Sample records for potential efp method
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Multipole moments in the effective fragment potential method
DOE Office of Scientific and Technical Information (OSTI.GOV)
Bertoni, Colleen; Slipchenko, Lyudmila V.; Misquitta, Alston J.
In the effective fragment potential (EFP) method the Coulomb potential is represented using a set of multipole moments generated by the distributed multipole analysis (DMA) method. Misquitta, Stone, and Fazeli recently developed a basis space-iterated stockholder atom (BS-ISA) method to generate multipole moments. This study assesses the accuracy of the EFP interaction energies using sets of multipole moments generated from the BS-ISA method, and from several versions of the DMA method (such as analytic and numeric grid-based), with varying basis sets. Both methods lead to reasonable results, although using certain implementations of the DMA method can result in large errors.more » With respect to the CCSD(T)/CBS interaction energies, the mean unsigned error (MUE) of the EFP method for the S22 data set using BS-ISA–generated multipole moments and DMA-generated multipole moments (using a small basis set and the analytic DMA procedure) is 0.78 and 0.72 kcal/mol, respectively. Here, the MUE accuracy is on the same order as MP2 and SCS-MP2. The MUEs are lower than in a previous study benchmarking the EFP method without the EFP charge transfer term, demonstrating that the charge transfer term increases the accuracy of the EFP method. Regardless of the multipole moment method used, it is likely that much of the error is due to an insufficient short-range electrostatic term (i.e., charge penetration term), as shown by comparisons with symmetry-adapted perturbation theory.« less
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Multipole moments in the effective fragment potential method
Bertoni, Colleen; Slipchenko, Lyudmila V.; Misquitta, Alston J.; ...
2017-02-17
In the effective fragment potential (EFP) method the Coulomb potential is represented using a set of multipole moments generated by the distributed multipole analysis (DMA) method. Misquitta, Stone, and Fazeli recently developed a basis space-iterated stockholder atom (BS-ISA) method to generate multipole moments. This study assesses the accuracy of the EFP interaction energies using sets of multipole moments generated from the BS-ISA method, and from several versions of the DMA method (such as analytic and numeric grid-based), with varying basis sets. Both methods lead to reasonable results, although using certain implementations of the DMA method can result in large errors.more » With respect to the CCSD(T)/CBS interaction energies, the mean unsigned error (MUE) of the EFP method for the S22 data set using BS-ISA–generated multipole moments and DMA-generated multipole moments (using a small basis set and the analytic DMA procedure) is 0.78 and 0.72 kcal/mol, respectively. Here, the MUE accuracy is on the same order as MP2 and SCS-MP2. The MUEs are lower than in a previous study benchmarking the EFP method without the EFP charge transfer term, demonstrating that the charge transfer term increases the accuracy of the EFP method. Regardless of the multipole moment method used, it is likely that much of the error is due to an insufficient short-range electrostatic term (i.e., charge penetration term), as shown by comparisons with symmetry-adapted perturbation theory.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Gaenko, Alexander; Windus, Theresa L.; Sosonkina, Masha
2012-10-19
The design and development of scientific software components to provide an interface to the effective fragment potential (EFP) methods are reported. Multiscale modeling of physical and chemical phenomena demands the merging of software packages developed by research groups in significantly different fields. Componentization offers an efficient way to realize new high performance scientific methods by combining the best models available in different software packages without a need for package readaptation after the initial componentization is complete. The EFP method is an efficient electronic structure theory based model potential that is suitable for predictive modeling of intermolecular interactions in large molecularmore » systems, such as liquids, proteins, atmospheric aerosols, and nanoparticles, with an accuracy that is comparable to that of correlated ab initio methods. The developed components make the EFP functionality accessible for any scientific component-aware software package. The performance of the component is demonstrated on a protein interaction model, and its accuracy is compared with results obtained with coupled cluster methods.« less
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Effective Fragment Potential Method for H-Bonding: How To Obtain Parameters for Nonrigid Fragments.
Dubinets, Nikita; Slipchenko, Lyudmila V
2017-07-20
Accuracy of the effective fragment potential (EFP) method was explored for describing intermolecular interaction energies in three dimers with strong H-bonded interactions, formic acid, formamide, and formamidine dimers, which are a part of HBC6 database of noncovalent interactions. Monomer geometries in these dimers change significantly as a function of intermonomer separation. Several EFP schemes were considered, in which fragment parameters were prepared for a fragment in its gas-phase geometry or recomputed for each unique fragment geometry. Additionally, a scheme in which gas-phase fragment parameters are shifted according to relaxed fragment geometries is introduced and tested. EFP data are compared against the coupled cluster with single, double, and perturbative triple excitations (CCSD(T)) method in a complete basis set (CBS) and the symmetry adapted perturbation theory (SAPT). All considered EFP schemes provide a good agreement with CCSD(T)/CBS for binding energies at equilibrium separations, with discrepancies not exceeding 2 kcal/mol. However, only the schemes that utilize relaxed fragment geometries remain qualitatively correct at shorter than equilibrium intermolecular distances. The EFP scheme with shifted parameters behaves quantitatively similar to the scheme in which parameters are recomputed for each monomer geometry and thus is recommended as a computationally efficient approach for large-scale EFP simulations of flexible systems.
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NASA Astrophysics Data System (ADS)
Kuroki, Nahoko; Mori, Hirotoshi
2018-02-01
Effective fragment potential version 2 - molecular dynamics (EFP2-MD) simulations, where the EFP2 is a polarizable force field based on ab initio electronic structure calculations were applied to water-methanol binary mixture. Comparing EFP2s defined with (aug-)cc-pVXZ (X = D,T) basis sets, it was found that large sets are necessary to generate sufficiently accurate EFP2 for predicting mixture properties. It was shown that EFP2-MD could predict the excess molar volume. Since the computational cost of EFP2-MD are far less than ab initio MD, the results presented herein demonstrate that EFP2-MD is promising for predicting physicochemical properties of novel mixed solvents.
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Guidez, Emilie B; Gordon, Mark S
2015-03-12
The modeling of dispersion interactions in density functional theory (DFT) is commonly performed using an energy correction that involves empirically fitted parameters for all atom pairs of the system investigated. In this study, the first-principles-derived dispersion energy from the effective fragment potential (EFP) method is implemented for the density functional theory (DFT-D(EFP)) and Hartree-Fock (HF-D(EFP)) energies. Overall, DFT-D(EFP) performs similarly to the semiempirical DFT-D corrections for the test cases investigated in this work. HF-D(EFP) tends to underestimate binding energies and overestimate intermolecular equilibrium distances, relative to coupled cluster theory, most likely due to incomplete accounting for electron correlation. Overall, this first-principles dispersion correction yields results that are in good agreement with coupled-cluster calculations at a low computational cost.
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Effective fragment potential study of the interaction of DNA bases.
Smith, Quentin A; Gordon, Mark S; Slipchenko, Lyudmila V
2011-10-20
Hydrogen-bonded and stacked structures of adenine-thymine and guanine-cytosine nucleotide base pairs, along with their methylated analogues, are examined with the ab inito based general effective fragment potential (EFP2) method. A comparison of coupled cluster with single, double, and perturbative triple (CCSD(T)) energies is presented, along with an EFP2 energy decomposition to illustrate the components of the interaction energy.
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Li, Hui
2009-11-14
Linear response and variational treatment are formulated for Hartree-Fock (HF) and Kohn-Sham density functional theory (DFT) methods and combined discrete-continuum solvation models that incorporate self-consistently induced dipoles and charges. Due to the variational treatment, analytic nuclear gradients can be evaluated efficiently for these discrete and continuum solvation models. The forces and torques on the induced point dipoles and point charges can be evaluated using simple electrostatic formulas as for permanent point dipoles and point charges, in accordance with the electrostatic nature of these methods. Implementation and tests using the effective fragment potential (EFP, a polarizable force field) method and the conductorlike polarizable continuum model (CPCM) show that the nuclear gradients are as accurate as those in the gas phase HF and DFT methods. Using B3LYP/EFP/CPCM and time-dependent-B3LYP/EFP/CPCM methods, acetone S(0)-->S(1) excitation in aqueous solution is studied. The results are close to those from full B3LYP/CPCM calculations.
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NASA Astrophysics Data System (ADS)
Ghosh, Debashree; Krylov, Anna I.
2011-06-01
Green fluorescent proteins (GFP) can be considered as a model for flurogenic dyes and are of importance in photovoltaic materials. It exhibits bright green fluorescence when exposed to blue light and has been an extremely powerful tool as non-invasive marker in living cells and extensibly used in molecular and cell biology. The understanding of the underlying electronic structure of these proteins and its chromophore is therefore crucial to the understanding of the mechanism for its optical properties. The chromophore of the GFP is p-hydroxybenzylidene-imidazolinone (HBDI) and is embedded in the center of the β barrel of the GFP. Calculating redox potential of this chromophore is a challenging problem, especially in diverse solvents and protein environment. It is possible to carry out high-level accurate ab-initio calculation of ionization potential or electron affinity of the microsolvated chromophore or the bare chromophore. But, it is not possible to extend these calculations to bulk solvents due to the high computational cost. Effective fragment potential (EFP)[1,2] method gives us a convenient tool to understand such systems. In our work, we have benchmarked the ionization energy and electron affinity of the microsolvated GFP chromophore calculated by combined EOM-IP-CCSD/EFP and EOM-EA-CCSD/EFP with the EOM-IP-CCSD and EOM-EA-CCSD calculations of the oxidized and reduced forms. We have carried out similar EFP-EOM-IP-CCSD and EFP-EOM-EA-CCSD calculations of ionization potential and electron affinity of GFP choromophore in bulk solvent generated by ab-initio molecular dynamics simulations. [1] M. S. Gordon, L. Slipchenko, H. Li, J. H. Jensen, Annual Reports in Computational Chemistry, Volume 3, 177 (2007). [2] D. Ghosh, D. Kosenkov, V. Vanovschi, C.F. Williams, J.M. Herbert, M.S. Gordon, M.W. Schmidt, L.V. Slipchenko, and A.I. Krylov, J. Phys. Chem. A 114, 12739 (2010).
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Developments toward more accurate molecular modeling of liquids
NASA Astrophysics Data System (ADS)
Evans, Tom J.
2000-12-01
The general goal of this research has been to improve upon existing combined quantum mechanics/molecular mechanics (QM/MM) methodologies. Error weighting functions have been introduced into the perturbative Monte Carlo (PMC) method for use with QM/MM. The PMC approach, introduced earlier, provides a means to reduce the number of full self-consistent field (SCF) calculations in simulations using the QM/MM potential by evoking perturbation theory to calculate energy changes due to displacements of a MM molecule. This will allow the ab initio QM/MM approach to be applied to systems that require more advanced, computationally demanding treatments of the QM and/or MM regions. Efforts have also been made to improve the accuracy of the representation of the solvent molecules usually represented by MM force fields. Results from an investigation of the applicability of the embedded density functional theory (EDFT) for studying physical properties of solutions will be presented. In this approach, the solute wavefunction is solved self- consistently in the field of individually frozen electron-density solvent molecules. To test its accuracy, the potential curves for interactions between Li+, Cl- and H2O with a single frozen-density H 2O molecule in different orientations have been calculated. With the development of the more sophisticated effective fragment potential (EFP) representation of solvent molecules, a QM/EFP technique was created. This hybrid QM/EFP approach was used to investigate the solvation of Li + by small clusters of water, as a test case for larger ionic dusters. The EFP appears to provide an accurate representation of the strong interactions that exist between Li+ and H2O. With the QM/EFP methodology comes an increased computational expense, resulting in an even greater need to rely on the PMC approach. However, while including the PMC into the hybrid QM/EFP technique, it was discovered that the previous implementation of the PMC was done incorrectly, invalidating earlier test results. The PMC implementation was therefore reworked, and tests were performed to investigate the methods usefulness in reducing the computational load of these types of simulations. The results that were obtained while studying F-(H2O) and F-(H 2O)2 show that PMC can be used cautiously to increase computational efficiency.
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Development and application of QM/MM methods to study the solvation effects and surfaces
DOE Office of Scientific and Technical Information (OSTI.GOV)
Dibya, Pooja Arora
2010-01-01
Quantum mechanical (QM) calculations have the advantage of attaining high-level accuracy, however QM calculations become computationally inefficient as the size of the system grows. Solving complex molecular problems on large systems and ensembles by using quantum mechanics still poses a challenge in terms of the computational cost. Methods that are based on classical mechanics are an inexpensive alternative, but they lack accuracy. A good trade off between accuracy and efficiency is achieved by combining QM methods with molecular mechanics (MM) methods to use the robustness of the QM methods in terms of accuracy and the MM methods to minimize themore » computational cost. Two types of QM combined with MM (QM/MM) methods are the main focus of the present dissertation: the application and development of QM/MM methods for solvation studies and reactions on the Si(100) surface. The solvation studies were performed using a discreet solvation model that is largely based on first principles called the effective fragment potential method (EFP). The main idea of combining the EFP method with quantum mechanics is to accurately treat the solute-solvent and solvent-solvent interactions, such as electrostatic, polarization, dispersion and charge transfer, that are important in correctly calculating solvent effects on systems of interest. A second QM/MM method called SIMOMM (surface integrated molecular orbital molecular mechanics) is a hybrid QM/MM embedded cluster model that mimics the real surface.3 This method was employed to calculate the potential energy surfaces for reactions of atomic O on the Si(100) surface. The hybrid QM/MM method is a computationally inexpensive approach for studying reactions on larger surfaces in a reasonably accurate and efficient manner. This thesis is comprised of four chapters: Chapter 1 describes the general overview and motivation of the dissertation and gives a broad background of the computational methods that have been employed in this work. Chapter 2 illustrates the methodology of the interface of the EFP method with the configuration interaction with single excitations (CIS) method to study solvent effects in excited states. Chapter 3 discusses the study of the adiabatic electron affinity of the hydroxyl radical in aqueous solution and in micro-solvated clusters using a QM/EFP method. Chapter 4 describes the study of etching and diffusion of oxygen atom on a reconstructed Si(100)-2 x 1 surface using a hybrid QM/MM embedded cluster model (SIMOMM). Chapter 4 elucidates the application of the EFP method towards the understanding of the aqueous ionization potential of Na atom. Finally, a general conclusion of this dissertation work and prospective future direction are presented in Chapter 6.« less
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Direct activation of the Mauthner cell by electric field pulses drives ultrarapid escape responses
Tabor, Kathryn M.; Bergeron, Sadie A.; Horstick, Eric J.; Jordan, Diana C.; Aho, Vilma; Porkka-Heiskanen, Tarja; Haspel, Gal
2014-01-01
Rapid escape swims in fish are initiated by the Mauthner cells, giant reticulospinal neurons with unique specializations for swift responses. The Mauthner cells directly activate motoneurons and facilitate predator detection by integrating acoustic, mechanosensory, and visual stimuli. In addition, larval fish show well-coordinated escape responses when exposed to electric field pulses (EFPs). Sensitization of the Mauthner cell by genetic overexpression of the voltage-gated sodium channel SCN5 increased EFP responsiveness, whereas Mauthner ablation with an engineered variant of nitroreductase with increased activity (epNTR) eliminated the response. The reaction time to EFPs is extremely short, with many responses initiated within 2 ms of the EFP. Large neurons, such as Mauthner cells, show heightened sensitivity to extracellular voltage gradients. We therefore tested whether the rapid response to EFPs was due to direct activation of the Mauthner cells, bypassing delays imposed by stimulus detection and transmission by sensory cells. Consistent with this, calcium imaging indicated that EFPs robustly activated the Mauthner cell but only rarely fired other reticulospinal neurons. Further supporting this idea, pharmacological blockade of synaptic transmission in zebrafish did not affect Mauthner cell activity in response to EFPs. Moreover, Mauthner cells transgenically expressing a tetrodotoxin (TTX)-resistant voltage-gated sodium channel retained responses to EFPs despite TTX suppression of action potentials in the rest of the brain. We propose that EFPs directly activate Mauthner cells because of their large size, thereby driving ultrarapid escape responses in fish. PMID:24848468
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Neural markers of emotional face perception across psychotic disorders and general population.
Sabharwal, Amri; Kotov, Roman; Szekely, Akos; Leung, Hoi-Chung; Barch, Deanna M; Mohanty, Aprajita
2017-07-01
There is considerable variation in negative and positive symptoms of psychosis, global functioning, and emotional face perception (EFP), not only in schizophrenia but also in other psychotic disorders and healthy individuals. However, EFP impairment and its association with worse symptoms and global functioning have been examined largely in the domain of schizophrenia. The present study adopted a dimensional approach to examine the association of behavioral and neural measures of EFP with symptoms of psychosis and global functioning across individuals with schizophrenia spectrum (SZ; N = 28) and other psychotic (OP; N = 29) disorders, and never-psychotic participants (NP; N = 21). Behavioral and functional MRI data were recorded as participants matched emotional expressions of faces and geometrical shapes. Lower accuracy and increased activity in early visual regions, hippocampus, and amygdala during emotion versus shape matching were associated with higher negative, but not positive, symptoms and lower global functioning, across all participants. This association remained even after controlling for group-related (SZ, OP, and NP) variance, dysphoria, and antipsychotic medication status, except in amygdala. Furthermore, negative symptoms mediated the relationship between behavioral and brain EFP measures and global functioning. This study provides some of the first evidence supporting the specific relationship of EFP measures with negative symptoms and global functioning across psychotic and never-psychotic samples, and transdiagnostically across different psychotic disorders. Present findings help bridge the gap between basic EFP-related neuroscience research and clinical research in psychosis, and highlight EFP as a potential symptom-specific marker that tracks global functioning. (PsycINFO Database Record (c) 2017 APA, all rights reserved).
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NASA Astrophysics Data System (ADS)
Li, R.; Li, W. B.; Wang, X. M.; Li, W. B.
2018-03-01
The effects of the initiation diameter and synchronicity error on the formation of fins and stable-flight velocity of an explosively formed projectile (EFP) with three-point initiation are investigated. The pressure and area of the Mach wave acting on the metal liner at different initiation diameters are calculated employing the Whitham method. LS-DYNA software is used to investigate the asymmetric collision of detonation waves resulting from three-point initiation synchronicity error, the distortion characteristics of the liner resulting from the composite detonation waves, and the performance parameters of the EFP with fins. Results indicate that deviations of the Y-shaped high-pressure zone and central ultrahigh-pressure zone from the liner center can be attributed to the error of three-point initiation, which leads to the irregular formation of EFP fins. It is noted that the area of the Mach wave decreases, but the pressure of the Mach wave and the final speed and length-to-diameter ( L/ D) ratio of the EFP increase, benefiting the formation of the EFP fins, as the initiation diameter increases.
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Drama in Dynamics: Boom, Splash, and Speed
DOE Office of Scientific and Technical Information (OSTI.GOV)
Netzloff, Heather Marie
2004-12-19
The full nature of chemistry and physics cannot be captured by static calculations alone. Dynamics calculations allow the simulation of time-dependent phenomena. This facilitates both comparisons with experimental data and the prediction and interpretation of details not easily obtainable from experiments. Simulations thus provide a direct link between theory and experiment, between microscopic details of a system and macroscopic observed properties. Many types of dynamics calculations exist. The most important distinction between the methods and the decision of which method to use can be described in terms of the size and type of molecule/reaction under consideration and the type andmore » level of accuracy required in the final properties of interest. These considerations must be balanced with available computational codes and resources as simulations to mimic ''real-life'' may require many time steps. As indicated in the title, the theme of this thesis is dynamics. The goal is to utilize the best type of dynamics for the system under study while trying to perform dynamics in the most accurate way possible. As a quantum chemist, this involves some level of first principles calculations by default. Very accurate calculations of small molecules and molecular systems are now possible with relatively high-level ab initio quantum chemistry. For example, a quantum chemical potential energy surface (PES) can be developed ''on-the-fly'' with dynamic reaction path (DRP) methods. In this way a classical trajectory is developed without prior knowledge of the PES. In order to treat solvation processes and the condensed phase, large numbers of molecules are required, especially in predicting bulk behavior. The Effective Fragment Potential (EFP) method for solvation decreases the cost of a fully quantum mechanical calculation by dividing a chemical system into an ab initio region that contains the solute and an ''effective fragment'' region that contains the remaining solvent molecules. But, despite the reduced cost relative to fully QM calculations, the EFP method, due to its complex, QM-based potential, does require more computation time than simple interaction potentials, especially when the method is used for large scale molecular dynamics simulations. Thus, the EFP method was parallelized to facilitate these calculations within the quantum chemistry program GAMESS. The EFP method provides relative energies and structures that are in excellent agreement with the analogous fully quantum results for small water clusters. The ability of the method to predict bulk water properties with a comparable accuracy is assessed by performing EFP molecular dynamics simulations. Molecular dynamics simulations can provide properties that are directly comparable with experimental results, for example radial distribution functions. The molecular PES is a fundamental starting point for chemical reaction dynamics. Many methods can be used to obtain a PES; for example, assuming a global functional form for the PES or, as mentioned above, performing ''on-the-fly'' dynamics with Al or semi-empirical calculations at every molecular configuration. But as the size of the system grows, using electronic structure theory to build a PES and, therefore, study reaction dynamics becomes virtually impossible. The program Grow builds a PES as an interpolation of Al data; the goal is to attempt to produce an accurate PES with the smallest number of Al calculations. The Grow-GAMESS interface was developed to obtain the Al data from GAMESS. Classical or quantum dynamics can be performed on the resulting surface. The interface includes the novel capability to build multi-reference PESs; these types of calculations are applicable to problems ranging from atmospheric chemistry to photochemical reaction mechanisms in organic and inorganic chemistry to fundamental biological phenomena such as photosynthesis.« less
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Optimizing Wellfield Operation in a Variable Power Price Regime.
Bauer-Gottwein, Peter; Schneider, Raphael; Davidsen, Claus
2016-01-01
Wellfield management is a multiobjective optimization problem. One important objective has been energy efficiency in terms of minimizing the energy footprint (EFP) of delivered water (MWh/m(3) ). However, power systems in most countries are moving in the direction of deregulated markets and price variability is increasing in many markets because of increased penetration of intermittent renewable power sources. In this context the relevant management objective becomes minimizing the cost of electric energy used for pumping and distribution of groundwater from wells rather than minimizing energy use itself. We estimated EFP of pumped water as a function of wellfield pumping rate (EFP-Q relationship) for a wellfield in Denmark using a coupled well and pipe network model. This EFP-Q relationship was subsequently used in a Stochastic Dynamic Programming (SDP) framework to minimize total cost of operating the combined wellfield-storage-demand system over the course of a 2-year planning period based on a time series of observed price on the Danish power market and a deterministic, time-varying hourly water demand. In the SDP setup, hourly pumping rates are the decision variables. Constraints include storage capacity and hourly water demand fulfilment. The SDP was solved for a baseline situation and for five scenario runs representing different EFP-Q relationships and different maximum wellfield pumping rates. Savings were quantified as differences in total cost between the scenario and a constant-rate pumping benchmark. Minor savings up to 10% were found in the baseline scenario, while the scenario with constant EFP and unlimited pumping rate resulted in savings up to 40%. Key factors determining potential cost savings obtained by flexible wellfield operation under a variable power price regime are the shape of the EFP-Q relationship, the maximum feasible pumping rate and the capacity of available storage facilities. © 2015 The Authors. Groundwater published by Wiley Periodicals, Inc. on behalf of National Ground Water Association.
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Federal Register 2010, 2011, 2012, 2013, 2014
2010-03-17
... economic and environmental performance benefits. Recreational Chilipepper EFP The California RFA and the... vessels participating in the EFP fisheries. The EFPs are necessary to allow activities that are otherwise... EFPs may be used to authorize fishing activities that would otherwise be prohibited. At the November...
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Shu, Zunpeng; Xing, Na; Wang, Qiuhong; Li, Xinli; Xu, Bingqing; Li, Zhenyu; Kuang, Haixue
2016-01-01
This study was designed to determine whether the 50% EtOH fraction from AB-8 macroporous resin fractionation of a 70% EtOH extract of P. Alkekengi (50-EFP) has antibacterial and/or anti-inflammatory activity both in vivo and in vitro and to investigate the mechanism of 50-EFP anti-inflammatory activity. Additionally, this study sought to define the chemical composition of 50-EFP. Results indicated that 50-EFP showed significant antibacterial activity in vitro and efficacy in vivo. Moreover, 50-EFP significantly reduced nitric oxide (NO), prostaglandin E2 (PGE2), tumor necrosis factor alpha (TNF-α), interleukin 1 (IL-1), and interleukin 6 (IL-6) production in lipopolysaccharide- (LPS-) stimulated THP-1 cells. Nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) (examined at the protein level) in THP-1 cells were suppressed by 50-EFP, which inhibited nuclear translocation of p65. Consistent with this anti-inflammatory activity in vitro, 50-EFP reduced inflammation in both animal models. Finally, seventeen compounds (8 physalins and 9 flavones) were isolated as major components of 50-EFP. Our data demonstrate that 50-EFP has antibacterial and anti-inflammatory activities both in vitro and in vivo. The anti-inflammatory effect appears to occur, at least in part, through the inhibition of nuclear translocation of p65. Moreover, physalins and flavones are probably the active components in 50-EFP that exert antibacterial and anti-inflammatory activities. PMID:27057196
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Perrier, Anthony; Peyraud, Rémi; Rengel, David; Barlet, Xavier; Lucasson, Emmanuel; Gouzy, Jérôme; Peeters, Nemo; Genin, Stéphane; Guidot, Alice
2016-12-01
Experimental evolution of the plant pathogen Ralstonia solanacearum, where bacteria were maintained on plant lineages for more than 300 generations, revealed that several independent single mutations in the efpR gene from populations propagated on beans were associated with fitness gain on bean. In the present work, novel allelic efpR variants were isolated from populations propagated on other plant species, thus suggesting that mutations in efpR were not solely associated to a fitness gain on bean, but also on additional hosts. A transcriptomic profiling and phenotypic characterization of the efpR deleted mutant showed that EfpR acts as a global catabolic repressor, directly or indirectly down-regulating the expression of multiple metabolic pathways. EfpR also controls virulence traits such as exopolysaccharide production, swimming and twitching motilities and deletion of efpR leads to reduced virulence on tomato plants after soil drenching inoculation. We studied the impact of the single mutations that occurred in efpR during experimental evolution and found that these allelic mutants displayed phenotypic characteristics similar to the deletion mutant, although not behaving as complete loss-of-function mutants. These adaptive mutations therefore strongly affected the function of efpR, leading to an expanded metabolic versatility that should benefit to the evolved clones. Altogether, these results indicated that EfpR is a novel central player of the R. solanacearum virulence regulatory network. Independent mutations therefore appeared during experimental evolution in the evolved clones, on a crucial node of this network, to favor adaptation to host vascular tissues through regulatory and metabolic rewiring.
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Rajkovic, Andrei; Hummels, Katherine R; Witzky, Anne; Erickson, Sarah; Gafken, Philip R; Whitelegge, Julian P; Faull, Kym F; Kearns, Daniel B; Ibba, Michael
2016-05-20
Elongation factor P (EF-P) accelerates diprolyl synthesis and requires a posttranslational modification to maintain proteostasis. Two phylogenetically distinct EF-P modification pathways have been described and are encoded in the majority of Gram-negative bacteria, but neither is present in Gram-positive bacteria. Prior work suggested that the EF-P-encoding gene (efp) primarily supports Bacillus subtilis swarming differentiation, whereas EF-P in Gram-negative bacteria has a more global housekeeping role, prompting our investigation to determine whether EF-P is modified and how it impacts gene expression in motile cells. We identified a 5-aminopentanol moiety attached to Lys(32) of B. subtilis EF-P that is required for swarming motility. A fluorescent in vivo B. subtilis reporter system identified peptide motifs whose efficient synthesis was most dependent on 5-aminopentanol EF-P. Examination of the B. subtilis genome sequence showed that these EF-P-dependent peptide motifs were represented in flagellar genes. Taken together, these data show that, in B. subtilis, a previously uncharacterized posttranslational modification of EF-P can modulate the synthesis of specific diprolyl motifs present in proteins required for swarming motility. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.
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Continuous decoding of human grasp kinematics using epidural and subdural signals
NASA Astrophysics Data System (ADS)
Flint, Robert D.; Rosenow, Joshua M.; Tate, Matthew C.; Slutzky, Marc W.
2017-02-01
Objective. Restoring or replacing function in paralyzed individuals will one day be achieved through the use of brain-machine interfaces. Regaining hand function is a major goal for paralyzed patients. Two competing prerequisites for the widespread adoption of any hand neuroprosthesis are accurate control over the fine details of movement, and minimized invasiveness. Here, we explore the interplay between these two goals by comparing our ability to decode hand movements with subdural and epidural field potentials (EFPs). Approach. We measured the accuracy of decoding continuous hand and finger kinematics during naturalistic grasping motions in five human subjects. We recorded subdural surface potentials (electrocorticography; ECoG) as well as with EFPs, with both standard- and high-resolution electrode arrays. Main results. In all five subjects, decoding of continuous kinematics significantly exceeded chance, using either EGoG or EFPs. ECoG decoding accuracy compared favorably with prior investigations of grasp kinematics (mean ± SD grasp aperture variance accounted for was 0.54 ± 0.05 across all subjects, 0.75 ± 0.09 for the best subject). In general, EFP decoding performed comparably to ECoG decoding. The 7-20 Hz and 70-115 Hz spectral bands contained the most information about grasp kinematics, with the 70-115 Hz band containing greater information about more subtle movements. Higher-resolution recording arrays provided clearly superior performance compared to standard-resolution arrays. Significance. To approach the fine motor control achieved by an intact brain-body system, it will be necessary to execute motor intent on a continuous basis with high accuracy. The current results demonstrate that this level of accuracy might be achievable not just with ECoG, but with EFPs as well. Epidural placement of electrodes is less invasive, and therefore may incur less risk of encephalitis or stroke than subdural placement of electrodes. Accurately decoding motor commands at the epidural level may be an important step towards a clinically viable brain-machine interface.
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Accurate Methods for Large Molecular Systems (Preprint)
2009-01-06
tensor, EFP calculations are basis set dependent. The smallest recommended basis set is 6- 31++G( d , p )52 The dependence of the computational cost of...and second order perturbation theory (MP2) levels with the 6-31G( d , p ) basis set. Additional SFM tests are presented for a small set of alpha...helices using the 6-31++G( d , p ) basis set. The larger 6-311++G(3df,2p) basis set is employed for creating all EFPs used for non- bonded interactions, since
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The Role and Regulatory Mechanism of 14-3-3 Sigma in Human Breast Cancer
Ko, SeungSang; Kim, Ji Young; Jeong, Joon; Lee, Jong Eun; Yang, Woo Ick
2014-01-01
Purpose 14-3-3 sigma (σ) is considered to be an important tumor suppressor and decreased expression of the same has been reported in many malignant tumors by hypermethylation at its promoter or ubiquitin-mediated proteolysis by estrogen-responsive ring finger protein (Efp). In this study, we investigated the significance of 14-3-3 σ expression in human breast cancer and its regulatory mechanism. Methods Efp was silenced using small interfering RNA (siRNA) in the MCF-7 breast cancer cell line in order to examine its influence on the level of 14-3-3 σ protein. The methylation status of the 14-3-3 σ promoter was also evaluated by methylation-specific polymerase chain reaction (PCR). The expression of Efp and 14-3-3 σ in 220 human breast carcinoma tissues was assessed by immunohistochemistry. Other clinicopathological parameters were also evaluated. Results Silencing Efp in the MCF-7 breast cancer cell line resulted in increased expression of 14-3-3 σ. The Efp-positive human breast cancers were more frequently 14-3-3 σ-negative (60.5% vs. 39.5%). Hypermethylation of 14-3-3 σ was common (64.9%) and had an inverse association with 14-3-3 σ positivity (p=0.072). Positive 14-3-3 σ expression was significantly correlated with poor prognosis: disease-free survival (p=0.008) and disease-specific survival (p=0.009). Conclusion Our data suggests that in human breast cancer, the regulation of 14-3-3 σ may involve two mechanisms: ubiquitin-mediated proteolysis by Efp and downregulation by hypermethylation. However, the inactivation of 14-3-3 σ is probably achieved mainly by hypermethylation. Interestingly, 14-3-3 σ turned out to be a very significant poor prognostic indicator, which is in contrast to its previously known function as a tumor suppressor, suggesting a different role of 14-3-3 σ in breast cancer. PMID:25320618
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Federal Register 2010, 2011, 2012, 2013, 2014
2012-11-21
...-year EFP. The experimental design requires this quantity of salmon to ensure statistically valid... of the groundfish harvested each year from the EFP is expected to be pollock. The experimental design... concentrations of salmon and pollock for addressing experimental design criteria. The activities under the EFP...
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Neuroprotective effects of adenosine deaminase in the striatum
Tamura, Risa; Satoh, Yasushi; Nonoyama, Shigeaki; Nishida, Yasuhiro; Nibuya, Masashi
2016-01-01
Adenosine deaminase (ADA) is a ubiquitous enzyme that catabolizes adenosine and deoxyadenosine. During cerebral ischemia, extracellular adenosine levels increase acutely and adenosine deaminase catabolizes the increased levels of adenosine. Since adenosine is a known neuroprotective agent, adenosine deaminase was thought to have a negative effect during ischemia. In this study, however, we demonstrate that adenosine deaminase has substantial neuroprotective effects in the striatum, which is especially vulnerable during cerebral ischemia. We used temporary oxygen/glucose deprivation (OGD) to simulate ischemia in rat corticostriatal brain slices. We used field potentials as the primary measure of neuronal damage. For stable and efficient electrophysiological assessment, we used transgenic rats expressing channelrhodopsin-2, which depolarizes neurons in response to blue light. Time courses of electrically evoked striatal field potential (eFP) and optogenetically evoked striatal field potential (optFP) were recorded during and after oxygen/glucose deprivation. The levels of both eFP and optFP decreased after 10 min of oxygen/glucose deprivation. Bath-application of 10 µg/ml adenosine deaminase during oxygen/glucose deprivation significantly attenuated the oxygen/glucose deprivation-induced reduction in levels of eFP and optFP. The number of injured cells decreased significantly, and western blot analysis indicated a significant decrease of autophagic signaling in the adenosine deaminase-treated oxygen/glucose deprivation slices. These results indicate that adenosine deaminase has protective effects in the striatum. PMID:26746865
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A chalcone isomerase-like protein enhances flavonoid production and flower pigmentation.
Morita, Yasumasa; Takagi, Kyoko; Fukuchi-Mizutani, Masako; Ishiguro, Kanako; Tanaka, Yoshikazu; Nitasaka, Eiji; Nakayama, Masayoshi; Saito, Norio; Kagami, Takashi; Hoshino, Atsushi; Iida, Shigeru
2014-04-01
Flavonoids are major pigments in plants, and their biosynthetic pathway is one of the best-studied metabolic pathways. Here we have identified three mutations within a gene that result in pale-colored flowers in the Japanese morning glory (Ipomoea nil). As the mutations lead to a reduction of the colorless flavonoid compound flavonol as well as of anthocyanins in the flower petal, the identified gene was designated enhancer of flavonoid production (EFP). EFP encodes a chalcone isomerase (CHI)-related protein classified as a type IV CHI protein. CHI is the second committed enzyme of the flavonoid biosynthetic pathway, but type IV CHI proteins are thought to lack CHI enzymatic activity, and their functions remain unknown. The spatio-temporal expression of EFP and structural genes encoding enzymes that produce flavonoids is very similar. Expression of both EFP and the structural genes is coordinately promoted by genes encoding R2R3-MYB and WD40 family proteins. The EFP gene is widely distributed in land plants, and RNAi knockdown mutants of the EFP homologs in petunia (Petunia hybrida) and torenia (Torenia hybrida) had pale-colored flowers and low amounts of anthocyanins. The flavonol and flavone contents in the knockdown petunia and torenia flowers, respectively, were also significantly decreased, suggesting that the EFP protein contributes in early step(s) of the flavonoid biosynthetic pathway to ensure production of flavonoid compounds. From these results, we conclude that EFP is an enhancer of flavonoid production and flower pigmentation, and its function is conserved among diverse land plant species. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.
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Continuous decoding of human grasp kinematics using epidural and subdural signals
Flint, Robert D.; Rosenow, Joshua M.; Tate, Matthew C.; Slutzky, Marc W.
2017-01-01
Objective Restoring or replacing function in paralyzed individuals will one day be achieved through the use of brain-machine interfaces (BMIs). Regaining hand function is a major goal for paralyzed patients. Two competing prerequisites for the widespread adoption of any hand neuroprosthesis are: accurate control over the fine details of movement, and minimized invasiveness. Here, we explore the interplay between these two goals by comparing our ability to decode hand movements with subdural and epidural field potentials. Approach We measured the accuracy of decoding continuous hand and finger kinematics during naturalistic grasping motions in five human subjects. We recorded subdural surface potentials (electrocorticography; ECoG) as well as with epidural field potentials (EFPs), with both standard- and high-resolution electrode arrays. Main results In all five subjects, decoding of continuous kinematics significantly exceeded chance, using either EGoG or EFPs. ECoG decoding accuracy compared favorably with prior investigations of grasp kinematics (mean± SD grasp aperture variance accounted for was 0.54± 0.05 across all subjects, 0.75± 0.09 for the best subject). In general, EFP decoding performed comparably to ECoG decoding. The 7–20 Hz and 70–115 Hz spectral bands contained the most information about grasp kinematics, with the 70–115 Hz band containing greater information about more subtle movements. Higher-resolution recording arrays provided clearly superior performance compared to standard-resolution arrays. Significance To approach the fine motor control achieved by an intact brain-body system, it will be necessary to execute motor intent on a continuous basis with high accuracy. The current results demonstrate that this level of accuracy might be achievable not just with ECoG, but with EFPs as well. Epidural placement of electrodes is less invasive, and therefore may incur less risk of encephalitis or stroke than subdural placement of electrodes. Accurately decoding motor commands at the epidural level may be an important step towards a clinically viable brain-machine interface. PMID:27900947
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Federal Register 2010, 2011, 2012, 2013, 2014
2011-08-12
... for Four Decimal Point Pricing for Block and Exchange for Physical (``EFPs'') Trades August 8, 2011... block trades and the futures component of EFP trades to be traded/priced in four decimals points. Regular trades (non-block or non EFP) will continue to trade in only two decimal points. The text of the...
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Villa, Chiara; Manzoli, Vita; Abreu, Maria M.; Verheyen, Connor A.; Seskin, Michael; Najjar, Mejdi; Molano, R. Damaris; Torrente, Yvan; Ricordi, Camillo; Tomei, Alice A.
2017-01-01
Background Understanding the effects of capsule composition and transplantation site on graft outcomes of encapsulated islets will aid in the development of more effective strategies for islet transplantation without immunosuppression. Methods Here, we evaluated the effects of transplanting alginate (ALG)-based microcapsules (Micro) in the confined and well-vascularized epididymal fat pad (EFP) site, a model of the human omentum, as opposed to free-floating in the intraperitoneal cavity (IP) in mice. We also examined the effects of reinforcing ALG with polyethylene glycol (PEG). To allow transplantation in the EFP site, we minimized capsule size to 500 ± 17 μm. Unlike ALG, PEG resists osmotic stress, hence we generated hybrid microcapsules by mixing PEG and ALG (MicroMix) or by coating ALG capsules with a 15 ± 2 μm PEG layer (Double). Results We found improved engraftment of fully allogeneic BALB/c islets in Micro capsules transplanted in the EFP (median reversal time [MRT], 1 day) versus the IP site (MRT, 5 days; P < 0.01) in diabetic C57BL/6 mice and of Micro encapsulated (MRT, 8 days) versus naked (MRT, 36 days; P < 0.01) baboon islets transplanted in the EFP site. Although in vitro viability and functionality of islets within MicroMix and Double capsules were comparable to Micro, addition of PEG to ALG in MicroMix capsules improved engraftment of allogeneic islets in the IP site, but resulted deleterious in the EFP site, probably due to lower biocompatibility. Conclusions Our results suggest that capsule composition and transplant site affect graft outcomes through their effects on nutrient availability, capsule stability, and biocompatibility. PMID:27525644
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Gaupels, Frank; Furch, Alexandra C. U.; Zimmermann, Matthias R.; Chen, Faxing; Kaever, Volkhard; Buhtz, Anja; Kehr, Julia; Sarioglu, Hakan; Kogel, Karl-Heinz; Durner, Jörg
2016-01-01
Cucurbits developed the unique extrafascicular phloem (EFP) as a defensive structure against herbivorous animals. Mechanical leaf injury was previously shown to induce a systemic wound response in the EFP of pumpkin (Cucurbita maxima). Here, we demonstrate that the phloem antioxidant system and protein modifications by NO are strongly regulated during this process. Activities of the central antioxidant enzymes dehydroascorbate reductase, glutathione reductase and ascorbate reductase were rapidly down-regulated at 30 min with a second minimum at 24 h after wounding. As a consequence levels of total ascorbate and glutathione also decreased with similar bi-phasic kinetics. These results hint toward a wound-induced shift in the redox status of the EFP. Nitric oxide (NO) is another important player in stress-induced redox signaling in plants. Therefore, we analyzed NO-dependent protein modifications in the EFP. Six to forty eight hours after leaf damage total S-nitrosothiol content and protein S-nitrosylation were clearly reduced, which was contrasted by a pronounced increase in protein tyrosine nitration. Collectively, these findings suggest that NO-dependent S-nitrosylation turned into peroxynitrite-mediated protein nitration upon a stress-induced redox shift probably involving the accumulation of reactive oxygen species within the EFP. Using the biotin switch assay and anti-nitrotyrosine antibodies we identified 9 candidate S-nitrosylated and 6 candidate tyrosine-nitrated phloem proteins. The wound-responsive Phloem Protein 16-1 (PP16-1) and Cyclophilin 18 (CYP18) as well as the 26.5 kD isoform of Phloem Protein 2 (PP2) were amenable to both NO modifications and could represent important redox-sensors within the cucurbit EFP. We also found that leaf injury triggered the systemic accumulation of cyclic guanosine monophosphate (cGMP) in the EFP and discuss the possible function of this second messenger in systemic NO and redox signaling within the EFP. PMID:26904092
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Sadybekov, Arman; Krylov, Anna I.
2017-07-07
A theoretical approach for calculating core-level states in condensed phase is presented. The approach is based on equation-of-motion coupled-cluster theory (EOMCC) and effective fragment potential (EFP) method. By introducing an approximate treatment of double excitations in the EOM-CCSD (EOM-CC with single and double substitutions) ansatz, we address poor convergence issues that are encountered for the core-level states and significantly reduce computational costs. While the approximations introduce relatively large errors in the absolute values of transition energies, the errors are systematic. Consequently, chemical shifts, changes in ionization energies relative to reference systems, are reproduced reasonably well. By using different protonation formsmore » of solvated glycine as a benchmark system, we show that our protocol is capable of reproducing the experimental chemical shifts with a quantitative accuracy. The results demonstrate that chemical shifts are very sensitive to the solvent interactions and that explicit treatment of solvent, such as EFP, is essential for achieving quantitative accuracy.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Sadybekov, Arman; Krylov, Anna I.
A theoretical approach for calculating core-level states in condensed phase is presented. The approach is based on equation-of-motion coupled-cluster theory (EOMCC) and effective fragment potential (EFP) method. By introducing an approximate treatment of double excitations in the EOM-CCSD (EOM-CC with single and double substitutions) ansatz, we address poor convergence issues that are encountered for the core-level states and significantly reduce computational costs. While the approximations introduce relatively large errors in the absolute values of transition energies, the errors are systematic. Consequently, chemical shifts, changes in ionization energies relative to reference systems, are reproduced reasonably well. By using different protonation formsmore » of solvated glycine as a benchmark system, we show that our protocol is capable of reproducing the experimental chemical shifts with a quantitative accuracy. The results demonstrate that chemical shifts are very sensitive to the solvent interactions and that explicit treatment of solvent, such as EFP, is essential for achieving quantitative accuracy.« less
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ERIC Educational Resources Information Center
Messaoudi, Belkacem; Granjon, Lionel; Mouly, Anne-Marie; Sevelinges, Yannick; Gervais, Remi
2004-01-01
The widely used Pavlovian fear-conditioning paradigms used for studying the neurobiology of learning and memory have mainly used auditory cues as conditioned stimuli (CS). The present work assessed the neural network involved in olfactory fear conditioning, using olfactory bulb stimulation-induced field potential signal (EFP) as a marker of…
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In-flight radiographic study of two nonaxisymmetric, explosively formed penetrators
DOE Office of Scientific and Technical Information (OSTI.GOV)
Schwalbe, L.A.; Mueller, K.H. Jr.; Christian, J.M.
1988-03-01
We present in-flight radiographic images of two explosively formed penetrators (EFPs) of tantalum. The data were obtained with Ecto, a flash x-ray source that delivers a single, 50-ns pulse of radiation with an effective mean energy of 1.4)pulse))minus) 0.1 MeV. The enrgy and flux of the beam are sufficient to penetrate the EFPs and reveal their internal structure. The subjects of this study are two warheads of an identical nonaxisymmetric design. One warhead was fired in each of two separate experiments. The warheads were oriented perpendicular to one another to provide separate orthogonal views of their EFPs. The radiographs weremore » then digitized and subjected to several numerical analyses, which include estimates of the masses of the EFPs, their center-of-mass coordinates, and plots of the attenuation lengths (or material thicknesses) at various positions. Optical photographs were also taken of the front and profile of one EFP. The optical data aid in interpretating the radioagraphy by allowing identification of the visible external features. 3 refs., 16 figs.« less
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Bachi, Keren; Terkel, Joseph; Teichman, Meir
2012-04-01
This article describes the theoretical-conceptual frame of equine-facilitated psychotherapy (EFP) for adolescents at-risk, the unique components of this intervention, and its implementation in an evaluation study. The study was conducted at a residential treatment facility for adolescents at-risk. We examined the outcomes of EFP on self-image, self-control, trust and general life satisfaction. Fourteen resident adolescents comprised the treatment group, and were compared with a matched group of 15 residents who did not receive EFP (control). The treatment comprised a weekly individual EFP session over a period of seven months. The study found a trend of positive change in all four research parameters within the treatment group. Additional indications of the intervention's positive influence were also found and are discussed.
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Elongation factor P is dispensable in Escherichia coli and Pseudomonas aeruginosa.
Balibar, Carl J; Iwanowicz, Dorothy; Dean, Charles R
2013-09-01
Elongation factor P (EF-P) is a highly conserved ribosomal initiation factor responsible for stimulating formation of the first peptide bond. Its essentiality has been debated and may differ depending on the organism. Here, we demonstrate that EF-P is dispensable in Escherichia coli and Pseudomonas aeruginosa under laboratory growth conditions. Although knockouts are viable, growth rates are diminished compared with wild-type strains. Despite this cost in fitness, these mutants are not more susceptible to a wide range of antibiotics; including ribosome targeting antibiotics, such as lincomycin, chloramphenicol, and streptomycin, which have been shown previously to disrupt EF-P function in vitro. In Pseudomonas, knockout of efp leads to an upregulation of mexX, a phenotype previously observed with other genetic lesions affecting ribosome function and that can be induced by the treatment with antibiotics affecting protein synthesis.
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Potential and limitations of inferring ecosystem photosynthetic capacity from leaf functional traits
Talie Musavi; Mirco Migliavacca; Martine Janet van de Weg; Jens Kattge; Georg Wohlfahrt; Peter M. van Bodegom; Markus Reichstein; Michael Bahn; Arnaud Carrara; Tomas F. Domingues; Michael Gavazzi; Damiano Gianelle; Cristina Gimeno; André Granier; Carsten Gruening; Kateřina Havránková; Mathias Herbst; Charmaine Hrynkiw; Aram Kalhori; Thomas Kaminski; Katja Klumpp; Pasi Kolari; Bernard Longdoz; Stefano Minerbi; Leonardo Montagnani; Eddy Moors; Walter C. Oechel; Peter B. Reich; Shani Rohatyn; Alessandra Rossi; Eyal Rotenberg; Andrej Varlagin; Matthew Wilkinson; Christian Wirth; Miguel D. Mahecha
2016-01-01
The aim of this study was to systematically analyze the potential and limitations of using plant functional trait observations from global databases versus in situ data to improve our understanding of vegetation impacts on ecosystem functional properties (EFPs). Using ecosystem photosynthetic capacity as an example, we first provide an objective approach to derive...
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Apparatus and methods for real-time detection of explosives devices
Blackburn, Brandon W [Idaho Falls, ID; Hunt, Alan W [Pocatello, ID; Chichester, David L [Idaho Falls, ID
2014-01-07
The present disclosure relates, according to some embodiments, to apparatus, devices, systems, and/or methods for real-time detection of a concealed or camouflaged explosive device (e.g., EFPs and IEDs) from a safe stand-off distance. Apparatus, system and/or methods of the disclosure may also be operable to identify and/or spatially locate and/or detect an explosive device. An apparatus or system may comprise an x-ray generator that generates high-energy x-rays and/or electrons operable to contact and activate a metal comprised in an explosive device from a stand-off distance; and a detector operable to detect activation of the metal. Identifying an explosive device may comprise detecting characteristic radiation signatures emitted by metals specific to an EFP, an IED or a landmine. Apparatus and systems of the disclosure may be mounted on vehicles and methods of the disclosure may be performed while moving in the vehicle and from a safe stand-off distance.
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Gaupels, Frank; Sarioglu, Hakan; Beckmann, Manfred; Hause, Bettina; Spannagl, Manuel; Draper, John; Lindermayr, Christian; Durner, Jörg
2012-01-01
In cucurbits, phloem latex exudes from cut sieve tubes of the extrafascicular phloem (EFP), serving in defense against herbivores. We analyzed inducible defense mechanisms in the EFP of pumpkin (Cucurbita maxima) after leaf damage. As an early systemic response, wounding elicited transient accumulation of jasmonates and a decrease in exudation probably due to partial sieve tube occlusion by callose. The energy status of the EFP was enhanced as indicated by increased levels of ATP, phosphate, and intermediates of the citric acid cycle. Gas chromatography coupled to mass spectrometry also revealed that sucrose transport, gluconeogenesis/glycolysis, and amino acid metabolism were up-regulated after wounding. Combining ProteoMiner technology for the enrichment of low-abundance proteins with stable isotope-coded protein labeling, we identified 51 wound-regulated phloem proteins. Two Sucrose-Nonfermenting1-related protein kinases and a 32-kD 14-3-3 protein are candidate central regulators of stress metabolism in the EFP. Other proteins, such as the Silverleaf Whitefly-Induced Protein1, Mitogen Activated Protein Kinase6, and Heat Shock Protein81, have known defensive functions. Isotope-coded protein labeling and western-blot analyses indicated that Cyclophilin18 is a reliable marker for stress responses of the EFP. As a hint toward the induction of redox signaling, we have observed delayed oxidation-triggered polymerization of the major Phloem Protein1 (PP1) and PP2, which correlated with a decline in carbonylation of PP2. In sum, wounding triggered transient sieve tube occlusion, enhanced energy metabolism, and accumulation of defense-related proteins in the pumpkin EFP. The systemic wound response was mediated by jasmonate and redox signaling. PMID:23085839
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Federal Register 2010, 2011, 2012, 2013, 2014
2010-02-18
... of federal management of the American lobster (lobster) resource. However, further review and... Republic Drive, Gloucester, MA 01930-2298. Mark the outside of the envelope ``Comments - Lobster EFP... identifier: ``Comments - Lobster EFP Proposal.'' FOR FURTHER INFORMATION CONTACT: Sarah Towne, Research...
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Federal Register 2010, 2011, 2012, 2013, 2014
2012-01-20
... data base on Gulf red snapper for the next stock assessment. The EFP, if approved, would authorize the... otoliths and gonads. LDWF would be responsible for providing all data collected under the EFP to NMFS for...
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50 CFR 665.17 - Experimental fishing.
Code of Federal Regulations, 2011 CFR
2011-10-01
... statement of the purposes and goals of the experiment for which an EFP is needed, including a general... the experiment. (7) For each vessel covered by the EFP, the approximate times and places fishing will... consistent with the purpose of the experiment including, but not limited to: (i) The maximum amount of each...
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50 CFR 665.17 - Experimental fishing.
Code of Federal Regulations, 2010 CFR
2010-10-01
... statement of the purposes and goals of the experiment for which an EFP is needed, including a general... the experiment. (7) For each vessel covered by the EFP, the approximate times and places fishing will... consistent with the purpose of the experiment including, but not limited to: (i) The maximum amount of each...
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Federal Register 2010, 2011, 2012, 2013, 2014
2012-04-24
... . Include in the subject line ``Comments on Fisheries Specialists 2012 Scallop RSA EFP.'' Mail: Daniel S... 01930. Mark the outside of the envelope ``Comments on Fisheries Specialists EFP.'' Fax: (978) 281-9135. FOR FURTHER INFORMATION CONTACT: Christopher Biegel, Fishery Management Specialist, 978-281-9112...
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Federal Register 2010, 2011, 2012, 2013, 2014
2012-04-06
... determination that an Exempted Fishing Permit (EFP) application submitted by the Northeast Fisheries Science... dependent catch data and biological samples. Regulations under the Magnuson-Stevens Fishery Conservation and...: NEFSC submitted a complete application for an EFP on February 28, 2012, to enable data collection...
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50 CFR 665.17 - Experimental fishing.
Code of Federal Regulations, 2013 CFR
2013-10-01
... statement of the purposes and goals of the experiment for which an EFP is needed, including a general... the experiment. (7) For each vessel covered by the EFP, the approximate times and places fishing will... consistent with the purpose of the experiment including, but not limited to: (i) The maximum amount of each...
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50 CFR 665.17 - Experimental fishing.
Code of Federal Regulations, 2014 CFR
2014-10-01
... statement of the purposes and goals of the experiment for which an EFP is needed, including a general... the experiment. (7) For each vessel covered by the EFP, the approximate times and places fishing will... consistent with the purpose of the experiment including, but not limited to: (i) The maximum amount of each...
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50 CFR 665.17 - Experimental fishing.
Code of Federal Regulations, 2012 CFR
2012-10-01
... statement of the purposes and goals of the experiment for which an EFP is needed, including a general... the experiment. (7) For each vessel covered by the EFP, the approximate times and places fishing will... consistent with the purpose of the experiment including, but not limited to: (i) The maximum amount of each...
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Federal Register 2010, 2011, 2012, 2013, 2014
2010-04-16
... consistent with the goals and objectives of the Monkfish Fishery Management Plan (FMP). However, further review and consultation may be necessary before a final determination is made to issue an EFP. The EFP would allow commercial fishing vessels to conduct research and compensation fishing operations that are...
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50 CFR 660.30 - Compensation with fish for collecting resource information-EFPs.
Code of Federal Regulations, 2010 CFR
2010-10-01
... research, as compensation for that survey. For each proposal, NMFS will present: (i) The maximum number of... NMFS to conduct a resource survey. NMFS may issue an EFP to the owner or operator of a vessel that conducted a resource survey according to a contract with NMFS. A vessel's total compensation from all...
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50 CFR 660.30 - Compensation with fish for collecting resource information-EFPs.
Code of Federal Regulations, 2014 CFR
2014-10-01
... research, as compensation for that survey. For each proposal, NMFS will present: (i) The maximum number of... NMFS to conduct a resource survey. NMFS may issue an EFP to the owner or operator of a vessel that conducted a resource survey according to a contract with NMFS. A vessel's total compensation from all...
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Study on the rheological properties and volatile release of cold-set emulsion-filled protein gels.
Mao, Like; Roos, Yrjö H; Miao, Song
2014-11-26
Emulsion-filled protein gels (EFP gels) were prepared through a cold-set gelation process, and they were used to deliver volatile compounds. An increase in the whey protein isolate (WPI) content from 4 to 6% w/w did not show significant effect on the gelation time, whereas an increase in the oil content from 5 to 20% w/w resulted in an earlier onset of gelation. Gels with a higher WPI content had a higher storage modulus and water-holding capacity (WHC), and they presented a higher force and strain at breaking, indicating that a more compact gel network was formed. An increase in the oil content contributed to gels with a higher storage modulus and force at breaking; however, this increase did not affect the WHC of the gels, and gels with a higher oil content became more brittle, resulting in a decreased strain at breaking. GC headspace analysis showed that volatiles released at lower rates and had lower air-gel partition coefficients in EFP gels than those in ungelled counterparts. Gels with a higher WPI content had lower release rates and partition coefficients of the volatiles. A change in the oil content significantly modified the partition of volatiles at equilibrium, but it produced a minor effect on the release rate of the volatiles. The findings indicated that EFP gels could be potentially used to modulate volatile release by varying the rheological properties of the gel.
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Moore, Keith Diaz
2014-01-01
This article presents an emergent heuristic framework for the core environmental gerontology concept of "place." Place has been a central concern in the field since the 1970s (Gubrium, 1978) for its hypothesized direct relationship to identity, the self, and agency--suggestive of the appropriateness of lateral theoretical linkages with developmental science. The Ecological Framework of Place (EFP) defines place as a socio-physical milieu involving people, the physical setting, and the program of the place, all catalyzed by situated human activity and fully acknowledging that all four may change over time. The article begins with a concise overview of the EFP before moving on to consider it within three theoretical terrains: place theory, developmental science theory, and environmental gerontology theory. The EFP will be argued to be a place theory which subsumes themes of emergent environmental gerontology theories within a developmental science perspective. Implications for theory, method and practice are discussed. One of the strengths of the model is its ability to serve both research and practice, as is exhibited in its ability to incorporate applied design research and inform architectural decision-making so often lacking in other environmental gerontology models. Place should be viewed as an integrative concept providing opportunities for both environmental gerontology and developmental science to more critically concern the profound role places have in terms of agency, identity and sense of self over the life course.
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Date palm pollen allergoid: characterization of its chemical-physical and immunological properties.
Mistrello, G; Harfi, H; Roncarolo, D; Kwaasi, A; Zanoni, D; Falagiani, P; Panzani, R
2008-01-01
Date palm (DP) pollen can cause allergic symptoms in people living in different countries. Specific immunotherapy with allergenic extracts by subcutaneous route is effective to cure allergic people. However, the risk of side effects has led to explore safer therapeutic modalities. The aim of our work was to evaluate IgE cross-reactivity between DP and autochthonous palm (European fan palm, EFP) pollen extracts, to chemically modify DP extract with potassium cyanate in order to obtain an allergoid, and to characterize it. By radioallergosorbent test inhibition, immunoblotting (IB) and skin prick test, in vitro and in vivo allergenic activities of native and modified DP extracts were compared. By SDS-PAGE and IB, we compared the protein profile and IgE-binding capacity of both native and modified DP, as well as of EFP extracts. By IB inhibition, IgE cross-reactivity of native DP and EFP extracts was evaluated. By ELISA, the capacity of modified DP-induced IgG to react with native DP extract was determined. Radioallergosorbent test inhibition, IB and skin prick test results demonstrated that modified DP was significantly less allergenic than native DP extract. The SDS-PAGE profile showed that potassium cyanate treatment of DP extract did not alter the molecular weight of its components. In addition, no difference was observed between native DP and EFP extracts. Subsequent IB inhibition data evidenced the existence of a strong IgE cross-reactivity between native DP and EFP extracts. ELISA results indicated that the administration of modified DP in mice was able to induce specific IgG also recognizing native DP extract. Modified DP extract (allergoid) seems to be a good candidate for immunotherapy of patients affected by specific allergy. 2007 S. Karger AG, Basel
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Extended Durability Testing of an External Fuel Processor for a Solid Oxide Fuel Cell (SOFC)
DOE Office of Scientific and Technical Information (OSTI.GOV)
Mark Perna; Anant Upadhyayula; Mark Scotto
2012-11-05
Durability testing was performed on an external fuel processor (EFP) for a solid oxide fuel cell (SOFC) power plant. The EFP enables the SOFC to reach high system efficiency (electrical efficiency up to 60%) using pipeline natural gas and eliminates the need for large quantities of bottled gases. LG Fuel Cell Systems Inc. (formerly known as Rolls-Royce Fuel Cell Systems (US) Inc.) (LGFCS) is developing natural gas-fired SOFC power plants for stationary power applications. These power plants will greatly benefit the public by reducing the cost of electricity while reducing the amount of gaseous emissions of carbon dioxide, sulfur oxides,more » and nitrogen oxides compared to conventional power plants. The EFP uses pipeline natural gas and air to provide all the gas streams required by the SOFC power plant; specifically those needed for start-up, normal operation, and shutdown. It includes a natural gas desulfurizer, a synthesis-gas generator and a start-gas generator. The research in this project demonstrated that the EFP could meet its performance and durability targets. The data generated helped assess the impact of long-term operation on system performance and system hardware. The research also showed the negative impact of ambient weather (both hot and cold conditions) on system operation and performance.« less
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Xu, Rosalind J; Blasiak, Bartosz; Cho, Minhaeng; Layfield, Joshua P; Londergan, Casey H
2018-05-17
A quantitative connection between molecular dynamics simulations and vibrational spectroscopy of probe-labeled systems would enable direct translation of experimental data into structural and dynamical information. To constitute this connection, all-atom molecular dynamics (MD) simulations were performed for two SCN probe sites (solvent-exposed and buried) in a calmodulin-target peptide complex. Two frequency calculation approaches with substantial nonelectrostatic components, a quantum mechanics/molecular mechanics (QM/MM)-based technique and a solvatochromic fragment potential (SolEFP) approach, were used to simulate the infrared probe line shapes. While QM/MM results disagreed with experiment, SolEFP results matched experimental frequencies and line shapes and revealed the physical and dynamic bases for the observed spectroscopic behavior. The main determinant of the CN probe frequency is the exchange repulsion between the probe and its local structural neighbors, and there is a clear dynamic explanation for the relatively broad probe line shape observed at the "buried" probe site. This methodology should be widely applicable to vibrational probes in many environments.
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Federal Register 2010, 2011, 2012, 2013, 2014
2013-08-02
... Federal lobster regulations in order to help determine the abundance and distribution of juvenile American lobsters at the Massachusetts and Rhode Island offshore wind farm area. The research is being conducted by... methods: Email: [email protected] . Include in the subject line ``Comments on CFRF Lobster EFP.'' Mail...
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Injuries from roadside improvised explosive devices.
Ramasamy, Arul; Harrisson, Stuart E; Clasper, Jon C; Stewart, Michael P M
2008-10-01
After the invasion of Iraq in April 2003, coalition forces have remained in the country in a bid to maintain stability and support the local security forces. The improvised explosive device (IED) has been widely used by the insurgents and is the leading cause of death and injury among Coalition troops in the region. From January 2006, data were prospectively collected on 100 consecutive casualties who were either injured or killed in hostile action. Mechanism of injury, new Injury Severity Score (NISS), The International Classification of Disease-9th edition diagnosis, anatomic pattern of wounding, and operative management were recorded in a trauma registry. The weapon incident reports were analyzed to ascertain the type of IED employed. Of the 100 casualties injured in hostile action, 53 casualties were injured by IEDs in 23 incidents (mean 2.3 casualties per incident). Twenty-one of 23 (91.3%) of the IEDs employed were explosive formed projectile (EFP) type. Twelve casualties (22.6%) were either killed or died of wounds. Median NISS score of survivors was 3 (range, 1-50). All fatalities sustained unsurvivable injuries with a NISS score of 75. Primary blast injuries were seen in only 2 (3.8%) and thermal injuries in 8 casualties (15.1%). Twenty (48.7%) of survivors underwent surgery by British surgeons in the field hospital. At 18 months follow, all but one of the United Kingdom Service personnel had returned to military employment. The injury profile seen with EFP-IEDs does not follow the traditional pattern of injuries seen with conventional high explosives. Primary blast injuries were uncommon despite all casualties being in close proximity to the explosion. When the EFP-IED is detonated, the EFP produced results in catastrophic injuries to casualties caught in its path, but causes relatively minor injuries to personnel sited adjacent to its trajectory. Improvements in vehicle protection may prevent the EFP from entering the passenger compartments and thereby reduce fatalities.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Not Available
1976-10-01
The Environmental Protection Agency is currently undertaking programs that measure the exhaust emissions of in-use vehicles. One of these programs, the Emission Factors Program (EFP), has generated data indicating that a high percentage of in-use 1975 automobiles have exhaust emissions exceeding the Federal emission standards for 1975-1976 light-duty vehicles. Typical failing vehicles have very high CO emissions. High CO emissions may be indicative of improper adjustment of either the idle mixture or the choke. Since idle mixture and choke adjustments are easily accessible and adjusted on most cars, it seems probable that the maladjustment of these two items may bemore » responsible for some of the high emission levels measured in the EFP. In order to further investigate these possibilities, a test program was conducted by the EPA to quantify the effects of various engine maladjustments on exhaust emissions. This test program would help identify maladjustments resulting in the types of failures encountered in the EFP.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Kobayashi, Kan; RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198; Suzuki, Takehiro
2014-08-27
E. coli YfcM was expressed, purified and crystallized. Crystals of YfcM were obtained by the in situ proteolysis crystallization method. Using these crystals, an X-ray diffraction data set was collected at 1.45 Å resolution. Elongation factor P (EF-P) plays an essential role in the translation of polyproline-containing proteins in bacteria. It becomes functional by the post-translational modification of its highly conserved lysine residue. It is first β-lysylated by PoxA and then hydroxylated by YfcM. In this work, the YfcM protein from Escherichia coli was overexpressed, purified and crystallized. The crystal of YfcM was obtained by the in situ proteolysis crystallizationmore » method and diffracted X-rays to 1.45 Å resolution. It belonged to space group C2, with unit-cell parameters a = 124.4, b = 37.0, c = 37.6 Å, β = 101.2°. The calculated Matthews coefficient (V{sub M}) of the crystal was 1.91 Å{sup 3} Da{sup −1}, indicating that one YfcM molecule is present in the asymmetric unit with a solvent content of 35.7%.« less
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Explosive shaped charge penetration into tuff rock
DOE Office of Scientific and Technical Information (OSTI.GOV)
Vigil, M.G.
1988-10-01
Analysis and data for the use of Explosive Shaped Charges (ESC) to generate holes in tuff rock formation is presented. The ESCs evaluated include Conical Shaped Charges (CSC) and Explosive Formed Projectiles (EFP). The CSCs vary in size from 0.158 to 9.1 inches inside cone diameter. The EFPs were 5.0 inches in diameter. Data for projectile impact angles of 30 and 90 degrees are presented. Analytically predicted depth of penetration data generally compared favorably with experimental data. Predicted depth of penetration versus ESC standoff data and hole profile dimensions in tuff are also presented. 24 refs., 45 figs., 6 tabs.
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NASA Astrophysics Data System (ADS)
Burr, Steven Reed
Dynamic Ionosphere Cubesat Experiment (DICE) is a satellite project funded by the National Science Foundation (NSF) to study the ionosphere, more particularly Storm Enhanced Densities (SED) with a payload consisting of plasma diagnostic instrumentation. Three instruments onboard DICE include an Electric Field Probe (EFP), Ion Langmuir Probe (ILP), and Three Axis Magnetometer (TAM). The EFP measures electric fields from +/-8V and consists of three channels a DC to 40Hz channel, a Floating Potential Probe (FPP), and an spectrographic channel with four bands from 16Hz to 512Hz. The ILP measures plasma densities from 1x104 cm--3 to 2x107 cm--3. The TAM measures magnetic field strength with a range +/-0.5 Gauss with a sensitivity of 2nT. To achieve desired mission requirements careful selection of instrument requirements and planning of the instrumentation design to achieve mission success. The analog design of each instrument is described in addition to the digital framework required to sample the science data at a 70Hz rate and prepare the data for the Command and Data Handing (C&DH) system. Calibration results are also presented and show fulfillment of the mission and instrumentation requirements.
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Effect of Mannitol on Glomerular Ultrafiltration in the Hydropenic Rat
Blantz, Roland C.
1974-01-01
The effect of mannitol upon glomerular ultrafiltration was examined in hydropenic Munich-Wistar rats. Superficial nephron filtration rate (sngfr) rose from 32.0±0.9 nl/min/g kidney wt to 42.0±1.6 (P < 0.001) in eight rats. Hydrostatic pressure gradients acting across the glomerular capillary (ΔP) were measured in glomerular capillaries and Bowman's space with a servo-nulling device, systemic (πA) and efferent arteriolar oncotic pressures (πE) were determined by microprotein analysis. These data were applied to a computer-based mathematical model of glomerular ultrafiltration to determine the profile of effective filtration pressure (EFP = ΔP — π) and total glomerular permeability (LpA) in both states. Filtration equilibrium obtained in hydropenia (LpA ≥ 0.099±0.006 nl/s/g kidney wt/mm Hg) and sngfr rose because EFP increased from a maximum value of 4.2±1.1 to 12.8±0.5 mm Hg after mannitol (P <0.01). This increase was due to both increased nephron plasma flow and decreased πA. Computer analysis of these data revealed that more than half (>58%) of this increase was due to decreased πA, consequent to dilution of protein. Since EFP was disequilibrated after mannitol, LpA could be calculated accurately (0.065 ± 0.003 nl/s/g kidney wt/mm Hg) and was significantly lower than the minimum estimate in hydropenia. Therefore, sngfr does increase with mannitol and this increase is not wholly dependent upon an increase in nephron plasma flow since the major factor increasing EFP was decreased πA. PMID:4418509
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Computational Study of the Malonic Acid Tautomerization Products in Highly Concentrated Particles
DOE Office of Scientific and Technical Information (OSTI.GOV)
Dick-Pérez, Marilú; Windus, Theresa L.
Knowing the tautomeric form of malonic acid (MA) in concentrated particles is critical to understanding its effect on the atmosphere. Energies and vibrational modes of hydrated MA particles were calculated using density functional theory (DFT) at the B3LYP/6-31G(d,p) level and the effective fragment potential (EFP) method. Visualization of the keto and enol isomer vibrational modes enabled the assignment of keto isomer peaks in the 1710–1750 cm –1 range, and previously unidentified experimental IR peaks in the 1690–1710 cm –1 can now be attributed to the enol isomer. Furthermore, a comparison of calculated spectra of pure hydrated enol or keto isomersmore » confirm recent experimental evidence, of a shift in the keto–enol tautomer equilibrium when MA exists as concentrated particles.« less
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Computational Study of the Malonic Acid Tautomerization Products in Highly Concentrated Particles
Dick-Pérez, Marilú; Windus, Theresa L.
2017-03-09
Knowing the tautomeric form of malonic acid (MA) in concentrated particles is critical to understanding its effect on the atmosphere. Energies and vibrational modes of hydrated MA particles were calculated using density functional theory (DFT) at the B3LYP/6-31G(d,p) level and the effective fragment potential (EFP) method. Visualization of the keto and enol isomer vibrational modes enabled the assignment of keto isomer peaks in the 1710–1750 cm –1 range, and previously unidentified experimental IR peaks in the 1690–1710 cm –1 can now be attributed to the enol isomer. Furthermore, a comparison of calculated spectra of pure hydrated enol or keto isomersmore » confirm recent experimental evidence, of a shift in the keto–enol tautomer equilibrium when MA exists as concentrated particles.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
NONE
The Electricity Market Module (EMM) is the electricity supply component of the National Energy Modeling System (NEMS). The EMM represents the generation, transmission, and pricing of electricity. It consists of four submodules: the Electricity Capacity Planning (ECP) Submodule, the Electricity Fuel Dispatch (EFD) Submodule, the Electricity Finance and Pricing (EFP) Submodule, and the Load and Demand-Side Management (LDSM) Submodule. For the Annual Energy Outlook 1998 (AEO98), the EMM has been modified to represent Renewable Portfolio Standards (RPS), which are included in many of the Federal and state proposals for deregulating the electric power industry. A RPS specifies that electricity suppliersmore » must produce a minimum level of generation using renewable technologies. Producers with insufficient renewable generating capacity can either build new plants or purchase {open_quotes}credits{close_quotes} from other suppliers with excess renewable generation. The representation of a RPS involves revisions to the ECP, EFD, and the EFP. The ECP projects capacity additions required to meet the minimum renewable generation levels in future years. The EFD determines the sales and purchases of renewable credits for the current year. The EFP incorporates the cost of building capacity and trading credits into the price of electricity.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Schwartz, Justin
Here we report the results from a project aimed at developing a fully superconducting joint between two REBCO coated conductors using electric field processing (EFP). Due to a reduction in the budget and time period of this contract, we reduced the project scope and focused first on the key scientific issues for forming a strong bond between conductors, and subsequently focused on improving through-the-joint transport. A modified timeline and task list is shown in Table 1, summarizing accomplishments to date. In the first period, we accomplished initial surface characterization as well as rounds of EFP experiments to begin to understandmore » processing parameters which produce well-bonded tapes. In the second phase, we explored the effects of two fundamental EFP parameters, voltage and pressure, and the limitations they place on the process. In the third phase, we achieved superconducting joints and established base characteristics of both the bonding process and the types of tapes best suited to this process. Finally, we investigated some of the parameters related to kinetics which appeared inhibit joint quality and performance.« less
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Klee, Sara M; Mostafa, Islam; Chen, Sixue; Dufresne, Craig; Lehman, Brian L; Sinn, Judith P; Peter, Kari A; McNellis, Timothy W
2018-07-01
The Gram-negative bacterium Erwinia amylovora causes fire blight, an economically important disease of apples and pears. Elongation factor P (EF-P) is a highly conserved protein that stimulates the formation of the first peptide bond of certain proteins and facilitates the translation of certain proteins, including those with polyproline motifs. YjeK and YjeA are two enzymes involved in the essential post-translational β-lysylation of EF-P at a conserved lysine residue, K34. EF-P, YjeA and YjeK have been shown to be essential for the full virulence of Escherichia coli, Salmonella species and Agrobacterium tumefaciens, with efp, yjeA and yjeK mutants having highly similar phenotypes. Here, we identified an E. amylovora yjeK::Tn5 transposon mutant with decreased virulence in apple fruit and trees. The yjeK::Tn5 mutant also showed pleiotropic phenotypes, including reduced growth in rich medium, lower extracellular polysaccharide production, reduced swimming motility and increased chemical sensitivity compared with the wild-type, whilst maintaining wild-type level growth in minimal medium. All yjeK::Tn5 mutant phenotypes were complemented in trans with a plasmid bearing a wild-type copy of yjeK. Comprehensive, quantitative proteomics analyses revealed numerous, environmentally dependent changes in the prevalence of a wide range of proteins, in higher abundance and lower abundance, in yjeK::Tn5 compared with the wild-type, and many of these alterations could be linked to yjeK::Tn5 mutant phenotypes. The environmental dependence of the yjeK::Tn5 mutant proteomic alterations suggests that YjeK could be required for aspects of the environmentally dependent regulation of protein translation. YjeK activity may be critical to overcoming stress, including the challenging host environment faced by invading pathogenic bacteria. © 2017 BSPP AND JOHN WILEY & SONS LTD.
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Code of Federal Regulations, 2012 CFR
2012-10-01
..., or territory catch reports or through creel surveys. Fisheries and research data from many of these..., and generally not retained for sale or personal use. EFP means an experimental fishing permit. First...
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Code of Federal Regulations, 2011 CFR
2011-10-01
..., or territory catch reports or through creel surveys. Fisheries and research data from many of these..., and generally not retained for sale or personal use. EFP means an experimental fishing permit. First...
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Code of Federal Regulations, 2013 CFR
2013-10-01
..., or territory catch reports or through creel surveys. Fisheries and research data from many of these... or overfished, and generally not retained for sale or personal use. EFP means an experimental fishing...
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Code of Federal Regulations, 2014 CFR
2014-10-01
..., or territory catch reports or through creel surveys. Fisheries and research data from many of these... or overfished, and generally not retained for sale or personal use. EFP means an experimental fishing...
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Code of Federal Regulations, 2010 CFR
2010-10-01
..., or territory catch reports or through creel surveys. Fisheries and research data from many of these... longer has any live coral polyps or tissue. EFP means an experimental fishing permit. First level buyer...
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Federal Register 2010, 2011, 2012, 2013, 2014
2010-02-25
... determination that the subject Exempted Fishing Permit (EFP) application for the Northeast Fisheries Science... for the purpose of collecting fishery dependent catch data and biological samples. Regulations under...
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NASA Astrophysics Data System (ADS)
Retsky, Michael
2008-04-01
Explosively formed projectiles (EFP) are a major problem in terrorism and asymmetrical warfare. EFPs are often triggered by ordinary infrared motion detectors. A potential weak link is that such electronics are not hardened to ionizing radiation and can latch-up or enter other inoperative states after exposure to a single short event of ionizing radiation. While these can often be repaired with a power restart, they also can produce shorts and permanent damage. A problem of course is that we do not want to add radiation exposure to the long list of war related hazards. Biological systems are highly sensitive to integrated dosage but show no particular sensitivity to short pulses. There may be a way to generate short pulsed subsoil radiation to deactivate concealed electronics without introducing radiation hazards to military personnel and civilian bystanders. Electron beams of 30 MeV that can be produced by portable linear accelerators (linacs) propagate >20 m in air and 10-12 cm in soil. X-radiation is produced by bremsstrahlung and occurs subsoil beneath the point of impact and is mostly forward directed. Linacs 1.5 m long can produce 66 MWatt pulses of subsoil x-radiation 1 microsecond or less in duration. Untested as yet, such a device could be mounted on a robotic vehicle that precedes a military convoy and deactivates any concealed electronics within 10-20 meters on either side of the road.
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Federal Register 2010, 2011, 2012, 2013, 2014
2012-07-26
... survey designed to estimate the population size of Pacific sardine. NMFS requests public comment on the... the use of 3,000 mt to replicate summer surveys conducted under EFPs approved in 2009, 2010, and 2011...
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Federal Register 2010, 2011, 2012, 2013, 2014
2013-07-08
... conduct a survey designed to estimate the population size of Pacific sardine. NMFS requests public comment... proposed the use of 3,000 mt to replicate summer surveys conducted under EFP's approved in 2009-2012. One...
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Federal Register 2010, 2011, 2012, 2013, 2014
2011-03-18
... Foundation, Inc. (CFFI), this EFP would grant exemptions from the limited access scallop days-at-sea (DAS... Atlantic sea scallop DAS regulations at 50 CFR 648.53(b) and to temporarily retain fish that would...
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Federal Register 2010, 2011, 2012, 2013, 2014
2013-01-10
... Francisco Community Fishing Association and Dan Platt; and (3) the Central Coast Sustainable Groundfish... Community Fishing Association and Dan Platt submitted an application for a 2-year EFP. The primary purpose...
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77 FR 62218 - Pacific Fishery Management Council; Public Meetings
Federal Register 2010, 2011, 2012, 2013, 2014
2012-10-12
... Management 1. NMFS Report 2. Exempted Fishing Permit (EFP) Process 3. Pacific Sardine Stock Assessment and... Groundfish Management Process) 3. Progress Report on Using Descending Devices to Mitigate Barotrauma in... Fishery Management Council; Public Meetings AGENCY: National Marine Fisheries Service (NMFS), National...
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Lin, Tamar; Gilam, Gadi; Raz, Gal; Or-Borichev, Ayelet; Bar-Haim, Yair; Fruchter, Eyal; Hendler, Talma
2017-01-01
Identifying vulnerable individuals prone to develop post-traumatic stress symptoms (PTSS) is of paramount importance, especially in populations at high risk for stress exposure such as combat soldiers. While several neural and psychological risk factors are known, no post-traumatic stress disorder (PTSD) biomarker has yet progressed to clinical use. Here we present novel and clinically applicable anger-related neurobehavioral risk markers for military-related PTSS in a large cohort of Israeli soldiers. The psychological, electrophysiological and neural (Simultaneous recording of scalp electroencephalography [EEG] and functional magnetic resonance imaging [fMRI]) reaction to an anger-inducing film were measured prior to advanced military training and PTSS were recorded at 1-year follow-up. Limbic modulation was measured using a novel approach that monitors amygdala modulation using fMRI-inspired EEG, hereafter termed amygdala electrical fingerprint (amyg-EFP). Inter-subject correlation (ISC) analysis on fMRI data indicated that during movie viewing participants’ brain activity was synchronized in limbic regions including the amygdala. Self-reported state-anger and amyg-EFP modulation successfully predicted PTSS levels. State-anger significantly accounted for 20% of the variance in PTSS, and amyg-EFP signal modulation significantly accounted for additional 15% of the variance. Our study was limited by the moderate PTSS levels and lack of systematic baseline symptoms assessment. These results suggest that pre-stress neurobehavioral measures of anger may predict risk for later PTSS, pointing to anger-related vulnerability factors that can be measured efficiently and at a low cost before stress exposure. Possible mechanisms underlying the association between the anger response and risk for PTSS are discussed. PMID:28326027
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Federal Register 2010, 2011, 2012, 2013, 2014
2013-04-09
...-Stevens Act Provisions; General Provisions for Domestic Fisheries; Application for Exempted Fishing... preliminary determination that an Exempted Fishing Permit (EFP) application contains all of the required information and warrants further consideration. This Exempted Fishing Permit would exempt commercial fishing...
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50 CFR 635.32 - Specifically authorized activities.
Code of Federal Regulations, 2013 CFR
2013-10-01
... prohibited by the regulations contained in this part for the conduct of scientific research, the acquisition... not limited to: scientific research resulting in, or likely to result in, the take, harvest, or... are subject to all conditions specified in any letter of acknowledgment, EFP, scientific research...
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Federal Register 2010, 2011, 2012, 2013, 2014
2011-01-11
... Collection; Comment Request; Scientific Research, Exempted Fishing, and Exempted Activity Submissions AGENCY... Exempted Fishing Permits (EFPs), Scientific Research Permits (SRPs), Display Permits, Letters of Acknowledgment (LOAs), and Shark Research Permits are issued under the authority of the Magnuson-Stevens Fishery...
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The SPoRT-WRF: Evaluating the Impact of NASA Datasets on Convective Forecasts
NASA Technical Reports Server (NTRS)
Zavodsky, Bradley; Kozlowski, Danielle; Case, Jonathan; Molthan, Andrew
2012-01-01
Short-term Prediction Research and Transition (SPoRT) seeks to improve short-term, regional weather forecasts using unique NASA products and capabilities SPoRT has developed a unique, real-time configuration of the NASA Unified Weather Research and Forecasting (WRF)WRF (ARW) that integrates all SPoRT modeling research data: (1) 2-km SPoRT Sea Surface Temperature (SST) Composite, (2) 3-km LIS with 1-km Greenness Vegetation Fraction (GVFs) (3) 45-km AIRS retrieved profiles. Transitioned this real-time forecast to NOAA's Hazardous Weather Testbed (HWT) as deterministic model at Experimental Forecast Program (EFP). Feedback from forecasters/participants and internal evaluation of SPoRT-WRF shows a cool, dry bias that appears to suppress convection likely related to methodology for assimilation of AIRS profiles Version 2 of the SPoRT-WRF will premier at the 2012 EFP and include NASA physics, cycling data assimilation methodology, better coverage of precipitation forcing, and new GVFs
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Federal Register 2010, 2011, 2012, 2013, 2014
2013-03-01
... Highly Migratory Species; Exempted Fishing, Scientific Research, Display, and Chartering Permits; Letters... Permits (EFPs), Scientific Research Permits (SRPs), Display Permits, Letters of Acknowledgment (LOAs), and... scientific research, the acquisition of information and data, the enhancement of safety at sea, the purpose...
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76 FR 23996 - North Pacific Fishery Management Council Public Meeting
Federal Register 2010, 2011, 2012, 2013, 2014
2011-04-29
... uncertainty/total catch accounting; review/approve Halibut Mortality on trawlers Exempted Fishing Permit (EFP... & Wildlife Service Report. 2. Catch Sharing Plan(CSP): Review CSP size limit algorithm. 3. BSAI Crab Draft Stock Assessment Fishery Evaluation report: Review and approve catch specifications for Norton Sound Red...
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Waldstreicher, J; Santoro, N F; Hall, J E; Filicori, M; Crowley, W F
1988-01-01
To examine gonadotropin secretory frequency as a component of the disordered neuroendocrine regulation of gonadotropin secretion in women with polycystic ovarian disease (PCOD), we measured serum gonadotropin concentrations in 12 women with PCOD at 10-min intervals for periods of 12-24 h. The patterns of LH and FSH release in these patients were compared to the findings of 24 studies in 21 age-matched normal women during the early, mid- and late follicular phases (EFP, MFP and LFP) of their cycles. Serum sex steroid levels during the 12-24 h of study in the women with PCOD were compared to those in normal women studied during the follicular phase. The mean serum estradiol (E2) level in the women with PCOD was similar to that in normal women studied in the EFP, but lower than those in normal women in the MFP (P less than 0.05) and LFP (P less than 0.01). Mean serum estrone, however, was significantly higher in women with PCOD than in women in the EFP and MFP (P less than 0.05 and P less than 0.02, respectively), but lower than that in women in the LFP (P less than 0.02). Total and unbound testosterone (T) levels were significantly elevated in women with PCOD compared to those in normal women at all stages of the follicular phase (P less than 0.001). The mean serum LH concentration and LH pulse amplitude were markedly elevated in the women with PCOD compared to normal women at all three stages of the follicular phase (P less than 0.05 or less). In addition, LH pulse frequency was faster in women with PCOD [24.8 +/- 0.9 ( +/- SE) pulses/24 h] than that in women in the EFP (15.6 +/- 0.7; P less than 0.01), MFP (22.2 +/- 1.1; P less than 0.05) and LFP (20.8 +/- 1.2; P less than 0.01). This increased LH pulse frequency in women with PCOD correlated with ambient serum E2 levels on the day of study (r = 0.84; P less than 0.001), but not with serum estrone, T, or unbound T. Repeat studies in four women with PCOD demonstrated a similarly abnormal gonadotropin secretory pattern in each. We conclude that 1) women with PCOD have an increase in both the amplitude and frequency of LH secretion compared to those in normally cycling women throughout the follicular phase; 2) the defect in women with PCOD is reproducible.(ABSTRACT TRUNCATED AT 400 WORDS)
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78 FR 43140 - Submission for OMB Review; Comment Request
Federal Register 2010, 2011, 2012, 2013, 2014
2013-07-19
... Control Number: 0648-0204. Form Number(s): NA. Type of Request: Regular submission (extension of a current... appeals, 2 hours; CPS transfers, 30 minutes; experimental fishing permits (EFPs), 1 hour. Burden Hours... persons to participate in Federally-managed fisheries off the West Coast. There are three types of permits...
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76 FR 8713 - Pacific Fishery Management Council; Public Meeting
Federal Register 2010, 2011, 2012, 2013, 2014
2011-02-15
... purpose of the joint conference call is to consider any CPS-related fisheries research proposals that will... consider adopting for public review any proposals that are submitted. The CPSMT and CPSAS will discuss any EFP proposals, and will develop statements to be included in the March Council meeting record. Special...
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Federal Register 2010, 2011, 2012, 2013, 2014
2013-06-06
..., fecundity, bioelectrical impedance analysis (BIA), food habits, and genetic research. The yellowtail... dependent catch data and biological samples. Regulations under the Magnuson-Stevens Fishery Conservation and... Exempted Fishing Permit (EFP) on April 11, 2013, to enable data collection activities that the regulations...
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Towards an Integrative Theory of Peace Education
ERIC Educational Resources Information Center
Danesh, H. B.
2006-01-01
This paper proposes the integrative theory of peace (ITP) and briefly outlines the education for peace curriculum (EFP) developed on the basis of this theory. ITP is based on the concept that peace is, at once, a psychological, social, political, ethical and spiritual state with its expressions in intrapersonal, interpersonal, intergroup,…
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50 CFR 660.516 - Exempted fishing.
Code of Federal Regulations, 2013 CFR
2013-10-01
... 50 Wildlife and Fisheries 13 2013-10-01 2013-10-01 false Exempted fishing. 660.516 Section 660.516... Exempted fishing. (a) General. In the interest of developing an efficient and productive fishery for CPS, the Regional Administrator may issue exempted fishing permits (EFP) for the harvest of CPS that...
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50 CFR 660.718 - Exempted fishing.
Code of Federal Regulations, 2010 CFR
2010-10-01
... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Exempted fishing. 660.718 Section 660.718... Exempted fishing. (a) In the interest of developing an efficient and productive fishery for HMS, the Regional Administrator may issue exempted fishing permits (EFP) for the harvest of HMS that otherwise would...
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50 CFR 660.516 - Exempted fishing.
Code of Federal Regulations, 2012 CFR
2012-10-01
... 50 Wildlife and Fisheries 13 2012-10-01 2012-10-01 false Exempted fishing. 660.516 Section 660.516... Exempted fishing. (a) General. In the interest of developing an efficient and productive fishery for CPS, the Regional Administrator may issue exempted fishing permits (EFP) for the harvest of CPS that...
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50 CFR 660.718 - Exempted fishing.
Code of Federal Regulations, 2014 CFR
2014-10-01
... 50 Wildlife and Fisheries 13 2014-10-01 2014-10-01 false Exempted fishing. 660.718 Section 660.718... Exempted fishing. (a) In the interest of developing an efficient and productive fishery for HMS, the Regional Administrator may issue exempted fishing permits (EFP) for the harvest of HMS that otherwise would...
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50 CFR 660.516 - Exempted fishing.
Code of Federal Regulations, 2010 CFR
2010-10-01
... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Exempted fishing. 660.516 Section 660.516... Exempted fishing. (a) General. In the interest of developing an efficient and productive fishery for CPS, the Regional Administrator may issue exempted fishing permits (EFP) for the harvest of CPS that...
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50 CFR 660.718 - Exempted fishing.
Code of Federal Regulations, 2012 CFR
2012-10-01
... 50 Wildlife and Fisheries 13 2012-10-01 2012-10-01 false Exempted fishing. 660.718 Section 660.718... Exempted fishing. (a) In the interest of developing an efficient and productive fishery for HMS, the Regional Administrator may issue exempted fishing permits (EFP) for the harvest of HMS that otherwise would...
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50 CFR 660.718 - Exempted fishing.
Code of Federal Regulations, 2013 CFR
2013-10-01
... 50 Wildlife and Fisheries 13 2013-10-01 2013-10-01 false Exempted fishing. 660.718 Section 660.718... Exempted fishing. (a) In the interest of developing an efficient and productive fishery for HMS, the Regional Administrator may issue exempted fishing permits (EFP) for the harvest of HMS that otherwise would...
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50 CFR 660.516 - Exempted fishing.
Code of Federal Regulations, 2011 CFR
2011-10-01
... 50 Wildlife and Fisheries 11 2011-10-01 2011-10-01 false Exempted fishing. 660.516 Section 660.516... Exempted fishing. (a) General. In the interest of developing an efficient and productive fishery for CPS, the Regional Administrator may issue exempted fishing permits (EFP) for the harvest of CPS that...
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50 CFR 660.718 - Exempted fishing.
Code of Federal Regulations, 2011 CFR
2011-10-01
... 50 Wildlife and Fisheries 11 2011-10-01 2011-10-01 false Exempted fishing. 660.718 Section 660.718... Exempted fishing. (a) In the interest of developing an efficient and productive fishery for HMS, the Regional Administrator may issue exempted fishing permits (EFP) for the harvest of HMS that otherwise would...
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Ballistically Initiated Fire Ball Generation Using M&S: Innovation Grant (Briefing Charts)
2012-01-26
isotropic in nature Phenomenological models for explosives initiation. – HVRB, forest fire etc. Equation of state – Ideal gas, Mie-Gruneisen, JWL ...perfectly plastic description • EOS • Mie Gruneisen • JWL for explosive • Phenomenological Model for EFP • High Explosive input for programmed burn
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Sahu, Nityananda; Gadre, Shridhar R.; Bandyopadhyay, Pradipta
We report new global minimum candidate structures for the (H2O)25 cluster that are lower in energy than the ones reported previously and correspond to hydrogen bonded networks with 42 hydrogen bonds and an interior, fully coordinated water molecule. These were obtained as a result of a hierarchical approach based on initial Monte Carlo Temperature Basin Paving (MCTBP) sampling of the cluster’s Potential Energy Surface (PES) with the Effective Fragment Potential (EFP), subsequent geometry optimization using the Molecular Tailoring fragmentation Approach (MTA) and final refinement at the second order Møller Plesset perturbation (MP2) level of theory. The MTA geometry optimizations usedmore » between 14 and 18 main fragments with maximum sizes between 11 and 14 water molecules and average size of 10 water molecules, whose energies and gradients were computed at the MP2 level. The MTA-MP2 optimized geometries were found to be quite close (within < 0.5 kcal/mol) to the ones obtained from the MP2 optimization of the whole cluster. The grafting of the MTA-MP2 energies yields electronic energies that are within < 5×10-4 a.u. from the MP2 results for the whole cluster while preserving their energy order. The MTA-MP2 method was also found to reproduce the MP2 harmonic vibrational frequencies in both the HOH bending and the OH stretching regions.« less
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Federal Register 2010, 2011, 2012, 2013, 2014
2013-04-02
... Federally-managed fisheries off the West Coast. There are three types of permits: Basic fishery permits for... fishing permits (EFPs). Appeals and certain waiver requests may also be submitted. Transfer applications... Species permits by April 30, 2013. III. Data OMB Control Number: 0648-0204. Form Number: None. Type of...
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The Education for Peace Integrative Curriculum: Concepts, Contents and Efficacy
ERIC Educational Resources Information Center
Danesh, H. B.
2008-01-01
This article presents the conceptual foundations of the Education for Peace (EFP) integrative curriculum, reviews its contents, and briefly describes its impact on students, teachers, staff and parents/guardians in Bosnia and Herzegovina. The curriculum was developed in 2000, first employed in six pilot schools and then implemented in 112 primary…
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Federal Register 2010, 2011, 2012, 2013, 2014
2011-04-08
... with the goals and objectives of the Monkfish Fishery Management Plan (FMP). However, further review... limit in the Southern Fishery Management Area (SFMA). The EFP issued to the gillnet tie-down study also...: (978) 281-9135. FOR FURTHER INFORMATION CONTACT: Jason Berthiaume, Fishery Management Specialist, 978...
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50 CFR 660.30 - Compensation with fish for collecting resource information-EFPs.
Code of Federal Regulations, 2011 CFR
2011-10-01
... 50 Wildlife and Fisheries 11 2011-10-01 2011-10-01 false Compensation with fish for collecting... COAST STATES West Coast Groundfish Fisheries § 660.30 Compensation with fish for collecting resource... retain fish as compensation in excess of trip limits or to be exempt from other specified management...
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50 CFR 660.30 - Compensation with fish for collecting resource information-EFPs.
Code of Federal Regulations, 2012 CFR
2012-10-01
... 50 Wildlife and Fisheries 13 2012-10-01 2012-10-01 false Compensation with fish for collecting... COAST STATES West Coast Groundfish Fisheries § 660.30 Compensation with fish for collecting resource... retain fish as compensation in excess of trip limits or to be exempt from other specified management...
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50 CFR 660.30 - Compensation with fish for collecting resource information-EFPs.
Code of Federal Regulations, 2013 CFR
2013-10-01
... 50 Wildlife and Fisheries 13 2013-10-01 2013-10-01 false Compensation with fish for collecting... COAST STATES West Coast Groundfish Fisheries § 660.30 Compensation with fish for collecting resource... retain fish as compensation in excess of trip limits or to be exempt from other specified management...
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Code of Federal Regulations, 2011 CFR
2011-10-01
..., the ACL or ACT when specified is reduced by the Pacific Coast treaty Indian Tribal harvest... in the non-groundfish fishery that is deducted from the ACL or ACT when specified. (2) The commercial... EFPs described at §§ 660.60(f) and 600.745, will be deducted from the ACL or ACT when specified. Set...
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50 CFR 635.4 - Permits and fees.
Code of Federal Regulations, 2011 CFR
2011-10-01
... and to fish for, take, retain or possess Atlantic tunas, swordfish, or sharks when engaged in.... (1) The owner of each vessel used to fish for or take Atlantic sharks or on which Atlantic sharks are... of a shark display or EFP issued pursuant to § 635.32, or fishes exclusively within State waters. It...
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76 FR 3616 - Gulf of Mexico Fishery Management Council; Public Meetings
Federal Register 2010, 2011, 2012, 2013, 2014
2011-01-20
... permits (EFPs), if any and hold an open public comment period regarding any fishery issue of concern... Policy; Habitat Protection; SEDAR Selection; AP Selection; Data Collection; Budget/Personnel; Shrimp... Essential Fish Habitat 5-year Review Report. 4:15 p.m.-4:45 p.m.--The Data Collection committee will meet to...
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EFP Delphi study on the trends in Periodontology and Periodontics in Europe for the year 2025.
Madianos, Phoebus; Papaioannou, William; Herrera, David; Sanz, Mariano; Baeumer, Amelie; Bogren, Anna; Bouchard, Philippe; Chomyszyn-Gajewska, Maria; Demirel, Korkud; Gaspersic, Rok; Giurgiu, Marina; Graziani, Filippo; Jepsen, Karin; Jepsen, Sören; O Brien, Tiernan; Polyzois, Ioannis; Preshaw, Philip M; Rakic, Mia; Reners, Michele; Rincic, Nives; Stavropoulos, Andreas; Sütcü, Serdar; Verner, Christian; Llodra, Juan Carlos
2016-06-01
The aim was to assess the potential trends in Periodontology and Periodontics in Europe that might be anticipated by the year 2025, using the Delphi method. The expert opinion of 120 experts was sought through the use of an open-ended questionnaire, developed by an advisory group, containing 40 questions concerning the various trends in periodontology. The experts (113 responders) expect a stabilization of the prevalence of periodontitis, both for the chronic as well as the aggressive cases, but an increase in implant-related diseases up to the year 2025. Concurrently, the importance of implants is seen to be increasing. They foresee an increased demand for postgraduate periodontology and implantology training. This is mirrored in an increase in publications for implant dentistry and increase in demand and need for training. Concerning the patients, better-informed individuals seeking more routine check-ups are expected. A continued need for specialized periodontists, but also well trained dental practitioners is foreseen for next decade in Europe. Apart from periodontology they will be increasingly exposed to and trained in implant dentistry. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
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Bose, Samik; Chakrabarty, Suman; Ghosh, Debashree
2016-05-19
Hybrid quantum mechanics/molecular mechanics (QM/MM) is applied to the fluorinated green fluorescent protein (GFP) chromophore (DFHBDI) in its deprotonated form to understand the solvatochromic shifts in its vertical detachment energy (VDE) and vertical excitation energy (VEE). This variant of the GFP chromophore becomes fluorescent in an RNA environment and has a wide range of applications in biomedical and biochemical fields. From microsolvation studies, we benchmark (with respect to full QM) the accuracy of our QM/MM calculations with effective fragment potential (EFP) as the MM method of choice. We show that while the solvatochromic shift in the VEE is minimal (0.1 eV blue shift) and its polarization component is only 0.03 eV, the effect of the solvent on the VDE is quite large (3.85 eV). We also show by accurate calculations on the solvatochromic shift of the VDE that polarization accounts for ∼0.23 eV and therefore cannot be neglected. The effect of the counterions on the VDE of the deprotonated chromophore in solvation is studied in detail, and a charge-smearing scheme is suggested for charged chromophores.
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Federal Register 2010, 2011, 2012, 2013, 2014
2012-05-29
... Management Act (16 U.S.C. 1801 et seq.), and regulations at 50 CFR 600.745(b) concerning exempted fishing... intended to involve recreational fishermen in the collection of fundamental biological information of Gulf... of Mexico Fishery Management Council (Council). The applicant requires authorization through the EFP...
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On Fibonacci Numbers Which Are Elliptic Korselt Numbers
2014-11-17
1, where (a|p) denotes the Legendre symbol of a with respect to p, then the order of group of points on E modulo p denoted #E(Fp), equals p+1. In...Fibonacci sequence, polynomials and the Euler function”, Indag. Math. (N.S.) 17 (2006), 611–625. [8] F. Luca and I. E. Shparlinski, “On the counting
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On Fibonacci Numbers Which Are Elliptic Carmichael
2014-12-27
d|p) = −1, where (a|p) denotes the Legendre symbol of a with respect to p. Then ap = 0, so, in particular, #E(Fp) = p + 1. Furthermore, if there...sequence, polynomials and the Euler function”, Indag. Math. (N.S.) 17 (2006), 611–625. [10] F. Luca and I. E. Shparlinski, “On the counting function of
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ERIC Educational Resources Information Center
Feldt, Ronald; Lindley, Kyla; Louison, Rebecca; Roe, Allison; Timm, Megan; Utinkova, Nikola
2015-01-01
The Emotional Regulation Related to Testing Scale (ERT Scale) assesses strategies students use to regulate emotion related to academic testing. It has four dimensions: Cognitive Appraising Processes (CAP), Emotion-Focusing Processes (EFP), Task-Focusing Processes (TFP), and Regaining Task-Focusing Processes (RTFP). The study examined the factor…
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Code of Federal Regulations, 2010 CFR
2010-10-01
... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Compensation with fish for collecting... Fisheries § 660.350 Compensation with fish for collecting resource information—exempted fishing permits off... EFP allowing a vessel to retain fish as compensation in excess of trip limits or to be exempt from...
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Federal Register 2010, 2011, 2012, 2013, 2014
2011-08-12
..., Shareholders Alliance, and would involve as many as 30 vessel owners associated with that organization... improve the scientific knowledge of red snapper and other reef fish taken from state and Federal waters of the Gulf and to use that knowledge to support fishery management decisions. The EFP, if approved...
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Federal Register 2010, 2011, 2012, 2013, 2014
2013-09-12
... authority of the Magnuson-Stevens Fishery Conservation and Management Act (16 U.S.C. 1801 et seq.), and... fundamental fisheries information. The described research is part of a long-term observer program that began... development and evaluation of fisheries management and regulatory options. The EFP would exempt the activities...
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Federal Register 2010, 2011, 2012, 2013, 2014
2010-06-03
... survey designed to estimate the population size of Pacific sardine. NMFS requests public comment on the... use of 4200 mt to replicate the summer survey conducted under the EFP approved in 2009 and expand the sample size and area covered. In addition to the summer survey, the applicants proposed to use 800 mt of...
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Federal Register 2010, 2011, 2012, 2013, 2014
2013-05-30
... 02543-1026, or online at: www.nefsc.noaa.gov/nefsc/publications/ . The revised EFP would exempt vessels.... Category F vessels would be charged monkfish RSA DAS at a higher pro- rated rate of 2.909:1 RSA DAS for... tail-to-whole-weight conversion factor from 3.32 to 2.91, which essentially reduced the whole weight...
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Federal Register 2010, 2011, 2012, 2013, 2014
2011-11-16
... into the observer and catch accounting systems. The applicant proposes to begin EFP fishing on April 1... experience and knowledge of the Amendment 80 catch accounting system. The AKSC would be limited to no more... end, bin, or conveyance system prior to being observed and counted by an at-sea observer; and...
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NASA Astrophysics Data System (ADS)
Sable, Peter; Helminiak, Nathaniel; Harstad, Eric; Gullerud, Arne; Hollenshead, Jeromy; Hertel, Eugene; Sandia National Laboratories Collaboration; Marquette University Collaboration
2017-06-01
With the increasing use of hydrocodes in modeling and system design, experimental benchmarking of software has never been more important. While this has been a large area of focus since the inception of computational design, comparisons with temperature data are sparse due to experimental limitations. A novel temperature measurement technique, magnetic diffusion analysis, has enabled the acquisition of in-flight temperature measurements of hyper velocity projectiles. Using this, an AC-14 bare shaped charge and an LX-14 EFP, both with copper linings, were simulated using CTH to benchmark temperature against experimental results. Particular attention was given to the slug temperature profiles after separation, and the effect of varying equation-of-state and strength models. Simulations are in agreement with experimental, attaining better than 2% error between observed shaped charge temperatures. This varied notably depending on the strength model used. Similar observations were made simulating the EFP case, with a minimum 4% deviation. Jet structures compare well with radiographic images and are consistent with ALEGRA simulations previously conducted. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.
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ERIC Educational Resources Information Center
Axelrod, Joseph
In this report of a project on curriculum planning, a new language is developed for analyzing and describing "the curricular-instructional subsystem." Some of the data come from the author's experiences in planning and directing the Experimental Freshman-Year Program (EFP) at San Francisco State College, but most were collected at the…
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Religion and Other Cultural Variables in Modern Operational Environments
2007-05-01
Contrary to Western media portrayals at the time, Babrak designed many of these programs to improve the quality of life for Afghanistan’s citizens...ammunition, advanced rocket propelled grenades, Katyusha rockets, and the particularly deadly explosive formed projectiles (EFP) designed to...trends toward insurgencies. It seemed however, that many chose to focus on major combat operations and conventional operational designs instead of truly
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Code of Federal Regulations, 2010 CFR
2010-10-01
... amount estimated to be taken as research catch and in non-groundfish fisheries is 3,000 mt. The... anticipated to be taken during research activity and 0.14 mt for the amount expected to be taken during EFP... unexploited rockfish population in the California Current ecosystem, a non-quantitative assessment was...
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Oocyte vitrification as an efficient option for elective fertility preservation.
Cobo, Ana; García-Velasco, Juan A; Coello, Aila; Domingo, Javier; Pellicer, Antonio; Remohí, José
2016-03-01
To provide a detailed description of the current oocyte vitrification status as a means of elective fertility preservation (EFP). Retrospective observational multicenter study. Private university-affiliated center. A total of 1,468 women who underwent EFP because of age or having associated a medical condition other than cancer (January 2007 to April 2015). None. Survival and cumulative live birth rate (CLBR) per consumed oocyte. Mean age was higher with EFP due to age versus having an associated medical reason (37.7 y [95% confidence interval (CI) 36.5-37.9] vs. 35.7 y [95% CI 34.9-36.3]). In total, 137 patients (9.3%) returned to use their oocytes. Overall survival rate was 85.2% (95% CI 83.2-87.2). Live birth rate per patient was higher in women ≤35 years old than ≥36 years old (50% [95% CI 32.7-67.3] vs. 22.9% [95% CI 14.9-30.9]). CLBR was higher and increased faster in younger women. The gain in CLBR was sharp from 5 (15.4%, 95% CI -4.2 to 35.0) to 8 oocytes (40.8%, 95% CI 13.2-68.4), with an 8.4% gain per additional oocyte, in the ≤35-year-old group. The increase was slower with 10-15 oocytes, reaching a plateau CLBR of 85.2%. A milder increase (4.9% gain) was observed in the ≥36-year-old group (from 5.1% [95% CI -0.6 to 10.7] to 19.9% [95% CI 8.7-31.1] when 5-8 oocytes were consumed), reaching the plateau with 11 oocytes (CLBR 35.6%). Forty babies were born. At least 8-10 metaphase II oocytes are necessary to achieve reasonable success. Numbers should be individualized in women >36 years old. We suggest encouraging women who are motivated exclusively by a desire to postpone childbearing because of age, to come at younger ages to increase success possibilities. Copyright © 2016 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.
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Electronically excited and ionized states in condensed phase: Theory and applications
NASA Astrophysics Data System (ADS)
Sadybekov, Arman
Predictive modeling of chemical processes in silico is a goal of XXI century. While robust and accurate methods exist for ground-state properties, reliable methods for excited states are still lacking and require further development. Electronically exited states are formed by interactions of matter with light and are responsible for key processes in solar energy harvesting, vision, artificial sensors, and photovoltaic applications. The greatest challenge to overcome on our way to a quantitative description of light-induced processes is accurate inclusion of the effect of the environment on excited states. All above mentioned processes occur in solution or solid state. Yet, there are few methodologies to study excited states in condensed phase. Application of highly accurate and robust methods, such as equation-of-motion coupled-cluster theory EOM-CC, is limited by a high computational cost and scaling precluding full quantum mechanical treatment of the entire system. In this thesis we present successful application of the EOM-CC family of methods to studies of excited states in liquid phase and build hierarchy of models for inclusion of the solvent effects. In the first part of the thesis we show that a simple gasphase model is sufficient to quantitatively analyze excited states in liquid benzene, while the latter part emphasizes the importance of explicit treatment of the solvent molecules in the case of glycine in water solution. In chapter 2, we use a simple dimer model to describe exciton formation in liquid and solid benzene. We show that sampling of dimer structures extracted from the liquid benzene is sufficient to correctly predict exited-state properties of the liquid. Our calculations explain experimentally observed features, which helped to understand the mechanism of the excimer formation in liquid benzene. Furthermore, we shed light on the difference between dimer configurations in the first solvation shell of liquid benzene and in unit cell of solid benzene and discussed the impact of these differences on the formation of the excimer state. In chapter 3, we present a theoretical approach for calculating core-level states in condensed phase. The approach is based on EOM-CC and effective fragment potential (EFP) method. By introducing an approximate treatment of double excitations in the EOM-CCSD (EOM-CC with single and double substitutions) ansatz, we addressed poor convergence issues that are encountered for the core-level states and significantly reduced computational costs. While the approximations introduce relatively large errors in the absolute values of transition energies, the errors are systematic. Consequently, chemical shifts, changes in ionization energies relative to the reference systems, are reproduced reasonably well. By using different protonation forms of solvated glycine as a benchmark system, we showed that our protocol is capable of reproducing the experimental chemical shifts with a quantitative accuracy. The results demonstrate that chemical shifts are very sensitive to the solvent interactions and that explicit treatment of solvent, such as EFP, is essential for achieving quantitative accuracy. In chapter 4, we outline future directions and discuss possible applications of the developed computational protocol for prediction of core chemical shifts in larger systems.
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Electricity Market Module - NEMS Documentation
2017-01-01
Documents the Electricity Market Module as it was used for the Annual Energy Outlook. The Electricity Market Module (EMM) is the electricity supply component of the National Energy Modeling System (NEMS). The EMM represents the generation, transmission, and pricing of electricity. It consists of four submodules: the Electricity Capacity Planning (ECP) Submodule, the Electricity Fuel Dispatch (EFD) Submodule, the Electricity Finance and Pricing (EFP) Submodule, and the Electricity Load and Demand (ELD) Submodule.
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ERIC Educational Resources Information Center
Danesh, H. B.
2008-01-01
In this article, the author describes the nature and dynamics of the culture of healing and the prerequisites for its creation. The concept of the culture of healing emerged over the course of 7 years of implementation of the Education for Peace (EFP) Program in over 100 primary and secondary schools in the ethnically divided Bosnia and…
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Structure-Function Based Molecular Relationships in Ewing's Sarcoma
2015-01-01
Ewing's Sarcoma Oncogene (ews) on chromosome 22q12 is encoding a ubiquitously expressed RNA-binding protein (EWS) with unknown function that is target of tumor-specific chromosomal translocations in Ewing's sarcoma family of tumors. A model of transcription complex was proposed in which the heterodimer Rpb4/7 binds to EAD, connecting it to Core RNA Pol II. The DNA-binding domain, provided by EFP, is bound to the promoter. Rpb4/7 binds RNA, stabilizing the transcription complex. The complex Rpb4/7 can stabilize the preinitiation complexes by converting the conformation of RNA Pol II. EWS may change its conformation, so that NTD becomes accessible. Two different mechanisms of interaction between EWS and RNA Pol II are proposed: (I) an intermolecular EWS-EWS interaction between two molecules, pushing conformation from “closed” to “open” state, or (II) an intramolecular interaction inside the molecule of EWS, pushing conformation of the molecule from “closed” to “open” state. The modified forms of EWS may interact with Pol II subunits hsRpb5 and hsRpb7. The EWS and EFPs binding partners are described schematically in a model, an attempt to link the transcription with the splicing. The proposed model helps to understand the functional molecular interactions in cancer, to find new partners and ways to treat cancer. PMID:25688366
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The melting temperature of liquid water with the effective fragment potential
DOE Office of Scientific and Technical Information (OSTI.GOV)
Brorsen, Kurt R.; Willow, Soohaeng Y.; Xantheas, Sotiris S.
2015-09-17
Direct simulation of the solid-liquid water interface with the effective fragment potential (EFP) via the constant enthalpy and pressure (NPH) ensemble was used to estimate the melting temperature (Tm) of ice-Ih. Initial configurations and velocities, taken from equilibrated constant pressure and temperature (NPT) simulations at T = 300 K, 350 K and 400 K, respectively, yielded corresponding Tm values of 378±16 K, 382±14 K and 384±15 K. These estimates are consistently higher than experiment, albeit to the same degree with previously reported estimates using density functional theory (DFT)-based Born-Oppenheimer simulations with the Becke-Lee-Yang-Parr functional plus dispersion corrections (BLYP-D). KRB wasmore » supported by a Computational Science Graduate Fellowship from the Department of Energy. MSG was supported by a U.S. National Science Foundation Software Infrastructure (SI2) grant (ACI – 1047772). SSX acknowledges support from the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle.« less
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Computer Systems Acquisition Metrics Handbook. Volume II. Quality Factor Modules.
1982-05-01
are unable to evil .mte) IPAW BrY: APFD If: i Ef-24 EFFICICYe: EfPDF.l L C1E PHASE: Sota S): PRELINARY DESIGN EfP. 1 EfDC. 2 = StSM NAM:. I. CUM...unable to evaluate) Iv. D6PB=’S C3#rm: PWAPM BY:______ APFD N _______ Po-30 MACHM NDE WM4 MEASE SO= Go&e:. PoII4LS LIM P E PHAiSE: SJRMCs): IMPLEME
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Miscoding-induced stalling of substrate translocation on the bacterial ribosome.
Alejo, Jose L; Blanchard, Scott C
2017-10-10
Directional transit of the ribosome along the messenger RNA (mRNA) template is a key determinant of the rate and processivity of protein synthesis. Imaging of the multistep translocation mechanism using single-molecule FRET has led to the hypothesis that substrate movements relative to the ribosome resolve through relatively long-lived late intermediates wherein peptidyl-tRNA enters the P site of the small ribosomal subunit via reversible, swivel-like motions of the small subunit head domain within the elongation factor G (GDP)-bound ribosome complex. Consistent with translocation being rate-limited by recognition and productive engagement of peptidyl-tRNA within the P site, we now show that base-pairing mismatches between the peptidyl-tRNA anticodon and the mRNA codon dramatically delay this rate-limiting, intramolecular process. This unexpected relationship between aminoacyl-tRNA decoding and translocation suggests that miscoding antibiotics may impact protein synthesis by impairing the recognition of peptidyl-tRNA in the small subunit P site during EF-G-catalyzed translocation. Strikingly, we show that elongation factor P (EF-P), traditionally known to alleviate ribosome stalling at polyproline motifs, can efficiently rescue translocation defects arising from miscoding. These findings help reveal the nature and origin of the rate-limiting steps in substrate translocation on the bacterial ribosome and indicate that EF-P can aid in resuming translation elongation stalled by miscoding errors.
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Miscoding-induced stalling of substrate translocation on the bacterial ribosome
Alejo, Jose L.; Blanchard, Scott C.
2017-01-01
Directional transit of the ribosome along the messenger RNA (mRNA) template is a key determinant of the rate and processivity of protein synthesis. Imaging of the multistep translocation mechanism using single-molecule FRET has led to the hypothesis that substrate movements relative to the ribosome resolve through relatively long-lived late intermediates wherein peptidyl-tRNA enters the P site of the small ribosomal subunit via reversible, swivel-like motions of the small subunit head domain within the elongation factor G (GDP)-bound ribosome complex. Consistent with translocation being rate-limited by recognition and productive engagement of peptidyl-tRNA within the P site, we now show that base-pairing mismatches between the peptidyl-tRNA anticodon and the mRNA codon dramatically delay this rate-limiting, intramolecular process. This unexpected relationship between aminoacyl-tRNA decoding and translocation suggests that miscoding antibiotics may impact protein synthesis by impairing the recognition of peptidyl-tRNA in the small subunit P site during EF-G–catalyzed translocation. Strikingly, we show that elongation factor P (EF-P), traditionally known to alleviate ribosome stalling at polyproline motifs, can efficiently rescue translocation defects arising from miscoding. These findings help reveal the nature and origin of the rate-limiting steps in substrate translocation on the bacterial ribosome and indicate that EF-P can aid in resuming translation elongation stalled by miscoding errors. PMID:28973849
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Complexity and specificity of the maize (Zea mays L.) root hair transcriptome.
Hey, Stefan; Baldauf, Jutta; Opitz, Nina; Lithio, Andrew; Pasha, Asher; Provart, Nicholas; Nettleton, Dan; Hochholdinger, Frank
2017-04-01
Root hairs are tubular extensions of epidermis cells. Transcriptome profiling demonstrated that the single cell-type root hair transcriptome was less complex than the transcriptome of multiple cell-type primary roots without root hairs. In total, 831 genes were exclusively and 5585 genes were preferentially expressed in root hairs [false discovery rate (FDR) ≤1%]. Among those, the most significantly enriched Gene Ontology (GO) functional terms were related to energy metabolism, highlighting the high energy demand for the development and function of root hairs. Subsequently, the maize homologs for 138 Arabidopsis genes known to be involved in root hair development were identified and their phylogenetic relationship and expression in root hairs were determined. This study indicated that the genetic regulation of root hair development in Arabidopsis and maize is controlled by common genes, but also shows differences which need to be dissected in future genetic experiments. Finally, a maize root view of the eFP browser was implemented including the root hair transcriptome of the present study and several previously published maize root transcriptome data sets. The eFP browser provides color-coded expression levels for these root types and tissues for any gene of interest, thus providing a novel resource to study gene expression and function in maize roots. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.
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1990-01-01
PERFORMED BY: In-house efforts accomplished by Program Executive Officer for Air De - fense Systems, Program Manager-Line of Sight-Forward- Heavy and U.S...evaluation of mechanisms involved in the recovery of heavy metals from waste sludges * (U) Complete determination of basic mechanisms responsible for...tities for characterization " (U) Refined computer model for design of effective heavy metal spin-insensitive EFP war- head liner * (U) Identified
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2009-06-01
Resistant Ambush Protected (MRAP) vehicles, which were designed to withstand an antitank mine (Eisler, 2007). An EFP can penetrate a thickness of armored...These robots weigh less than 100 pounds, are man-portable, and move on small treads with seven speed settings. The TALON is controlled with a...is powered by a two-stroke piston engine and has a steerable nose and main gear, with tires suitable for rough terrain. The Tern utilizes a GPS
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Helicopter/Ship Qualification Testing (Les essais de qualification helicoptere/navire)
2003-02-01
maximum all-up masses of the helicopter; • wind limitations. The data are presented as a polar diagramme , the radius representing the wind speed and the...Systems CAD Cartridge Actuated Device CG Center of Gravity DI Dynamic Interface EFP Elevated Fixed Platform FA Fore Aft FFG Guided Missile Fast Frigate...not be able to complete all the planned data points. The nature of DI testing results in a fast paced test program once flight testing begins. It is
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The RNA-binding protein repertoire of embryonic stem cells.
Kwon, S Chul; Yi, Hyerim; Eichelbaum, Katrin; Föhr, Sophia; Fischer, Bernd; You, Kwon Tae; Castello, Alfredo; Krijgsveld, Jeroen; Hentze, Matthias W; Kim, V Narry
2013-09-01
RNA-binding proteins (RBPs) have essential roles in RNA-mediated gene regulation, and yet annotation of RBPs is limited mainly to those with known RNA-binding domains. To systematically identify the RBPs of embryonic stem cells (ESCs), we here employ interactome capture, which combines UV cross-linking of RBP to RNA in living cells, oligo(dT) capture and MS. From mouse ESCs (mESCs), we have defined 555 proteins constituting the mESC mRNA interactome, including 283 proteins not previously annotated as RBPs. Of these, 68 new RBP candidates are highly expressed in ESCs compared to differentiated cells, implicating a role in stem-cell physiology. Two well-known E3 ubiquitin ligases, Trim25 (also called Efp) and Trim71 (also called Lin41), are validated as RBPs, revealing a potential link between RNA biology and protein-modification pathways. Our study confirms and expands the atlas of RBPs, providing a useful resource for the study of the RNA-RBP network in stem cells.
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Zhang, Baichen; Tolstikov, Vladimir; Turnbull, Colin; Hicks, Leslie M.; Fiehn, Oliver
2010-01-01
Cucurbitaceous plants (cucurbits) have long been preferred models for studying phloem physiology. However, these species are unusual in that they possess two different phloem systems, one within the main vascular bundles [fascicular phloem (FP)] and another peripheral to the vascular bundles and scattered through stem and petiole cortex tissues [extrafascicular phloem (EFP)]. We have revisited the assumption that the sap released after shoot incision originates from the FP, and also investigated the long-standing question of why the sugar content of this sap is ~30-fold less than predicted for requirements of photosynthate delivery. Video microscopy and phloem labeling experiments unexpectedly reveal that FP very quickly becomes blocked upon cutting, whereas the extrafascicular phloem bleeds for extended periods. Thus, all cucurbit phloem sap studies to date have reported metabolite, protein, and RNA composition and transport in the relatively minor extrafascicular sieve tubes. Using tissue dissection and direct sampling of sieve tube contents, we show that FP in fact does contain up to 1 M sugars, in contrast to low-millimolar levels in the EFP. Moreover, major phloem proteins in sieve tubes of FP differ from those that predominate in the extrafascicular sap, and include several previously uncharacterized proteins with little or no homology to databases. The overall compositional differences of the two phloem systems strongly indicate functional isolation. On this basis, we propose that the fascicular phloem is largely responsible for sugar transport, whereas the extrafascicular phloem may function in signaling, defense, and transport of other metabolites. PMID:20566864
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NASA Astrophysics Data System (ADS)
Adamowicz, B.; Miczek, M.; Ikeya, K.; Mutoh, M.; Saitoh, T.; Fujikura, H.; Hasegawa, H.
1999-03-01
The photoluminescence surface state spectroscopy (PLS 3) method was applied to a study of the surface state distribution ( NSS), effective surface recombination velocity ( Seff), electron ( EFn) and hole ( EFp) quasi-Fermi levels and band bending ( VS) on the Al 0.33Ga 0.67As surface air-exposed and passivated by the Si interface control layer (ICL) technique. Using the detailed measurements of the PL quantum efficiency for different excitation intensities, combined with the rigorous computer simulations of the bulk and surface recombination processes, the behavior and correlation among the surface characteristics under photo-excitation was determined. The present analysis indicated that forming of a Si 3N 4/Si ICL double layer (with a monolayer level control) on AlGaAs surface reduces the minimum interface state density down to 10 10 cm -2 eV -1 and surface recombination velocity to the range of 10 4 cm/s under low excitations.
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NASA Astrophysics Data System (ADS)
Miller, Steven David
1999-10-01
A consistent extension of the Oppenheimer-Snyder gravitational collapse formalism is presented which incorporates stochastic, conformal, vacuum fluctuations of the metric tensor. This results in a tractable approach to studying the possible effects of vacuum fluctuations on collapse and singularity formation. The motivation here, is that it is known that coupling stochastic noise to a classical field theory can lead to workable methodologies that accommodate or reproduce many aspects of quantum theory, turbulence or structure formation. The effect of statistically averaging over the metric fluctuations gives the appearance of a deterministic Riemannian structure, with an induced non-vanishing cosmological constant arising from the nonlinearity. The Oppenheimer-Snyder collapse of a perfect fluid or dust star in the fluctuating or `turbulent' spacetime, is reformulated in terms of nonlinear Einstein-Langevin field equations, with an additional noise source in the energy-momentum tensor. The smooth deterministic worldlines of collapsing matter within the classical Oppenheimer-Snyder model, now become nonlinear Brownian motions due to the backreaction induced by vacuum fluctuations. As the star collapses, the matter worldlines become increasingly randomized since the backreaction coupling to the vacuum fluctuations is nonlinear; the input assumptions of the Hawking-Penrose singularity theorems should then be violated. Solving the nonlinear Einstein-Langevin field equation for collapse - via the Ito interpretation - gives a singularity-free solution, which is equivalent to the original Oppenheimer solution but with higher-order stochastic corrections; the original singular solution is recovered in the limit of zero vacuum fluctuations. The `geometro-hydrodynamics' of noisy gravitational collapse, were also translated into an equivalent mathematical formulation in terms of nonlinear Einstein-Fokker-Planck (EFP) continuity equations with respect to comoving coordinates: these describe the collapse as a conserved flow of probability. A solution was found in the dilute limit of weak fluctuations where the EFP equation is linearized. There is zero probability that the star collapses to a singular state in the presence of background vacuum fluctuations, but the singularity returns with unit probability when the fluctuations are reduced to zero. Finally, an EFP equation was considered with respect to standard exterior coordinates. Using the thermal Brownian motion paradigm, an exact stationary or equilibrium solution was found in the infinite standard time relaxation limit. The solution gives the conditions required for the final collapsed object (a black hole) to be in thermal equilibrium with the background vacuum fluctuations. From this solution, one recovers the Hawking temperature without using field theory. The stationary solution then seems to correspond to a black hole in thermal equilibrium with a fluctuating conformal scalar field; or the Hawking-Hartle state.
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Efflux Pump Gene Expression in Multidrug-Resistant Mycobacterium tuberculosis Clinical Isolates
Jiang, Yi; Wei, Jianhao; Zhao, Li-li; Zhao, Xiuqin; Lu, Jianxin; Wan, Kanglin
2015-01-01
Isoniazid (INH) and rifampicin (RIF) are the two most effective drugs in tuberculosis therapy. Understanding the molecular mechanisms of resistance to these two drugs is essential to quickly diagnose multidrug-resistant (MDR) tuberculosis and extensive drug-resistant tuberculosis. Nine clinical Mycobacterium tuberculosis isolates resistant to only INH and RIF and 10 clinical pan-sensitive isolates were included to evaluate the expression of 20 putative drug efflux pump genes and sequence mutations in rpoB (RIF), katG (INH), the inhA promoter (INH), and oxyR-ahpC (INH). Nine and three MDR isolates were induced to overexpress efflux pump genes by INH and RIF, respectively. Eight and two efflux pump genes were induced to overexpress by INH and RIF in MDR isolates, respectively. drrA, drrB, efpA, jefA (Rv2459), mmr, Rv0849, Rv1634, and Rv1250 were overexpressed under INH or RIF stress. Most efflux pump genes were overexpressed under INH stress in a MDR isolates that carried the wild-type katG, inhA, and oxyR-ahpC associated with INH resistance than in those that carried mutations. The expression levels of 11 genes (efpA, Rv0849, Rv1250, P55 (Rv1410c), Rv1634, Rv2994, stp, Rv2459, pstB, drrA, and drrB) without drug inducement were significantly higher (P < 0.05) in nine MDR isolates than in 10 pan-sensitive isolates. In conclusion, efflux pumps may play an important role in INH acquired resistance in MDR M. tuberculosis, especially in those strains having no mutations in genes associated with INH resistance; basal expression levels of some efflux pump genes are higher in MDR isolates than in pan-sensitive isolates and the basal expressional differences may be helpful to diagnose and treat resistant tuberculosis. PMID:25695504
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Wang, Jian; Ben, Weiwei; Yang, Min; Zhang, Yu; Qiang, Zhimin
2016-01-01
Swine feedlots are an important pollution source of antibiotics and antibiotic resistance genes (ARGs) to the environment. This study investigated the dissemination of two classes of commonly-used veterinary antibiotics, namely, tetracyclines (TCs) and sulfonamides (SAs), and their corresponding ARGs along the waste treatment paths from a concentrated swine feedlot located in Beijing, China. The highest total TC and total SA concentrations detected were 166.7mgkg(-1) and 64.5μgkg(-1) in swine manure as well as 388.7 and 7.56μgL(-1) in swine wastewater, respectively. Fourteen tetracycline resistance genes (TRGs) encoding ribosomal protection proteins (RPP), efflux proteins (EFP) and enzymatic inactivation proteins, three sulfonamide resistance genes (SRGs), and two integrase genes were detected along the waste treatment paths with detection frequencies of 33.3-75.0%. The relative abundances of target ARGs ranged from 2.74×10(-6) to 1.19. The antibiotics and ARGs generally declined along both waste treatment paths, but their degree of reduction was more significant along the manure treatment path. The RPP TRGs dominated in the upstream samples and then decreased continuously along both waste treatment paths, whilst the EFP TRGs and SRGs maintained relatively stable. Strong correlations between antibiotic concentrations and ARGs were observed among both manure and wastewater samples. In addition, seasonal temperature, and integrase genes, moisture content and nutrient level of tested samples could all impact the relative abundances of ARGs along the swine waste treatment paths. This study helps understand the evolution and spread of ARGs from swine feedlots to the environment as well as assess the environmental risk arising from swine waste treatment. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Freely Drifting Swallow Float Array: May 1987 Trip Report
1988-05-01
co’-4 v-4~ I00 I.U I6z oJy 2ZIWO Is Y)L Figur X.4x ca C)CD U) Lo Cc r(no _0 I IC VV ~.N L) Figue X. 4bD !K U.n a1 u iP K ( o 0) 1 1(: I.,L Il 4, U ch...La. Pw ~’(rh I y- El - tD Efp KL Cr) -- - If MaIKuOOPzlwO FigreXr)b. -~ jtn x4 a(I-~)WIo u- _0 c ca CO _ -4 I’a) Fic’uX15~ 4-0C es ~ -J-L p -S.7e -f-i
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Nebgen, Benjamin Tyler; Magurudeniya, Harsha D.; Kwock, Kevin Wen Chi; ...
2017-07-18
Molecular dynamics simulations (up to the nanoscale) were performed on the 3-methyl-1-pentylimidazolium ionic liquid cation paired with three anions; chloride, nitrate, and thiocyanate as aqueous mixtures, using the effective fragment potential (EFP) method, a computationally inexpensive way of modeling intermolecular interactions. The simulations provided insight (preferred geometries, radial distribution functions and theoretical proton NMR resonances) into the interactions within the ionic domain and are validated against 1H NMR spectroscopy and small- and wide-angle X-ray scattering experiments on 1-decyl-3-methylimidazolium. Ionic liquids containing thiocyanate typically resist gelation and form poorly ordered lamellar structures upon mixing with water. Conversely, chloride, a strongly coordinatingmore » anion, normally forms strong physical gels and produces well-ordered nanostructures adopting a variety of structural motifs over a very wide range of water compositions. Nitrate is intermediate in character, whereby upon dispersal in water it displays a range of viscosities and self-assembles into nanostructures with considerable variability in the fidelity of ordering and symmetry, as a function of water content in the binary mixtures. The observed changes in the macro and nanoscale characteristics were directly correlated to ionic domain structures and intermolecular interactions as theoretically predicted by the analysis of MD trajectories and calculated RDFs. Specifically, both chloride and nitrate are positioned in the plane of the cation. Anion to cation proximity is dependent on water content. Thiocyanate is more susceptible to water insertion into the second solvent shell. Experimental 1H NMR chemical shifts monitor the site-specific competition dependence with water content in the binary mixtures. As a result, thiocyanate preferentially sits above and below the aromatic ring plane, a state disallowing interaction with the protons on the imidazolium ring.« less
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Nebgen, Benjamin T; Magurudeniya, Harsha D; Kwock, Kevin W C; Ringstrand, Bryan S; Ahmed, Towfiq; Seifert, Sönke; Zhu, Jian-Xin; Tretiak, Sergei; Firestone, Millicent A
2017-12-14
Molecular dynamics simulations (up to the nanoscale) were performed on the 3-methyl-1-pentylimidazolium ionic liquid cation paired with three anions; chloride, nitrate, and thiocyanate as aqueous mixtures, using the effective fragment potential (EFP) method, a computationally inexpensive way of modeling intermolecular interactions. The simulations provided insight (preferred geometries, radial distribution functions and theoretical proton NMR resonances) into the interactions within the ionic domain and are validated against 1 H NMR spectroscopy and small- and wide-angle X-ray scattering experiments on 1-decyl-3-methylimidazolium. Ionic liquids containing thiocyanate typically resist gelation and form poorly ordered lamellar structures upon mixing with water. Conversely, chloride, a strongly coordinating anion, normally forms strong physical gels and produces well-ordered nanostructures adopting a variety of structural motifs over a very wide range of water compositions. Nitrate is intermediate in character, whereby upon dispersal in water it displays a range of viscosities and self-assembles into nanostructures with considerable variability in the fidelity of ordering and symmetry, as a function of water content in the binary mixtures. The observed changes in the macro and nanoscale characteristics were directly correlated to ionic domain structures and intermolecular interactions as theoretically predicted by the analysis of MD trajectories and calculated RDFs. Specifically, both chloride and nitrate are positioned in the plane of the cation. Anion to cation proximity is dependent on water content. Thiocyanate is more susceptible to water insertion into the second solvent shell. Experimental 1 H NMR chemical shifts monitor the site-specific competition dependence with water content in the binary mixtures. Thiocyanate preferentially sits above and below the aromatic ring plane, a state disallowing interaction with the protons on the imidazolium ring.
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Mandal, Ajeet; Mandal, Swati; Park, Myung Hee
2014-01-01
The eukaryotic translation factor, eIF5A has been recently reported as a sequence-specific elongation factor that facilitates peptide bond formation at consecutive prolines in Saccharomyces cerevisiae, as its ortholog elongation factor P (EF-P) does in bacteria. We have searched the genome databases of 35 representative organisms from six kingdoms of life for PPP (Pro-Pro-Pro) and/or PPG (Pro-Pro-Gly)-encoding genes whose expression is expected to depend on eIF5A. We have made detailed analyses of proteome data of 5 selected species, Escherichia coli, Saccharomyces cerevisiae, Drosophila melanogaster, Mus musculus and Homo sapiens. The PPP and PPG motifs are low in the prokaryotic proteomes. However, their frequencies markedly increase with the biological complexity of eukaryotic organisms, and are higher in newly derived proteins than in those orthologous proteins commonly shared in all species. Ontology classifications of S. cerevisiae and human genes encoding the highest level of polyprolines reveal their strong association with several specific biological processes, including actin/cytoskeletal associated functions, RNA splicing/turnover, DNA binding/transcription and cell signaling. Previously reported phenotypic defects in actin polarity and mRNA decay of eIF5A mutant strains are consistent with the proposed role for eIF5A in the translation of the polyproline-containing proteins. Of all the amino acid tandem repeats (≥3 amino acids), only the proline repeat frequency correlates with functional complexity of the five organisms examined. Taken together, these findings suggest the importance of proline repeat-rich proteins and a potential role for eIF5A and its hypusine modification pathway in the course of eukaryotic evolution. PMID:25364902
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Acute Stress Affects the Expression of Hippocampal Mu Oscillations in an Age-Dependent Manner
Takillah, Samir; Naudé, Jérémie; Didienne, Steve; Sebban, Claude; Decros, Brigitte; Schenker, Esther; Spedding, Michael; Mourot, Alexandre; Mariani, Jean; Faure, Philippe
2017-01-01
Anxiolytic drugs are widely used in the elderly, a population particularly sensitive to stress. Stress, aging and anxiolytics all affect low-frequency oscillations in the hippocampus and prefrontal cortex (PFC) independently, but the interactions between these factors remain unclear. Here, we compared the effects of stress (elevated platform, EP) and anxiolytics (diazepam, DZP) on extracellular field potentials (EFP) in the PFC, parietal cortex and hippocampus (dorsal and ventral parts) of adult (8 months) and aged (18 months) Wistar rats. A potential source of confusion in the experimental studies in rodents comes from locomotion-related theta (6–12 Hz) oscillations, which may overshadow the direct effects of anxiety on low-frequency and especially on the high-amplitude oscillations in the Mu range (7–12 Hz), related to arousal. Animals were restrained to avoid any confound and isolate the direct effects of stress from theta oscillations related to stress-induced locomotion. We identified transient, high-amplitude oscillations in the 7–12 Hz range (“Mu-bursts”) in the PFC, parietal cortex and only in the dorsal part of hippocampus. At rest, aged rats displayed more Mu-bursts than adults. Stress acted differently on Mu-bursts depending on age: it increases vs. decreases burst, in adult and aged animals, respectively. In contrast DZP (1 mg/kg) acted the same way in stressed adult and age animal: it decreased the occurrence of Mu-bursts, as well as their co-occurrence. This is consistent with DZP acting as a positive allosteric modulator of GABAA receptors, which globally potentiates inhibition and has anxiolytic effects. Overall, the effect of benzodiazepines on stressed animals was to restore Mu burst activity in adults but to strongly diminish them in aged rats. This work suggests Mu-bursts as a neural marker to study the impact of stress and DZP on age. PMID:29033825
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The on-orbit calibration of geometric parameters of the Tian-Hui 1 (TH-1) satellite
NASA Astrophysics Data System (ADS)
Wang, Jianrong; Wang, Renxiang; Hu, Xin; Su, Zhongbo
2017-02-01
The on-orbit calibration of geometric parameters is a key step in improving the location accuracy of satellite images without using Ground Control Points (GCPs). Most methods of on-orbit calibration are based on the self-calibration using additional parameters. When using additional parameters, different number of additional parameters may lead to different results. The triangulation bundle adjustment is another way to calibrate the geometric parameters of camera, which can describe the changes in each geometric parameter. When triangulation bundle adjustment method is applied to calibrate geometric parameters, a prerequisite is that the strip model can avoid systematic deformation caused by the rate of attitude changes. Concerning the stereo camera, the influence of the intersection angle should be considered during calibration. The Equivalent Frame Photo (EFP) bundle adjustment based on the Line-Matrix CCD (LMCCD) image can solve the systematic distortion of the strip model, and obtain high accuracy location without using GCPs. In this paper, the triangulation bundle adjustment is used to calibrate the geometric parameters of TH-1 satellite cameras based on LMCCD image. During the bundle adjustment, the three-line array cameras are reconstructed by adopting the principle of inverse triangulation. Finally, the geometric accuracy is validated before and after on-orbit calibration using 5 testing fields. After on-orbit calibration, the 3D geometric accuracy is improved to 11.8 m from 170 m. The results show that the location accuracy of TH-1 without using GCPs is significantly improved using the on-orbit calibration of the geometric parameters.
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Identification and Herc5-mediated ISGylation of novel target proteins.
Takeuchi, Tomoharu; Inoue, Satoshi; Yokosawa, Hideyoshi
2006-09-22
ISG15, a protein containing two ubiquitin-like domains, is an interferon-stimulated gene product that functions in antiviral response and is conjugated to various cellular proteins (ISGylation) upon interferon stimulation. ISGylation occurs via a pathway similar to the pathway for ubiquitination that requires the sequential action of E1/E2/E3: the E1 (UBE1L), E2 (UbcH8), and E3 (Efp/Herc5) enzymes for ISGylation have been hitherto identified. In this study, we identified six novel candidate target proteins for ISGylation by a proteomic approach. Four candidate target proteins were demonstrated to be ISGylated in UBE1L- and UbcH8-dependent manners, and ISGylation of the respective target proteins was stimulated by Herc5. In addition, Herc5 was capable of binding with the respective target proteins. Thus, these results suggest that Herc5 functions as a general E3 ligase for protein ISGylation.
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An EEG Finger-Print of fMRI deep regional activation.
Meir-Hasson, Yehudit; Kinreich, Sivan; Podlipsky, Ilana; Hendler, Talma; Intrator, Nathan
2014-11-15
This work introduces a general framework for producing an EEG Finger-Print (EFP) which can be used to predict specific brain activity as measured by fMRI at a given deep region. This new approach allows for improved EEG spatial resolution based on simultaneous fMRI activity measurements. Advanced signal processing and machine learning methods were applied on EEG data acquired simultaneously with fMRI during relaxation training guided by on-line continuous feedback on changing alpha/theta EEG measure. We focused on demonstrating improved EEG prediction of activation in sub-cortical regions such as the amygdala. Our analysis shows that a ridge regression model that is based on time/frequency representation of EEG data from a single electrode, can predict the amygdala related activity significantly better than a traditional theta/alpha activity sampled from the best electrode and about 1/3 of the times, significantly better than a linear combination of frequencies with a pre-defined delay. The far-reaching goal of our approach is to be able to reduce the need for fMRI scanning for probing specific sub-cortical regions such as the amygdala as the basis for brain-training procedures. On the other hand, activity in those regions can be characterized with higher temporal resolution than is obtained by fMRI alone thus revealing additional information about their processing mode. Copyright © 2013 Elsevier Inc. All rights reserved.
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HSIAO, Chien-Yu; CHEN, Yi-Ming; HSU, Yi-Ju; HUANG, Chi-Chang; SUNG, Hsin-Ching; CHEN, Sheng-Shih
2017-01-01
Hualian No. 4 wild bitter gourd (WBG) is a specific vegetable cultivated by the Hualien District Agricultural Research and Extension Station in Taiwan. WBG is commonly consumed as a vegetable and used as a popular folk medicine. However, few studies have demonstrated the effects of WBG supplementation on exercise performance, physical fatigue and the biochemical profile. The purpose of this study was to evaluate the potential beneficial effects of WBG extract on fatigue and ergogenic functions following physiological challenge. Three groups of male ICR mice (n=8 per group) were orally administered 0, 1 or 2.5 g/kg/day of WBG for 4 weeks. They were respectively designated the vehicle, WBG-1X and WBG-2.5X groups. WBG significantly decreased body weight (BW) and epididymal fat pad (EFP) weight. Concerning physical performance, WBG supplementation dose-dependently increased grip strength and endurance swimming time. Concerning anti-fatigue activity, WBG decreased levels of serum lactate, ammonia, creatine kinase and blood urea nitrogen, and economized glucose metabolism after acute exercise challenge. Glycogen in the liver and gastrocnemius muscle dose-dependently increased with WBG treatment. Concerning the biochemical profile, WBG treatment significantly decreased alanine aminotransferase (ALT), blood urea nitrogen (BUN) and urea acid (UA), and increased total protein (TP). Therefore, 4-week supplementation with WBG may decrease white adipose weight, enhance energy economy, increase glycogen storage to enhance exercise performance and reduce fatigue. PMID:28458274
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Improvised explosive devices: pathophysiology, injury profiles and current medical management.
Ramasamy, A; Hill, A M; Clasper, J C
2009-12-01
The improvised explosive device (IED), in all its forms, has become the most significant threat to troops operating in Afghanistan and Iraq. These devices range from rudimentary home made explosives to sophisticated weapon systems containing high-grade explosives. Within this broad definition they may be classified as roadside explosives and blast mines, explosive formed pojectile (EFP) devices and suicide bombings. Each of these groups causeinjury through a number of different mechanisms and can result in vastly different injury profiles. The "Global War on Terror" has meant that incidents which were previously exclusively seen in conflict areas, can occur anywhere, and clinicians who are involved in emergency trauma care may be required to manage casualties from similar terrorist attacks. An understanding of the types of devices and their pathophysiological effects is necessary to allow proper planning of mass casualty events and to allow appropriate management of the complex poly-trauma casualties they invariably cause. The aim of this review article is to firstly describe the physics and injury profile from these different devices and secondly to present the current clinical evidence that underpins their medical management.
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SoyFN: a knowledge database of soybean functional networks.
Xu, Yungang; Guo, Maozu; Liu, Xiaoyan; Wang, Chunyu; Liu, Yang
2014-01-01
Many databases for soybean genomic analysis have been built and made publicly available, but few of them contain knowledge specifically targeting the omics-level gene-gene, gene-microRNA (miRNA) and miRNA-miRNA interactions. Here, we present SoyFN, a knowledge database of soybean functional gene networks and miRNA functional networks. SoyFN provides user-friendly interfaces to retrieve, visualize, analyze and download the functional networks of soybean genes and miRNAs. In addition, it incorporates much information about KEGG pathways, gene ontology annotations and 3'-UTR sequences as well as many useful tools including SoySearch, ID mapping, Genome Browser, eFP Browser and promoter motif scan. SoyFN is a schema-free database that can be accessed as a Web service from any modern programming language using a simple Hypertext Transfer Protocol call. The Web site is implemented in Java, JavaScript, PHP, HTML and Apache, with all major browsers supported. We anticipate that this database will be useful for members of research communities both in soybean experimental science and bioinformatics. Database URL: http://nclab.hit.edu.cn/SoyFN.
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G Caton, Jack; Armitage, Gary; Berglundh, Tord; Chapple, Iain L C; Jepsen, Søren; S Kornman, Kenneth; L Mealey, Brian; Papapanou, Panos N; Sanz, Mariano; S Tonetti, Maurizio
2018-06-01
A classification scheme for periodontal and peri-implant diseases and conditions is necessary for clinicians to properly diagnose and treat patients as well as for scientists to investigate etiology, pathogenesis, natural history, and treatment of the diseases and conditions. This paper summarizes the proceedings of the World Workshop on the Classification of Periodontal and Peri-implant Diseases and Conditions. The workshop was co-sponsored by the American Academy of Periodontology (AAP) and the European Federation of Periodontology (EFP) and included expert participants from all over the world. Planning for the conference, which was held in Chicago on November 9 to 11, 2017, began in early 2015. An organizing committee from the AAP and EFP commissioned 19 review papers and four consensus reports covering relevant areas in periodontology and implant dentistry. The authors were charged with updating the 1999 classification of periodontal diseases and conditions and developing a similar scheme for peri-implant diseases and conditions. Reviewers and workgroups were also asked to establish pertinent case definitions and to provide diagnostic criteria to aid clinicians in the use of the new classification. All findings and recommendations of the workshop were agreed to by consensus. This introductory paper presents an overview for the new classification of periodontal and peri-implant diseases and conditions, along with a condensed scheme for each of four workgroup sections, but readers are directed to the pertinent consensus reports and review papers for a thorough discussion of the rationale, criteria, and interpretation of the proposed classification. Changes to the 1999 classification are highlighted and discussed. Although the intent of the workshop was to base classification on the strongest available scientific evidence, lower level evidence and expert opinion were inevitably used whenever sufficient research data were unavailable. The scope of this workshop was to align and update the classification scheme to the current understanding of periodontal and peri-implant diseases and conditions. This introductory overview presents the schematic tables for the new classification of periodontal and peri-implant diseases and conditions and briefly highlights changes made to the 1999 classification. It cannot present the wealth of information included in the reviews, case definition papers, and consensus reports that has guided the development of the new classification, and reference to the consensus and case definition papers is necessary to provide a thorough understanding of its use for either case management or scientific investigation. Therefore, it is strongly recommended that the reader use this overview as an introduction to these subjects. Accessing this publication online will allow the reader to use the links in this overview and the tables to view the source papers (Table ). © 2018 American Academy of Periodontology and European Federation of Periodontology.
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G Caton, Jack; Armitage, Gary; Berglundh, Tord; Chapple, Iain L C; Jepsen, Søren; S Kornman, Kenneth; L Mealey, Brian; Papapanou, Panos N; Sanz, Mariano; S Tonetti, Maurizio
2018-06-01
A classification scheme for periodontal and peri-implant diseases and conditions is necessary for clinicians to properly diagnose and treat patients as well as for scientists to investigate etiology, pathogenesis, natural history, and treatment of the diseases and conditions. This paper summarizes the proceedings of the World Workshop on the Classification of Periodontal and Peri-implant Diseases and Conditions. The workshop was co-sponsored by the American Academy of Periodontology (AAP) and the European Federation of Periodontology (EFP) and included expert participants from all over the world. Planning for the conference, which was held in Chicago on November 9 to 11, 2017, began in early 2015. An organizing committee from the AAP and EFP commissioned 19 review papers and four consensus reports covering relevant areas in periodontology and implant dentistry. The authors were charged with updating the 1999 classification of periodontal diseases and conditions and developing a similar scheme for peri-implant diseases and conditions. Reviewers and workgroups were also asked to establish pertinent case definitions and to provide diagnostic criteria to aid clinicians in the use of the new classification. All findings and recommendations of the workshop were agreed to by consensus. This introductory paper presents an overview for the new classification of periodontal and peri-implant diseases and conditions, along with a condensed scheme for each of four workgroup sections, but readers are directed to the pertinent consensus reports and review papers for a thorough discussion of the rationale, criteria, and interpretation of the proposed classification. Changes to the 1999 classification are highlighted and discussed. Although the intent of the workshop was to base classification on the strongest available scientific evidence, lower level evidence and expert opinion were inevitably used whenever sufficient research data were unavailable. The scope of this workshop was to align and update the classification scheme to the current understanding of periodontal and peri-implant diseases and conditions. This introductory overview presents the schematic tables for the new classification of periodontal and peri-implant diseases and conditions and briefly highlights changes made to the 1999 classification. It cannot present the wealth of information included in the reviews, case definition papers, and consensus reports that has guided the development of the new classification, and reference to the consensus and case definition papers is necessary to provide a thorough understanding of its use for either case management or scientific investigation. Therefore, it is strongly recommended that the reader use this overview as an introduction to these subjects. Accessing this publication online will allow the reader to use the links in this overview and the tables to view the source papers (Table 1). © 2018 American Academy of Periodontology and European Federation of Periodontology.
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2012-01-01
Background The molecular mechanisms altered by the traditional mutation and screening approach during the improvement of antibiotic-producing microorganisms are still poorly understood although this information is essential to design rational strategies for industrial strain improvement. In this study, we applied comparative genomics to identify all genetic changes occurring during the development of an erythromycin overproducer obtained using the traditional mutate-and- screen method. Results Compared with the parental Saccharopolyspora erythraea NRRL 2338, the genome of the overproducing strain presents 117 deletion, 78 insertion and 12 transposition sites, with 71 insertion/deletion sites mapping within coding sequences (CDSs) and generating frame-shift mutations. Single nucleotide variations are present in 144 CDSs. Overall, the genomic variations affect 227 proteins of the overproducing strain and a considerable number of mutations alter genes of key enzymes in the central carbon and nitrogen metabolism and in the biosynthesis of secondary metabolites, resulting in the redirection of common precursors toward erythromycin biosynthesis. Interestingly, several mutations inactivate genes coding for proteins that play fundamental roles in basic transcription and translation machineries including the transcription anti-termination factor NusB and the transcription elongation factor Efp. These mutations, along with those affecting genes coding for pleiotropic or pathway-specific regulators, affect global expression profile as demonstrated by a comparative analysis of the parental and overproducer expression profiles. Genomic data, finally, suggest that the mutate-and-screen process might have been accelerated by mutations in DNA repair genes. Conclusions This study helps to clarify the mechanisms underlying antibiotic overproduction providing valuable information about new possible molecular targets for rationale strain improvement. PMID:22401291
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Identifing Atmospheric Pollutant Sources Using Artificial Neural Networks
NASA Astrophysics Data System (ADS)
Paes, F. F.; Campos, H. F.; Luz, E. P.; Carvalho, A. R.
2008-05-01
The estimation of the area source pollutant strength is a relevant issue for atmospheric environment. This characterizes an inverse problem in the atmospheric pollution dispersion. In the inverse analysis, an area source domain is considered, where the strength of such area source term is assumed unknown. The inverse problem is solved by using a supervised artificial neural network: multi-layer perceptron. The conection weights of the neural network are computed from delta rule - learning process. The neural network inversion is compared with results from standard inverse analysis (regularized inverse solution). In the regularization method, the inverse problem is formulated as a non-linear optimization approach, whose the objective function is given by the square difference between the measured pollutant concentration and the mathematical models, associated with a regularization operator. In our numerical experiments, the forward problem is addressed by a source-receptor scheme, where a regressive Lagrangian model is applied to compute the transition matrix. The second order maximum entropy regularization is used, and the regularization parameter is calculated by the L-curve technique. The objective function is minimized employing a deterministic scheme (a quasi-Newton algorithm) [1] and a stochastic technique (PSO: particle swarm optimization) [2]. The inverse problem methodology is tested with synthetic observational data, from six measurement points in the physical domain. The best inverse solutions were obtained with neural networks. References: [1] D. R. Roberti, D. Anfossi, H. F. Campos Velho, G. A. Degrazia (2005): Estimating Emission Rate and Pollutant Source Location, Ciencia e Natura, p. 131-134. [2] E.F.P. da Luz, H.F. de Campos Velho, J.C. Becceneri, D.R. Roberti (2007): Estimating Atmospheric Area Source Strength Through Particle Swarm Optimization. Inverse Problems, Desing and Optimization Symposium IPDO-2007, April 16-18, Miami (FL), USA, vol 1, p. 354-359.
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Chen, Yi-Ming; Lin, Che-Li; Wei, Li; Hsu, Yi-Ju; Chen, Kuan-Neng; Huang, Chi-Chang; Kao, Chin-Hsung
2016-01-01
Exercise and fitness training programs have attracted the public’s attention in recent years. Sports nutrition supplementation is an important issue in the global sports market. Purpose: In this study, we designed a power exercise training (PET) program with a mouse model based on a strength and conditional training protocol for humans. We tested the effect of supplementation with functional branched-chain amino acid (BCAA)-rich sake protein (SP) to determine whether the supplement had a synergistic effect during PET and enhanced athletic performance and resistance to fatigue. Methods: Male ICR mice were divided into three groups (n = 8 per group) for four-week treatment: sedentary controls with vehicle (SC), and PET and PET groups with SP supplementation (3.8 g/kg, PET + SP). Exercise performance was evaluated by forelimb grip strength and exhaustive swimming time as well as changes in body composition and anti-fatigue activity levels of serum lactate, ammonia, glucose, and creatine kinase (CK) after a 15-min swimming exercise. The biochemical parameters were measured at the end of the experiment. Results: four-week PET significantly increased grip strength and exhaustive swimming time and decreased epididymal fat pad (EFP) weight and area. Levels of aspartate aminotransferase (AST), alanine aminotransferase (ALT), creatinine, and uric acid (UA) were significantly increased. PET + SP supplementation significantly decreased serum lactate, ammonia and CK levels after the 15-min swimming exercise. The resting serum levels of AST, ALT, CREA and UA were all significantly decreased with PET + SP. Conclusion: The PET program could increase the exercise performance and modulate the body composition of mice. PET with SP conferred better anti-fatigue activity, improved biochemical profiles, and may be an effective ergogenic aid in strength training. PMID:26907336
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Correlation Between Cometary Gas/Dust Ratios and Heliocentric Distance
NASA Astrophysics Data System (ADS)
Harrington, Olga; Womack, Maria; Lastra, Nathan
2017-10-01
We compiled CO-based gas/dust ratios for several comets out to heliocentric distances, rh, of 8 au to probe whether there is a noticeable change in comet behavior over the range that water-ice sublimation starts. Previously, gas/dust ratios were calculated for an ensemble of comets using Q(CO2)/efp values derived from infrared measurements, which showed that the gas/dust ratio follows a rh-2 within 4 AU, but is flat at greater distances (Bauer et al. 2015). Our project focuses on gas/dust ratios for which CO is assumed to be the dominant gas, in order to test whether similar breaks in slope occur for CO. The gas/dust ratios were calculated from measurements of CO production rates (mostly from millimeter-wavelength spectroscopy) and reflected sunlight of comets (mostly via reported visual magnitudes of dusty comets). We present our new CO-based gas/dust ratios at different heliocentric distances, compare them to existing CO2-based gas/dust ratios, and discuss implications for CO-driven and CO2-driven activity. We discuss O.H. acknowledges support from the Hartmann Student Travel Grant program. M.W. acknowledges support from NSF grant AST-1615917.
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Comparative proteomic analysis of outer membrane protein 43 (omp43)-deficient Bartonella henselae.
Kang, Jun-Gu; Lee, Hee-Woo; Ko, Sungjin; Chae, Joon-Seok
2018-01-31
Outer membrane proteins (OMPs) of Gram-negative bacteria constitute the first line of defense protecting cells against environmental stresses including chemical, biophysical, and biological attacks. Although the 43-kDa OMP (OMP43) is major porin protein among Bartonella henselae -derived OMPs, its function remains unreported. In this study, OMP43-deficient mutant B. henselae (Δomp43) was generated to investigate OMP43 function. Interestingly, Δ omp 43 exhibited weaker proliferative ability than that of wild-type (WT) B. henselae . To study the differences in proteomic expression between WT and Δ omp 43, two-dimensional gel electrophoresis-based proteomic analysis was performed. Based on Clusters of Orthologus Groups functional assignments, 12 proteins were associated with metabolism, 7 proteins associated with information storage and processing, and 3 proteins associated with cellular processing and signaling. By semi-quantitative reverse transcriptase polymerase chain reaction, increases in tld D, efp, ntr X, pdh A, pur B, and ATPA mRNA expression and decreases in Rho and yfe A mRNA expression were confirmed in Δ omp 43. In conclusion, this is the first report showing that a loss of OMP43 expression in B. henselae leads to retarded proliferation. Furthermore, our proteomic data provide useful information for the further investigation of mechanisms related to the growth of B. henselae.
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Dissecting limiting factors of the Protein synthesis Using Recombinant Elements (PURE) system
Li, Jun; Zhang, Chi; Huang, Poyi; Kuru, Erkin; Forster-Benson, Eliot T. C.; Church, George M.
2017-01-01
ABSTRACT Reconstituted cell-free protein synthesis systems such as the Protein synthesis Using Recombinant Elements (PURE) system give high-throughput and controlled access to in vitro protein synthesis. Here we show that compared with the commercial S30 crude extract based RTS 100 E. coli HY system, the PURE system has less mRNA degradation and produces up to ∼6-fold full-length proteins. However the majority of polypeptides PURE produces are partially translated or inactive since the signal from firefly luciferase (Fluc) translated in PURE is only ∼2/3rd of that measured using the RTS 100 E. coli HY S30 system. Both of the 2 batch systems suffer from low ribosome recycling efficiency when translating proteins from 82 kD to 224 kD. A systematic fed-batch analysis of PURE shows replenishment of 6 small molecule substrates individually or in combination before energy depletion increased Fluc protein yield by ∼1.5 to ∼2-fold, while creatine phosphate and magnesium have synergistic effects when added to the PURE system. Additionally, while adding EF-P to PURE reduced full-length protein translated, it increased the fraction of functional protein and reduced partially translated protein probably by slowing down the translation process. Finally, ArfA, rather than YaeJ or PrfH, helped reduce ribosome stalling when translating Fluc and improved system productivity in a template-dependent fashion. PMID:28702280
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Crystal structure of the TRIM25 B30.2 (PRYSPRY) domain: a key component of antiviral signalling.
D'Cruz, Akshay A; Kershaw, Nadia J; Chiang, Jessica J; Wang, May K; Nicola, Nicos A; Babon, Jeffrey J; Gack, Michaela U; Nicholson, Sandra E
2013-12-01
TRIM (tripartite motif) proteins primarily function as ubiquitin E3 ligases that regulate the innate immune response to infection. TRIM25 [also known as Efp (oestrogen-responsive finger protein)] has been implicated in the regulation of oestrogen receptor α signalling and in the regulation of innate immune signalling via RIG-I (retinoic acid-inducible gene-I). RIG-I senses cytosolic viral RNA and is subsequently ubiquitinated by TRIM25 at its N-terminal CARDs (caspase recruitment domains), leading to type I interferon production. The interaction with RIG-I is dependent on the TRIM25 B30.2 domain, a protein-interaction domain composed of the PRY and SPRY tandem sequence motifs. In the present study we describe the 1.8 Å crystal structure of the TRIM25 B30.2 domain, which exhibits a typical B30.2/SPRY domain fold comprising two N-terminal α-helices, thirteen β-strands arranged into two β-sheets and loop regions of varying lengths. A comparison with other B30.2/SPRY structures and an analysis of the loop regions identified a putative binding pocket, which is likely to be involved in binding target proteins. This was supported by mutagenesis and functional analyses, which identified two key residues (Asp(488) and Trp(621)) in the TRIM25 B30.2 domain as being critical for binding to the RIG-I CARDs.
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Crystal structure of the TRIM25 B30.2 (PRYSPRY) domain: a key component of antiviral signalling
D'Cruz, Akshay A.; Kershaw, Nadia J.; Chiang, Jessica J.; Wang, May K.; Nicola, Nicos A.; Babon, Jeffrey J.; Gack, Michaela U.; Nicholson, Sandra E.
2014-01-01
TRIM (tripartite motif) proteins primarily function as ubiquitin E3 ligases that regulate the innate immune response to infection. TRIM25 [also known as Efp (oestrogen-responsive finger protein)] has been implicated in the regulation of oestrogen receptor α signalling and in the regulation of innate immune signalling via RIG-I (retinoic acid-inducible gene-I). RIG-I senses cytosolic viral RNA and is subsequently ubiquitinated by TRIM25 at its N-terminal CARDs (caspase recruitment domains), leading to type I interferon production. The interaction with RIG-I is dependent on the TRIM25 B30.2 domain, a protein-interaction domain composed of the PRY and SPRY tandem sequence motifs. In the present study we describe the 1.8 Å crystal structure of the TRIM25 B30.2 domain, which exhibits a typical B30.2/SPRY domain fold comprising two N-terminal α-helices, thirteen β-strands arranged into two β-sheets and loop regions of varying lengths. A comparison with other B30.2/SPRY structures and an analysis of the loop regions identified a putative binding pocket, which is likely to be involved in binding target proteins. This was supported by mutagenesis and functional analyses, which identified two key residues (Asp488 and Trp621) in the TRIM25 B30.2 domain as being critical for binding to the RIG-I CARDs. PMID:24015671
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Dissecting limiting factors of the Protein synthesis Using Recombinant Elements (PURE) system
DOE Office of Scientific and Technical Information (OSTI.GOV)
Li, Jun; Zhang, Chi; Huang, Poyi
Reconstituted cell-free protein synthesis systems such as the Protein synthesis Using Recombinant Elements (PURE) system give high-throughput and controlled access to in vitro protein synthesis. Here we show that compared with the commercial S30 crude extract based RTS 100 E. coli HY system, the PURE system has less mRNA degradation and produces up to ~6-fold full-length proteins. However the majority of polypeptides PURE produces are partially translated or inactive since the signal from firefly luciferase (Fluc) translated in PURE is only ~2/3 rd of that measured using the RTS 100 E. coli HY S30 system. Both of the 2 batchmore » systems suffer from low ribosome recycling efficiency when translating proteins from 82 k D to 224 k D. A systematic fed-batch analysis of PURE shows replenishment of 6 small molecule substrates individually or in combination before energy depletion increased Fluc protein yield by ~1.5 to ~2-fold, while creatine phosphate and magnesium have synergistic effects when added to the PURE system. Additionally, while adding EF-P to PURE reduced full-length protein translated, it increased the fraction of functional protein and reduced partially translated protein probably by slowing down the translation process. Finally, ArfA, rather than YaeJ or PrfH, helped reduce ribosome stalling when translating Fluc and improved system productivity in a template-dependent fashion.« less
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Champoiseau, P; Daugrois, J-H; Pieretti, I; Cociancich, S; Royer, M; Rott, P
2006-10-01
ABSTRACT Pathogenicity of 75 strains of Xanthomonas albilineans from Guadeloupe was assessed by inoculation of sugarcane cv. B69566, which is susceptible to leaf scald, and 19 of the strains were selected as representative of the variation in pathogenicity observed based on stalk colonization. In vitro production of albicidin varied among these 19 strains, but the restriction fragment length polymorphism pattern of their albicidin biosynthesis genes was identical. Similarly, no genomic variation was found among strains by pulsed-field gel electrophoresis. Some variation among strains was found by amplified fragment length polymorphism, but no relationship between this genetic variation and variation in pathogenicity was found. Only 3 (pilB, rpfA, and xpsE) of 40 genes involved in pathogenicity of bacterial species closely related to X. albilineans could be amplified by polymerase chain reaction from total genomic DNA of all nine strains tested of X. albilineans differing in pathogenicity in Guadeloupe. Nucleotide sequences of these genes were 100% identical among strains, and a phylogenetic study with these genes and housekeeping genes efp and ihfA suggested that X. albilineans is on an evolutionary road between the X. campestris group and Xylella fastidiosa, another vascular plant pathogen. Sequencing of the complete genome of Xanthomonas albilineans could be the next step in deciphering molecular mechanisms involved in pathogenicity of X. albilineans.
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Dissecting limiting factors of the Protein synthesis Using Recombinant Elements (PURE) system
Li, Jun; Zhang, Chi; Huang, Poyi; ...
2017-05-09
Reconstituted cell-free protein synthesis systems such as the Protein synthesis Using Recombinant Elements (PURE) system give high-throughput and controlled access to in vitro protein synthesis. Here we show that compared with the commercial S30 crude extract based RTS 100 E. coli HY system, the PURE system has less mRNA degradation and produces up to ~6-fold full-length proteins. However the majority of polypeptides PURE produces are partially translated or inactive since the signal from firefly luciferase (Fluc) translated in PURE is only ~2/3 rd of that measured using the RTS 100 E. coli HY S30 system. Both of the 2 batchmore » systems suffer from low ribosome recycling efficiency when translating proteins from 82 k D to 224 k D. A systematic fed-batch analysis of PURE shows replenishment of 6 small molecule substrates individually or in combination before energy depletion increased Fluc protein yield by ~1.5 to ~2-fold, while creatine phosphate and magnesium have synergistic effects when added to the PURE system. Additionally, while adding EF-P to PURE reduced full-length protein translated, it increased the fraction of functional protein and reduced partially translated protein probably by slowing down the translation process. Finally, ArfA, rather than YaeJ or PrfH, helped reduce ribosome stalling when translating Fluc and improved system productivity in a template-dependent fashion.« less
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Boudon, Sylvain; Manceau, Charles; Nottéghem, Jean-Loup
2005-09-01
ABSTRACT Xanthomonas arboricola pv. pruni, the causal agent of bacterial spot on stone fruit, was found in 1995 in several orchards in southeastern France. We studied population genetics of this emerging pathogen in comparison with populations from the United States, where the disease was first described, and from Italy, where the disease has occurred since 1920. Four housekeeping genes (atpD, dnaK, efp, and glnA) and the intergenic transcribed spacer region were sequenced from a total of 3.9 kb of sequences, and fluorescent amplified fragment length polymorphism (FAFLP) analysis was performed. A collection of 64 X. arboricola pv. pruni strains, including 23 strains from France, was analyzed. The X. arboricola pv. pruni population had a low diversity because no sequence polymorphisms were observed. Population diversity revealed by FAFLP was lower for the West European population than for the American population. The same bacterial genotype was detected from five countries on three continents, a geographic distribution that can be explained by human-aided migration of bacteria. Our data support the hypothesis that the pathogen originated in the United States and subsequently has been disseminated to other stone-fruit-growing regions of the world. In France, emergence of this disease was due to a recent introduction of the most prevalent genotype of the bacterium found worldwide.
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Chen, Li-Han; Chien, Yi-Wen; Liang, Chung-Tiang; Chan, Ching-Hung; Fan, Meng-Han; Huang, Hui-Yu
2017-01-01
Background: A wealth of research has reported on the anti-obesity effects of green tea extract (GTE). Although browning of white adipose tissue (WAT) has been reported to attenuate obesity, no study has disclosed the effects of GTE on browning in Sprague Dawley rats. Objectives: The aims of the study were to investigate the effects of GTE on anti-obesity and browning, and their underlying mechanisms. Methods: Four groups of rats (n=10/group) were used including a normal diet with vehicle treatment, and a high-energy diet (HED) with vehicle or GTE by oral gavage at 77.5 or 155 mg/kg/day for 8 weeks. Body weight, fat accumulation, and serum biochemical parameters were used to evaluate obesity. The gene expressions were analyzed using RT-qPCR and western blotting. Results: GTE modulated HED-induced body weight, fat accumulation, and serum levels of triacylglycerol, total cholesterol, low-density lipoprotein, free fatty acids, aspartate aminotransferase, and alanine aminotransferase. Moreover, GTE enhanced the serum high-density lipoprotein. Most importantly, the biomarkers of beige adipose tissue were up-regulated in WAT in GTE-given groups. GTE induced genes involved in different pathways of browning, and reduced transducin-like enhancer protein-3 in WAT. Conclusion: Our results suggest that GTE may improve obesity through inducing browning in HED-fed rats. Abbreviations : ALT: Alanine transaminase; AST: Aspartate transaminase; BAT: Brown adipose tissue; BMP-7: Bone morphogenetic protein-7; BW: Body weight; CIDEA: Cell death activator; CPT-1: Carnitine palmitoyltransferase-1; EFP: Epididymal fat pad; FFA: Free fatty acid; FGF-21: Fibroblast growth factor-21; GTE: Green tea extract; HDL: High-density lipoprotein; HED: high-energy diet; LDL: Low-density lipoprotein; MFP: Mesenteric fat pad; PGC-1α: Activates PPAR-γ coactivator-1; PPAR-γ: Peroxisome proliferator-activated receptor-γ; PRDM-16: PR domain containing 16; RFP: Renal fat pad; SD: Sprague Dawley; TC: Total cholesterol; TG: Triacylglycerol; TLE-3: Transducin-like enhancer protein-3: UCP-1: Uncoupling protein-1; WAT: White adipose tissue.
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Sanz, Mariano; Beighton, David; Curtis, Michael A; Cury, Jaime A; Dige, Irene; Dommisch, Henrik; Ellwood, Roger; Giacaman, Rodrigo A; Herrera, David; Herzberg, Mark C; Könönen, Eija; Marsh, Philip D; Meyle, Joerg; Mira, Alex; Molina, Ana; Mombelli, Andrea; Quirynen, Marc; Reynolds, Eric C; Shapira, Lior; Zaura, Egija
2017-03-01
The scope of this working group was to review (1) ecological interactions at the dental biofilm in health and disease, (2) the role of microbial communities in the pathogenesis of periodontitis and caries, and (3) the innate host response in caries and periodontal diseases. A health-associated biofilm includes genera such as Neisseria, Streptococcus, Actinomyces, Veillonella and Granulicatella. Microorganisms associated with both caries and periodontal diseases are metabolically highly specialized and organized as multispecies microbial biofilms. Progression of these diseases involves multiple microbial interactions driven by different stressors. In caries, the exposure of dental biofilms to dietary sugars and their fermentation to organic acids results in increasing proportions of acidogenic and aciduric species. In gingivitis, plaque accumulation at the gingival margin leads to inflammation and increasing proportions of proteolytic and often obligately anaerobic species. The natural mucosal barriers and saliva are the main innate defence mechanisms against soft tissue bacterial invasion. Similarly, enamel and dentin are important hard tissue barriers to the caries process. Given that the present state of knowledge suggests that the aetiologies of caries and periodontal diseases are mutually independent, the elements of innate immunity that appear to contribute to resistance to both are somewhat coincidental. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
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Amino acid substrates impose polyamine, eIF5A, or hypusine requirement for peptide synthesis
Shin, Byung-Sik; Katoh, Takayuki; Gutierrez, Erik; Kim, Joo-Ran; Suga, Hiroaki
2017-01-01
Abstract Whereas ribosomes efficiently catalyze peptide bond synthesis by most amino acids, the imino acid proline is a poor substrate for protein synthesis. Previous studies have shown that the translation factor eIF5A and its bacterial ortholog EF-P bind in the E site of the ribosome where they contact the peptidyl-tRNA in the P site and play a critical role in promoting the synthesis of polyproline peptides. Using misacylated Pro-tRNAPhe and Phe-tRNAPro, we show that the imino acid proline and not tRNAPro imposes the primary eIF5A requirement for polyproline synthesis. Though most proline analogs require eIF5A for efficient peptide synthesis, azetidine-2-caboxylic acid, a more flexible four-membered ring derivative of proline, shows relaxed eIF5A dependency, indicating that the structural rigidity of proline might contribute to the requirement for eIF5A. Finally, we examine the interplay between eIF5A and polyamines in promoting translation elongation. We show that eIF5A can obviate the polyamine requirement for general translation elongation, and that this activity is independent of the conserved hypusine modification on eIF5A. Thus, we propose that the body of eIF5A functionally substitutes for polyamines to promote general protein synthesis and that the hypusine modification on eIF5A is critically important for poor substrates like proline. PMID:28637321
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Hindt, Maria; Socha, Amanda L.; Zuber, Hélène
2013-01-01
Here we present approaches for using multi-elemental imaging (specifically synchrotron X-ray fluorescence microscopy, SXRF) in ionomics, with examples using the model plant Arabidopsis thaliana. The complexity of each approach depends on the amount of a priori information available for the gene and/or phenotype being studied. Three approaches are outlined, which apply to experimental situations where a gene of interest has been identified but has an unknown phenotype (Phenotyping), an unidentified gene is associated with a known phenotype (Gene Cloning) and finally, a Screening approach, where both gene and phenotype are unknown. These approaches make use of open-access, online databases with which plant molecular genetics researchers working in the model plant Arabidopsis will be familiar, in particular the Ionomics Hub and online transcriptomic databases such as the Arabidopsis eFP browser. The approaches and examples we describe are based on the assumption that altering the expression of ion transporters can result in changes in elemental distribution. We provide methodological details on using elemental imaging to aid or accelerate gene functional characterization by narrowing down the search for candidate genes to the tissues in which elemental distributions are altered. We use synchrotron X-ray microprobes as a technique of choice, which can now be used to image all parts of an Arabidopsis plant in a hydrated state. We present elemental images of leaves, stem, root, siliques and germinating hypocotyls. PMID:23912758
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Kong, Hee Jeong; Lee, Ye Ji; Shin, Jihye; Cho, Hyun Kook; Kim, Woo-Jin; Kim, Hyung Soo; Cheong, Jaehun; Sohn, Young Chang; Lee, Sang-Jun; Kim, Bong-Seok
2012-09-01
Tripartite motif-containing 25 (TRIM25), also known as estrogen-responsive finger protein (EFP), plays an essential role in cell proliferation and innate immunity. In the present study, we isolated and characterized the TRIM25 cDNA of the Korean rose bitterling Rhodeus uyekii, designated RuTRIM25. It encodes an open reading frame of 669 amino acids containing an N-terminal RBCC motif composed of a RING domain, two B boxes, and a coiled-coil domain and a C-terminal B30.2 (PRY/SPRY) domain. RuTRIM25 shows strong homology (79.7%) to zebrafish TRIM25 and shared 32.4-28.8% homology with TRIM25 from other species, including mammals. RuTRIM25 mRNA was expressed ubiquitously. It was highly expressed in the ovary, spleen, and liver and moderately in the stomach and intestine of normal Korean rose bitterling. The intracellular localization of RuTRIM25 in HEK293T cells was diffusely localized in the cytoplasm and its RING domain deletion mutant (RuTRIM25ΔR) was detected diffusely with some aggregates in the cytoplasm. RuTRIM25, but not RuTRIM25ΔR, is ubiquitinated in vivo. Ectopic expression of RuTRIM25 synergistically activated the estrogen receptor (ER)-mediated luciferase reporter activity in a dose-dependent manner in HEK293T cells. Together, these results suggest that the RuTRIM25 regulates the ER-mediated transcription in fish similarly to its mammalian counterpart. Copyright © 2012 Elsevier Inc. All rights reserved.
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Amino acid substrates impose polyamine, eIF5A, or hypusine requirement for peptide synthesis.
Shin, Byung-Sik; Katoh, Takayuki; Gutierrez, Erik; Kim, Joo-Ran; Suga, Hiroaki; Dever, Thomas E
2017-08-21
Whereas ribosomes efficiently catalyze peptide bond synthesis by most amino acids, the imino acid proline is a poor substrate for protein synthesis. Previous studies have shown that the translation factor eIF5A and its bacterial ortholog EF-P bind in the E site of the ribosome where they contact the peptidyl-tRNA in the P site and play a critical role in promoting the synthesis of polyproline peptides. Using misacylated Pro-tRNAPhe and Phe-tRNAPro, we show that the imino acid proline and not tRNAPro imposes the primary eIF5A requirement for polyproline synthesis. Though most proline analogs require eIF5A for efficient peptide synthesis, azetidine-2-caboxylic acid, a more flexible four-membered ring derivative of proline, shows relaxed eIF5A dependency, indicating that the structural rigidity of proline might contribute to the requirement for eIF5A. Finally, we examine the interplay between eIF5A and polyamines in promoting translation elongation. We show that eIF5A can obviate the polyamine requirement for general translation elongation, and that this activity is independent of the conserved hypusine modification on eIF5A. Thus, we propose that the body of eIF5A functionally substitutes for polyamines to promote general protein synthesis and that the hypusine modification on eIF5A is critically important for poor substrates like proline. Published by Oxford University Press on behalf of Nucleic Acids Research 2017.
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Narang, Anshika; Giri, Astha; Gupta, Shraddha; Garima, Kushal; Bose, Mridula; Varma-Basil, Mandira
2017-01-01
Isoniazid (INH) resistance in Mycobacterium tuberculosis has been mainly attributed to mutations in katG (64%) and inhA (19%). However, 20%-30% resistance to INH cannot be explained by mutations alone. Hence, other mechanisms besides mutations may play a significant role in providing drug resistance. Here, we explored the role of 24 putative efflux pump genes conferring INH-resistance in M. tuberculosis. Real-time expression profiling of the efflux pump genes was performed in five INH-susceptible and six high-level INH-resistant clinical isolates of M. tuberculosis exposed to the drug. Isolates were also analyzed for mutations in katG and inhA. Four high-level INH-resistant isolates (minimum inhibitory concentration [MIC] ≥2.5 mg/L) with mutations at codon 315 (AGC-ACC) of katG showed upregulation of one of the efflux genes Rv1634, Rv0849, efpA, or p55. Another high-level INH-resistant isolate (MIC 1.5 mg/L), with no mutations at katG or inhA overexpressed 8/24 efflux genes, namely, Rv1273c, Rv0194, Rv1634, Rv1250, Rv3823c, Rv0507, jefA, and p55. Five of these, namely, Rv0194, Rv1634, Rv1250, Rv0507, and p55 were induced only in resistant isolates. The high number of efflux genes overexpressed in an INH-resistant isolate with no known INH resistance associated mutations, suggests a role for efflux pumps in resistance to this antituberculous agent, with the role of Rv0194 and Rv0507 in INH resistance being reported for the first time.
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Takayama, Ken-Ichi; Suzuki, Takashi; Tanaka, Tomoaki; Fujimura, Tetsuya; Takahashi, Satoru; Urano, Tomohiko; Ikeda, Kazuhiro; Inoue, Satoshi
2018-04-01
Prostate cancer growth is promoted by the gene regulatory action of androgen receptor (AR) and its downstream signals. The aberrant dysfunction of tumor suppressor p53 has an important role in the prognosis of cancer. We previously found that androgen treatments translocate p53 to the cytoplasm. The mechanism of this translocation depends on sumoylation of p53 by complex of SUMO E3 ligase RanBP2 with androgen-induced GTPase-activating protein-binding protein 2 (G3BP2). Here, we identified tripartite motif-containing protein 25 (TRIM25)/estrogen-responsive finger protein (Efp) as a novel interacting partner of G3BP2 protein complex. Then, we demonstrated that TRIM25 knockdown resulted in p53 downstream activation for cell cycle inhibition and apoptosis induction in LNCaP and 22Rv1 cells. In contrast, overexpression of TRIM25 promoted prostate cancer cell proliferation and inhibited apoptosis by docetaxel treatment in LNCaP cells. We observed that p53 activity was reduced by mechanism of G3BP2-mediated nuclear export in TRIM25-overexpressing prostate cancer cells. We also found TRIM25 is important for G3BP2/RanBP2-mediated p53 modification. Clinically, we newly demonstrated that TRIM25 is a prognostic factor for prostate cancer patients. Expression of TRIM25 is significantly associated with cytoplasmic p53 expression and G3BP2. Moreover, TRIM25 knockdown results in reduced tumor growth and increased p53 activity in the mouse xenograft model of prostate cancer. Thus, our findings show that overexpression of TRIM25 promoted prostate cancer cell proliferation and cell survival by modulating p53 nuclear export mechanism with G3BP2 interaction.
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Perkins, R B; Hall, J E; Martin, K A
1999-06-01
To characterize the neuroendocrine patterns of abnormal GnRH secretion in hypothalamic amenorrhea (HA), 49 women with primary and secondary HA underwent frequent sampling of LH in a total of 72 baseline studies over 12-24 h. A subset of women participated in more than one study to address 1) the variability of LH pulse patterns over time; and 2) the impact of modulating opioid, dopaminergic, and adrenergic tone on LH secretory patterns. The frequency and amplitude of LH secretion was compared with that seen in the early follicular phase (EFP) of normally cycling women. The spectrum of abnormalities of LH pulses was 8% apulsatile, 27% low frequency/low amplitude, 8% low amplitude/normal frequency, 43% low frequency/normal amplitude, 14% normal frequency/normal amplitude. Of patients studied overnight, 45% demonstrated a pubertal pattern of augmented LH secretion during sleep. Of patients studied repeatedly, 75% demonstrated at least 2 different patterns of LH secretion, and 33% reverted at least once to a normal pattern of secretion. An increase in LH pulse frequency was seen in 12 of 15 subjects in response to naloxone (opioid receptor antagonist). Clonidine (alpha-2 adrenergic agonist) was associated with a decrease in mean LH in 3 of 3 subjects. An increase in LH pulse frequency was seen in 4 of 8 subjects in response to metoclopramide (dopamine receptor antagonist), but the response was not statistically significant. Baseline abnormalities in LH secretion did not appear to influence response to neurotransmitter modulation. 1) HA represents a spectrum of disordered GnRH secretion that can vary over time; 2) LH pulse patterns at baseline do not appear to influence the ability to respond to neurotransmitter modulation; 3) Opioid and adrenergic tone appear to influence the hypothalamic GnRH pulse generator in some individuals with HA.
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Ancestral European roots of Helicobacter pylori in India
Devi, S Manjulata; Ahmed, Irshad; Francalacci, Paolo; Hussain, M Abid; Akhter, Yusuf; Alvi, Ayesha; Sechi, Leonardo A; Mégraud, Francis; Ahmed, Niyaz
2007-01-01
Background The human gastric pathogen Helicobacter pylori is co-evolved with its host and therefore, origins and expansion of multiple populations and sub populations of H. pylori mirror ancient human migrations. Ancestral origins of H. pylori in the vast Indian subcontinent are debatable. It is not clear how different waves of human migrations in South Asia shaped the population structure of H. pylori. We tried to address these issues through mapping genetic origins of present day H. pylori in India and their genomic comparison with hundreds of isolates from different geographic regions. Results We attempted to dissect genetic identity of strains by multilocus sequence typing (MLST) of the 7 housekeeping genes (atpA, efp, ureI, ppa, mutY, trpC, yphC) and phylogeographic analysis of haplotypes using MEGA and NETWORK software while incorporating DNA sequences and genotyping data of whole cag pathogenicity-islands (cagPAI). The distribution of cagPAI genes within these strains was analyzed by using PCR and the geographic type of cagA phosphorylation motif EPIYA was determined by gene sequencing. All the isolates analyzed revealed European ancestry and belonged to H. pylori sub-population, hpEurope. The cagPAI harbored by Indian strains revealed European features upon PCR based analysis and whole PAI sequencing. Conclusion These observations suggest that H. pylori strains in India share ancestral origins with their European counterparts. Further, non-existence of other sub-populations such as hpAfrica and hpEastAsia, at least in our collection of isolates, suggest that the hpEurope strains enjoyed a special fitness advantage in Indian stomachs to out-compete any endogenous strains. These results also might support hypotheses related to gene flow in India through Indo-Aryans and arrival of Neolithic practices and languages from the Fertile Crescent. PMID:17584914
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Chen, Yi-Ming; Lin, Che-Li; Wei, Li; Hsu, Yi-Ju; Chen, Kuan-Neng; Huang, Chi-Chang; Kao, Chin-Hsung
2016-02-20
Exercise and fitness training programs have attracted the public's attention in recent years. Sports nutrition supplementation is an important issue in the global sports market. In this study, we designed a power exercise training (PET) program with a mouse model based on a strength and conditional training protocol for humans. We tested the effect of supplementation with functional branched-chain amino acid (BCAA)-rich sake protein (SP) to determine whether the supplement had a synergistic effect during PET and enhanced athletic performance and resistance to fatigue. Male ICR mice were divided into three groups (n = 8 per group) for four-week treatment: sedentary controls with vehicle (SC), and PET and PET groups with SP supplementation (3.8 g/kg, PET + SP). Exercise performance was evaluated by forelimb grip strength and exhaustive swimming time as well as changes in body composition and anti-fatigue activity levels of serum lactate, ammonia, glucose, and creatine kinase (CK) after a 15-min swimming exercise. The biochemical parameters were measured at the end of the experiment. four-week PET significantly increased grip strength and exhaustive swimming time and decreased epididymal fat pad (EFP) weight and area. Levels of aspartate aminotransferase (AST), alanine aminotransferase (ALT), creatinine, and uric acid (UA) were significantly increased. PET + SP supplementation significantly decreased serum lactate, ammonia and CK levels after the 15-min swimming exercise. The resting serum levels of AST, ALT, CREA and UA were all significantly decreased with PET + SP. The PET program could increase the exercise performance and modulate the body composition of mice. PET with SP conferred better anti-fatigue activity, improved biochemical profiles, and may be an effective ergogenic aid in strength training.
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Chapple, Iain L C; Bouchard, Philippe; Cagetti, Maria Grazia; Campus, Guglielmo; Carra, Maria-Clotilde; Cocco, Fabio; Nibali, Luigi; Hujoel, Philippe; Laine, Marja L; Lingstrom, Peter; Manton, David J; Montero, Eduardo; Pitts, Nigel; Rangé, Hélène; Schlueter, Nadine; Teughels, Wim; Twetman, Svante; Van Loveren, Cor; Van der Weijden, Fridus; Vieira, Alexandre R; Schulte, Andreas G
2017-03-01
Periodontal diseases and dental caries are the most common diseases of humans and the main cause of tooth loss. Both diseases can lead to nutritional compromise and negative impacts upon self-esteem and quality of life. As complex chronic diseases, they share common risk factors, such as a requirement for a pathogenic plaque biofilm, yet they exhibit distinct pathophysiologies. Multiple exposures contribute to their causal pathways, and susceptibility involves risk factors that are inherited (e.g. genetic variants), and those that are acquired (e.g. socio-economic factors, biofilm load or composition, smoking, carbohydrate intake). Identification of these factors is crucial in the prevention of both diseases as well as in their management. To systematically appraise the scientific literature to identify potential risk factors for caries and periodontal diseases. One systematic review (genetic risk factors), one narrative review (role of diet and nutrition) and reference documentation for modifiable acquired risk factors common to both disease groups, formed the basis of the report. There is moderately strong evidence for a genetic contribution to periodontal diseases and caries susceptibility, with an attributable risk estimated to be up to 50%. The genetics literature for periodontal disease is more substantial than for caries and genes associated with chronic periodontitis are the vitamin D receptor (VDR), Fc gamma receptor IIA (Fc-γRIIA) and Interleukin 10 (IL10) genes. For caries, genes involved in enamel formation (AMELX, AMBN, ENAM, TUFT, MMP20, and KLK4), salivary characteristics (AQP5), immune regulation and dietary preferences had the largest impact. No common genetic variants were found. Fermentable carbohydrates (sugars and starches) were the most relevant common dietary risk factor for both diseases, but associated mechanisms differed. In caries, the fermentation process leads to acid production and the generation of biofilm components such as Glucans. In periodontitis, glycaemia drives oxidative stress and advanced glycation end-products may also trigger a hyper inflammatory state. Micronutrient deficiencies, such as for vitamin C, vitamin D or vitamin B12, may be related to the onset and progression of both diseases. Functional foods or probiotics could be helpful in caries prevention and periodontal disease management, although evidence is limited and biological mechanisms not fully elucidated. Hyposalivation, rheumatoid arthritis, smoking/tobacco use, undiagnosed or sub-optimally controlled diabetes and obesity are common acquired risk factors for both caries and periodontal diseases. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
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Mao, Yuezhi; Shao, Yihan; Dziedzic, Jacek; Skylaris, Chris-Kriton; Head-Gordon, Teresa; Head-Gordon, Martin
2017-05-09
The importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized with respect to both the QM electronic density and the MM induced dipoles. This QM/AMOEBA model is implemented through the Q-Chem/LibEFP code interface and then applied to the evaluation of solute-solvent interaction energies for various systems ranging from the water dimer to neutral and ionic solutes (NH 3 , NH 4 + , CN - ) surrounded by increasing numbers of water molecules (up to 100). In order to analyze the resulting interaction energies, we also utilize an energy decomposition analysis (EDA) scheme which identifies contributions from permanent electrostatics, polarization, and van der Waals (vdW) interaction for the interaction between the QM solute and the solvent molecules described by AMOEBA. This facilitates a component-wise comparison against full QM calculations where the corresponding energy components are obtained via a modified version of the absolutely localized molecular orbitals (ALMO)-EDA. The results show that the present QM/AMOEBA model can yield reasonable solute-solvent interaction energies for neutral and cationic species, while further scrutiny reveals that this accuracy highly relies on the delicate balance between insufficiently favorable permanent electrostatics and softened vdW interaction. For anionic solutes where the charge penetration effect becomes more pronounced, the QM/MM interface turns out to be unbalanced. These results are consistent with and further elucidate our findings in a previous study using a slightly different QM/AMOEBA model ( Dziedzic et al. J. Chem. Phys. 2016 , 145 , 124106 ). The implications of these results for further refinement of this model are also discussed.
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Machado, Diana; Coelho, Tatiane S; Perdigão, João; Pereira, Catarina; Couto, Isabel; Portugal, Isabel; Maschmann, Raquel De Abreu; Ramos, Daniela F; von Groll, Andrea; Rossetti, Maria L R; Silva, Pedro A; Viveiros, Miguel
2017-01-01
Numerous studies show efflux as a universal bacterial mechanism contributing to antibiotic resistance and also that the activity of the antibiotics subject to efflux can be enhanced by the combined use of efflux inhibitors. Nevertheless, the contribution of efflux to the overall drug resistance levels of clinical isolates of Mycobacterium tuberculosis is poorly understood and still is ignored by many. Here, we evaluated the contribution of drug efflux plus target-gene mutations to the drug resistance levels in clinical isolates of M. tuberculosis . A panel of 17 M. tuberculosis clinical strains were characterized for drug resistance associated mutations and antibiotic profiles in the presence and absence of efflux inhibitors. The correlation between the effect of the efflux inhibitors and the resistance levels was assessed by quantitative drug susceptibility testing. The bacterial growth/survival vs. growth inhibition was analyzed through the comparison between the time of growth in the presence and absence of an inhibitor. For the same mutation conferring antibiotic resistance, different MICs were observed and the different resistance levels found could be reduced by efflux inhibitors. Although susceptibility was not restored, the results demonstrate the existence of a broad-spectrum synergistic interaction between antibiotics and efflux inhibitors. The existence of efflux activity was confirmed by real-time fluorometry. Moreover, the efflux pump genes mmr, mmpL7, Rv1258c, p55 , and efpA were shown to be overexpressed in the presence of antibiotics, demonstrating the contribution of these efflux pumps to the overall resistance phenotype of the M. tuberculosis clinical isolates studied, independently of the genotype of the strains. These results showed that the drug resistance levels of multi- and extensively-drug resistant M. tuberculosis clinical strains are a combination between drug efflux and the presence of target-gene mutations, a reality that is often disregarded by the tuberculosis specialists in favor of the almost undisputed importance of antibiotic target-gene mutations for the resistance in M. tuberculosis .
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Pharmacy discounts on generic medicines in France: is there room for further efficiency savings?
Kanavos, Panos; Taylor, David
2007-10-01
In France control of pharmaceutical expenditure has been a policy priority for many years and generic policies have featured prominently on the policy agenda. Measures including reference pricing, generic substitution and international non-proprietary name (INN) prescribing have been introduced in recent years. Generic manufacturers and wholesalers may offer discounts, rebates or promotions to pharmacies in order to gain an edge over their competitors, but their true extent is unknown. To identify the amplitude of discounts on generic medicines, and whether wholesalers or generic manufacturers offer these beyond officially negotiated margins and allowable discounts, by conducting a pilot study. Data on net prices were acquired for all available presentations of 11 generic molecules selected across different therapeutic categories included in the 40 most selling generic products in 2005. Data were obtained via a questionnaire survey followed by interview with selected pharmacies (n = 4) and whole-salers (n = 2). Pharmacies and wholesalers participated in this study subject to confidentiality and anonymity. Pharmacies usually prefer to buy generic products directly from manufacturers rather than from wholesalers in order to avoid paying additional margins imposed by wholesalers. Discounts are mostly price-related and generally vary from 20 to 70% off the wholesaler selling price (WSP), on top of the officially allowed 10.74%. Discounts on the ex-factory price (EFP) are much lower, typically around 7.5%. Discounts are prohibited for branded products, beyond the officially allowed ceiling of 2.5%. While horizontal integration among pharmacies is disallowed, pharmacies may form purchasing groups allowing them to realise greater discounts from suppliers. Overall, the evidence suggests that discounts occur in France beyond what may be allowable and their extent can be significant. If general discount levels for generic medicines are as high as this pilot study suggests, then this may imply that health insurance in France may be overpaying for commodity generic medicines.
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NASA Astrophysics Data System (ADS)
Nathalia Wea, Kristiana; Suparmi, A.; Cari, C.; Wahyulianti
2017-11-01
The solution of the Schrodinger equation with physical potential is the important part in quantum physics. Many methods have been developed to resolve the Schrodinger equation. The Nikiforov-Uvarov method and supersymmetric method are the most methods that interesting to be explored. The supersymmetric method not only used to solve the Schrodinger equation but also used to construct the partner potential from a general potential. In this study, the Nikiforov-Uvarov method was used to solve the Schrodinger equation while the supersymmetric method was used to construction partner potential. The study about the construction of the partner potential from general potential Rosen-Morse and Manning Rosen in D-dimensional Schrodinger system has been done. The partner potential was obtained are solvable. By using the Nikiforov-Uvarov method the eigenfunction of the Schrodinger equation in D-dimensional system with general potential Rosen-Morse and Manning Rosen and the Schrodinger equation in D-dimensional system with partner potential Rosen-Morse and Manning Rosen are determined. The eigenfunctions are different between the Schrodinger equation with general potential and the Schrodinger potential with the partner potential.
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Local discretization method for overdamped Brownian motion on a potential with multiple deep wells.
Nguyen, P T T; Challis, K J; Jack, M W
2016-11-01
We present a general method for transforming the continuous diffusion equation describing overdamped Brownian motion on a time-independent potential with multiple deep wells to a discrete master equation. The method is based on an expansion in localized basis states of local metastable potentials that match the full potential in the region of each potential well. Unlike previous basis methods for discretizing Brownian motion on a potential, this approach is valid for periodic potentials with varying multiple deep wells per period and can also be applied to nonperiodic systems. We apply the method to a range of potentials and find that potential wells that are deep compared to five times the thermal energy can be associated with a discrete localized state while shallower wells are better incorporated into the local metastable potentials of neighboring deep potential wells.
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Local discretization method for overdamped Brownian motion on a potential with multiple deep wells
NASA Astrophysics Data System (ADS)
Nguyen, P. T. T.; Challis, K. J.; Jack, M. W.
2016-11-01
We present a general method for transforming the continuous diffusion equation describing overdamped Brownian motion on a time-independent potential with multiple deep wells to a discrete master equation. The method is based on an expansion in localized basis states of local metastable potentials that match the full potential in the region of each potential well. Unlike previous basis methods for discretizing Brownian motion on a potential, this approach is valid for periodic potentials with varying multiple deep wells per period and can also be applied to nonperiodic systems. We apply the method to a range of potentials and find that potential wells that are deep compared to five times the thermal energy can be associated with a discrete localized state while shallower wells are better incorporated into the local metastable potentials of neighboring deep potential wells.
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White, Alec F.; Head-Gordon, Martin; McCurdy, C. William
2017-01-30
The computation of Siegert energies by analytic continuation of bound state energies has recently been applied to shape resonances in polyatomic molecules by several authors. Here, we critically evaluate a recently proposed analytic continuation method based on low order (type III) Padé approximants as well as an analytic continuation method based on high order (type II) Padé approximants. We compare three classes of stabilizing potentials: Coulomb potentials, Gaussian potentials, and attenuated Coulomb potentials. These methods are applied to a model potential where the correct answer is known exactly and to the 2Π g shape resonance of N 2 - whichmore » has been studied extensively by other methods. Both the choice of stabilizing potential and method of analytic continuation prove to be important to the accuracy of the results. We then conclude that an attenuated Coulomb potential is the most effective of the three for bound state analytic continuation methods. With the proper potential, such methods show promise for algorithmic determination of the positions and widths of molecular shape resonances.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
White, Alec F.; Head-Gordon, Martin; McCurdy, C. William
The computation of Siegert energies by analytic continuation of bound state energies has recently been applied to shape resonances in polyatomic molecules by several authors. Here, we critically evaluate a recently proposed analytic continuation method based on low order (type III) Padé approximants as well as an analytic continuation method based on high order (type II) Padé approximants. We compare three classes of stabilizing potentials: Coulomb potentials, Gaussian potentials, and attenuated Coulomb potentials. These methods are applied to a model potential where the correct answer is known exactly and to the 2Π g shape resonance of N 2 - whichmore » has been studied extensively by other methods. Both the choice of stabilizing potential and method of analytic continuation prove to be important to the accuracy of the results. We then conclude that an attenuated Coulomb potential is the most effective of the three for bound state analytic continuation methods. With the proper potential, such methods show promise for algorithmic determination of the positions and widths of molecular shape resonances.« less
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Comparison of the dye method with the thermocouple psychrometer for measuring leaf water potentials.
Knipling, E B; Kramer, P J
1967-10-01
The dye method for measuring water potential was examined and compared with the thermocouple psychrometer method in order to evaluate its usefulness for measuring leaf water potentials of forest trees and common laboratory plants. Psychrometer measurements are assumed to represent the true leaf water potentials. Because of the contamination of test solutions by cell sap and leaf surface residues, dye method values of most species varied about 1 to 5 bars from psychrometer values over the leaf water potential range of 0 to -30 bars. The dye method is useful for measuring changes and relative values in leaf potential. Because of species differences in the relationships of dye method values to true leaf water potentials, dye method values should be interpreted with caution when comparing different species or the same species growing in widely different environments. Despite its limitations the dye method has a usefulness to many workers because it is simple, requires no elaborate equipment, and can be used in both the laboratory and field.
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Electric potential calculation in molecular simulation of electric double layer capacitors
NASA Astrophysics Data System (ADS)
Wang, Zhenxing; Olmsted, David L.; Asta, Mark; Laird, Brian B.
2016-11-01
For the molecular simulation of electric double layer capacitors (EDLCs), a number of methods have been proposed and implemented to determine the one-dimensional electric potential profile between the two electrodes at a fixed potential difference. In this work, we compare several of these methods for a model LiClO4-acetonitrile/graphite EDLC simulated using both the traditional fixed-charged method (FCM), in which a fixed charge is assigned a priori to the electrode atoms, or the recently developed constant potential method (CPM) (2007 J. Chem. Phys. 126 084704), where the electrode charges are allowed to fluctuate to keep the potential fixed. Based on an analysis of the full three-dimensional electric potential field, we suggest a method for determining the averaged one-dimensional electric potential profile that can be applied to both the FCM and CPM simulations. Compared to traditional methods based on numerically solving the one-dimensional Poisson’s equation, this method yields better accuracy and no supplemental assumptions.
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Knipling, Edward B.; Kramer, Paul J.
1967-01-01
The dye method for measuring water potential was examined and compared with the thermocouple psychrometer method in order to evaluate its usefulness for measuring leaf water potentials of forest trees and common laboratory plants. Psychrometer measurements are assumed to represent the true leaf water potentials. Because of the contamination of test solutions by cell sap and leaf surface residues, dye method values of most species varied about 1 to 5 bars from psychrometer values over the leaf water potential range of 0 to −30 bars. The dye method is useful for measuring changes and relative values in leaf potential. Because of species differences in the relationships of dye method values to true leaf water potentials, dye method values should be interpreted with caution when comparing different species or the same species growing in widely different environments. Despite its limitations the dye method has a usefulness to many workers because it is simple, requires no elaborate equipment, and can be used in both the laboratory and field. PMID:16656657
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Path Planning for Robot based on Chaotic Artificial Potential Field Method
NASA Astrophysics Data System (ADS)
Zhang, Cheng
2018-03-01
Robot path planning in unknown environments is one of the hot research topics in the field of robot control. Aiming at the shortcomings of traditional artificial potential field methods, we propose a new path planning for Robot based on chaotic artificial potential field method. The path planning adopts the potential function as the objective function and introduces the robot direction of movement as the control variables, which combines the improved artificial potential field method with chaotic optimization algorithm. Simulations have been carried out and the results demonstrate that the superior practicality and high efficiency of the proposed method.
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NASA Astrophysics Data System (ADS)
Mamat, Siti Salwana; Ahmad, Tahir; Awang, Siti Rahmah
2017-08-01
Analytic Hierarchy Process (AHP) is a method used in structuring, measuring and synthesizing criteria, in particular ranking of multiple criteria in decision making problems. On the other hand, Potential Method is a ranking procedure in which utilizes preference graph ς (V, A). Two nodes are adjacent if they are compared in a pairwise comparison whereby the assigned arc is oriented towards the more preferred node. In this paper Potential Method is used to solve problem on a catering service selection. The comparison of result by using Potential method is made with Extent Analysis. The Potential Method is found to produce the same rank as Extent Analysis in AHP.
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NASA Astrophysics Data System (ADS)
Fasnacht, Marc
We develop adaptive Monte Carlo methods for the calculation of the free energy as a function of a parameter of interest. The methods presented are particularly well-suited for systems with complex energy landscapes, where standard sampling techniques have difficulties. The Adaptive Histogram Method uses a biasing potential derived from histograms recorded during the simulation to achieve uniform sampling in the parameter of interest. The Adaptive Integration method directly calculates an estimate of the free energy from the average derivative of the Hamiltonian with respect to the parameter of interest and uses it as a biasing potential. We compare both methods to a state of the art method, and demonstrate that they compare favorably for the calculation of potentials of mean force of dense Lennard-Jones fluids. We use the Adaptive Integration Method to calculate accurate potentials of mean force for different types of simple particles in a Lennard-Jones fluid. Our approach allows us to separate the contributions of the solvent to the potential of mean force from the effect of the direct interaction between the particles. With contributions of the solvent determined, we can find the potential of mean force directly for any other direct interaction without additional simulations. We also test the accuracy of the Adaptive Integration Method on a thermodynamic cycle, which allows us to perform a consistency check between potentials of mean force and chemical potentials calculated using the Adaptive Integration Method. The results demonstrate a high degree of consistency of the method.
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Johnson
1999-01-01
The electrokinetic behavior of granular quartz sand in aqueous solution is investigated by both microelectrophoresis and streaming potential methods. zeta potentials of surfaces composed of granular quartz obtained via streaming potential methods are compared to electrophoretic mobility zeta potential values of colloid-sized quartz fragments. The zeta values generated by these alternate methods are in close agreement over a wide pH range and electrolyte concentrations spanning several orders of magnitude. Streaming measurements performed on chemically heterogeneous mixtures of physically homogeneous sand are shown to obey a simple mixing model based on the surface area-weighted average of the streaming potentials associated with the individual end members. These experimental results support the applicability of the streaming potential method as a means of determining the zeta potential of granular porous media surfaces. Copyright 1999 Academic Press.
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NASA Astrophysics Data System (ADS)
Matsumoto, Kensaku; Okada, Takashi; Takeuchi, Atsuo; Yazawa, Masato; Uchibori, Sumio; Shimizu, Yoshihiko
Field Measurement of Self Potential Method using Copper Sulfate Electrode was performed in base of riverbank in WATARASE River, where has leakage problem to examine leakage characteristics. Measurement results showed typical S-shape what indicates existence of flow groundwater. The results agreed with measurement results by Ministry of Land, Infrastructure and Transport with good accuracy. Results of 1m depth ground temperature detection and Chain-Array detection showed good agreement with results of the Self Potential Method. Correlation between Self Potential value and groundwater velocity was examined model experiment. The result showed apparent correlation. These results indicate that the Self Potential Method was effective method to examine the characteristics of ground water of base of riverbank in leakage problem.
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NASA Technical Reports Server (NTRS)
Wang, R.; Demerdash, N. A.
1991-01-01
A method of combined use of magnetic vector potential based finite-element (FE) formulations and magnetic scalar potential (MSP) based formulations for computation of three-dimensional magnetostatic fields is introduced. In this method, the curl-component of the magnetic field intensity is computed by a reduced magnetic vector potential. This field intensity forms the basic of a forcing function for a global magnetic scalar potential solution over the entire volume of the region. This method allows one to include iron portions sandwiched in between conductors within partitioned current-carrying subregions. The method is most suited for large-scale global-type 3-D magnetostatic field computations in electrical devices, and in particular rotating electric machinery.
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NASA Technical Reports Server (NTRS)
Hafez, M.
1989-01-01
Vector potential and related methods, for the simulation of both inviscid and viscous flows over aerodynamic configurations, are briefly reviewed. The advantages and disadvantages of several formulations are discussed and alternate strategies are recommended. Scalar potential, modified potential, alternate formulations of Euler equations, least-squares formulation, variational principles, iterative techniques and related methods, and viscous flow simulation are discussed.
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Quadratic adaptive algorithm for solving cardiac action potential models.
Chen, Min-Hung; Chen, Po-Yuan; Luo, Ching-Hsing
2016-10-01
An adaptive integration method is proposed for computing cardiac action potential models accurately and efficiently. Time steps are adaptively chosen by solving a quadratic formula involving the first and second derivatives of the membrane action potential. To improve the numerical accuracy, we devise an extremum-locator (el) function to predict the local extremum when approaching the peak amplitude of the action potential. In addition, the time step restriction (tsr) technique is designed to limit the increase in time steps, and thus prevent the membrane potential from changing abruptly. The performance of the proposed method is tested using the Luo-Rudy phase 1 (LR1), dynamic (LR2), and human O'Hara-Rudy dynamic (ORd) ventricular action potential models, and the Courtemanche atrial model incorporating a Markov sodium channel model. Numerical experiments demonstrate that the action potential generated using the proposed method is more accurate than that using the traditional Hybrid method, especially near the peak region. The traditional Hybrid method may choose large time steps near to the peak region, and sometimes causes the action potential to become distorted. In contrast, the proposed new method chooses very fine time steps in the peak region, but large time steps in the smooth region, and the profiles are smoother and closer to the reference solution. In the test on the stiff Markov ionic channel model, the Hybrid blows up if the allowable time step is set to be greater than 0.1ms. In contrast, our method can adjust the time step size automatically, and is stable. Overall, the proposed method is more accurate than and as efficient as the traditional Hybrid method, especially for the human ORd model. The proposed method shows improvement for action potentials with a non-smooth morphology, and it needs further investigation to determine whether the method is helpful during propagation of the action potential. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Proteomic analysis of Chromobacterium violaceum and its adaptability to stress.
Castro, Diogo; Cordeiro, Isabelle Bezerra; Taquita, Paula; Eberlin, Marcos Nogueira; Garcia, Jerusa Simone; Souza, Gustavo Henrique M F; Arruda, Marco Aurélio Zezzi; Andrade, Edmar V; Filho, Spartaco A; Crainey, J Lee; Lozano, Luis Lopez; Nogueira, Paulo A; Orlandi, Patrícia P
2015-12-01
Chromobacterium violaceum (C. violaceum) occurs abundantly in a variety of ecosystems, including ecosystems that place the bacterium under stress. This study assessed the adaptability of C. violaceum by submitting it to nutritional and pH stresses and then analyzing protein expression using bi-dimensional electrophoresis (2-DE) and Maldi mass spectrometry. Chromobacterium violaceum grew best in pH neutral, nutrient-rich medium (reference conditions); however, the total protein mass recovered from stressed bacteria cultures was always higher than the total protein mass recovered from our reference culture. The diversity of proteins expressed (repressed by the number of identifiable 2-DE spots) was seen to be highest in the reference cultures, suggesting that stress reduces the overall range of proteins expressed by C. violaceum. Database comparisons allowed 43 of the 55 spots subjected to Maldi mass spectrometry to be characterized as containing a single identifiable protein. Stress-related expression changes were noted for C. violaceum proteins related to the previously characterized bacterial proteins: DnaK, GroEL-2, Rhs, EF-Tu, EF-P; MCP, homogentisate 1,2-dioxygenase, Arginine deiminase and the ATP synthase β-subunit protein as well as for the ribosomal protein subunits L1, L3, L5 and L6. The ability of C. violaceum to adapt its cellular mechanics to sub-optimal growth and protein production conditions was well illustrated by its regulation of ribosomal protein subunits. With the exception of the ribosomal subunit L3, which plays a role in protein folding and maybe therefore be more useful in stressful conditions, all the other ribosomal subunit proteins were seen to have reduced expression in stressed cultures. Curiously, C. violeaceum cultures were also observed to lose their violet color under stress, which suggests that the violacein pigment biosynthetic pathway is affected by stress. Analysis of the proteomic signatures of stressed C. violaceum indicates that nutrient-starvation and pH stress can cause changes in the expression of the C. violaceum receptors, transporters, and proteins involved with biosynthetic pathways, molecule recycling, energy production. Our findings complement the recent publication of the C. violeaceum genome sequence and could help with the future commercial exploitation of C. violeaceum.
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An entropy correction method for unsteady full potential flows with strong shocks
NASA Technical Reports Server (NTRS)
Whitlow, W., Jr.; Hafez, M. M.; Osher, S. J.
1986-01-01
An entropy correction method for the unsteady full potential equation is presented. The unsteady potential equation is modified to account for entropy jumps across shock waves. The conservative form of the modified equation is solved in generalized coordinates using an implicit, approximate factorization method. A flux-biasing differencing method, which generates the proper amounts of artificial viscosity in supersonic regions, is used to discretize the flow equations in space. Comparisons between the present method and solutions of the Euler equations and between the present method and experimental data are presented. The comparisons show that the present method more accurately models solutions of the Euler equations and experiment than does the isentropic potential formulation.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Stiegler, Thomas; Sadus, Richard J., E-mail: rsadus@swin.edu.au
General methods for combining interactions between particles characterised by non-identical intermolecular potentials are investigated. The combination methods are tested by performing molecular dynamics simulations to determine the pressure, energy, isochoric and isobaric heat capacities, thermal expansion coefficient, isothermal compressibility, Joule-Thomson coefficient, and speed of sound of 10-5 + 12-6 Mie potential binary mixtures. In addition to the two non-identical Mie potentials, mixtures are also studied with non-identical intermolecular parameters. The combination methods are compared with results obtained by simply averaging the Mie exponents. When either the energy or size parameters are non-identical, very significant differences emerge in the thermodynamic propertiesmore » predicted by the alternative combination methods. The isobaric heat capacity is the thermodynamic property that is most affected by the relative magnitude of the intermolecular potential parameters and the method for combining non-identical potentials. Either the arithmetic or geometric combination of potentials provides a simple and effective way of performing simulations involving mixtures of components characterised by non-identical intermolecular potentials, which is independent of their functional form.« less
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Minimizing Higgs potentials via numerical polynomial homotopy continuation
NASA Astrophysics Data System (ADS)
Maniatis, M.; Mehta, D.
2012-08-01
The study of models with extended Higgs sectors requires to minimize the corresponding Higgs potentials, which is in general very difficult. Here, we apply a recently developed method, called numerical polynomial homotopy continuation (NPHC), which guarantees to find all the stationary points of the Higgs potentials with polynomial-like non-linearity. The detection of all stationary points reveals the structure of the potential with maxima, metastable minima, saddle points besides the global minimum. We apply the NPHC method to the most general Higgs potential having two complex Higgs-boson doublets and up to five real Higgs-boson singlets. Moreover the method is applicable to even more involved potentials. Hence the NPHC method allows to go far beyond the limits of the Gröbner basis approach.
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Patching the Exchange-Correlation Potential in Density Functional Theory.
Huang, Chen
2016-05-10
A method for directly patching exchange-correlation (XC) potentials in materials is derived. The electron density of a system is partitioned into subsystem densities by dividing its Kohn-Sham (KS) potential among the subsystems. Inside each subsystem, its projected KS potential is required to become the total system's KS potential. This requirement, together with the nearsightedness principle of electronic matters, ensures that the electronic structures inside subsystems can be good approximations to the total system's electronic structure. The nearsightedness principle also ensures that subsystem densities could be well localized in their regions, making it possible to use high-level methods to invert the XC potentials for subsystem densities. Two XC patching methods are developed. In the local XC patching method, the total system's XC potential is improved in the cluster region. We show that the coupling between a cluster and its environment is important for achieving a fast convergence of the electronic structure in the cluster region. In the global XC patching method, we discuss how to patch the subsystem XC potentials to construct the XC potential in the total system, aiming to scale up high-level quantum mechanics simulations of materials. Proof-of-principle examples are given.
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NASA Astrophysics Data System (ADS)
Suparmi; Cari, C.; Wea, K. N.; Wahyulianti
2018-03-01
The Schrodinger equation is the fundamental equation in quantum physics. The characteristic of the particle in physics potential field can be explained by using the Schrodinger equation. In this study, the solution of 4 dimensional Schrodinger equation for the anharmonic potential and the anharmonic partner potential have done. The method that used to solve the Schrodinger equation was the ansatz wave method, while to construction the partner potential was the supersymmetric method. The construction of partner potential used to explain the experiment result that cannot be explained by the original potential. The eigenvalue for anharmonic potential and the anharmonic partner potential have the same characteristic. Every increase of quantum orbital number the eigenvalue getting smaller. This result corresponds to Bohrn’s atomic theory that the eigenvalue is inversely proportional to the atomic shell. But the eigenvalue for the anharmonic partner potential higher than the eigenvalue for the anharmonic original potential.
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Resonances for Symmetric Two-Barrier Potentials
ERIC Educational Resources Information Center
Fernandez, Francisco M.
2011-01-01
We describe a method for the accurate calculation of bound-state and resonance energies for one-dimensional potentials. We calculate the shape resonances for symmetric two-barrier potentials and compare them with those coming from the Siegert approximation, the complex scaling method and the box-stabilization method. A comparison of the…
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NASA Astrophysics Data System (ADS)
Aoki, Sinya
2013-07-01
We review the potential method in lattice QCD, which has recently been proposed to extract nucleon-nucleon interactions via numerical simulations. We focus on the methodology of this approach by emphasizing the strategy of the potential method, the theoretical foundation behind it, and special numerical techniques. We compare the potential method with the standard finite volume method in lattice QCD, in order to make pros and cons of the approach clear. We also present several numerical results for nucleon-nucleon potentials.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Yao, Jie, E-mail: yjie2@uh.edu; Lesage, Anne-Cécile; Hussain, Fazle
2014-12-15
The reversion of the Born-Neumann series of the Lippmann-Schwinger equation is one of the standard ways to solve the inverse acoustic scattering problem. One limitation of the current inversion methods based on the reversion of the Born-Neumann series is that the velocity potential should have compact support. However, this assumption cannot be satisfied in certain cases, especially in seismic inversion. Based on the idea of distorted wave scattering, we explore an inverse scattering method for velocity potentials without compact support. The strategy is to decompose the actual medium as a known single interface reference medium, which has the same asymptoticmore » form as the actual medium and a perturbative scattering potential with compact support. After introducing the method to calculate the Green’s function for the known reference potential, the inverse scattering series and Volterra inverse scattering series are derived for the perturbative potential. Analytical and numerical examples demonstrate the feasibility and effectiveness of this method. Besides, to ensure stability of the numerical computation, the Lanczos averaging method is employed as a filter to reduce the Gibbs oscillations for the truncated discrete inverse Fourier transform of each order. Our method provides a rigorous mathematical framework for inverse acoustic scattering with a non-compact support velocity potential.« less
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Crepeau, Kathryn L.; Fram, Miranda S.; Bush, Noel
2004-01-01
An analytical method for the determination of the trihalomethane formation potential of water samples has been developed. The trihalomethane formation potential is measured by dosing samples with chlorine under specified conditions of pH, temperature, incubation time, darkness, and residual-free chlorine, and then analyzing the resulting trihalomethanes by purge and trap/gas chromatography equipped with an electron capture detector. Detailed explanations of the method and quality-control practices are provided. Method validation experiments showed that the trihalomethane formation potential varies as a function of time between sample collection and analysis, residual-free chlorine concentration, method of sample dilution, and the concentration of bromide in the sample.
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A novel knowledge-based potential for RNA 3D structure evaluation
NASA Astrophysics Data System (ADS)
Yang, Yi; Gu, Qi; Zhang, Ben-Gong; Shi, Ya-Zhou; Shao, Zhi-Gang
2018-03-01
Ribonucleic acids (RNAs) play a vital role in biology, and knowledge of their three-dimensional (3D) structure is required to understand their biological functions. Recently structural prediction methods have been developed to address this issue, but a series of RNA 3D structures are generally predicted by most existing methods. Therefore, the evaluation of the predicted structures is generally indispensable. Although several methods have been proposed to assess RNA 3D structures, the existing methods are not precise enough. In this work, a new all-atom knowledge-based potential is developed for more accurately evaluating RNA 3D structures. The potential not only includes local and nonlocal interactions but also fully considers the specificity of each RNA by introducing a retraining mechanism. Based on extensive test sets generated from independent methods, the proposed potential correctly distinguished the native state and ranked near-native conformations to effectively select the best. Furthermore, the proposed potential precisely captured RNA structural features such as base-stacking and base-pairing. Comparisons with existing potential methods show that the proposed potential is very reliable and accurate in RNA 3D structure evaluation. Project supported by the National Science Foundation of China (Grants Nos. 11605125, 11105054, 11274124, and 11401448).
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Palani, Damodharan; Pekala, Dobromila; Baginskas, Armantas; Szkudlarek, Hanna; Raastad, Morten
2012-07-15
We investigated the ability of a grease-gap method to record fast and slow changes of the membrane potential from bundles of gray matter axons. Their membrane potentials are of particular interest because these axons are different from most axons that have been investigated using intra-axonal or gap techniques. One of the main differences is that gray matter axons typically have closely spaced presynaptic specializations, called boutons or varicosities, distributed along their entire paths. In response to electrical activation of bundles of parallel fiber axons we were able to record small (128-416μV) but stable signals that we show most likely represented a fraction of the trans-membrane action potentials. A less-than 100% fraction prevents measurements of absolute values for membrane potentials, but the good signal-to-noise ratio (typically 10-16) allows detection of changes in resting membrane potential, action potentials and their after-potentials. Because very little is known about the shape of action potentials and after-potentials in these axons we used several independent methods to make it likely that the grease-gap signal was of intra-axonal origin. We demonstrate the utility of the method by showing that the action potentials in cerebellar parallel fibers and hippocampal Schaffer collaterals had a slowly decaying, depolarized after-potential. The method is ideal for pharmacological tests, which we demonstrate by showing that the slow after-potential was sensitive to 4-AP, and that the membrane potential was reduced by 200μM Ba(2+). Copyright © 2012 Elsevier B.V. All rights reserved.
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A joint sparse representation-based method for double-trial evoked potentials estimation.
Yu, Nannan; Liu, Haikuan; Wang, Xiaoyan; Lu, Hanbing
2013-12-01
In this paper, we present a novel approach to solving an evoked potentials estimating problem. Generally, the evoked potentials in two consecutive trials obtained by repeated identical stimuli of the nerves are extremely similar. In order to trace evoked potentials, we propose a joint sparse representation-based double-trial evoked potentials estimation method, taking full advantage of this similarity. The estimation process is performed in three stages: first, according to the similarity of evoked potentials and the randomness of a spontaneous electroencephalogram, the two consecutive observations of evoked potentials are considered as superpositions of the common component and the unique components; second, making use of their characteristics, the two sparse dictionaries are constructed; and finally, we apply the joint sparse representation method in order to extract the common component of double-trial observations, instead of the evoked potential in each trial. A series of experiments carried out on simulated and human test responses confirmed the superior performance of our method. © 2013 Elsevier Ltd. Published by Elsevier Ltd. All rights reserved.
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Advances in visual representation of molecular potentials.
Du, Qi-Shi; Huang, Ri-Bo; Chou, Kuo-Chen
2010-06-01
The recent advances in visual representations of molecular properties in 3D space are summarized, and their applications in molecular modeling study and rational drug design are introduced. The visual representation methods provide us with detailed insights into protein-ligand interactions, and hence can play a major role in elucidating the structure or reactivity of a biomolecular system. Three newly developed computation and visualization methods for studying the physical and chemical properties of molecules are introduced, including their electrostatic potential, lipophilicity potential and excess chemical potential. The newest application examples of visual representations in structure-based rational drug are presented. The 3D electrostatic potentials, calculated using the empirical method (EM-ESP), in which the classical Coulomb equation and traditional atomic partial changes are discarded, are highly consistent with the results by the higher level quantum chemical method. The 3D lipophilicity potentials, computed by the heuristic molecular lipophilicity potential method based on the principles of quantum mechanics and statistical mechanics, are more accurate and reliable than those by using the traditional empirical methods. The 3D excess chemical potentials, derived by the reference interaction site model-hypernetted chain theory, provide a new tool for computational chemistry and molecular modeling. For structure-based drug design, the visual representations of molecular properties will play a significant role in practical applications. It is anticipated that the new advances in computational chemistry will stimulate the development of molecular modeling methods, further enriching the visual representation techniques for rational drug design, as well as other relevant fields in life science.
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Baryon interactions in lattice QCD: the direct method vs. the HAL QCD potential method
NASA Astrophysics Data System (ADS)
Iritani, T.; HAL QCD Collaboration
We make a detailed comparison between the direct method and the HAL QCD potential method for the baryon-baryon interactions, taking the $\\Xi\\Xi$ system at $m_\\pi= 0.51$ GeV in 2+1 flavor QCD and using both smeared and wall quark sources. The energy shift $\\Delta E_\\mathrm{eff}(t)$ in the direct method shows the strong dependence on the choice of quark source operators, which means that the results with either (or both) source are false. The time-dependent HAL QCD method, on the other hand, gives the quark source independent $\\Xi\\Xi$ potential, thanks to the derivative expansion of the potential, which absorbs the source dependence to the next leading order correction. The HAL QCD potential predicts the absence of the bound state in the $\\Xi\\Xi$($^1$S$_0$) channel at $m_\\pi= 0.51$ GeV, which is also confirmed by the volume dependence of finite volume energy from the potential. We also demonstrate that the origin of the fake plateau in the effective energy shift $\\Delta E_\\mathrm{eff}(t)$ at $t \\sim 1$ fm can be clarified by a few low-lying eigenfunctions and eigenvalues on the finite volume derived from the HAL QCD potential, which implies that the ground state saturation of $\\Xi\\Xi$($^1$S$_0$) requires $t \\sim 10$ fm in the direct method for the smeared source on $(4.3 \\ \\mathrm{fm})^3$ lattice, while the HAL QCD method does not suffer from such a problem.
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NASA Astrophysics Data System (ADS)
Bonitati, Joey; Slimmer, Ben; Li, Weichuan; Potel, Gregory; Nunes, Filomena
2017-09-01
The calculable form of the R-matrix method has been previously shown to be a useful tool in approximately solving the Schrodinger equation in nuclear scattering problems. We use this technique combined with the Gauss quadrature for the Lagrange-mesh method to efficiently solve for the wave functions of projectile nuclei in low energy collisions (1-100 MeV) involving an arbitrary number of channels. We include the local Woods-Saxon potential, the non-local potential of Perey and Buck, a Coulomb potential, and a coupling potential to computationally solve for the wave function of two nuclei at short distances. Object oriented programming is used to increase modularity, and parallel programming techniques are introduced to reduce computation time. We conclude that the R-matrix method is an effective method to predict the wave functions of nuclei in scattering problems involving both multiple channels and non-local potentials. Michigan State University iCER ACRES REU.
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NASA Astrophysics Data System (ADS)
Jia, Weile; Lin, Lin
2017-10-01
Fermi operator expansion (FOE) methods are powerful alternatives to diagonalization type methods for solving Kohn-Sham density functional theory (KSDFT). One example is the pole expansion and selected inversion (PEXSI) method, which approximates the Fermi operator by rational matrix functions and reduces the computational complexity to at most quadratic scaling for solving KSDFT. Unlike diagonalization type methods, the chemical potential often cannot be directly read off from the result of a single step of evaluation of the Fermi operator. Hence multiple evaluations are needed to be sequentially performed to compute the chemical potential to ensure the correct number of electrons within a given tolerance. This hinders the performance of FOE methods in practice. In this paper, we develop an efficient and robust strategy to determine the chemical potential in the context of the PEXSI method. The main idea of the new method is not to find the exact chemical potential at each self-consistent-field (SCF) iteration but to dynamically and rigorously update the upper and lower bounds for the true chemical potential, so that the chemical potential reaches its convergence along the SCF iteration. Instead of evaluating the Fermi operator for multiple times sequentially, our method uses a two-level strategy that evaluates the Fermi operators in parallel. In the regime of full parallelization, the wall clock time of each SCF iteration is always close to the time for one single evaluation of the Fermi operator, even when the initial guess is far away from the converged solution. We demonstrate the effectiveness of the new method using examples with metallic and insulating characters, as well as results from ab initio molecular dynamics.
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Jia, Weile; Lin, Lin
2017-10-14
Fermi operator expansion (FOE) methods are powerful alternatives to diagonalization type methods for solving Kohn-Sham density functional theory (KSDFT). One example is the pole expansion and selected inversion (PEXSI) method, which approximates the Fermi operator by rational matrix functions and reduces the computational complexity to at most quadratic scaling for solving KSDFT. Unlike diagonalization type methods, the chemical potential often cannot be directly read off from the result of a single step of evaluation of the Fermi operator. Hence multiple evaluations are needed to be sequentially performed to compute the chemical potential to ensure the correct number of electrons within a given tolerance. This hinders the performance of FOE methods in practice. In this paper, we develop an efficient and robust strategy to determine the chemical potential in the context of the PEXSI method. The main idea of the new method is not to find the exact chemical potential at each self-consistent-field (SCF) iteration but to dynamically and rigorously update the upper and lower bounds for the true chemical potential, so that the chemical potential reaches its convergence along the SCF iteration. Instead of evaluating the Fermi operator for multiple times sequentially, our method uses a two-level strategy that evaluates the Fermi operators in parallel. In the regime of full parallelization, the wall clock time of each SCF iteration is always close to the time for one single evaluation of the Fermi operator, even when the initial guess is far away from the converged solution. We demonstrate the effectiveness of the new method using examples with metallic and insulating characters, as well as results from ab initio molecular dynamics.
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Electrical Methods: Self-Potential (SP) Method
Various potentials are produced in native ground or within the subsurface altered by our actions. Natural potentials occur about dissimilar materials, near varying concentrations of electrolytic solutions, and due to the flow of fluids.
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Eigenenergies of a Relativistic Particle in an Infinite Range Linear Potential Using WKB Method
ERIC Educational Resources Information Center
Shivalingaswamy, T.; Kagali, B. A.
2011-01-01
Energy eigenvalues for a non-relativistic particle in a linear potential well are available. In this paper we obtain the eigenenergies for a relativistic spin less particle in a similar potential using an extension of the well-known WKB method treating the potential as the time component of a four-vector potential. Since genuine bound states do…
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ERIC Educational Resources Information Center
Ikram, I. Mohamed; Rabinal, M. K.; Mulimani, B. G.
2009-01-01
Here, we propose a simple method for measuring the built-in potential and its temperature dependence of a photodiode by a photosaturation technique. The experimental design facilitates both current-voltage and null voltage measurements as a function of white light intensity. This method gives the built-in potential directly; as a result its…
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Improving Cardiac Action Potential Measurements: 2D and 3D Cell Culture.
Daily, Neil J; Yin, Yue; Kemanli, Pinar; Ip, Brian; Wakatsuki, Tetsuro
2015-11-01
Progress in the development of assays for measuring cardiac action potential is crucial for the discovery of drugs for treating cardiac disease and assessing cardiotoxicity. Recently, high-throughput methods for assessing action potential using induced pluripotent stem cell (iPSC) derived cardiomyocytes in both two-dimensional monolayer cultures and three-dimensional tissues have been developed. We describe an improved method for assessing cardiac action potential using an ultra-fast cost-effective plate reader with commercially available dyes. Our methods improve dramatically the detection of the fluorescence signal from these dyes and make way for the development of more high-throughput methods for cardiac drug discovery and cardiotoxicity.
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Ohura, Hiroki; Imato, Toshihiko
2011-01-01
Two analytical methods, which prove the utility of a potentiometric flow injection technique for determining various redox species, based on the use of some redox potential buffers, are reviewed. The first is a potentiometric flow injection method in which a redox couple such as Fe(III)-Fe(II), Fe(CN)6 3−-Fe(CN)(CN)6 4−, and bromide-bromine and a redox electrode or a combined platinum-bromide ion selective electrode are used. The analytical principle and advantages of the method are discussed, and several examples of its application are reported. Another example is a highly sensitive potentiometric flow injection method, in which a large transient potential change due to bromine or chlorine as an intermediate, generated during the reaction of the oxidative species with an Fe(III)-Fe(II) potential buffer containing bromide or chloride, is utilized. The analytical principle and details of the proposed method are described, and examples of several applications are described. The determination of trace amounts of hydrazine, based on the detection of a transient change in potential caused by the reaction with a Ce(IV)-Ce(III) potential buffer, is also described. PMID:21584280
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Hirshberg, Barak; Sagiv, Lior; Gerber, R Benny
2017-03-14
Algorithms for quantum molecular dynamics simulations that directly use ab initio methods have many potential applications. In this article, the ab initio classical separable potentials (AICSP) method is proposed as the basis for approximate algorithms of this type. The AICSP method assumes separability of the total time-dependent wave function of the nuclei and employs mean-field potentials that govern the dynamics of each degree of freedom. In the proposed approach, the mean-field potentials are determined by classical ab initio molecular dynamics simulations. The nuclear wave function can thus be propagated in time using the effective potentials generated "on the fly". As a test of the method for realistic systems, calculations of the stationary anharmonic frequencies of hydrogen stretching modes were carried out for several polyatomic systems, including three amino acids and the guanine-cytosine pair of nucleobases. Good agreement with experiments was found. The method scales very favorably with the number of vibrational modes and should be applicable for very large molecules, e.g., peptides. The method should also be applicable for properties such as vibrational line widths and line shapes. Work in these directions is underway.
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Mohammadi, Zohreh; Modabberi, Soroush; Jafari, Mohammad Reza; Ajayebi, Kimia Sadat
2015-06-01
Acid mine drainage (AMD) gives rise to several problems in sulfide-bearing mineral deposits whether in an ore body or in the mining wastes and tailings. Hence, several methods and parameters have been proposed to evaluate the acid-producing and acid-neutralizing potential of a material. This research compares common static methods for evaluation of acid-production potential of mining wastes in the Muteh gold mines by using 62 samples taken from six waste dumps around Senjedeh and Chah-Khatoun mines. According to a detailed mineralogical study, the waste materials are composed of mica-schist and quartz veins with a high amount of pyrite and are supposed to be susceptible to acid production, and upon a rainfall, they release acid drainage. All parameters introduced in different methods were calculated and compared in this research in order to predict the acid-generating and neutralization potential, including APP, NNP, MPA, NPR, and NAGpH. Based on the analytical results and calculation of different parameters, all methods are in a general consensus that DWS-02 and DWS-03 waste dumps are acid-forming which is clearly attributed to high content of pyrite in samples. DWS-04 is considered as non-acid forming in all methods except method 8 which is uncertain about its acid-forming potential and method 7 which considers a low potential for it. DWC-01 is acid-forming based on all methods except 8, 9, 10, and 11 which are also uncertain about its potential. The methods used are not reached to a compromise on DWS-01 and DWC-02 waste dumps. It is supposed that method 7 gives the conservationist results in all cases. Method 8 is unable to decide on some cases. It is recommended to use and rely on results provided by methods 1, 2, 3, and 12 for taking decisions for further studies. Therefore, according to the static tests used, the aforementioned criteria in selected methods can be used with much confidence as a rule of thumb estimation.
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Single-scale renormalisation group improvement of multi-scale effective potentials
NASA Astrophysics Data System (ADS)
Chataignier, Leonardo; Prokopec, Tomislav; Schmidt, Michael G.; Świeżewska, Bogumiła
2018-03-01
We present a new method for renormalisation group improvement of the effective potential of a quantum field theory with an arbitrary number of scalar fields. The method amounts to solving the renormalisation group equation for the effective potential with the boundary conditions chosen on the hypersurface where quantum corrections vanish. This hypersurface is defined through a suitable choice of a field-dependent value for the renormalisation scale. The method can be applied to any order in perturbation theory and it is a generalisation of the standard procedure valid for the one-field case. In our method, however, the choice of the renormalisation scale does not eliminate individual logarithmic terms but rather the entire loop corrections to the effective potential. It allows us to evaluate the improved effective potential for arbitrary values of the scalar fields using the tree-level potential with running coupling constants as long as they remain perturbative. This opens the possibility of studying various applications which require an analysis of multi-field effective potentials across different energy scales. In particular, the issue of stability of the scalar potential can be easily studied beyond tree level.
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A method of solid-solid phase equilibrium calculation by molecular dynamics
NASA Astrophysics Data System (ADS)
Karavaev, A. V.; Dremov, V. V.
2016-12-01
A method for evaluation of solid-solid phase equilibrium curves in molecular dynamics simulation for a given model of interatomic interaction is proposed. The method allows to calculate entropies of crystal phases and provides an accuracy comparable with that of the thermodynamic integration method by Frenkel and Ladd while it is much simpler in realization and less intense computationally. The accuracy of the proposed method was demonstrated in MD calculations of entropies for EAM potential for iron and for MEAM potential for beryllium. The bcc-hcp equilibrium curves for iron calculated for the EAM potential by the thermodynamic integration method and by the proposed one agree quite well.
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Recursion-transform method and potential formulae of the m × n cobweb and fan networks
NASA Astrophysics Data System (ADS)
Tan, Zhi-Zhong
2017-08-01
In this paper, we made a new breakthrough, which proposes a new Recursion-Transform (RT) method with potential parameters to evaluate the nodal potential in arbitrary resistor networks. For the first time, we found the exact potential formulae of arbitrary m× n cobweb and fan networks by the RT method, and the potential formulae of infinite and semi-infinite networks are derived. As applications, a series of interesting corollaries of potential formulae are given by using the general formula, the equivalent resistance formula is deduced by using the potential formula, and we find a new trigonometric identity by comparing two equivalence results with different forms. Project supported by the Natural Science Foundation of Jiangsu Province, China (Grant No. BK20161278).
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The imagework method in health and social science research.
Edgar, I R
1999-03-01
Existing alongside the traditional forms of qualitative social science research, there is a set of potential research methods that derive from experiential groupwork and the humanistic human potential movement and are only slightly used by researchers. Social science research has barely begun to use these powerful strategies that were developed originally for personal and group change but that are potentially applicable to the research domain. This article will locate these methods within the qualitative research domain and propose a novel view of their value. The study of the actual and potential use of one of these methods, imagework, will be the particular focus of this article. References to the use of artwork, sculpting, psychodrama, gestalt, and dreamwork will also be made. The hypothesis underpinning the author's approach is that experiential research methods such as imagework can elicit implicit knowledge and self-identifies of respondents in a way that other methods cannot.
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NASA Astrophysics Data System (ADS)
Kondrat'ev, B. P.
1993-06-01
A method is developed for the representation of the potential energy of homogeneous gravitating, as well as electrically charged, bodies in the form of special series. These series contain members consisting of products of the corresponding coefficients appearing in the expansion of external and internal Newtonian potentials in Legendre polynomial series. Several versions of the representation of potential energy through these series are possible. A formula which expresses potential energy not as a volume integral, as is the convention, but as an integral over the body surface is derived. The method is tested for the particular cases of sphere and ellipsoid, and the convergence of the found series is shown.
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A method to assess the potential effects of air pollution mitigation on healthcare costs.
Sætterstrøm, Bjørn; Kruse, Marie; Brønnum-Hansen, Henrik; Bønløkke, Jakob Hjort; Flachs, Esben Meulengracht; Sørensen, Jan
2012-01-01
The aim of this study was to develop a method to assess the potential effects of air pollution mitigation on healthcare costs and to apply this method to assess the potential savings related to a reduction in fine particle matter in Denmark. The effects of air pollution on health were used to identify "exposed" individuals (i.e., cases). Coronary heart disease, stroke, chronic obstructive pulmonary disease, and lung cancer were considered to be associated with air pollution. We used propensity score matching, two-part estimation, and Lin's method to estimate healthcare costs. Subsequently, we multiplied the number of saved cases due to mitigation with the healthcare costs to arrive to an expression for healthcare cost savings. The potential cost saving in the healthcare system arising from a modelled reduction in air pollution was estimated at €0.1-2.6 million per 100,000 inhabitants for the four diseases. We have illustrated an application of a method to assess the potential changes in healthcare costs due to a reduction in air pollution. The method relies on a large volume of administrative data and combines a number of established methods for epidemiological analysis.
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Reconstructing free-energy landscapes for nonequilibrium periodic potentials
NASA Astrophysics Data System (ADS)
López-Alamilla, N. J.; Jack, Michael W.; Challis, K. J.
2018-03-01
We present a method for reconstructing the free-energy landscape of overdamped Brownian motion on a tilted periodic potential. Our approach exploits the periodicity of the system by using the k -space form of the Smoluchowski equation and we employ an iterative approach to determine the nonequilibrium tilt. We reconstruct landscapes for a number of example potentials to show the applicability of the method to both deep and shallow wells and near-to- and far-from-equilibrium regimes. The method converges logarithmically with the number of Fourier terms in the potential.
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On numerical solution of the Schrödinger equation: the shooting method revisited
NASA Astrophysics Data System (ADS)
Indjin, D.; Todorović, G.; Milanović, V.; Ikonić, Z.
1995-09-01
An alternative formulation of the "shooting" method for a numerical solution of the Schrödinger equation is described for cases of general asymmetric one-dimensional potential (planar geometry), and spherically symmetric potential. The method relies on matching the asymptotic wavefunctions and the potential core region wavefunctions, in course of finding bound states energies. It is demonstrated in the examples of Morse and Kratzer potentials, where a high accuracy of the calculated eigenvalues is found, together with a considerable saving of the computation time.
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Programmable Potentials: Approximate N-body potentials from coarse-level logic.
Thakur, Gunjan S; Mohr, Ryan; Mezić, Igor
2016-09-27
This paper gives a systematic method for constructing an N-body potential, approximating the true potential, that accurately captures meso-scale behavior of the chemical or biological system using pairwise potentials coming from experimental data or ab initio methods. The meso-scale behavior is translated into logic rules for the dynamics. Each pairwise potential has an associated logic function that is constructed using the logic rules, a class of elementary logic functions, and AND, OR, and NOT gates. The effect of each logic function is to turn its associated potential on and off. The N-body potential is constructed as linear combination of the pairwise potentials, where the "coefficients" of the potentials are smoothed versions of the associated logic functions. These potentials allow a potentially low-dimensional description of complex processes while still accurately capturing the relevant physics at the meso-scale. We present the proposed formalism to construct coarse-grained potential models for three examples: an inhibitor molecular system, bond breaking in chemical reactions, and DNA transcription from biology. The method can potentially be used in reverse for design of molecular processes by specifying properties of molecules that can carry them out.
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Programmable Potentials: Approximate N-body potentials from coarse-level logic
NASA Astrophysics Data System (ADS)
Thakur, Gunjan S.; Mohr, Ryan; Mezić, Igor
2016-09-01
This paper gives a systematic method for constructing an N-body potential, approximating the true potential, that accurately captures meso-scale behavior of the chemical or biological system using pairwise potentials coming from experimental data or ab initio methods. The meso-scale behavior is translated into logic rules for the dynamics. Each pairwise potential has an associated logic function that is constructed using the logic rules, a class of elementary logic functions, and AND, OR, and NOT gates. The effect of each logic function is to turn its associated potential on and off. The N-body potential is constructed as linear combination of the pairwise potentials, where the “coefficients” of the potentials are smoothed versions of the associated logic functions. These potentials allow a potentially low-dimensional description of complex processes while still accurately capturing the relevant physics at the meso-scale. We present the proposed formalism to construct coarse-grained potential models for three examples: an inhibitor molecular system, bond breaking in chemical reactions, and DNA transcription from biology. The method can potentially be used in reverse for design of molecular processes by specifying properties of molecules that can carry them out.
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Programmable Potentials: Approximate N-body potentials from coarse-level logic
Thakur, Gunjan S.; Mohr, Ryan; Mezić, Igor
2016-01-01
This paper gives a systematic method for constructing an N-body potential, approximating the true potential, that accurately captures meso-scale behavior of the chemical or biological system using pairwise potentials coming from experimental data or ab initio methods. The meso-scale behavior is translated into logic rules for the dynamics. Each pairwise potential has an associated logic function that is constructed using the logic rules, a class of elementary logic functions, and AND, OR, and NOT gates. The effect of each logic function is to turn its associated potential on and off. The N-body potential is constructed as linear combination of the pairwise potentials, where the “coefficients” of the potentials are smoothed versions of the associated logic functions. These potentials allow a potentially low-dimensional description of complex processes while still accurately capturing the relevant physics at the meso-scale. We present the proposed formalism to construct coarse-grained potential models for three examples: an inhibitor molecular system, bond breaking in chemical reactions, and DNA transcription from biology. The method can potentially be used in reverse for design of molecular processes by specifying properties of molecules that can carry them out. PMID:27671683
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Dual stage potential field method for robotic path planning
NASA Astrophysics Data System (ADS)
Singh, Pradyumna Kumar; Parida, Pramod Kumar
2018-04-01
Path planning for autonomous mobile robots are the root for all autonomous mobile systems. Various methods are used for optimization of path to be followed by the autonomous mobile robots. Artificial potential field based path planning method is one of the most used methods for the researchers. Various algorithms have been proposed using the potential field approach. But in most of the common problems are encounters while heading towards the goal or target. i.e. local minima problem, zero potential regions problem, complex shaped obstacles problem, target near obstacle problem. In this paper we provide a new algorithm in which two types of potential functions are used one after another. The former one is to use to get the probable points and later one for getting the optimum path. In this algorithm we consider only the static obstacle and goal.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Zhang, Zhiqiang; Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706; Geng, Dalong
A simple and effective decoupled finite element analysis method was developed for simulating both the piezoelectric and flexoelectric effects of zinc oxide (ZnO) and barium titanate (BTO) nanowires (NWs). The piezoelectric potential distribution on a ZnO NW was calculated under three deformation conditions (cantilever, three-point, and four-point bending) and compared to the conventional fully coupled method. The discrepancies of the electric potential maximums from these two methods were found very small, validating the accuracy and effectiveness of the decoupled method. Both ZnO and BTO NWs yielded very similar potential distributions. Comparing the potential distributions induced by the piezoelectric and flexoelectricmore » effects, we identified that the middle segment of a four-point bending NW beam is the ideal place for measuring the flexoelectric coefficient, because the uniform parallel plate capacitor-like potential distribution in this region is exclusively induced by the flexoelectric effect. This decoupled method could provide a valuable guideline for experimental measurements of the piezoelectric effects and flexoelectric effects in the nanometer scale.« less
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NASA Astrophysics Data System (ADS)
Izmaylov, Artur F.; Staroverov, Viktor N.; Scuseria, Gustavo E.; Davidson, Ernest R.; Stoltz, Gabriel; Cancès, Eric
2007-02-01
We have recently formulated a new approach, named the effective local potential (ELP) method, for calculating local exchange-correlation potentials for orbital-dependent functionals based on minimizing the variance of the difference between a given nonlocal potential and its desired local counterpart [V. N. Staroverov et al., J. Chem. Phys. 125, 081104 (2006)]. Here we show that under a mildly simplifying assumption of frozen molecular orbitals, the equation defining the ELP has a unique analytic solution which is identical with the expression arising in the localized Hartree-Fock (LHF) and common energy denominator approximations (CEDA) to the optimized effective potential. The ELP procedure differs from the CEDA and LHF in that it yields the target potential as an expansion in auxiliary basis functions. We report extensive calculations of atomic and molecular properties using the frozen-orbital ELP method and its iterative generalization to prove that ELP results agree with the corresponding LHF and CEDA values, as they should. Finally, we make the case for extending the iterative frozen-orbital ELP method to full orbital relaxation.
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Charge-transfer modified embedded atom method dynamic charge potential for Li-Co-O system
NASA Astrophysics Data System (ADS)
Kong, Fantai; Longo, Roberto C.; Liang, Chaoping; Nie, Yifan; Zheng, Yongping; Zhang, Chenxi; Cho, Kyeongjae
2017-11-01
To overcome the limitation of conventional fixed charge potential methods for the study of Li-ion battery cathode materials, a dynamic charge potential method, charge-transfer modified embedded atom method (CT-MEAM), has been developed and applied to the Li-Co-O ternary system. The accuracy of the potential has been tested and validated by reproducing a variety of structural and electrochemical properties of LiCoO2. A detailed analysis on the local charge distribution confirmed the capability of this potential for dynamic charge modeling. The transferability of the potential is also demonstrated by its reliability in describing Li-rich Li2CoO2 and Li-deficient LiCo2O4 compounds, including their phase stability, equilibrium volume, charge states and cathode voltages. These results demonstrate that the CT-MEAM dynamic charge potential could help to overcome the challenge of modeling complex ternary transition metal oxides. This work can promote molecular dynamics studies of Li ion cathode materials and other important transition metal oxides systems that involve complex electrochemical and catalytic reactions.
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Charge-transfer modified embedded atom method dynamic charge potential for Li-Co-O system.
Kong, Fantai; Longo, Roberto C; Liang, Chaoping; Nie, Yifan; Zheng, Yongping; Zhang, Chenxi; Cho, Kyeongjae
2017-11-29
To overcome the limitation of conventional fixed charge potential methods for the study of Li-ion battery cathode materials, a dynamic charge potential method, charge-transfer modified embedded atom method (CT-MEAM), has been developed and applied to the Li-Co-O ternary system. The accuracy of the potential has been tested and validated by reproducing a variety of structural and electrochemical properties of LiCoO 2 . A detailed analysis on the local charge distribution confirmed the capability of this potential for dynamic charge modeling. The transferability of the potential is also demonstrated by its reliability in describing Li-rich Li 2 CoO 2 and Li-deficient LiCo 2 O 4 compounds, including their phase stability, equilibrium volume, charge states and cathode voltages. These results demonstrate that the CT-MEAM dynamic charge potential could help to overcome the challenge of modeling complex ternary transition metal oxides. This work can promote molecular dynamics studies of Li ion cathode materials and other important transition metal oxides systems that involve complex electrochemical and catalytic reactions.
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The Calculation of Potential Energy Curves of Diatomic Molecules: The RKR Method.
ERIC Educational Resources Information Center
Castano, F.; And Others
1983-01-01
The RKR method for determining accurate potential energy curves is described. Advantages of using the method (compared to Morse procedure) and a TRS-80 computer program which calculates the classical turning points by an RKR method are also described. The computer program is available from the author upon request. (Author/JN)
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NASA Astrophysics Data System (ADS)
Russel, Fhillipo; Damayanti, Astrid; Pin, Tjiong Giok
2018-02-01
This research is about geothermal potential of Mount Karang, Banten Province which is based on the characteristics of the region. This research method used is geochemistry sample of hot springs and integrated with GIS method for spatial of geothermal potential. Based on the geothermal potential, Mount Karang is divided into three regions, ie high potential, normal potential, and low potential. The high geothermal potential region covers an area of 24.16 Km2 and which there are Cisolong and Banjar 2 hot springs. The normal potential covers Kawah hot spring. Index of the fault of Mount Karang region is one of the significant physical characteristics to determine geothermal potential.
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Exploring a potential energy surface by machine learning for characterizing atomic transport
NASA Astrophysics Data System (ADS)
Kanamori, Kenta; Toyoura, Kazuaki; Honda, Junya; Hattori, Kazuki; Seko, Atsuto; Karasuyama, Masayuki; Shitara, Kazuki; Shiga, Motoki; Kuwabara, Akihide; Takeuchi, Ichiro
2018-03-01
We propose a machine-learning method for evaluating the potential barrier governing atomic transport based on the preferential selection of dominant points for atomic transport. The proposed method generates numerous random samples of the entire potential energy surface (PES) from a probabilistic Gaussian process model of the PES, which enables defining the likelihood of the dominant points. The robustness and efficiency of the method are demonstrated on a dozen model cases for proton diffusion in oxides, in comparison with a conventional nudge elastic band method.
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An assessment of two methods for identifying undocumented levees using remotely sensed data
Czuba, Christiana R.; Williams, Byron K.; Westman, Jack; LeClaire, Keith
2015-01-01
Many undocumented and commonly unmaintained levees exist in the landscape complicating flood forecasting, risk management, and emergency response. This report describes a pilot study completed by the U.S. Geological Survey in cooperation with the U.S. Army Corps of Engineers to assess two methods to identify undocumented levees by using remotely sensed, high-resolution topographic data. For the first method, the U.S. Army Corps of Engineers examined hillshades computed from a digital elevation model that was derived from light detection and ranging (lidar) to visually identify potential levees and then used detailed site visits to assess the validity of the identifications. For the second method, the U.S. Geological Survey applied a wavelet transform to a lidar-derived digital elevation model to identify potential levees. The hillshade method was applied to Delano, Minnesota, and the wavelet-transform method was applied to Delano and Springfield, Minnesota. Both methods were successful in identifying levees but also identified other features that required interpretation to differentiate from levees such as constructed barriers, high banks, and bluffs. Both methods are complementary to each other, and a potential conjunctive method for testing in the future includes (1) use of the wavelet-transform method to rapidly identify slope-break features in high-resolution topographic data, (2) further examination of topographic data using hillshades and aerial photographs to classify features and map potential levees, and (3) a verification check of each identified potential levee with local officials and field visits.
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FINITE EXPANSION METHOD FOR THE CALCULATION AND INTERPRETATION OF MOLECULAR ELECTROSTATIC POTENTIALS
Because it is useful to have the molecular electrostatic potential as an element in a complex scheme to assess the toxicity of large molecules, efficient and reliable methods are needed for the calculation and characterization of these potentials. A multicenter multipole expansio...
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Alvarez, Isaac; de la Torre, Angel; Sainz, Manuel; Roldan, Cristina; Schoesser, Hansjoerg; Spitzer, Philipp
2007-09-15
Stimulus artifact is one of the main limitations when considering electrically evoked compound action potential for clinical applications. Alternating stimulation (average of recordings obtained with anodic-cathodic and cathodic-anodic bipolar stimulation pulses) is an effective method to reduce stimulus artifact when evoked potentials are recorded. In this paper we extend the concept of alternating stimulation by combining anodic-cathodic and cathodic-anodic recordings with a weight in general different to 0.5. We also provide an automatic method to obtain an estimation of the optimal weights. Comparison with conventional alternating, triphasic stimulation and masker-probe paradigm shows that the generalized alternating method improves the quality of electrically evoked compound action potential responses.
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Analysis on Potential of Electric Energy Market based on Large Industrial Consumer
NASA Astrophysics Data System (ADS)
Lin, Jingyi; Zhu, Xinzhi; Yang, Shuo; Xia, Huaijian; Yang, Di; Li, Hao; Lin, Haiying
2018-01-01
The implementation of electric energy substitution by enterprises plays an important role in promoting the development of energy conservation and emission reduction in china. In order to explore alternative energy potential of industrial enterprises, to simulate and analyze the process of industrial enterprises, identify high energy consumption process and equipment, give priority to alternative energy technologies, and determine the enterprise electric energy substitution potential predictive value, this paper constructs the evaluation model of the influence factors of the electric energy substitution potential of industrial enterprises, and uses the combined weight method to determine the weight value of the evaluation factors to calculate the target value of the electric energy substitution potential. Taking the iron and steel industry as an example, this method is used to excavate the potential. The results show that the method can effectively tap the potential of the electric power industry
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Toyama, F.M.; Nogami, Y.; Zhao, Z.
1993-02-01
For the Dirac equation in one space dimension with a potential of the Lorentz scalar type, we present a complete solution for the problem of constructing a transparent potential. This is a relativistic extension of the Kay-Moses method which was developed for the nonrelativistic Schroedinger equation. There is an infinite family of transparent potentials. The potentials are all related to solutions of a class of coupled, nonlinear Dirac equations. In addition, it is argued that an admixture of a Lorentz vector component in the potential impairs perfect transparency.
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ERIC Educational Resources Information Center
Wilder, David A; Therrien, Kelly; Wine, Byron
2006-01-01
Two methods of assessing preference for stimuli (i.e., potential reinforcers) were compared for adult administrative assistant employees. During Phase 1, a survey method and a verbal choice method of assessing preference for 6 stimuli were administered. During Phase 2, a coupon system was used to determine which categories of stimuli actually…
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Electrochemical nitridation of metal surfaces
Wang, Heli; Turner, John A.
2015-06-30
Electrochemical nitridation of metals and the produced metals are disclosed. An exemplary method of electrochemical nitridation of metals comprises providing an electrochemical solution at low temperature. The method also comprises providing a three-electrode potentiostat system. The method also comprises stabilizing the three-electrode potentiostat system at open circuit potential. The method also comprises applying a cathodic potential to a metal.
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NASA Technical Reports Server (NTRS)
Jones, Henry E.
1997-01-01
A study of the full-potential modeling of a blade-vortex interaction was made. A primary goal of this study was to investigate the effectiveness of the various methods of modeling the vortex. The model problem restricts the interaction to that of an infinite wing with an infinite line vortex moving parallel to its leading edge. This problem provides a convenient testing ground for the various methods of modeling the vortex while retaining the essential physics of the full three-dimensional interaction. A full-potential algorithm specifically tailored to solve the blade-vortex interaction (BVI) was developed to solve this problem. The basic algorithm was modified to include the effect of a vortex passing near the airfoil. Four different methods of modeling the vortex were used: (1) the angle-of-attack method, (2) the lifting-surface method, (3) the branch-cut method, and (4) the split-potential method. A side-by-side comparison of the four models was conducted. These comparisons included comparing generated velocity fields, a subcritical interaction, and a critical interaction. The subcritical and critical interactions are compared with experimentally generated results. The split-potential model was used to make a survey of some of the more critical parameters which affect the BVI.
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Gordeev, S A; Voronin, S G
2016-01-01
To analyze the efficacy of modified (passive radiocarpal articulation flexion/extension) and «standard» (passive radiocarpal articulation flexion) methods of kinesthetic evoked potentials for proprioceptive sensitivity assessment in healthy subjects and patients with spondylotic cervical myelopathy. The study included 14 healthy subjects (4 women and 10 men, mean age 54.1±10.5 years) and 8 patients (2 women and 6 men, mean age 55.8±10.9 years) with spondylotic cervical myelopathy. Muscle-joint sensation was examined during the clinical study. A modified method of kinesthetic evoked potentials was developed. This method differed from the "standard" one by the organization of a cycle including several passive movements,where each new movement differed from the preceding one by the direction. The modified method of kinesthetic evoked potentials ensures more reliable kinesthetic sensitivity assessment due to movement variability. Asignificant increaseof the latent periods of the early components of the response was found in patients compared to healthy subjects. The modified method of kinesthetic evoked potentials can be used for objective diagnosis of proprioceptive sensitivity disorders in patients with spondylotic cervical myelopathy.
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Erdősi, Orsolya; Szakmár, Katalin; Reichart, Olivér; Szili, Zsuzsanna; László, Noémi; Székely Körmöczy, Péter; Laczay, Péter
2014-09-01
The incidence of outbreaks of foodborne listeriosis has indicated the need for a reliable and rapid detection of the microbe in different foodstuffs. A method combining redox potential measurement and real-time polymerase chain reaction (PCR) was developed to detect Listeria monocytogenes in artificially contaminated raw milk and soft cheese. Food samples of 25 g or 25 ml were homogenised in 225 ml of Listeria Enrichment Broth (LEB) with Oxford supplement, and the redox potential measurement technique was applied. For Listeria species the measuring time was maximum 34 h. The absence of L. monocytogenes could reliably be proven by the redox potential measurement method, but Listeria innocua and Bacillus subtilis could not be differentiated from L. monocytogenes on the basis of the redox curves. The presence of L. monocytogenes had to be confirmed by real-time PCR. The combination of these two methods proved to detect < 10 cfu/g of L. monocytogenes in a cost- and time-effective manner. This method can potentially be used as an alternative to the standard nutrient method for the rapid detection of L. monocytogenes in food.
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40 CFR 63.1046 - Test methods and procedures.
Code of Federal Regulations, 2013 CFR
2013-07-01
... Method 21 of 40 CFR part 60, appendix A. Each potential leak interface (i.e., a location where organic vapor leakage could occur) on the cover and associated closure devices shall be checked. Potential leak... 60, appendix A. (7) Each potential leak interface shall be checked by traversing the instrument probe...
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40 CFR 63.1046 - Test methods and procedures.
Code of Federal Regulations, 2011 CFR
2011-07-01
... Method 21 of 40 CFR part 60, appendix A. Each potential leak interface (i.e., a location where organic vapor leakage could occur) on the cover and associated closure devices shall be checked. Potential leak... 60, appendix A. (7) Each potential leak interface shall be checked by traversing the instrument probe...
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40 CFR 63.1046 - Test methods and procedures.
Code of Federal Regulations, 2012 CFR
2012-07-01
... Method 21 of 40 CFR part 60, appendix A. Each potential leak interface (i.e., a location where organic vapor leakage could occur) on the cover and associated closure devices shall be checked. Potential leak... 60, appendix A. (7) Each potential leak interface shall be checked by traversing the instrument probe...
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40 CFR 63.945 - Test methods and procedures.
Code of Federal Regulations, 2011 CFR
2011-07-01
..., appendix A. Each potential leak interface (i.e., a location where organic vapor leakage could occur) on the cover and associated closure devices shall be checked. Potential leak interfaces that are associated... determined according to the procedures in Method 21 of 40 CFR part 60, appendix A. (7) Each potential leak...
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40 CFR 63.945 - Test methods and procedures.
Code of Federal Regulations, 2013 CFR
2013-07-01
..., appendix A. Each potential leak interface (i.e., a location where organic vapor leakage could occur) on the cover and associated closure devices shall be checked. Potential leak interfaces that are associated... determined according to the procedures in Method 21 of 40 CFR part 60, appendix A. (7) Each potential leak...
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40 CFR 63.925 - Test methods and procedures.
Code of Federal Regulations, 2013 CFR
2013-07-01
.... Each potential leak interface (i.e., a location where organic vapor leakage could occur) on the cover and associated closure devices shall be checked. Potential leak interfaces that are associated with... according to the procedures in Method 21 of 40 CFR part 60, appendix A. (7) Each potential leak interface...
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40 CFR 63.925 - Test methods and procedures.
Code of Federal Regulations, 2012 CFR
2012-07-01
.... Each potential leak interface (i.e., a location where organic vapor leakage could occur) on the cover and associated closure devices shall be checked. Potential leak interfaces that are associated with... according to the procedures in Method 21 of 40 CFR part 60, appendix A. (7) Each potential leak interface...
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40 CFR 63.905 - Test methods and procedures.
Code of Federal Regulations, 2012 CFR
2012-07-01
.... Each potential leak interface (i.e., a location where organic vapor leakage could occur) on the cover and associated closure devices shall be checked. Potential leak interfaces that are associated with... according to the procedures in Method 21 of 40 CFR part 60, appendix A. (7) Each potential leak interface...
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40 CFR 63.905 - Test methods and procedures.
Code of Federal Regulations, 2011 CFR
2011-07-01
.... Each potential leak interface (i.e., a location where organic vapor leakage could occur) on the cover and associated closure devices shall be checked. Potential leak interfaces that are associated with... according to the procedures in Method 21 of 40 CFR part 60, appendix A. (7) Each potential leak interface...
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40 CFR 63.905 - Test methods and procedures.
Code of Federal Regulations, 2013 CFR
2013-07-01
.... Each potential leak interface (i.e., a location where organic vapor leakage could occur) on the cover and associated closure devices shall be checked. Potential leak interfaces that are associated with... according to the procedures in Method 21 of 40 CFR part 60, appendix A. (7) Each potential leak interface...
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40 CFR 63.925 - Test methods and procedures.
Code of Federal Regulations, 2011 CFR
2011-07-01
.... Each potential leak interface (i.e., a location where organic vapor leakage could occur) on the cover and associated closure devices shall be checked. Potential leak interfaces that are associated with... according to the procedures in Method 21 of 40 CFR part 60, appendix A. (7) Each potential leak interface...
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40 CFR 63.945 - Test methods and procedures.
Code of Federal Regulations, 2012 CFR
2012-07-01
..., appendix A. Each potential leak interface (i.e., a location where organic vapor leakage could occur) on the cover and associated closure devices shall be checked. Potential leak interfaces that are associated... determined according to the procedures in Method 21 of 40 CFR part 60, appendix A. (7) Each potential leak...
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Constructing a multidimensional free energy surface like a spider weaving a web.
Chen, Changjun
2017-10-15
Complete free energy surface in the collective variable space provides important information of the reaction mechanisms of the molecules. But, sufficient sampling in the collective variable space is not easy. The space expands quickly with the number of the collective variables. To solve the problem, many methods utilize artificial biasing potentials to flatten out the original free energy surface of the molecule in the simulation. Their performances are sensitive to the definitions of the biasing potentials. Fast-growing biasing potential accelerates the sampling speed but decreases the accuracy of the free energy result. Slow-growing biasing potential gives an optimized result but needs more simulation time. In this article, we propose an alternative method. It adds the biasing potential to a representative point of the molecule in the collective variable space to improve the conformational sampling. And the free energy surface is calculated from the free energy gradient in the constrained simulation, not given by the negative of the biasing potential as previous methods. So the presented method does not require the biasing potential to remove all the barriers and basins on the free energy surface exactly. Practical applications show that the method in this work is able to produce the accurate free energy surfaces for different molecules in a short time period. The free energy errors are small in the cases of various biasing potentials. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
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NASA Astrophysics Data System (ADS)
Orozco Cortés, Luis Fernando; Fernández García, Nicolás
2014-05-01
A method to obtain the general solution of any constant piecewise potential is presented, this is achieved by means of the analysis of the transfer matrices in each cutoff. The resonance phenomenon together with the supersymmetric quantum mechanics technique allow us to construct a wide family of complex potentials which can be used as theoretical models for optical systems. The method is applied to the particular case for which the potential function has six cutoff points.
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The Noninvasive Measurement of X-Ray Tube Potential.
NASA Astrophysics Data System (ADS)
Ranallo, Frank Nunzio
In this thesis I briefly describe the design of clinical x-ray imaging systems and also the various methods of measuring x-ray tube potential, both invasive and noninvasive. I also discuss the meaning and usage of the quantities tube potential (kV) and peak tube potential (kVp) with reference to x-ray systems used in medical imaging. I propose that there exist several quantities which describe different important aspects of the tube potential as a function of time. These quantities are measurable and can be well defined. I have developed a list of definitions of these quantities along with suggested names and symbols. I describe the development and physical principles of a superior noninvasive method of tube potential measurement along with the instrumentation used to implement this method. This thesis research resulted in the development of several commercial kVp test devices (or "kVp Meters") for which the actual measurement procedure is simple, rapid, and reliable compared to other methods, invasive or noninvasive. These kVp test devices provide measurements with a high level of accuracy and reliability over a wide range of test conditions. They provide results which are more reliable and clinically meaningful than many other, more primary and invasive methods. The errors inherent in these new kVp test devices were investigated and methods to minimize them are discussed.
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Yang, Yunze; Liu, Xian-Wei; Wang, Hui; Yu, Hui; Guan, Yan; Wang, Shaopeng; Tao, Nongjian
2018-03-28
Action potentials in neurons have been studied traditionally by intracellular electrophysiological recordings and more recently by the fluorescence detection methods. Here we describe a label-free optical imaging method that can measure mechanical motion in single cells with a sub-nanometer detection limit. Using the method, we have observed sub-nanometer mechanical motion accompanying the action potential in single mammalian neurons by averaging the repeated action potential spikes. The shape and width of the transient displacement are similar to those of the electrically recorded action potential, but the amplitude varies from neuron to neuron, and from one region of a neuron to another, ranging from 0.2-0.4 nm. The work indicates that action potentials may be studied noninvasively in single mammalian neurons by label-free imaging of the accompanying sub-nanometer mechanical motion.
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Novel scheme to compute chemical potentials of chain molecules on a lattice
NASA Astrophysics Data System (ADS)
Mooij, G. C. A. M.; Frenkel, D.
We present a novel method that allows efficient computation of the total number of allowed conformations of a chain molecule in a dense phase. Using this method, it is possible to estimate the chemical potential of such a chain molecule. We have tested the present method in simulations of a two-dimensional monolayer of chain molecules on a lattice (Whittington-Chapman model) and compared it with existing schemes to compute the chemical potential. We find that the present approach is two to three orders of magnitude faster than the most efficient of the existing methods.
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Streaming potentials in gramicidin channels measured with ion-selective microelectrodes.
Tripathi, S; Hladky, S B
1998-01-01
Streaming potentials have been measured for gramicidin channels with a new method employing ion-selective microelectrodes. It is shown that ideally ion-selective electrodes placed at the membrane surface record the true streaming potential. Using this method for ion concentrations below 100 mM, approximately seven water molecules are transported whenever a sodium, potassium, or cesium ion, passes through the channel. This new method confirms earlier measurements (Rosenberg, P.A., and A. Finkelstein. 1978. Interaction of ions and water in gramicidin A channels. J. Gen. Physiol. 72:327-340) in which the streaming potentials were calculated as the difference between electrical potentials measured in the presence of gramicidin and in the presence of the ion carriers valinomycin and nonactin. PMID:9635745
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A regularization method for extrapolation of solar potential magnetic fields
NASA Technical Reports Server (NTRS)
Gary, G. A.; Musielak, Z. E.
1992-01-01
The mathematical basis of a Tikhonov regularization method for extrapolating the chromospheric-coronal magnetic field using photospheric vector magnetograms is discussed. The basic techniques show that the Cauchy initial value problem can be formulated for potential magnetic fields. The potential field analysis considers a set of linear, elliptic partial differential equations. It is found that, by introducing an appropriate smoothing of the initial data of the Cauchy potential problem, an approximate Fourier integral solution is found, and an upper bound to the error in the solution is derived. This specific regularization technique, which is a function of magnetograph measurement sensitivities, provides a method to extrapolate the potential magnetic field above an active region into the chromosphere and low corona.
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Research on social communication network evolution based on topology potential distribution
NASA Astrophysics Data System (ADS)
Zhao, Dongjie; Jiang, Jian; Li, Deyi; Zhang, Haisu; Chen, Guisheng
2011-12-01
Aiming at the problem of social communication network evolution, first, topology potential is introduced to measure the local influence among nodes in networks. Second, from the perspective of topology potential distribution the method of network evolution description based on topology potential distribution is presented, which takes the artificial intelligence with uncertainty as basic theory and local influence among nodes as essentiality. Then, a social communication network is constructed by enron email dataset, the method presented is used to analyze the characteristic of the social communication network evolution and some useful conclusions are got, implying that the method is effective, which shows that topology potential distribution can effectively describe the characteristic of sociology and detect the local changes in social communication network.
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NASA Astrophysics Data System (ADS)
Jensen, Daniel; Wasserman, Adam; Baczewski, Andrew
The construction of approximations to the exchange-correlation potential for warm dense matter (WDM) is a topic of significant recent interest. In this work, we study the inverse problem of Kohn-Sham (KS) DFT as a means of guiding functional design at zero temperature and in WDM. Whereas the forward problem solves the KS equations to produce a density from a specified exchange-correlation potential, the inverse problem seeks to construct the exchange-correlation potential from specified densities. These two problems require different computational methods and convergence criteria despite sharing the same mathematical equations. We present two new inversion methods based on constrained variational and PDE-constrained optimization methods. We adapt these methods to finite temperature calculations to reveal the exchange-correlation potential's temperature dependence in WDM-relevant conditions. The different inversion methods presented are applied to both non-interacting and interacting model systems for comparison. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Security Administration under contract DE-AC04-94.
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Mendelev, M. I.; Underwood, T. L.; Ackland, G. J.
2016-10-17
New interatomic potentials describing defects, plasticity, and high temperature phase transitions for Ti are presented. Fitting the martensitic hcp-bcc phase transformation temperature requires an efficient and accurate method to determine it. We apply a molecular dynamics method based on determination of the melting temperature of competing solid phases, and Gibbs-Helmholtz integration, and a lattice-switch Monte Carlo method: these agree on the hcp-bcc transformation temperatures to within 2 K. We were able to develop embedded atom potentials which give a good fit to either low or high temperature data, but not both. The first developed potential (Ti1) reproduces the hcp-bcc transformationmore » and melting temperatures and is suitable for the simulation of phase transitions and bcc Ti. Two other potentials (Ti2 and Ti3) correctly describe defect properties and can be used to simulate plasticity or radiation damage in hcp Ti. The fact that a single embedded atom method potential cannot describe both low and high temperature phases may be attributed to neglect of electronic degrees of freedom, notably bcc has a much higher electronic entropy. As a result, a temperature-dependent potential obtained from the combination of potentials Ti1 and Ti2 may be used to simulate Ti properties at any temperature.« less
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Exact exchange-correlation potentials of singlet two-electron systems
NASA Astrophysics Data System (ADS)
Ryabinkin, Ilya G.; Ospadov, Egor; Staroverov, Viktor N.
2017-10-01
We suggest a non-iterative analytic method for constructing the exchange-correlation potential, v XC ( r ) , of any singlet ground-state two-electron system. The method is based on a convenient formula for v XC ( r ) in terms of quantities determined only by the system's electronic wave function, exact or approximate, and is essentially different from the Kohn-Sham inversion technique. When applied to Gaussian-basis-set wave functions, the method yields finite-basis-set approximations to the corresponding basis-set-limit v XC ( r ) , whereas the Kohn-Sham inversion produces physically inappropriate (oscillatory and divergent) potentials. The effectiveness of the procedure is demonstrated by computing accurate exchange-correlation potentials of several two-electron systems (helium isoelectronic series, H2, H3 + ) using common ab initio methods and Gaussian basis sets.
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Neural network approach for the calculation of potential coefficients in quantum mechanics
NASA Astrophysics Data System (ADS)
Ossandón, Sebastián; Reyes, Camilo; Cumsille, Patricio; Reyes, Carlos M.
2017-05-01
A numerical method based on artificial neural networks is used to solve the inverse Schrödinger equation for a multi-parameter class of potentials. First, the finite element method was used to solve repeatedly the direct problem for different parametrizations of the chosen potential function. Then, using the attainable eigenvalues as a training set of the direct radial basis neural network a map of new eigenvalues was obtained. This relationship was later inverted and refined by training an inverse radial basis neural network, allowing the calculation of the unknown parameters and therefore estimating the potential function. Three numerical examples are presented in order to prove the effectiveness of the method. The results show that the method proposed has the advantage to use less computational resources without a significant accuracy loss.
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Using the Screened Coulomb Potential to Illustrate the Variational Method
ERIC Educational Resources Information Center
Zuniga, Jose; Bastida, Adolfo; Requena, Alberto
2012-01-01
The screened Coulomb potential, or Yukawa potential, is used to illustrate the application of the single and linear variational methods. The trial variational functions are expressed in terms of Slater-type functions, for which the integrals needed to carry out the variational calculations are easily evaluated in closed form. The variational…
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Cruff, R.W.; Thompson, T.H.
1967-01-01
This study compared potential evapotranspiration, computed from climatological data by each of six empirical methods, with pan evaporation adjusted to equivalent lake evaporation by regional coefficients. The six methods tested were the Thornthwaite, U.S. Weather Bureau (a modification of the Permian method), Lowry-Johnson, Blaney-Criddle, Lane, and Hamon methods. The test was limited to 25 sites in the arid and subhumid parts of Arizona, California, and Nevada, where pan evaporation and concurrent climatological data were available. However, some of the sites lacked complete climatological data for the application of all six methods. Average values of adjusted pan evaporation and computed potential evapotransp4ration were compared for two periods---the calendar year and the 6-month period from May 1 through October 31. The 25 sites sampled a wide range of climatic conditions. Ten sites (group 1) were in a highly arid environment and four (group 2) were in an arid environment that was modified by extensive irrigation. The remaining 11 sites (group 3) were in a subhumid environment. Only the Weather Bureau method gave estimates of potential evapotranspiration that closely agreed with the adjusted pan evaporation at all sites where the method was used. However, lack of climatological data restricted the use of the Weather Bureau method to seven sites. Results obtained by use of the Thornthwaite, Lowry-Johnson, and Hamon methods were consistently low. Results obtained by use of the Lane method agreed with adjusted pan evaporation at the group 1 sites but were consistently high at the group 2 and 3 sites. During the analysis it became apparent that adjusted pan evaporation in an arid environment (group 1 sites) was a spurious standard for evaluating the reliability of .the methods that were tested. Group 1 data were accordingly not considered when making conclusions as ,to which of the six methods tested was best. The results of this study for group 2 and 3 data indicated that the Blaney-Criddle method, which uses climatological data that can be readily obtained or deduced, was the most practical of the six methods for estimating potential evapotranspiration. At all 15 sites in the two environments, potential evapotranspiration computed by the Blaney-Criddle method checked the adjusted pan evaporation within ?22 percent. This percentage range is generally considered to be the range of reliability for estimating lake evaporation from evaporation pans.
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Validating a Coarse-Grained Potential Energy Function through Protein Loop Modelling
MacDonald, James T.; Kelley, Lawrence A.; Freemont, Paul S.
2013-01-01
Coarse-grained (CG) methods for sampling protein conformational space have the potential to increase computational efficiency by reducing the degrees of freedom. The gain in computational efficiency of CG methods often comes at the expense of non-protein like local conformational features. This could cause problems when transitioning to full atom models in a hierarchical framework. Here, a CG potential energy function was validated by applying it to the problem of loop prediction. A novel method to sample the conformational space of backbone atoms was benchmarked using a standard test set consisting of 351 distinct loops. This method used a sequence-independent CG potential energy function representing the protein using -carbon positions only and sampling conformations with a Monte Carlo simulated annealing based protocol. Backbone atoms were added using a method previously described and then gradient minimised in the Rosetta force field. Despite the CG potential energy function being sequence-independent, the method performed similarly to methods that explicitly use either fragments of known protein backbones with similar sequences or residue-specific /-maps to restrict the search space. The method was also able to predict with sub-Angstrom accuracy two out of seven loops from recently solved crystal structures of proteins with low sequence and structure similarity to previously deposited structures in the PDB. The ability to sample realistic loop conformations directly from a potential energy function enables the incorporation of additional geometric restraints and the use of more advanced sampling methods in a way that is not possible to do easily with fragment replacement methods and also enable multi-scale simulations for protein design and protein structure prediction. These restraints could be derived from experimental data or could be design restraints in the case of computational protein design. C++ source code is available for download from http://www.sbg.bio.ic.ac.uk/phyre2/PD2/. PMID:23824634
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Direct current electrical potential measurement of the growth of small cracks
NASA Technical Reports Server (NTRS)
Gangloff, Richard P.; Slavik, Donald C.; Piascik, Robert S.; Van Stone, Robert H.
1992-01-01
The analytical and experimental aspects of the direct-current electrical potential difference (dcEPD) method for continuous monitoring of the growth kinetics of short (50 to 500 microns) fatigue cracks are reviewed, and successful applications of the deEPD method to study fatigue crack propagation in a variety of metallic alloys exposed to various environments are described. Particular attention is given to the principle of the dcEPD method, the analytical electrical potential calibration relationships, and the experimental procedures and equipment.
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2017-01-01
Methodology 3 2.1 Modified Embedded-Atom Method Theory 3 2.1.1 Embedding Energy Function 3 2.1.2 Screening Factor 8 2.1.3 Modified Embedded-Atom...Simulation Methodology 2.1 Modified Embedded-Atom Method Theory In the EAM and MEAM formalisms1,2,5 the total energy of a system of atoms (Etot) is...An interatomic potential for saturated hydrocarbons using the modified embedded-atom method (MEAM), a semiempirical many-body potential based on
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Using the surface panel method to predict the steady performance of ducted propellers
NASA Astrophysics Data System (ADS)
Cai, Hao-Peng; Su, Yu-Min; Li, Xin; Shen, Hai-Long
2009-12-01
A new numerical method was developed for predicting the steady hydrodynamic performance of ducted propellers. A potential based surface panel method was applied both to the duct and the propeller, and the interaction between them was solved by an induced velocity potential iterative method. Compared with the induced velocity iterative method, the method presented can save programming and calculating time. Numerical results for a JD simplified ducted propeller series showed that the method presented is effective for predicting the steady hydrodynamic performance of ducted propellers.
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NASA Astrophysics Data System (ADS)
Mokadem, Naziha; Boughariou, Emna; Mudarra, Matías; Ben Brahim, Fatma; Andreo, Bartolome; Hamed, Younes; Bouri, Salem
2018-05-01
With the progressive evolution of industrial sector, agricultural, urbanization, population and drinking water supply, the water demand continuously increases which necessitates the planning of groundwater recharge particularly in arid and semi-arid regions. This paper gives a comprehensive review of various recharges studies in the North Gafsa basin (South Tunisia). This latter is characterized by a natural groundwater recharge that is deeply affected by the lack of precipitations. The aim of this study is to determine the recharge potential zones and to quantify (or estimate) the rainfall recharge of the shallow aquifers. The mapping of the potential recharge zones was established in North Gafsa basin, using geological and hydrological parameters such as slope, lithology, topography and stream network. Indeed, GIS provide tools to reclassify these input layers to produce the final map of groundwater potential zones of the study area. The final output map reveals two distinct zones representing moderate and low groundwater potential recharge. Recharge estimations were based on the four methods: (1) Chloride Method, (2) ERAS Method, (3) DGRE coefficient and (4) Fersi equations. Therefore, the overall results of the different methods demonstrate that the use of the DGRE method applying on the potential zones is more validated.
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The orbital PDF: general inference of the gravitational potential from steady-state tracers
NASA Astrophysics Data System (ADS)
Han, Jiaxin; Wang, Wenting; Cole, Shaun; Frenk, Carlos S.
2016-02-01
We develop two general methods to infer the gravitational potential of a system using steady-state tracers, I.e. tracers with a time-independent phase-space distribution. Combined with the phase-space continuity equation, the time independence implies a universal orbital probability density function (oPDF) dP(λ|orbit) ∝ dt, where λ is the coordinate of the particle along the orbit. The oPDF is equivalent to Jeans theorem, and is the key physical ingredient behind most dynamical modelling of steady-state tracers. In the case of a spherical potential, we develop a likelihood estimator that fits analytical potentials to the system and a non-parametric method (`phase-mark') that reconstructs the potential profile, both assuming only the oPDF. The methods involve no extra assumptions about the tracer distribution function and can be applied to tracers with any arbitrary distribution of orbits, with possible extension to non-spherical potentials. The methods are tested on Monte Carlo samples of steady-state tracers in dark matter haloes to show that they are unbiased as well as efficient. A fully documented C/PYTHON code implementing our method is freely available at a GitHub repository linked from http://icc.dur.ac.uk/data/#oPDF.
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A direct potential fitting RKR method: Semiclassical vs. quantal comparisons
NASA Astrophysics Data System (ADS)
Tellinghuisen, Joel
2016-12-01
Quantal and semiclassical (SC) eigenvalues are compared for three diatomic molecular potential curves: the X state of CO, the X state of Rb2, and the A state of I2. The comparisons show higher levels of agreement than generally recognized, when the SC calculations incorporate a quantum defect correction to the vibrational quantum number, in keeping with the Kaiser modification. One particular aspect of this is better agreement between quantal and SC estimates of the zero-point vibrational energy, supporting the need for the Y00 correction in this context. The pursuit of a direct-potential-fitting (DPF) RKR method is motivated by the notion that some of the limitations of RKR potentials may be innate, from their generation by an exact inversion of approximate quantities: the vibrational energy Gυ and rotational constant Bυ from least-squares analysis of spectroscopic data. In contrast, the DPF RKR method resembles the quantal DPF methods now increasingly used to analyze diatomic spectral data, but with the eigenvalues obtained from SC phase integrals. Application of this method to the analysis of 9500 assigned lines in the I2A ← X spectrum fails to alter the quantal-SC disparities found for the A-state RKR curve from a previous analysis. On the other hand, the SC method can be much faster than the quantal method in exploratory work with different potential functions, where it is convenient to use finite-difference methods to evaluate the partial derivatives required in nonlinear fitting.
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Quadratic String Method for Locating Instantons in Tunneling Splitting Calculations.
Cvitaš, Marko T
2018-03-13
The ring-polymer instanton (RPI) method is an efficient technique for calculating approximate tunneling splittings in high-dimensional molecular systems. In the RPI method, tunneling splitting is evaluated from the properties of the minimum action path (MAP) connecting the symmetric wells, whereby the extensive sampling of the full potential energy surface of the exact quantum-dynamics methods is avoided. Nevertheless, the search for the MAP is usually the most time-consuming step in the standard numerical procedures. Recently, nudged elastic band (NEB) and string methods, originaly developed for locating minimum energy paths (MEPs), were adapted for the purpose of MAP finding with great efficiency gains [ J. Chem. Theory Comput. 2016 , 12 , 787 ]. In this work, we develop a new quadratic string method for locating instantons. The Euclidean action is minimized by propagating the initial guess (a path connecting two wells) over the quadratic potential energy surface approximated by means of updated Hessians. This allows the algorithm to take many minimization steps between the potential/gradient calls with further reductions in the computational effort, exploiting the smoothness of potential energy surface. The approach is general, as it uses Cartesian coordinates, and widely applicable, with computational effort of finding the instanton usually lower than that of determining the MEP. It can be combined with expensive potential energy surfaces or on-the-fly electronic-structure methods to explore a wide variety of molecular systems.
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Transonic Flow Computations Using Nonlinear Potential Methods
NASA Technical Reports Server (NTRS)
Holst, Terry L.; Kwak, Dochan (Technical Monitor)
2000-01-01
This presentation describes the state of transonic flow simulation using nonlinear potential methods for external aerodynamic applications. The presentation begins with a review of the various potential equation forms (with emphasis on the full potential equation) and includes a discussion of pertinent mathematical characteristics and all derivation assumptions. Impact of the derivation assumptions on simulation accuracy, especially with respect to shock wave capture, is discussed. Key characteristics of all numerical algorithm types used for solving nonlinear potential equations, including steady, unsteady, space marching, and design methods, are described. Both spatial discretization and iteration scheme characteristics are examined. Numerical results for various aerodynamic applications are included throughout the presentation to highlight key discussion points. The presentation ends with concluding remarks and recommendations for future work. Overall. nonlinear potential solvers are efficient, highly developed and routinely used in the aerodynamic design environment for cruise conditions. Published by Elsevier Science Ltd. All rights reserved.
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The dimension split element-free Galerkin method for three-dimensional potential problems
NASA Astrophysics Data System (ADS)
Meng, Z. J.; Cheng, H.; Ma, L. D.; Cheng, Y. M.
2018-06-01
This paper presents the dimension split element-free Galerkin (DSEFG) method for three-dimensional potential problems, and the corresponding formulae are obtained. The main idea of the DSEFG method is that a three-dimensional potential problem can be transformed into a series of two-dimensional problems. For these two-dimensional problems, the improved moving least-squares (IMLS) approximation is applied to construct the shape function, which uses an orthogonal function system with a weight function as the basis functions. The Galerkin weak form is applied to obtain a discretized system equation, and the penalty method is employed to impose the essential boundary condition. The finite difference method is selected in the splitting direction. For the purposes of demonstration, some selected numerical examples are solved using the DSEFG method. The convergence study and error analysis of the DSEFG method are presented. The numerical examples show that the DSEFG method has greater computational precision and computational efficiency than the IEFG method.
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The analytical transfer matrix method for PT-symmetric complex potential
NASA Astrophysics Data System (ADS)
Naceri, Leila; Hammou, Amine B.
2017-07-01
We have extended the analytical transfer matrix (ATM) method to solve quantum mechanical bound state problems with complex PT-symmetric potentials. Our work focuses on a class of models studied by Bender and Jones, we calculate the energy eigenvalues, discuss the critical values of g and compare the results with those obtained from other methods such as exact numerical computation and WKB approximation method.
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NASA Astrophysics Data System (ADS)
Schröder, Markus; Meyer, Hans-Dieter
2017-08-01
We propose a Monte Carlo method, "Monte Carlo Potfit," for transforming high-dimensional potential energy surfaces evaluated on discrete grid points into a sum-of-products form, more precisely into a Tucker form. To this end we use a variational ansatz in which we replace numerically exact integrals with Monte Carlo integrals. This largely reduces the numerical cost by avoiding the evaluation of the potential on all grid points and allows a treatment of surfaces up to 15-18 degrees of freedom. We furthermore show that the error made with this ansatz can be controlled and vanishes in certain limits. We present calculations on the potential of HFCO to demonstrate the features of the algorithm. To demonstrate the power of the method, we transformed a 15D potential of the protonated water dimer (Zundel cation) in a sum-of-products form and calculated the ground and lowest 26 vibrationally excited states of the Zundel cation with the multi-configuration time-dependent Hartree method.
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NASA Technical Reports Server (NTRS)
Mavris, Dimitri; Roth, Bryce; McDonald, Rob
2002-01-01
The objective of this report is to provide a tool to facilitate the application of thermodynamic work potential methods to aircraft and engine analysis. This starts with a discussion of the theoretical background underlying these methods, which is then used to derive various equations useful for thermodynamic analysis of aircraft engines. The work potential analysis method is implemented in the form of a set of working charts and tables that can be used to graphically evaluate work potential stored in high-enthalpy gas. The range of validity for these tables is 300 to 36,000 R, pressures between between 0.01 atm and 100 atm, and fuel-air ratios from zero to stoichiometric. The derivations and charts assume mixtures of Jet-A and air as the working fluid. The thermodynamic properties presented in these charts were calculated based upon standard thermodynamic curve fits.
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NASA Technical Reports Server (NTRS)
Stern, D. P.
1976-01-01
Several mathematical methods which are available for the description of magnetic fields in space are reviewed. Examples of the application of such methods are given, with particular emphasis on work related to the geomagnetic field, and their individual properties and associated problems are described. The methods are grouped in five main classes: (1) methods based on the current density, (2) methods using the scalar magnetic potential, (3) toroidal and poloidal components of the field and spherical vector harmonics, (4) Euler potentials, and (5) local expansions of the field near a given reference point. Special attention is devoted to models of the magnetosphere, to the uniqueness of the scalar potential as derived from observed data, and to the L parameter.
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Hubbell, Joel M.; Sisson, James B.
2001-01-01
A method of determining matric potential of a sample, the method comprising placing the sample in a container, the container having an opening; and contacting the sample with a tensiometer via the opening. An apparatus for determining matric potential of a sample, the apparatus comprising a housing configured to receive a sample; a portable matric potential sensing device extending into the housing and having a porous member; and a wall closing the housing to insulate the sample and at least a portion of the matric potential sensing device including the porous member.
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ERIC Educational Resources Information Center
Verdini, Roxana A.; Lagier, Claudia M.
2004-01-01
Voltammetry principles are introduced to students by means of a bipotentiometric method to determine vitamin C in fruits and vegetables. The aim is to draw attention to voltammetric methods, particular to the study of current-potential curves, stressing the potential applicability in areas of food quality control.
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Federal Register 2010, 2011, 2012, 2013, 2014
2012-02-14
... development of BG1Luc ER TA test method performance standards. ICCVAM assigned the activities a high priority... Vitro Test Methods for Detecting Potential Endocrine Disruptors. Research Triangle Park, NC: National...Final.pdf . ICCVAM. 2003a. ICCVAM Evaluation of In Vitro Test Methods For Detecting Potential Endocrine...
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An induced current method for measuring zeta potential of electrolyte solution-air interface.
Song, Yongxin; Zhao, Kai; Wang, Junsheng; Wu, Xudong; Pan, Xinxiang; Sun, Yeqing; Li, Dongqing
2014-02-15
This paper reports a novel and very simple method for measuring the zeta potential of electrolyte solution-air interface. When a measuring electrode contacts the electrolyte solution-air interface, an electrical current will be generated due to the potential difference between the electrode-air surface and the electrolyte solution-air interface. The amplitude of the measured electric signal is linearly proportional to this potential difference; and depends only on the zeta potential at the electrolyte solution-air interface, regardless of the types and concentrations of the electrolyte. A correlation between the zeta potential and the measured voltage signal is obtained based on the experimental data. Using this equation, the zeta potential of any electrolyte solution-air interface can be evaluated quickly and easily by inserting an electrode through the electrolyte solution-air interface and measuring the electrical signal amplitude. This method was verified by comparing the obtained results of NaCl, MgCl2 and CaCl2 solutions of different pH values and concentrations with the zeta potential data reported in the published journal papers. Copyright © 2013 Elsevier Inc. All rights reserved.
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Phase shifts in I = 2 ππ-scattering from two lattice approaches
NASA Astrophysics Data System (ADS)
Kurth, T.; Ishii, N.; Doi, T.; Aoki, S.; Hatsuda, T.
2013-12-01
We present a lattice QCD study of the phase shift of I = 2 ππ scattering on the basis of two different approaches: the standard finite volume approach by Lüscher and the recently introduced HAL QCD potential method. Quenched QCD simulations are performed on lattices with extents N s = 16 , 24 , 32 , 48 and N t = 128 as well as lattice spacing a ~ 0 .115 fm and a pion mass of m π ~ 940 MeV. The phase shift and the scattering length are calculated in these two methods. In the potential method, the error is dominated by the systematic uncertainty associated with the violation of rotational symmetry due to finite lattice spacing. In Lüscher's approach, such systematic uncertainty is difficult to be evaluated and thus is not included in this work. A systematic uncertainty attributed to the quenched approximation, however, is not evaluated in both methods. In case of the potential method, the phase shift can be calculated for arbitrary energies below the inelastic threshold. The energy dependence of the phase shift is also obtained from Lüscher's method using different volumes and/or nonrest-frame extension of it. The results are found to agree well with the potential method.
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Conductivity map from scanning tunneling potentiometry.
Zhang, Hao; Li, Xianqi; Chen, Yunmei; Durand, Corentin; Li, An-Ping; Zhang, X-G
2016-08-01
We present a novel method for extracting two-dimensional (2D) conductivity profiles from large electrochemical potential datasets acquired by scanning tunneling potentiometry of a 2D conductor. The method consists of a data preprocessing procedure to reduce/eliminate noise and a numerical conductivity reconstruction. The preprocessing procedure employs an inverse consistent image registration method to align the forward and backward scans of the same line for each image line followed by a total variation (TV) based image restoration method to obtain a (nearly) noise-free potential from the aligned scans. The preprocessed potential is then used for numerical conductivity reconstruction, based on a TV model solved by accelerated alternating direction method of multiplier. The method is demonstrated on a measurement of the grain boundary of a monolayer graphene, yielding a nearly 10:1 ratio for the grain boundary resistivity over bulk resistivity.
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Chi, Xiaowei; Tang, Yongan; Zeng, Xiangqun
2016-10-20
Water and oxygen are ubiquitous present in ambient conditions. This work studies the unique oxygen, trace water and a volatile organic compound (VOC) acetaldehyde redox chemistry in a hydrophobic and aprotic ionic liquid (IL), 1-butyl-1-methylpyrrolidinium bis(trifluoromethanesulfonyl)imide ([Bmpy] [NTf 2 ]) by cyclic voltammetry and potential step methods. One electron oxygen reduction leads to superoxide radical formation in the IL. Trace water in the IL acts as a protic species that reacts with the superoxide radical. Acetaldehyde is a stronger protic species than water for reacting with the superoxide radical. The presence of trace water in the IL was also demonstrated to facilitate the electro-oxidation of acetaldehyde, with similar mechanism to that in the aqueous solutions. A multiple-step coupling reaction mechanism between water, superoxide radical and acetaldehyde has been described. The unique characteristics of redox chemistry of acetaldehyde in [Bmpy][NTf 2 ] in the presence of oxygen and trace water can be controlled by electrochemical potentials. By controlling the electrode potential windows, several methods including cyclic voltammetry, potential step methods (single-potential, double-potential and triple-potential step methods) were established for the quantification of acetaldehyde. Instead of treating water and oxygen as frustrating interferents to ILs, we found that oxygen and trace water chemistry in [Bmpy][NTf 2 ] can be utilized to develop innovative electrochemical methods for electroanalysis of acetaldehyde.
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NASA Astrophysics Data System (ADS)
Hale, Lucas M.; Trautt, Zachary T.; Becker, Chandler A.
2018-07-01
Atomistic simulations using classical interatomic potentials are powerful investigative tools linking atomic structures to dynamic properties and behaviors. It is well known that different interatomic potentials produce different results, thus making it necessary to characterize potentials based on how they predict basic properties. Doing so makes it possible to compare existing interatomic models in order to select those best suited for specific use cases, and to identify any limitations of the models that may lead to unrealistic responses. While the methods for obtaining many of these properties are often thought of as simple calculations, there are many underlying aspects that can lead to variability in the reported property values. For instance, multiple methods may exist for computing the same property and values may be sensitive to certain simulation parameters. Here, we introduce a new high-throughput computational framework that encodes various simulation methodologies as Python calculation scripts. Three distinct methods for evaluating the lattice and elastic constants of bulk crystal structures are implemented and used to evaluate the properties across 120 interatomic potentials, 18 crystal prototypes, and all possible combinations of unique lattice site and elemental model pairings. Analysis of the results reveals which potentials and crystal prototypes are sensitive to the calculation methods and parameters, and it assists with the verification of potentials, methods, and molecular dynamics software. The results, calculation scripts, and computational infrastructure are self-contained and openly available to support researchers in performing meaningful simulations.
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Chi, Xiaowei; Tang, Yongan; Zeng, Xiangqun
2017-01-01
Water and oxygen are ubiquitous present in ambient conditions. This work studies the unique oxygen, trace water and a volatile organic compound (VOC) acetaldehyde redox chemistry in a hydrophobic and aprotic ionic liquid (IL), 1-butyl-1-methylpyrrolidinium bis(trifluoromethanesulfonyl)imide ([Bmpy] [NTf2]) by cyclic voltammetry and potential step methods. One electron oxygen reduction leads to superoxide radical formation in the IL. Trace water in the IL acts as a protic species that reacts with the superoxide radical. Acetaldehyde is a stronger protic species than water for reacting with the superoxide radical. The presence of trace water in the IL was also demonstrated to facilitate the electro-oxidation of acetaldehyde, with similar mechanism to that in the aqueous solutions. A multiple-step coupling reaction mechanism between water, superoxide radical and acetaldehyde has been described. The unique characteristics of redox chemistry of acetaldehyde in [Bmpy][NTf2] in the presence of oxygen and trace water can be controlled by electrochemical potentials. By controlling the electrode potential windows, several methods including cyclic voltammetry, potential step methods (single-potential, double-potential and triple-potential step methods) were established for the quantification of acetaldehyde. Instead of treating water and oxygen as frustrating interferents to ILs, we found that oxygen and trace water chemistry in [Bmpy][NTf2] can be utilized to develop innovative electrochemical methods for electroanalysis of acetaldehyde. PMID:29142331
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The use of spectral methods in bidomain studies.
Trayanova, N; Pilkington, T
1992-01-01
A Fourier transform method is developed for solving the bidomain coupled differential equations governing the intracellular and extracellular potentials on a finite sheet of cardiac cells undergoing stimulation. The spectral formulation converts the system of differential equations into a "diagonal" system of algebraic equations. Solving the algebraic equations directly and taking the inverse transform of the potentials proved numerically less expensive than solving the coupled differential equations by means of traditional numerical techniques, such as finite differences; the comparison between the computer execution times showed that the Fourier transform method was about 40 times faster than the finite difference method. By application of the Fourier transform method, transmembrane potential distributions in the two-dimensional myocardial slice were calculated. For a tissue characterized by a ratio of the intra- to extracellular conductivities that is different in all principal directions, the transmembrane potential distribution exhibits a rather complicated geometrical pattern. The influence of the different anisotropy ratios, the finite tissue size, and the stimuli configuration on the pattern of membrane polarization is investigated.
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Optical model potentials for 6He+64Zn from 63Cu(7Li,6He)64Zn reactions
NASA Astrophysics Data System (ADS)
Yang, L.; Lin, C. J.; Jia, H. M.; Wang, D. X.; Sun, L. J.; Ma, N. R.; Yang, F.; Wu, Z. D.; Xu, X. X.; Zhang, H. Q.; Liu, Z. H.; Bao, P. F.
2017-03-01
Angular distributions of the transfer reaction 63Cu(7Li,6He )64Zn were measured at Elab(7Li) =12.67 , 15.21, 16.33, 23.30, 27.30, and 30.96 MeV. With the interaction potentials of the entrance channel 7Li+63Cu obtained from elastic scattering data as input, the optical potentials of the halo nuclear system 6He+64Zn in the exit channel were extracted by fitting the experimental data with the distorted-wave Born approximation (DWBA) and coupled reaction channels (CRC) methods, respectively. The results show that the threshold anomaly presents in the weakly bound system of 7Li+63Cu and the dispersion relation can be adopted to describe the connection between the real and imaginary potentials, while both the real and imaginary potentials nearly keep constant within the researched energy region for the halo system of 6He+64Zn . Moreover, calculations by the potentials extracted from the CRC method can reproduce the experimental elastic scattering of the 6He+64Zn system rather well, but those by the potentials from the DWBA method cannot, where the couplings between 7Li and 6He are absent. This work verifies the validity of the transfer method in the medium-mass target region and lays a solid foundation for the further study of optical potentials for exotic nuclear systems.
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Supersonic full-potential methods for missile body analysis
NASA Technical Reports Server (NTRS)
Pittman, James L.
1992-01-01
Accounts are presented of representative applications to missile bodies of arbitrary shape of methods based on the steady form of the full potential equation. The NCOREL and SIMP full-potential codes are compared, and their results are evaluated for the cases of an arrow wing and a wing-body configuration. Attention is given to the effect of cross-sectional and longitudinal geometries. Comparisons of surface pressure and longitudinal force and moment data for circular and elliptic bodies have shown that the full-potential methods yielded excellent results in attached-flow conditions. Results are presented for a conical star body, waveriders, the Shuttle Orbiter, and a highly swept wing-body cruising at Mach 4.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Kato, Tsuyoshi; Ide, Yoshihiro; Yamanouchi, Kaoru
We first calculate the ground-state molecular wave function of 1D model H{sub 2} molecule by solving the coupled equations of motion formulated in the extended multi-configuration time-dependent Hartree-Fock (MCTDHF) method by the imaginary time propagation. From the comparisons with the results obtained by the Born-Huang (BH) expansion method as well as with the exact wave function, we observe that the memory size required in the extended MCTDHF method is about two orders of magnitude smaller than in the BH expansion method to achieve the same accuracy for the total energy. Second, in order to provide a theoretical means to understandmore » dynamical behavior of the wave function, we propose to define effective adiabatic potential functions and compare them with the conventional adiabatic electronic potentials, although the notion of the adiabatic potentials is not used in the extended MCTDHF approach. From the comparison, we conclude that by calculating the effective potentials we may be able to predict the energy differences among electronic states even for a time-dependent system, e.g., time-dependent excitation energies, which would be difficult to be estimated within the BH expansion approach.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Al Sdran, N.; Najran University, Faculty of Sciences and Arts, Najran; Maiz, F., E-mail: fethimaiz@gmail.com
2016-06-15
The numerical solutions of the time independent Schrödinger equation of different one-dimensional potentials forms are sometime achieved by the asymptotic iteration method. Its importance appears, for example, on its efficiency to describe vibrational system in quantum mechanics. In this paper, the Airy function approach and the Numerov method have been used and presented to study the oscillator anharmonic potential V(x) = Ax{sup 2α} + Bx{sup 2}, (A>0, B<0), with (α = 2) for quadratic, (α =3) for sextic and (α =4) for octic anharmonic oscillators. The Airy function approach is based on the replacement of the real potential V(x) bymore » a piecewise-linear potential v(x), while, the Numerov method is based on the discretization of the wave function on the x-axis. The first energies levels have been calculated and the wave functions for the sextic system have been evaluated. These specific values are unlimited by the magnitude of A, B and α. It’s found that the obtained results are in good agreement with the previous results obtained by the asymptotic iteration method for α =3.« less
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NASA Astrophysics Data System (ADS)
Resita Arum, Sari; A, Suparmi; C, Cari
2016-01-01
The Dirac equation for Eckart potential and trigonometric Manning Rosen potential with exact spin symmetry is obtained using an asymptotic iteration method. The combination of the two potentials is substituted into the Dirac equation, then the variables are separated into radial and angular parts. The Dirac equation is solved by using an asymptotic iteration method that can reduce the second order differential equation into a differential equation with substitution variables of hypergeometry type. The relativistic energy is calculated using Matlab 2011. This study is limited to the case of spin symmetry. With the asymptotic iteration method, the energy spectra of the relativistic equations and equations of orbital quantum number l can be obtained, where both are interrelated between quantum numbers. The energy spectrum is also numerically solved using the Matlab software, where the increase in the radial quantum number nr causes the energy to decrease. The radial part and the angular part of the wave function are defined as hypergeometry functions and visualized with Matlab 2011. The results show that the disturbance of a combination of the Eckart potential and trigonometric Manning Rosen potential can change the radial part and the angular part of the wave function. Project supported by the Higher Education Project (Grant No. 698/UN27.11/PN/2015).
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Comparison of optical vortex detection methods for use with a Shack-Hartmann wavefront sensor.
Murphy, Kevin; Dainty, Chris
2012-02-27
In this paper we compare experimentally two methods of detecting optical vortices from Shack-Hartmann wavefront sensor (SHWFS) data, the vortex potential and the contour sum methods. The experimental setup uses a spatial light modulator (SLM) to generate turbulent fields with vortices. In the experiment, many fields are generated and detected by a SHWFS, and data is analysed by the two vortex detection methods. We conclude that the vortex potential method is more successful in locating vortices in these fields.
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Optical potential from first principles
Rotureau, J.; Danielewicz, P.; Hagen, G.; ...
2017-02-15
Here, we develop a method to construct a microscopic optical potential from chiral interactions for nucleon-nucleus scattering. The optical potential is constructed by combining the Green’s function approach with the coupled-cluster method. To deal with the poles of the Green’s function along the real energy axis we employ a Berggren basis in the complex energy plane combined with the Lanczos method. Using this approach, we perform a proof-of-principle calculation of the optical potential for the elastic neutron scattering on 16O. For the computation of the ground-state of 16O, we use the coupled-cluster method in the singles-and-doubles approximation, while for themore » A ±1 nuclei we use particle-attached/removed equation-of-motion method truncated at two-particle-one-hole and one-particle-two-hole excitations, respectively. We verify the convergence of the optical potential and scattering phase shifts with respect to the model-space size and the number of discretized complex continuum states. We also investigate the absorptive component of the optical potential (which reflects the opening of inelastic channels) by computing its imaginary volume integral and find an almost negligible absorptive component at low-energies. To shed light on this result, we computed excited states of 16O using equation-of-motion coupled-cluster method with singles-and- doubles excitations and we found no low-lying excited states below 10 MeV. Furthermore, most excited states have a dominant two-particle-two-hole component, making higher-order particle-hole excitations necessary to achieve a precise description of these core-excited states. We conclude that the reduced absorption at low-energies can be attributed to the lack of correlations coming from the low-order cluster truncation in the employed coupled-cluster method.« less
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Finite difference methods for the solution of unsteady potential flows
NASA Technical Reports Server (NTRS)
Caradonna, F. X.
1982-01-01
Various problems which are confronted in the development of an unsteady finite difference potential code are reviewed mainly in the context of what is done for a typical small disturbance and full potential method. The issues discussed include choice of equations, linearization and conservation, differencing schemes, and algorithm development. A number of applications, including unsteady three dimensional rotor calculations, are demonstrated.
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Optimized Free Energies from Bidirectional Single-Molecule Force Spectroscopy
NASA Astrophysics Data System (ADS)
Minh, David D. L.; Adib, Artur B.
2008-05-01
An optimized method for estimating path-ensemble averages using data from processes driven in opposite directions is presented. Based on this estimator, bidirectional expressions for reconstructing free energies and potentials of mean force from single-molecule force spectroscopy—valid for biasing potentials of arbitrary stiffness—are developed. Numerical simulations on a model potential indicate that these methods perform better than unidirectional strategies.
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NASA Astrophysics Data System (ADS)
Kang, In-Je; Park, In-Sun; Wackerbarth, Eugene; Bae, Min-Keun; Hershkowitz, Noah; Severn, Greg; Chung, Kyu-Sun
2017-10-01
Plasma potential structures are measured with an emissive probe near a negatively biased grid ( - 100 V , 80mm diam., 40 lines/cm) immersed in a hot filament DC discharge in Kr. Three different methods of analysis are compared: inflection point (IP), floating potential (FP) and separation point (SE) methods. The plasma device at the University of San Diego (length = 64 cm, diameter = 32 cm, source = filament DC discharge) was operated with 5 ×108
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Modeling potential evapotranspiration of two forested watersheds in the southern Appalachians
L.Y. Rao; G. Sun; C.R. Ford; J.M. Vose
2011-01-01
Global climate change has direct impacts on watershed hydrology through altering evapotranspiration (ET) processes at multiple scales. There are many methods to estimate forest ET with models, but the most practical and the most popular one is the potential ET (PET) based method. However, the choice of PET methods for AET estimation remains challenging. This study...
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NASA Astrophysics Data System (ADS)
Huang, Wen-Min; Mou, Chung-Yu; Chang, Cheng-Hung
2010-02-01
While the scattering phase for several one-dimensional potentials can be exactly derived, less is known in multi-dimensional quantum systems. This work provides a method to extend the one-dimensional phase knowledge to multi-dimensional quantization rules. The extension is illustrated in the example of Bogomolny's transfer operator method applied in two quantum wells bounded by step potentials of different heights. This generalized semiclassical method accurately determines the energy spectrum of the systems, which indicates the substantial role of the proposed phase correction. Theoretically, the result can be extended to other semiclassical methods, such as Gutzwiller trace formula, dynamical zeta functions, and semiclassical Landauer-Büttiker formula. In practice, this recipe enhances the applicability of semiclassical methods to multi-dimensional quantum systems bounded by general soft potentials.
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On the use of the exact exchange optimized effective potential method for static response properties
NASA Astrophysics Data System (ADS)
Krykunov, Mykhaylo; Ziegler, Tom
In the present work, we question the notion that the modified Kohn-Sham orbital energies and smaller HOMO-LUMO gaps, produced from the exact exchange optimized effective potential (EXX-OEP) method, might significantly improve the paramagnetic contribution to the NMR chemical shifts compared with the regular Hartree-Fock (HF) scheme. First of all, it is shown analytically that if there is such a local potential that produces the HF energy, and the Kohn-Sham orbitals are obtained as a result of separate rotations of the occupied and virtual HF orbitals, any static magnetic property obtained from the coupled perturbed HF method will be identical to that obtained from the EXX-OEP approach. In fact the EXX-OEP method is equivalent to the improved virtual orbitals (IVO) scheme in which the energies of the virtual orbitals are modified by an effective potential. It is shown that the IVO procedure leaves static response properties unchanged. To test our analysis numerically we have employed several variants of the EXX-OEP method, based on the expansion of the local exchange potential into a linear combination of fit functions. The different EXX-OEP schemes have been used to calculate the NMR chemical shifts for a set of small molecules containing C, H, N, O, and F atoms. Comparison of the deviation between experimental and calculated chemical shifts from the HF, the EXX-OEP, and the common energy denominator approximation (CEDA) approximation to the EXX-OEP methods has shown that for carbon, hydrogen, and fluorine the EXX-OEP methods do not yield any improvement over the HF method. For nitrogen and oxygen we have found that the EXX-OEP performs better than the HF method. However, in the limit of infinite fit basis set and, as a consequence of it, a perfect fit of the HF potential the EXX-OEP and the HF methods would afford the same chemical shifts according to our theoretical analysis. Unfortunately, without a perfect fit the chemical shifts from the EXX-OEP method strongly depend on the fit convergence. In our opinion, the EXX-OEP method should not be used for response properties as it is numerically unstable. Thus, any apparent improvement of the EXX-OEP method over the HF scheme for a finite fit basis set must be considered spurious.
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Quantum mechanical fragment methods based on partitioning atoms or partitioning coordinates.
Wang, Bo; Yang, Ke R; Xu, Xuefei; Isegawa, Miho; Leverentz, Hannah R; Truhlar, Donald G
2014-09-16
Conspectus The development of more efficient and more accurate ways to represent reactive potential energy surfaces is a requirement for extending the simulation of large systems to more complex systems, longer-time dynamical processes, and more complete statistical mechanical sampling. One way to treat large systems is by direct dynamics fragment methods. Another way is by fitting system-specific analytic potential energy functions with methods adapted to large systems. Here we consider both approaches. First we consider three fragment methods that allow a given monomer to appear in more than one fragment. The first two approaches are the electrostatically embedded many-body (EE-MB) expansion and the electrostatically embedded many-body expansion of the correlation energy (EE-MB-CE), which we have shown to yield quite accurate results even when one restricts the calculations to include only electrostatically embedded dimers. The third fragment method is the electrostatically embedded molecular tailoring approach (EE-MTA), which is more flexible than EE-MB and EE-MB-CE. We show that electrostatic embedding greatly improves the accuracy of these approaches compared with the original unembedded approaches. Quantum mechanical fragment methods share with combined quantum mechanical/molecular mechanical (QM/MM) methods the need to treat a quantum mechanical fragment in the presence of the rest of the system, which is especially challenging for those parts of the rest of the system that are close to the boundary of the quantum mechanical fragment. This is a delicate matter even for fragments that are not covalently bonded to the rest of the system, but it becomes even more difficult when the boundary of the quantum mechanical fragment cuts a bond. We have developed a suite of methods for more realistically treating interactions across such boundaries. These methods include redistributing and balancing the external partial atomic charges and the use of tuned fluorine atoms for capping dangling bonds, and we have shown that they can greatly improve the accuracy. Finally we present a new approach that goes beyond QM/MM by combining the convenience of molecular mechanics with the accuracy of fitting a potential function to electronic structure calculations on a specific system. To make the latter practical for systems with a large number of degrees of freedom, we developed a method to interpolate between local internal-coordinate fits to the potential energy. A key issue for the application to large systems is that rather than assigning the atoms or monomers to fragments, we assign the internal coordinates to reaction, secondary, and tertiary sets. Thus, we make a partition in coordinate space rather than atom space. Fits to the local dependence of the potential energy on tertiary coordinates are arrayed along a preselected reaction coordinate at a sequence of geometries called anchor points; the potential energy function is called an anchor points reactive potential. Electrostatically embedded fragment methods and the anchor points reactive potential, because they are based on treating an entire system by quantum mechanical electronic structure methods but are affordable for large and complex systems, have the potential to open new areas for accurate simulations where combined QM/MM methods are inadequate.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Ho, T.; Rabitz, H.
1996-02-01
A general interpolation method for constructing smooth molecular potential energy surfaces (PES{close_quote}s) from {ital ab} {ital initio} data are proposed within the framework of the reproducing kernel Hilbert space and the inverse problem theory. The general expression for an {ital a} {ital posteriori} error bound of the constructed PES is derived. It is shown that the method yields globally smooth potential energy surfaces that are continuous and possess derivatives up to second order or higher. Moreover, the method is amenable to correct symmetry properties and asymptotic behavior of the molecular system. Finally, the method is generic and can be easilymore » extended from low dimensional problems involving two and three atoms to high dimensional problems involving four or more atoms. Basic properties of the method are illustrated by the construction of a one-dimensional potential energy curve of the He{endash}He van der Waals dimer using the exact quantum Monte Carlo calculations of Anderson {ital et} {ital al}. [J. Chem. Phys. {bold 99}, 345 (1993)], a two-dimensional potential energy surface of the HeCO van der Waals molecule using recent {ital ab} {ital initio} calculations by Tao {ital et} {ital al}. [J. Chem. Phys. {bold 101}, 8680 (1994)], and a three-dimensional potential energy surface of the H{sup +}{sub 3} molecular ion using highly accurate {ital ab} {ital initio} calculations of R{umlt o}hse {ital et} {ital al}. [J. Chem. Phys. {bold 101}, 2231 (1994)]. In the first two cases the constructed potentials clearly exhibit the correct asymptotic forms, while in the last case the constructed potential energy surface is in excellent agreement with that constructed by R{umlt o}hse {ital et} {ital al}. using a low order polynomial fitting procedure. {copyright} {ital 1996 American Institute of Physics.}« less
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Nguyen, Phuong H; Derreumaux, Philippe
2012-01-14
One challenge in computational biophysics and biology is to develop methodologies able to estimate accurately the configurational entropy of macromolecules. Among many methods, the quasiharmonic approximation (QH) is most widely used as it is simple in both theory and implementation. However, it has been shown that this method becomes inaccurate by overestimating entropy for systems with rugged free energy landscapes. Here, we propose a simple method to improve the QH approximation, i.e., to reduce QH entropy. We approximate the potential energy landscape of the system by an effective harmonic potential, and request that this potential must produce exactly the configurational temperature of the system. Due to this constraint, the force constants associated with the effective harmonic potential are increased, or equivalently, entropy of motion governed by this effective harmonic potential is reduced. We also introduce the effective configurational temperature concept which can be used as an indicator to check the anharmonicity of the free energy landscape. To validate the new method we compare it with the recently developed expansion approximate method by calculating entropy of one simple model system and two peptides with 3 and 16 amino acids either in gas phase or in explicit solvent. We show that the new method appears to be a good choice in practice as it is a compromise between accuracy and computational speed. A modification of the expansion approximate method is also introduced and advantages are discussed in some detail.
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Object detection and tracking system
Ma, Tian J.
2017-05-30
Methods and apparatuses for analyzing a sequence of images for an object are disclosed herein. In a general embodiment, the method identifies a region of interest in the sequence of images. The object is likely to move within the region of interest. The method divides the region of interest in the sequence of images into sections and calculates signal-to-noise ratios for a section in the sections. A signal-to-noise ratio for the section is calculated using the section in the image, a prior section in a prior image to the image, and a subsequent section in a subsequent image to the image. The signal-to-noise ratios are for potential velocities of the object in the section. The method also selects a velocity from the potential velocities for the object in the section using a potential velocity in the potential velocities having a highest signal-to-noise ratio in the signal-to-noise ratios.
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Method for discriminative particle selection
Post, Richard F.
1992-01-01
The invention is a method and means for separating ions or providing an ion beam. The invention generates ions of the isotopes to be separated, and then provides a traveling electric potential hill created by a sequential series of quasi static electric potential hills. By regulating the velocity and potential amplitude of the traveling electric potential hill ionized isotopes are selectively positively or negatively accelerated. Since the ionized isotopes have differing final velocities, the isotopes may be collected separately or used to produce an ion beam of a selected isotope.
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NASA Technical Reports Server (NTRS)
Ko, William L.
1995-01-01
Thermal buckling characteristics of hypersonic aircraft sandwich panels of various aspect ratios were investigated. The panel is fastened at its four edges to the substructures under four different edge conditions and is subjected to uniform temperature loading. Minimum potential energy theory and finite element methods were used to calculate the panel buckling temperatures. The two methods gave fairly close buckling temperatures. However, the finite element method gave slightly lower buckling temperatures than those given by the minimum potential energy theory. The reasons for this slight discrepancy in eigensolutions are discussed in detail. In addition, the effect of eigenshifting on the eigenvalue convergence rate is discussed.
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Structural issues affecting mixed methods studies in health research: a qualitative study.
O'Cathain, Alicia; Nicholl, Jon; Murphy, Elizabeth
2009-12-09
Health researchers undertake studies which combine qualitative and quantitative methods. Little attention has been paid to the structural issues affecting this mixed methods approach. We explored the facilitators and barriers to undertaking mixed methods studies in health research. Face-to-face semi-structured interviews with 20 researchers experienced in mixed methods research in health in the United Kingdom. Structural facilitators for undertaking mixed methods studies included a perception that funding bodies promoted this approach, and the multidisciplinary constituency of some university departments. Structural barriers to exploiting the potential of these studies included a lack of education and training in mixed methods research, and a lack of templates for reporting mixed methods articles in peer-reviewed journals. The 'hierarchy of evidence' relating to effectiveness studies in health care research, with the randomised controlled trial as the gold standard, appeared to pervade the health research infrastructure. Thus integration of data and findings from qualitative and quantitative components of mixed methods studies, and dissemination of integrated outputs, tended to occur through serendipity and effort, further highlighting the presence of structural constraints. Researchers are agents who may also support current structures - journal reviewers and editors, and directors of postgraduate training courses - and thus have the ability to improve the structural support for exploiting the potential of mixed methods research. The environment for health research in the UK appears to be conducive to mixed methods research but not to exploiting the potential of this approach. Structural change, as well as change in researcher behaviour, will be necessary if researchers are to fully exploit the potential of using mixed methods research.
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Clinical Trials Methods for Evaluation of Potential Reduced Exposure Products
Hatsukami, Dorothy K.; Hanson, Karen; Briggs, Anna; Parascandola, Mark; Genkinger, Jeanine M.; O'Connor, Richard; Shields, Peter
2009-01-01
Potential reduced exposure tobacco products (PREPs) may have promise in reducing tobacco-related morbidity or mortality or may promote greater harm to individuals or the population. Critical to determining the risks or benefits from these products are valid human clinical trial PREP assessment methods. Assessment involves determining the effects of these products on biomarkers of exposure and of effect, which serve as proxies for harm, and assessing the potential for consumer uptake and abuse of the product. This article raises the critical methodological issues associated with PREP assessment, reviews the methods that have been used to assess PREPs, and describes the strengths and limitations of these methods. Additionally, recommendations for clinical trials PREP assessment methods and future research directions in this area based on this review and on the deliberations from a National Cancer Institute sponsored Clinical Trials PREP Methods Workshop are provided. PMID:19959672
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Bender, Jason D.; Doraiswamy, Sriram; Candler, Graham V., E-mail: truhlar@umn.edu, E-mail: candler@aem.umn.edu
2014-02-07
Fitting potential energy surfaces to analytic forms is an important first step for efficient molecular dynamics simulations. Here, we present an improved version of the local interpolating moving least squares method (L-IMLS) for such fitting. Our method has three key improvements. First, pairwise interactions are modeled separately from many-body interactions. Second, permutational invariance is incorporated in the basis functions, using permutationally invariant polynomials in Morse variables, and in the weight functions. Third, computational cost is reduced by statistical localization, in which we statistically correlate the cutoff radius with data point density. We motivate our discussion in this paper with amore » review of global and local least-squares-based fitting methods in one dimension. Then, we develop our method in six dimensions, and we note that it allows the analytic evaluation of gradients, a feature that is important for molecular dynamics. The approach, which we call statistically localized, permutationally invariant, local interpolating moving least squares fitting of the many-body potential (SL-PI-L-IMLS-MP, or, more simply, L-IMLS-G2), is used to fit a potential energy surface to an electronic structure dataset for N{sub 4}. We discuss its performance on the dataset and give directions for further research, including applications to trajectory calculations.« less
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A theoretical treatment of technical risk in modern propulsion system design
NASA Astrophysics Data System (ADS)
Roth, Bryce Alexander
2000-09-01
A prevalent trend in modern aerospace systems is increasing complexity and cost, which in turn drives increased risk. Consequently, there is a clear and present need for the development of formalized methods to analyze the impact of risk on the design of aerospace vehicles. The objective of this work is to develop such a method that enables analysis of risk via a consistent, comprehensive treatment of aerothermodynamic and mass properties aspects of vehicle design. The key elements enabling the creation of this methodology are recent developments in the analytical estimation of work potential based on the second law of thermodynamics. This dissertation develops the theoretical foundation of a vehicle analysis method based on work potential and validates it using the Northrop F-5E with GE J85-GE-21 engines as a case study. Although the method is broadly applicable, emphasis is given to aircraft propulsion applications. Three work potential figures of merit are applied using this method: exergy, available energy, and thrust work potential. It is shown that each possesses unique properties making them useful for specific vehicle analysis tasks, though the latter two are actually special cases of exergy. All three are demonstrated on the analysis of the J85-GE-21 propulsion system, resulting in a comprehensive description of propulsion system thermodynamic loss. This "loss management" method is used to analyze aerodynamic drag loss of the F-5E and is then used in conjunction with the propulsive loss model to analyze the usage of fuel work potential throughout the F-5E design mission. The results clearly show how and where work potential is used during flight and yield considerable insight as to where the greatest opportunity for design improvement is. Next, usage of work potential is translated into fuel weight so that the aerothermodynamic performance of the F-5E can be expressed entirely in terms of vehicle gross weight. This technique is then applied as a means to quantify the impact of engine cycle technologies on the F-5E airframe. Finally, loss management methods are used in conjunction with probabilistic analysis methods to quantify the impact of risk on F-5E aerothermodynamic performance.
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Accelerating atomistic simulations through self-learning bond-boost hyperdynamics
DOE Office of Scientific and Technical Information (OSTI.GOV)
Perez, Danny; Voter, Arthur F
2008-01-01
By altering the potential energy landscape on which molecular dynamics are carried out, the hyperdynamics method of Voter enables one to significantly accelerate the simulation state-to-state dynamics of physical systems. While very powerful, successful application of the method entails solving the subtle problem of the parametrization of the so-called bias potential. In this study, we first clarify the constraints that must be obeyed by the bias potential and demonstrate that fast sampling of the biased landscape is key to the obtention of proper kinetics. We then propose an approach by which the bond boost potential of Miron and Fichthorn canmore » be safely parametrized based on data acquired in the course of a molecular dynamics simulation. Finally, we introduce a procedure, the Self-Learning Bond Boost method, in which the parametrization is step efficiently carried out on-the-fly for each new state that is visited during the simulation by safely ramping up the strength of the bias potential up to its optimal value. The stability and accuracy of the method are demonstrated.« less
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A method for locating potential tree-planting sites in urban areas: a case study of Los Angeles, USA
Chunxia Wua; Qingfu Xiaoa; Gregory E. McPherson
2008-01-01
A GIS-based method for locating potential tree-planting sites based on land cover data is introduced. Criteria were developed to identify locations that are spatially available for potential tree planting based on land cover, sufficient distance from impervious surfaces, a minimum amount of pervious surface, and no crown overlap with other trees. In an ArcGIS...
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NASA Technical Reports Server (NTRS)
Duncan, Comer; Jones, Jim
1993-01-01
A key ingredient in the simulation of self-gravitating astrophysical fluid dynamical systems is the gravitational potential and its gradient. This paper focuses on the development of a mixed method multigrid solver of the Poisson equation formulated so that both the potential and the Cartesian components of its gradient are self-consistently and accurately generated. The method achieves this goal by formulating the problem as a system of four equations for the gravitational potential and the three Cartesian components of the gradient and solves them using a distributed relaxation technique combined with conventional full multigrid V-cycles. The method is described, some tests are presented, and the accuracy of the method is assessed. We also describe how the method has been incorporated into our three-dimensional hydrodynamics code and give an example of an application to the collision of two stars. We end with some remarks about the future developments of the method and some of the applications in which it will be used in astrophysics.
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Numerical computation of gravitational field for general axisymmetric objects
NASA Astrophysics Data System (ADS)
Fukushima, Toshio
2016-10-01
We developed a numerical method to compute the gravitational field of a general axisymmetric object. The method (I) numerically evaluates a double integral of the ring potential by the split quadrature method using the double exponential rules, and (II) derives the acceleration vector by numerically differentiating the numerically integrated potential by Ridder's algorithm. Numerical comparison with the analytical solutions for a finite uniform spheroid and an infinitely extended object of the Miyamoto-Nagai density distribution confirmed the 13- and 11-digit accuracy of the potential and the acceleration vector computed by the method, respectively. By using the method, we present the gravitational potential contour map and/or the rotation curve of various axisymmetric objects: (I) finite uniform objects covering rhombic spindles and circular toroids, (II) infinitely extended spheroids including Sérsic and Navarro-Frenk-White spheroids, and (III) other axisymmetric objects such as an X/peanut-shaped object like NGC 128, a power-law disc with a central hole like the protoplanetary disc of TW Hya, and a tear-drop-shaped toroid like an axisymmetric equilibrium solution of plasma charge distribution in an International Thermonuclear Experimental Reactor-like tokamak. The method is directly applicable to the electrostatic field and will be easily extended for the magnetostatic field. The FORTRAN 90 programs of the new method and some test results are electronically available.
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ERIC Educational Resources Information Center
Thomas, Val
2014-01-01
The disciplines of counselling and psychotherapy have generated a range of innovative qualitative research methods. There is the potential for further developments, particularly in relation to methods that reveal how the researcher is implicated in the research. Practitioner-researchers could help to identify potential new methods through a…
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An improved reaction path optimization method using a chain of conformations
NASA Astrophysics Data System (ADS)
Asada, Toshio; Sawada, Nozomi; Nishikawa, Takuya; Koseki, Shiro
2018-05-01
The efficient fast path optimization (FPO) method is proposed to optimize the reaction paths on energy surfaces by using chains of conformations. No artificial spring force is used in the FPO method to ensure the equal spacing of adjacent conformations. The FPO method is applied to optimize the reaction path on two model potential surfaces. The use of this method enabled the optimization of the reaction paths with a drastically reduced number of optimization cycles for both potentials. It was also successfully utilized to define the MEP of the isomerization of the glycine molecule in water by FPO method.
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Jahanfar, Ali; Amirmojahedi, Mohsen; Gharabaghi, Bahram; Dubey, Brajesh; McBean, Edward; Kumar, Dinesh
2017-03-01
Rapid population growth of major urban centres in many developing countries has created massive landfills with extraordinary heights and steep side-slopes, which are frequently surrounded by illegal low-income residential settlements developed too close to landfills. These extraordinary landfills are facing high risks of catastrophic failure with potentially large numbers of fatalities. This study presents a novel method for risk assessment of landfill slope failure, using probabilistic analysis of potential failure scenarios and associated fatalities. The conceptual framework of the method includes selecting appropriate statistical distributions for the municipal solid waste (MSW) material shear strength and rheological properties for potential failure scenario analysis. The MSW material properties for a given scenario is then used to analyse the probability of slope failure and the resulting run-out length to calculate the potential risk of fatalities. In comparison with existing methods, which are solely based on the probability of slope failure, this method provides a more accurate estimate of the risk of fatalities associated with a given landfill slope failure. The application of the new risk assessment method is demonstrated with a case study for a landfill located within a heavily populated area of New Delhi, India.
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Structural issues affecting mixed methods studies in health research: a qualitative study
2009-01-01
Background Health researchers undertake studies which combine qualitative and quantitative methods. Little attention has been paid to the structural issues affecting this mixed methods approach. We explored the facilitators and barriers to undertaking mixed methods studies in health research. Methods Face-to-face semi-structured interviews with 20 researchers experienced in mixed methods research in health in the United Kingdom. Results Structural facilitators for undertaking mixed methods studies included a perception that funding bodies promoted this approach, and the multidisciplinary constituency of some university departments. Structural barriers to exploiting the potential of these studies included a lack of education and training in mixed methods research, and a lack of templates for reporting mixed methods articles in peer-reviewed journals. The 'hierarchy of evidence' relating to effectiveness studies in health care research, with the randomised controlled trial as the gold standard, appeared to pervade the health research infrastructure. Thus integration of data and findings from qualitative and quantitative components of mixed methods studies, and dissemination of integrated outputs, tended to occur through serendipity and effort, further highlighting the presence of structural constraints. Researchers are agents who may also support current structures - journal reviewers and editors, and directors of postgraduate training courses - and thus have the ability to improve the structural support for exploiting the potential of mixed methods research. Conclusion The environment for health research in the UK appears to be conducive to mixed methods research but not to exploiting the potential of this approach. Structural change, as well as change in researcher behaviour, will be necessary if researchers are to fully exploit the potential of using mixed methods research. PMID:20003210
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Simulation of electric double-layer capacitors: evaluation of constant potential method
NASA Astrophysics Data System (ADS)
Wang, Zhenxing; Laird, Brian; Yang, Yang; Olmsted, David; Asta, Mark
2014-03-01
Atomistic simulations can play an important role in understanding electric double-layer capacitors (EDLCs) at a molecular level. In such simulations, typically the electrode surface is modeled using fixed surface charges, which ignores the charge fluctuation induced by local fluctuations in the electrolyte solution. In this work we evaluate an explicit treatment of charges, namely constant potential method (CPM)[1], in which the electrode charges are dynamically updated to maintain constant electrode potential. We employ a model system with a graphite electrode and a LiClO4/acetonitrile electrolyte, examined as a function of electrode potential differences. Using various molecular and macroscopic properties as metrics, we compare CPM simulations on this system to results using fixed surface charges. Specifically, results for predicted capacity, electric potential gradient and solvent density profile are identical between the two methods; However, ion density profiles and solvation structure yield significantly different results.
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Marques, J M C; Pais, A A C C; Abreu, P E
2012-02-05
The efficiency of the so-called big-bang method for the optimization of atomic clusters is analysed in detail for Morse pair potentials with different ranges; here, we have used Morse potentials with four different ranges, from long- ρ = 3) to short-ranged ρ = 14) interactions. Specifically, we study the efficacy of the method in discovering low-energy structures, including the putative global minimum, as a function of the potential range and the cluster size. A new global minimum structure for long-ranged ρ = 3) Morse potential at the cluster size of n= 240 is reported. The present results are useful to assess the maximum cluster size for each type of interaction where the global minimum can be discovered with a limited number of big-bang trials. Copyright © 2011 Wiley Periodicals, Inc.
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Assessment of geothermal energy potential by geophysical methods: Nevşehir Region, Central Anatolia
NASA Astrophysics Data System (ADS)
Kıyak, Alper; Karavul, Can; Gülen, Levent; Pekşen, Ertan; Kılıç, A. Rıza
2015-03-01
In this study, geothermal potential of the Nevşehir region (Central Anatolia) was assessed by using vertical electrical sounding (VES), self-potential (SP), magnetotelluric (MT), gravity and gravity 3D Euler deconvolution structure analysis methods. Extensive volcanic activity occurred in this region from Upper Miocene to Holocene time. Due to the young volcanic activity Nevşehir region can be viewed as a potential geothermal area. We collected data from 54 VES points along 5 profiles, from 28 MT measurement points along 2 profiles (at frequency range between 320 and 0.0001 Hz), and from 4 SP profiles (total 19 km long). The obtained results based on different geophysical methods are consistent with each other. Joint interpretation of all geological and geophysical data suggests that this region has geothermal potential and an exploration well validated this assessment beyond doubt.
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Vrabel, Joseph; Teeple, Andrew; Kress, Wade H.
2009-01-01
With increasing demands for reliable water supplies and availability estimates, groundwater flow models often are developed to enhance understanding of surface-water and groundwater systems. Specific hydraulic variables must be known or calibrated for the groundwater-flow model to accurately simulate current or future conditions. Surface geophysical surveys, along with selected test-hole information, can provide an integrated framework for quantifying hydrogeologic conditions within a defined area. In 2004, the U.S. Geological Survey, in cooperation with the North Platte Natural Resources District, performed a surface geophysical survey using a capacitively coupled resistivity technique to map the lithology within the top 8 meters of the near-surface for 110 kilometers of the Interstate and Tri-State Canals in western Nebraska and eastern Wyoming. Assuming that leakage between the surface-water and groundwater systems is affected primarily by the sediment directly underlying the canal bed, leakage potential was estimated from the simple vertical mean of inverse-model resistivity values for depth levels with geometrically increasing layer thickness with depth which resulted in mean-resistivity values biased towards the surface. This method generally produced reliable results, but an improved analysis method was needed to account for situations where confining units, composed of less permeable material, underlie units with greater permeability. In this report, prepared by the U.S. Geological Survey in cooperation with the North Platte Natural Resources District, the authors use geostatistical analysis to develop the minimum-unadjusted method to compute a relative leakage potential based on the minimum resistivity value in a vertical column of the resistivity model. The minimum-unadjusted method considers the effects of homogeneous confining units. The minimum-adjusted method also is developed to incorporate the effect of local lithologic heterogeneity on water transmission. Seven sites with differing geologic contexts were selected following review of the capacitively coupled resistivity data collected in 2004. A reevaluation of these sites using the mean, minimum-unadjusted, and minimum-adjusted methods was performed to compare the different approaches for estimating leakage potential. Five of the seven sites contained underlying confining units, for which the minimum-unadjusted and minimum-adjusted methods accounted for the confining-unit effect. Estimates of overall leakage potential were lower for the minimum-unadjusted and minimum-adjusted methods than those estimated by the mean method. For most sites, the local heterogeneity adjustment procedure of the minimum-adjusted method resulted in slightly larger overall leakage-potential estimates. In contrast to the mean method, the two minimum-based methods allowed the least permeable areas to control the overall vertical permeability of the subsurface. The minimum-adjusted method refined leakage-potential estimation by additionally including local lithologic heterogeneity effects.
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Potential Landslide Early Detection Near Wenchuan by a Qualitatively Multi-Baseline Dinsar Method
NASA Astrophysics Data System (ADS)
Dai, K.; Chen, G.; Xu, Q.; Li, Z.; Qu, T.; Hu, L.; Lu, H.
2018-04-01
Early detection of landslides is important for disaster prevention, which was still very hard work with traditional surveying methods. Interferometric Synthetic Aperture Radar (InSAR) technology provided us the ability to monitor displacements along the slope with wide coverage and high accuracy. In this paper, we proposed a qualitatively multi-baseline DInSAR method to early detect and map the potential landslides. Two sections of China National Highway 317 and 213 were selected as study area. With this method 10 potential landslide areas were early detected and mapped in a quick and effective way. One of them (i.e. Shidaguan landslide) collapsed on August 2017, which was coincident with our results, suggesting that this method could become an effective way to acquire the landslide early detection map to assist the future disaster prevention work.
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DOT National Transportation Integrated Search
2015-03-01
This report examines potential methods for evaluating the economic benefits from nonmotorized transportation investments. The variety of potential economic benefits of bicycle and pedestrian infrastructure and programming investments discussed includ...
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ABSTRACT BODY: Thousands of chemicals lack adequate testing for adverse effects on nervous system development, stimulating research into alternative methods to screen chemicals for potential developmental neurotoxicity. Microelectrode arrays (MEA) collect action potential spiking...
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Vibrational properties of TaW alloy using modified embedded atom method potential
DOE Office of Scientific and Technical Information (OSTI.GOV)
Chand, Manesh, E-mail: maneshchand@gmail.com; Uniyal, Shweta; Joshi, Subodh
2016-05-06
Force-constants up to second neighbours of pure transition metal Ta and TaW alloy are determined using the modified embedded atom method (MEAM) potential. The obtained force-constants are used to calculate the phonon dispersion of pure Ta and TaW alloy. As a further application of MEAM potential, the force-constants are used to calculate the local vibrational density of states and mean square thermal displacements of pure Ta and W impurity atoms with Green’s function method. The calculated results are found to be in agreement with the experimental measurements.
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Estimating soil matric potential in Owens Valley, California
Sorenson, Stephen K.; Miller, R.F.; Welch, M.R.; Groeneveld, D.P.; Branson, F.A.
1988-01-01
Much of the floor of the Owens Valley, California, is covered with alkaline scrub and alkaline meadow plant communities, whose existence is dependent partly on precipitation and partly on water infiltrated into the rooting zone from the shallow water table. The extent to which these plant communities are capable of adapting to and surviving fluctuations in the water table depends on physiological adaptations of the plants and on the water content, matric potential characteristics of the soils. Two methods were used to estimate soil matric potential in test sites in Owens Valley. The first was the filter-paper method, which uses water content of filter papers equilibrated to water content of soil samples taken with a hand auger. The other method of estimating soil matric potential was a modeling approach based on data from this and previous investigations. These data indicate that the base 10 logarithm of soil matric potential is a linear function of gravimetric soil water content for a particular soil. Estimates of soil water characteristic curves were made at two sites by averaging the gravimetric soil water content and soil matric potential values from multiple samples at 0.1 m depths derived by using the hand auger and filter paper method and entering these values in the soil water model. The characteristic curves then were used to estimate soil matric potential from estimates of volumetric soil water content derived from neutron-probe readings. Evaluation of the modeling technique at two study sites indicated that estimates of soil matric potential within 0.5 pF units of the soil matric potential value derived by using the filter paper method could be obtained 90 to 95% of the time in soils where water content was less than field capacity. The greatest errors occurred at depths where there was a distinct transition between soils of different textures. (Lantz-PTT)
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Finite elements and finite differences for transonic flow calculations
NASA Technical Reports Server (NTRS)
Hafez, M. M.; Murman, E. M.; Wellford, L. C.
1978-01-01
The paper reviews the chief finite difference and finite element techniques used for numerical solution of nonlinear mixed elliptic-hyperbolic equations governing transonic flow. The forms of the governing equations for unsteady two-dimensional transonic flow considered are the Euler equation, the full potential equation in both conservative and nonconservative form, the transonic small-disturbance equation in both conservative and nonconservative form, and the hodograph equations for the small-disturbance case and the full-potential case. Finite difference methods considered include time-dependent methods, relaxation methods, semidirect methods, and hybrid methods. Finite element methods include finite element Lax-Wendroff schemes, implicit Galerkin method, mixed variational principles, dual iterative procedures, optimal control methods and least squares.
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NASA Astrophysics Data System (ADS)
Raff, L. M.; Malshe, M.; Hagan, M.; Doughan, D. I.; Rockley, M. G.; Komanduri, R.
2005-02-01
A neural network/trajectory approach is presented for the development of accurate potential-energy hypersurfaces that can be utilized to conduct ab initio molecular dynamics (AIMD) and Monte Carlo studies of gas-phase chemical reactions, nanometric cutting, and nanotribology, and of a variety of mechanical properties of importance in potential microelectromechanical systems applications. The method is sufficiently robust that it can be applied to a wide range of polyatomic systems. The overall method integrates ab initio electronic structure calculations with importance sampling techniques that permit the critical regions of configuration space to be determined. The computed ab initio energies and gradients are then accurately interpolated using neural networks (NN) rather than arbitrary parametrized analytical functional forms, moving interpolation or least-squares methods. The sampling method involves a tight integration of molecular dynamics calculations with neural networks that employ early stopping and regularization procedures to improve network performance and test for convergence. The procedure can be initiated using an empirical potential surface or direct dynamics. The accuracy and interpolation power of the method has been tested for two cases, the global potential surface for vinyl bromide undergoing unimolecular decomposition via four different reaction channels and nanometric cutting of silicon. The results show that the sampling methods permit the important regions of configuration space to be easily and rapidly identified, that convergence of the NN fit to the ab initio electronic structure database can be easily monitored, and that the interpolation accuracy of the NN fits is excellent, even for systems involving five atoms or more. The method permits a substantial computational speed and accuracy advantage over existing methods, is robust, and relatively easy to implement.
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Mehdi, Mohammad Murtaza; Rizvi, Syed Ibrahim
2013-05-15
N,N-Dimethyl-p-phenylenediamine dihydrochloride (DMPD) is a compound that is normally used to measure the antioxidant potential. In the presence of Fe(3+), it gets converted to DMPD(∙+) radical, which is scavenged by antioxidant molecules present in test samples. In plasma, due to the presence of iron, this method cannot be applied for the measurement of antioxidant potential. The modified DMPD method proposed by us measures with great accuracy the oxidant potential of plasma using the oxidizing effect of plasma to oxidize DMPD into producing a stable pink color. The method is fast and reproducible. We show that plasma oxidative capacity increases significantly during human aging. Copyright © 2013 Elsevier Inc. All rights reserved.
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Comparison of interpretation methods of thermocouple psychrometer readouts
NASA Astrophysics Data System (ADS)
Guz, Łukasz; Majerek, Dariusz; Sobczuk, Henryk; Guz, Ewa; Połednik, Bernard
2017-07-01
Thermocouple psychrometers allow to determine the water potential, which can be easily recalculated into relative humidity of air in cavity of porous materials. The available typical measuring range of probe is very narrow. The lower limit of water potential measurements is about -200 kPa. On the other hand, the upper limit is approximately equal to -7000 kPa and depends on many factors. These paper presents a comparison of two interpretation methods of thermocouple microvolt output regarding: i) amplitude of voltage during wet-bulb temperature depression, ii) field under microvolt output curve. Previous results of experiments indicate that there is a robust correlation between water potential and field under microvolt output curve. In order to obtain correct results of water potential, each probe should be calibrated. The range of NaCl salt solutions with molality from 0.75M to 2.25M was used for calibration, which enable to obtain the osmotic potential from -3377 kPa to -10865 kPa. During measurements was applied 5mA heating current over a span 5 s and 5 mA cooling current aver a span 30s. The conducted study proves that using only different interpretation method based on field under microvolt output it is possible to achieve about 1000 kPa wider range of water potential. The average relative mean square error (RMSE) of this interpretation method is 1199 kPa while voltage amplitude based method yields average RMSE equaling 1378 kPa during calibration in temperature not stabilized conditions.
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Real-time obstacle avoidance using harmonic potential functions
NASA Technical Reports Server (NTRS)
Kim, Jin-Oh; Khosla, Pradeep K.
1992-01-01
This paper presents a new formulation of the artificial potential approach to the obstacle avoidance problem for a mobile robot or a manipulator in a known environment. Previous formulations of artificial potentials for obstacle avoidance have exhibited local minima in a cluttered environment. To build an artificial potential field, harmonic functions that completely eliminate local minima even for a cluttered environment are used. The panel method is employed to represent arbitrarily shaped obstacles and to derive the potential over the whole space. Based on this potential function, an elegant control strategy is proposed for the real-time control of a robot. The harmonic potential, the panel method, and the control strategy are tested with a bar-shaped mobile robot and a three-degree-of-freedom planar redundant manipulator.
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Accurate and Efficient Approximation to the Optimized Effective Potential for Exchange
NASA Astrophysics Data System (ADS)
Ryabinkin, Ilya G.; Kananenka, Alexei A.; Staroverov, Viktor N.
2013-07-01
We devise an efficient practical method for computing the Kohn-Sham exchange-correlation potential corresponding to a Hartree-Fock electron density. This potential is almost indistinguishable from the exact-exchange optimized effective potential (OEP) and, when used as an approximation to the OEP, is vastly better than all existing models. Using our method one can obtain unambiguous, nearly exact OEPs for any reasonable finite one-electron basis set at the same low cost as the Krieger-Li-Iafrate and Becke-Johnson potentials. For all practical purposes, this solves the long-standing problem of black-box construction of OEPs in exact-exchange calculations.
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Active invisibility cloaks in one dimension
NASA Astrophysics Data System (ADS)
Mostafazadeh, Ali
2015-06-01
We outline a general method of constructing finite-range cloaking potentials which render a given finite-range real or complex potential, v (x ) , unidirectionally reflectionless or invisible at a wave number, k0, of our choice. We give explicit analytic expressions for three classes of cloaking potentials which achieve this goal while preserving some or all of the other scattering properties of v (x ) . The cloaking potentials we construct are the sum of up to three constituent unidirectionally invisible potentials. We discuss their utility in making v (x ) bidirectionally invisible at k0 and demonstrate the application of our method to obtain antireflection and invisibility cloaks for a Bragg reflector.
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Finite difference methods for the solution of unsteady potential flows
NASA Technical Reports Server (NTRS)
Caradonna, F. X.
1985-01-01
A brief review is presented of various problems which are confronted in the development of an unsteady finite difference potential code. This review is conducted mainly in the context of what is done for a typical small disturbance and full potential methods. The issues discussed include choice of equation, linearization and conservation, differencing schemes, and algorithm development. A number of applications including unsteady three-dimensional rotor calculation, are demonstrated.
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Quantitative method of measuring cancer cell urokinase and metastatic potential
NASA Technical Reports Server (NTRS)
Morrison, Dennis R. (Inventor)
1993-01-01
The metastatic potential of tumors can be evaluated by the quantitative detection of urokinase and DNA. The cell sample selected for examination is analyzed for the presence of high levels of urokinase and abnormal DNA using analytical flow cytometry and digital image analysis. Other factors such as membrane associated urokinase, increased DNA synthesis rates and certain receptors can be used in the method for detection of potentially invasive tumors.
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Rodriguez-Falces, Javier
2013-12-01
In electrophysiology studies, it is becoming increasingly common to explain experimental observations using both descriptive methods and quantitative approaches. However, some electrophysiological phenomena, such as the generation of extracellular potentials that results from the propagation of the excitation source along the muscle fiber, are difficult to describe and conceptualize. In addition, most traditional approaches aimed at describing extracellular potentials consist of complex mathematical machinery that gives no chance for physical interpretation. The aim of the present study is to present a new method to teach the formation of extracellular potentials around a muscle fiber from both a descriptive and quantitative perspective. The implementation of this method was tested through a written exam and a satisfaction survey. The new method enhanced the ability of students to visualize the generation of bioelectrical potentials. In addition, the new approach improved students' understanding of how changes in the fiber-to-electrode distance and in the shape of the excitation source are translated into changes in the extracellular potential. The survey results show that combining general principles of electrical fields with accurate graphic imagery gives students an intuitive, yet quantitative, feel for electrophysiological signals and enhances their motivation to continue their studies in the biomedical engineering field.
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Berente, Imre; Czinki, Eszter; Náray-Szabó, Gábor
2007-09-01
We report an approach for the determination of atomic monopoles of macromolecular systems using connectivity and geometry parameters alone. The method is appropriate also for the calculation of charge distributions based on the quantum mechanically determined wave function and does not suffer from the mathematical instability of other electrostatic potential fit methods. Copyright 2007 Wiley Periodicals, Inc.
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Customer-Specific Transaction Risk Management in E-Commerce
NASA Astrophysics Data System (ADS)
Ruch, Markus; Sackmann, Stefan
Increasing potential for turnover in e-commerce is inextricably linked with an increase in risk. Online retailers (e-tailers), aiming for a company-wide value orientation should manage this risk. However, current approaches to risk management either use average retail prices elevated by an overall risk premium or restrict the payment methods offered to customers. Thus, they neglect customer-specific value and risk attributes and leave turnover potentials unconsidered. To close this gap, an innovative valuation model is proposed in this contribution that integrates customer-specific risk and potential turnover. The approach presented evaluates different payment methods using their risk-turnover characteristic, provides a risk-adjusted decision basis for selecting payment methods and allows e-tailers to derive automated risk management decisions per customer and transaction without reducing turnover potential.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Kolb, Brian; Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; Zhao, Bin
2016-06-14
The applicability and accuracy of the Behler-Parrinello atomistic neural network method for fitting reactive potential energy surfaces is critically examined in three systems, H + H{sub 2} → H{sub 2} + H, H + H{sub 2}O → H{sub 2} + OH, and H + CH{sub 4} → H{sub 2} + CH{sub 3}. A pragmatic Monte Carlo method is proposed to make efficient choice of the atom-centered mapping functions. The accuracy of the potential energy surfaces is not only tested by fitting errors but also validated by direct comparison in dynamically important regions and by quantum scattering calculations. Our results suggestmore » this method is both accurate and efficient in representing multidimensional potential energy surfaces even when dissociation continua are involved.« less
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Volgushev, Maxim; Malyshev, Aleksey; Balaban, Pavel; Chistiakova, Marina; Volgushev, Stanislav; Wolf, Fred
2008-04-09
The generation of action potentials (APs) is a key process in the operation of nerve cells and the communication between neurons. Action potentials in mammalian central neurons are characterized by an exceptionally fast onset dynamics, which differs from the typically slow and gradual onset dynamics seen in identified snail neurons. Here we describe a novel method of analysis which provides a quantitative measure of the onset dynamics of action potentials. This method captures the difference between the fast, step-like onset of APs in rat neocortical neurons and the gradual, exponential-like AP onset in identified snail neurons. The quantitative measure of the AP onset dynamics, provided by the method, allows us to perform quantitative analyses of factors influencing the dynamics.
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Volgushev, Maxim; Malyshev, Aleksey; Balaban, Pavel; Chistiakova, Marina; Volgushev, Stanislav; Wolf, Fred
2008-01-01
The generation of action potentials (APs) is a key process in the operation of nerve cells and the communication between neurons. Action potentials in mammalian central neurons are characterized by an exceptionally fast onset dynamics, which differs from the typically slow and gradual onset dynamics seen in identified snail neurons. Here we describe a novel method of analysis which provides a quantitative measure of the onset dynamics of action potentials. This method captures the difference between the fast, step-like onset of APs in rat neocortical neurons and the gradual, exponential-like AP onset in identified snail neurons. The quantitative measure of the AP onset dynamics, provided by the method, allows us to perform quantitative analyses of factors influencing the dynamics. PMID:18398478
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The Chemical Potential of Plasma Membrane Cholesterol: Implications for Cell Biology.
Ayuyan, Artem G; Cohen, Fredric S
2018-02-27
Cholesterol is abundant in plasma membranes and exhibits a variety of interactions throughout the membrane. Chemical potential accounts for thermodynamic consequences of molecular interactions, and quantifies the effective concentration (i.e., activity) of any substance participating in a process. We have developed, to our knowledge, the first method to measure cholesterol chemical potential in plasma membranes. This was accomplished by complexing methyl-β-cyclodextrin with cholesterol in an aqueous solution and equilibrating it with an organic solvent containing dissolved cholesterol. The chemical potential of cholesterol was thereby equalized in the two phases. Because cholesterol is dilute in the organic phase, here activity and concentration were equivalent. This equivalence allowed the amount of cholesterol bound to methyl-β-cyclodextrin to be converted to cholesterol chemical potential. Our method was used to determine the chemical potential of cholesterol in erythrocytes and in plasma membranes of nucleated cells in culture. For erythrocytes, the chemical potential did not vary when the concentration was below a critical value. Above this value, the chemical potential progressively increased with concentration. We used standard cancer lines to characterize cholesterol chemical potential in plasma membranes of nucleated cells. This chemical potential was significantly greater for highly metastatic breast cancer cells than for nonmetastatic breast cancer cells. Chemical potential depended on density of the cancer cells. A method to alter and fix the cholesterol chemical potential to any value (i.e., a cholesterol chemical potential clamp) was also developed. Cholesterol content did not change when cells were clamped for 24-48 h. It was found that the level of activation of the transcription factor STAT3 increased with increasing cholesterol chemical potential. The cholesterol chemical potential may regulate signaling pathways. Copyright © 2018. Published by Elsevier Inc.
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Free energy calculations: an efficient adaptive biasing potential method.
Dickson, Bradley M; Legoll, Frédéric; Lelièvre, Tony; Stoltz, Gabriel; Fleurat-Lessard, Paul
2010-05-06
We develop an efficient sampling and free energy calculation technique within the adaptive biasing potential (ABP) framework. By mollifying the density of states we obtain an approximate free energy and an adaptive bias potential that is computed directly from the population along the coordinates of the free energy. Because of the mollifier, the bias potential is "nonlocal", and its gradient admits a simple analytic expression. A single observation of the reaction coordinate can thus be used to update the approximate free energy at every point within a neighborhood of the observation. This greatly reduces the equilibration time of the adaptive bias potential. This approximation introduces two parameters: strength of mollification and the zero of energy of the bias potential. While we observe that the approximate free energy is a very good estimate of the actual free energy for a large range of mollification strength, we demonstrate that the errors associated with the mollification may be removed via deconvolution. The zero of energy of the bias potential, which is easy to choose, influences the speed of convergence but not the limiting accuracy. This method is simple to apply to free energy or mean force computation in multiple dimensions and does not involve second derivatives of the reaction coordinates, matrix manipulations nor on-the-fly adaptation of parameters. For the alanine dipeptide test case, the new method is found to gain as much as a factor of 10 in efficiency as compared to two basic implementations of the adaptive biasing force methods, and it is shown to be as efficient as well-tempered metadynamics with the postprocess deconvolution giving a clear advantage to the mollified density of states method.
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NASA Astrophysics Data System (ADS)
Quintero-Chavarria, E.; Ochoa Gutierrez, L. H.
2016-12-01
Applications of the Self-potential Method in the fields of Hydrogeology and Environmental Sciences have had significant developments during the last two decades with a strong use on groundwater flows identification. Although only few authors deal with the forward problem's solution -especially in geophysics literature- different inversion procedures are currently being developed but in most cases they are compared with unconventional groundwater velocity fields and restricted to structured meshes. This research solves the forward problem based on the finite element method using the St. Venant's Principle to transform a point dipole, which is the field generated by a single vector, into a distribution of electrical monopoles. Then, two simple aquifer models were generated with specific boundary conditions and head potentials, velocity fields and electric potentials in the medium were computed. With the model's surface electric potential, the inverse problem is solved to retrieve the source of electric potential (vector field associated to groundwater flow) using deterministic and stochastic approaches. The first approach was carried out by implementing a Tikhonov regularization with a stabilized operator adapted to the finite element mesh while for the second a hierarchical Bayesian model based on Markov chain Monte Carlo (McMC) and Markov Random Fields (MRF) was constructed. For all implemented methods, the result between the direct and inverse models was contrasted in two ways: 1) shape and distribution of the vector field, and 2) magnitude's histogram. Finally, it was concluded that inversion procedures are improved when the velocity field's behavior is considered, thus, the deterministic method is more suitable for unconfined aquifers than confined ones. McMC has restricted applications and requires a lot of information (particularly in potentials fields) while MRF has a remarkable response especially when dealing with confined aquifers.
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Estimating soil matric potential in Owens Valley, California
Sorenson, Stephen K.; Miller, Reuben F.; Welch, Michael R.; Groeneveld, David P.; Branson, Farrel A.
1989-01-01
Much of the floor of Owens Valley, California, is covered with alkaline scrub and alkaline meadow plant communities, whose existence is dependent partly on precipitation and partly on water infiltrated into the rooting zone from the shallow water table. The extent to which these plant communities are capable of adapting to and surviving fluctuations in the water table depends on physiological adaptations of the plants and on the water content, matric potential characteristics of the soils. Two methods were used to estimate soil matric potential in test sites in Owens Valley. The first, the filter-paper method, uses water content of filter papers equilibrated to water content of soil samples taken with a hand auger. The previously published calibration relations used to estimate soil matric potential from the water content of the filter papers were modified on the basis of current laboratory data. The other method of estimating soil matric potential was a modeling approach based on data from this and previous investigations. These data indicate that the base-10 logarithm of soil matric potential is a linear function of gravimetric soil water content for a particular soil. The slope and intercepts of this function vary with the texture and saturation capacity of the soil. Estimates of soil water characteristic curves were made at two sites by averaging the gravimetric soil water content and soil matric potential values from multiple samples at 0.1-m depth intervals derived by using the hand auger and filter-paper method and entering these values in the soil water model. The characteristic curves then were used to estimate soil matric potential from estimates of volumetric soil water content derived from neutron-probe readings. Evaluation of the modeling technique at two study sites indicated that estimates of soil matric potential within 0.5 pF units of the soil matric potential value derived by using the filter-paper method could be obtained 90 to 95 percent of the time in soils where water content was less than field capacity. The greatest errors occurred at depths where there was a distinct transition between soils of different textures.
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Schwinger-variational-principle theory of collisions in the presence of multiple potentials
NASA Astrophysics Data System (ADS)
Robicheaux, F.; Giannakeas, P.; Greene, Chris H.
2015-08-01
A theoretical method for treating collisions in the presence of multiple potentials is developed by employing the Schwinger variational principle. The current treatment agrees with the local (regularized) frame transformation theory and extends its capabilities. Specifically, the Schwinger variational approach gives results without the divergences that need to be regularized in other methods. Furthermore, it provides a framework to identify the origin of these singularities and possibly improve the local frame transformation. We have used the method to obtain the scattering parameters for different confining potentials symmetric in x ,y . The method is also used to treat photodetachment processes in the presence of various confining potentials, thereby highlighting effects of the infinitely many closed channels. Two general features predicted are the vanishing of the total photoabsorption probability at every channel threshold and the occurrence of resonances below the channel thresholds for negative scattering lengths. In addition, the case of negative-ion photodetachment in the presence of uniform magnetic fields is also considered where unique features emerge at large scattering lengths.
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Wang, Han-Chun; Ernst, Siegfried; Baltruschat, Helmut
2010-03-07
The apparent transfer coefficient, which gives the magnitude of the potential dependence of the electrochemical reaction rates, is the key quantity for the elucidation of electrochemical reaction mechanisms. We introduce the application of an ac method to determine the apparent transfer coefficient alpha' for the oxidation of pre-adsorbed CO at polycrystalline and single-crystalline Pt electrodes in sulfuric acid. The method allows to record alpha' quasi continuously as a function of potential (and time) in cyclic voltammetry or at a fixed potential, with the reaction rate varying with time. At all surfaces (Pt(poly), Pt(111), Pt(665), and Pt(332)) we clearly observed a transition of the apparent transfer coefficient from values around 1.5 at low potentials to values around 0.5 at higher potentials. Changes of the apparent transfer coefficients for the CO oxidation with potential were observed previously, but only from around 0.7 to values as low as 0.2. In contrast, our experimental findings completely agree with the simulation by Koper et al., J. Chem. Phys., 1998, 109, 6051-6062. They can be understood in the framework of a Langmuir-Hinshelwood mechanism. The transition occurs when the sum of the rate constants for the forward reaction (first step: potential dependent OH adsorption, second step: potential dependent oxidation of CO(ad) with OH(ad)) exceeds the rate constant for the back-reaction of the first step. We expect that the ac method for the determination of the apparent transfer coefficient, which we used here, will be of great help also in many other cases, especially under steady conditions, where the major limitations of the method are avoided.
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Podsakoff, Philip M; MacKenzie, Scott B; Lee, Jeong-Yeon; Podsakoff, Nathan P
2003-10-01
Interest in the problem of method biases has a long history in the behavioral sciences. Despite this, a comprehensive summary of the potential sources of method biases and how to control for them does not exist. Therefore, the purpose of this article is to examine the extent to which method biases influence behavioral research results, identify potential sources of method biases, discuss the cognitive processes through which method biases influence responses to measures, evaluate the many different procedural and statistical techniques that can be used to control method biases, and provide recommendations for how to select appropriate procedural and statistical remedies for different types of research settings.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Revil, Andre
2013-01-15
Understanding the influence of coupled biological, chemical, and hydrological processes on subsurface contaminant behavior at multiple scales is a prerequisite for developing effective remedial approaches, whether they are active remediation or natural attenuation strategies. To develop this understanding, methods are needed that can measure critical components of the natural system in real time. The self-potential method corresponds to the passive measurement of the distribution of the electrical potential at the surface of the Earth or in boreholes. This method is very complemetary to other geophysical methods like DC resistivity and induced polarization. In this report, we summarize of research effortsmore » to advance the theory of low-frequency geoelectrical methods and their applications to the contaminant plumes in the vicinity of the former S-3 settling basins at Oak Ridge, TN.« less
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Subsonic panel method for designing wing surfaces from pressure distribution
NASA Technical Reports Server (NTRS)
Bristow, D. R.; Hawk, J. D.
1983-01-01
An iterative method has been developed for designing wing section contours corresponding to a prescribed subcritical distribution of pressure. The calculations are initialized by using a surface panel method to analyze a baseline wing or wing-fuselage configuration. A first-order expansion to the baseline panel method equations is then used to calculate a matrix containing the partial derivative of potential at each control point with respect to each unknown geometry parameter. In every iteration cycle, the matrix is used both to calculate the geometry perturbation and to analyze the perturbed geometry. The distribution of potential on the perturbed geometry is established by simple linear extrapolation from the baseline solution. The extrapolated potential is converted to pressure by Bernoulli's equation. Not only is the accuracy of the approach good for very large perturbations, but the computing cost of each complete iteration cycle is substantially less than one analysis solution by a conventional panel method.
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Numerical simulation using vorticity-vector potential formulation
NASA Technical Reports Server (NTRS)
Tokunaga, Hiroshi
1993-01-01
An accurate and efficient computational method is needed for three-dimensional incompressible viscous flows in engineering applications. On solving the turbulent shear flows directly or using the subgrid scale model, it is indispensable to resolve the small scale fluid motions as well as the large scale motions. From this point of view, the pseudo-spectral method is used so far as the computational method. However, the finite difference or the finite element methods are widely applied for computing the flow with practical importance since these methods are easily applied to the flows with complex geometric configurations. However, there exist several problems in applying the finite difference method to direct and large eddy simulations. Accuracy is one of most important problems. This point was already addressed by the present author on the direct simulations on the instability of the plane Poiseuille flow and also on the transition to turbulence. In order to obtain high efficiency, the multi-grid Poisson solver is combined with the higher-order, accurate finite difference method. The formulation method is also one of the most important problems in applying the finite difference method to the incompressible turbulent flows. The three-dimensional Navier-Stokes equations have been solved so far in the primitive variables formulation. One of the major difficulties of this method is the rigorous satisfaction of the equation of continuity. In general, the staggered grid is used for the satisfaction of the solenoidal condition for the velocity field at the wall boundary. However, the velocity field satisfies the equation of continuity automatically in the vorticity-vector potential formulation. From this point of view, the vorticity-vector potential method was extended to the generalized coordinate system. In the present article, we adopt the vorticity-vector potential formulation, the generalized coordinate system, and the 4th-order accurate difference method as the computational method. We present the computational method and apply the present method to computations of flows in a square cavity at large Reynolds number in order to investigate its effectiveness.
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Inferring the gravitational potential of the Milky Way with a few precisely measured stars
DOE Office of Scientific and Technical Information (OSTI.GOV)
Price-Whelan, Adrian M.; Johnston, Kathryn V.; Hendel, David
2014-10-10
The dark matter halo of the Milky Way is expected to be triaxial and filled with substructure. It is hoped that streams or shells of stars produced by tidal disruption of stellar systems will provide precise measures of the gravitational potential to test these predictions. We develop a method for inferring the Galactic potential with tidal streams based on the idea that the stream stars were once close in phase space. Our method can flexibly adapt to any form for the Galactic potential: it works in phase-space rather than action-space and hence relies neither on our ability to derive actionsmore » nor on the integrability of the potential. Our model is probabilistic, with a likelihood function and priors on the parameters. The method can properly account for finite observational uncertainties and missing data dimensions. We test our method on synthetic data sets generated from N-body simulations of satellite disruption in a static, multi-component Milky Way, including a triaxial dark matter halo with observational uncertainties chosen to mimic current and near-future surveys of various stars. We find that with just eight well-measured stream stars, we can infer properties of a triaxial potential with precisions of the order of 5%-7%. Without proper motions, we obtain 10% constraints on most potential parameters and precisions around 5%-10% for recovering missing phase-space coordinates. These results are encouraging for the goal of using flexible, time-dependent potential models combined with larger data sets to unravel the detailed shape of the dark matter distribution around the Milky Way.« less
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Zazzi, Barbara C.; Crepeau, Kathryn L.; Fram, Miranda S.; Bergamaschi, Brian A.
2005-01-01
An analytical method for the determination of haloacetic acid formation potential of water samples has been developed by the U.S. Geological Survey California Water Science Center Sacramento Laboratory. The haloacetic acid formation potential is measured by dosing water samples with chlorine under specified conditions of pH, temperature, incubation time, darkness, and residual-free chlorine. The haloacetic acids formed are bromochloroacetic acid, bromodichloroacetic acid, dibromochloroacetic acid, dibromoacetic acid, dichloroacetic acid, monobromoacetic acid, monochloroacetic acid, tribromoacetic acid, and trichloroacetic acid. They are extracted, methylated, and then analyzed using a gas chromatograph equipped with an electron capture detector. Method validation experiments were performed to determine the method accuracy, precision, and detection limit for each of the compounds. Method detection limits for these nine haloacetic acids ranged from 0.11 to 0.45 microgram per liter. Quality-control practices include the use of blanks, quality-control samples, calibration verification standards, surrogate recovery, internal standard, matrix spikes, and duplicates.
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1997-11-01
status can sometimes be reflected in the infectious potential or drug resistance of those pathogens. For example, in Mycobacterium tuberculosis ... Mycobacterium tuberculosis , its antibiotic resistance and prediction of pathogenicity amongst Mycobacterium spp. based on signature lipid biomarkers ...TITLE AND SUBTITLE Rapid, Potentially Automatable, Method Extract Biomarkers for HPLC/ESI/MS/MS to Detect and Identify BW Agents 5a. CONTRACT NUMBER 5b
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Thermal conductivity of silicon using reverse non-equilibrium molecular dynamics
NASA Astrophysics Data System (ADS)
El-Genk, Mohamed S.; Talaat, Khaled; Cowen, Benjamin J.
2018-05-01
Simulations are performed using the reverse non-equilibrium molecular dynamics (rNEMD) method and the Stillinger-Weber (SW) potential to determine the input parameters for achieving ±1% convergence of the calculated thermal conductivity of silicon. These parameters are then used to investigate the effects of the interatomic potentials of SW, Tersoff II, Environment Dependent Interatomic Potential (EDIP), Second Nearest Neighbor, Modified Embedded-Atom Method (MEAM), and Highly Optimized Empirical Potential MEAM on determining the bulk thermal conductivity as a function of temperature (400-1000 K). At temperatures > 400 K, data collection and swap periods of 15 ns and 150 fs, system size ≥6 × 6 UC2 and system lengths ≥192 UC are adequate for ±1% convergence with all potentials, regardless of the time step size (0.1-0.5 fs). This is also true at 400 K, except for the SW potential, which requires a data collection period ≥30 ns. The calculated bulk thermal conductivities using the rNEMD method and the EDIP potential are close to, but lower than experimental values. The 10% difference at 400 K increases gradually to 20% at 1000 K.
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GIS-based bivariate statistical techniques for groundwater potential analysis (an example of Iran)
NASA Astrophysics Data System (ADS)
Haghizadeh, Ali; Moghaddam, Davoud Davoudi; Pourghasemi, Hamid Reza
2017-12-01
Groundwater potential analysis prepares better comprehension of hydrological settings of different regions. This study shows the potency of two GIS-based data driven bivariate techniques namely statistical index (SI) and Dempster-Shafer theory (DST) to analyze groundwater potential in Broujerd region of Iran. The research was done using 11 groundwater conditioning factors and 496 spring positions. Based on the ground water potential maps (GPMs) of SI and DST methods, 24.22% and 23.74% of the study area is covered by poor zone of groundwater potential, and 43.93% and 36.3% of Broujerd region is covered by good and very good potential zones, respectively. The validation of outcomes displayed that area under the curve (AUC) of SI and DST techniques are 81.23% and 79.41%, respectively, which shows SI method has slightly a better performance than the DST technique. Therefore, SI and DST methods are advantageous to analyze groundwater capacity and scrutinize the complicated relation between groundwater occurrence and groundwater conditioning factors, which permits investigation of both systemic and stochastic uncertainty. Finally, it can be realized that these techniques are very beneficial for groundwater potential analyzing and can be practical for water-resource management experts.
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Effective numerical method of spectral analysis of quantum graphs
NASA Astrophysics Data System (ADS)
Barrera-Figueroa, Víctor; Rabinovich, Vladimir S.
2017-05-01
We present in the paper an effective numerical method for the determination of the spectra of periodic metric graphs equipped by Schrödinger operators with real-valued periodic electric potentials as Hamiltonians and with Kirchhoff and Neumann conditions at the vertices. Our method is based on the spectral parameter power series method, which leads to a series representation of the dispersion equation, which is suitable for both analytical and numerical calculations. Several important examples demonstrate the effectiveness of our method for some periodic graphs of interest that possess potentials usually found in quantum mechanics.
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A new approach to the Schrödinger equation with rational potentials
NASA Astrophysics Data System (ADS)
Dong, Ming-de; Chu, Jue-Hui
1984-04-01
A new analytic theory is established for the Schrödinger equation with a rational potential, including a complete classification of the regular eigenfunctions into three different types, an exact method of obtaining wavefunctions, an explicit formulation of the spectral equation (3 x 3 determinant) etc. All representations are exhibited in a unifying way via function-theoretic methods and therefore given in explicit form, in contrast to the prevailing discussion appealing to perturbation or variation methods or continued-fraction techniques. The irregular eigenfunctions at infinity can be obtained analogously and will be discussed separately as another solvable case for singular potentials.
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Methodology for vocational psychodiagnostics of senior schoolchildren using information technologies
NASA Astrophysics Data System (ADS)
Bogdanovskaya, I. M.; Kosheleva, A. N.; Kiselev, P. B.; Davydova, Yu. A.
2017-01-01
The article identifies the role and main problems of vocational psychodiagnostics in modern socio-cultural conditions. It analyzes the potentials of information technologies in vocational psychodiagnostics of senior schoolchildren. The article describes the theoretical and methodological grounds, content and diagnostic potentials of the computerized method in vocational psychodiagnostics. The computerized method includes three blocks of sub-tests to identify intellectual potential, personal qualities, professional interests and values, career orientations, as well as subtests to analyze the specific life experience of senior schoolchildren. The results of diagnostics allow developing an integrated psychodiagnostic conclusion with recommendations. The article contains options of software architecture for the given method.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Sundararaman, Ravishankar; Goddard, III, William A.; Arias, Tomas A.
First-principles calculations combining density-functional theory and continuum solvation models enable realistic theoretical modeling and design of electrochemical systems. When a reaction proceeds in such systems, the number of electrons in the portion of the system treated quantum mechanically changes continuously, with a balancing charge appearing in the continuum electrolyte. A grand-canonical ensemble of electrons at a chemical potential set by the electrode potential is therefore the ideal description of such systems that directly mimics the experimental condition. We present two distinct algorithms: a self-consistent field method and a direct variational free energy minimization method using auxiliary Hamiltonians (GC-AuxH), to solvemore » the Kohn-Sham equations of electronic density-functional theory directly in the grand canonical ensemble at fixed potential. Both methods substantially improve performance compared to a sequence of conventional fixed-number calculations targeting the desired potential, with the GC-AuxH method additionally exhibiting reliable and smooth exponential convergence of the grand free energy. Lastly, we apply grand-canonical density-functional theory to the under-potential deposition of copper on platinum from chloride-containing electrolytes and show that chloride desorption, not partial copper monolayer formation, is responsible for the second voltammetric peak.« less
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Sundararaman, Ravishankar; Goddard, William A; Arias, Tomas A
2017-03-21
First-principles calculations combining density-functional theory and continuum solvation models enable realistic theoretical modeling and design of electrochemical systems. When a reaction proceeds in such systems, the number of electrons in the portion of the system treated quantum mechanically changes continuously, with a balancing charge appearing in the continuum electrolyte. A grand-canonical ensemble of electrons at a chemical potential set by the electrode potential is therefore the ideal description of such systems that directly mimics the experimental condition. We present two distinct algorithms: a self-consistent field method and a direct variational free energy minimization method using auxiliary Hamiltonians (GC-AuxH), to solve the Kohn-Sham equations of electronic density-functional theory directly in the grand canonical ensemble at fixed potential. Both methods substantially improve performance compared to a sequence of conventional fixed-number calculations targeting the desired potential, with the GC-AuxH method additionally exhibiting reliable and smooth exponential convergence of the grand free energy. Finally, we apply grand-canonical density-functional theory to the under-potential deposition of copper on platinum from chloride-containing electrolytes and show that chloride desorption, not partial copper monolayer formation, is responsible for the second voltammetric peak.
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Sundararaman, Ravishankar; Goddard, III, William A.; Arias, Tomas A.
2017-03-16
First-principles calculations combining density-functional theory and continuum solvation models enable realistic theoretical modeling and design of electrochemical systems. When a reaction proceeds in such systems, the number of electrons in the portion of the system treated quantum mechanically changes continuously, with a balancing charge appearing in the continuum electrolyte. A grand-canonical ensemble of electrons at a chemical potential set by the electrode potential is therefore the ideal description of such systems that directly mimics the experimental condition. We present two distinct algorithms: a self-consistent field method and a direct variational free energy minimization method using auxiliary Hamiltonians (GC-AuxH), to solvemore » the Kohn-Sham equations of electronic density-functional theory directly in the grand canonical ensemble at fixed potential. Both methods substantially improve performance compared to a sequence of conventional fixed-number calculations targeting the desired potential, with the GC-AuxH method additionally exhibiting reliable and smooth exponential convergence of the grand free energy. Lastly, we apply grand-canonical density-functional theory to the under-potential deposition of copper on platinum from chloride-containing electrolytes and show that chloride desorption, not partial copper monolayer formation, is responsible for the second voltammetric peak.« less
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Vella, Joseph R.; Stillinger, Frank H.; Panagiotopoulos, Athanassios Z.; ...
2015-07-23
Here, we compare six lithium potentials by examining their ability to predict coexistence properties and liquid structure using molecular dynamics. All potentials are of the embedded-atom-method (EAM) type. The coexistence properties we focus on are the melting curve, vapor pressure, saturated liquid density, and vapor-liquid surface tension. For each property studied, the simulation results are compared to available experimental data in order to properly assess the accuracy of each potential. We find that the Cui 2NN MEAM is the most robust potential, giving adequate agreement with most of the properties examined. For example, the zero-pressure melting point of this potentialmore » is shown to be around 443 K, while experimentally is it about 454 K. This potential also gives excellent agreement with saturated liquid densities, even though no liquid properties were used in the fitting procedure. Our study allows us to conclude that the Cui 2NN MEAM should be used for further simulations of lithiums.« less
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Symmetric and anti-symmetric LS hyperon potentials from lattice QCD
NASA Astrophysics Data System (ADS)
Ishii, Noriyoshi; Murano, Keiko; Nemura, Hidekatsu; Sasaki, Kenji; Inoue, Takashi; HAL QCD Collaboration
2014-09-01
We present recent results of odd-parity hyperon-hyperon potentials from lattice QCD. By using HAL QCD method, we generate hyperon-hyperon potentials from Nambu-Bethe-Salpeter (NBS) wave functions generated by lattice QCD simulation in the flavor SU(3) limit. Potentials in the irreducible flavor SU(3) representations are combined to make a Lambda-N potential which has a strong symmetric LS potential and a weak anti-symmetric LS potential. We discuss a possible cancellation between symmetric and anti-symmetric LS (Lambda-N) potentials after the coupled Sigma-N sector is integrated out. We present recent results of odd-parity hyperon-hyperon potentials from lattice QCD. By using HAL QCD method, we generate hyperon-hyperon potentials from Nambu-Bethe-Salpeter (NBS) wave functions generated by lattice QCD simulation in the flavor SU(3) limit. Potentials in the irreducible flavor SU(3) representations are combined to make a Lambda-N potential which has a strong symmetric LS potential and a weak anti-symmetric LS potential. We discuss a possible cancellation between symmetric and anti-symmetric LS (Lambda-N) potentials after the coupled Sigma-N sector is integrated out. This work is supported by JSPS KAKENHI Grant Number 25400244.
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Realizing the Potential of Mobile Mental Health: New Methods for New Data in Psychiatry
Staples, Patrick; Onnela, Jukka-Pekka
2015-01-01
Smartphones are now ubiquitous and can be harnessed to offer psychiatry a wealth of real-time data regarding patient behavior, self-reported symptoms, and even physiology. The data collected from smartphones meet the three criteria of big data: velocity, volume, and variety. Although these data have tremendous potential, transforming them into clinically valid and useful information requires using new tools and methods as a part of assessment in psychiatry. In this paper, we introduce and explore numerous analytical methods and tools from the computational and statistical sciences that appear readily applicable to psychiatric data collected using smartphones. By matching smartphone data with appropriate statistical methods, psychiatry can better realize the potential of mobile mental health and empower both patients and providers with novel clinical tools. PMID:26073363
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NASA Astrophysics Data System (ADS)
Nadzir, Z. A.; Karondia, L. A.; Jaelani, L. M.; Sulaiman, A.; Pamungkas, A.; Koenhardono, E. S.; Sulisetyono, A.
2015-10-01
Ocean wave energy is one of the ORE (Ocean Renewable Energies) sources, which potential, in which this energy has several advantages over fossil energy and being one of the most researched energy in developed countries nowadays. One of the efforts for mapping ORE potential is by computing energy potential generated from ocean wave, symbolized by Watt per area unit using various methods of observation. SAR (Synthetic Aperture Radar) is one of the hyped and most developed Remote Sensing method used to monitor and map the ocean wave energy potential effectively and fast. SAR imagery processing can be accomplished not only in remote sensing data applications, but using Matrices processing application as well such as MATLAB that utilizing Fast Fourier Transform and Band-Pass Filtering methods undergoing Pre-Processing stage. In this research, the processing and energy estimation from ALOSPALSAR satellite imagery acquired on the 5/12/2009 was accomplished using 2 methods (i.e Magnitude and Wavelength). This resulted in 9 potential locations of ocean wave energy between 0-228 W/m2, and 7 potential locations with ranged value between 182-1317 W/m2. After getting through buffering process with value of 2 km (to facilitate the construction of power plant installation), 9 sites of location were estimated to be the most potential location of ocean wave energy generation in the ocean with average depth of 8.058 m and annual wind speed of 6.553 knot.
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Application of the string method to the study of critical nuclei in capillary condensation.
Qiu, Chunyin; Qian, Tiezheng; Ren, Weiqing
2008-10-21
We adopt a continuum description for liquid-vapor phase transition in the framework of mean-field theory and use the string method to numerically investigate the critical nuclei for capillary condensation in a slit pore. This numerical approach allows us to determine the critical nuclei corresponding to saddle points of the grand potential function in which the chemical potential is given in the beginning. The string method locates the minimal energy path (MEP), which is the most probable transition pathway connecting two metastable/stable states in configuration space. From the MEP, the saddle point is determined and the corresponding energy barrier also obtained (for grand potential). Moreover, the MEP shows how the new phase (liquid) grows out of the old phase (vapor) along the most probable transition pathway, from the birth of a critical nucleus to its consequent expansion. Our calculations run from partial wetting to complete wetting with a variable strength of attractive wall potential. In the latter case, the string method presents a unified way for computing the critical nuclei, from film formation at solid surface to bulk condensation via liquid bridge. The present application of the string method to the numerical study of capillary condensation shows the great power of this method in evaluating the critical nuclei in various liquid-vapor phase transitions.
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Sources of method bias in social science research and recommendations on how to control it.
Podsakoff, Philip M; MacKenzie, Scott B; Podsakoff, Nathan P
2012-01-01
Despite the concern that has been expressed about potential method biases, and the pervasiveness of research settings with the potential to produce them, there is disagreement about whether they really are a problem for researchers in the behavioral sciences. Therefore, the purpose of this review is to explore the current state of knowledge about method biases. First, we explore the meaning of the terms "method" and "method bias" and then we examine whether method biases influence all measures equally. Next, we review the evidence of the effects that method biases have on individual measures and on the covariation between different constructs. Following this, we evaluate the procedural and statistical remedies that have been used to control method biases and provide recommendations for minimizing method bias.
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The current matrix elements from HAL QCD method
NASA Astrophysics Data System (ADS)
Watanabe, Kai; Ishii, Noriyoshi
2018-03-01
HAL QCD method is a method to construct a potential (HAL QCD potential) that reproduces the NN scattering phase shift faithful to the QCD. The HAL QCD potential is obtained from QCD by eliminating the degrees of freedom of quarks and gluons and leaving only two particular hadrons. Therefor, in the effective quantum mechanics of two nucleons defined by HAL QCD potential, the conserved current consists not only of the nucleon current but also an extra current originating from the potential (two-body current). Though the form of the two-body current is closely related to the potential, it is not straight forward to extract the former from the latter. In this work, we derive the the current matrix element formula in the quantum mechanics defined by the HAL QCD potential. As a first step, we focus on the non-relativistic case. To give an explicit example, we consider a second quantized non-relativistic two-channel coupling model which we refer to as the original model. From the original model, the HAL QCD potential for the open channel is constructed by eliminating the closed channel in the elastic two-particle scattering region. The current matrix element formula is derived by demanding the effective quantum mechanics defined by the HAL QCD potential to respond to the external field in the same way as the original two-channel coupling model.
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Methods for Developing Evidence Reviews in Short Periods of Time: A Scoping Review
Abou-Setta, Ahmed M.; Jeyaraman, Maya; Attia, Abdelhamid; Al-Inany, Hesham G.; Ferri, Mauricio; Ansari, Mohammed T.; Garritty, Chantelle M.; Bond, Kenneth; Norris, Susan L.
2016-01-01
Introduction Rapid reviews (RR), using abbreviated systematic review (SR) methods, are becoming more popular among decision-makers. This World Health Organization commissioned study sought to summarize RR methods, identify differences, and highlight potential biases between RR and SR. Methods Review of RR methods (Key Question 1 [KQ1]), meta-epidemiologic studies comparing reliability/ validity of RR and SR methods (KQ2), and their potential associated biases (KQ3). We searched Medline, EMBASE, Cochrane Library, grey literature, and checked reference lists, used personal contacts, and crowdsourcing (e.g. email listservs). Selection and data extraction was conducted by one reviewer (KQ1) or two reviewers independently (KQ2-3). Results Across all KQs, we identified 42,743 citations through the literature searches. KQ1: RR methods from 29 organizations were reviewed. There was no consensus on which aspects of the SR process to abbreviate. KQ2: Studies comparing the conclusions of RR and SR (n = 9) found them to be generally similar. Where major differences were identified, it was attributed to the inclusion of evidence from different sources (e.g. searching different databases or including different study designs). KQ3: Potential biases introduced into the review process were well-identified although not necessarily supported by empirical evidence, and focused mainly on selective outcome reporting and publication biases. Conclusion RR approaches are context and organization specific. Existing comparative evidence has found similar conclusions derived from RR and SR, but there is a lack of evidence comparing the potential of bias in both evidence synthesis approaches. Further research and decision aids are needed to help decision makers and reviewers balance the benefits of providing timely evidence with the potential for biased findings. PMID:27930662
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Gordeev, S A; Voronin, S G
2015-01-01
The proprioceptive sensitivity of healthy volunteers and convalescents after acute cerebrovascular episodes was studied by a new neurophysiological method for registration of kinesthetic evoked potentials emerging in response to passive 50(o) bending of the hand in the wrist joint with the angular acceleration of 350 rad/sec(2). Kinesthetic evoked potentials were recorded above the somatosensory cortex projection areas in the hemispheres contra- and ipsilateral to the stimulated limb. The patients exhibited significantly longer latencies and lesser amplitudes of the early components of response in the involved hemisphere in comparison with normal subjects. The method for registration of the kinesthetic evoked potentials allows a more detailed study of the mechanisms of kinesthetic sensitivity in health and in organic involvement of the brain.
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Neural Network and Nearest Neighbor Algorithms for Enhancing Sampling of Molecular Dynamics.
Galvelis, Raimondas; Sugita, Yuji
2017-06-13
The free energy calculations of complex chemical and biological systems with molecular dynamics (MD) are inefficient due to multiple local minima separated by high-energy barriers. The minima can be escaped using an enhanced sampling method such as metadynamics, which apply bias (i.e., importance sampling) along a set of collective variables (CV), but the maximum number of CVs (or dimensions) is severely limited. We propose a high-dimensional bias potential method (NN2B) based on two machine learning algorithms: the nearest neighbor density estimator (NNDE) and the artificial neural network (ANN) for the bias potential approximation. The bias potential is constructed iteratively from short biased MD simulations accounting for correlation among CVs. Our method is capable of achieving ergodic sampling and calculating free energy of polypeptides with up to 8-dimensional bias potential.
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Interaction Analysis through Proteomic Phage Display
2014-01-01
Phage display is a powerful technique for profiling specificities of peptide binding domains. The method is suited for the identification of high-affinity ligands with inhibitor potential when using highly diverse combinatorial peptide phage libraries. Such experiments further provide consensus motifs for genome-wide scanning of ligands of potential biological relevance. A complementary but considerably less explored approach is to display expression products of genomic DNA, cDNA, open reading frames (ORFs), or oligonucleotide libraries designed to encode defined regions of a target proteome on phage particles. One of the main applications of such proteomic libraries has been the elucidation of antibody epitopes. This review is focused on the use of proteomic phage display to uncover protein-protein interactions of potential relevance for cellular function. The method is particularly suited for the discovery of interactions between peptide binding domains and their targets. We discuss the largely unexplored potential of this method in the discovery of domain-motif interactions of potential biological relevance. PMID:25295249
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Inversion of potential field data using the finite element method on parallel computers
NASA Astrophysics Data System (ADS)
Gross, L.; Altinay, C.; Shaw, S.
2015-11-01
In this paper we present a formulation of the joint inversion of potential field anomaly data as an optimization problem with partial differential equation (PDE) constraints. The problem is solved using the iterative Broyden-Fletcher-Goldfarb-Shanno (BFGS) method with the Hessian operator of the regularization and cross-gradient component of the cost function as preconditioner. We will show that each iterative step requires the solution of several PDEs namely for the potential fields, for the adjoint defects and for the application of the preconditioner. In extension to the traditional discrete formulation the BFGS method is applied to continuous descriptions of the unknown physical properties in combination with an appropriate integral form of the dot product. The PDEs can easily be solved using standard conforming finite element methods (FEMs) with potentially different resolutions. For two examples we demonstrate that the number of PDE solutions required to reach a given tolerance in the BFGS iteration is controlled by weighting regularization and cross-gradient but is independent of the resolution of PDE discretization and that as a consequence the method is weakly scalable with the number of cells on parallel computers. We also show a comparison with the UBC-GIF GRAV3D code.
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An Excel‐based implementation of the spectral method of action potential alternans analysis
Pearman, Charles M.
2014-01-01
Abstract Action potential (AP) alternans has been well established as a mechanism of arrhythmogenesis and sudden cardiac death. Proper interpretation of AP alternans requires a robust method of alternans quantification. Traditional methods of alternans analysis neglect higher order periodicities that may have greater pro‐arrhythmic potential than classical 2:1 alternans. The spectral method of alternans analysis, already widely used in the related study of microvolt T‐wave alternans, has also been used to study AP alternans. Software to meet the specific needs of AP alternans analysis is not currently available in the public domain. An AP analysis tool is implemented here, written in Visual Basic for Applications and using Microsoft Excel as a shell. This performs a sophisticated analysis of alternans behavior allowing reliable distinction of alternans from random fluctuations, quantification of alternans magnitude, and identification of which phases of the AP are most affected. In addition, the spectral method has been adapted to allow detection and quantification of higher order regular oscillations. Analysis of action potential morphology is also performed. A simple user interface enables easy import, analysis, and export of collated results. PMID:25501439
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Molecular methods, such as DNA barcoding, have the potential in enhance biomonitoring programs worldwide. Altering routinely used sample preservation methods to protect DNA from degradation may pose a potential impediment to application of DNA barcoding and metagenomics for biom...
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Leisman, Gerald; Ashkenazi, Maureen
1979-01-01
Objective psychophysical techniques for investigating visual fields are described. The paper concerns methods for the collection and analysis of evoked potentials using a small laboratory computer and provides efficient methods for obtaining information about the conduction pathways of the visual system.
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Effective conservation of woodland vernal pools – important components of regional amphibian diversity and ecosystem services – depends on locating and mapping these pools accurately. Current methods for identifying potential vernal pools are primarily based on visual interpretat...
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Miscellaneous methods for measuring matric or water potential
Scanlon, Bridget R.; Andraski, Brian J.; Bilskie, Jim; Dane, Jacob H.; Topp, G. Clarke
2002-01-01
A variety of techniques to measure matric potential or water potential in the laboratory and in the field are described in this section. The techniques described herein require equilibration of some medium whose matric or water potential can be determined from previous calibration or can be measured directly. Under equilibrium conditions the matric or water potential of the medium is equal to that of the soil. The techniques can be divided into: (i) those that measure matric potential and (ii) those that measure water potential (sum of matric and osmotic potentials). Matric potential is determined when the sensor matrix is in direct contact with the soil, so salts are free to diffuse in or out of the sensor matrix, and the equilibrium measurement therefore reflects matric forces acting on the water. Water potential is determined when the sensor is separated from the soil by a vapor gap, so salts are not free to move in or out of the sensor, and the equilibrium measurement reflects the sum of the matric and osmotic forces acting on the water.Seven different techniques are described in this section. Those that measure matric potential include (i) heat dissipation sensors, (ii) electrical resistance sensors, (iii) frequency domain and time domain sensors, and (iv) electro-optical switches. A method that can be used to measure matric potential or water potential is the (v) filter paper method. Techniques that measure water potential include (vi) the Dew Point Potentiameter (Decagon Devices, Inc., Pullman, WA1) (water activity meter) and (vii) vapor equilibration.The first four techniques are electronically based methods for measuring matric potential. Heat dissipation sensors and electrical resistance sensors infer matric potential from previously determined calibration relations between sensor heat dissipation or electrical resistance and matric potential. Frequency-domain and timedomain matric potential sensors measure water content, which is related to matric potential of the sensor through calibration. Electro-optical switches measure changes in light transmission through thin, nylon filters as they absorb or desorb water in response to changes in matric potential. Heat dissipation sensors and electrical resistance sensors are used primarily in the field to provide information on matric potential. Frequency domain matric potential sensors are new and have not been widely used. Time domain matric potential sensors and electro-optical switches are new and have not been commercialized. For the fifth technique, filter paper is used as the standard matrix. The filter paper technique measures matric potential when the filter paper is in direct contact with soil or water potential when separated from soil by a vapor gap. The Dew Point Potentiameter calculates water potential from the measured dew point and sample temperature. The vapor equilibration technique involves equilibration of soil samples with salt solutions of known osmotic potential. The filter paper, Dew Point Potentiameter, and vapor equilibration techniques are generally used in the laboratory to measure water potential of disturbed field samples or to measure water potential for water retention functions.
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Daily air temperature interpolated at high spatial resolution over a large mountainous region
Dodson, R.; Marks, D.
1997-01-01
Two methods are investigated for interpolating daily minimum and maximum air temperatures (Tmin and Tmax) at a 1 km spatial resolution over a large mountainous region (830 000 km2) in the U.S. Pacific Northwest. The methods were selected because of their ability to (1) account for the effect of elevation on temperature and (2) efficiently handle large volumes of data. The first method, the neutral stability algorithm (NSA), used the hydrostatic and potential temperature equations to convert measured temperatures and elevations to sea-level potential temperatures. The potential temperatures were spatially interpolated using an inverse-squared-distance algorithm and then mapped to the elevation surface of a digital elevation model (DEM). The second method, linear lapse rate adjustment (LLRA), involved the same basic procedure as the NSA, but used a constant linear lapse rate instead of the potential temperature equation. Cross-validation analyses were performed using the NSA and LLRA methods to interpolate Tmin and Tmax each day for the 1990 water year, and the methods were evaluated based on mean annual interpolation error (IE). The NSA method showed considerable bias for sites associated with vertical extrapolation. A correction based on climate station/grid cell elevation differences was developed and found to successfully remove the bias. The LLRA method was tested using 3 lapse rates, none of which produced a serious extrapolation bias. The bias-adjusted NSA and the 3 LLRA methods produced almost identical levels of accuracy (mean absolute errors between 1.2 and 1.3??C), and produced very similar temperature surfaces based on image difference statistics. In terms of accuracy, speed, and ease of implementation, LLRA was chosen as the best of the methods tested.
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Derivation of aerodynamic kernel functions
NASA Technical Reports Server (NTRS)
Dowell, E. H.; Ventres, C. S.
1973-01-01
The method of Fourier transforms is used to determine the kernel function which relates the pressure on a lifting surface to the prescribed downwash within the framework of Dowell's (1971) shear flow model. This model is intended to improve upon the potential flow aerodynamic model by allowing for the aerodynamic boundary layer effects neglected in the potential flow model. For simplicity, incompressible, steady flow is considered. The proposed method is illustrated by deriving known results from potential flow theory.
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Time delayed Ensemble Nudging Method
NASA Astrophysics Data System (ADS)
An, Zhe; Abarbanel, Henry
Optimal nudging method based on time delayed embedding theory has shows potentials on analyzing and data assimilation in previous literatures. To extend the application and promote the practical implementation, new nudging assimilation method based on the time delayed embedding space is presented and the connection with other standard assimilation methods are studied. Results shows the incorporating information from the time series of data can reduce the sufficient observation needed to preserve the quality of numerical prediction, making it a potential alternative in the field of data assimilation of large geophysical models.
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Metastable Autoionizing States of Molecules and Radicals in Highly Energetic Environment
2016-03-22
electronic states. The specific aims are to develop and calibrate complex-scaled equation-of-motion coupled cluster (cs-EOM- CC ) and CAP (complex...absorbing potential) augmented EOM- CC methods. We have implemented and benchmarked cs-EOM-CCSD and CAP- augmented EOM-CCSD methods for excitation energies...motion coupled cluster (cs-EOM- CC ) and CAP (complex absorbing potential) augmented EOM- CC methods. We have implemented and benchmarked cs-EOM-CCSD and
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Park, H M; Hong, S M
2006-12-15
In this paper we develop a method for the determination of the zeta potential zeta and the dielectric constant epsilon by exploiting velocity measurements of the electroosmotic flow in microchannels. The inverse problem is solved through the minimization of a performance function utilizing the conjugate gradient method. The present method is found to estimate zeta and epsilon with reasonable accuracy even with noisy velocity measurements.
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Intracellular recording of action potentials by nanopillar electroporation.
Xie, Chong; Lin, Ziliang; Hanson, Lindsey; Cui, Yi; Cui, Bianxiao
2012-02-12
Action potentials have a central role in the nervous system and in many cellular processes, notably those involving ion channels. The accurate measurement of action potentials requires efficient coupling between the cell membrane and the measuring electrodes. Intracellular recording methods such as patch clamping involve measuring the voltage or current across the cell membrane by accessing the cell interior with an electrode, allowing both the amplitude and shape of the action potentials to be recorded faithfully with high signal-to-noise ratios. However, the invasive nature of intracellular methods usually limits the recording time to a few hours, and their complexity makes it difficult to simultaneously record more than a few cells. Extracellular recording methods, such as multielectrode arrays and multitransistor arrays, are non-invasive and allow long-term and multiplexed measurements. However, extracellular recording sacrifices the one-to-one correspondence between the cells and electrodes, and also suffers from significantly reduced signal strength and quality. Extracellular techniques are not, therefore, able to record action potentials with the accuracy needed to explore the properties of ion channels. As a result, the pharmacological screening of ion-channel drugs is usually performed by low-throughput intracellular recording methods. The use of nanowire transistors, nanotube-coupled transistors and micro gold-spine and related electrodes can significantly improve the signal strength of recorded action potentials. Here, we show that vertical nanopillar electrodes can record both the extracellular and intracellular action potentials of cultured cardiomyocytes over a long period of time with excellent signal strength and quality. Moreover, it is possible to repeatedly switch between extracellular and intracellular recording by nanoscale electroporation and resealing processes. Furthermore, vertical nanopillar electrodes can detect subtle changes in action potentials induced by drugs that target ion channels.
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Intracellular recording of action potentials by nanopillar electroporation
NASA Astrophysics Data System (ADS)
Xie, Chong; Lin, Ziliang; Hanson, Lindsey; Cui, Yi; Cui, Bianxiao
2012-03-01
Action potentials have a central role in the nervous system and in many cellular processes, notably those involving ion channels. The accurate measurement of action potentials requires efficient coupling between the cell membrane and the measuring electrodes. Intracellular recording methods such as patch clamping involve measuring the voltage or current across the cell membrane by accessing the cell interior with an electrode, allowing both the amplitude and shape of the action potentials to be recorded faithfully with high signal-to-noise ratios. However, the invasive nature of intracellular methods usually limits the recording time to a few hours, and their complexity makes it difficult to simultaneously record more than a few cells. Extracellular recording methods, such as multielectrode arrays and multitransistor arrays, are non-invasive and allow long-term and multiplexed measurements. However, extracellular recording sacrifices the one-to-one correspondence between the cells and electrodes, and also suffers from significantly reduced signal strength and quality. Extracellular techniques are not, therefore, able to record action potentials with the accuracy needed to explore the properties of ion channels. As a result, the pharmacological screening of ion-channel drugs is usually performed by low-throughput intracellular recording methods. The use of nanowire transistors, nanotube-coupled transistors and micro gold-spine and related electrodes can significantly improve the signal strength of recorded action potentials. Here, we show that vertical nanopillar electrodes can record both the extracellular and intracellular action potentials of cultured cardiomyocytes over a long period of time with excellent signal strength and quality. Moreover, it is possible to repeatedly switch between extracellular and intracellular recording by nanoscale electroporation and resealing processes. Furthermore, vertical nanopillar electrodes can detect subtle changes in action potentials induced by drugs that target ion channels.
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Joint inversion of hydraulic head and self-potential data associated with harmonic pumping tests
NASA Astrophysics Data System (ADS)
Soueid Ahmed, A.; Jardani, A.; Revil, A.; Dupont, J. P.
2016-09-01
Harmonic pumping tests consist in stimulating an aquifer by the means of hydraulic stimulations at some discrete frequencies. The inverse problem consisting in retrieving the hydraulic properties is inherently ill posed and is usually underdetermined when considering the number of well head data available in field conditions. To better constrain this inverse problem, we add self-potential data recorded at the ground surface to the head data. The self-potential method is a passive geophysical method. Its signals are generated by the groundwater flow through an electrokinetic coupling. We showed using a 3-D saturated unconfined synthetic aquifer that the self-potential method significantly improves the results of the harmonic hydraulic tomography. The hydroelectric forward problem is obtained by solving first the Richards equation, describing the groundwater flow, and then using the result in an electrical Poisson equation describing the self-potential problem. The joint inversion problem is solved using a reduction model based on the principal component geostatistical approach. In this method, the large prior covariance matrix is truncated and replaced by its low-rank approximation, allowing thus for notable computational time and storage savings. Three test cases are studied, to assess the validity of our approach. In the first test, we show that when the number of harmonic stimulations is low, combining the harmonic hydraulic and self-potential data does not improve the inversion results. In the second test where enough harmonic stimulations are performed, a significant improvement of the hydraulic parameters is observed. In the last synthetic test, we show that the electrical conductivity field required to invert the self-potential data can be determined with enough accuracy using an electrical resistivity tomography survey using the same electrodes configuration as used for the self-potential investigation.
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Precise determination of lattice phase shifts and mixing angles
Lu, Bing -Nan; Lähde, Timo A.; Lee, Dean; ...
2016-07-09
Here, we introduce a general and accurate method for determining lattice phase shifts and mixing angles, which is applicable to arbitrary, non-cubic lattices. Our method combines angular momentum projection, spherical wall boundaries and an adjustable auxiliary potential. This allows us to construct radial lattice wave functions and to determine phase shifts at arbitrary energies. For coupled partial waves, we use a complex-valued auxiliary potential that breaks time-reversal invariance. We benchmark our method using a system of two spin-1/2 particles interacting through a finite-range potential with a strong tensor component. We are able to extract phase shifts and mixing angles formore » all angular momenta and energies, with precision greater than that of extant methods. We discuss a wide range of applications from nuclear lattice simulations to optical lattice experiments.« less
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NASA Technical Reports Server (NTRS)
Jekeli, C.
1979-01-01
Through the method of truncation functions, the oceanic geoid undulation is divided into two constituents: an inner zone contribution expressed as an integral of surface gravity disturbances over a spherical cap; and an outer zone contribution derived from a finite set of potential harmonic coefficients. Global, average error estimates are formulated for undulation differences, thereby providing accuracies for a relative geoid. The error analysis focuses on the outer zone contribution for which the potential coefficient errors are modeled. The method of computing undulations based on gravity disturbance data for the inner zone is compared to the similar, conventional method which presupposes gravity anomaly data within this zone.
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A constructive model potential method for atomic interactions
NASA Technical Reports Server (NTRS)
Bottcher, C.; Dalgarno, A.
1974-01-01
A model potential method is presented that can be applied to many electron single centre and two centre systems. The development leads to a Hamiltonian with terms arising from core polarization that depend parametrically upon the positions of the valence electrons. Some of the terms have been introduced empirically in previous studies. Their significance is clarified by an analysis of a similar model in classical electrostatics. The explicit forms of the expectation values of operators at large separations of two atoms given by the model potential method are shown to be equivalent to the exact forms when the assumption is made that the energy level differences of one atom are negligible compared to those of the other.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Joshi, Subodh, E-mail: subodhssgk@gmail.com; Chand, Manesh, E-mail: maneshchand@gmail.com; Dabral, Krishna, E-mail: kmkrishna.dabral@gmail.com
2016-05-06
A modified embedded atom method (MEAM) potential model up to second neighbours has been used to calculate the phonon dispersions for Ni{sub 0.55}Pd{sub 0.45} alloy in which Pd is introduced as substitutional impurity. Using the force-constants obtained from MEAM potential, the local vibrational density of states in host Ni and substitutional Pd atoms using Green’s function method has been calculated. The calculation of phonon dispersions of NiPd alloy shows a good agreement with the experimental results. Condition of resonance mode has also been investigated and resonance mode in the frequency spectrum of impurity atom at low frequency is observed.
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Exponential integrators in time-dependent density-functional calculations
NASA Astrophysics Data System (ADS)
Kidd, Daniel; Covington, Cody; Varga, Kálmán
2017-12-01
The integrating factor and exponential time differencing methods are implemented and tested for solving the time-dependent Kohn-Sham equations. Popular time propagation methods used in physics, as well as other robust numerical approaches, are compared to these exponential integrator methods in order to judge the relative merit of the computational schemes. We determine an improvement in accuracy of multiple orders of magnitude when describing dynamics driven primarily by a nonlinear potential. For cases of dynamics driven by a time-dependent external potential, the accuracy of the exponential integrator methods are less enhanced but still match or outperform the best of the conventional methods tested.
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Likelihood-based methods for evaluating principal surrogacy in augmented vaccine trials.
Liu, Wei; Zhang, Bo; Zhang, Hui; Zhang, Zhiwei
2017-04-01
There is growing interest in assessing immune biomarkers, which are quick to measure and potentially predictive of long-term efficacy, as surrogate endpoints in randomized, placebo-controlled vaccine trials. This can be done under a principal stratification approach, with principal strata defined using a subject's potential immune responses to vaccine and placebo (the latter may be assumed to be zero). In this context, principal surrogacy refers to the extent to which vaccine efficacy varies across principal strata. Because a placebo recipient's potential immune response to vaccine is unobserved in a standard vaccine trial, augmented vaccine trials have been proposed to produce the information needed to evaluate principal surrogacy. This article reviews existing methods based on an estimated likelihood and a pseudo-score (PS) and proposes two new methods based on a semiparametric likelihood (SL) and a pseudo-likelihood (PL), for analyzing augmented vaccine trials. Unlike the PS method, the SL method does not require a model for missingness, which can be advantageous when immune response data are missing by happenstance. The SL method is shown to be asymptotically efficient, and it performs similarly to the PS and PL methods in simulation experiments. The PL method appears to have a computational advantage over the PS and SL methods.
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STOCK Mechanics:. a General Theory and Method of Energy Conservation with Applications on Djia
NASA Astrophysics Data System (ADS)
Tuncay, Çağlar
A new method, based on the original theory of conservation of sum of kinetic and potential energy defined for prices is proposed and applied on the Dow Jones Industrials Average (DJIA). The general trends averaged over months or years gave a roughly conserved total energy, with three different potential energies, i.e., positive definite quadratic, negative definite quadratic and linear potential energy for exponential rises (and falls), sinusoidal oscillations and parabolic trajectories, respectively. Corresponding expressions for force (impact) are also given.
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NASA Astrophysics Data System (ADS)
Nurhidayati, I.; Suparmi, A.; Cari, C.
2018-03-01
The Schrödinger equation has been extended by applying the minimal length formalism for trigonometric potential. The wave function and energy spectra were used to describe the behavior of subatomic particle. The wave function and energy spectra were obtained by using hypergeometry method. The result showed that the energy increased by the increasing both of minimal length parameter and the potential parameter. The energy were calculated numerically using MatLab.
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NASA Astrophysics Data System (ADS)
Akpan, N. Ikot; Hassan, Hassanabadi; Tamunoimi, M. Abbey
2015-12-01
The Dirac equation with Hellmann potential is presented in the presence of Coulomb-like tensor (CLT), Yukawa-like tensor (YLT), and Hulthen-type tensor (HLT) interactions by using Nikiforov-Uvarov method. The bound state energy spectra and the radial wave functions are obtained approximately within the framework of spin and pseudospin symmetries limit. We have also reported some numerical results and figures to show the effects of the tensor interactions. Special cases of the potential are also discussed.
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NASA Astrophysics Data System (ADS)
Assi, I. A.; Sous, A. J.
2018-05-01
The goal of this work is to derive a new class of short-range potentials that could have a wide range of physical applications, specially in molecular physics. The tridiagonal representation approach has been developed beyond its limitations to produce new potentials by requiring the representation of the Schrödinger wave operator to be multidiagonal and symmetric. This produces a family of Hulthén potentials that has a specific structure, as mentioned in the introduction. As an example, we have solved the nonrelativistic wave equation for the new four-parameter short-range screening potential numerically using the asymptotic iteration method, where we tabulated the eigenvalues for both s -wave and arbitrary l -wave cases in tables.
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Frappier, Vincent; Najmanovich, Rafael J.
2014-01-01
Normal mode analysis (NMA) methods are widely used to study dynamic aspects of protein structures. Two critical components of NMA methods are coarse-graining in the level of simplification used to represent protein structures and the choice of potential energy functional form. There is a trade-off between speed and accuracy in different choices. In one extreme one finds accurate but slow molecular-dynamics based methods with all-atom representations and detailed atom potentials. On the other extreme, fast elastic network model (ENM) methods with Cα−only representations and simplified potentials that based on geometry alone, thus oblivious to protein sequence. Here we present ENCoM, an Elastic Network Contact Model that employs a potential energy function that includes a pairwise atom-type non-bonded interaction term and thus makes it possible to consider the effect of the specific nature of amino-acids on dynamics within the context of NMA. ENCoM is as fast as existing ENM methods and outperforms such methods in the generation of conformational ensembles. Here we introduce a new application for NMA methods with the use of ENCoM in the prediction of the effect of mutations on protein stability. While existing methods are based on machine learning or enthalpic considerations, the use of ENCoM, based on vibrational normal modes, is based on entropic considerations. This represents a novel area of application for NMA methods and a novel approach for the prediction of the effect of mutations. We compare ENCoM to a large number of methods in terms of accuracy and self-consistency. We show that the accuracy of ENCoM is comparable to that of the best existing methods. We show that existing methods are biased towards the prediction of destabilizing mutations and that ENCoM is less biased at predicting stabilizing mutations. PMID:24762569
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Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials.
Olsen, Jógvan Magnus Haugaard; List, Nanna Holmgaard; Kristensen, Kasper; Kongsted, Jacob
2015-04-14
Quantum-mechanical embedding methods have in recent years gained significant interest and may now be applied to predict a wide range of molecular properties calculated at different levels of theory. To reach a high level of accuracy in embedding methods, both the electronic structure model of the active region and the embedding potential need to be of sufficiently high quality. In fact, failures in quantum mechanics/molecular mechanics (QM/MM)-based embedding methods have often been associated with the QM/MM methodology itself; however, in many cases the reason for such failures is due to the use of an inaccurate embedding potential. In this paper, we investigate in detail the quality of the electronic component of embedding potentials designed for calculations on protein biostructures. We show that very accurate explicitly polarizable embedding potentials may be efficiently designed using fragmentation strategies combined with single-fragment ab initio calculations. In fact, due to the self-interaction error in Kohn-Sham density functional theory (KS-DFT), use of large full-structure quantum-mechanical calculations based on conventional (hybrid) functionals leads to less accurate embedding potentials than fragment-based approaches. We also find that standard protein force fields yield poor embedding potentials, and it is therefore not advisable to use such force fields in general QM/MM-type calculations of molecular properties other than energies and structures.
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Electro-quasistatic analysis of an electrostatic induction micromotor using the cell method.
Monzón-Verona, José Miguel; Santana-Martín, Francisco Jorge; García-Alonso, Santiago; Montiel-Nelson, Juan Antonio
2010-01-01
An electro-quasistatic analysis of an induction micromotor has been realized by using the Cell Method. We employed the direct Finite Formulation (FF) of the electromagnetic laws, hence, avoiding a further discretization. The Cell Method (CM) is used for solving the field equations at the entire domain (2D space) of the micromotor. We have reformulated the field laws in a direct FF and analyzed physical quantities to make explicit the relationship between magnitudes and laws. We applied a primal-dual barycentric discretization of the 2D space. The electric potential has been calculated on each node of the primal mesh using CM. For verification purpose, an analytical electric potential equation is introduced as reference. In frequency domain, results demonstrate the error in calculating potential quantity is neglected (<3‰). In time domain, the potential value in transient state tends to the steady state value.
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Electro-Quasistatic Analysis of an Electrostatic Induction Micromotor Using the Cell Method
Monzón-Verona, José Miguel; Santana-Martín, Francisco Jorge; García–Alonso, Santiago; Montiel-Nelson, Juan Antonio
2010-01-01
An electro-quasistatic analysis of an induction micromotor has been realized by using the Cell Method. We employed the direct Finite Formulation (FF) of the electromagnetic laws, hence, avoiding a further discretization. The Cell Method (CM) is used for solving the field equations at the entire domain (2D space) of the micromotor. We have reformulated the field laws in a direct FF and analyzed physical quantities to make explicit the relationship between magnitudes and laws. We applied a primal-dual barycentric discretization of the 2D space. The electric potential has been calculated on each node of the primal mesh using CM. For verification purpose, an analytical electric potential equation is introduced as reference. In frequency domain, results demonstrate the error in calculating potential quantity is neglected (<3‰). In time domain, the potential value in transient state tends to the steady state value. PMID:22163397
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Adaptive-numerical-bias metadynamics.
Khanjari, Neda; Eslami, Hossein; Müller-Plathe, Florian
2017-12-05
A metadynamics scheme is presented in which the free energy surface is filled with progressively adding adaptive biasing potentials, obtained from the accumulated probability distribution of the collective variables. Instead of adding Gaussians with assigned height and width in conventional metadynamics method, here we add a more realistic adaptive biasing potential to the Hamiltonian of the system. The shape of the adaptive biasing potential is adjusted on the fly by sampling over the visited states. As the top of the barrier is approached, the biasing potentials become wider. This decreases the problem of trapping the system in the niches, introduced by the addition of Gaussians of fixed height in metadynamics. Our results for the free energy profiles of three test systems show that this method is more accurate and converges more quickly than the conventional metadynamics, and is quite comparable (in accuracy and convergence rate) with the well-tempered metadynamics method. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
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Recent studies have shown the detection of pharmaceuticals in surface waters across the United States. The objective of this study was to develop methods, and apply them, to evaluate the potential for food chain transfer when pharmaceutical containing wastewaters are used for cr...
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NASA Technical Reports Server (NTRS)
Khayat, Michael A.; Wilton, Donald R.; Fink, Patrick W.
2007-01-01
Simple and efficient numerical procedures using singularity cancellation methods are presented for evaluating singular and near-singular potential integrals. Four different transformations are compared and the advantages of the Radial-angular transform are demonstrated. A method is then described for optimizing this integration scheme.
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Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity.
Clark, Stephen J; Lee, Heather J; Smallwood, Sébastien A; Kelsey, Gavin; Reik, Wolf
2016-04-18
Emerging single-cell epigenomic methods are being developed with the exciting potential to transform our knowledge of gene regulation. Here we review available techniques and future possibilities, arguing that the full potential of single-cell epigenetic studies will be realized through parallel profiling of genomic, transcriptional, and epigenetic information.
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Lithologic composition and rock weathering potential of forested, glacial-till soils
Scott W. Bailey; James W. Hornbeck; James W. Hornbeck
1992-01-01
Describes methods for predicting lithologies present in soils developed on glacial till, and the potential weathering contributions from rock particles >2 mm in diameter. The methods are not quantitative in terms of providing weathering rates, but provide information that can further the understanding of forest nutrient cycles, and possibly assist with decisions...
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USDA-ARS?s Scientific Manuscript database
Using catfish gill cells G1B and four chemicals (hydrogen peroxide, sodium chloride, potassium permanganate, and D-mannose), the feasibility of using an in vitro screening method to identify potential effective chemotherapeutants was evaluated in this study. In vitro screening results revealed that,...
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First Generation College Student Leadership Potential: A Mixed Methods Analysis
ERIC Educational Resources Information Center
Hojan-Clark, Jane M.
2010-01-01
This mixed methods research compared the leadership potential of traditionally aged first generation college students to that of college students whose parents are college educated. A college education provides advantages to those who can obtain it (Baum & Payea, 2004; Black Issues in Higher Education, 2005; Education and the Value of…
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Electrical resistance tomography using steel cased boreholes as electrodes
Daily, W.D.; Ramirez, A.L.
1999-06-22
An electrical resistance tomography method is described which uses steel cased boreholes as electrodes. The method enables mapping the electrical resistivity distribution in the subsurface from measurements of electrical potential caused by electrical currents injected into an array of electrodes in the subsurface. By use of current injection and potential measurement electrodes to generate data about the subsurface resistivity distribution, which data is then used in an inverse calculation, a model of the electrical resistivity distribution can be obtained. The inverse model may be constrained by independent data to better define an inverse solution. The method utilizes pairs of electrically conductive (steel) borehole casings as current injection electrodes and as potential measurement electrodes. The greater the number of steel cased boreholes in an array, the greater the amount of data is obtained. The steel cased boreholes may be utilized for either current injection or potential measurement electrodes. The subsurface model produced by this method can be 2 or 3 dimensional in resistivity depending on the detail desired in the calculated resistivity distribution and the amount of data to constrain the models. 2 figs.
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Electrical resistance tomography using steel cased boreholes as electrodes
Daily, William D.; Ramirez, Abelardo L.
1999-01-01
An electrical resistance tomography method using steel cased boreholes as electrodes. The method enables mapping the electrical resistivity distribution in the subsurface from measurements of electrical potential caused by electrical currents injected into an array of electrodes in the subsurface. By use of current injection and potential measurement electrodes to generate data about the subsurface resistivity distribution, which data is then used in an inverse calculation, a model of the electrical resistivity distribution can be obtained. The inverse model may be constrained by independent data to better define an inverse solution. The method utilizes pairs of electrically conductive (steel) borehole casings as current injection electrodes and as potential measurement electrodes. The greater the number of steel cased boreholes in an array, the greater the amount of data is obtained. The steel cased boreholes may be utilized for either current injection or potential measurement electrodes. The subsurface model produced by this method can be 2 or 3 dimensional in resistivity depending on the detail desired in the calculated resistivity distribution and the amount of data to constain the models.
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Computed Potential Energy Surfaces and Minimum Energy Pathways for Chemical Reactions
NASA Technical Reports Server (NTRS)
Walch, Stephen P.; Langhoff, S. R. (Technical Monitor)
1994-01-01
Computed potential energy surfaces are often required for computation of such parameters as rate constants as a function of temperature, product branching ratios, and other detailed properties. For some dynamics methods, global potential energy surfaces are required. In this case, it is necessary to obtain the energy at a complete sampling of all the possible arrangements of the nuclei, which are energetically accessible, and then a fitting function must be obtained to interpolate between the computed points. In other cases, characterization of the stationary points and the reaction pathway connecting them is sufficient. These properties may be readily obtained using analytical derivative methods. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method to obtain accurate energetics, gives usefull results for a number of chemically important systems. The talk will focus on a number of applications including global potential energy surfaces, H + O2, H + N2, O(3p) + H2, and reaction pathways for complex reactions, including reactions leading to NO and soot formation in hydrocarbon combustion.
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Embedded atom method potential for studying mechanical properties of binary Cu–Au alloys
NASA Astrophysics Data System (ADS)
Gola, Adrien; Pastewka, Lars
2018-07-01
We present an embedded atom method (EAM) potential for the binary Cu–Au system. The unary phases are described by two well-tested unary EAM potentials for Cu and Au. We fitted the interaction between Cu and Au to experimental properties of the binary intermetallic phases Cu3Au, CuAu and CuAu3. Particular attention has been paid to reproducing stacking fault energies in order to obtain a potential suitable for studying deformation in this binary system. The resulting energies, lattice constant, elastic properties and melting points are in good agreement with available experimental data. We use nested sampling to show that our potential reproduces the phase boundaries between intermetallic phases and the disordered face-centered cubic solid solution. We benchmark our potential against four popular Cu–Au EAM parameterizations and density-functional theory calculations.
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NASA Technical Reports Server (NTRS)
Davis, J. E.; Bonnett, W. S.; Medan, R. T.
1976-01-01
A computer program known as SOLN was developed as an independent segment of the NASA-Ames three-dimensional potential flow analysis systems of linear algebraic equations. Methods used include: LU decomposition, Householder's method, a partitioning scheme, and a block successive relaxation method. Due to the independent modular nature of the program, it may be used by itself and not necessarily in conjunction with other segments of the POTFAN system.
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Fully-relativistic full-potential multiple scattering theory: A pathology-free scheme
NASA Astrophysics Data System (ADS)
Liu, Xianglin; Wang, Yang; Eisenbach, Markus; Stocks, G. Malcolm
2018-03-01
The Green function plays an essential role in the Korringa-Kohn-Rostoker(KKR) multiple scattering method. In practice, it is constructed from the regular and irregular solutions of the local Kohn-Sham equation and robust methods exist for spherical potentials. However, when applied to a non-spherical potential, numerical errors from the irregular solutions give rise to pathological behaviors of the charge density at small radius. Here we present a full-potential implementation of the fully-relativistic KKR method to perform ab initio self-consistent calculation by directly solving the Dirac differential equations using the generalized variable phase (sine and cosine matrices) formalism Liu et al. (2016). The pathology around the origin is completely eliminated by carrying out the energy integration of the single-site Green function along the real axis. By using an efficient pole-searching technique to identify the zeros of the well-behaved Jost matrices, we demonstrated that this scheme is numerically stable and computationally efficient, with speed comparable to the conventional contour energy integration method, while free of the pathology problem of the charge density. As an application, this method is utilized to investigate the crystal structures of polonium and their bulk properties, which is challenging for a conventional real-energy scheme. The noble metals are also calculated, both as a test of our method and to study the relativistic effects.
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Thostenson, J O; Mourouvin, R; Hawkins, B T; Ngaboyamahina, E; Sellgren, K L; Parker, C B; Deshusses, M A; Stoner, B R; Glass, J T
2018-09-01
Electrochemical disinfection (ECD) has become an important blackwater disinfection technology. ECD is a promising solution for the 2 billion people without access to conventional sanitation practices and in areas deficient in basic utilities (e.g., sewers, electricity, waste treatment). Here, we report on the disinfection of blackwater using potential cycling compared to potentiostatic treatment methods in chloride-containing and chloride-free solutions of blackwater (i.e., untreated wastewater containing feces, urine, and flushwater from a toilet). Potentiodynamic treatment is demonstrated to improve disinfection energy efficiency of blackwater by 24% and 124% compared to static oxidation and reduction methods, respectively. The result is shown to be caused by electrochemical advanced oxidation processes (EAOP) and regeneration of sp 2 -surface-bonded carbon functional groups that serve the dual purpose of catalysts and adsorption sites of oxidant intermediates. Following 24 h electrolysis in blackwater, electrode fouling is shown to be minimized by the potential cycling method when compared to equivalent potentiostatic methods. The potential cycling current density is 40% higher than both the static oxidative and reductive methods. This work enhances the understanding of oxygen reduction catalysts using functionalized carbon materials and electrochemical disinfection anodes, both of which have the potential to bring a cost-effective, energy efficient, and practical solution to the problem of disinfecting blackwater. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.
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Fully-relativistic full-potential multiple scattering theory: A pathology-free scheme
DOE Office of Scientific and Technical Information (OSTI.GOV)
Liu, Xianglin; Wang, Yang; Eisenbach, Markus
The Green function plays an essential role in the Korringa–Kohn–Rostoker(KKR) multiple scattering method. In practice, it is constructed from the regular and irregular solutions of the local Kohn–Sham equation and robust methods exist for spherical potentials. However, when applied to a non-spherical potential, numerical errors from the irregular solutions give rise to pathological behaviors of the charge density at small radius. Here we present a full-potential implementation of the fully-relativistic KKR method to perform ab initio self-consistent calculation by directly solving the Dirac differential equations using the generalized variable phase (sine and cosine matrices) formalism Liu et al. (2016). Themore » pathology around the origin is completely eliminated by carrying out the energy integration of the single-site Green function along the real axis. Here, by using an efficient pole-searching technique to identify the zeros of the well-behaved Jost matrices, we demonstrated that this scheme is numerically stable and computationally efficient, with speed comparable to the conventional contour energy integration method, while free of the pathology problem of the charge density. As an application, this method is utilized to investigate the crystal structures of polonium and their bulk properties, which is challenging for a conventional real-energy scheme. The noble metals are also calculated, both as a test of our method and to study the relativistic effects.« less
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Fully-relativistic full-potential multiple scattering theory: A pathology-free scheme
Liu, Xianglin; Wang, Yang; Eisenbach, Markus; ...
2017-10-28
The Green function plays an essential role in the Korringa–Kohn–Rostoker(KKR) multiple scattering method. In practice, it is constructed from the regular and irregular solutions of the local Kohn–Sham equation and robust methods exist for spherical potentials. However, when applied to a non-spherical potential, numerical errors from the irregular solutions give rise to pathological behaviors of the charge density at small radius. Here we present a full-potential implementation of the fully-relativistic KKR method to perform ab initio self-consistent calculation by directly solving the Dirac differential equations using the generalized variable phase (sine and cosine matrices) formalism Liu et al. (2016). Themore » pathology around the origin is completely eliminated by carrying out the energy integration of the single-site Green function along the real axis. Here, by using an efficient pole-searching technique to identify the zeros of the well-behaved Jost matrices, we demonstrated that this scheme is numerically stable and computationally efficient, with speed comparable to the conventional contour energy integration method, while free of the pathology problem of the charge density. As an application, this method is utilized to investigate the crystal structures of polonium and their bulk properties, which is challenging for a conventional real-energy scheme. The noble metals are also calculated, both as a test of our method and to study the relativistic effects.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Gastegger, Michael; Kauffmann, Clemens; Marquetand, Philipp, E-mail: philipp.marquetand@univie.ac.at
Many approaches, which have been developed to express the potential energy of large systems, exploit the locality of the atomic interactions. A prominent example is the fragmentation methods in which the quantum chemical calculations are carried out for overlapping small fragments of a given molecule that are then combined in a second step to yield the system’s total energy. Here we compare the accuracy of the systematic molecular fragmentation approach with the performance of high-dimensional neural network (HDNN) potentials introduced by Behler and Parrinello. HDNN potentials are similar in spirit to the fragmentation approach in that the total energy ismore » constructed as a sum of environment-dependent atomic energies, which are derived indirectly from electronic structure calculations. As a benchmark set, we use all-trans alkanes containing up to eleven carbon atoms at the coupled cluster level of theory. These molecules have been chosen because they allow to extrapolate reliable reference energies for very long chains, enabling an assessment of the energies obtained by both methods for alkanes including up to 10 000 carbon atoms. We find that both methods predict high-quality energies with the HDNN potentials yielding smaller errors with respect to the coupled cluster reference.« less
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Enhanced regeneration potential of mobilized dental pulp stem cells from immature teeth.
Nakayama, H; Iohara, K; Hayashi, Y; Okuwa, Y; Kurita, K; Nakashima, M
2017-07-01
We have previously demonstrated that dental pulp stem cells (DPSCs) isolated from mature teeth by granulocyte colony-stimulating factor (G-CSF)-induced mobilization method can enhance angiogenesis/vasculogenesis and improve pulp regeneration when compared with colony-derived DPSCs. However, the efficacy of this method in immature teeth with root-formative stage has never been investigated. Therefore, the aim of this study was to examine the stemness, biological characteristics, and regeneration potential in mobilized DPSCs compared with colony-derived DPSCs from immature teeth. Mobilized DPSCs isolated from immature teeth were compared to colony-derived DPSCs using methods including flow cytometry, migration assays, mRNA expression of angiogenic/neurotrophic factor, and induced differentiation assays. They were also compared in trophic effects of the secretome. Regeneration potential was further compared in an ectopic tooth transplantation model. Mobilized DPSCs had higher migration ability and expressed more angiogenic/neurotrophic factors than DPSCs. The mobilized DPSC secretome produced a higher stimulatory effect on migration, immunomodulation, anti-apoptosis, endothelial differentiation, and neurite extension. In addition, vascularization and pulp regeneration potential were higher in mobilized DPSCs than in DPSCs. G-CSF-induced mobilization method enhances regeneration potential of colony-derived DPSCs from immature teeth. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
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Temperature scaling method for Markov chains.
Crosby, Lonnie D; Windus, Theresa L
2009-01-22
The use of ab initio potentials in Monte Carlo simulations aimed at investigating the nucleation kinetics of water clusters is complicated by the computational expense of the potential energy determinations. Furthermore, the common desire to investigate the temperature dependence of kinetic properties leads to an urgent need to reduce the expense of performing simulations at many different temperatures. A method is detailed that allows a Markov chain (obtained via Monte Carlo) at one temperature to be scaled to other temperatures of interest without the need to perform additional large simulations. This Markov chain temperature-scaling (TeS) can be generally applied to simulations geared for numerous applications. This paper shows the quality of results which can be obtained by TeS and the possible quantities which may be extracted from scaled Markov chains. Results are obtained for a 1-D analytical potential for which the exact solutions are known. Also, this method is applied to water clusters consisting of between 2 and 5 monomers, using Dynamical Nucleation Theory to determine the evaporation rate constant for monomer loss. Although ab initio potentials are not utilized in this paper, the benefit of this method is made apparent by using the Dang-Chang polarizable classical potential for water to obtain statistical properties at various temperatures.
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Short-time quantum dynamics of sharp boundaries potentials
NASA Astrophysics Data System (ADS)
Granot, Er'el; Marchewka, Avi
2015-02-01
Despite the high prevalence of singular potential in general, and rectangular potentials in particular, in applied scattering models, to date little is known about their short time effects. The reason is that singular potentials cause a mixture of complicated local as well as non-local effects. The object of this work is to derive a generic method to calculate analytically the short-time impact of any singular potential. In this paper it is shown that the scattering of a smooth wavefunction on a singular potential is totally equivalent, in the short-time regime, to the free propagation of a singular wavefunction. However, the latter problem was totally addressed analytically in Ref. [7]. Therefore, this equivalency can be utilized in solving analytically the short time dynamics of any smooth wavefunction at the presence of a singular potentials. In particular, with this method the short-time dynamics of any problem where a sharp boundaries potential (e.g., a rectangular barrier) is turned on instantaneously can easily be solved analytically.
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Analysis of Self-Potential Response beyond the Fixed Geometry Technique
NASA Astrophysics Data System (ADS)
Mahardika, Harry
2018-03-01
The self-potential (SP) method is one of the oldest geophysical methods that are still available for today’s application. Since its early days SP data interpretation has been done qualitatively until the emerging of the fixed geometry analysis that was used to characterize the orientation and the electric-dipole properties of a mineral ore structure. Through the expansion of fundamental theories, computational methods, field-and-lab experiments in the last fifteen years, SP method has emerge from its low-class reputation to become more respectable. It became a complementary package alongside electric-resistivity tomography (ERT) for detecting groundwater flow in the subsurface, and extends to the hydrothermal flow in geothermal areas. As the analysis of SP data becomes more quantitative, its potential applications become more diverse. In this paper, we will show examples of our current SP studies such as the groundwater flow characterization inside a fault area. Lastly we will introduce the application of the "active" SP method - that is the seismoelectric method - which can be used for 4D real-time monitoring systems.
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Computing pKa Values with a Mixing Hamiltonian Quantum Mechanical/Molecular Mechanical Approach.
Liu, Yang; Fan, Xiaoli; Jin, Yingdi; Hu, Xiangqian; Hu, Hao
2013-09-10
Accurate computation of the pKa value of a compound in solution is important but challenging. Here, a new mixing quantum mechanical/molecular mechanical (QM/MM) Hamiltonian method is developed to simulate the free-energy change associated with the protonation/deprotonation processes in solution. The mixing Hamiltonian method is designed for efficient quantum mechanical free-energy simulations by alchemically varying the nuclear potential, i.e., the nuclear charge of the transforming nucleus. In pKa calculation, the charge on the proton is varied in fraction between 0 and 1, corresponding to the fully deprotonated and protonated states, respectively. Inspired by the mixing potential QM/MM free energy simulation method developed previously [H. Hu and W. T. Yang, J. Chem. Phys. 2005, 123, 041102], this method succeeds many advantages of a large class of λ-coupled free-energy simulation methods and the linear combination of atomic potential approach. Theory and technique details of this method, along with the calculation results of the pKa of methanol and methanethiol molecules in aqueous solution, are reported. The results show satisfactory agreement with the experimental data.
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NASA Technical Reports Server (NTRS)
Chen, T.; Raju, I. S.
2002-01-01
A coupled finite element (FE) method and meshless local Petrov-Galerkin (MLPG) method for analyzing two-dimensional potential problems is presented in this paper. The analysis domain is subdivided into two regions, a finite element (FE) region and a meshless (MM) region. A single weighted residual form is written for the entire domain. Independent trial and test functions are assumed in the FE and MM regions. A transition region is created between the two regions. The transition region blends the trial and test functions of the FE and MM regions. The trial function blending is achieved using a technique similar to the 'Coons patch' method that is widely used in computer-aided geometric design. The test function blending is achieved by using either FE or MM test functions on the nodes in the transition element. The technique was evaluated by applying the coupled method to two potential problems governed by the Poisson equation. The coupled method passed all the patch test problems and gave accurate solutions for the problems studied.
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Alternative methods of salt disposal at the seven salt sites for a nuclear waste repository
DOE Office of Scientific and Technical Information (OSTI.GOV)
Not Available
1987-02-01
This study discusses the various alternative salt management techniques for the disposal of excess mined salt at seven potentially acceptable nuclear waste repository sites: Deaf Smith and Swisher Counties, Texas; Richton and Cypress Creek Domes, Mississippi; Vacherie Dome, Louisiana; and Davis and Lavender Canyons, Utah. Because the repository development involves the underground excavation of corridors and waste emplacement rooms, in either bedded or domed salt formations, excess salt will be mined and must be disposed of offsite. The salt disposal alternatives examined for all the sites include commercial use, ocean disposal, deep well injection, landfill disposal, and underground mine disposal.more » These alternatives (and other site-specific disposal methods) are reviewed, using estimated amounts of excavated, backfilled, and excess salt. Methods of transporting the excess salt are discussed, along with possible impacts of each disposal method and potential regulatory requirements. A preferred method of disposal is recommended for each potentially acceptable repository site. 14 refs., 5 tabs.« less
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Finite Element Analysis in Concurrent Processing: Computational Issues
NASA Technical Reports Server (NTRS)
Sobieszczanski-Sobieski, Jaroslaw; Watson, Brian; Vanderplaats, Garrett
2004-01-01
The purpose of this research is to investigate the potential application of new methods for solving large-scale static structural problems on concurrent computers. It is well known that traditional single-processor computational speed will be limited by inherent physical limits. The only path to achieve higher computational speeds lies through concurrent processing. Traditional factorization solution methods for sparse matrices are ill suited for concurrent processing because the null entries get filled, leading to high communication and memory requirements. The research reported herein investigates alternatives to factorization that promise a greater potential to achieve high concurrent computing efficiency. Two methods, and their variants, based on direct energy minimization are studied: a) minimization of the strain energy using the displacement method formulation; b) constrained minimization of the complementary strain energy using the force method formulation. Initial results indicated that in the context of the direct energy minimization the displacement formulation experienced convergence and accuracy difficulties while the force formulation showed promising potential.
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NASA Technical Reports Server (NTRS)
Phillips, J. R.
1996-01-01
In this paper we derive error bounds for a collocation-grid-projection scheme tuned for use in multilevel methods for solving boundary-element discretizations of potential integral equations. The grid-projection scheme is then combined with a precorrected FFT style multilevel method for solving potential integral equations with 1/r and e(sup ikr)/r kernels. A complexity analysis of this combined method is given to show that for homogeneous problems, the method is order n natural log n nearly independent of the kernel. In addition, it is shown analytically and experimentally that for an inhomogeneity generated by a very finely discretized surface, the combined method slows to order n(sup 4/3). Finally, examples are given to show that the collocation-based grid-projection plus precorrected-FFT scheme is competitive with fast-multipole algorithms when considering realistic problems and 1/r kernels, but can be used over a range of spatial frequencies with only a small performance penalty.
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Wroblewska, Katarzyna; Kucinska, Małgorzata; Murias, Marek; Lulek, Janina
2015-09-01
The aim of our study was to examine the irritation potential of new eye drops containing 2% choline salicylate (CS) as an active pharmaceutical ingredient (API) and various polymers increasing eye drop viscosity (hydroxyethylcellulose, hydroxypropyl methylcellulose, methylcellulose, polyvinyl alcohol, polyvinylpyrrolidone). The standard method for assessing the potential of irritating substances has been the Draize rabbit eye test. However the European Centre for Validation of Alternative Methods and the Coordinating Committee for Validation of Alternative Methods recommend, short time exposure (STE) in vitro tests as an alternative method for assessing eye irritation. The eye irritation potential was determined using cytotoxicity test methods for rabbit corneal cell line (SIRC) after 5 min exposure. The viability of cells was determined using two cytotoxicity assays: MTT and Neutral Red Uptake. According to the irritation rankings for the short time exposure test, all tested eye drops are classified as non-irritating (cell viability >70%).
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Wroblewska, Katarzyna; Kucinska, Małgorzata; Murias, Marek; Lulek, Janina
2014-01-01
The aim of our study was to examine the irritation potential of new eye drops containing 2% choline salicylate (CS) as an active pharmaceutical ingredient (API) and various polymers increasing eye drop viscosity (hydroxyethylcellulose, hydroxypropyl methylcellulose, methylcellulose, polyvinyl alcohol, polyvinylpyrrolidone). The standard method for assessing the potential of irritating substances has been the Draize rabbit eye test. However the European Centre for Validation of Alternative Methods and the Coordinating Committee for Validation of Alternative Methods recommend, short time exposure (STE) in vitro tests as an alternative method for assessing eye irritation. The eye irritation potential was determined using cytotoxicity test methods for rabbit corneal cell line (SIRC) after 5 min exposure. The viability of cells was determined using two cytotoxicity assays: MTT and Neutral Red Uptake. According to the irritation rankings for the short time exposure test, all tested eye drops are classified as non-irritating (cell viability >70%). PMID:27134543
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Sodium influxes in internally perfused squid giant axon during voltage clamp.
Atwater, I; Bezanilla, F; Rojas, E
1969-05-01
1. An experimental method for measuring ionic influxes during voltage clamp in the giant axon of Dosidicus is described; the technique combines intracellular perfusion with a method for controlling membrane potential.2. Sodium influx determinations were carried out while applying rectangular pulses of membrane depolarization. The ratio ;measured sodium influx/computed ionic flux during the early current' is 0.92 +/- 0.12.3. Plots of measured sodium influx and computed ionic flux during the early current against membrane potential are very similar. There was evidence that the membrane potential at which the sodium influx vanishes is the potential at which the early current reverses.
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Conformational Sampling of a Biomolecular Rugged Energy Landscape.
Rydzewski, Jakub; Jakubowski, Rafal; Nicosia, Giuseppe; Nowak, Wieslaw
2018-01-01
The protein structure refinement using conformational sampling is important in hitherto protein studies. In this paper, we examined the protein structure refinement by means of potential energy minimization using immune computing as a method of sampling conformations. The method was tested on the x-ray structure and 30 decoys of the mutant of [Leu]Enkephalin, a paradigmatic example of the biomolecular multiple-minima problem. In order to score the refined conformations, we used a standard potential energy function with the OPLSAA force field. The effectiveness of the search was assessed using a variety of methods. The robustness of sampling was checked by the energy yield function which measures quantitatively the number of the peptide decoys residing in an energetic funnel. Furthermore, the potential energy-dependent Pareto fronts were calculated to elucidate dissimilarities between peptide conformations and the native state as observed by x-ray crystallography. Our results showed that the probed potential energy landscape of [Leu]Enkephalin is self-similar on different metric scales and that the local potential energy minima of the peptide decoys are metastable, thus they can be refined to conformations whose potential energy is decreased by approximately 250 kJ/mol.
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Comparison of methods for the analysis of relatively simple mediation models.
Rijnhart, Judith J M; Twisk, Jos W R; Chinapaw, Mai J M; de Boer, Michiel R; Heymans, Martijn W
2017-09-01
Statistical mediation analysis is an often used method in trials, to unravel the pathways underlying the effect of an intervention on a particular outcome variable. Throughout the years, several methods have been proposed, such as ordinary least square (OLS) regression, structural equation modeling (SEM), and the potential outcomes framework. Most applied researchers do not know that these methods are mathematically equivalent when applied to mediation models with a continuous mediator and outcome variable. Therefore, the aim of this paper was to demonstrate the similarities between OLS regression, SEM, and the potential outcomes framework in three mediation models: 1) a crude model, 2) a confounder-adjusted model, and 3) a model with an interaction term for exposure-mediator interaction. Secondary data analysis of a randomized controlled trial that included 546 schoolchildren. In our data example, the mediator and outcome variable were both continuous. We compared the estimates of the total, direct and indirect effects, proportion mediated, and 95% confidence intervals (CIs) for the indirect effect across OLS regression, SEM, and the potential outcomes framework. OLS regression, SEM, and the potential outcomes framework yielded the same effect estimates in the crude mediation model, the confounder-adjusted mediation model, and the mediation model with an interaction term for exposure-mediator interaction. Since OLS regression, SEM, and the potential outcomes framework yield the same results in three mediation models with a continuous mediator and outcome variable, researchers can continue using the method that is most convenient to them.
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NASA Astrophysics Data System (ADS)
Jougnot, D.; Roubinet, D.; Linde, N.; Irving, J.
2016-12-01
Quantifying fluid flow in fractured media is a critical challenge in a wide variety of research fields and applications. To this end, geophysics offers a variety of tools that can provide important information on subsurface physical properties in a noninvasive manner. Most geophysical techniques infer fluid flow by data or model differencing in time or space (i.e., they are not directly sensitive to flow occurring at the time of the measurements). An exception is the self-potential (SP) method. When water flows in the subsurface, an excess of charge in the pore water that counterbalances electric charges at the mineral-pore water interface gives rise to a streaming current and an associated streaming potential. The latter can be measured with the SP technique, meaning that the method is directly sensitive to fluid flow. Whereas numerous field experiments suggest that the SP method may allow for the detection of hydraulically active fractures, suitable tools for numerically modeling streaming potentials in fractured media do not exist. Here, we present a highly efficient two-dimensional discrete-dual-porosity approach for solving the fluid-flow and associated self-potential problems in fractured domains. Our approach is specifically designed for complex fracture networks that cannot be investigated using standard numerical methods due to computational limitations. We then simulate SP signals associated with pumping conditions for a number of examples to show that (i) accounting for matrix fluid flow is essential for accurate SP modeling and (ii) the sensitivity of SP to hydraulically active fractures is intimately linked with fracture-matrix fluid interactions. This implies that fractures associated with strong SP amplitudes are likely to be hydraulically conductive, attracting fluid flow from the surrounding matrix.
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NASA Astrophysics Data System (ADS)
Poursina, Mohammad; Anderson, Kurt S.
2014-08-01
This paper presents a novel algorithm to approximate the long-range electrostatic potential field in the Cartesian coordinates applicable to 3D coarse-grained simulations of biopolymers. In such models, coarse-grained clusters are formed via treating groups of atoms as rigid and/or flexible bodies connected together via kinematic joints. Therefore, multibody dynamic techniques are used to form and solve the equations of motion of such coarse-grained systems. In this article, the approximations for the potential fields due to the interaction between a highly negatively/positively charged pseudo-atom and charged particles, as well as the interaction between clusters of charged particles, are presented. These approximations are expressed in terms of physical and geometrical properties of the bodies such as the entire charge, the location of the center of charge, and the pseudo-inertia tensor about the center of charge of the clusters. Further, a novel substructuring scheme is introduced to implement the presented far-field potential evaluations in a binary tree framework as opposed to the existing quadtree and octree strategies of implementing fast multipole method. Using the presented Lagrangian grids, the electrostatic potential is recursively calculated via sweeping two passes: assembly and disassembly. In the assembly pass, adjacent charged bodies are combined together to form new clusters. Then, the potential field of each cluster due to its interaction with faraway resulting clusters is recursively calculated in the disassembly pass. The method is highly compatible with multibody dynamic schemes to model coarse-grained biopolymers. Since the proposed method takes advantage of constant physical and geometrical properties of rigid clusters, improvement in the overall computational cost is observed comparing to the tradition application of fast multipole method.
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NASA Astrophysics Data System (ADS)
Pan, Kok-Kwei
We have generalized the linked cluster expansion method to solve more many-body quantum systems, such as quantum spin systems with crystal-field potentials and the Hubbard model. The technique sums up all connected diagrams to a certain order of the perturbative Hamiltonian. The modified multiple-site Wick reduction theorem and the simple tau dependence of the standard basis operators have been used to facilitate the evaluation of the integration procedures in the perturbation expansion. Computational methods are developed to calculate all terms in the series expansion. As a first example, the perturbation series expansion of thermodynamic quantities of the single-band Hubbard model has been obtained using a linked cluster series expansion technique. We have made corrections to all previous results of several papers (up to fourth order). The behaviors of the three dimensional simple cubic and body-centered cubic systems have been discussed from the qualitative analysis of the perturbation series up to fourth order. We have also calculated the sixth-order perturbation series of this model. As a second example, we present the magnetic properties of spin-one Heisenberg model with arbitrary crystal-field potential using a linked cluster series expansion. The calculation of the thermodynamic properties using this method covers the whole range of temperature, in both magnetically ordered and disordered phases. The series for the susceptibility and magnetization have been obtained up to fourth order for this model. The method sums up all perturbation terms to certain order and estimates the result using a well -developed and highly successful extrapolation method (the standard ratio method). The dependence of critical temperature on the crystal-field potential and the magnetization as a function of temperature and crystal-field potential are shown. The critical behaviors at zero temperature are also shown. The range of the crystal-field potential for Ni(2+) compounds is roughly estimated based on this model using known experimental results.
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In vitro methods for hazard assessment of industrial chemicals – opportunities and challenges
Wong, Chin Lin; Ghassabian, Sussan; Smith, Maree T.; Lam, Ai-Leen
2015-01-01
Allergic contact dermatitis (ACD) is a delayed-type hypersensitivity immune reaction mediated by T-lymphocytes as a result of repeated exposure of an allergen primarily on skin. ACD accounts for up to 95% of occupational skin diseases, with epoxy resins implicated as one of the most common causes of ACD. Efficient high-throughput in vitro screening for accurate identification of compounds and materials that may pose hazardous risks in the workplace is crucial. At present, the murine local lymph node assay is the ‘method of choice’ for predicting the sensitizing potency of contact allergens. As the 3Rs principles of reduction, refinement, and replacement in animal testing has gained political and economic momentum, several in vitro screening methods have been developed for identifying potential contact allergens. To date, these latter methods have been utilized primarily to assess the skin sensitizing potential of the chemical components of cosmetic products with scant research attention as to the applicability of these methods to industrial chemicals, particularly epoxy resins. Herein we review the currently utilized in vitro methods and identify the knowledge gaps with regard to assessing the generalizability of in vitro screening methods for assessing the skin sensitizing potential of industrial chemicals. PMID:25999858
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NASA Astrophysics Data System (ADS)
Baraliya, Jagdish D.; Rakhashiya, Purvi M.; Patel, Pooja P.; Thaker, Vrinda S.; Joshi, Hiren H.
2017-05-01
In this study, novel multifunctional magnetic iron-based nanoparticles (CoFe2O4) coated with silica, silica-DEG (diethylene glycol), PEG (polyethylene glycol) were synthesized using Auto Combustion Method (ACM), Co-precipitation Method (COPM), Citrate Precursor Method (CPM), Flash Combustion Method (FCM). These spinel ferrite nanoparticles also contain very high antibacterial properties to fulfill the requirements of a drug delivery system so that the antibiotic concentration could be minimized. A potential delivery system could be based on a ferromagnetic fluid. The effects of various preparation methods on the physical properties of the nanoparticles were examined. The nanoparticles were also tested against four human pathogenic bacteria (Gram negative E.coli, P. aeruginosa, Gram positive S. aureus, S. pyogenus) and two fungi (C. albicans, A.niger). It was revealed that a nanoparticle has strong antibacterial activity as compared to antifungal. Further, Gram positive bacteria are more affected than Gram negative bacteria. It was also clear that different methods of coating have great influence on the antimicrobial properties. It was observed that these nanoparticles have significantly different but potentially very high antimicrobial activities against the tested organisms than found elsewhere by other nanoparticles on the same organisms.
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In vitro methods for hazard assessment of industrial chemicals - opportunities and challenges.
Wong, Chin Lin; Ghassabian, Sussan; Smith, Maree T; Lam, Ai-Leen
2015-01-01
Allergic contact dermatitis (ACD) is a delayed-type hypersensitivity immune reaction mediated by T-lymphocytes as a result of repeated exposure of an allergen primarily on skin. ACD accounts for up to 95% of occupational skin diseases, with epoxy resins implicated as one of the most common causes of ACD. Efficient high-throughput in vitro screening for accurate identification of compounds and materials that may pose hazardous risks in the workplace is crucial. At present, the murine local lymph node assay is the 'method of choice' for predicting the sensitizing potency of contact allergens. As the 3Rs principles of reduction, refinement, and replacement in animal testing has gained political and economic momentum, several in vitro screening methods have been developed for identifying potential contact allergens. To date, these latter methods have been utilized primarily to assess the skin sensitizing potential of the chemical components of cosmetic products with scant research attention as to the applicability of these methods to industrial chemicals, particularly epoxy resins. Herein we review the currently utilized in vitro methods and identify the knowledge gaps with regard to assessing the generalizability of in vitro screening methods for assessing the skin sensitizing potential of industrial chemicals.
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NASA Astrophysics Data System (ADS)
Gurk, M.; Bosch, F. P.; Tougiannidis, N.
2013-04-01
Common studies on the static electric field distribution over a conductivity anomaly use the self-potential method. However, this method is time consuming and requires nonpolarizable electrodes to be placed in the ground. Moreover, the information gained by this method is restricted to the horizontal variations of the electric field. To overcome the limitation in the self-potential technique, we conducted a field experiment using a non conventional technique to assess the static electric field over a conductivity anomaly. We use two metallic potential probes arranged on an insulated boom with a separation of 126 cm. When placed into the electric field of the free air, a surface charge will be induced on each probe trying to equalize with the potential of the surrounding atmosphere. The use of a plasma source at both probes facilitated continuous and quicker measurement of the electric field in the air. The present study shows first experimental measurements with a modified potential probe technique (MPP) along a 600-meter-long transect to demonstrate the general feasibility of this method for studying the static electric field distribution over shallow conductivity anomalies. Field measurements were carried out on a test site on top of the Bramsche Massif near Osnabrück (Northwest Germany) to benefit from a variety of available near surface data over an almost vertical conductivity anomaly. High resolution self-potential data served in a numerical analysis to estimate the expected individual components of the electric field vector. During the experiment we found more anomalies in the vertical and horizontal components of the electric field than self-potential anomalies. These contrasting findings are successfully cross-validated with conventional near surface geophysical methods. Among these methods, we used self-potential, radiomagnetotelluric, electric resistivity tomography and induced polarization data to derive 2D conductivity models of the subsurface in order to infer the geometrical properties and the origin of the conductivity anomaly in the survey area. The presented study demonstrates the feasibility of electric field measurements in free air to detect and study near surface conductivity anomalies. Variations in Ez correlate well with the conductivity distribution obtained from resistivity methods. Compared to the self-potential technique, continuously free air measurements of the electric field are more rapid and of better lateral resolution combined with the unique ability to analyze vertical components of the electric field which are of particular importance to detect lateral conductivity contrasts. Mapping Ez in free air is a good tool to precisely map lateral changes of the electric field distribution in areas where SP generation fails. MPP offers interesting application in other geophysical techniques e.g. in time domain electromagnetics, DC and IP. With this method we were able to reveal a ca. 150 m broad zone of enhanced electric field strength.
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Grid-based Continual Analysis of Molecular Interior for Drug Discovery, QSAR and QSPR.
Potemkin, Andrey V; Grishina, Maria A; Potemkin, Vladimir A
2017-01-01
In 1979, R.D.Cramer and M.Milne made a first realization of 3D comparison of molecules by aligning them in space and by mapping their molecular fields to a 3D grid. Further, this approach was developed as the DYLOMMS (Dynamic Lattice- Oriented Molecular Modelling System) approach. In 1984, H.Wold and S.Wold proposed the use of partial least squares (PLS) analysis, instead of principal component analysis, to correlate the field values with biological activities. Then, in 1988, the method which was called CoMFA (Comparative Molecular Field Analysis) was introduced and the appropriate software became commercially available. Since 1988, a lot of 3D QSAR methods, algorithms and their modifications are introduced for solving of virtual drug discovery problems (e.g., CoMSIA, CoMMA, HINT, HASL, GOLPE, GRID, PARM, Raptor, BiS, CiS, ConGO,). All the methods can be divided into two groups (classes):1. Methods studying the exterior of molecules; 2) Methods studying the interior of molecules. A series of grid-based computational technologies for Continual Molecular Interior analysis (CoMIn) are invented in the current paper. The grid-based analysis is fulfilled by means of a lattice construction analogously to many other grid-based methods. The further continual elucidation of molecular structure is performed in various ways. (i) In terms of intermolecular interactions potentials. This can be represented as a superposition of Coulomb, Van der Waals interactions and hydrogen bonds. All the potentials are well known continual functions and their values can be determined in all lattice points for a molecule. (ii) In the terms of quantum functions such as electron density distribution, Laplacian and Hamiltonian of electron density distribution, potential energy distribution, the highest occupied and the lowest unoccupied molecular orbitals distribution and their superposition. To reduce time of calculations using quantum methods based on the first principles, an original quantum free-orbital approach AlteQ is proposed. All the functions can be calculated using a quantum approach at a sufficient level of theory and their values can be determined in all lattice points for a molecule. Then, the molecules of a dataset can be superimposed in the lattice for the maximal coincidence (or minimal deviations) of the potentials (i) or the quantum functions (ii). The methods and criteria of the superimposition are discussed. After that a functional relationship between biological activity or property and characteristics of potentials (i) or functions (ii) is created. The methods of the quantitative relationship construction are discussed. New approaches for rational virtual drug design based on the intermolecular potentials and quantum functions are invented. All the invented methods are realized at www.chemosophia.com web page. Therefore, a set of 3D QSAR approaches for continual molecular interior study giving a lot of opportunities for virtual drug discovery, virtual screening and ligand-based drug design are invented. The continual elucidation of molecular structure is performed in the terms of intermolecular interactions potentials and in the terms of quantum functions such as electron density distribution, Laplacian and Hamiltonian of electron density distribution, potential energy distribution, the highest occupied and the lowest unoccupied molecular orbitals distribution and their superposition. To reduce time of calculations using quantum methods based on the first principles, an original quantum free-orbital approach AlteQ is proposed. The methods of the quantitative relationship construction are discussed. New approaches for rational virtual drug design based on the intermolecular potentials and quantum functions are invented. All the invented methods are realized at www.chemosophia.com web page. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.
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Parallelized Three-Dimensional Resistivity Inversion Using Finite Elements And Adjoint State Methods
NASA Astrophysics Data System (ADS)
Schaa, Ralf; Gross, Lutz; Du Plessis, Jaco
2015-04-01
The resistivity method is one of the oldest geophysical exploration methods, which employs one pair of electrodes to inject current into the ground and one or more pairs of electrodes to measure the electrical potential difference. The potential difference is a non-linear function of the subsurface resistivity distribution described by an elliptic partial differential equation (PDE) of the Poisson type. Inversion of measured potentials solves for the subsurface resistivity represented by PDE coefficients. With increasing advances in multichannel resistivity acquisition systems (systems with more than 60 channels and full waveform recording are now emerging), inversion software require efficient storage and solver algorithms. We developed the finite element solver Escript, which provides a user-friendly programming environment in Python to solve large-scale PDE-based problems (see https://launchpad.net/escript-finley). Using finite elements, highly irregular shaped geology and topography can readily be taken into account. For the 3D resistivity problem, we have implemented the secondary potential approach, where the PDE is decomposed into a primary potential caused by the source current and the secondary potential caused by changes in subsurface resistivity. The primary potential is calculated analytically, and the boundary value problem for the secondary potential is solved using nodal finite elements. This approach removes the singularity caused by the source currents and provides more accurate 3D resistivity models. To solve the inversion problem we apply a 'first optimize then discretize' approach using the quasi-Newton scheme in form of the limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) method (see Gross & Kemp 2013). The evaluation of the cost function requires the solution of the secondary potential PDE for each source current and the solution of the corresponding adjoint-state PDE for the cost function gradients with respect to the subsurface resistivity. The Hessian of the regularization term is used as preconditioner which requires an additional PDE solution in each iteration step. As it turns out, the relevant PDEs are naturally formulated in the finite element framework. Using the domain decomposition method provided in Escript, the inversion scheme has been parallelized for distributed memory computers with multi-core shared memory nodes. We show numerical examples from simple layered models to complex 3D models and compare with the results from other methods. The inversion scheme is furthermore tested on a field data example to characterise localised freshwater discharge in a coastal environment.. References: L. Gross and C. Kemp (2013) Large Scale Joint Inversion of Geophysical Data using the Finite Element Method in escript. ASEG Extended Abstracts 2013, http://dx.doi.org/10.1071/ASEG2013ab306
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Identification of selection footprints on the X chromosome in pig.
Ma, Yunlong; Zhang, Haihan; Zhang, Qin; Ding, Xiangdong
2014-01-01
Identifying footprints of selection can provide a straightforward insight into the mechanism of artificial selection and further dig out the causal genes related to important traits. In this study, three between-population and two within-population approaches, the Cross Population Extend Haplotype Homozygosity Test (XPEHH), the Cross Population Composite Likelihood Ratio (XPCLR), the F-statistics (Fst), the Integrated Haplotype Score (iHS) and the Tajima's D, were implemented to detect the selection footprints on the X chromosome in three pig breeds using Illumina Porcine60K SNP chip. In the detection of selection footprints using between-population methods, 11, 11 and 7 potential selection regions with length of 15.62 Mb, 12.32 Mb and 9.38 Mb were identified in Landrace, Chinese Songliao and Yorkshire by XPEHH, respectively, and 16, 13 and 17 potential selection regions with length of 15.20 Mb, 13.00 Mb and 19.21 Mb by XPCLR, 4, 2 and 4 potential selection regions with length of 3.20 Mb, 1.60 Mb and 3.20 Mb by Fst. For within-population methods, 7, 10 and 9 potential selection regions with length of 8.12 Mb, 8.40 Mb and 9.99 Mb were identified in Landrace, Chinese Songliao and Yorkshire by iHS, and 4, 3 and 2 potential selection regions with length of 3.20 Mb, 2.40 Mb and 1.60 Mb by Tajima's D. Moreover, the selection regions from different methods were partly overlapped, especially the regions around 22∼25 Mb were detected under selection in Landrace and Yorkshire while no selection in Chinese Songliao by all three between-population methods. Only quite few overlap of selection regions identified by between-population and within-population methods were found. Bioinformatics analysis showed that the genes relevant with meat quality, reproduction and immune were found in potential selection regions. In addition, three out of five significant SNPs associated with hematological traits reported in our genome-wide association study were harbored in potential selection regions.
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NASA Technical Reports Server (NTRS)
Beatty, T. D.
1975-01-01
A theoretical method is presented for the computation of the flow field about an axisymmetric body operating in a viscous, incompressible fluid. A potential flow method was used to determine the inviscid flow field and to yield the boundary conditions for the boundary layer solutions. Boundary layer effects in the forces of displacement thickness and empirically modeled separation streamlines are accounted for in subsequent potential flow solutions. This procedure is repeated until the solutions converge. An empirical method was used to determine base drag allowing configuration drag to be computed.
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NASA Astrophysics Data System (ADS)
Fu, Yuan; Zhang, Da-peng; Xie, Xi-lin
2018-04-01
In this study, a vorticity vector-potential method for two-dimensional viscous incompressible rotating driven flows is developed in the time-dependent curvilinear coordinates. The method is applicable in both inertial and non-inertial frames of reference with the advantage of a fixed and regular calculation domain. The numerical method is applied to triangle and curved triangle configurations in constant and varying rotational angular velocity cases respectively. The evolutions of flow field are studied. The geostrophic effect, unsteady effect and curvature effect on the evolutions are discussed.
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Generation of Cardiomyocytes from Pluripotent Stem Cells.
Nakahama, Hiroko; Di Pasquale, Elisa
2016-01-01
The advent of pluripotent stem cells (PSCs) enabled a multitude of studies for modeling the development of diseases and testing pharmaceutical therapeutic potential in vitro. These PSCs have been differentiated to multiple cell types to demonstrate its pluripotent potential, including cardiomyocytes (CMs). However, the efficiency and efficacy of differentiation vary greatly between different cell lines and methods. Here, we describe two different methods for acquiring CMs from human pluripotent lines. One method involves the generation of embryoid bodies, which emulates the natural developmental process, while the other method chemically activates the canonical Wnt signaling pathway to induce a monolayer of cardiac differentiation.
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Applications of fuzzy ranking methods to risk-management decisions
NASA Astrophysics Data System (ADS)
Mitchell, Harold A.; Carter, James C., III
1993-12-01
The Department of Energy is making significant improvements to its nuclear facilities as a result of more stringent regulation, internal audits, and recommendations from external review groups. A large backlog of upgrades has resulted. Currently, a prioritization method is being utilized which relies on a matrix of potential consequence and probability of occurrence. The attributes of the potential consequences considered include likelihood, exposure, public health and safety, environmental impact, site personnel safety, public relations, legal liability, and business loss. This paper describes an improved method which utilizes fuzzy multiple attribute decision methods to rank proposed improvement projects.
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General design method for three-dimensional potential flow fields. 1: Theory
NASA Technical Reports Server (NTRS)
Stanitz, J. D.
1980-01-01
A general design method was developed for steady, three dimensional, potential, incompressible or subsonic-compressible flow. In this design method, the flow field, including the shape of its boundary, was determined for arbitrarily specified, continuous distributions of velocity as a function of arc length along the boundary streamlines. The method applied to the design of both internal and external flow fields, including, in both cases, fields with planar symmetry. The analytic problems associated with stagnation points, closure of bodies in external flow fields, and prediction of turning angles in three dimensional ducts were reviewed.
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NASA Astrophysics Data System (ADS)
Fu, Yuan; Zhang, Da-peng; Xie, Xi-lin
2018-03-01
In this study, a vorticity vector-potential method for two-dimensional viscous incompressible rotating driven flows is developed in the time-dependent curvilinear coordinates. The method is applicable in both inertial and non-inertial frames of reference with the advantage of a fixed and regular calculation domain. The numerical method is applied to triangle and curved triangle configurations in constant and varying rotational angular velocity cases respectively. The evolutions of flow field are studied. The geostrophic effect, unsteady effect and curvature effect on the evolutions are discussed.
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NASA Astrophysics Data System (ADS)
Lu, Tiao; Cai, Wei
2008-10-01
In this paper, we propose a high order Fourier spectral-discontinuous Galerkin method for time-dependent Schrödinger-Poisson equations in 3-D spaces. The Fourier spectral Galerkin method is used for the two periodic transverse directions and a high order discontinuous Galerkin method for the longitudinal propagation direction. Such a combination results in a diagonal form for the differential operators along the transverse directions and a flexible method to handle the discontinuous potentials present in quantum heterojunction and supperlattice structures. As the derivative matrices are required for various time integration schemes such as the exponential time differencing and Crank Nicholson methods, explicit derivative matrices of the discontinuous Galerkin method of various orders are derived. Numerical results, using the proposed method with various time integration schemes, are provided to validate the method.
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Inverting Residual Self-Potential Data for Redox Potentials of Contaminant Plumes
NASA Astrophysics Data System (ADS)
Linde, N.; Revil, A.
2007-05-01
Self-potential (SP) data can be separated into a streaming potential component that is associated with pore water flow and a redox potential component, which is sensitive to differences in the redox potentials of organic-rich contaminant plumes and the surroundings. This work presents the first inversion method that uses residual SP (i.e., corrected for the streaming potential component) to invert for the redox potentials of contaminant plumes. We consider a two-layered electrical conductivity structure, where the boundary corresponds to the water table. We assume that the electrical dipole sources are associated with microbial breakdown of contaminants at the water table. This geobattery model is hypothesized to exist (1) because the water table is associated with a strong redox gradient between highly reducing conditions within the contaminated groundwater (due to biodegradation and oxygen depletion) and the oxidized vadose zone, and (2) because the microbial biofilms and precipitation of metallic particles can provide an electron conductor to complete the circuit required for the geobattery. The inverse method was applied to residual SP estimated from SP measurements collected at the ground surface in the vicinity of the Entressen landfill, South of France. The estimated redox potentials correlate well with in situ measurements (correlation coefficient is 0.93) and the estimated amplitudes of the redox potentials are similar to those measured in situ. A sensitivity analysis reveals that meaningful estimates of the redox potential can be derived even if the electrical conductivity structure is only known within an order of magnitude. These results provide further evidence that the SP method can be useful to monitor the spreading of contaminants around landfills and to evaluate the efficiency of remediation programs.
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Comparative Measurement of Microcystins in Diverse Surface ...
The measurement of microcystins, cyanotoxins associated with cyanobacterial blooms which are increasingly prevalent in inland waters, is complicated by the diversity of congeners which have been observed in the environment. At present, more than 150 microcystin congeners have been identified, and this poses a significant challenge to analytical methods intended to assess human health risks in surface and drinking water systems. The most widely employed analytical method at present is the ADDA-ELISA technique which is potentially sensitive to all microcystins, but it is primarily intended as a semi-quantitative method, and questions have been raised regarding the potential for cross-reactivity and false positives. LC-MS/MS methods targeting specific congeners, such as US EPA Method 544, are intended for use as a secondary confirmation following a positive ELISA response, but these techniques can target only those congeners for which commercial standards are available. Accordingly, they are not suitable for ascertaining the safety of a given water sample, given the potential for omitting unknown microcystin congeners which might be present.An alternative approach involves oxidative transformation of microcystins to a common product, 2-methyl-3-methoxy-4-phenylbutyric acid, or MMPB. Measuring MMPB by LC-MS/MS can potentially provide a metric for the sum of all microcystin congeners present in a sample, subject to the efficiency and overall yield of conversion. The
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An Excel-based implementation of the spectral method of action potential alternans analysis.
Pearman, Charles M
2014-12-01
Action potential (AP) alternans has been well established as a mechanism of arrhythmogenesis and sudden cardiac death. Proper interpretation of AP alternans requires a robust method of alternans quantification. Traditional methods of alternans analysis neglect higher order periodicities that may have greater pro-arrhythmic potential than classical 2:1 alternans. The spectral method of alternans analysis, already widely used in the related study of microvolt T-wave alternans, has also been used to study AP alternans. Software to meet the specific needs of AP alternans analysis is not currently available in the public domain. An AP analysis tool is implemented here, written in Visual Basic for Applications and using Microsoft Excel as a shell. This performs a sophisticated analysis of alternans behavior allowing reliable distinction of alternans from random fluctuations, quantification of alternans magnitude, and identification of which phases of the AP are most affected. In addition, the spectral method has been adapted to allow detection and quantification of higher order regular oscillations. Analysis of action potential morphology is also performed. A simple user interface enables easy import, analysis, and export of collated results. © 2014 The Author. Physiological Reports published by Wiley Periodicals, Inc. on behalf of the American Physiological Society and The Physiological Society.
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Potential of Progressive Construction Systems in Slovakia
NASA Astrophysics Data System (ADS)
Kozlovska, Maria; Spisakova, Marcela; Mackova, Daniela
2017-10-01
Construction industry is a sector with rapid development. Progressive technologies of construction and new construction materials also called modern methods of construction (MMC) are developed constantly. MMC represent the adoption of construction industrialisation and the use of prefabrication of components in building construction. One of these modern methods is also system Varianthaus, which is based on, insulated concrete forms principle and provides complete production plant for wall, ceiling and roof elements for a high thermal insulation house construction. Another progressive construction system is EcoB, which represents an insulated precast concrete panel based on combination of two layers, insulation and concrete, produced in a factory as a whole. Both modern methods of construction are not yet known and wide-spread in the Slovak construction market. The aim of this paper is focused on demonstration of MMC using potential in Slovakia. MMC potential is proved based on comparison of the selected parameters of construction process - construction costs and construction time. The subject of this study is family house modelled in three material variants - masonry construction (as a representative of traditional methods of construction), Varianthaus and EcoB (as the representatives of modern methods of construction). The results of this study provide the useful information in decision-making process for potential investors of construction.
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Ohyu, Shigeharu; Okamoto, Yoshiwo; Kuriki, Shinya
2002-06-01
A novel magnetocardiographic inverse method for reconstructing the action potential amplitude (APA) and the activation time (AT) on the ventricular myocardium is proposed. This method is based on the propagated excitation model, in which the excitation is propagated through the ventricle with nonuniform height of action potential. Assumption of stepwise waveform on the transmembrane potential was introduced in the model. Spatial gradient of transmembrane potential, which is defined by APA and AT distributed in the ventricular wall, is used for the computation of a current source distribution. Based on this source model, the distributions of APA and AT are inversely reconstructed from the QRS interval of magnetocardiogram (MCG) utilizing a maximum a posteriori approach. The proposed reconstruction method was tested through computer simulations. Stability of the methods with respect to measurement noise was demonstrated. When reference APA was provided as a uniform distribution, root-mean-square errors of estimated APA were below 10 mV for MCG signal-to-noise ratios greater than, or equal to, 20 dB. Low-amplitude regions located at several sites in reference APA distributions were correctly reproduced in reconstructed APA distributions. The goal of our study is to develop a method for detecting myocardial ischemia through the depression of reconstructed APA distributions.
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Comparative measurement of microcystins in diverse surface ...
The measurement of microcystins, cyanotoxins associated with cyanobacterial blooms which are increasingly prevalent in inland waters, is complicated by the diversity of congeners which have been observed in the environment. At present, more than 150 microcystin congeners have been identified, and this poses a significant challenge to analytical methods intended to assess human health risks in surface and drinking water systems. The most widely employed analytical method at present is the ADDA-ELISA technique which is potentially sensitive to all microcystins, but it is primarily intended as a semi-quantitative method, and questions have been raised regarding the potential for cross-reactivity and false positives. LC-MS/MS methods targeting specific congeners, such as US EPA Method 544, are intended for use as a secondary confirmation following a positive ELISA response, but these techniques can target only those congeners for which commercial standards are available. Accordingly, they not suitable for ascertaining the safety of a given water sample, given the potential for omitting unknown microcystin congeners which might be present.An alternative approach involves oxidative transformation of microcystins to a common product, 2-methyl-3-methoxy-4-phenylbutyric acid, or MMPB. Measuring MMPB by LC-MS/MS can potentially provide a metric for the sum of all microcystin congeners present in a sample, subject to the efficiency and overall yield of conversion. The pres
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Blowers, Paul; Hollingshead, Kyle
2009-05-21
In this work, the global warming potential (GWP) of methylene fluoride (CH(2)F(2)), or HFC-32, is estimated through computational chemistry methods. We find our computational chemistry approach reproduces well all phenomena important for predicting global warming potentials. Geometries predicted using the B3LYP/6-311g** method were in good agreement with experiment, although some other computational methods performed slightly better. Frequencies needed for both partition function calculations in transition-state theory and infrared intensities needed for radiative forcing estimates agreed well with experiment compared to other computational methods. A modified CBS-RAD method used to obtain energies led to superior results to all other previous heat of reaction estimates and most barrier height calculations when the B3LYP/6-311g** optimized geometry was used as the base structure. Use of the small-curvature tunneling correction and a hindered rotor treatment where appropriate led to accurate reaction rate constants and radiative forcing estimates without requiring any experimental data. Atmospheric lifetimes from theory at 277 K were indistinguishable from experimental results, as were the final global warming potentials compared to experiment. This is the first time entirely computational methods have been applied to estimate a global warming potential for a chemical, and we have found the approach to be robust, inexpensive, and accurate compared to prior experimental results. This methodology was subsequently used to estimate GWPs for three additional species [methane (CH(4)); fluoromethane (CH(3)F), or HFC-41; and fluoroform (CHF(3)), or HFC-23], where estimations also compare favorably to experimental values.
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Paff, Marc G.; Monterial, Mateusz; Marleau, Peter; ...
2014-06-21
A series of simulations and experiments were undertaken to explore and evaluate the potential for a novel new technique for fissile material detection and characterization, the timecorrelated pulse-height (TCPH) method, to be used concurrent with active stimulation of potential nuclear materials. In previous work TCPH has been established as a highly sensitive method for the detection and characterization of configurations of fissile material containing Plutonium in passive measurements. By actively stimulating fission with the introduction of an external radiation source, we have shown that TCPH is also an effective method of detecting and characterizing configurations of fissile material containing Highlymore » Enriched Uranium (HEU). The TCPH method is shown to be robust in the presence of the proper choice of external radiation source. An evaluation of potential interrogation sources is presented.« less
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Decoding spike timing: the differential reverse correlation method
Tkačik, Gašper; Magnasco, Marcelo O.
2009-01-01
It is widely acknowledged that detailed timing of action potentials is used to encode information, for example in auditory pathways; however the computational tools required to analyze encoding through timing are still in their infancy. We present a simple example of encoding, based on a recent model of time-frequency analysis, in which units fire action potentials when a certain condition is met, but the timing of the action potential depends also on other features of the stimulus. We show that, as a result, spike-triggered averages are smoothed so much they do not represent the true features of the encoding. Inspired by this example, we present a simple method, differential reverse correlations, that can separate an analysis of what causes a neuron to spike, and what controls its timing. We analyze with this method the leaky integrate-and-fire neuron and show the method accurately reconstructs the model's kernel. PMID:18597928
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NASA Technical Reports Server (NTRS)
Chen, L. T.
1975-01-01
A general method for analyzing aerodynamic flows around complex configurations is presented. By applying the Green function method, a linear integral equation relating the unknown, small perturbation potential on the surface of the body, to the known downwash is obtained. The surfaces of the aircraft, wake and diaphragm (if necessary) are divided into small quadrilateral elements which are approximated with hyperboloidal surfaces. The potential and its normal derivative are assumed to be constant within each element. This yields a set of linear algebraic equations and the coefficients are evaluated analytically. By using Gaussian elimination method, equations are solved for the potentials at the centroids of elements. The pressure coefficient is evaluated by the finite different method; the lift and moment coefficients are evaluated by numerical integration. Numerical results are presented, and applications to flutter are also included.
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A new treatment of nonlocality in scattering process
NASA Astrophysics Data System (ADS)
Upadhyay, N. J.; Bhagwat, A.; Jain, B. K.
2018-01-01
Nonlocality in the scattering potential leads to an integro-differential equation. In this equation nonlocality enters through an integral over the nonlocal potential kernel. The resulting Schrödinger equation is usually handled by approximating r,{r}{\\prime }-dependence of the nonlocal kernel. The present work proposes a novel method to solve the integro-differential equation. The method, using the mean value theorem of integral calculus, converts the nonhomogeneous term to a homogeneous term. The effective local potential in this equation turns out to be energy independent, but has relative angular momentum dependence. This method is accurate and valid for any form of nonlocality. As illustrative examples, the total and differential cross sections for neutron scattering off 12C, 56Fe and 100Mo nuclei are calculated with this method in the low energy region (up to 10 MeV) and are found to be in reasonable accord with the experiments.
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Fingerprinting of music scores
NASA Astrophysics Data System (ADS)
Irons, Jonathan; Schmucker, Martin
2004-06-01
Publishers of sheet music are generally reluctant in distributing their content via the Internet. Although online sheet music distribution's advantages are numerous the potential risk of Intellectual Property Rights (IPR) infringement, e.g. illegal online distributions, disables any innovation propensity. While active protection techniques only deter external risk factors, additional technology is necessary to adequately treat further risk factors. For several media types including music scores watermarking technology has been developed, which ebeds information in data by suitable data modifications. Furthermore, fingerprinting or perceptual hasing methods have been developed and are being applied especially for audio. These methods allow the identification of content without prior modifications. In this article we motivate the development of watermarking and fingerprinting technologies for sheet music. Outgoing from potential limitations of watermarking methods we explain why fingerprinting methods are important for sheet music and address potential applications. Finally we introduce a condept for fingerprinting of sheet music.
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Effect of Applied Potential on Fatigue Life of Electropolished Nitinol Wires
NASA Astrophysics Data System (ADS)
Sivan, Shiril; Di Prima, Matthew; Weaver, Jason D.
2017-09-01
Nitinol is used as a metallic biomaterial in medical devices due to its shape memory and pseudoelastic properties. The clinical performance of nitinol depends on factors which include the surface finish, the local environment, and the mechanical loads to which the device is subjected. Preclinical evaluations of device durability are performed with fatigue tests while electrochemical characterization methods such as ASTM F2129 are employed to evaluate corrosion susceptibility by determining the rest potential and breakdown potential. However, it is well established that the rest potential of a metal surface can vary with the local environment. Very little is known regarding the influence of voltage on fatigue life of nitinol. In this study, we developed a fatigue testing method in which an electrochemical system was integrated with a rotary bend wire fatigue tester. Samples were fatigued at various strain levels at electropotentials anodic and cathodic to the rest potential to determine if it could influence fatigue life. Wires at potentials negative to the rest potential had a significantly higher number of cycles to fracture than wires held at potentials above the breakdown potential. For wires for which no potential was applied, they had fatigue life similar to wires at negative potentials.
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Interior-Point Methods for Linear Programming: A Review
ERIC Educational Resources Information Center
Singh, J. N.; Singh, D.
2002-01-01
The paper reviews some recent advances in interior-point methods for linear programming and indicates directions in which future progress can be made. Most of the interior-point methods belong to any of three categories: affine-scaling methods, potential reduction methods and central path methods. These methods are discussed together with…
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Stresses and elastic constants of crystalline sodium, from molecular dynamics
DOE Office of Scientific and Technical Information (OSTI.GOV)
Schiferl, S.K.
1985-02-01
The stresses and the elastic constants of bcc sodium are calculated by molecular dynamics (MD) for temperatures to T = 340K. The total adiabatic potential of a system of sodium atoms is represented by pseudopotential model. The resulting expression has two terms: a large, strictly volume-dependent potential, plus a sum over ion pairs of a small, volume-dependent two-body potential. The stresses and the elastic constants are given as strain derivatives of the Helmholtz free energy. The resulting expressions involve canonical ensemble averages (and fluctuation averages) of the position and volume derivatives of the potential. An ensemble correction relates the resultsmore » to MD equilibrium averages. Evaluation of the potential and its derivatives requires the calculation of integrals with infinite upper limits of integration, and integrand singularities. Methods for calculating these integrals and estimating the effects of integration errors are developed. A method is given for choosing initial conditions that relax quickly to a desired equilibrium state. Statistical methods developed earlier for MD data are extended to evaluate uncertainties in fluctuation averages, and to test for symmetry. 45 refs., 10 figs., 4 tabs.« less
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An Extension of the Krieger-Li-Iafrate Approximation to the Optimized-Effective-Potential Method
DOE Office of Scientific and Technical Information (OSTI.GOV)
Wilson, B.G.
1999-11-11
The Krieger-Li-Iafrate approximation can be expressed as the zeroth order result of an unstable iterative method for solving the integral equation form of the optimized-effective-potential method. By pre-conditioning the iterate a first order correction can be obtained which recovers the bulk of quantal oscillations missing in the zeroth order approximation. A comparison of calculated total energies are given with Krieger-Li-Iafrate, Local Density Functional, and Hyper-Hartree-Fock results for non-relativistic atoms and ions.
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NASA Technical Reports Server (NTRS)
Khodadad, Christina L.; Birmele, Michele N.; Hummerick, Mary E.; Roman, Monsi; Smith, David J.
2015-01-01
Microorganisms including potential human pathogens have been detected on the International Space Station (ISS). The potential to introduce new microorganisms occurs with every exchange of crew or addition of equipment or supplies. Current microbial monitoring methods require enrichment of microorganisms and a 48-hour incubation time resulting in an increase in microbial load, detecting a limited number of unidentified microorganisms. An expedient, low-cost, in-flight method of microbial detection, identification, and enumeration is warranted.
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Development of a Method to Determine The Autoxidation of Turbine Fuels.
1992-05-01
By 6 G.E. Fodor D.W. Naegeli Belvoir Fuels and Lubricants Research Facility (SwRI) Southwest Research Institute San Antonio, Texas Under Contract to -6...G.E., Naegeli , D.W., Kohl, K.B., and Cuellar, Jr., J.P., "Development of a Test Method to Determine Potential Peroxide Content in Turbine Fuels...June 1985. 5. Fodor, G.E. and Naegeli , D.W., "Development of a Test Method to Determine Potential Peroxide Content in Turbine Fuels," Conference
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NASA Astrophysics Data System (ADS)
Lea, J.
2017-12-01
The quantification of glacier change is a key variable within glacier monitoring, with the method used potentially being crucial to ensuring that data can be appropriately compared with environmental data. The topic and timescales of study (e.g. land/marine terminating environments; sub-annual/decadal/centennial/millennial timescales) often mean that different methods are more suitable for different problems. However, depending on the GIS/coding expertise of the user, some methods can potentially be time consuming to undertake, making large-scale studies problematic. In addition, examples exist where different users have nominally applied the same methods in different studies, though with minor methodological inconsistencies in their approach. In turn, this will have implications for data homogeneity where regional/global datasets may be constructed. Here, I present a simple toolbox scripted in a Matlab® environment that requires only glacier margin and glacier centreline data to quantify glacier length, glacier change between observations, rate of change, in addition to other metrics. The toolbox includes the option to apply the established centreline or curvilinear box methods, or a new method: the variable box method - designed for tidewater margins where box width is defined as the total width of the individual terminus observation. The toolbox is extremely flexible, and has the option to be applied as either Matlab® functions within user scripts, or via a graphical user interface (GUI) for those unfamiliar with a coding environment. In both instances, there is potential to apply the methods quickly to large datasets (100s-1000s of glaciers, with potentially similar numbers of observations each), thus ensuring large scale methodological consistency (and therefore data homogeneity) and allowing regional/global scale analyses to be achievable for those with limited GIS/coding experience. The toolbox has been evaluated against idealised scenarios demonstrating its accuracy, while feedback from undergraduate students who have trialled the toolbox is that it is intuitive and simple to use. When released, the toolbox will be free and open source allowing users to potentially modify, improve and expand upon the current version.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Jannik, G. T.; Dixon, K. L.
This report presents the environmental dose assessment methods and the estimated potential doses to the offsite public from 2015 Savannah River Site (SRS) atmospheric and liquid radioactive releases. Also documented are potential doses from special-case exposure scenarios - such as the consumption of deer meat, fish, and goat milk.
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A New Approach to Aircraft Robust Performance Analysis
NASA Technical Reports Server (NTRS)
Gregory, Irene M.; Tierno, Jorge E.
2004-01-01
A recently developed algorithm for nonlinear system performance analysis has been applied to an F16 aircraft to begin evaluating the suitability of the method for aerospace problems. The algorithm has a potential to be much more efficient than the current methods in performance analysis for aircraft. This paper is the initial step in evaluating this potential.
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ERIC Educational Resources Information Center
Eckberg, Deborah A.
2015-01-01
This study explores race as a potential predictor of research methods anxiety among a sample of undergraduates. While differences in academic achievement based on race and ethnicity have been well documented, few studies have examined racial differences in anxiety with regard to specific subject matter in undergraduate curricula. This exploratory…
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Systematic Convergence in Applying Variational Method to Double-Well Potential
ERIC Educational Resources Information Center
Mei, Wai-Ning
2016-01-01
In this work, we demonstrate the application of the variational method by computing the ground- and first-excited state energies of a double-well potential. We start with the proper choice of the trial wave functions using optimized parameters, and notice that accurate expectation values in excellent agreement with the numerical results can be…
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Work function measurements by the field emission retarding potential method
NASA Technical Reports Server (NTRS)
Swanson, L. W.; Strayer, R. W.; Mackie, W. A.
1971-01-01
Using the field emission retarding potential method true work functions have been measured for the following monocrystalline substrates: W(110), W(111), W(100), Nb(100), Ni(100), Cu(100), Ir(110) and Ir(111). The electron elastic and inelastic reflection coefficients from several of these surfaces have also been examined near zero primary beam energy.
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Identifying High Academic Potential in Australian Aboriginal Children Using Dynamic Testing
ERIC Educational Resources Information Center
Chaffey, Graham W.; Bailey, Stan B.; Vine, Ken W.
2015-01-01
The primary purpose of this study was to determine the effectiveness of dynamic testing as a method for identifying high academic potential in Australian Aboriginal children. The 79 participating Aboriginal children were drawn from Years 3-5 in rural schools in northern New South Wales. The dynamic testing method used in this study involved a…
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Random Walk Method for Potential Problems
NASA Technical Reports Server (NTRS)
Krishnamurthy, T.; Raju, I. S.
2002-01-01
A local Random Walk Method (RWM) for potential problems governed by Lapalace's and Paragon's equations is developed for two- and three-dimensional problems. The RWM is implemented and demonstrated in a multiprocessor parallel environment on a Beowulf cluster of computers. A speed gain of 16 is achieved as the number of processors is increased from 1 to 23.
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Oak regeneration potential increased by shelterwood treatments
Richard C. Schlesinger; Ivan L. Sander; Kenneth R. Davidson
1993-01-01
In much of the Central Hardwood Forest Region, oak species are not regenerating well, even though large oak trees are common within the existing forests. The shelterwood method has been suggested as a potential tool for establishing and developing advanced regeneration where it is lacking. The 10-yr results from a study of several variants of the shelterwood method...
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Roncero, Octavio; Aguado, Alfredo; Batista-Romero, Fidel A; Bernal-Uruchurtu, Margarita I; Hernández-Lamoneda, Ramón
2015-03-10
A variant of the density difference driven optimized embedding potential (DDD-OEP) method, proposed by Roncero et al. (J. Chem. Phys. 2009, 131, 234110), has been applied to the calculation of excited states of Br2 within small water clusters. It is found that the strong interaction of Br2 with the lone electronic pair of the water molecules makes necessary to optimize specific embedding potentials for ground and excited electronic states, separately and using the corresponding densities. Diagnosis and convergence studies are presented with the aim of providing methods to be applied for the study of chromophores in solution. Also, some preliminary results obtained for the study of electronic states of Br2 in clathrate cages are presented.
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Computer simulation of surface and film processes
NASA Technical Reports Server (NTRS)
Tiller, W. A.; Halicioglu, M. T.
1983-01-01
Adequate computer methods, based on interactions between discrete particles, provide information leading to an atomic level understanding of various physical processes. The success of these simulation methods, however, is related to the accuracy of the potential energy function representing the interactions among the particles. The development of a potential energy function for crystalline SiO2 forms that can be employed in lengthy computer modelling procedures was investigated. In many of the simulation methods which deal with discrete particles, semiempirical two body potentials were employed to analyze energy and structure related properties of the system. Many body interactions are required for a proper representation of the total energy for many systems. Many body interactions for simulations based on discrete particles are discussed.
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System and method for evaluating a wire conductor
Panozzo, Edward; Parish, Harold
2013-10-22
A method of evaluating an electrically conductive wire segment having an insulated intermediate portion and non-insulated ends includes passing the insulated portion of the wire segment through an electrically conductive brush. According to the method, an electrical potential is established on the brush by a power source. The method also includes determining a value of electrical current that is conducted through the wire segment by the brush when the potential is established on the brush. The method additionally includes comparing the value of electrical current conducted through the wire segment with a predetermined current value to thereby evaluate the wire segment. A system for evaluating an electrically conductive wire segment is also disclosed.