases with improved catalytic properties. PMID:24959852

  2. Oxidative decomposition of formaldehyde catalyzed by a bituminous coal

    SciTech Connect

    Haim Cohen; Uri Green

    2009-05-15

    It has been observed that molecular hydrogen is formed during long-term storage of bituminous coals via oxidative decomposition of formaldehyde by coal surface peroxides. This study has investigated the effects of coal quantity, temperature, and water content on the molecular hydrogen formation with a typical American coal (Pittsburgh No. 6). The results indicate that the coal's surface serves as a catalyst in the formation processes of molecular hydrogen. Furthermore, the results also indicate that low temperature emission of molecular hydrogen may possibly be the cause of unexplained explosions in confined spaces containing bituminous coals, for example, underground mines or ship holds. 20 refs., 4 figs., 6 tabs.

  3. Molecular Analysis of Asymptomatic Bacteriuria Escherichia coli Strain VR50 Reveals Adaptation to the Urinary Tract by Gene Acquisition

    PubMed Central

    Ben Zakour, Nouri L.; Totsika, Makrina; Forde, Brian M.; Watts, Rebecca E.; Mabbett, Amanda N.; Szubert, Jan M.; Sarkar, Sohinee; Phan, Minh-Duy; Peters, Kate M.; Petty, Nicola K.; Alikhan, Nabil-Fareed; Sullivan, Mitchell J.; Gawthorne, Jayde A.; Stanton-Cook, Mitchell; Nhu, Nguyen Thi Khanh; Chong, Teik Min; Yin, Wai-Fong; Chan, Kok-Gan; Hancock, Viktoria; Ussery, David W.; Ulett, Glen C.

    2015-01-01

    Urinary tract infections (UTIs) are among the most common infectious diseases of humans, with Escherichia coli responsible for >80% of all cases. One extreme of UTI is asymptomatic bacteriuria (ABU), which occurs as an asymptomatic carrier state that resembles commensalism. To understand the evolution and molecular mechanisms that underpin ABU, the genome of the ABU E. coli strain VR50 was sequenced. Analysis of the complete genome indicated that it most resembles E. coli K-12, with the addition of a 94-kb genomic island (GI-VR50-pheV), eight prophages, and multiple plasmids. GI-VR50-pheV has a mosaic structure and contains genes encoding a number of UTI-associated virulence factors, namely, Afa (afimbrial adhesin), two autotransporter proteins (Ag43 and Sat), and aerobactin. We demonstrated that the presence of this island in VR50 confers its ability to colonize the murine bladder, as a VR50 mutant with GI-VR50-pheV deleted was attenuated in a mouse model of UTI in vivo. We established that Afa is the island-encoded factor responsible for this phenotype using two independent deletion (Afa operon and AfaE adhesin) mutants. E. coli VR50afa and VR50afaE displayed significantly decreased ability to adhere to human bladder epithelial cells. In the mouse model of UTI, VR50afa and VR50afaE displayed reduced bladder colonization compared to wild-type VR50, similar to the colonization level of the GI-VR50-pheV mutant. Our study suggests that E. coli VR50 is a commensal-like strain that has acquired fitness factors that facilitate colonization of the human bladder. PMID:25667270

  4. Molecular Analysis of Asymptomatic Bacteriuria Escherichia coli Strain VR50 Reveals Adaptation to the Urinary Tract by Gene Acquisition

    DOE PAGESBeta

    Beatson, Scott A.; Ben Zakour, Nouri L.; Totsika, Makrina; Forde, Brian M.; Watts, Rebecca E.; Mabbett, Amanda N.; Szubert, Jan M.; Sarkar, Sohinee; Phan, Minh-Duy; Peters, Kate M.; et al

    2015-05-01

    Urinary tract infections (UTIs) are among the most common infectious diseases of humans, with Escherichia coli for >80% of all cases. One extreme of UTI is asymptomatic bacteriuria (ABU), which occurs as an asymptomatic carrier state that resembles commensalism. Here, to understand the evolution and molecular mechanisms that underpin ABU, the genome of the ABU E. coli strain VR50 was sequenced. Analysis of the complete genome indicated that it most resembles E. coli K-12, with the addition of a 94-kb genomic island (GI-VR50-pheV), eight prophages, and multiple plasmids. GI-VR50-pheV has a mosaic structure and contains genes encoding a number ofmore » UTI-associated virulence factors, namely, Afa (afimbrial adhesin), two autotransporter proteins (Ag43 and Sat), and aerobactin. We demonstrated that the presence of this island in VR50 confers its ability to colonize the murine bladder, as a VR50 mutant with GI-VR50-pheV deleted was attenuated in a mouse model of UTI in vivo. We established that Afa is the island-encoded factor responsible for this phenotype using two independent deletion (Afa operon and AfaE adhesin) mutants. E. coli VR50afa and VR50afaE displayed significantly decreased ability to adhere to human bladder epithelial cells. In the mouse model of UTI, VR50afa and VR50afaE displayed reduced bladder colonization compared to wild-type VR50, similar to the colonization level of the GI-VR50-pheV mutant. In conlusion, our study suggests that E. coli VR50 is a commensal-like strain that has acquired fitness factors that facilitate colonization of the human bladder.« less

  5. Molecular analysis of asymptomatic bacteriuria Escherichia coli strain VR50 reveals adaptation to the urinary tract by gene acquisition.

    PubMed

    Beatson, Scott A; Ben Zakour, Nouri L; Totsika, Makrina; Forde, Brian M; Watts, Rebecca E; Mabbett, Amanda N; Szubert, Jan M; Sarkar, Sohinee; Phan, Minh-Duy; Peters, Kate M; Petty, Nicola K; Alikhan, Nabil-Fareed; Sullivan, Mitchell J; Gawthorne, Jayde A; Stanton-Cook, Mitchell; Nhu, Nguyen Thi Khanh; Chong, Teik Min; Yin, Wai-Fong; Chan, Kok-Gan; Hancock, Viktoria; Ussery, David W; Ulett, Glen C; Schembri, Mark A

    2015-05-01

    Urinary tract infections (UTIs) are among the most common infectious diseases of humans, with Escherichia coli responsible for >80% of all cases. One extreme of UTI is asymptomatic bacteriuria (ABU), which occurs as an asymptomatic carrier state that resembles commensalism. To understand the evolution and molecular mechanisms that underpin ABU, the genome of the ABU E. coli strain VR50 was sequenced. Analysis of the complete genome indicated that it most resembles E. coli K-12, with the addition of a 94-kb genomic island (GI-VR50-pheV), eight prophages, and multiple plasmids. GI-VR50-pheV has a mosaic structure and contains genes encoding a number of UTI-associated virulence factors, namely, Afa (afimbrial adhesin), two autotransporter proteins (Ag43 and Sat), and aerobactin. We demonstrated that the presence of this island in VR50 confers its ability to colonize the murine bladder, as a VR50 mutant with GI-VR50-pheV deleted was attenuated in a mouse model of UTI in vivo. We established that Afa is the island-encoded factor responsible for this phenotype using two independent deletion (Afa operon and AfaE adhesin) mutants. E. coli VR50afa and VR50afaE displayed significantly decreased ability to adhere to human bladder epithelial cells. In the mouse model of UTI, VR50afa and VR50afaE displayed reduced bladder colonization compared to wild-type VR50, similar to the colonization level of the GI-VR50-pheV mutant. Our study suggests that E. coli VR50 is a commensal-like strain that has acquired fitness factors that facilitate colonization of the human bladder. PMID:25667270

  6. Decomposition in northern Minnesota peatlands

    SciTech Connect

    Farrish, K.W.

    1985-01-01

    Decomposition in peatlands was investigated in northern Minnesota. Four sites, an ombrotrophic raised bog, an ombrotrophic perched bog and two groundwater minerotrophic fens, were studied. Decomposition rates of peat and paper were estimated using mass-loss techniques. Environmental and substrate factors that were most likely to be responsible for limiting decomposition were monitored. Laboratory incubation experiments complemented the field work. Mass-loss over one year in one of the bogs, ranged from 11 percent in the upper 10 cm of hummocks to 1 percent at 60 to 100 cm depth in hollows. Regression analysis of the data for that bog predicted no mass-loss below 87 cm. Decomposition estimates on an area basis were 2720 and 6460 km/ha yr for the two bogs; 17,000 and 5900 kg/ha yr for the two fens. Environmental factors found to limit decomposition in these peatlands were reducing/anaerobic conditions below the water table and cool peat temperatures. Substrate factors found to limit decomposition were low pH, high content of resistant organics such as lignin, and shortages of available N and K. Greater groundwater influence was found to favor decomposition through raising the pH and perhaps by introducing limited amounts of dissolved oxygen.

  7. The loss of the hemoglobin H2S-binding function in annelids from sulfide-free habitats reveals molecular adaptation driven by Darwinian positive selection.

    PubMed

    Bailly, Xavier; Leroy, Riwanon; Carney, Susan; Collin, Olivier; Zal, Franck; Toulmond, Andre; Jollivet, Didier

    2003-05-13

    The hemoglobin of the deep-sea hydrothermal vent vestimentiferan Riftia pachyptila (annelid) is able to bind toxic hydrogen sulfide (H(2)S) to free cysteine residues and to transport it to fuel endosymbiotic sulfide-oxidising bacteria. The cysteine residues are conserved key amino acids in annelid globins living in sulfide-rich environments, but are absent in annelid globins from sulfide-free environments. Synonymous and nonsynonymous substitution analysis from two different sets of orthologous annelid globin genes from sulfide rich and sulfide free environments have been performed to understand how the sulfide-binding function of hemoglobin appeared and has been maintained during the course of evolution. This study reveals that the sites occupied by free-cysteine residues in annelids living in sulfide-rich environments and occupied by other amino acids in annelids from sulfide-free environments, have undergone positive selection in annelids from sulfide-free environments. We assumed that the high reactivity of cysteine residues became a disadvantage when H(2)S disappeared because free cysteines without their natural ligand had the capacity to interact with other blood components, disturb homeostasis, reduce fitness and thus could have been counterselected. To our knowledge, we pointed out for the first time a case of function loss driven by molecular adaptation rather than genetic drift. If constraint relaxation (H(2)S disappearance) led to the loss of the sulfide-binding function in modern annelids from sulfide-free environments, our work suggests that adaptation to sulfide-rich environments is a plesiomorphic feature, and thus that the annelid ancestor could have emerged in a sulfide-rich environment. PMID:12721359

  8. The loss of the hemoglobin H2S-binding function in annelids from sulfide-free habitats reveals molecular adaptation driven by Darwinian positive selection

    PubMed Central

    Bailly, Xavier; Leroy, Riwanon; Carney, Susan; Collin, Olivier; Zal, Franck; Toulmond, André; Jollivet, Didier

    2003-01-01

    The hemoglobin of the deep-sea hydrothermal vent vestimentiferan Riftia pachyptila (annelid) is able to bind toxic hydrogen sulfide (H2S) to free cysteine residues and to transport it to fuel endosymbiotic sulfide-oxidising bacteria. The cysteine residues are conserved key amino acids in annelid globins living in sulfide-rich environments, but are absent in annelid globins from sulfide-free environments. Synonymous and nonsynonymous substitution analysis from two different sets of orthologous annelid globin genes from sulfide rich and sulfide free environments have been performed to understand how the sulfide-binding function of hemoglobin appeared and has been maintained during the course of evolution. This study reveals that the sites occupied by free-cysteine residues in annelids living in sulfide-rich environments and occupied by other amino acids in annelids from sulfide-free environments, have undergone positive selection in annelids from sulfide-free environments. We assumed that the high reactivity of cysteine residues became a disadvantage when H2S disappeared because free cysteines without their natural ligand had the capacity to interact with other blood components, disturb homeostasis, reduce fitness and thus could have been counterselected. To our knowledge, we pointed out for the first time a case of function loss driven by molecular adaptation rather than genetic drift. If constraint relaxation (H2S disappearance) led to the loss of the sulfide-binding function in modern annelids from sulfide-free environments, our work suggests that adaptation to sulfide-rich environments is a plesiomorphic feature, and thus that the annelid ancestor could have emerged in a sulfide-rich environment. PMID:12721359

  9. Evolution and ecology meet molecular genetics: adaptive phenotypic plasticity in two isolated Negev desert populations of Acacia raddiana at either end of a rainfall gradient

    PubMed Central

    Ward, David; Shrestha, Madan K.; Golan-Goldhirsh, Avi

    2012-01-01

    Background and Aims The ecological, evolutionary and genetic bases of population differentiation in a variable environment are often related to the selection pressures that plants experience. We compared differences in several growth- and defence-related traits in two isolated populations of Acacia raddiana trees from sites at either end of an extreme environmental gradient in the Negev desert. Methods We used random amplified polymorphic DNA (RAPD) to determine the molecular differences between populations. We grew plants under two levels of water, three levels of nutrients and three levels of herbivory to test for phenotypic plasticity and adaptive phenotypic plasticity. Key Results The RAPD analyses showed that these populations are highly genetically differentiated. Phenotypic plasticity in various morphological traits in A. raddiana was related to patterns of population genetic differentiation between the two study sites. Although we did not test for maternal effects in these long-lived trees, significant genotype × environment (G × E) interactions in some of these traits indicated that such plasticity may be adaptive. Conclusions The main selection pressure in this desert environment, perhaps unsurprisingly, is water. Increased water availability resulted in greater growth in the southern population, which normally receives far less rain than the northern population. Even under the conditions that we defined as low water and/or nutrients, the performance of the seedlings from the southern population was significantly better, perhaps reflecting selection for these traits. Consistent with previous studies of this genus, there was no evidence of trade-offs between physical and chemical defences and plant growth parameters in this study. Rather, there appeared to be positive correlations between plant size and defence parameters. The great variation in several traits in both populations may result in a diverse potential for responding to selection pressures in

  10. Molecular physiology and functional morphology of SO₄²⁻ excretion by the kidney of seawater-adapted eels.

    PubMed

    Watanabe, Taro; Takei, Yoshio

    2011-05-15

    Marine teleosts actively excrete SO₄²⁻ and keep the plasma concentration of this ion much lower than that of environmental seawater (SW). We used the eel as a model to study the excretory mechanism of SO₄²⁻ because this euryhaline species changes SO₄²⁻ regulation drastically after transfer from freshwater (FW) to SW. Time-course studies showed that plasma SO₄²⁻ concentration decreased 3 days after transfer of eels from FW to SW, while urine SO₄²⁻ concentration increased on 1 day. Detailed analyses showed that urine SO₄²⁻ concentration increased linearly from 6 h after SW transfer; however, this did not immediately translate to increased SO₄²⁻ excretion because the volume of urine was decreased. We identified five SO₄²⁻ transporters in the eel kidney. Three of these (Slc26a1, Slc26a6b and Slc26a6c) are expressed in both SW- and FW-acclimated eels while Slc26a6a and Slc13a1 are expressed in SW-acclimated eels and FW-acclimated eels, respectively. We showed that changes in Slc26a6a and Slc13a1 gene expression occurred 1-3 days after SW transfer. In SW eel kidneys, immunohistochemistry using specific antisera against each transporter protein showed that Slc26a6a and Slc26a6c are localized on the apical membrane of the P1 segment of the proximal tubule, while Slc26a6b is localized on the apical membrane and Slc26a1 on the basolateral membrane of the P2 segment. The current study revealed complex molecular mechanisms of SO₄²⁻ excretion in the SW eel kidney that involve segment-specific localization of multiple Slc transporters in proximal tubules and modulation of their expression in different SO₄²⁻ environments. This precise regulatory mechanism may endow the eel with euryhalinity. PMID:21525326

  11. 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.

  12. 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.

  13. Autonomous Gaussian Decomposition

    NASA Astrophysics Data System (ADS)

    Lindner, Robert R.; Vera-Ciro, Carlos; Murray, Claire E.; Stanimirović, Snežana; Babler, Brian; Heiles, Carl; Hennebelle, Patrick; Goss, W. M.; Dickey, John

    2015-04-01

    We present a new algorithm, named Autonomous Gaussian Decomposition (AGD), for automatically decomposing spectra into Gaussian components. AGD uses derivative spectroscopy and machine learning to provide optimized guesses for the number of Gaussian components in the data, and also their locations, widths, and amplitudes. We test AGD and find that it produces results comparable to human-derived solutions on 21 cm absorption spectra from the 21 cm SPectral line Observations of Neutral Gas with the EVLA (21-SPONGE) survey. We use AGD with Monte Carlo methods to derive the H i line completeness as a function of peak optical depth and velocity width for the 21-SPONGE data, and also show that the results of AGD are stable against varying observational noise intensity. The autonomy and computational efficiency of the method over traditional manual Gaussian fits allow for truly unbiased comparisons between observations and simulations, and for the ability to scale up and interpret the very large data volumes from the upcoming Square Kilometer Array and pathfinder telescopes.

  14. Lignocellulose decomposition by microbial secretions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Carbon storage in terrestrial ecosystems is contingent upon the natural resistance of plant cell wall polymers to rapid biological degradation. Nevertheless, certain microorganisms have evolved remarkable means to overcome this natural resistance. Lignocellulose decomposition by microorganisms com...

  15. Some nonlinear space decomposition algorithms

    SciTech Connect

    Tai, Xue-Cheng; Espedal, M.

    1996-12-31

    Convergence of a space decomposition method is proved for a general convex programming problem. The space decomposition refers to methods that decompose a space into sums of subspaces, which could be a domain decomposition or a multigrid method for partial differential equations. Two algorithms are proposed. Both can be used for linear as well as nonlinear elliptic problems and they reduce to the standard additive and multiplicative Schwarz methods for linear elliptic problems. Two {open_quotes}hybrid{close_quotes} algorithms are also presented. They converge faster than the additive one and have better parallelism than the multiplicative method. Numerical tests with a two level domain decomposition for linear, nonlinear and interface elliptic problems are presented for the proposed algorithms.

  16. 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.

  17. Nontraditional tensor decompositions and applications.

    SciTech Connect

    Bader, Brett William

    2010-07-01

    This presentation will discuss two tensor decompositions that are not as well known as PARAFAC (parallel factors) and Tucker, but have proven useful in informatics applications. Three-way DEDICOM (decomposition into directional components) is an algebraic model for the analysis of 3-way arrays with nonsymmetric slices. PARAFAC2 is a related model that is less constrained than PARAFAC and allows for different objects in one mode. Applications of both models to informatics problems will be shown.

  18. Construction of diabatic Hamiltonian matrix from ab initio calculated molecular symmetry adapted nonadiabatic coupling terms and nuclear dynamics for the excited states of Na3 cluster.

    PubMed

    Mukherjee, Saikat; Bandyopadhyay, Sudip; Paul, Amit Kumar; Adhikari, Satrajit

    2013-04-25

    We present the molecular symmetry (MS) adapted treatment of nonadiabatic coupling terms (NACTs) for the excited electronic states (2(2)E' and 1(2)A1') of Na3 cluster, where the adiabatic potential energy surfaces (PESs) and the NACTs are calculated at the MRCI level by using an ab initio quantum chemistry package (MOLPRO). The signs of the NACTs at each point of the configuration space (CS) are determined by employing appropriate irreducible representations (IREPs) arising due to MS group, and such terms are incorporated into the adiabatic to diabatic transformation (ADT) equations to obtain the ADT angles. Since those sign corrected NACTs and the corresponding ADT angles demonstrate the validity of curl condition for the existence of three-state (2(2)E' and 1(2)A1') sub-Hilbert space, it becomes possible to construct the continuous, single-valued, symmetric, and smooth 3 × 3 diabatic Hamiltonian matrix. Finally, nuclear dynamics has been carried out on such diabatic surfaces to explore whether our MS-based treatment of diabatization can reproduce the pattern of the experimental spectrum for system B of Na3 cluster. PMID:23521047

  19. A fast tree-based method for estimating column densities in adaptive mesh refinement codes. Influence of UV radiation field on the structure of molecular clouds

    NASA Astrophysics Data System (ADS)

    Valdivia, Valeska; Hennebelle, Patrick

    2014-11-01

    Context. Ultraviolet radiation plays a crucial role in molecular clouds. Radiation and matter are tightly coupled and their interplay influences the physical and chemical properties of gas. In particular, modeling the radiation propagation requires calculating column densities, which can be numerically expensive in high-resolution multidimensional simulations. Aims: Developing fast methods for estimating column densities is mandatory if we are interested in the dynamical influence of the radiative transfer. In particular, we focus on the effect of the UV screening on the dynamics and on the statistical properties of molecular clouds. Methods: We have developed a tree-based method for a fast estimate of column densities, implemented in the adaptive mesh refinement code RAMSES. We performed numerical simulations using this method in order to analyze the influence of the screening on the clump formation. Results: We find that the accuracy for the extinction of the tree-based method is better than 10%, while the relative error for the column density can be much more. We describe the implementation of a method based on precalculating the geometrical terms that noticeably reduces the calculation time. To study the influence of the screening on the statistical properties of molecular clouds we present the probability distribution function of gas and the associated temperature per density bin and the mass spectra for different density thresholds. Conclusions: The tree-based method is fast and accurate enough to be used during numerical simulations since no communication is needed between CPUs when using a fully threaded tree. It is then suitable to parallel computing. We show that the screening for far UV radiation mainly affects the dense gas, thereby favoring low temperatures and affecting the fragmentation. We show that when we include the screening, more structures are formed with higher densities in comparison to the case that does not include this effect. We

  20. 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. PMID:18467759

  1. Domain decomposition methods in computational fluid dynamics

    NASA Technical Reports Server (NTRS)

    Gropp, William D.; Keyes, David E.

    1992-01-01

    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.

  2. 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.

  3. Generalized spectral decomposition for stochastic nonlinear problems

    SciTech Connect

    Nouy, Anthony Le Maitre, Olivier P.

    2009-01-10

    We present an extension of the generalized spectral decomposition method for the resolution of nonlinear stochastic problems. The method consists in the construction of a reduced basis approximation of the Galerkin solution and is independent of the stochastic discretization selected (polynomial chaos, stochastic multi-element or multi-wavelets). Two algorithms are proposed for the sequential construction of the successive generalized spectral modes. They involve decoupled resolutions of a series of deterministic and low-dimensional stochastic problems. Compared to the classical Galerkin method, the algorithms allow for significant computational savings and require minor adaptations of the deterministic codes. The methodology is detailed and tested on two model problems, the one-dimensional steady viscous Burgers equation and a two-dimensional nonlinear diffusion problem. These examples demonstrate the effectiveness of the proposed algorithms which exhibit convergence rates with the number of modes essentially dependent on the spectrum of the stochastic solution but independent of the dimension of the stochastic approximation space.

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

    SciTech Connect

    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. 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.

  5. Fever, immunity, and molecular adaptations.

    PubMed

    Hasday, Jeffrey D; Thompson, Christopher; Singh, Ishwar S

    2014-01-01

    The heat shock response (HSR) is an ancient and highly conserved process that is essential for coping with environmental stresses, including extremes of temperature. Fever is a more recently evolved response, during which organisms temporarily subject themselves to thermal stress in the face of infections. We review the phylogenetically conserved mechanisms that regulate fever and discuss the effects that febrile-range temperatures have on multiple biological processes involved in host defense and cell death and survival, including the HSR and its implications for patients with severe sepsis, trauma, and other acute systemic inflammatory states. Heat shock factor-1, a heat-induced transcriptional enhancer is not only the central regulator of the HSR but also regulates expression of pivotal cytokines and early response genes. Febrile-range temperatures exert additional immunomodulatory effects by activating mitogen-activated protein kinase cascades and accelerating apoptosis in some cell types. This results in accelerated pathogen clearance, but increased collateral tissue injury, thus the net effect of exposure to febrile range temperature depends in part on the site and nature of the pathologic process and the specific treatment provided. PMID:24692136

  6. Autocatalytic behavior of trimethylindium during thermal decomposition

    SciTech Connect

    McDaniel, A.H.; Allendorf, M.D.

    2000-02-01

    Pyrolysis of trimethylindium (TMIn) in a hot-wall flow-tube reactor has been investigated at temperatures between 573 and 723 K using a modulated molecular-beam mass-sampling technique and detailed numerical modeling. The TMIn was exposed to various mixtures of carrier gases: He, H{sub 2}, D{sub 2}, and C{sub 2}H{sub 4}, in an effort to elucidated the behavior exhibited by this compound in different chemical environments. The decomposition of TMIn is a heterogeneous, autocatalytic process with an induction period that is carrier-gas dependent and lasts on the order of minutes. After activation of the tube wall, the thermolysis exhibits a steady-state behavior that is surface mediated. This result is contrary to prior literature reports, which state that decomposition occurs in the gas phase via successive loss of the CH{sub 3} ligands. This finding also suggests that the bond dissociation energy for the (CH{sub 3}){sub 2}In-CH{sub 3} bond derived from flow-tube investigations is erroneous and should be reevaluated.

  7. Thermal Decomposition of Furan Generates Propargyl Radicals

    SciTech Connect

    Vasiliou, A.; Nimlos, M. R.; Daily, J. W.; Ellison, G. B.

    2009-07-01

    The thermal decomposition of furan has been studied by a 1 mm x 2 cm tubular silicon carbide reactor, C{sub 4}H{sub 4}O + {Delta} {yields} products. Unlike previous studies, these experiments are able to identify the initial furan decomposition products. Furan is entrained in either He or Ar carrier gas and is passed through a heated (1600 K) SiC tubular reactor. Furan decomposes during transit through the tubular reactor (approximately 65 {micro}s) and exits to a vacuum chamber. Within one nozzle diameter of leaving the nozzle, the gases cool to less than 50 K, and all reactions cease. The resultant molecular beam is interrogated by photoionization mass spectroscopy as well as infrared spectroscopy. Earlier G2(MP2) electronic structure calculations predicted that furan will thermally decompose to acetylene, ketene, carbon monoxide, and propyne at lower temperatures. At higher temperatures, these calculations forecast that propargyl radical could result. We observe all of these species (see Scheme 1). As the pressure in the tubular reactor is raised, the photoionization mass spectra show clear evidence for the formation of aromatic hydrocarbons.

  8. Structure and function of cytochrome P450S in insect adaptation to natural and synthetic toxins: insights gained from molecular modeling.

    PubMed

    Schuler, Mary A; Berenbaum, May R

    2013-09-01

    Over evolutionary time, insect herbivores have adapted to the presence of natural toxins and more recently to synthetic insecticides in or on the plants they consume. Biochemical analyses and molecular modeling of the cytochrome P450 monooxygenases (P450s) that metabolize these compounds have provided insight into the many variations affecting their catalytic activity. Phylogenetically distinct P450s may metabolize similar substrates, and phylogenetically similar P450s may metabolize different substrates; as well, some P450s process broad arrays of both phytochemicals and synthetic insecticides, while closely related P450s are restricted to a narrow range of phytochemicals. Mapped on the predicted three-dimensional structures of insect P450s developed from available mammalian P450 crystal structures, differences in multiple regions of the insect proteins reveal the evolutionary processes occurring as P450 genes have duplicated and diverged. Analyses of site-directed mutants in select lepidopteran and dipteran P450s demonstrate that slight changes in the catalytic site, the putative product release channel, and the proximal surface (interacting with electron transfer partners such as cytochrome P450 reductase and cytochrome b5) yield pronounced activity differences. Additionally, changes in the catalytic site and in the linker region preceding the proline-hinge influence P450 folding. With predicted structures available for many mammalian P450s involved in metabolism of xenobiotics, it is possible to record allelic variation relative to catalytically important regions in the overall P450 structure and to predict functionally critical differences. Together with information on the relative levels of allelic variant transcripts, comprehensive characterization of the mechanisms that modulate metabolism of natural and synthetic xenobiotics in insects can yield insights into plant-insect coevolution and into novel approaches for chemical pest management. PMID:24036972

  9. 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

  10. 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.

  11. Updating the singular value decomposition

    NASA Astrophysics Data System (ADS)

    Davies, Philip I.; Smith, M. I. Matthew I.

    2004-09-01

    The spectral decomposition of a symmetric matrix A with small off-diagonal and distinct diagonal elements can be approximated using a direct scheme of R. Davies and Modi (Linear Algebra Appl. 77 (1986) 61). In this paper a generalization of this method for computing the singular value decomposition of close-to-diagonal is presented. When A has repeated or "close" singular values it is possible to apply the direct method to split the problem in two with one part containing the well-separated singular values and one requiring the computation of the "close" singular values.

  12. Symmetry-related decompositions of uncertainty

    NASA Astrophysics Data System (ADS)

    Viana, Marlos

    2012-10-01

    In statistics, the sample mean and variance are intimately related to the symmetries of the full symmetric group describing all possible permutations of assignments of observations to sampling units. While those symmetries yield exactly two invariant subspaces (in a sense to be defined in the text) in correspondence to those summary statistics, the invariant subspaces associated with specific subgroups of the full symmetric group may then lead to much detailed decompositions of the experimental uncertainty. In the present chapter we discuss the symmetry-related summaries of data arising from dihedral experiments, specifically in the context of multinomial models for frequency counts in symbolic sequences. Special examples are given to dihedral summaries that can be potentially interpreted as measures of (molecular) chirality or handedness.

  13. Evolution-Based Functional Decomposition of Proteins.

    PubMed

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

    2016-06-01

    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

  14. 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.

  15. 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.

  16. The ecology of carrion decomposition

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Carrion, or the remains of dead animals, is something that most people would like to avoid. It is visually unpleasant, emits foul odors, and may be the source of numerous pathogens. Decomposition of carrion, however, provides a unique opportunity for scientists to investigate how nutrients cycle t...

  17. How Is Morphological Decomposition Achieved?

    ERIC Educational Resources Information Center

    Libben, Gary

    1994-01-01

    Two experiments investigated morphological decomposition in ambiguous novel compounds such as "busheater," which can be parsed as either "bus-heater" or "bush-heater." It was found that subjects' parsing choices for such words are influenced by orthographic constraints but that these constraints do not operate prelexically. (33 references) (MDM)

  18. Microbial interactions during carrion decomposition

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This addresses the microbial ecology of carrion decomposition in the age of metagenomics. It describes what is known about the microbial communities on carrion, including a brief synopsis about the communities on other organic matter sources. It provides a description of studies using state-of-the...

  19. 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. PMID:21395512

  20. An Iterative Reweighted Method for Tucker Decomposition of Incomplete Tensors

    NASA Astrophysics Data System (ADS)

    Yang, Linxiao; Fang, Jun; Li, Hongbin; Zeng, Bing

    2016-09-01

    We consider the problem of low-rank decomposition of incomplete multiway tensors. Since many real-world data lie on an intrinsically low dimensional subspace, tensor low-rank decomposition with missing entries has applications in many data analysis problems such as recommender systems and image inpainting. In this paper, we focus on Tucker decomposition which represents an Nth-order tensor in terms of N factor matrices and a core tensor via multilinear operations. To exploit the underlying multilinear low-rank structure in high-dimensional datasets, we propose a group-based log-sum penalty functional to place structural sparsity over the core tensor, which leads to a compact representation with smallest core tensor. The method for Tucker decomposition is developed by iteratively minimizing a surrogate function that majorizes the original objective function, which results in an iterative reweighted process. In addition, to reduce the computational complexity, an over-relaxed monotone fast iterative shrinkage-thresholding technique is adapted and embedded in the iterative reweighted process. The proposed method is able to determine the model complexity (i.e. multilinear rank) in an automatic way. Simulation results show that the proposed algorithm offers competitive performance compared with other existing algorithms.

  1. Roaming radical kinetics in the decomposition of acetaldehyde.

    SciTech Connect

    Harding, L. B.; Georgievskii, Y.; Klippenstein, S. J.; Chemical Sciences and Engineering Division

    2010-01-01

    A novel theoretical framework for predicting the branching between roaming and bond fission channels in molecular dissociations is described and applied to the decomposition of acetaldehyde. This reduced dimensional trajectory (RDT) approach, which is motivated by the long-range nature of the roaming, bond fission, and abstraction dynamical bottlenecks, involves the propagation of rigid-body trajectories on an analytic potential energy surface. The analytic potential is obtained from fits to large-scale multireference ab initio electronic structure calculations. The final potential includes one-dimensional corrections from higher-level electronic structure calculations and for the effect of conserved mode variations along both the addition and abstraction paths. The corrections along the abstraction path play a significant role in the predicted branching. Master equation simulations are used to transform the microcanonical branching ratios obtained from the RDT simulations to the temperature- and pressure-dependent branching ratios observed in thermal decomposition experiments. For completeness, a transition-state theory treatment of the contributions of the tight transition states for the molecular channels is included in the theoretical analyses. The theoretically predicted branching between molecules and radicals in the thermal decomposition of acetaldehyde is in reasonable agreement with the corresponding shock tube measurement described in the companion paper. The prediction for the ratio of the tight to roaming contributions to the molecular channel also agrees well with results extracted from recent experimental and experimental/theoretical photodissociation studies.

  2. 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.

  3. Cold adaptation of zinc metalloproteases in the thermolysin family from deep sea and arctic sea ice bacteria revealed by catalytic and structural properties and molecular dynamics: new insights into relationship between conformational flexibility and hydrogen bonding.

    PubMed

    Xie, Bin-Bin; Bian, Fei; Chen, Xiu-Lan; He, Hai-Lun; Guo, Jun; Gao, Xiang; Zeng, Yin-Xin; Chen, Bo; Zhou, Bai-Cheng; Zhang, Yu-Zhong

    2009-04-01

    Increased conformational flexibility is the prevailing explanation for the high catalytic efficiency of cold-adapted enzymes at low temperatures. However, less is known about the structural determinants of flexibility. We reported two novel cold-adapted zinc metalloproteases in the thermolysin family, vibriolysin MCP-02 from a deep sea bacterium and vibriolysin E495 from an Arctic sea ice bacterium, and compared them with their mesophilic homolog, pseudolysin from a terrestrial bacterium. Their catalytic efficiencies, k(cat)/K(m) (10-40 degrees C), followed the order pseudolysin < MCP-02 < E495 with a ratio of approximately 1:2:4. MCP-02 and E495 have the same optimal temperature (T(opt), 57 degrees C, 5 degrees C lower than pseudolysin) and apparent melting temperature (T(m) = 64 degrees C, approximately 10 degrees C lower than pseudolysin). Structural analysis showed that the slightly lower stabilities resulted from a decrease in the number of salt bridges. Fluorescence quenching experiments and molecular dynamics simulations showed that the flexibilities of the proteins were pseudolysin < MCP-02 < E495, suggesting that optimization of flexibility is a strategy for cold adaptation. Molecular dynamics results showed that the ordinal increase in flexibility from pseudolysin to MCP-02 and E495, especially the increase from MCP-02 to E495, mainly resulted from the decrease of hydrogen-bond stability in the dynamic structure, which was due to the increase in asparagine, serine, and threonine residues. Finally, a model for the cold adaptation of MCP-02 and E495 was proposed. This is the first report of the optimization of hydrogen-bonding dynamics as a strategy for cold adaptation and provides new insights into the structural basis underlying conformational flexibility. PMID:19181663

  4. Investigating hydrogel dosimeter decomposition by chemical methods

    NASA Astrophysics Data System (ADS)

    Jordan, Kevin

    2015-01-01

    The chemical oxidative decomposition of leucocrystal violet micelle hydrogel dosimeters was investigated using the reaction of ferrous ions with hydrogen peroxide or sodium bicarbonate with hydrogen peroxide. The second reaction is more effective at dye decomposition in gelatin hydrogels. Additional chemical analysis is required to determine the decomposition products.

  5. Trade-Offs in Resource Allocation Among Moss Species Control Decomposition in Boreal Peatlands

    SciTech Connect

    Turetsky, M. R.; Crow, S. E.; Evans, R. J.; Vitt, D. H.; Wieder, R. K.

    2008-01-01

    We separated the effects of plant species controls on decomposition rates from environmental controls in northern peatlands using a full factorial, reciprocal transplant experiment of eight dominant bryophytes in four distinct peatland types in boreal Alberta, Canada. Standard fractionation techniques as well as compound-specific pyrolysis molecular beam mass spectrometry were used to identify a biochemical mechanism underlying any interspecific differences in decomposition rates. We found that over a 3-year field incubation, individual moss species and not micro-environmental conditions controlled early stages of decomposition. Across species, Sphagnum mosses exhibited a trade-off in resource partitioning into metabolic and structural carbohydrates, a pattern that served as a strong predictor of litter decomposition. Decomposition rates showed a negative co-variation between species and their microtopographic position, as species that live in hummocks decomposed slowly but hummock microhabitats themselves corresponded to rapid decomposition rates. By forming litter that degrades slowly, hummock mosses appear to promote the maintenance of macropore structure in surface peat hummocks that aid in water retention. Many northern regions are experiencing rapid climate warming that is expected to accelerate the decomposition of large soil carbon pools stored within peatlands. However, our results suggest that some common peatland moss species form tissue that resists decomposition across a range of peatland environments, suggesting that moss resource allocation could stabilize peatland carbon losses under a changing climate.

  6. Separation Surfaces in the Spectral TV Domain for Texture Decomposition

    NASA Astrophysics Data System (ADS)

    Horesh, Dikla; Gilboa, Guy

    2016-09-01

    In this paper we introduce a novel notion of separation surfaces for image decomposition. A surface is embedded in the spectral total-variation (TV) three dimensional domain and encodes a spatially-varying separation scale. The method allows good separation of textures with gradually varying pattern-size, pattern-contrast or illumination. The recently proposed total variation spectral framework is used to decompose the image into a continuum of textural scales. A desired texture, within a scale range, is found by fitting a surface to the local maximal responses in the spectral domain. A band above and below the surface, referred to as the \\textit{Texture Stratum}, defines for each pixel the adaptive scale-range of the texture. Based on the decomposition an application is proposed which can attenuate or enhance textures in the image in a very natural and visually convincing manner.

  7. 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. PMID:20608697

  8. 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.

  9. Thermal decomposition of isooctyl nitrate

    SciTech Connect

    Pritchard, H.O.

    1989-03-01

    The diesel ignition improver DII-3, made by Ethyl Corporation, also known as isooctyl nitrate, is a mixture whose principal constituent (about 95%) is 2-ethyl hexyl nitrate. This note describes an investigation of the thermal decomposition that is not exhaustive, but that is intended to provide sufficient information on the rate and the mechanism so as to make possible the educated guesses needed for modeling the effect of isooctyl nitrate on the diesel ignition process. As is the case with other alkyl nitrates, the decomposition of the neat material is a complex one giving a complicated pressure versus time curve, unsuitable for a quick derivation of the rate constant. However, in the presence of toluene, whose intended purpose is to trap reactive free radicals and thereby simplify the overall mechanism, the pressure rises approximately exponentially to a limit; thus, on the assumption that the reaction is homogeneous and of first order, the rate constants can be determined from the half-life.

  10. Variance decomposition in stochastic simulators

    SciTech Connect

    Le Maître, O. P.; Knio, O. M.; Moraes, A.

    2015-06-28

    This work aims at the development of a mathematical and computational approach that enables quantification of the inherent sources of stochasticity and of the corresponding sensitivities in stochastic simulations of chemical reaction networks. The approach is based on reformulating the system dynamics as being generated by independent standardized Poisson processes. This reformulation affords a straightforward identification of individual realizations for the stochastic dynamics of each reaction channel, and consequently a quantitative characterization of the inherent sources of stochasticity in the system. By relying on the Sobol-Hoeffding decomposition, the reformulation enables us to perform an orthogonal decomposition of the solution variance. Thus, by judiciously exploiting the inherent stochasticity of the system, one is able to quantify the variance-based sensitivities associated with individual reaction channels, as well as the importance of channel interactions. Implementation of the algorithms is illustrated in light of simulations of simplified systems, including the birth-death, Schlögl, and Michaelis-Menten models.

  11. Variance decomposition in stochastic simulators

    NASA Astrophysics Data System (ADS)

    Le Maître, O. P.; Knio, O. M.; Moraes, A.

    2015-06-01

    This work aims at the development of a mathematical and computational approach that enables quantification of the inherent sources of stochasticity and of the corresponding sensitivities in stochastic simulations of chemical reaction networks. The approach is based on reformulating the system dynamics as being generated by independent standardized Poisson processes. This reformulation affords a straightforward identification of individual realizations for the stochastic dynamics of each reaction channel, and consequently a quantitative characterization of the inherent sources of stochasticity in the system. By relying on the Sobol-Hoeffding decomposition, the reformulation enables us to perform an orthogonal decomposition of the solution variance. Thus, by judiciously exploiting the inherent stochasticity of the system, one is able to quantify the variance-based sensitivities associated with individual reaction channels, as well as the importance of channel interactions. Implementation of the algorithms is illustrated in light of simulations of simplified systems, including the birth-death, Schlögl, and Michaelis-Menten models.

  12. Thermal decomposition of allylbenzene ozonide

    SciTech Connect

    Ewing, J.C.; Church, D.F.; Pryor, W.A. )

    1989-07-19

    Thermal decomposition of allylbenzene ozonide (ABO) at 98{degree}C in the liquid phase yields toluene, bibenzyl, phenylacetaldehyde, formic acid, and (benzyloxy)methyl formate as major products; benzyl chloride is formed when chlorinated solvents are employed. These products, as well as benzyl formate, are formed when ABO is decomposed at 37{degree}C. When the decomposition of ABO is carried out in the presence of 1-butanethiol, the product distribution changes: yields of toluene increase, no bibenzyl is formed, and decreases in yields of (benzyloxy)methyl formate, phenylacetladehyde, and benzyl chloride are observed. The decomposition of 1-octene ozonide (OTO) also was studied for comparison. The activation parameters for both ABO and OTO are similar (28.2 kcal/mol, log A = 13.6 and 26.6 kcal/mol, log A = 12.5, respectively); these data suggest that ozonides decompose by homolysis of the O-O bond, rather than by an alternative synchronous two-bond scission process. When ABO is decomposed at 37{degree}C in the presence of the spin traps 5,5-dimethyl-1-pyrroline N-oxide (DMPO) or 3,3,5,5-tetramethyl-1-pyrroline N-oxide (M{sub 4}PO), ESR signals are observed that are consistent with the trapping of benzyl and other carbon- and oxygen-centered radicals. A mechanism for the thermal decomposition of ABO that involves peroxide bond homolysis and subsequent {beta}-scission is proposed. Thus, Criegee ozonides decompose to give free radicals at quite modest temperatures.

  13. 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. PMID:26264421

  14. Methanethiol decomposition on Ni(100)

    SciTech Connect

    Castro, M.E.; Ahkter, S.; Golchet, A.; White, J.M. ); Sahin, T. )

    1991-01-01

    Static secondary ion mass spectroscopy (SSIMS), temperature programmed desorption (TPD), and Auger electron spectroscopy (AES) were used under ultrahigh vacuum conditions to study the decomposition of CH{sub 3}SH on Ni(100). Only methane, hydrogen, and the parent molecule are observed in TPD. Complete decomposition to C(a), S(a) and desorbing H{sub 2} is the preferred reaction pathway for low exposures, while desorption of methane is observed at higher coverages. Preadsorbed hydrogen promoted methane desorption. Upon adsorption, and for low coverages, SSIMS evidence indicates S-H bond cleavage into CH{sub 3}S and surface hydrogen. S-H bond cleavage is inhibited for high coverages. The TP-SSIMS data are consistent with an activated C-S bond cleavage in CH{sub 3}S, with an activation energy of 8.81 kcal/mol and preexponential factor of 10{sup 6.5}s{sup {minus}1}. The low preexponential factor is taken as indicating a complex decomposition pathway. A mechanism consistent with the observed data is discussed.

  15. 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.

  16. Thermal decomposition mechanism of disilane.

    PubMed

    Yoshida, Kazumasa; Matsumoto, Keiji; Oguchi, Tatsuo; Tonokura, Kenichi; Koshi, Mitsuo

    2006-04-13

    Thermal decomposition of disilane was investigated using time-of-flight (TOF) mass spectrometry coupled with vacuum ultraviolet single-photon ionization (VUV-SPI) at a temperature range of 675-740 K and total pressure of 20-40 Torr. Si(n)H(m) species were photoionized by VUV radiation at 10.5 eV (118 nm). Concentrations of disilane and trisilane during thermal decomposition of disilane were quantitatively measured using the VUV-SPI method. Formation of Si(2)H(4) species was also examined. On the basis of pressure-dependent rate constants of disilane dissociation reported by Matsumoto et al. [J. Phys. Chem. A 2005, 109, 4911], kinetic simulation including gas-phase and surface reactions was performed to analyze thermal decomposition mechanisms of disilane. The branching ratio for (R1) Si(2)H(6) --> SiH(4) + SiH(2)/(R2) Si(2)H(6) --> H(2) + H(3)SiSiH was derived by the pressure-dependent rate constants. Temperature and reaction time dependences of disilane loss and formation of trisilane were well represented by the kinetic simulation. Comparison between the experimental results and the kinetic simulation results suggested that about 70% of consumed disilane was converted to trisilane, which was observed as one of the main reaction products under the present experimental conditions. PMID:16599440

  17. Comparison of different methods to determine the degree of peat decomposition in peat bogs

    NASA Astrophysics Data System (ADS)

    Biester, H.; Knorr, K.-H.; Schellekens, J.; Basler, A.; Hermanns, Y.-M.

    2014-05-01

    Peat humification or decomposition is a frequently used proxy to extract past time changes in hydrology and climate from peat bogs. During the past century several methods to determine changes in peat decomposition have been introduced. Most of these methods are operationally defined only and the chemical changes underlying the decomposition process are often poorly understood and lack validation. Owing to the chemically undefined nature of many humification analyses the comparison of results obtained by different methods is difficult. In this study we compared changes in peat decomposition proxies in cores of two peat bogs (Königsmoor, KK; Kleines Rotes Bruch, KRB) from the Harz Mountains (Germany) using C / N ratios, Fourier transform infrared spectra absorption (FTIR) intensities, Rock Eva® oxygen and hydrogen indices, δ13C and δ15N isotopic signatures and UV-absorption (UV-ABS) of NaOH peat extracts. In order to explain parallels and discrepancies between these methods, one of the cores was additionally analysed by pyrolysis gas chromatography mass spectrometry (pyrolysis-GC-MS). Pyrolysis-GC-MS data provide detailed information on a molecular level, which allows differentiation of both changes attributed to decomposition processes and changes in vegetation. Principal component analysis was used to identify and separate the effects of changes in vegetation pattern and decomposition processes because both may occur simultaneously upon changes in bog hydrology. Records of decomposition proxies show similar historical development at both sites, indicating external forcing such as climate as controlling the process. All decomposition proxies except UV-ABS and δ15N isotopes show similar patterns in their records and reflect to different extents signals of decomposition. The molecular composition of the KK core reveals that these changes are mainly attributed to decomposition processes and to a lesser extent to changes in vegetation. Changes in the molecular

  18. 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

  19. 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.

  20. Applications of domain decomposition methods to turbomachinery flows

    NASA Astrophysics Data System (ADS)

    Rai, M. M.

    Domain decomposition techniques can be used to great advantage by computational fluid dynamicists in computing flows about complex geometries and adapting the grid to the solution. These techniques are particularly useful in computing flows about several bodies that are in relative motion such as rotor/stator configurations in turbomachinery or helicopter rotor/fuselage configurations. This paper discusses some of the basic ideas involved in transferring information between subdomains in a multidomain calculation and presents results for a simple rotor/stator configuration.

  1. Next-Generation Force Fields from Symmetry-Adapted Perturbation Theory

    NASA Astrophysics Data System (ADS)

    McDaniel, Jesse G.; Schmidt, J. R.

    2016-05-01

    Symmetry-adapted perturbation theory (SAPT) provides a unique set of advantages for parameterizing next-generation force fields from first principles. SAPT provides a direct, basis-set superposition error free estimate of molecular interaction energies, a physically intuitive energy decomposition, and a seamless transition to an asymptotic picture of intermolecular interactions. These properties have been exploited throughout the literature to develop next-generation force fields for a variety of applications, including classical molecular dynamics simulations, crystal structure prediction, and quantum dynamics/spectroscopy. This review provides a brief overview of the formalism and theory of SAPT, along with a practical discussion of the various methodologies utilized to parameterize force fields from SAPT calculations. It also highlights a number of applications of SAPT-based force fields for chemical systems of particular interest. Finally, the review ends with a brief outlook on the future opportunities and challenges that remain for next-generation force fields based on SAPT.

  2. Next-Generation Force Fields from Symmetry-Adapted Perturbation Theory.

    PubMed

    McDaniel, Jesse G; Schmidt, J R

    2016-05-27

    Symmetry-adapted perturbation theory (SAPT) provides a unique set of advantages for parameterizing next-generation force fields from first principles. SAPT provides a direct, basis-set superposition error free estimate of molecular interaction energies, a physically intuitive energy decomposition, and a seamless transition to an asymptotic picture of intermolecular interactions. These properties have been exploited throughout the literature to develop next-generation force fields for a variety of applications, including classical molecular dynamics simulations, crystal structure prediction, and quantum dynamics/spectroscopy. This review provides a brief overview of the formalism and theory of SAPT, along with a practical discussion of the various methodologies utilized to parameterize force fields from SAPT calculations. It also highlights a number of applications of SAPT-based force fields for chemical systems of particular interest. Finally, the review ends with a brief outlook on the future opportunities and challenges that remain for next-generation force fields based on SAPT. PMID:27070322

  3. Atomic decomposition of conceptual DFT descriptors: application to proton transfer reactions.

    PubMed

    Inostroza-Rivera, Ricardo; Yahia-Ouahmed, Meziane; Tognetti, Vincent; Joubert, Laurent; Herrera, Bárbara; Toro-Labbé, Alejandro

    2015-07-21

    In this study, we present an atomic decomposition, in principle exact, at any point on a given reaction path, of the molecular energy, reaction force and reaction flux, which is based on Bader's atoms-in-molecules theory and on Pendás' interacting quantum atoms scheme. This decomposition enables the assessment of the importance and the contribution of each atom or molecular group to these global properties, and may cast the light on the physical factors governing bond formation or bond breaking. The potential use of this partition is finally illustrated by proton transfers in model biological systems. PMID:26089126

  4. Combinatorial drug screening and molecular profiling reveal diverse mechanisms of intrinsic and adaptive resistance to BRAF inhibition in V600E BRAF mutant melanomas

    PubMed Central

    Roller, Devin G.; Capaldo, Brian; Bekiranov, Stefan; Mackey, Aaron J.; Conaway, Mark R.; Petricoin, Emanuel F.; Gioeli, Daniel; Weber, Michael J.

    2016-01-01

    Over half of BRAFV600E melanomas display intrinsic resistance to BRAF inhibitors, in part due to adaptive signaling responses. In this communication we ask whether BRAFV600E melanomas share common adaptive responses to BRAF inhibition that can provide clinically relevant targets for drug combinations. We screened a panel of 12 treatment-naïve BRAFV600E melanoma cell lines with MAP Kinase pathway inhibitors in pairwise combination with 58 signaling inhibitors, assaying for synergistic cytotoxicity. We found enormous diversity in the drug combinations that showed synergy, with no two cell lines having an identical profile. Although the 6 lines most resistant to BRAF inhibition showed synergistic benefit from combination with lapatinib, the signaling mechanisms by which this combination generated synergistic cytotoxicity differed between the cell lines. We conclude that adaptive responses to inhibition of the primary oncogenic driver (BRAFV600E) are determined not only by the primary oncogenic driver but also by diverse secondary genetic and epigenetic changes (“back-seat drivers”) and hence optimal drug combinations will be variable. Because upregulation of receptor tyrosine kinases is a major source of drug resistance arising from diverse adaptive responses, we propose that inhibitors of these receptors may have substantial clinical utility in combination with inhibitors of the MAP Kinase pathway. PMID:26673621

  5. Decomposition and humification of soil organic carbon after land use change on erosion prone slopes

    NASA Astrophysics Data System (ADS)

    Häring, Volker; Fischer, Holger; Cadisch, Georg; Stahr, Karl

    2014-05-01

    Soil organic carbon decline after land use change from forest to maize usually lead to soil degradation and elevated CO2 emissions. However, limited knowledge is available on the interactions between rates of SOC change and soil erosion and how SOC dynamics vary with soil depth and clay contents. The 13C isotope based CIDE approach (Carbon Input, Decomposition and Erosion) was developed to determine SOC dynamics on erosion prone slopes. The aims of the present study were: (1) to test the applicability of the CIDE approach to determine rates of decomposition and SOC input under particular considerations of concurrent erosion events on three soil types (Alisol, Luvisol, Vertisol), (2) to adapt the CIDE approach to deeper soil layers (10-20 and 20-30 cm) and (3) to determine the variation of decomposition and SOC input with soil depth and soil texture. SOC dynamics were determined for bulk soil and physically separated SOC fractions along three chronosequences after land use change from forest to maize (up to 21 years) in northwestern Vietnam. Consideration of the effects of soil erosion on SOC dynamics by the CIDE approach yielded a higher total SOC loss (6 to 32%), a lower decomposition (13 to 40%) and a lower SOC input (14 to 31%) relative to the values derived from a commonly applied 13C isotope based mass balance approach. Comparison of decomposition between depth layers revealed that tillage accelerated decomposition in the plough layer (0-10 cm), accounting for 3 to 34% of total decomposition. With increasing clay contents SOC input increased. In addition, decomposition increased with increasing clay contents, too, being attributed to decomposition of exposed labile SOC which was attached to clay particles in the sand sized stable aggregate fraction. This study suggests that in situ SOC dynamics on erosion prone slopes are commonly misrepresented by erosion unadjusted approaches.

  6. 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

  7. 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.

  8. 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.

  9. Condensed-phase thermal decomposition of TATB investigated by atomic force microscopy (AFM) and simultaneous thermogravimetric modulated beam mass spectrometry (STMBMS)

    SciTech Connect

    Land, T.A.; Siekhaus, W.J.; Foltz, M.F.; Behrens, R. Jr.

    1993-05-01

    A combination of techniques has been used to investigate the condensed-phase thermal decomposition of TATB. STMBMS has been used to identify the thermal decomposition products and their temporal correlation`s. These experiments have shown that the condensed-phase decomposition proceeds through several autocatalytic pathways. Both low and high molecular weight decomposition products have been identified. Mono-, di- and tri-furazans products have been identified and, their temporal behaviors are consistent with a stepwise loss of water. AFM has been used to correlate the decomposition chemistry with morphological changes occurring as a function of heating. Patches of small 25-140 nm round holes were observed throughout the lattice of TATB crystals that were heated briefly to 300C. It is likely that these holes show where decomposition reactions have started. Evidence of decomposition products have been seen in TATB that has been held at 250C for one hour.

  10. Quantum mechanical simulations of condensed-phase decomposition dynamics in molten RDX

    NASA Astrophysics Data System (ADS)

    Schweigert, Igor

    2013-03-01

    A reaction model for condensed-phase decomposition of RDX under pressures up to several GPa is needed to support mesoscale simulations of the energetic material's sensitivity to thermal and shock loading. A prerequisite to developing such a model is the identification of the chemical pathways that control the rate of the initial dissociation and the subsequent decomposition of the dissociation products. We use quantum mechanics based molecular dynamics simulations to follow the decomposition dynamics under high-pressure conditions and to identify the reaction mechanisms. This presentation will describe current applications to liquid-phase decomposition of molten RDX. 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.

  11. Variance decomposition in stochastic simulators.

    PubMed

    Le Maître, O P; Knio, O M; Moraes, A

    2015-06-28

    This work aims at the development of a mathematical and computational approach that enables quantification of the inherent sources of stochasticity and of the corresponding sensitivities in stochastic simulations of chemical reaction networks. The approach is based on reformulating the system dynamics as being generated by independent standardized Poisson processes. This reformulation affords a straightforward identification of individual realizations for the stochastic dynamics of each reaction channel, and consequently a quantitative characterization of the inherent sources of stochasticity in the system. By relying on the Sobol-Hoeffding decomposition, the reformulation enables us to perform an orthogonal decomposition of the solution variance. Thus, by judiciously exploiting the inherent stochasticity of the system, one is able to quantify the variance-based sensitivities associated with individual reaction channels, as well as the importance of channel interactions. Implementation of the algorithms is illustrated in light of simulations of simplified systems, including the birth-death, Schlögl, and Michaelis-Menten models. PMID:26133418

  12. 9 CFR 354.131 - Decomposition.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 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...

  13. Adaptive Management

    EPA Science Inventory

    Adaptive management is an approach to natural resource management that emphasizes learning through management where knowledge is incomplete, and when, despite inherent uncertainty, managers and policymakers must act. Unlike a traditional trial and error approach, adaptive managem...

  14. The formation of carbonic and silicon dioxide structured films through the decomposition of molecules on the surface of ionic crystals under the action of IR femtosecond laser radiation

    NASA Astrophysics Data System (ADS)

    Kompanets, V. O.; Laptev, V. B.; Pigul’skii, S. V.; Ryabov, E. A.; Chekalin, S. V.; Blank, V. D.; Denisov, V. N.; Kravchuk, K. S.; Kulnitskiy, B. A.; Perezhogin, I. A.

    2016-06-01

    This study relates to the formation of carbon and silicon dioxide films that occurs as a result of the decomposition of organic and silicon-containing molecules on the surface of ionic crystals under IR femtosecond laser radiation of moderate intensity (~1011 W cm‑2) without molecular decomposition in the gas phase. We found that transparent graphite oxide films formed in the case of CO2 molecule decomposition.

  15. Elucidation of the molecular basis for the attenuation of a live, attenuated influenza A H5N1 cold-adapted vaccine virus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A recombinant, live influenza A H5N1 vaccine candidate with the hemagglutinin (HA) and neuraminidase (NA) genes derived from A/VietNam/1203/04 (H5N1) (H5N1 2004 wt) and the internal protein genes from A/Ann Arbor/6/60 (AA) (H2N2) cold-adapted (ca) virus has been previously shown to be attenuated in ...

  16. Salinity adaptation of the invasive New Zealand mud snail (Potamopyrgus antipodarum) in the Columbia River estuary (Pacific Northwest, USA): Physiological and molecular studies

    USGS Publications Warehouse

    Hoy, Marshal; Boese, Bruce L.; Taylor, Louise; Reusser, Deborah; Rodriguez, Rusty

    2012-01-01

    In this study, we examine salinity stress tolerances of two populations of the invasive species New Zealand mud snail Potamopyrgus antipodarum, one population from a high salinity environment in the Columbia River estuary and the other from a fresh water lake. In 1996, New Zealand mud snails were discovered in the tidal reaches of the Columbia River estuary that is routinely exposed to salinity at near full seawater concentrations. In contrast, in their native habitat and throughout its spread in the western US, New Zealand mud snails are found only in fresh water ecosystems. Our aim was to determine whether the Columbia River snails have become salt water adapted. Using a modification of the standard amphipod sediment toxicity test, salinity tolerance was tested using a range of concentrations up to undiluted seawater, and the snails were sampled for mortality at daily time points. Our results show that the Columbia River snails were more tolerant of acute salinity stress with the LC50 values averaging 38 and 22 Practical Salinity Units for the Columbia River and freshwater snails, respectively. DNA sequence analysis and morphological comparisons of individuals representing each population indicate that they were all P. antipodarum. These results suggest that this species is salt water adaptable and in addition, this investigation helps elucidate the potential of this aquatic invasive organism to adapt to adverse environmental conditions.

  17. Incorporating Functional Gene Quantification into Traditional Decomposition Models

    NASA Astrophysics Data System (ADS)

    Todd-Brown, K. E.; Zhou, J.; Yin, H.; Wu, L.; Tiedje, J. M.; Schuur, E. A. G.; Konstantinidis, K.; Luo, Y.

    2014-12-01

    Incorporating new genetic quantification measurements into traditional substrate pool models represents a substantial challenge. These decomposition models are built around the idea that substrate availablity, with environmental drivers, limit carbon dioxide respiration rates. In this paradigm, microbial communities optimally adapt to a given substrate and environment on much shorter time scales then the carbon flux of interest. By characterizing the relative shift in biomass of these microbial communities, we informed previously poorly constrained parameters in traditional decomposition models. In this study we coupled a 9 month laboratory incubation study with quantitative gene measurements with traditional CO2 flux measurements plus initial soil organic carbon quantification. GeoChip 5.0 was used to quantify the functional genes associated with carbon cycling at 2 weeks, 3 months and 9 months. We then combined the genes which 'collapsed' over the experiment and assumed that this tracked the relative change in the biomass associated with the 'fast' pool. We further assumed that this biomass was proportional to the 'fast' SOC pool and thus were able to constrain the relative change in the fast SOC pool in our 3-pool decomposition model. We found that biomass quantification described above, combined with traditional CO2 flux and SOC measurements, improve the transfer coefficient estimation in traditional decomposition models. Transfer coefficients are very difficult to characterized using traditional CO2 flux measurements, thus DNA quantification provides new and significant information about the system. Over a 100 year simulation, these new biologically informed parameters resulted in an additional 10% of SOC loss over the traditionally informed parameters.

  18. Molecular energies from an incremental fragmentation method

    NASA Astrophysics Data System (ADS)

    Meitei, Oinam Romesh; Heßelmann, Andreas

    2016-02-01

    The systematic molecular fragmentation method by Collins and Deev [J. Chem. Phys. 125, 104104 (2006)] has been used to calculate total energies and relative conformational energies for a number of small and extended molecular systems. In contrast to the original approach by Collins, we have tested the accuracy of the fragmentation method by utilising an incremental scheme in which the energies at the lowest level of the fragmentation are calculated on an accurate quantum chemistry level while lower-cost methods are used to correct the low-level energies through a high-level fragmentation. In this work, the fragment energies at the lowest level of fragmentation were calculated using the random-phase approximation (RPA) and two recently developed extensions to the RPA while the incremental corrections at higher levels of the fragmentation were calculated using standard density functional theory (DFT) methods. The complete incremental fragmentation method has been shown to reproduce the supermolecule results with a very good accuracy, almost independent on the molecular type, size, or type of decomposition. The fragmentation method has also been used in conjunction with the DFT-SAPT (symmetry-adapted perturbation theory) method which enables a breakdown of the total nonbonding energy contributions into individual interaction energy terms. Finally, the potential problems of the method connected with the use of capping hydrogen atoms are analysed and two possible solutions are supplied.

  19. Unsupervised polarimetric SAR urban area classification based on model-based decomposition with cross scattering

    NASA Astrophysics Data System (ADS)

    Xiang, Deliang; Tang, Tao; Ban, Yifang; Su, Yi; Kuang, Gangyao

    2016-06-01

    Since it has been validated that cross-polarized scattering (HV) is caused not only by vegetation but also by rotated dihedrals, in this study, we use rotated dihedral corner reflectors to form a cross scattering matrix and propose an extended four-component model-based decomposition method for PolSAR data over urban areas. Unlike other urban area decomposition techniques which need to discriminate the urban and natural areas before decomposition, this proposed method is applied on PolSAR image directly. The building orientation angle is considered in this scattering matrix, making it flexible and adaptive in the decomposition. Therefore, we can separate cross scattering of urban areas from the overall HV component. Further, the cross and helix scattering components are also compared. Then, using these decomposed scattering powers, the buildings and natural areas can be easily discriminated from each other using a simple unsupervised K-means classifier. Moreover, buildings aligned and not aligned along the radar flight direction can be also distinguished clearly. Spaceborne RADARSAT-2 and airborne AIRSAR full polarimetric SAR data are used to validate the performance of our proposed method. The cross scattering power of oriented buildings is generated, leading to a better decomposition result for urban areas with respect to other state-of-the-art urban decomposition techniques. The decomposed scattering powers significantly improve the classification accuracy for urban areas.

  20. Determining the degree of peat decomposition - A comparison of different methods

    NASA Astrophysics Data System (ADS)

    Biester, Harald; Knorr, Klaus-Holger; Schellekens, Judith; Basler, Anna; Hermanns, Yvonne-Marie

    2014-05-01

    Peat humification or decomposition is a frequently used proxy to extract past time changes in hydrology and climate from peat bogs. During the past century several methods to determine changes in peat decomposition have been introduced. Most of these methods are operationally defined only and the chemical changes underlying the decomposition process are often poorly understood and lack validation. Due to the chemically undefined nature of many humification analyses the comparison of results obtained by different methods is difficult if not misleading. In this study we compared changes in peat decomposition in cores of two peat bogs (Königsmoor (KK), Kleines Rotes Bruch (KRB)) from the Harz Mountains (Germany) using C/N ratios, Fourier Transform Infrared spectra absorption (FTIR) intensities, Rock Eval® oxygen- and hydrogen indices, δ13C and δ15N isotopic signatures and UV-absorption of NaOH peat extracts. In addition, one of the cores was analysed for changes in the peat's molecular composition using pyrolysis gas chromatography mass spectrometry (pyrolysis-GC-MS). Records of decomposition proxies show similar historical development at both sites, indicating external forcing such as climate as controlling process. Moreover, all decomposition proxies except UV-ABS and δ15N isotopes show similar patterns in their records and thus reflect in different extents signals of decomposition. Pyrolysis-GC-MS analyses of the KK core reveal that changes in peat molecular chemistry are mainly attributed to decomposition processes and to a lesser extend to changes in vegetation. Changes in the abundance of molecular compounds indicate that peat decomposition in the KK bog is mainly characterized by preferential decomposition of phenols and polysaccharides and relative enrichment of aliphatics during drier periods. Enrichment of lignin and other aromatics during decomposition was also observed but showed less variation, and presumably reflects changes in vegetation associated

  1. Comparison of different methods to determine the degree of peat decomposition in peat bogs

    NASA Astrophysics Data System (ADS)

    Biester, H.; Knorr, K.-H.; Schellekens, J.; Basler, A.; Hermanns, Y.-M.

    2013-11-01

    Peat humification or decomposition is a frequently used proxy to extract past time changes in hydrology and climate from peat bogs. During the past century several methods to determine changes in peat decomposition have been introduced. Most of these methods are operationally defined only and the chemical changes underlying the decomposition process are often poorly understood and lack validation. Due to the chemically undefined nature of many humification analyses the comparison of results obtained by different methods is difficult if not misleading. In this study we compared changes in peat decomposition in cores of two peat bogs (Königsmoor (KK), Kleines Rotes Bruch, KRB) from the Harz Mountains (Germany) using C / N ratios, Fourier Transform Infrared spectra absorption (FTIR) intensities, Rock Eval® oxygen- and hydrogen indices, δ13C and δ15N isotopic signatures and UV-absorption of NaOH peat extracts. In addition, one of the cores was analysed for changes in the peat's molecular composition using pyrolysis gas chromatography mass spectrometry (pyrolysis-GC-MS). Records of decomposition proxies show similar historical development at both sites, indicating external forcing such as climate as controlling process. Moreover, all decomposition proxies except UV-ABS and δ15N isotopes show similar patterns in their records and thus reflect in different extents signals of decomposition. Pyrolysis-GC-MS analyses of the KK core reveal that changes in peat molecular chemistry are mainly attributed to decomposition processes and to a lesser extend to changes in vegetation. Changes in the abundance of molecular compounds indicate that peat decomposition in the KK bog is mainly characterized by preferential decomposition of phenols and polysaccharides and relative enrichment of aliphatics during drier periods. Enrichment of lignin and other aromatics during decomposition was also observed but showed less variation, and presumably reflects changes in vegetation

  2. A full variational calculation based on a tensor product decomposition

    NASA Astrophysics Data System (ADS)

    Senese, Frederick A.; Beattie, Christopher A.; Schug, John C.; Viers, Jimmy W.; Watson, Layne T.

    1989-08-01

    A new direct full variational approach exploits a tensor (Kronecker) product decomposition of the Hamiltonian. Explicit assembly and storage of the Hamiltonian matrix is avoided by using the Kronecker product structure to form matrix-vector products directly from the molecular integrals. Computation-intensive integral transformations and formula tapes are unnecessary. The wavefunction is expanded in terms of spin-free primitive kets rather than Slater determinants or configuration state functions, and the expansion is equivalent to a full configuration interaction expansion. The approach suggests compact storage schemes and algorithms which are naturally suited to parallel and pipelined machines.

  3. Wavefront reconstruction by modal decomposition.

    PubMed

    Schulze, Christian; Naidoo, Darryl; Flamm, Daniel; Schmidt, Oliver A; Forbes, Andrew; Duparré, Michael

    2012-08-27

    We propose a new method to determine the wavefront of a laser beam based on modal decomposition by computer-generated holograms. The hologram is encoded with a transmission function suitable for measuring the amplitudes and phases of the modes in real-time. This yields the complete information about the optical field, from which the Poynting vector and the wavefront are deduced. Two different wavefront reconstruction options are outlined: reconstruction from the phase for scalar beams, and reconstruction from the Poynting vector for inhomogeneously polarized beams. Results are compared to Shack-Hartmann measurements that serve as a reference and are shown to reproduce the wavefront and phase with very high fidelity. PMID:23037024

  4. Thermal decomposition of HN(3).

    PubMed

    Knyazev, Vadim D; Korobeinichev, Oleg P

    2010-01-21

    The two-channel thermal decomposition of hydrogen azide, HN(3), was studied computationally. The reaction produces triplet or singlet NH and N(2). A model of the reaction was created on the basis of the theoretical study of the reaction potential-energy surface and microscopic reaction rates by Besora and Harvey (Besora, M.; Harvey, J. N. J. Chem. Phys. 2008, 129, 044303) and the experimental data on the energy-dependent rate constants reported by Foy et al. (Foy, B. R.; Casassa, M. P.; Stephenson, J. C.; King, D. S. J. Chem. Phys. 1990, 92, 2782) The properties of the model were adjusted to fit the calculated k(E) dependence to the experimental one. The experiments on thermal decomposition of HN(3) described in the literature were analyzed via kinetic modeling; the results of the analysis demonstrate that all but one of the existing studies were affected by contributions from secondary kinetics. The model of the reaction was then used in master-equation calculations of the pressure effects and the value of the critical energy transfer parameter, DeltaE(down), was adjusted based on agreement with the experimental k(T,P) data. Finally, the model was used to determine pressure- and temperature-dependent rate constants for both channels of reaction 1, which do not conform to the traditional formalism of low-pressure-limit and falloff description. Uncertainties of the model and their influence on the calculated thermal rate constant values were analyzed. Finally, parametrized expression for rate coefficients were provided for a wide range of temperatures and pressures. PMID:19916540

  5. Surface-Accelerated Decomposition of δ-HMX.

    PubMed

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

    2013-03-01

    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. PMID:26281926

  6. Ground state for CH2 and symmetry for methane decomposition

    NASA Astrophysics Data System (ADS)

    Zhang, Li; Luo, Wen-Lang; Ruan, Wen; Jiang, Gang; Zhu, Zheng-He

    2008-06-01

    Using the different level of methods B3P86, BLYP, B3PW91, HF, QCISD, CASSCF (4,4) and MP2 with the various basis functions 6-311G**, D95, cc-pVTZ and DGDZVP, the calculations of this paper confirm that the ground state is tilde X3B1 with C2v group for CH2. Furthermore, the three kinds of theoretical methods, i.e. B3P86, CCSD(T, MP4) and G2 with the same basis set cc-pVTZ only are used to recalculate the zero-point energy revision which are modified by scaling factor 0.989 for the high level based on the virial theorem, and also with the correction for basis set superposition error. These results are also contrary to tilde X3Σ-g for the ground state of CH2 in reference. Based on the atomic and molecular reaction statics, this paper proves that the decomposition type (1) i.e. CH4 → CH2+H2, is forbidden and the decomposition type (2) i.e. CH4 → CH3+H is allowed for CH4. This is similar to the decomposition of SiH4.

  7. Metallo-Organic Decomposition (MOD) film development

    NASA Technical Reports Server (NTRS)

    Parker, J.

    1986-01-01

    The processing techniques and problems encountered in formulating metallo-organic decomposition (MOD) films used in contracting structures for thin solar cells are described. The use of thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) techniques performed at Jet Propulsion Laboratory (JPL) in understanding the decomposition reactions lead to improvements in process procedures. The characteristics of the available MOD films were described in detail.

  8. 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...

  9. 9 CFR 354.131 - Decomposition.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 9 Animals and Animal Products 2 2011-01-01 2011-01-01 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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…

  14. 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…

  15. 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...

  16. Sampling Stoichiometry: The Decomposition of Hydrogen Peroxide.

    ERIC Educational Resources Information Center

    Clift, Philip A.

    1992-01-01

    Describes a demonstration of the decomposition of hydrogen peroxide to provide an interesting, quantitative illustration of the stoichiometric relationship between the decomposition of hydrogen peroxide and the formation of oxygen gas. This 10-minute demonstration uses ordinary hydrogen peroxide and yeast that can be purchased in a supermarket.…

  17. Regular Decompositions for H(div) Spaces

    SciTech Connect

    Kolev, Tzanio; Vassilevski, Panayot

    2012-01-01

    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.

  18. Chronic N(G)-nitro-L-arginine methyl ester-induced hypertension : novel molecular adaptation to systolic load in absence of hypertrophy

    NASA Technical Reports Server (NTRS)

    Bartunek, J.; Weinberg, E. O.; Tajima, M.; Rohrbach, S.; Katz, S. E.; Douglas, P. S.; Lorell, B. H.; Schneider, M. (Principal Investigator)

    2000-01-01

    BACKGROUND: Chronic N(G)-nitro-L-arginine methyl ester (L-NAME), which inhibits nitric oxide synthesis, causes hypertension and would therefore be expected to induce robust cardiac hypertrophy. However, L-NAME has negative metabolic effects on protein synthesis that suppress the increase in left ventricular (LV) mass in response to sustained pressure overload. In the present study, we used L-NAME-induced hypertension to test the hypothesis that adaptation to pressure overload occurs even when hypertrophy is suppressed. METHODS AND RESULTS: Male rats received L-NAME (50 mg. kg(-1). d(-1)) or no drug for 6 weeks. Rats with L-NAME-induced hypertension had levels of systolic wall stress similar to those of rats with aortic stenosis (85+/-19 versus 92+/-16 kdyne/cm). Rats with aortic stenosis developed a nearly 2-fold increase in LV mass compared with controls. In contrast, in the L-NAME rats, no increase in LV mass (1. 00+/-0.03 versus 1.04+/-0.04 g) or hypertrophy of isolated myocytes occurred (3586+/-129 versus 3756+/-135 microm(2)) compared with controls. Nevertheless, chronic pressure overload was not accompanied by the development of heart failure. LV systolic performance was maintained by mechanisms of concentric remodeling (decrease of in vivo LV chamber dimension relative to wall thickness) and augmented myocardial calcium-dependent contractile reserve associated with preserved expression of alpha- and beta-myosin heavy chain isoforms and sarcoplasmic reticulum Ca(2+) ATPase (SERCA-2). CONCLUSIONS: When the expected compensatory hypertrophic response is suppressed during L-NAME-induced hypertension, severe chronic pressure overload is associated with a successful adaptation to maintain systolic performance; this adaptation depends on both LV remodeling and enhanced contractility in response to calcium.

  19. How to Make a Non-Antigenic Protein (Auto) Antigenic: Molecular Complementarity Alters Antigen Processing and Activates Adaptive-Innate Immunity Synergy.

    PubMed

    Root-Bernstein, Robert

    2015-01-01

    Evidence is reviewed that complementary proteins and peptides form complexes with increased antigenicity and/or autoimmunogenicity. Five case studies are highlighted: 1) diphtheria toxin-antitoxin (antibody), which induces immunity to the normally non-antigenic toxin, and autoimmune neuritis; 2) tryptophan peptide of myelin basic protein and muramyl dipeptide ("adjuvant peptide"), which form a complex that induces experimental allergic encephalomyelitis; 3) an insulin and glucagon complex that is far more antigenic than either component individually; 4) various causes of experimental autoimmune myocarditis such as C protein in combination with its antibody, or coxsackie B virus in combination with the coxsackie and adenovirus receptor; 5) influenza A virus haemagglutinin with the outer membrane protein of the Haemophilus influenzae, which increases antigenicity. Several mechanisms cooperate to alter immunogenicity. Complexation alters antigen processing, protecting the components against proteolysis, altering fragmentation and presenting novel antigens to the immune system. Complementary antigens induce complementary adaptive immune responses (complementary antibodies and/or T cell receptors) that produce circulating immune complexes (CIC). CIC stimulate innate immunity. Concurrently, complementary antigens stimulate multiple Toll-like receptors that synergize to over-produce cytokines, which further stimulate adaptive immunity. Thus innate and adaptive immunity form a positive feedback loop. If components of the complex mimic a host protein, then autoimmunity may result. Enhanced antigenicity for production of improved vaccines and/or therapeutic autoimmunity (e.g., against cancer cells) might be achieved by using information from antibody or TCR recognition sites to complement an antigen; by panning for complements in randomized peptide libraries; or using antisense peptide strategies to design complements. PMID:26179268

  20. In situ GaN decomposition analysis by quadrupole mass spectrometry and reflection high-energy electron diffraction

    SciTech Connect

    Fernandez-Garrido, S.; Calleja, E.; Koblmueller, G.; Speck, J. S.

    2008-08-01

    Thermal decomposition of wurtzite (0001)-oriented GaN was analyzed: in vacuum, under active N exposure, and during growth by rf plasma-assisted molecular beam epitaxy. The GaN decomposition rate was determined by measurements of the Ga desorption using in situ quadrupole mass spectrometry, which showed Arrhenius behavior with an apparent activation energy of 3.1 eV. Clear signatures of intensity oscillations during reflection high-energy electron diffraction measurements facilitated complementary evaluation of the decomposition rate and highlighted a layer-by-layer decomposition mode in vacuum. Exposure to active nitrogen, either under vacuum or during growth under N-rich growth conditions, strongly reduced the GaN losses due to GaN decomposition.

  1. Thermal decomposition of magnesium and calcium sulfates

    SciTech Connect

    Roche, S L

    1982-04-01

    The effect of catalyst on the thermal decomposition of MgSO/sub 4/ and CaSO/sub 4/ in vacuum was studied as a function of time in Knudsen cells and for MgSO/sub 4/, in open crucibles in vacuum in a Thermal Gravimetric Apparatus. Platinum and Fe/sub 2/O/sub 3/ were used as catalysts. The CaSO/sub 4/ decomposition rate was approximately doubled when Fe/sub 2/O/sub 3/ was present in a Knudsen cell. Platinum did not catalyze the CaSO/sub 4/ decomposition reaction. The initial decomposition rate for MgSO/sub 4/ was approximately 5 times greater than when additives were present in Knudsen cells but only about 1.5 times greater when decomposition was done in an open crucible.

  2. Multilinear operators for higher-order decompositions.

    SciTech Connect

    Kolda, Tamara Gibson

    2006-04-01

    We propose two new multilinear operators for expressing the matrix compositions that are needed in the Tucker and PARAFAC (CANDECOMP) decompositions. The first operator, which we call the Tucker operator, is shorthand for performing an n-mode matrix multiplication for every mode of a given tensor and can be employed to concisely express the Tucker decomposition. The second operator, which we call the Kruskal operator, is shorthand for the sum of the outer-products of the columns of N matrices and allows a divorce from a matricized representation and a very concise expression of the PARAFAC decomposition. We explore the properties of the Tucker and Kruskal operators independently of the related decompositions. Additionally, we provide a review of the matrix and tensor operations that are frequently used in the context of tensor decompositions.

  3. 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.

  4. Multi-decadal variability in the Greenland ice core records obtained using intrinsic timescale decomposition

    NASA Astrophysics Data System (ADS)

    Zhou, Jiansong; Tung, Ka-Kit; Li, King-Fai

    2015-10-01

    By performing a new adaptive time series decomposition on the composite average of multiple ice core records obtained from the Arctic and Greenland, we extracted a robust quasi-oscillatory signal with a period of ~70 years throughout the preceding millennium, and showed that it is strongly connected to the Atlantic Multidecadal Oscillation (AMO). In the same decomposition there exists the Greenland signature of the Little Ice Age and Medieval Warm Period. Throughout the warm and cold periods the AMO properties remained robust. It implies that the evolution of the AMO has its own coherent mechanism and was little affected by these large climatic excursions.

  5. Polymer electrolyte membrane fuel cell fault diagnosis based on empirical mode decomposition

    NASA Astrophysics Data System (ADS)

    Damour, Cédric; Benne, Michel; Grondin-Perez, Brigitte; Bessafi, Miloud; Hissel, Daniel; Chabriat, Jean-Pierre

    2015-12-01

    Diagnosis tool for water management is relevant to improve the reliability and lifetime of polymer electrolyte membrane fuel cells (PEMFCs). This paper presents a novel signal-based diagnosis approach, based on Empirical Mode Decomposition (EMD), dedicated to PEMFCs. EMD is an empirical, intuitive, direct and adaptive signal processing method, without pre-determined basis functions. The proposed diagnosis approach relies on the decomposition of FC output voltage to detect and isolate flooding and drying faults. The low computational cost of EMD, the reduced number of required measurements, and the high diagnosis accuracy of flooding and drying faults diagnosis make this approach a promising online diagnosis tool for PEMFC degraded modes management.

  6. Multi-decadal variability in the Greenland ice core records obtained using intrinsic timescale decomposition

    NASA Astrophysics Data System (ADS)

    Zhou, Jiansong; Tung, Ka-Kit; Li, King-Fai

    2016-08-01

    By performing a new adaptive time series decomposition on the composite average of multiple ice core records obtained from the Arctic and Greenland, we extracted a robust quasi-oscillatory signal with a period of ~70 years throughout the preceding millennium, and showed that it is strongly connected to the Atlantic Multidecadal Oscillation (AMO). In the same decomposition there exists the Greenland signature of the Little Ice Age and Medieval Warm Period. Throughout the warm and cold periods the AMO properties remained robust. It implies that the evolution of the AMO has its own coherent mechanism and was little affected by these large climatic excursions.

  7. Draft Genome Sequence of thermoalkaliphilic Caldalkalibacillus thermarum strain TA2.A1 Reveals Molecular Adaptations to Extreme pH and Temperature

    SciTech Connect

    Kalamorz, Falk; Keis, Stefanie; Stanton, Jo-Ann; Brown, Steven D; Klingeman, Dawn Marie; Land, Miriam L; Han, Cliff; Martin, S L.; Morgan, Hugh; Cook, Greg

    2011-01-01

    The genes and molecular machines that allow for a thermoalkaliphilic lifestyle have not been defined. To address this goal, we report on the improved high-quality draft genome sequence of Caldalkalibacillus thermarum strain TA2.A1, an obligately aerobic bacterium that grows optimally at pH 9.5 and 65 to 70 C on a wide variety of carbon and energy sources.

  8. 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

  9. Molecular phylogenetics of the Espeletia complex (Asteraceae): evidence from nrDNA ITS sequences on the closest relatives of an Andean adaptive radiation.

    PubMed

    Rauscher, Jason T

    2002-07-01

    The subtribe Espeletiinae (Asteraceae, Heliantheae) comprises morphologically and ecologically diverse plants endemic to the tropical montane paramos of the Andes of Venezuela, Colombia, and Ecuador. Though the ecophysiology and ecology of this adaptive radiation have been well studied, relationships among taxa in the subtribe and between the subtribe and other taxa in the Heliantheae are poorly known. In this study, sequences from the internal transcribed spacer (ITS) region of nuclear ribosomal DNA are used to test previous hypotheses about the phylogenetic position of the Espeletiinae within the Heliantheae and to determine which taxa are the subtribe's closest relatives. Gene phylogenies based on maximum parsimony analyses reveal that the Espeletiinae clade is nested well within the subtribe Melampodiinae and thus should be considered a monophyletic complex of species, not a separate subtribe. The most parsimonious gene trees suggest that the genus Ichthyothere may be the sister taxon to the Espeletia complex and that the genus Smallanthus and a species of Rumfordia are likely among the complex's other closest living relatives. These data offer preliminary insights into the origins of this adaptive radiation and the broader phylogenetic context in which it occurred. PMID:21665707

  10. Identification of Molecular Fingerprints in Human Heat Pain Thresholds by Use of an Interactive Mixture Model R Toolbox (AdaptGauss).

    PubMed

    Ultsch, Alfred; Thrun, Michael C; Hansen-Goos, Onno; Lötsch, Jörn

    2015-01-01

    Biomedical data obtained during cell experiments, laboratory animal research, or human studies often display a complex distribution. Statistical identification of subgroups in research data poses an analytical challenge. Here were introduce an interactive R-based bioinformatics tool, called "AdaptGauss". It enables a valid identification of a biologically-meaningful multimodal structure in the data by fitting a Gaussian mixture model (GMM) to the data. The interface allows a supervised selection of the number of subgroups. This enables the expectation maximization (EM) algorithm to adapt more complex GMM than usually observed with a noninteractive approach. Interactively fitting a GMM to heat pain threshold data acquired from human volunteers revealed a distribution pattern with four Gaussian modes located at temperatures of 32.3, 37.2, 41.4, and 45.4 °C. Noninteractive fitting was unable to identify a meaningful data structure. Obtained results are compatible with known activity temperatures of different TRP ion channels suggesting the mechanistic contribution of different heat sensors to the perception of thermal pain. Thus, sophisticated analysis of the modal structure of biomedical data provides a basis for the mechanistic interpretation of the observations. As it may reflect the involvement of different TRP thermosensory ion channels, the analysis provides a starting point for hypothesis-driven laboratory experiments. PMID:26516852

  11. Adaptive SPECT

    PubMed Central

    Barrett, Harrison H.; Furenlid, Lars R.; Freed, Melanie; Hesterman, Jacob Y.; Kupinski, Matthew A.; Clarkson, Eric; Whitaker, Meredith K.

    2008-01-01

    Adaptive imaging systems alter their data-acquisition configuration or protocol in response to the image information received. An adaptive pinhole single-photon emission computed tomography (SPECT) system might acquire an initial scout image to obtain preliminary information about the radiotracer distribution and then adjust the configuration or sizes of the pinholes, the magnifications, or the projection angles in order to improve performance. This paper briefly describes two small-animal SPECT systems that allow this flexibility and then presents a framework for evaluating adaptive systems in general, and adaptive SPECT systems in particular. The evaluation is in terms of the performance of linear observers on detection or estimation tasks. Expressions are derived for the ideal linear (Hotelling) observer and the ideal linear (Wiener) estimator with adaptive imaging. Detailed expressions for the performance figures of merit are given, and possible adaptation rules are discussed. PMID:18541485

  12. Adapting SAFT-γ perturbation theory to site-based molecular dynamics simulation. II. Confined fluids and vapor-liquid interfaces

    NASA Astrophysics Data System (ADS)

    Ghobadi, Ahmadreza F.; Elliott, J. Richard

    2014-07-01

    In this work, a new classical density functional theory is developed for group-contribution equations of state (EOS). Details of implementation are demonstrated for the recently-developed SAFT-γ WCA EOS and selective applications are studied for confined fluids and vapor-liquid interfaces. The acronym WCA (Weeks-Chandler-Andersen) refers to the characterization of the reference part of the third-order thermodynamic perturbation theory applied in formulating the EOS. SAFT-γ refers to the particular form of "statistical associating fluid theory" that is applied to the fused-sphere, heteronuclear, united-atom molecular models of interest. For the monomer term, the modified fundamental measure theory is extended to WCA-spheres. A new chain functional is also introduced for fused and soft heteronuclear chains. The attractive interactions are taken into account by considering the structure of the fluid, thus elevating the theory beyond the mean field approximation. The fluctuations of energy are also included via a non-local third-order perturbation theory. The theory includes resolution of the density profiles of individual groups such as CH2 and CH3 and satisfies stoichiometric constraints for the density profiles. New molecular simulations are conducted to demonstrate the accuracy of each Helmholtz free energy contribution in reproducing the microstructure of inhomogeneous systems at the united-atom level of coarse graining. At each stage, comparisons are made to assess where the present theory stands relative to the current state of the art for studying inhomogeneous fluids. Overall, it is shown that the characteristic features of real molecular fluids are captured both qualitatively and quantitatively. For example, the average pore density deviates ˜2% from simulation data for attractive pentadecane in a 2-nm slit pore. Another example is the surface tension of ethane/heptane mixture, which deviates ˜1% from simulation data while the theory reproduces the excess

  13. Adapting SAFT-γ perturbation theory to site-based molecular dynamics simulation. II. Confined fluids and vapor-liquid interfaces

    SciTech Connect

    Ghobadi, Ahmadreza F.; Elliott, J. Richard

    2014-07-14

    In this work, a new classical density functional theory is developed for group-contribution equations of state (EOS). Details of implementation are demonstrated for the recently-developed SAFT-γ WCA EOS and selective applications are studied for confined fluids and vapor-liquid interfaces. The acronym WCA (Weeks-Chandler-Andersen) refers to the characterization of the reference part of the third-order thermodynamic perturbation theory applied in formulating the EOS. SAFT-γ refers to the particular form of “statistical associating fluid theory” that is applied to the fused-sphere, heteronuclear, united-atom molecular models of interest. For the monomer term, the modified fundamental measure theory is extended to WCA-spheres. A new chain functional is also introduced for fused and soft heteronuclear chains. The attractive interactions are taken into account by considering the structure of the fluid, thus elevating the theory beyond the mean field approximation. The fluctuations of energy are also included via a non-local third-order perturbation theory. The theory includes resolution of the density profiles of individual groups such as CH{sub 2} and CH{sub 3} and satisfies stoichiometric constraints for the density profiles. New molecular simulations are conducted to demonstrate the accuracy of each Helmholtz free energy contribution in reproducing the microstructure of inhomogeneous systems at the united-atom level of coarse graining. At each stage, comparisons are made to assess where the present theory stands relative to the current state of the art for studying inhomogeneous fluids. Overall, it is shown that the characteristic features of real molecular fluids are captured both qualitatively and quantitatively. For example, the average pore density deviates ∼2% from simulation data for attractive pentadecane in a 2-nm slit pore. Another example is the surface tension of ethane/heptane mixture, which deviates ∼1% from simulation data while the theory

  14. Molecular Characterization and Functional Regulation of Melanocortin 2 Receptor (MC2R) in the Sea Bass. A Putative Role in the Adaptation to Stress

    PubMed Central

    Agulleiro, Maria Josep; Sánchez, Elisa; Leal, Esther; Cortés, Raúl; Fernández-Durán, Begoña; Guillot, Raúl; Davis, Perry; Dores, Robert M.; Gallo-Payet, Nicole; Cerdá-Reverter, José Miguel

    2013-01-01

    The activation of melanocortin 2 receptor (MC2R) by ACTH mediates the signaling cascade leading to steroid synthesis in the interrenal tissue (analogous to the adrenal cortex in mammals) of fish. However, little is known about the functional regulation of this receptor in fish. In this work described, we cloned sea bass MC2R from a liver cDNA. SbMC2R requires the melanocortin 2 receptor accessory protein (MRAP) for its functional expression. Dietary cortisol but not long-term stress protocols downregulated interrenal sbMC2R expression. Data suggest the existence of a negative feedback on interrenal sbMC2R expression imposed by local or systemic glucocorticoids. This feedback could be involved in long-term stress adaptation by regulating interrenal sensitivity to ACTH. ACTH-induced MC2R activation stimulates hepatic lipolysis, suggesting that ACTH may mediate stress-induced effects upstream of cortisol release. PMID:23724142

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

    PubMed Central

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

    2016-01-01

    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. PMID:26924084

  16. Thermal Decomposition Kinetics of HMX

    SciTech Connect

    Burnham, A K; Weese, R K

    2004-05-05

    Nucleation-growth kinetic expressions are derived for thermal decomposition of HMX from a variety of types of data, including mass loss for isothermal and constant rate heating in an open pan, and heat flow for isothermal and constant rate heating in open and closed pans. Conditions are identified in which thermal runaway is small to nonexistent, which typically means temperatures less than 255 C and heating rates less than 1 C/min. Activation energies are typically in the 140 to 150 kJ/mol regime for open pan experiments and about 160 kJ/mol for sealed pan experiments. Our activation energies are about 10% lower than those derived from data supplied by the University of Utah, which we consider the best previous work. The reaction clearly displays more than one process, and most likely three processes, which are most clearly evident in open pan experiments. The reaction is accelerated for closed pan experiments, and one global reaction appears to fit the data well.

  17. Thermal Decomposition Kinetics of HMX

    SciTech Connect

    Burnham, A K; Weese, R K

    2005-03-17

    Nucleation-growth kinetic expressions are derived for thermal decomposition of HMX from a variety of types of data, including mass loss for isothermal and constant rate heating in an open pan, and heat flow for isothermal and constant rate heating in open and closed pans. Conditions are identified in which thermal runaway is small to nonexistent, which typically means temperatures less than 255 C and heating rates less than 1 C/min. Activation energies are typically in the 140 to 165 kJ/mol regime for open pan experiments and about 150-165 kJ/mol for sealed-pan experiments. The reaction clearly displays more than one process, and most likely three processes, which are most clearly evident in open pan experiments. The reaction is accelerated for closed pan experiments, and one global reaction fits the data fairly well. Our A-E values lie in the middle of the values given in a compensation-law plot by Brill et al. (1994). Comparison with additional open and closed low temperature pyrolysis experiments support an activation energy of 165 kJ/mol at 10% conversion.

  18. Thermal Decomposition Kinetics of HMX

    SciTech Connect

    Burnham, A K; Weese, R K

    2004-11-18

    Nucleation-growth kinetic expressions are derived for thermal decomposition of HMX from a variety of thermal analysis data types, including mass loss for isothermal and constant rate heating in an open pan and heat flow for isothermal and constant rate heating in open and closed pans. Conditions are identified in which thermal runaway is small to nonexistent, which typically means temperatures less than 255 C and heating rates less than 1 C/min. Activation energies are typically in the 140 to 165 kJ/mol range for open pan experiments and about 150 to 165 kJ/mol for sealed pan experiments. Our activation energies tend to be slightly lower than those derived from data supplied by the University of Utah, which we consider the best previous thermal analysis work. The reaction clearly displays more than one process, and most likely three processes, which are most clearly evident in open pan experiments. The reaction is accelerated in closed pan experiments, and one global reaction appears to fit the data well. Comparison of our rate measurements with additional literature sources for open and closed low temperature pyrolysis from Sandia gives a likely activation energy of 165 kJ/mol at 10% conversion.

  19. Unimolecular thermal decomposition of dimethoxybenzenes

    NASA Astrophysics Data System (ADS)

    Robichaud, David J.; Scheer, Adam M.; Mukarakate, Calvin; Ormond, Thomas K.; Buckingham, Grant T.; Ellison, G. Barney; Nimlos, Mark R.

    2014-06-01

    The unimolecular thermal decomposition mechanisms of o-, m-, and p-dimethoxybenzene (CH3O-C6H4-OCH3) have been studied using a high temperature, microtubular (μtubular) SiC reactor with a residence time of 100 μs. Product detection was carried out using single photon ionization (SPI, 10.487 eV) and resonance enhanced multiphoton ionization (REMPI) time-of-flight mass spectrometry and matrix infrared absorption spectroscopy from 400 K to 1600 K. The initial pyrolytic step for each isomer is methoxy bond homolysis to eliminate methyl radical. Subsequent thermolysis is unique for each isomer. In the case of o-CH3O-C6H4-OCH3, intramolecular H-transfer dominates leading to the formation of o-hydroxybenzaldehyde (o-HO-C6H4-CHO) and phenol (C6H5OH). Para-CH3O-C6H4-OCH3 immediately breaks the second methoxy bond to form p-benzoquinone, which decomposes further to cyclopentadienone (C5H4=O). Finally, the m-CH3O-C6H4-OCH3 isomer will predominantly follow a ring-reduction/CO-elimination mechanism to form C5H4=O. Electronic structure calculations and transition state theory are used to confirm mechanisms and comment on kinetics. Implications for lignin pyrolysis are discussed.

  20. Downstream evolution of proper orthogonal decomposition eigenfunctions in a lobed mixer

    NASA Technical Reports Server (NTRS)

    Ukeiley, L.; Glauser, M.; Wick, D.

    1993-01-01

    A two-dimensional (one space and time) scalar adaptation of the proper orthogonal decomposition was applied to streamwise velocity data obtained in a lobed mixer flowfield, using a rake of 15 single-component hot wires. Through the application of the proper orthogonal decomposition, the amount of streamwise turbulent kinetic energy contained in the various proper orthogonal modes was examined for two different downstream locations (z/h = 2.6 and 3.9). The large eddy or dominant mode was shown to have a measurable decrease in the relative streamwise component of the kinetic energy between these two downstream locations. This indicates that the large eddy, as defined by the proper orthogonal decomposition, breaks down, and the flow becomes more homogeneous. A pseudoflow visualization technique was then employed to help visualize this process.

  1. 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.

  2. Morphological features of different polyploids for adaptation and molecular characterization of CC-NBS-LRR and LEA gene families in Agave L.

    PubMed

    Tamayo-Ordóñez, M C; Rodriguez-Zapata, L C; Narváez-Zapata, J A; Tamayo-Ordóñez, Y J; Ayil-Gutiérrez, B A; Barredo-Pool, F; Sánchez-Teyer, L F

    2016-05-20

    Polyploidy has been widely described in many Agave L. species, but its influence on environmental response to stress is still unknown. With the objective of knowing the morphological adaptations and regulation responses of genes related to biotic (LEA) and abiotic (NBS-LRR) stress in species of Agave with different levels of ploidy, and how these factors contribute to major response of Agave against environmental stresses, we analyzed 16 morphological trials on five accessions of three species (Agave tequilana Weber, Agave angustifolia Haw. and Agave fourcroydes Lem.) with different ploidy levels (2n=2x=60 2n=3x=90, 2n=5x=150, 2n=6x=180) and evaluated the expression of NBS-LRR and LEA genes regulated by biotic and abiotic stress. It was possible to associate some morphological traits (spines, nuclei, and stomata) to ploidy level. The genetic characterization of stress-related genes NBS-LRR induced by pathogenic infection and LEA by heat or saline stresses indicated that amino acid sequence analysis in these genes showed more substitutions in higher ploidy level accessions of A. fourcroydes Lem. 'Sac Ki' (2n=5x=150) and A. angustifolia Haw. 'Chelem Ki' (2n=6x=180), and a higher LEA and NBS-LRR representativeness when compared to their diploid and triploid counterparts. In all studied Agave accessions expression of LEA and NBS-LRR genes was induced by saline or heat stresses or by infection with Erwinia carotovora, respectively. The transcriptional activation was also higher in A. angustifolia Haw. 'Chelem Ki' (2n=6x=180) and A. fourcroydes 'Sac Ki' (2n=5x=150) than in their diploid and triploid counterparts, which suggests higher adaptation to stress. Finally, the diploid accession A. tequilana Weber 'Azul' showed a differentiated genetic profile relative to other Agave accessions. The differences include similar or higher genetic representativeness and transcript accumulation of LEA and NBS-LRR genes than in polyploid (2n=5x=150 and 2n=6x=180) Agave accessions

  3. The Chick Chorioallantoic Membrane: A Model of Molecular, Structural, and Functional Adaptation to Transepithelial Ion Transport and Barrier Function during Embryonic Development

    PubMed Central

    Gabrielli, Maria Gabriella; Accili, Daniela

    2010-01-01

    The chick chorioallantoic membrane is a very simple extraembryonic membrane which serves multiple functions during embryo development; it is the site of exchange of respiratory gases, calcium transport from the eggshell, acid-base homeostasis in the embryo, and ion and H2O reabsorption from the allantoic fluid. All these functions are accomplished by its epithelia, the chorionic and the allantoic epithelium, by differentiation of a wide range of structural and molecular peculiarities which make them highly specialized, ion transporting epithelia. Studying the different aspects of such a developmental strategy emphasizes the functional potential of the epithelium and offers an excellent model system to gain insights into questions partly still unresolved. PMID:20339524

  4. Decomposition of dissolved organic matter released by an isolate of Microcystis aeruginosa and morphological profile of the associated bacterial community.

    PubMed

    Moreira, I C; Bianchini Jr, I; Vieira, A A H

    2011-02-01

    This study concerns the kinetics of bacterial degradation of two fractions (molecular mass) of dissolved organic matter (DOM) released by Microcystis aeruginosa. Barra Bonita Reservoir (SP, Brazil) conditions were simulated in the laboratory using the associated local bacterial community. The extent of degradation was quantified as the amount of organic carbon transferred from each DOM fraction (< 3 kDa and 3-30 kDa) to bacteria. The variation of bacteria morphotypes associated with the decomposition of each fraction was observed. To find the degradation rate constants (kT), the time profiles of the total, dissolved and particulate organic carbon concentrations were fitted to a first-order kinetic model. These rate constants were higher for the 3-30 kDa fraction than for the lighter fraction. Only in the latter fraction the formation of refractory dissolved organic carbon (DOCR) compounds could be detected and its rate of mass loss was low. The higher bacterial density was reached at 24 and 48 hours for small and higher fractions, respectively. In the first 48 hours of decomposition of both fractions, there was an early predominance of bacillus, succeeded by coccobacillus, vibrios and coccus, and from day 5 to 27, the bacterial density declined and there was greater evenness among the morphotypes. Both fractions of DOM were consumed rapidly, corroborating the hypothesis that DOM is readily available in the environment. This also suggests that the bacterial community in the inocula readily uses the labile part of the DOM, until this community is able to metabolise efficiently the remaining of DOM not degraded in the first moment. Given that M. aeruginosa blooms recur throughout the year in some eutrophic reservoirs, there is a constant supply of the same DOM which could maintain a consortium of bacterial morphotypes adapted to consuming this substrate. PMID:21437399

  5. [Molecular-genetic and epidemiologic examination of personnel subjected to occupational irradiation in Russian Federal Nuclear Center (Sarov). Report 3. Genetic characteristics of adaptive norm].

    PubMed

    Korzeneva, I B; Malinina, T V; Afanas'ev, K I; Zaichkina, S I; Dubrova, Iu E; Skorodumova, E N; Samsonova, V F; Volkova, I V; Shishova, R T; Shcherbakova, I L

    2008-01-01

    Was undertaken the effort to define the limits of the adaptive norms and of high risk groups in regard to the work connected with fissile materials (FM), radioactive materials (RM) and ionizing radiation sources (IRS). In view of the aforementioned goal it was made a comparative evaluation of the individual radiosensitivity measurements and anthropometric indicators in the cohort formed from VNIIEF personnel, which was exposed to a constant occupational gamma-neutron irradiation, as well as the non-irradiated cohort. There were analyzed the dispersion dependencies on height, on chest and on head circumference and heterozygosis by 9 loci. It was found that the minimum chest circumference dispersion is observed in people with average heterozygosis equal to 3 (at the 95% credibility). The minimum head circumference and height dispersion is observed in people with average heterozygosis equal to 3-5. The largest jitter in metric indicators is characteristic for people with heterozygosis 2. The highest radiosensitivity is typical for such individuals as well. It was formulated the assumption that this category of people present the limit heterozygosis case. So, additional research looking at people with the limit heterozygosis values (2 and 7; 8) is required, in order to define individual radiosensitivity limits. PMID:19004326

  6. Physiological and molecular characterization of atypical lipid-dependent Malassezia yeasts from a dog with skin lesions: adaptation to a new host?

    PubMed

    Cafarchia, C; Latrofa, M S; Figueredo, L A; da Silva Machado, M L; Ferreiro, L; Guillot, J; Boekhout, T; Otranto, D

    2011-05-01

    Three lipid-dependent Malassezia isolates (here named 114A, 114B and 114C) recovered from a dog with skin lesions were phenotypically and genotypically characterized. All presented ovoid cells and buds formed on a narrow base. Most of the results from physiological tests were consistent with those of Malassezia furfur. The phylogenetic analysis of ITS-1 and LSU nucleotide sequences was concordant in placing all three clinical Malassezia isolates close to M. furfur. However, the phylogenetic data on the chs-2 sequence revealed that clinical isolate 114A is distinct from M. furfur and was closely affiliated to the sequence of M. pachydermatis with high nodal support. In particular, lipid-dependent isolates 114A displayed chs-2 sequences similar (100%) to that of the non-lipid dependent species Malassezia pachydermatis. The presence of the genetic and physiological polymorphisms detected in these three isolates of M. furfur could have resulted from a process of adaptation of this anthropophilic species to a new host. PMID:21070187

  7. Unimolecular decomposition of methyltrichlorosilane: RRKM calculations

    SciTech Connect

    Osterheld, T.H.; Allendorf, M.D.; Melius, C.F.

    1993-06-01

    Based on reaction thermochemistry and estimates of Arrhenius A-factors, it is expected that Si-C bond cleavage, C-H bond cleavage, and HCl elimination will be the primary channels for the unimolecular decomposition of methyltrichlorosilane. Using RRKM theory, we calculated rate constants for these three reactions. The calculations support the conclusion that these three reactions are the major decomposition pathways. Rate constants for each reaction were calculated in the high-pressure limit (800--1500 K) and in the falloff regime (1300--1500 K) for bath gases of both helium and hydrogen. These calculations thus provide branching fractions as well as decomposition rates. We also calculated bimolecular rate constants for the overall decomposition in the low-pressure limit. Interesting and surprising kinetic behavior of this system and the individual reactions is discussed. The reactivity of this chlorinated organosilane is compared to that of other organosilanes.

  8. A Decomposition Theorem for Finite Automata.

    ERIC Educational Resources Information Center

    Santa Coloma, Teresa L.; Tucci, Ralph P.

    1990-01-01

    Described is automata theory which is a branch of theoretical computer science. A decomposition theorem is presented that is easier than the Krohn-Rhodes theorem. Included are the definitions, the theorem, and a proof. (KR)

  9. Headspace analysis gas-phase infrared spectroscopy: a study of xanthate decomposition on mineral surfaces

    NASA Astrophysics Data System (ADS)

    Vreugdenhil, Andrew J.; Brienne, Stephane H. R.; Markwell, Ross D.; Butler, Ian S.; Finch, James A.

    1997-03-01

    The O-ethyldithiocarbonate (ethyl xanthate, CH 3CH 2OCS -2) anion is a widely used reagent in mineral processing for the separation of sulphide minerals by froth flotation. Ethyl xanthate interacts with mineral powders to produce a hydrophobic layer on the mineral surface. A novel infrared technique, headspace analysis gas-phase infrared spectroscopy (HAGIS) has been used to study the in situ thermal decomposition products of ethyl xanthate on mineral surfaces. These products include CS 2, COS, CO 2, CH 4, SO 2, and higher molecular weight alkyl-containing species. Decomposition pathways have been proposed with some information determined from 2H- and 13C-isotope labelling experiments.

  10. [Capacity of hyperthermophilic Crenarchaeota for decomposition of refractory protiens (α- and β-keratins)].

    PubMed

    Bidzhieva, S Kh; Derbikova, K S; Kublanov, I V; Bonch-Osmolovskaya, E A

    2014-01-01

    Anaerobic thermophilic archaea of the genera Thermogladius and Desulfurococcus capable of a- and P3-keratin decomposition were isolated from hot springs of Kamchatka and Kunashir Island. For two of them (strains 2355k and 3008g), the presence of high-molecular mass, cell-bound endopeptidases active against nonhydrolyzed and partially hydrolyzed proteins at high values of temperature and pH was shown. Capacity for β-keratin decomposition was also found in collection strains (type strains of Desulfurococcus amylolyticus subsp. amylolyticus, D. mucosus subsp. mobilis, and D. fermentans). PMID:25941724

  11. Domain decomposition for the SPN solver MINOS

    SciTech Connect

    Jamelot, Erell; Baudron, Anne-Marie; Lautard, Jean-Jacques

    2012-07-01

    In this article we present a domain decomposition method for the mixed SPN equations, discretized with Raviart-Thomas-Nedelec finite elements. This domain decomposition is based on the iterative Schwarz algorithm with Robin interface conditions to handle communications. After having described this method, we give details on how to optimize the convergence. Finally, we give some numerical results computed in a realistic 3D domain. The computations are done with the MINOS solver of the APOLLO3 (R) code. (authors)

  12. 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.

  13. Hardware Implementation of Singular Value Decomposition

    NASA Astrophysics Data System (ADS)

    Majumder, Swanirbhar; Shaw, Anil Kumar; Sarkar, Subir Kumar

    2016-06-01

    Singular value decomposition (SVD) is a useful decomposition technique which has important role in various engineering fields such as image compression, watermarking, signal processing, and numerous others. SVD does not involve convolution operation, which make it more suitable for hardware implementation, unlike the most popular transforms. This paper reviews the various methods of hardware implementation for SVD computation. This paper also studies the time complexity and hardware complexity in various methods of SVD computation.

  14. 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.

  15. 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.

  16. Unimolecular thermal decomposition of dimethoxybenzenes

    SciTech Connect

    Robichaud, David J. Mukarakate, Calvin; Nimlos, Mark R.; Scheer, Adam M.; Ormond, Thomas K.; Buckingham, Grant T.; Ellison, G. Barney

    2014-06-21

    The unimolecular thermal decomposition mechanisms of o-, m-, and p-dimethoxybenzene (CH{sub 3}O-C{sub 6}H{sub 4}-OCH{sub 3}) have been studied using a high temperature, microtubular (μtubular) SiC reactor with a residence time of 100 μs. Product detection was carried out using single photon ionization (SPI, 10.487 eV) and resonance enhanced multiphoton ionization (REMPI) time-of-flight mass spectrometry and matrix infrared absorption spectroscopy from 400 K to 1600 K. The initial pyrolytic step for each isomer is methoxy bond homolysis to eliminate methyl radical. Subsequent thermolysis is unique for each isomer. In the case of o-CH{sub 3}O-C{sub 6}H{sub 4}-OCH{sub 3}, intramolecular H-transfer dominates leading to the formation of o-hydroxybenzaldehyde (o-HO-C{sub 6}H{sub 4}-CHO) and phenol (C{sub 6}H{sub 5}OH). Para-CH{sub 3}O-C{sub 6}H{sub 4}-OCH{sub 3} immediately breaks the second methoxy bond to form p-benzoquinone, which decomposes further to cyclopentadienone (C{sub 5}H{sub 4}=O). Finally, the m-CH{sub 3}O-C{sub 6}H{sub 4}-OCH{sub 3} isomer will predominantly follow a ring-reduction/CO-elimination mechanism to form C{sub 5}H{sub 4}=O. Electronic structure calculations and transition state theory are used to confirm mechanisms and comment on kinetics. Implications for lignin pyrolysis are discussed.

  17. 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.

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

    SciTech Connect

    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-O 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 supported

  19. 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.

  20. Frequency filtering decompositions for unsymmetric matrices and matrices with strongly varying coefficients

    SciTech Connect

    Wagner, C.

    1996-12-31

    In 1992, Wittum introduced the frequency filtering decompositions (FFD), which yield a fast method for the iterative solution of large systems of linear equations. Based on this method, the tangential frequency filtering decompositions (TFFD) have been developed. The TFFD allow the robust and efficient treatment of matrices with strongly varying coefficients. The existence and the convergence of the TFFD can be shown for symmetric and positive definite matrices. For a large class of matrices, it is possible to prove that the convergence rate of the TFFD and of the FFD is independent of the number of unknowns. For both methods, schemes for the construction of frequency filtering decompositions for unsymmetric matrices have been developed. Since, in contrast to Wittums`s FFD, the TFFD needs only one test vector, an adaptive test vector can be used. The TFFD with respect to the adaptive test vector can be combined with other iterative methods, e.g. multi-grid methods, in order to improve the robustness of these methods. The frequency filtering decompositions have been successfully applied to the problem of the decontamination of a heterogeneous porous medium by flushing.

  1. Molecular cloning and expression studies of the adapter molecule myeloid differentiation factor 88 (MyD88) in turbot (Scophthalmus maximus).

    PubMed

    Lin, Jing-Yun; Hu, Guo-Bin; Yu, Chang-Hong; Li, Song; Liu, Qiu-Ming; Zhang, Shi-Cui

    2015-10-01

    Myeloid differentiation factor 88 (MyD88) is an adapter protein involved in the interleukin-1 receptor (IL-1R) and Toll-like receptor (TLR)-mediated activation of nuclear factor-kappaB (NF-κB). In this study, a full length cDNA of MyD88 was cloned from turbot, Scophthalmus maximus. It is 1619 bp in length and contains an 858-bp open reading frame that encodes a peptide of 285 amino acid residues. The putative turbot (Sm)MyD88 protein possesses a N-terminal death domain and a C-terminal Toll/IL-1 receptor (TIR) domain known to be important for the functions of MyD88 in mammals. Phylogenetic analysis grouped SmMyD88 with other fish MyD88s. SmMyD88 mRNA was ubiquitously expressed in all examined tissues of healthy turbots, with higher levels observed in immune-relevant organs. To explore the role of SmMyD88, its gene expression profile in response to stimulation of lipopolysaccharide (LPS), CpG oligodeoxynucleotide (CpG-ODN) or turbot reddish body iridovirus (TRBIV) was studied in the head kidney, spleen, gills and muscle over a 7-day time course. The results showed an up-regulation of SmMyD88 transcript levels by the three immunostimulants in all four examined tissues, with the induction by CpG-ODN strongest and initiated earliest and inducibility in the muscle very weak. Additionally, TRBIV challenge resulted in a quite high level of SmMyD88 expression in the spleen, whereas the two synthetic immunostimulants induced the higher levels in the head kidney. These data provide insights into the roles of SmMyD88 in the TLR/IL-1R signaling pathway of the innate immune system in turbot. PMID:26025195

  2. The Periplasmic Bacterial Molecular Chaperone SurA Adapts Its Structure to Bind Peptides in Different Conformations to Assert a Sequence Preference for Aromatic Residues

    SciTech Connect

    Xu, X.; Wang, S.; Hu, Y.-X.; McKay, D.B.

    2009-06-04

    The periplasmic molecular chaperone protein SurA facilitates correct folding and maturation of outer membrane proteins in Gram-negative bacteria. It preferentially binds peptides that have a high fraction of aromatic amino acids. Phage display selections, isothermal titration calorimetry and crystallographic structure determination have been used to elucidate the basis of the binding specificity. The peptide recognition is imparted by the first peptidyl-prolyl isomerase (PPIase) domain of SurA. Crystal structures of complexes between peptides of sequence WEYIPNV and NFTLKFWDIFRK with the first PPIase domain of the Escherichia coli SurA protein at 1.3 A resolution, and of a complex between the dodecapeptide and a SurA fragment lacking the second PPIase domain at 3.4 A resolution, have been solved. SurA binds as a monomer to the heptapeptide in an extended conformation. It binds as a dimer to the dodecapeptide in an alpha-helical conformation, predicated on a substantial structural rearrangement of the SurA protein. In both cases, side-chains of aromatic residues of the peptides contribute a large fraction of the binding interactions. SurA therefore asserts a recognition preference for aromatic amino acids in a variety of sequence configurations by adopting alternative tertiary and quaternary structures to bind peptides in different conformations.

  3. Molecular Cloning and Optimization for High Level Expression of Cold-Adapted Serine Protease from Antarctic Yeast Glaciozyma antarctica PI12

    PubMed Central

    Ahmad Mazian, Mu'adz; Salleh, Abu Bakar; Basri, Mahiran; Rahman, Raja Noor Zaliha Raja Abd.

    2014-01-01

    Psychrophilic basidiomycete yeast, Glaciozyma antarctica strain PI12, was shown to be a protease-producer. Isolation of the PI12 protease gene from genomic and mRNA sequences allowed determination of 19 exons and 18 introns. Full-length cDNA of PI12 protease gene was amplified by rapid amplification of cDNA ends (RACE) strategy with an open reading frame (ORF) of 2892 bp, coded for 963 amino acids. PI12 protease showed low homology with the subtilisin-like protease from fungus Rhodosporidium toruloides (42% identity) and no homology to other psychrophilic proteases. The gene encoding mature PI12 protease was cloned into Pichia pastoris expression vector, pPIC9, and positioned under the induction of methanol-alcohol oxidase (AOX) promoter. The recombinant PI12 protease was efficiently secreted into the culture medium driven by the Saccharomyces cerevisiae α-factor signal sequence. The highest protease production (28.3 U/ml) was obtained from P. pastoris GS115 host (GpPro2) at 20°C after 72 hours of postinduction time with 0.5% (v/v) of methanol inducer. The expressed protein was detected by SDS-PAGE and activity staining with a molecular weight of 99 kDa. PMID:25093119

  4. Molecular Cloning and Optimization for High Level Expression of Cold-Adapted Serine Protease from Antarctic Yeast Glaciozyma antarctica PI12.

    PubMed

    Alias, Norsyuhada; Ahmad Mazian, Mu'adz; Salleh, Abu Bakar; Basri, Mahiran; Rahman, Raja Noor Zaliha Raja Abd

    2014-01-01

    Psychrophilic basidiomycete yeast, Glaciozyma antarctica strain PI12, was shown to be a protease-producer. Isolation of the PI12 protease gene from genomic and mRNA sequences allowed determination of 19 exons and 18 introns. Full-length cDNA of PI12 protease gene was amplified by rapid amplification of cDNA ends (RACE) strategy with an open reading frame (ORF) of 2892 bp, coded for 963 amino acids. PI12 protease showed low homology with the subtilisin-like protease from fungus Rhodosporidium toruloides (42% identity) and no homology to other psychrophilic proteases. The gene encoding mature PI12 protease was cloned into Pichia pastoris expression vector, pPIC9, and positioned under the induction of methanol-alcohol oxidase (AOX) promoter. The recombinant PI12 protease was efficiently secreted into the culture medium driven by the Saccharomyces cerevisiae α-factor signal sequence. The highest protease production (28.3 U/ml) was obtained from P. pastoris GS115 host (GpPro2) at 20°C after 72 hours of postinduction time with 0.5% (v/v) of methanol inducer. The expressed protein was detected by SDS-PAGE and activity staining with a molecular weight of 99 kDa. PMID:25093119

  5. Empirical modal decomposition applied to cardiac signals analysis

    NASA Astrophysics Data System (ADS)

    Beya, O.; Jalil, B.; Fauvet, E.; Laligant, O.

    2010-01-01

    In this article, we present the method of empirical modal decomposition (EMD) applied to the electrocardiograms and phonocardiograms signals analysis and denoising. The objective of this work is to detect automatically cardiac anomalies of a patient. As these anomalies are localized in time, therefore the localization of all the events should be preserved precisely. The methods based on the Fourier Transform (TFD) lose the localization property [13] and in the case of Wavelet Transform (WT) which makes possible to overcome the problem of localization, but the interpretation remains still difficult to characterize the signal precisely. In this work we propose to apply the EMD (Empirical Modal Decomposition) which have very significant properties on pseudo periodic signals. The second section describes the algorithm of EMD. In the third part we present the result obtained on Phonocardiograms (PCG) and on Electrocardiograms (ECG) test signals. The analysis and the interpretation of these signals are given in this same section. Finally, we introduce an adaptation of the EMD algorithm which seems to be very efficient for denoising.

  6. Exploring Multimodal Data Fusion Through Joint Decompositions with Flexible Couplings

    NASA Astrophysics Data System (ADS)

    Cabral Farias, Rodrigo; Cohen, Jeremy Emile; Comon, Pierre

    2016-09-01

    A Bayesian framework is proposed to define flexible coupling models for joint tensor decompositions of multiple data sets. Under this framework, a natural formulation of the data fusion problem is to cast it in terms of a joint maximum a posteriori (MAP) estimator. Data driven scenarios of joint posterior distributions are provided, including general Gaussian priors and non Gaussian coupling priors. We present and discuss implementation issues of algorithms used to obtain the joint MAP estimator. We also show how this framework can be adapted to tackle the problem of joint decompositions of large datasets. In the case of a conditional Gaussian coupling with a linear transformation, we give theoretical bounds on the data fusion performance using the Bayesian Cramer-Rao bound. Simulations are reported for hybrid coupling models ranging from simple additive Gaussian models, to Gamma-type models with positive variables and to the coupling of data sets which are inherently of different size due to different resolution of the measurement devices.

  7. Mechanisms of intestinal adaptation.

    PubMed

    Rubin, Deborah C; Levin, Marc S

    2016-04-01

    Following loss of functional small bowel surface area due to surgical resection for therapy of Crohn's disease, ischemia, trauma or other disorders, the remnant gut undergoes a morphometric and functional compensatory adaptive response which has been best characterized in preclinical models. Increased crypt cell proliferation results in increased villus height, crypt depth and villus hyperplasia, accompanied by increased nutrient, fluid and electrolyte absorption. Clinical observations suggest that functional adaptation occurs in humans. In the immediate postoperative period, patients with substantial small bowel resection have massive fluid and electrolyte loss with reduced nutrient absorption. For many patients, the adaptive response permits partial or complete weaning from parenteral nutrition (PN), within two years following resection. However, others have life-long PN dependence. An understanding of the molecular mechanisms that regulate the gut adaptive response is critical for developing novel therapies for short bowel syndrome. Herein we present a summary of key studies that seek to elucidate the mechanisms that regulate post-resection adaptation, focusing on stem and crypt cell proliferation, epithelial differentiation, apoptosis, enterocyte function and the role of growth factors and the enteric nervous system. PMID:27086888

  8. An extended-Lagrangian scheme for charge equilibration in reactive molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Nomura, Ken-ichi; Small, Patrick E.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

    2015-07-01

    Reactive molecular dynamics (RMD) simulations describe chemical reactions at orders-of-magnitude faster computing speed compared with quantum molecular dynamics (QMD) simulations. A major computational bottleneck of RMD is charge-equilibration (QEq) calculation to describe charge transfer between atoms. Here, we eliminate the speed-limiting iterative minimization of the Coulombic energy in QEq calculation by adapting an extended-Lagrangian scheme that was recently proposed in the context of QMD simulations, Souvatzis and Niklasson (2014). The resulting XRMD simulation code drastically improves energy conservation compared with our previous RMD code, Nomura et al. (2008), while substantially reducing the time-to-solution. The XRMD code has been implemented on parallel computers based on spatial decomposition, achieving a weak-scaling parallel efficiency of 0.977 on 786,432 IBM Blue Gene/Q cores for a 67.6 billion-atom system.

  9. 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

  10. Molecular adaptations of apoptotic pathways and signaling partners in the cerebral cortex of human cocaine addicts and cocaine-treated rats.

    PubMed

    Alvaro-Bartolomé, M; La Harpe, R; Callado, L F; Meana, J J; García-Sevilla, J A

    2011-11-24

    could reflect the induction of contraregulatory adaptations or non-apoptotic (neuroplastic) actions induced by the psychostimulant. The enhanced degradation of nuclear PARP-1, a hallmark of apoptosis, indicates the possibility of aberrant cell death. PMID:21925237

  11. 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.

  12. 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.

  13. Molecular Analysis of Asymptomatic Bacteriuria Escherichia coli Strain VR50 Reveals Adaptation to the Urinary Tract by Gene Acquisition

    SciTech Connect

    Beatson, Scott A.; Ben Zakour, Nouri L.; Totsika, Makrina; Forde, Brian M.; Watts, Rebecca E.; Mabbett, Amanda N.; Szubert, Jan M.; Sarkar, Sohinee; Phan, Minh-Duy; Peters, Kate M.; Petty, Nicola K.; Alikhan, Nabil-Fareed; Sullivan, Mitchell J.; Gawthorne, Jayde A.; Stanton-Cook, Mitchell; Nhu, Nguyen Thi Khanh; Chong, Teik Min; Yin, Wai-Fong; Chan, Kok-Gan; Hancock, Viktoria; Ussery, David W.; Ulett, Glen C.; Schembri, Mark A

    2015-05-01

    Urinary tract infections (UTIs) are among the most common infectious diseases of humans, with Escherichia coli for >80% of all cases. One extreme of UTI is asymptomatic bacteriuria (ABU), which occurs as an asymptomatic carrier state that resembles commensalism. Here, to understand the evolution and molecular mechanisms that underpin ABU, the genome of the ABU E. coli strain VR50 was sequenced. Analysis of the complete genome indicated that it most resembles E. coli K-12, with the addition of a 94-kb genomic island (GI-VR50-pheV), eight prophages, and multiple plasmids. GI-VR50-pheV has a mosaic structure and contains genes encoding a number of UTI-associated virulence factors, namely, Afa (afimbrial adhesin), two autotransporter proteins (Ag43 and Sat), and aerobactin. We demonstrated that the presence of this island in VR50 confers its ability to colonize the murine bladder, as a VR50 mutant with GI-VR50-pheV deleted was attenuated in a mouse model of UTI in vivo. We established that Afa is the island-encoded factor responsible for this phenotype using two independent deletion (Afa operon and AfaE adhesin) mutants. E. coli VR50afa and VR50afaE displayed significantly decreased ability to adhere to human bladder epithelial cells. In the mouse model of UTI, VR50afa and VR50afaE displayed reduced bladder colonization compared to wild-type VR50, similar to the colonization level of the GI-VR50-pheV mutant. In conlusion, our study suggests that E. coli VR50 is a commensal-like strain that has acquired fitness factors that facilitate colonization of the human bladder.

  14. Thermal decomposition of 1,1-dimethylhydrazine on Si(100)-2 × 1

    NASA Astrophysics Data System (ADS)

    Armstrong, J. L.; Sun, Y.-M.; White, J. M.

    1997-12-01

    The surface reaction of 1,1-dimethylhydrazine (DMH) with Si(100) has been studied with temperature programmed desorption spectroscopy (TPD), temperature programmed static secondary ion mass spectrometry (TPSSIMS), X-ray photoelectron spectroscopy (XPS), and Auger electron spectroscopy (AES). Adsorption of DMH on Si(100) at 170 K followed by annealing to 1100 K results in significant decomposition to form surface carbide and nitride. TPD results show that the only gas phase desoprtion products are hydrogen and dimethylamine. Furthermore, decomposition occurs over a broad temperature range; XPS and TPSIMS results indicate C sbnd N bond cleavage beginning at 400 K and by 600 K, all the C sbnd N bonds have dissociated. We propose a molecular level mechanism that involves partial decomposition upon adsorption followed by extensive bond cleavage to form surface carbide and nitride.

  15. Ammonia decomposition activity on monolayer Ni supported on Ru, Pt and WC substrates

    NASA Astrophysics Data System (ADS)

    Hansgen, Danielle A.; Vlachos, Dionisios G.; Chen, Jingguang G.

    2011-12-01

    Catalyst design for specific reactions currently involves using atomic or molecular descriptors to identify promising catalysts. In this paper, we explore three surfaces that have similar computed nitrogen binding energies, which is a descriptor for the ammonia decomposition reaction. The surfaces studied include a monolayer of Ni on Pt(111), Ru(0001) and tungsten monocarbide (WC). The activity of these surfaces toward the ammonia decomposition reaction was compared using density functional theory and temperature programmed desorption. It was found that while the NHx-H bond scission is similar on each of the surfaces, the temperature of nitrogen desorption is very different. The differences are explained and the implications for ammonia decomposition activity and catalyst design are discussed.

  16. CT-perfusion imaging of the human brain: advanced deconvolution analysis using circulant singular value decomposition.

    PubMed

    Wittsack, H J; Wohlschläger, A M; Ritzl, E K; Kleiser, R; Cohnen, M; Seitz, R J; Mödder, U

    2008-01-01

    According to indicator dilution theory tissue time-concentration curves have to be deconvolved with arterial input curves in order to get valid perfusion results. Our aim was to adapt and validate a deconvolution method originating from magnetic resonance techniques and apply it to the calculation of dynamic contrast enhanced computed tomography perfusion imaging. The application of a block-circulant matrix approach for singular value decomposition renders the analysis independent of tracer arrival time to improve the results. PMID:18029143

  17. Decomposition of forest products buried in landfills

    SciTech Connect

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

    2013-11-15

    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 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 2.5 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 higher than

  18. 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

  19. Plant roots alter microbial potential for mediation of soil organic carbon decomposition

    NASA Astrophysics Data System (ADS)

    Firestone, M.; Shi, S.; Herman, D.; He, Z.; Zhou, J.

    2014-12-01

    Plant root regulation of soil organic carbon (SOC) decomposition is a key controller of terrestrial C-cycling. Although many studies have tested possible mechanisms underlying plant "priming" of decomposition, few have investigated the microbial mediators of decomposition, which can be greatly influenced by plant activities. Here we examined effects of Avena fatua roots on decomposition of 13C-labeled root litter in a California grassland soil over two simulated growing-seasons. The presence of plant roots consistently suppressed rates of litter decomposition. Reduction of inorganic nitrogen (N) concentration in soil reduced but did not completely relieve this suppressive effect. The presence of plants significantly altered the abundance, composition and functional potential of microbial communities. Significantly higher signal intensities of genes capable of degrading low molecular weight organic compounds (e.g., glucose, formate and malate) were observed in microbial communities from planted soils, while microorganisms in unplanted soils had higher relative abundances of genes involved in degradation of some macromolecules (e.g., hemicellulose and lignin). Additionally, compared to unplanted soils, microbial communities from planted soils had higher signal intensities of proV and proW, suggesting microbial osmotic stress in planted soils. Possible mechanisms for the observed inhibition of decomposition are 1) microbes preferentially using simple substrates from root exudates and 2) soil drying by plant evapotranspiration impairing microbial activity. We propose a simple data-based model suggesting that the impacts of roots, the soil environment, and microbial community composition on decomposition processes result from impacts of these factors on the soil microbial functional gene potential.

  20. Revisiting formic acid decomposition on metallic powder catalysts: Exploding the HCOOH decomposition volcano curve

    NASA Astrophysics Data System (ADS)

    Tang, Yadan; Roberts, Charles A.; Perkins, Ryan T.; Wachs, Israel E.

    2016-08-01

    This study revisits the classic volcano curve for HCOOH decomposition by metal catalysts by taking a modern catalysis approach. The metal catalysts (Au, Ag, Cu, Pt, Pd, Ni, Rh, Co and Fe) were prepared by H2 reduction of the corresponding metal oxides. The number of surface active sites (Ns) was determined by formic acid chemisorption. In situ IR indicated that both monodentate and bidentate/bridged surface HCOO* were present on the metals. Heats of adsorption (ΔHads) for surface HCOO* values on metals were taken from recently reported DFT calculations. Kinetics for surface HCOO* decomposition (krds) were determined with TPD spectroscopy. Steady-state specific activity (TOF = activity/Ns) for HCOOH decomposition over the metals was calculated from steady-state activity (μmol/g-s) and Ns (μmol/g). Steady-state TOFs for HCOOH decomposition weakly correlated with surface HCOO* decomposition kinetics (krds) and ΔHads of surface HCOO* intermediates. The plot of TOF vs. ΔHads for HCOOH decomposition on metal catalysts does not reproduce the classic volcano curve, but shows that TOF depends on both ΔHads and decomposition kinetics (krds) of surface HCOO* intermediates. This is the first time that the classic catalysis study of HCOOH decomposition on metallic powder catalysts has been repeated since its original publication.

  1. Geochemical drivers of organic matter decomposition in Arctic tundra soils

    DOE PAGESBeta

    Herndon, Elizabeth M.; Yang, Ziming; Graham, David E.; Wullschleger, Stan D.; Gu, Baohua; Liang, Liyuan; Bargar, John; Janot, Noemie; Regier, Tom Z.

    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 (CO2) and methane (CH4) 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 seasonal patterns ofmore » 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 CH4 increased relative to dissolved CO2 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

  2. Geochemical drivers of organic matter decomposition in Arctic tundra soils

    SciTech Connect

    Herndon, Elizabeth M.; Yang, Ziming; Graham, David E.; Wullschleger, Stan D.; Gu, Baohua; Liang, Liyuan; Bargar, John; Janot, Noemie; Regier, Tom Z.

    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 (CO2) and methane (CH4) 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 seasonal 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 CH4 increased relative to dissolved CO2 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.

  3. In situ dynamics of microbial communities during decomposition of wheat, rape, and alfalfa residues.

    PubMed

    Pascault, Noémie; Cécillon, Lauric; Mathieu, Olivier; Hénault, Catherine; Sarr, Amadou; Lévêque, Jean; Farcy, Pascal; Ranjard, Lionel; Maron, Pierre-Alain

    2010-11-01

    Microbial communities are of major importance in the decomposition of soil organic matter. However, the identities and dynamics of the populations involved are still poorly documented. We investigated, in an 11-month field experiment, how the initial biochemical quality of crop residues could lead to specific decomposition patterns, linking biochemical changes undergone by the crop residues to the respiration, biomass, and genetic structure of the soil microbial communities. Wheat, alfalfa, and rape residues were incorporated into the 0-15 cm layer of the soil of field plots by tilling. Biochemical changes in the residues occurring during degradation were assessed by near-infrared spectroscopy. Qualitative modifications in the genetic structure of the bacterial communities were determined by bacterial-automated ribosomal intergenic spacer analysis. Bacterial diversity in the three crop residues at early and late stages of decomposition process was further analyzed from a molecular inventory of the 16S rDNA. The decomposition of plant residues in croplands was shown to involve specific biochemical characteristics and microbial community dynamics which were clearly related to the quality of the organic inputs. Decay stage and seasonal shifts occurred by replacement of copiotrophic bacterial groups such as proteobacteria successful on younger residues with those successful on more extensively decayed material such as Actinobacteria. However, relative abundance of proteobacteria depended greatly on the composition of the residues, with a gradient observed from alfalfa to wheat, suggesting that this bacterial group may represent a good indicator of crop residues degradability and modifications during the decomposition process. PMID:20593174

  4. Decomposition of condensed phase energetic materials: interplay between uni- and bimolecular mechanisms.

    PubMed

    Furman, David; Kosloff, Ronnie; Dubnikova, Faina; Zybin, Sergey V; Goddard, William A; Rom, Naomi; Hirshberg, Barak; Zeiri, Yehuda

    2014-03-19

    Activation energy for the decomposition of explosives is a crucial parameter of performance. The dramatic suppression of activation energy in condensed phase decomposition of nitroaromatic explosives has been an unresolved issue for over a decade. We rationalize the reduction in activation energy as a result of a mechanistic change from unimolecular decomposition in the gas phase to a series of radical bimolecular reactions in the condensed phase. This is in contrast to other classes of explosives, such as nitramines and nitrate esters, whose decomposition proceeds via unimolecular reactions both in the gas and in the condensed phase. The thermal decomposition of a model nitroaromatic explosive, 2,4,6-trinitrotoluene (TNT), is presented as a prime example. Electronic structure and reactive molecular dynamics (ReaxFF-lg) calculations enable to directly probe the condensed phase chemistry under extreme conditions of temperature and pressure, identifying the key bimolecular radical reactions responsible for the low activation route. This study elucidates the origin of the difference between the activation energies in the gas phase (~62 kcal/mol) and the condensed phase (~35 kcal/mol) of TNT and identifies the corresponding universal principle. On the basis of these findings, the different reactivities of nitro-based organic explosives are rationalized as an interplay between uni- and bimolecular processes. PMID:24495109

  5. 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.

  6. Global decomposition experiment shows soil animal impacts on decomposition are climate-dependent

    PubMed Central

    WALL, DIANA H; BRADFORD, MARK A; ST JOHN, MARK G; TROFYMOW, JOHN A; BEHAN-PELLETIER, VALERIE; BIGNELL, DAVID E; DANGERFIELD, J MARK; PARTON, WILLIAM J; RUSEK, JOSEF; VOIGT, WINFRIED; WOLTERS, VOLKMAR; GARDEL, HOLLEY ZADEH; AYUKE, FRED O; BASHFORD, RICHARD; BELJAKOVA, OLGA I; BOHLEN, PATRICK J; BRAUMAN, ALAIN; FLEMMING, STEPHEN; HENSCHEL, JOH R; JOHNSON, DAN L; JONES, T HEFIN; KOVAROVA, MARCELA; KRANABETTER, J MARTY; KUTNY, LES; LIN, KUO-CHUAN; MARYATI, MOHAMED; MASSE, DOMINIQUE; POKARZHEVSKII, ANDREI; RAHMAN, HOMATHEVI; SABARÁ, MILLOR G; SALAMON, JOERG-ALFRED; SWIFT, MICHAEL J; VARELA, AMANDA; VASCONCELOS, HERALDO L; WHITE, DON; ZOU, XIAOMING

    2008-01-01

    Climate and litter quality are primary drivers of terrestrial decomposition and, based on evidence from multisite experiments at regional and global scales, are universally factored into global decomposition models. In contrast, soil animals are considered key regulators of decomposition at local scales but their role at larger scales is unresolved. Soil animals are consequently excluded from global models of organic mineralization processes. Incomplete assessment of the roles of soil animals stems from the difficulties of manipulating invertebrate animals experimentally across large geographic gradients. This is compounded by deficient or inconsistent taxonomy. We report a global decomposition experiment to assess the importance of soil animals in C mineralization, in which a common grass litter substrate was exposed to natural decomposition in either control or reduced animal treatments across 30 sites distributed from 43°S to 68°N on six continents. Animals in the mesofaunal size range were recovered from the litter by Tullgren extraction and identified to common specifications, mostly at the ordinal level. The design of the trials enabled faunal contribution to be evaluated against abiotic parameters between sites. Soil animals increase decomposition rates in temperate and wet tropical climates, but have neutral effects where temperature or moisture constrain biological activity. Our findings highlight that faunal influences on decomposition are dependent on prevailing climatic conditions. We conclude that (1) inclusion of soil animals will improve the predictive capabilities of region- or biome-scale decomposition models, (2) soil animal influences on decomposition are important at the regional scale when attempting to predict global change scenarios, and (3) the statistical relationship between decomposition rates and climate, at the global scale, is robust against changes in soil faunal abundance and diversity.

  7. Thermal Decomposition of 3-Bromopropene. A Theoretical Kinetic Investigation.

    PubMed

    Tucceri, María E; Badenes, María P; Bracco, Larisa L B; Cobos, Carlos J

    2016-04-21

    A detailed kinetic study of the gas-phase thermal decomposition of 3-bromopropene over wide temperature and pressure ranges was performed. Quantum chemical calculations employing the density functional theory methods B3LYP, BMK, and M06-2X and the CBS-QB3 and G4 ab initio composite models provide the relevant part of the potential energy surfaces and the molecular properties of the species involved in the CH2═CH-CH2Br → CH2═C═CH2 + HBr (1) and CH2═CH-CH2Br → CH2═CH-CH2 + Br (2) reaction channels. Transition-state theory and unimolecular reaction rate theory calculations show that the simple bond fission reaction ( 2 ) is the predominant decomposition channel and that all reported experimental studies are very close to the high-pressure limit of this process. Over the 500-1400 K range a rate constant for the primary dissociation of k2,∞ = 4.8 × 10(14) exp(-55.0 kcal mol(-1)/RT) s(-1) is predicted at the G4 level. The calculated k1,∞ values lie between 50 to 260 times smaller. A value of 10.6 ± 1.5 kcal mol(-1) for the standard enthalpy of formation of 3-bromopropene at 298 K was estimated from G4 thermochemical calculations. PMID:27023718

  8. The Autocatalytic Behavior of Trimethylindium During Thermal Decomposition

    SciTech Connect

    Anthony H. McDaniel; M. D. Allendorf

    2000-02-02

    Pyrolysis of trimethylindium (TMIn) in a hot-wall flow-tube reactor has been investigated at temperatures between 573 and 723 K using a modulated molecular-beam mass-sampling technique and detailed numerical modeling. The TMIn was exposed to various mixtures of carrier gases: He, H{sub 2}, D{sub 2}, and C{sub 2}H{sub 4}, in an effort to elucidate the behavior exhibited by this compound in different chemical environments. The decomposition of TMIn is a heterogeneous, autocatalytic process with an induction period that is carrier-gas dependent and lasts on the order of minutes. After activation of the tube wall, the thermolysis exhibits a steady-state behavior that is surface mediated. This result is contrary to prior literature reports, which state that decomposition occurs in the gas phase via successive loss of the CH{sub 3} ligands. This finding also suggests that the bond dissociation energy for the (CH{sub 3}){sub 2}In-CH{sub 3} bond derived from flow-tube investigations is erroneous and should be reevaluated.

  9. Adaptive Development

    NASA Technical Reports Server (NTRS)

    2005-01-01

    The goal of this research is to develop and demonstrate innovative adaptive seal technologies that can lead to dramatic improvements in engine performance, life, range, and emissions, and enhance operability for next generation gas turbine engines. This work is concentrated on the development of self-adaptive clearance control systems for gas turbine engines. Researchers have targeted the high-pressure turbine (HPT) blade tip seal location for following reasons: Current active clearance control (ACC) systems (e.g., thermal case-cooling schemes) cannot respond to blade tip clearance changes due to mechanical, thermal, and aerodynamic loads. As such they are prone to wear due to the required tight running clearances during operation. Blade tip seal wear (increased clearances) reduces engine efficiency, performance, and service life. Adaptive sealing technology research has inherent impact on all envisioned 21st century propulsion systems (e.g. distributed vectored, hybrid and electric drive propulsion concepts).

  10. [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. PMID:18069332

  11. Multilevel domain decomposition for electronic structure calculations

    SciTech Connect

    Barrault, M. . E-mail: maxime.barrault@edf.fr; Cances, E. . E-mail: cances@cermics.enpc.fr; Hager, W.W. . E-mail: hager@math.ufl.edu; Le Bris, C. . E-mail: lebris@cermics.enpc.fr

    2007-03-01

    We introduce a new multilevel domain decomposition method (MDD) for electronic structure calculations within semi-empirical and density functional theory (DFT) frameworks. This method iterates between local fine solvers and global coarse solvers, in the spirit of domain decomposition methods. Using this approach, calculations have been successfully performed on several linear polymer chains containing up to 40,000 atoms and 200,000 atomic orbitals. Both the computational cost and the memory requirement scale linearly with the number of atoms. Additional speed-up can easily be obtained by parallelization. We show that this domain decomposition method outperforms the density matrix minimization (DMM) method for poor initial guesses. Our method provides an efficient preconditioner for DMM and other linear scaling methods, variational in nature, such as the orbital minimization (OM) procedure.

  12. 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. PMID:16154263

  13. 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.

  14. Electrostatic interactions play an essential role in DNA repair and cold-adaptation of uracil DNA glycosylase.

    PubMed

    Olufsen, Magne; Smalås, Arne O; Brandsdal, Bjørn O

    2008-03-01

    Life has adapted to most environments on earth, including low and high temperature niches. The increased catalytic efficiency and thermoliability observed for enzymes from organisms living in constantly cold regions when compared to their mesophilic and thermophilic cousins are poorly understood at the molecular level. Uracil DNA glycosylase (UNG) from cod (cUNG) catalyzes removal of uracil from DNA with an increased k(cat) and reduced K(m) relative to its warm-active human (hUNG) counterpart. Specific issues related to DNA repair and substrate binding/recognition (K(m)) are here investigated by continuum electrostatics calculations, MD simulations and free energy calculations. Continuum electrostatic calculations reveal that cUNG has surface potentials that are more complementary to the DNA potential at and around the catalytic site when compared to hUNG, indicating improved substrate binding. Comparative MD simulations combined with free energy calculations using the molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) method show that large opposing energies are involved when forming the enzyme-substrate complexes. Furthermore, the binding free energies obtained reveal that the Michaelis-Menten complex is more stable for cUNG, primarily due to enhanced electrostatic properties, suggesting that energetic fine-tuning of electrostatics can be utilized for enzymatic temperature adaptation. Energy decomposition pinpoints the residual determinants responsible for this adaptation. PMID:18196298

  15. A framework for constructing adaptive and reconfigurable systems

    SciTech Connect

    Poirot, Pierre-Etienne; Nogiec, Jerzy; Ren, Shangping; /IIT, Chicago

    2007-05-01

    This paper presents a software approach to augmenting existing real-time systems with self-adaptation capabilities. In this approach, based on the control loop paradigm commonly used in industrial control, self-adaptation is decomposed into observing system events, inferring necessary changes based on a system's functional model, and activating appropriate adaptation procedures. The solution adopts an architectural decomposition that emphasizes independence and separation of concerns. It encapsulates observation, modeling and correction into separate modules to allow for easier customization of the adaptive behavior and flexibility in selecting implementation technologies.

  16. 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. PMID:23942265

  17. Excess Sodium Tetraphenylborate and Intermediates Decomposition Studies

    SciTech Connect

    Barnes, M.J.

    1998-12-07

    The stability of excess amounts of sodium tetraphenylborate (NaTPB) in the In-Tank Precipitation (ITP) facility depends on a number of variables. Concentration of palladium, initial benzene, and sodium ion as well as temperature provide the best opportunities for controlling the decomposition rate. This study examined the influence of these four variable on the reactivity of palladium-catalyzed sodium tetraphenylborate decomposition. Also, single effects tests investigated the reactivity of simulants with continuous stirring and nitrogen ventilation, with very high benzene concentrations, under washed sodium concentrations, with very high palladium concentrations, and with minimal quantities of excess NaTPB.

  18. A mathematical analysis of the scattered decomposition

    SciTech Connect

    Salmon, J.

    1988-01-01

    A theoretical basis for the scattered decomposition is worked out in some detail. The basic result has been part of the /open quotes/folklore/close quotes/ for some time, but has never been proved. The load imbalance expected from a scattered decomposition of a set of computational tasks is proportional to the number of tasks assigned to each processor, the mean time per task and root mean square deviation timer per task. The constant of proportionality is a very slowly increasing function of the number of processors. 4 refs.

  19. 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.

  20. 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.